changeset 20:c265f13066d8

Deleted selected files

--- a/commons/launcher/BlatClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch BlatProgramLauncher on several files in parallel on a cluster.
-
-
-from pyRepet.launcher.AbstractClusterLauncher import *
-from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
-from commons.core.coord.AlignUtils import AlignUtils
-from commons.tools import srptBlasterMatcher
-
-
-class BlatClusterLauncher( AbstractClusterLauncher ):
-    """
-    Launch Blat on several files in parallel on a cluster.
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractClusterLauncher.__init__( self )
-        AbstractClusterLauncher.setAcronym( self, "Blat" )
-        
-        self._cmdLineSpecificOptions = "s:p:A"
-        
-        self._exeWrapper = "BlatProgramLauncher.py"
-        self._prgLauncher = BlatProgramLauncher()
-        self._prgLauncher.setInputFile( GENERIC_IN_FILE )
-        self._prgLauncher.setClean()
-        self._prgLauncher.setVerbosityLevel( 1 )
-        self._prgLauncher.setListFilesToKeep()
-        self._prgLauncher.setListFilesToRemove()
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (format='fasta')"
-        string += "\n     -p: parameters for '%s'" % ( self._prgLauncher.getProgramName() )
-        string += "\n     -Z: concatenate output files"
-        string += "\n     -A: same sequences (all-by-all)"
-        return string
-    
-    
-    def getSubjectFile( self ):
-        return self._prgLauncher.getSubjectFile()
-    
-    
-    def getProgramParameters( self ):
-        return self._prgLauncher.getProgramParameters()
-    
-    
-    def processOutputFile( self, tmpFile, outFile ):
-        sortFile = "%s.sort" % ( tmpFile )
-        AlignUtils.sortAlignFile( tmpFile, sortFile )
-        if self._prgLauncher.getAllByAll():
-            srptBlasterMatcher.filterRedundantMatches( sortFile,
-                                                                  outFile )
-            os.remove( sortFile )
-        else:
-            os.rename( sortFile, outFile )
-            
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        if o =="-s":
-            self._prgLauncher.setSubjectFile( a )
-            
-if __name__ == "__main__":
-    i = BlatClusterLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/BlatProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,192 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch Blat (pairwise alignment).
-#
-# options:
-#      -h: this help
-#      -i: name of the input file (queries, format='fasta')
-#      -s: name of the subject file (format='fasta')
-#      -p: parameters for 'blat' (default='-d 2')
-#      -o: name of the output file (format='align', default=inFile+'.align')
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import os
-import sys
-
-from commons.pyRepetUnit.components.AbstractProgramLauncher import  AbstractProgramLauncher
-
-
-class BlatProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch Blat (pairwise alignment).
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "blat"
-        self._formatInFile = "fasta"
-        self._sbjFile = ""
-        self._prgParam = ""
-        self._allByAll = False
-        
-        
-    def getHelpAsString( self ):
-        string = AbstractProgramLauncher.getHelpAsString(self)
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (database, format='fasta')"
-        string += "\n     -p: parameters for '%s'" % ( self.getProgramName() )
-        string += "\n     -A: same sequences (all-by-all)"
-        string += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        return string
-    
-    def getCmdLineOptions(self):
-        return AbstractProgramLauncher.getCmdLineOptions(self) + "s:p:Ao:"
-
-    def setAttributesFromCmdLine( self, o, a = "" ):
-        AbstractProgramLauncher.setAttributesFromCmdLine(self, o, a)
-        if o == "-s":
-            self.setSubjectFile( a )
-        elif o == "-p":
-            self.setProgramParameters( a )
-        elif o == "-A":
-            self.setAllByAll()
-        elif o == "-o":
-            self.setOutputFile( a )
-            
-            
-    def setSubjectFile( self, arg ):
-        self._sbjFile = arg
-        
-        
-    def getSubjectFile( self ):
-        return self._sbjFile
-    
-    
-    def setAllByAll( self ):
-        self._allByAll = True
-        
-        
-    def getAllByAll( self ):
-        return self._allByAll
-    
-    
-    def check( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        AbstractProgramLauncher.check(self)
-        if self._sbjFile == "":
-            string = "ERROR: missing subject file (-s)"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-            
-            
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for BlatClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
-        if self.getProgramParameters() != "":
-            self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
-        if self.getAllByAll():
-            self._wrpCmdLine += " -A"
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        
-        
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        self._prgCmdLine += " %s" % ( self.getSubjectFile() )
-        self._prgCmdLine += " %s" % ( self.getInputFile() )
-        if self.getProgramParameters() != "":
-            self._prgCmdLine += " %s" % ( self.getProgramParameters() )
-        self._prgCmdLine += " -out=blast8"
-        self._prgCmdLine += " %s.blast" % ( self.getInputFile() )
-        
-        
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        
-        
-    def setListFilesToRemove( self ):
-        """
-        Set the list of files to remove.
-        """
-        self.appendFileToRemove( "%s.blast" % ( self.getInputFile() ) )
-        
-        
-    def convertBlastIntoAlign( self ):
-        """
-        Convert a 'blast' file into the 'align' format.
-        """
-        cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py"
-        cmd += " -i %s.blast" % ( self.getInputFile() )
-        cmd += " -o %s" % ( self.getOutputFile() )
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR while converting 'blast' file into 'align' format"
-            print string
-            sys.exit(1)
-            
-            
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
-        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
-        if self.getAllByAll():
-            self._summary += "\nall-by-all"
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
-            print string
-            sys.exit(1)
-            
-        self.convertBlastIntoAlign()
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = BlatProgramLauncher()
-    i.checkAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/LaunchBlastclust.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,372 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Launch Blastclust on nucleotide sequences and return a fasta file.
-"""
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import sys
-import subprocess
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.core.seq.Bioseq import Bioseq
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-class LaunchBlastclust(object):
-    """
-    Launch Blastclust on nucleotide sequences and return a fasta file.
-    """
-    
-    def __init__(self, input = "", outFilePrefix = "", clean = False, verbose = 0):
-        """
-        Constructor.
-        """
-        self._inFileName = input
-        self._identityThreshold = 95
-        self._coverageThreshold = 0.9
-        self._bothSeq = "T"
-        self._filterUnclusteredSeq = False
-        self._outFilePrefix = outFilePrefix
-        self._isBlastToMap = False
-        self._isHeaderForTEdenovo = False
-        self._nbCPUs = 1
-        self._clean = clean
-        self._verbose = verbose
-        self._tmpFileName = ""
-        
-    def setAttributesFromCmdLine(self):
-        """
-        Set the attributes from the command-line.
-        """
-        
-        description = "Launch Blastclust on nucleotide sequences and return a fasta file."
-        usage = "LaunchBlastclust.py -i inputFileName [options]"
-        
-        examples = "\nExample 1: launch Blastclust with default options, highest verbose and clean temporary files.\n"
-        examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -v 2 -c"
-        examples += "\n\t"
-        examples += "\t\nExample 2: launch Blastclust with an identity threshold of 90%, rename output files and generate a map file corresponding to the fasta output.\n"
-        examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -S 90 -o SpecialOutputName -m"
-        examples += "\n\tWARNING: Please refer to -m option limitations in the description above.\n"
-        
-        #TODO: check if the optionParser can handle '\' into strings for a better code readability in -m option
-        
-        parser = RepetOptionParser(description = description, usage = usage, version = "v1.0", epilog = examples)
-        parser.add_option("-i", "--input",          dest = "inFileName",            type = "string",    help = "name of the input fasta file (nucleotides)",                    default = "")
-        parser.add_option("-L", "--length",         dest = "coverageThreshold",     type = "float",     help = "length coverage threshold (default=0.9)",                       default = 0.9)
-        parser.add_option("-S", "--ident",          dest = "identityThreshold",     type = "int",       help = "identity threshold (default=95)",                               default = 95)
-        parser.add_option("-b", "--both",           dest = "bothSeq",               type = "string",    help = "require coverage on both neighbours (default=T/F)",             default = "T")
-        parser.add_option("-f", "--filter",         dest = "filterUnclusteredSeq",                      help = "filter unclustered sequences",                                  default = False,    action="store_true")
-        parser.add_option("-o", "--out",            dest = "outFilePrefix",         type = "string",    help = "prefix of the output files (default=input fasta file name)",    default = "")
-        parser.add_option("-m", "--map",            dest = "isBlast2Map",                               help = "generate an additional output file in map format (Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output)",   default = False,    action="store_true")
-        parser.add_option("", "--TEdenovoHeader",   dest = "isHeaderForTEdenovo",                       help = "format headers for TEdenovo pipeline",                          default = False,    action="store_true")
-        parser.add_option("-n", "--num",            dest = "nbCPUs",                type = "int",       help = "number of CPU's to use (default=1)",                            default = 1)
-        parser.add_option("-c", "--clean",          dest = "clean",                                     help = "clean temporary files",                                         default = False,    action="store_true")
-        parser.add_option("-v", "--verbose",        dest = "verbose",               type = "int",       help = "verbosity level (default=0/1/2)",                               default = 0)
-
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setInputFileName(options.inFileName)
-        self.setCoverageThreshold(options.coverageThreshold)
-        self.setIdentityThreshold(options.identityThreshold)
-        self.setBothSequences(options.bothSeq)
-        self.setNbCPUs(options.nbCPUs)
-        self.setIsHeaderForTEdenovo(options.isHeaderForTEdenovo)
-        if options.filterUnclusteredSeq:
-            self.setFilterUnclusteredSequences()
-        if options.outFilePrefix != "":
-            self.setOutputFilePrefix(options.outFilePrefix)
-        else:
-            self._outFilePrefix = self._inFileName
-        if options.isBlast2Map:
-            self.setIsBlastToMap()
-        if options.clean:
-            self.setClean()
-        self.setVerbosityLevel(options.verbose)
-                
-    def setInputFileName(self , inFileName):
-        self._inFileName = inFileName
-        
-    def setCoverageThreshold(self, lengthThresh):
-        self._coverageThreshold = float(lengthThresh)
-                
-    def setIdentityThreshold(self, identityThresh):
-        self._identityThreshold = int(identityThresh)
-        
-    def setBothSequences(self, bothSeq):
-        self._bothSeq = bothSeq
-        
-    def setNbCPUs(self, nbCPUs):
-        self._nbCPUs = int(nbCPUs)
-        
-    def setFilterUnclusteredSequences(self):
-        self._filterUnclusteredSeq = True
-        
-    def setOutputFilePrefix(self, outFilePrefix):
-        self._outFilePrefix = outFilePrefix
-        
-    def setIsBlastToMap(self):
-        self._isBlastToMap = True
-        
-    def setIsHeaderForTEdenovo(self, isHeaderForTEdenovo):
-        self._isHeaderForTEdenovo = isHeaderForTEdenovo
-        
-    def setClean(self):
-        self._clean = True
-        
-    def setVerbosityLevel(self, verbose):
-        self._verbose = int(verbose)
-    
-    def setTmpFileName(self, tmpFileName):    
-        self._tmpFileName = tmpFileName
-        
-        
-    def checkAttributes(self):
-        """
-        Check the attributes are valid before running the algorithm.
-        """
-        if self._inFileName == "":
-            print "ERROR: missing input file name (-i)"
-            sys.exit(1)
-        if self._outFilePrefix == "":
-            self._outFilePrefix = self._inFileName
-        self._tmpFileName = "%s_blastclust.txt" % (self._outFilePrefix)
-        
-        
-    def launchBlastclust(self, inFile):
-        """
-        Launch Blastclust in command-line.
-        """
-        if os.path.exists(os.path.basename(inFile)):
-            inFile = os.path.basename(inFile)
-        prg = "blastclust"
-        cmd = prg
-        cmd += " -i %s" % (inFile)
-        cmd += " -o %s" % (self._tmpFileName)
-        cmd += " -S %i" % (self._identityThreshold)
-        cmd += " -L %f" % (self._coverageThreshold)
-        cmd += " -b %s" % (self._bothSeq)
-        cmd += " -p F"
-        cmd += " -a %i" % (self._nbCPUs)
-        if self._verbose == 0:
-            cmd += " -v blastclust.log"
-        if self._verbose > 0:
-            print cmd
-            sys.stdout.flush()
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        if process.returncode != 0:
-            raise Exception("ERROR when launching '%s'" % cmd)
-        if self._clean and os.path.exists("error.log"):
-            os.remove("error.log")
-        if self._clean and os.path.exists("blastclust.log"):
-            os.remove("blastclust.log")
-            
-            
-    def getClustersFromTxtFile(self):
-        """
-        Return a dictionary with cluster IDs as keys and sequence headers as values.
-        """
-        dClusterId2SeqHeaders = {}
-        inF = open(self._tmpFileName, "r")
-        line = inF.readline()
-        clusterId = 1
-        while True:
-            if line == "":
-                break
-            tokens = line[:-1].split(" ")
-            dClusterId2SeqHeaders[clusterId] = []
-            for seqHeader in tokens:
-                if seqHeader != "":
-                    dClusterId2SeqHeaders[clusterId].append(seqHeader)
-            line = inF.readline()
-            clusterId += 1
-        inF.close()
-        if self._verbose > 0:
-            print "nb of clusters: %i" % (len(dClusterId2SeqHeaders.keys()))
-            sys.stdout.flush()
-        return dClusterId2SeqHeaders
-    
-    
-    def filterUnclusteredSequences(self, dClusterId2SeqHeaders):
-        """
-        Filter clusters having only one sequence.
-        """
-        for clusterId in dClusterId2SeqHeaders.keys():
-            if len(dClusterId2SeqHeaders[clusterId]) == 1:
-                del dClusterId2SeqHeaders[clusterId]
-        if self._verbose > 0:
-            print "nb of clusters (>1seq): %i" % (len(dClusterId2SeqHeaders.keys()))
-            sys.stdout.flush()
-        return dClusterId2SeqHeaders
-    
-    
-    def getClusteringResultsInFasta(self, inFile):
-        """
-        Write a fasta file whose sequence headers contain the clustering IDs.
-        """
-        dClusterId2SeqHeaders = self.getClustersFromTxtFile()
-        if self._filterUnclusteredSeq:
-            dClusterId2SeqHeaders = self.filterUnclusteredSequences(dClusterId2SeqHeaders)
-        inDB = BioseqDB(inFile)
-        outFileName = "%s_Blastclust.fa" % (inFile)
-        outF = open(outFileName, "w")
-        for clusterId in dClusterId2SeqHeaders.keys():
-            memberId = 1
-            for seqHeader in dClusterId2SeqHeaders[clusterId]:
-                bs = inDB.fetch(seqHeader)
-                bs.header = "BlastclustCluster%iMb%i_%s" % (clusterId, memberId, seqHeader)
-                bs.write(outF)
-                memberId += 1
-        outF.close()
-        
-        
-    def getLinkInitNewHeaders(self):
-        dNew2Init = {}
-        linkFileName = "%s.shortHlink" % (self._inFileName)
-        linkFile = open(linkFileName,"r")
-        line = linkFile.readline()
-        while True:
-            if line == "":
-                break
-            data = line.split("\t")
-            dNew2Init[data[0]] = data[1]
-            line = linkFile.readline()
-        linkFile.close()
-        return dNew2Init
-    
-    
-    def retrieveInitHeaders(self, dNewH2InitH):
-        tmpFaFile = "%s.shortH_Blastclust.fa" % (self._inFileName)
-        tmpFaFileHandler = open(tmpFaFile, "r")
-        outFaFile = "%s_Blastclust.fa" % (self._outFilePrefix)
-        outFaFileHandler = open(outFaFile, "w")
-        while True:
-            line = tmpFaFileHandler.readline()
-            if line == "":
-                break
-            if line[0] == ">":
-                tokens = line[1:-1].split("_")
-                initHeader = dNewH2InitH[tokens[1]]
-                if self._isHeaderForTEdenovo:
-                    classif = initHeader.split("_")[0]
-                    consensusName = "_".join(initHeader.split("_")[1:])
-                    clusterId = tokens[0].split("Cluster")[1].split("Mb")[0]
-                    newHeader = "%s_Blc%s_%s" % (classif, clusterId, consensusName)
-                else:
-                    newHeader = "%s_%s" % (tokens[0], initHeader)
-                outFaFileHandler.write(">%s\n" % (newHeader))
-            else:
-                outFaFileHandler.write(line)
-        tmpFaFileHandler.close()
-        outFaFileHandler.close()
-        if self._clean:
-            os.remove(tmpFaFile)
-
-
-    def blastclustToMap(self, blastclustFastaOut):
-        """
-        Write a map file from blastclust fasta output.
-        Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output.
-        """
-        fileDb = open(blastclustFastaOut , "r")
-        mapFilename = "%s.map" % (os.path.splitext(blastclustFastaOut)[0])
-        fileMap = open(mapFilename, "w")
-        seq = Bioseq()
-        numseq = 0
-        while 1:
-            seq.read(fileDb)
-            if seq.sequence == None:
-                break
-            numseq = numseq + 1
-            ID = seq.header.split(' ')[0].split('_')[0]
-            chunk = seq.header.split(' ')[0].split('_')[1]
-            start = seq.header.split(' ')[-1].split(',')[0][1:]
-            end = seq.header.split(' ')[-1].split(',')[1][:-1]
-            line= '%s\t%s\t%s\t%s' % (ID, chunk, start, end)
-            fileMap.write(line + "\n")
-    
-        fileDb.close()
-        fileMap.close()
-        print "saved in %s" % mapFilename 
-        
-        
-    def start(self):
-        """
-        Useful commands before running the program.
-        """
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START %s" % (type(self).__name__)
-            
-            
-    def end(self):
-        """
-        Useful commands before ending the program.
-        """
-        if self._verbose > 0:
-            print "END %s" % (type(self).__name__)
-            
-            
-    def run(self):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        iCSH = ChangeSequenceHeaders(inFile = self._inFileName, format = "fasta", step = 1, outFile = "%s.shortH" % self._inFileName, linkFile = "%s.shortHlink" % self._inFileName)
-        iCSH.run()
-        
-        self.launchBlastclust("%s.shortH" % (self._inFileName))
-        
-        self.getClusteringResultsInFasta("%s.shortH" % (self._inFileName))
-        
-        dNewH2InitH = self.getLinkInitNewHeaders()
-        self.retrieveInitHeaders(dNewH2InitH)
-        
-        if self._isBlastToMap:
-            blastclustFileName = "%s_Blastclust.fa" % (self._outFilePrefix)
-            self.blastclustToMap(blastclustFileName)
-        
-        if self._clean:
-            os.remove("%s.shortH" % (self._inFileName))
-            os.remove("%s.shortHlink" % (self._inFileName))
-        
-        self.end()
-        
-if __name__ == "__main__":
-    i = LaunchBlastclust()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/LaunchLastZ.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import sys
-import os
-import optparse
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.FileUtils import FileUtils
-from subprocess import Popen
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-import tempfile
-  
-class LaunchLastZ(object):
-
-    def __init__(self,queryFileName="", refFileName ="", outputFileName=None,outputFileFormat="axt",noTransition=True, ambiguous=None, step=1,gfextend=False, chain=False, verbosity=1 ):
-        self.queryFileName = queryFileName
-        self.refFileName = refFileName
-        self.outputFileName = outputFileName
-        self.outputFileFormat = outputFileFormat
-        self.noTransition = noTransition
-        self.step = step
-        self.ambiguous = ambiguous
-        self.gfextend = gfextend
-        self.chain = chain
-        self.verbosity = verbosity
-        
-    def setAttributesFromCmdLine(self):
-        description = "LaunchLastZ runs the LastZ program ."    
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-q", "--query", dest="queryFileName", default = None,  action="store", type="string", help="input query file [compulsory] [format: fasta]")
-        parser.add_option("-r", "--ref", dest="refFileName", default = None,  action="store", type="string", help="input ref file [compulsory] [format: fasta]")
-        parser.add_option("-o", "--output", dest="outputFileName", default = None,  action="store", type="string", help="output file [compulsory] ")
-        parser.add_option("-f", "--format", dest="outputFileFormat", default = "axt",  action="store", type="string", help="output file format[optional] ")
-        parser.add_option("-n", "--notransition", dest="noTransition", action="store_false", default=True, help="noTransition (default True) [optional] ")
-        parser.add_option("-a", "--ambiguous", dest="ambiguous", action="store",  type="string", help="ambiguous [optional] ")
-        parser.add_option("-s", "--step", dest="step", default = 1,  action="store", type="int", help="stepsize (default 1) [optional] ")
-        parser.add_option("-g", "--gfextend", dest="gfextend",  action="store_true",  help="extend gf (default false)[optional] ")
-        parser.add_option("-c", "--chain", dest="chain",  action="store_true", help="chain (default false)[optional] ")
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 1,  action="store", type="int", help="verbosity [optional] ")
-        (self._options, args) = parser.parse_args()
-        self._setAttributesFromOptions(self._options)
-
-    def _setAttributesFromOptions(self, options):
-        self.queryFileName = options.queryFileName
-        self.refFileName = options.refFileName
-        self.outputFileName = options.outputFileName
-        self.outputFileFormat = options.outputFileFormat
-	self.ambiguous = options.ambiguous
-        self.noTransition = options.noTransition
-        self.step = options.step
-        self.gfextend = options.gfextend
-        self.chain = options.chain
-        self.verbosity = options.verbosity
-      
-    def checkOptions(self):       
-        if self.queryFileName != "":
-            if not FileUtils.isRessourceExists(self.queryFileName):
-                raise Exception("ERROR: Query file does not exist!")
-        else:
-            raise Exception("ERROR: No specified --query option!")
-        if self.refFileName != "":
-            if not FileUtils.isRessourceExists(self.refFileName):
-                raise Exception("ERROR: Ref file does not exist!")
-        else:
-            raise Exception("ERROR: No specified --ref option!")
-        if self.outputFileName == None:
-            self.outputFileName = "%s_%s.axt" % (os.path.basename(self.queryFileName), os.path.basename(self.refFileName))
-                                
-    def run(self):
-        if not CheckerUtils.isExecutableInUserPath("lastz") :
-            print ("ERROR: LastZ must be in your path")
-        else:
-            self.checkOptions()
-            
-            transition = "" 
-            if self.noTransition:
-                transition = "--notransition"
-            ambiguous = ""    
-            if self.ambiguous is not None:
-                ambiguous =  "--ambiguous=%s" % self.ambiguous
-                
-            gfextend = ""
-            if self.gfextend:
-                gfextend = "--gfextend"
-                
-            chain = ""
-            if self.chain:
-                chain = "--chain"
-                
-            cmd = "lastz %s[format=fasta] %s[format=fasta] --output=%s --format=%s %s %s --step=%i %s %s" % (self.refFileName, self.queryFileName, self.outputFileName
-                                                                           , self.outputFileFormat, ambiguous, transition,self.step, gfextend, chain)
-            if self.verbosity>0:
-                print("Running LastZ with following commands : %s" %cmd)
-            sys.stdout.flush()
-            cmd = cmd.split()
-            process = subprocess.Popen(cmd)
-            process.wait()
-            return process.returncode
-
-if __name__ == "__main__":
-    iLaunchLastZ = LaunchLastZ()
-    iLaunchLastZ.setAttributesFromCmdLine()
-    iLaunchLastZ.run()

--- a/commons/launcher/LaunchMCL.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.coord.MatchUtils import MatchUtils
-import subprocess
-import os
-import time
-import shutil
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-LOG_DEPTH = "repet.base"
-
-##Launch MCL
-#
-class LaunchMCL(object):
-    
-    def __init__(self, fastaFileName = "", outFilePrefix = "", inflate = 1.5, covThres = 0.0, isJoined = False, isCluster2Map = False, isClusterConsensusHeaders = False, doClean = False, verbosity = 0):
-        self._fastaFileName = fastaFileName
-        self.setOutFilePrefix(outFilePrefix)
-        self._inflate = inflate
-        self._coverageThreshold = covThres
-        self._isJoined = isJoined
-        self._isCluster2Map = isCluster2Map
-        self._isClusterConsensusHeaders = isClusterConsensusHeaders
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch MCL clustering program."
-        epilog = "\nExample: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchMCL.py -i file.fa -v 0\n"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--fasta",      dest = "fastaFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFilePrefix", action = "store",       type = "string", help = "prefix of the output files [default=input fasta file name]",    default = "")
-        parser.add_option("-I", "--inflate",    dest = "inflate",       action = "store",       type = "float",  help = "inflate parameter of MCL [optional] [default: 1.5]", default = 1.5)
-        parser.add_option("-T", "--coverage",   dest = "coverageThreshold", action = "store",   type = "float",  help = "length coverage threshold (default=0.0, 0.0 <= value <= 1.0)",              default = 0.0)
-        parser.add_option("-j", "--join",       dest = "isJoined",          action = "store_true",               help = "join hits after alignement [optional] [default: False]" , default = False)
-        parser.add_option("-m", "--map",        dest = "isCluster2Map", action = "store_true",                   help = "generate an additional output file in map format (Warning: only works if MCL's fasta input headers are formated like LTRharvest fasta output)",   default = False)
-        parser.add_option("", "--isClusterConsensusHeaders", dest = "isClusterConsensusHeaders", action="store_true", help = "format headers for Cluster Consensus tool", default = False)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setFastaFileName(options.fastaFileName)
-        self.setOutFilePrefix(options.outFilePrefix)
-        self.setInflate(options.inflate)
-        self.setCoverageThreshold(options.coverageThreshold)
-        self.setIsJoined(options.isJoined)
-        self.setIsCluster2Map(options.isCluster2Map)
-        self.setIsClusterConsensusHeaders(options.isClusterConsensusHeaders)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def setFastaFileName(self, fastaFileName):
-        self._fastaFileName = fastaFileName
-        
-    def setOutFilePrefix(self, outFilePrefix):
-        if outFilePrefix == "":
-            self._outFilePrefix = os.path.splitext(self._fastaFileName)[0]
-        else:
-            self._outFilePrefix = outFilePrefix
-            
-    def setInflate(self, inflate):
-        self._inflate = inflate
-        
-    def setCoverageThreshold(self, covThres):
-        self._coverageThreshold = float(covThres)
-    
-    def setIsJoined(self, isJoined):
-        self._isJoined = isJoined       
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setIsCluster2Map(self, isCluster2Map):
-        self._isCluster2Map = isCluster2Map
-        
-    def setIsClusterConsensusHeaders(self, isClusterConsensusHeaders):
-        self._isClusterConsensusHeaders = isClusterConsensusHeaders
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._fastaFileName == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-        if self._isCluster2Map and self._isClusterConsensusHeaders:
-            self._logAndRaise("ERROR: You can't use both '--isClusterConsensusHeaders' and '-m' options")
-        if self._coverageThreshold > 1 or self._coverageThreshold < 0:
-            self._logAndRaise("ERROR: Coverage Threshold must be in [0.0 , 1.0]")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START Launch MCL")
-        self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f -j %r -m %r -clusterHeaders %r " % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold, self._isJoined, self._isCluster2Map, self._isClusterConsensusHeaders))
-        #self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f" % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold))
-        self._log.debug("Fasta file name: %s" % self._fastaFileName)
-        workingDir = "MCLtmpDirectory"
-        if os.path.exists(workingDir):
-            self._logAndRaise("ERROR: %s already exists." % workingDir)
-        os.mkdir(workingDir)
-        os.chdir(workingDir)
-        linkToFastaFile = "%s2.fa" % os.path.splitext(self._fastaFileName)[0]
-        os.symlink("../%s" % self._fastaFileName, self._fastaFileName)
-        fastaFileNameShorten = "%s.shortH" % self._fastaFileName
-        iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=self._fastaFileName, format="fasta", step=1, outFile=fastaFileNameShorten, verbosity=self._verbosity - 1)
-        iChangeSequenceHeaders.run()
-        os.symlink(fastaFileNameShorten, linkToFastaFile)     
-        
-        self._log.info("START Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
-        cmd = "LaunchBlaster.py"
-        cmd += " -q %s" % fastaFileNameShorten
-        cmd += " -s %s" % linkToFastaFile
-        cmd += " -a"
-        cmd += " 1>&2 >> blasterMatcher.log"
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        outBlasterFileName = "%s.align" % fastaFileNameShorten
-        
-        cmd = "matcher"
-        cmd += " -m %s" % outBlasterFileName
-        cmd += " -q %s" % fastaFileNameShorten
-        cmd += " -s %s" % linkToFastaFile
-        cmd += " -a"
-        if self._isJoined:
-            cmd += " -j"
-        cmd += " 1>&2 >> blasterMatcher.log"
-        process = subprocess.Popen(cmd, shell=True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        self._log.info("END Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
-        
-        outMatcherFileName = "%s.match.tab" % outBlasterFileName
-        inputABCFileName = "%s.shortH.abc" % os.path.splitext(fastaFileNameShorten)[0]
-        MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(outMatcherFileName, inputABCFileName, coverage = self._coverageThreshold)
-        outMCLPreprocessFileName = "MCLPreprocess.out"
-        
-        self._log.info("START MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
-        cmd = "mcxload"
-        cmd += " -abc %s" % inputABCFileName
-        cmd += " --stream-mirror"
-        cmd += " --stream-neg-log10"
-        cmd += " -stream-tf 'ceil(200)'"
-        cmd += " -o %s" % outMCLPreprocessFileName
-        cmd += " -write-tab %s.tab" % outMCLPreprocessFileName
-        cmd += " 1>&2 > MCLpreprocess.log"
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        
-        outMCLFileName = "out.shortH.mcl"
-        cmd = "mcl"
-        cmd += " %s" % outMCLPreprocessFileName
-        cmd += " -I %s" % self._inflate
-        cmd += " -use-tab %s.tab" % outMCLPreprocessFileName
-        cmd += " -o %s" % outMCLFileName
-        cmd += " 1>&2 > MCL.log"
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        self._log.info("END MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
-
-        outFastaFileNameShorten = "%s.fa" % os.path.splitext(outMCLFileName)[0]
-
-        FastaUtils.convertClusterFileToFastaFile(outMCLFileName, fastaFileNameShorten, outFastaFileNameShorten, "MCL", verbosity = self._verbosity - 1)
-        
-        outFastaFileName = "%s_MCL.fa" % self._outFilePrefix
-        linkFileName = "%s.newHlink" % self._fastaFileName
-        headerStyle = "A"
-        if self._isClusterConsensusHeaders:
-            headerStyle = "B"
-        iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=outFastaFileNameShorten, format="fasta", step=2, outFile=outFastaFileName, linkFile=linkFileName, whichCluster = headerStyle, verbosity=self._verbosity - 1)
-        iChangeSequenceHeaders.run()
-        
-        if self._isCluster2Map:
-            outMapFileName = "%s_MCL.map" % self._outFilePrefix
-            FastaUtils.convertClusteredFastaFileToMapFile(outFastaFileName, outMapFileName)
-            shutil.move(outMapFileName, "..")
-
-        shutil.move(outFastaFileName, "..")
-        os.chdir("..")
-        if self._doClean:
-            self._log.warning("Working directory will be cleaned")
-            shutil.rmtree(workingDir)
-        self._log.info("END Launch MCL")
-
-if __name__ == "__main__":
-    iLaunch = LaunchMCL()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()

--- a/commons/launcher/LaunchMap.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-from commons.core.utils.FileUtils import FileUtils
-import os
-import subprocess
-
-LOG_DEPTH = "repet.tools"
-
-##Reference launcher implementation
-#
-class LaunchMap(object):
-    
-    def __init__(self, fastaFileName = "", outFileName = "", gapSize = 50, mismatchPenalty = -8, gapOpenPenalty = 16, gapExtendPenalty = 4, doClean = False, verbosity = 0):
-        self._fastaFileName = fastaFileName
-        self.setOutFileName(outFileName)
-        self._gapSize = gapSize
-        self._mismatchPenalty = mismatchPenalty
-        self._gapOpenPenalty = gapOpenPenalty
-        self._gapExtendPenalty = gapExtendPenalty
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-#        description = "Launch template to create a launcher."
-#        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-#        epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
-#        epilog += "\n\t"
-#        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
-#        epilog += "\t$ python LaunchTemplate.py -i file.fa -c -v 2"
-#        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser = RepetOptionParser(description = "", epilog = "")
-        parser.add_option("-i", "--fasta",      dest = "fastaFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.fa_aln]", default = "")
-        parser.add_option("-s", "--gapSize",    dest = "gapSize",       action = "store",       type = "int",    help = "size above which a gap is not penalized anymore [optional] [default: 50]", default = 50)
-        parser.add_option("-m", "--mismatch",   dest = "mismatch",      action = "store",       type = "int",    help = "penalty for a mismatch [optional] [default: -8]", default = -8)
-        parser.add_option("-O", "--gapOpen",    dest = "gapOpen",       action = "store",       type = "int",    help = "penalty for a gap opening [optional] [default: 16]", default = 16)
-        parser.add_option("-e", "--gapExtend",  dest = "gapExtend",     action = "store",       type = "int",    help = "penalty for a gap extension [optional] [default: 4]", default = 4)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setFastaFileName(options.fastaFileName)
-        self.setOutFileName(options.outFileName)
-        self.setGapSize(options.gapSize)
-        self.setMismatchPenalty(options.mismatch)
-        self.setGapOpenPenalty(options.gapOpen)
-        self.setGapExtendPenalty(options.gapExtend)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def setFastaFileName(self, fastaFileName):
-        self._fastaFileName = fastaFileName
-        
-    def setOutFileName(self, outFileName):
-        if outFileName == "":
-            self._outFileName = "%s.fa_aln" % self._fastaFileName
-        else:
-            self._outFileName = outFileName
-        
-    def setGapSize(self, gapSize):
-        self._gapSize = gapSize
-
-    def setMismatchPenalty(self, mismatchPenalty):
-        self._mismatchPenalty = mismatchPenalty
-        
-    def setGapOpenPenalty(self, gapOpenPenalty):
-        self._gapOpenPenalty = gapOpenPenalty
-        
-    def setGapExtendPenalty(self, gapExtendPenalty):
-        self._gapExtendPenalty = gapExtendPenalty
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._fastaFileName == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-        if not FileUtils.isRessourceExists(self._fastaFileName):
-            self._logAndRaise("ERROR: Input fasta file name %s doesn't exist." % self._fastaFileName)
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def getMapCmd(self):
-        cmd = "rpt_map"
-        cmd += " %s.shortH" % self._fastaFileName
-        cmd += " %i" % self._gapSize
-        cmd += " %i" % self._mismatchPenalty
-        cmd += " %i" % self._gapOpenPenalty
-        cmd += " %i" % self._gapExtendPenalty
-        cmd += " > %s.shortH.fa_aln" % self._fastaFileName
-        return cmd
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START LaunchMap")
-        self._log.debug("Fasta file name: %s" % self._fastaFileName)
-        
-        lInitHeaders = FastaUtils.dbHeaders(self._fastaFileName, self._verbosity - 1)
-        
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile(self._fastaFileName)
-        csh.setFormat("fasta")
-        csh.setStep(1)
-        csh.setPrefix("seq")
-        csh.setLinkFile("%s.shortHlink" % self._fastaFileName)
-        csh.setOutputFile("%s.shortH" % self._fastaFileName)
-        csh.setVerbosityLevel(self._verbosity - 1)
-        csh.run()
-        
-        cmd = self.getMapCmd()
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-            
-        csh.setInputFile("%s.shortH.fa_aln" % self._fastaFileName)
-        csh.setFormat("fasta")
-        csh.setStep(2)
-        csh.setLinkFile("%s.shortHlink" % self._fastaFileName)
-        csh.setOutputFile("%s.shortH.fa_aln.initH" % self._fastaFileName)
-        csh.setVerbosityLevel(self._verbosity - 1)
-        csh.run()
-        
-        absDB = AlignedBioseqDB("%s.shortH.fa_aln.initH" % self._fastaFileName)
-        outFileHandler = open(self._outFileName, "w")
-        for header in lInitHeaders:
-            bs = absDB.fetch(header)
-            bs.upCase()
-            bs.write(outFileHandler)
-        outFileHandler.close()
-        if self._doClean:
-            os.remove("%s.shortH" % self._fastaFileName)
-            os.remove("%s.shortHlink" % self._fastaFileName)
-            os.remove("%s.shortH.fa_aln" % self._fastaFileName)
-            os.remove("%s.shortH.fa_aln.initH" % self._fastaFileName)
-        self._log.info("END Launch")
-
-if __name__ == "__main__":
-    iLaunch = LaunchMap()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/launcher/LaunchMatcher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-
-LOG_DEPTH = "repet.tools"
-
-##Launch MATCHER
-#
-class LaunchMatcher(object):
-
-    def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", doClean = False, verbosity = 0):
-        self._alignFileName = align
-        self._queryFileName = queryFileName
-        self.setSubjectFileName(subjectFileName)
-        self.setOutPrefix(prefix)
-        self._doJoin = doJoin
-        self._eValue = evalue
-        self._keepConflict = keepConflict
-        
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch Matcher."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchMatcher.py -a in.align -v 0"
-        epilog += "\n\t"
-        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
-        epilog += "\t$ python LaunchMatcher.py -a in.align -q query.fa -s nr.fa -c -v 2"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-a", "--align",      dest = "align",         action = "store",       type = "string", help = "input align file name [compulsory] [format: align]",       default = "")
-        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [optional] [format: fasta]",         default = "")
-        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [optional] [format: fasta]",       default = "")
-        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "E-value filter [default: 1e-10]",                          default = "1e-10")
-        parser.add_option("-j", "--join",       dest = "doJoin",        action = "store_true",                   help = "join matches [default: False]",                            default = False)
-        parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true",                   help = "keep conflicting subjects [default: False]",               default = False)
-        parser.add_option("-o", "--outPrefix",  dest = "outPrefix",     action = "store",       type = "string", help = "output file prefix [default: align file name]",            default = "")
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setAlignFileName(options.align)
-        self.setQueryFileName(options.query)
-        self.setSubjectFileName(options.subject)
-        self.setEvalue(options.evalue)
-        self.setDoJoin(options.doJoin)
-        self.setKeepConflicts(options.keepConflict)
-        self.setOutPrefix(options.outPrefix)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-        
-    def setAlignFileName(self, alignFileName):
-        self._alignFileName = alignFileName
-        
-    def setQueryFileName(self, queryFileName):
-        self._queryFileName = queryFileName
-        
-    def setSubjectFileName(self, subjectFileName):
-        self._subjectFileName = subjectFileName
-        
-    def setEvalue(self, evalue):
-        self._eValue = evalue
-        
-    def setDoJoin(self, doJoin):
-        self._doJoin = doJoin
-        
-    def setKeepConflicts(self, keepConflict):
-        self._keepConflict = keepConflict
-        
-    def setOutPrefix(self, outPrefix):
-        if outPrefix == "":
-            self._outPrefix = self._alignFileName
-        else:
-            self._outPrefix = outPrefix
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._alignFileName == "":
-            self._logAndRaise("ERROR: Missing input align file name")
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-
-    def _getMatcherCmd(self):
-        lArgs = []
-        lArgs.append("-m %s" % self._alignFileName)
-        if self._queryFileName:
-            lArgs.append("-q %s" % self._queryFileName)
-        if self._subjectFileName:
-            lArgs.append("-s %s" % self._subjectFileName)
-        if self._doJoin:
-            lArgs.append("-j")
-        lArgs.append("-E %s" % self._eValue)
-        lArgs.append("-B %s" % self._outPrefix)
-        if self._keepConflict:
-            lArgs.append("-a")
-        lArgs.append("-v %i" % (self._verbosity - 1))
-        return self._getSystemCommand("matcher", lArgs)
-    
-    def _getSystemCommand(self, prg, lArgs):
-        systemCmd = prg 
-        for arg in lArgs:
-            systemCmd += " " + arg
-        return systemCmd
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START LaunchMatcher")
-        self._log.debug("Align file name: %s" % self._alignFileName)
-        self._log.debug("Query file name: %s" % self._queryFileName)
-        self._log.debug("Subject file name: %s" % self._subjectFileName)
-        #TODO: clean files
-#        if self._doClean:
-#            self._log.warning("Files will be cleaned")
-        cmd = self._getMatcherCmd()
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        self._log.info("END LaunchMatcher")
-
-if __name__ == "__main__":
-    iLaunch = LaunchMatcher()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/launcher/LaunchMummerPlot.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-from commons.core.LoggerFactory import LoggerFactory
-import os
-import shutil
-  
-LOG_DEPTH = "repet.tools"  
-  
-class LaunchMummerPlot(object):
-
-    def __init__(self, inputFileName="", queryFileName="", refFileName ="", prefix = None, fat=False, filter=False,clean=False, verbosity=0):
-        self._inputFileName = inputFileName
-        self._queryFileName = queryFileName
-        self._refFileName = refFileName
-        self._prefix = prefix
-        self._fat = fat
-        self._filter = filter
-        self.doClean = clean
-        self.verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-             
-    def setAttributesFromCmdLine(self):
-        description = "LaunchMummerPlot runs the MummerPlot program (part of the mummer package) ."    
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-i", "--input", dest="inputFileName", default = None,  action="store", type="string", help="input file[mandatory] [format: delta]")      
-        parser.add_option("-q", "--Qfile", dest="queryFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Qfile [optional] [format: fasta]")
-        parser.add_option("-r", "--Rfile", dest="refFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Rfile [optional] [format: fasta]")
-        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [mandatory]")
-        parser.add_option("-o","--fat", dest="fat",action="store_true", help="Layout sequences using fattest alignment only[optional] ")
-        parser.add_option("-s","--filter", dest="filter",action="store_true", help="Only display .delta alignments which represent the 'best' hit [optional] ")      
-        parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true")  
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")
-        
-        (self._options, args) = parser.parse_args()
-        self._setAttributesFromOptions(self._options)
-
-    def _setAttributesFromOptions(self, options):
-        self._inputFileName = options.inputFileName
-        self._queryFileName = options.queryFileName
-        self._refFileName = options.refFileName
-        self._prefix = options.prefix
-        self._fat = options.fat
-        self._filter = options.filter
-        self.verbosity = options.verbosity
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-            
-    def checkOptions(self):  
-        if self._inputFileName != "":
-            if not FileUtils.isRessourceExists(self._inputFileName):
-                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._inputFileName)
-        else:
-            self._logAndRaise("ERROR: No specified --query option!")     
-        
-        if self._queryFileName != "":
-            if not FileUtils.isRessourceExists(self._queryFileName):
-                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
-        
-        if self._refFileName != "":
-            if not FileUtils.isRessourceExists(self._refFileName):
-                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
-                
-    def clean(self):
-        try:
-            os.remove("%s.filter" % self._prefix)
-        except Exception as inst: 
-            self._log.error(inst)
-        try:
-            os.remove("%s.fplot" % self._prefix)
-        except Exception as inst: 
-            self._log.error(inst)
-        try:
-            os.remove("%s.rplot" % self._prefix)
-        except Exception as inst: 
-            self._log.error(inst)
-                                
-    def run(self):
-        if not CheckerUtils.isExecutableInUserPath("mummerplot") :
-            self._logAndRaise("ERROR: mummerplot must be in your path")
-        self.checkOptions()
-        
-        ref=""
-        if self._refFileName != "":
-            ref = "-R %s"  % self._refFileName
-           
-        query=""
-        if self._queryFileName != "":
-            query = "-Q %s"  % self._queryFileName
-           
-        fat = ""
-        if self._fat:
-            fat =  "--fat"
-            
-        filter = ""
-        if self._filter:
-            filter = "-f" 
-            
-        prefix = ""
-        if self._prefix is not None:
-            prefix = "--prefix=%s" %(self._prefix)
-            
-        cmd = "mummerplot %s %s %s %s %s %s --png" % (self._inputFileName, prefix, ref, query, fat, filter)
-        self._log.debug("Running mummerplot with following commands : %s" %cmd)
-        cmd = cmd.split()         
-        process = subprocess.Popen(cmd)
-        process.wait()
-        
-        self.clean()
-        return process.returncode
-            
-if __name__ == "__main__":
-    iLaunchNucmer = LaunchMummerPlot()
-    iLaunchNucmer.setAttributesFromCmdLine()
-    iLaunchNucmer.run()
\ No newline at end of file

--- a/commons/launcher/LaunchNucmer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,158 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-from commons.core.LoggerFactory import LoggerFactory
-import os
-  
-LOG_DEPTH = "repet.tools"  
-  
-class LaunchNucmer(object):
-
-    def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=90, minMatch=20, nooptimize=False,mincluster=65, minIdentity=50, minLength=100, verbosity=0):
-        self._queryFileName = queryFileName
-        self._refFileName = refFileName
-        self._prefix = prefix
-        self._genCoords = genCoords
-        self._showCoords = showCoords
-        self._mum = mum
-        self._maxgaps = maxGaps
-        self._minMatch = minMatch
-        self._nooptimize = nooptimize
-        self._mincluster = mincluster
-        self._minIdentity = minIdentity
-        self._minLength = minLength
-        self.verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-        
-    def setMincluster(self, value):
-        self._mincluster = value
-    def getMincluster(self):
-        return self._mincluster
-    
-    mincluster = property(getMincluster, setMincluster)
-         
-    def setAttributesFromCmdLine(self):
-        description = "LaunchNucmer runs the Nucmer program (part of the mummer package) ."    
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-q", "--query", dest="queryFileName", default = "",  action="store", type="string", help="input query file [compulsory] [format: fasta]")
-        parser.add_option("-r", "--ref", dest="refFileName", default = "",  action="store", type="string", help="input ref file [compulsory] [format: fasta]")
-        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [optional]")
-        parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ")
-        parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ")        
-        parser.add_option("-m", "--mum", dest="mum",  action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ")      
-        parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 90,  action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 90) [optional] ")
-        parser.add_option("-l", "--minmatch", dest="minMatch", default = 20,  action="store", type="int", help="Minimum length of an maximal exact match (default 20) [optional] ")
-        parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ")  
-        parser.add_option("-j", "--mincluster", dest="mincluster", default = 65,  action="store", type="int", help="Minimum length of a cluster of matches (default 65) [optional] ")
-        
-        parser.add_option("-i", "--minIdentity", dest="minIdentity", default = 50,  action="store", type="int", help="Minimum identity for show_coords (default 50) [optional] ")
-        parser.add_option("-u", "--minLength", dest="minLength", default = 100,  action="store", type="int", help="Minimum alignment length for show_coords (default 100) [optional] ")
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")
-        
-        (self._options, args) = parser.parse_args()
-        self._setAttributesFromOptions(self._options)
-
-    def _setAttributesFromOptions(self, options):
-        self._queryFileName = options.queryFileName
-        self._refFileName = options.refFileName
-        self._prefix = options.prefix
-        self._genCoords = options.genCoords
-        self._showCoords = options.showCoords
-        self._mum = options.mum  
-        self._maxgaps = options.maxgaps
-        self._minMatch = options.minMatch
-        self._nooptimize =  options.nooptimize
-        self._mincluster = options.mincluster
-        
-        self._minIdentity = options.minIdentity
-        self._minLength = options.minLength
-        
-        self.verbosity = options.verbosity
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-            
-    def checkOptions(self):       
-        if self._queryFileName != "":
-            if not FileUtils.isRessourceExists(self._queryFileName):
-                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
-        else:
-            self._logAndRaise("ERROR: No specified --query option!")
-        
-        if self._refFileName != "":
-            if not FileUtils.isRessourceExists(self._refFileName):
-                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
-        else:
-            self._logAndRaise("ERROR: No specified --ref option!")
-                                
-    def run(self):
-        LoggerFactory.setLevel(self._log, self.verbosity)
-        if not CheckerUtils.isExecutableInUserPath("nucmer") :
-            self._logAndRaise("ERROR: nucmer must be in your path")
-        self.checkOptions()
-        
-        genCoords = ""
-        if self._genCoords:
-            genCoords = "-o"     
-        mum = ""
-        if self._mum:
-            mum =  "--mum"
-        nooptimize = "--optimize"
-        if self._nooptimize:
-            nooptimize = "--nooptimize" 
-        prefix = ""
-        if self._prefix is not None:
-            prefix = "--prefix=%s" %(self._prefix) 
-        cmd = "nucmer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster)
-        self._log.debug("Running nucmer with following commands : %s" %cmd)
-        cmd = cmd.split()
-        process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        process.wait()
-        
-        if self._showCoords:
-            #use of os.system because redirect on process is broken in python < 3.0
-            cmd = "show-coords -r -c -l -d -I %d -L %d -T %s.delta > %s.coords" % (self._minIdentity, self._minLength, self._prefix, self._prefix)
-            self._log.debug("Running show-coords with following commands : %s" %cmd)
-            os.system(cmd)
-
-            
-        return process.returncode
-            
-if __name__ == "__main__":
-    iLaunchNucmer = LaunchNucmer()
-    iLaunchNucmer.setAttributesFromCmdLine()
-    iLaunchNucmer.run()
\ No newline at end of file

--- a/commons/launcher/LaunchPhyML.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,177 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-import subprocess
-import os
-from commons.core.seq.Bioseq import Bioseq
-import shutil
-
-LOG_DEPTH = "repet.core.launchers"
-
-
-
-class LaunchPhyML(object):
-    """
-    Launch 'PhyML'
-    """
-    def __init__(self, inputFileName="", outFileName="",dataType= "nt", interleavedFormat= True, nbDataSets=1, nbBootDataSets=0, substModel="HKY85", ratioTsTv=4.0, propInvSites= 0.0, nbCat=1, gammaParam=1.0, startTree="BIONJ", paramOptimisation = "tlr", clean=False, verbosity=3 ):
-        self.inputFileName = inputFileName
-        self.outFileName=outFileName
-        self.dataType = dataType                    #"nt or aa"
-        self._setSeqFormat(interleavedFormat)       #if False -q"
-        self.nbDataSets = nbDataSets
-        self.nbBootDataSets = nbBootDataSets
-        self.substModel = substModel
-        self.ratioTsTv = ratioTsTv
-        self.propInvSites = propInvSites            # propInvSites="e" replaced by 0.0; should be in [0-1]
-        self.nbCat = nbCat                          # Number of categories less than four or higher than eight are not recommended.
-        self.gammaParam = gammaParam
-        self.startTree = startTree                  #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead
-        self.paramOptimisation = paramOptimisation  # used instead of self.optTopology="y", self.optBranchRate="y" 
-                                                    #This option focuses on specific parameter optimisation.
-                                                    #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
-                                                    #tl  : tree topology and branch length are optimised.
-                                                    #lr  : branch length and rate parameters are optimised.
-                                                    #l   : branch length are optimised.
-                                                    #r   : rate parameters are optimised.
-                                                    #n   : no parameter is optimised.
-
-        self._clean = clean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-    
-    def _setSeqFormat(self, interleavedFormat):
-        if not (interleavedFormat) :
-            self.seqFormat = " -q"
-        else :
-            self.seqFormat = ""
-            
-    def setAttributesFromCmdLine(self):
-        description = "usage: LaunchPhyML.py [ options ]"
-        epilog = "\n -h: this help\n"
-        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
-        epilog += "\n\t"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--fasta",      dest = "inputFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.out]", default = "")
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.inputFileName = options.inputFileName
-        self.setOutFileName = options.outFileName
-        self._verbosity = options.verbosity
-
-    def _checkOptions(self):
-        if self.inputFileName == "":
-            self._logAndRaise("ERROR: Missing input file name")
-    
-        if self.outFileName == "":
-            self.outFileName = "%s_phyml.newick" % (self.inputFileName)
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-         
-    def _shortenHeaders(self):
-        self.csh = ChangeSequenceHeaders()
-        self.csh.setInputFile(self.inputFileName)
-        self.csh.setFormat("fasta")
-        self.csh.setStep(1)
-        self.csh.setPrefix("seq")
-        self.csh.setLinkFile(self.inputFileName+".shortHlink")
-        self.csh.setOutputFile(self.inputFileName+".shortH")
-        self.csh.setVerbosityLevel(self._verbosity-1)
-        self.csh.run()
-        self.shortInputFileName = self.inputFileName+".shortH" 
-        
-    def _renameHeaders(self):
-        self.csh.setInputFile(self.phyml_tree)
-        self.csh.setFormat("newick")
-        self.csh.setStep(2)
-        self.csh.setLinkFile(self.inputFileName+".shortHlink" )
-        self.csh.setOutputFile(self.outFileName)
-        self.csh.setVerbosityLevel(self._verbosity-1)
-        self.csh.run()
-          
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START LaunchPhyML")
-        self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
-        
-        inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
-        if not os.path.exists(inputFileName):
-            os.symlink(self.inputFileName, inputFileName)
-        self.inputFileName = inputFileName
-        
-        self._shortenHeaders()
-
-        cmd = "sreformat phylip %s" % (self.shortInputFileName)
-        
-        with open (self.reformatedInputFileName, "w") as fPhylip :
-            
-            process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE)
-            self._log.debug("Running : %s" % cmd)
-            output = process.communicate()
-            self._log.debug("Output:\n%s" % output[0])
-            if process.returncode != 0:
-                self._logAndRaise("ERROR when launching '%s'" % cmd)
-        
-        self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName
-        self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName 
-        cpyPhyml_tree = "%s_cpy" %self.phyml_tree
-        shutil.copyfile(self.phyml_tree,cpyPhyml_tree)
-                          
-        cmd = "phyml -i %s -d %s%s -n %d -b %d -m %s -t %f -v %f -c %d -a %f -u %s -o %s" % (self.reformatedInputFileName, self.dataType, self.seqFormat, self.nbDataSets,self.nbBootDataSets,self.substModel, self.ratioTsTv, self.propInvSites,self.nbCat,self.gammaParam, cpyPhyml_tree , self.paramOptimisation )
-        print cmd    
-        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._log.debug("Running : %s" % cmd)
-        output = process.communicate()
-        self._log.debug("Output:\n%s" % output[0])
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        
-        self._renameHeaders()
-        
-        if self._clean:
-            for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]:
-                os.remove(f)
-            os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) )
-        
-        self._log.info("Finished running LaunchPhyML")
-        
-        

--- a/commons/launcher/LaunchPromer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-from commons.core.LoggerFactory import LoggerFactory
-import os
-  
-LOG_DEPTH = "repet.tools"  
-  
-class LaunchPromer(object):
-
-    def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=30, minMatch=6, nooptimize=False,mincluster=20, verbosity=0):
-        self._queryFileName = queryFileName
-        self._refFileName = refFileName
-        self._prefix = prefix
-        self._genCoords = genCoords
-        self._showCoords = showCoords
-        self._mum = mum
-        self._maxgaps = maxGaps
-        self._minMatch = minMatch
-        self._nooptimize = nooptimize
-        self._mincluster = mincluster
-        self.verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-        
-    def setMincluster(self, value):
-        self._mincluster = value
-    def getMincluster(self):
-        return self._mincluster
-    
-    mincluster = property(getMincluster, setMincluster)
-         
-    def setAttributesFromCmdLine(self):
-        description = "LaunchPromer runs the Promer program (part of the mummer package) ."    
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-q", "--query", dest="queryFileName", default = "",  action="store", type="string", help="input query file [compulsory] [format: fasta]")
-        parser.add_option("-r", "--ref", dest="refFileName", default = "",  action="store", type="string", help="input ref file [compulsory] [format: fasta]")
-        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [optional]")
-        parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ")
-        parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ")        
-        parser.add_option("-m", "--mum", dest="mum",  action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ")      
-        parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 30,  action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 30) [optional] ")
-        parser.add_option("-l", "--minmatch", dest="minMatch", default = 6,  action="store", type="int", help="Minimum length of an maximal exact match (default 6) [optional] ")
-        parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ")  
-        parser.add_option("-j", "--mincluster", dest="mincluster", default = 20,  action="store", type="int", help="Minimum length of a cluster of matches (default 20) [optional] ")
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")
-        
-        (self._options, args) = parser.parse_args()
-        self._setAttributesFromOptions(self._options)
-
-    def _setAttributesFromOptions(self, options):
-        self._queryFileName = options.queryFileName
-        self._refFileName = options.refFileName
-        self._prefix = options.prefix
-        self._genCoords = options.genCoords
-        self._showCoords = options.showCoords
-        self._mum = options.mum  
-        self._maxgaps = options.maxgaps
-        self._minMatch = options.minMatch
-        self._nooptimize =  options.nooptimize
-        self._mincluster = options.mincluster
-        self.verbosity = options.verbosity
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-            
-    def checkOptions(self):       
-        if self._queryFileName != "":
-            if not FileUtils.isRessourceExists(self._queryFileName):
-                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
-        else:
-            self._logAndRaise("ERROR: No specified --query option!")
-        
-        if self._refFileName != "":
-            if not FileUtils.isRessourceExists(self._refFileName):
-                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
-        else:
-            self._logAndRaise("ERROR: No specified --ref option!")
-                                
-    def run(self):
-        if not CheckerUtils.isExecutableInUserPath("promer") :
-            self._logAndRaise("ERROR: promer must be in your path")
-        self.checkOptions()
-        
-        genCoords = ""
-        if self._genCoords:
-            genCoords = "-o"     
-        mum = ""
-        if self._mum:
-            mum =  "--mum"
-        nooptimize = "--optimize"
-        if self._nooptimize:
-            nooptimize = "--nooptimize" 
-        prefix = ""
-        if self._prefix is not None:
-            prefix = "--prefix=%s" %(self._prefix)
-            
-        cmd = "promer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster)
-        self._log.debug("Running promer with following commands : %s" %cmd)
-        cmd = cmd.split()         
-        process = subprocess.Popen(cmd)
-        process.wait()
-        
-        if self._showCoords:
-            #use of os.system because redirect on process is broken in python < 3.0
-            cmd = "show-coords -r -c -l -d -I 50 -L 100 -T %s.delta > %s.coords" % (self._prefix, self._prefix)
-            os.system(cmd)
-
-        return process.returncode
-            
-if __name__ == "__main__":
-    iLaunchPromer = LaunchPromer()
-    iLaunchPromer.setAttributesFromCmdLine()
-    iLaunchPromer.run()
\ No newline at end of file

--- a/commons/launcher/LaunchRefAlign.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,208 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules
-from commons.core.checker.ConfigChecker import ConfigChecker
-import subprocess
-import os
-from commons.core.seq.Bioseq import Bioseq
-
-LOG_DEPTH = "repet.core.launchers"
-
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-class LaunchRefAlign(object):
-    """
-    Launch 'refalign' to build a master-slave multiple sequence alignment.
-    """
-    def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ):
-        self.inputFileName = inputFileName
-        self.outFileName=outFileName
-        self.gapSize = gapSize
-        self.match = match
-        self.mismatch = mismatch
-        self.gapOpen = gapOpen
-        self.gapExtend = gapExtend
-        self.gapExtend = gapExtend
-        self.refseqName = refseqName
-        self.keepRefseq = keepRefseq
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "usage: LaunchRefalign.py [ options ]"
-        epilog = "\n -h: this help\n"
-        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
-        epilog += "\t -r: keep the reference sequence"
-        epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')"
-        epilog += "\t -v: verbosity (default=0)"
-        epilog += "\n\t"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--fasta",      dest = "inputFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.out]", default = "")
-        parser.add_option("-r", "--keepRefseq", dest = "keepRefseq",    action = "store_true",                   help = "keep reference sequence [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.inputFileName = options.inputFileName
-        self.setOutFileName = options.outFileName
-        self.keepRefseq = options.keepRefseq
-        self._verbosity = options.verbosity
-
-    def _checkOptions(self):
-        if self.inputFileName == "":
-            self._logAndRaise("ERROR: Missing input file name")
-    
-        if self.outFileName == "":
-            self.outFileName = "%s.fa_aln" % (self.inputFileName)
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-         
-    def _prepareRefAlign(self):
-        self.shortInputFileName = self.inputFileName+".shortH" 
-        self.refFileName= self.shortInputFileName + ".ref"
-        self.cpyFileName=self.shortInputFileName + ".cpy"
-        
-        file_db = open(self.shortInputFileName)
-        file_ref = open(self.refFileName,"w")
-        file_cpy = open(self.cpyFileName,"w")
-        
-        self._numseq=0
-        while 1:
-            seq=Bioseq()
-            seq.read(file_db)
-            if seq.sequence==None:
-                break
-            self._numseq+=1
-            if self._numseq==1:
-                seq.write(file_ref)
-            else:
-                seq.write(file_cpy)
-        file_db.close()
-        file_ref.close()
-        file_cpy.close()
-    
-    def _shortenHeaders(self):
-        self.csh = ChangeSequenceHeaders()
-        self.csh.setInputFile(self.inputFileName)
-        self.csh.setFormat("fasta")
-        self.csh.setStep(1)
-        self.csh.setPrefix("seq")
-        self.csh.setLinkFile(self.inputFileName+".shortHlink")
-        self.csh.setOutputFile(self.inputFileName+".shortH")
-        self.csh.setVerbosityLevel(self._verbosity-1)
-        self.csh.run()
-        
-        bsDB = BioseqDB(self.inputFileName+".shortH")
-        bsDB.upCase()
-        bsDB.save(self.inputFileName+".shortHtmp")
-        del bsDB
-        os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH")
-        
-    def _renameHeaders(self):
-        self.csh.setInputFile(self.inputFileName+".shortH.fa_aln")
-        self.csh.setFormat("fasta")
-        self.csh.setStep(2)
-        self.csh.setLinkFile(self.inputFileName+".shortHlink" )
-        self.csh.setOutputFile(self.outFileName)
-        self.csh.setVerbosityLevel(self._verbosity-1)
-        self.csh.run()
-          
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START LaunchRefAlign")
-        self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
-        
-        inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
-        if not os.path.exists(inputFileName):
-            os.symlink(self.inputFileName, inputFileName)
-        self.inputFileName = inputFileName
-        
-        self._shortenHeaders()
-        if self.keepRefseq:
-            self.refseqName="seq1"
-        self._prepareRefAlign()
-        
-        if self._numseq > 1:
-            cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend)
-            
-            process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-            self._log.debug("Running : %s" % cmd)
-            output = process.communicate()
-            self._log.debug("Output:\n%s" % output[0])
-            if process.returncode != 0:
-                self._logAndRaise("ERROR when launching '%s'" % cmd)
-            refseqNameParam = ""
-            if self.refseqName != "":
-                refseqNameParam = "-r %s " % (self.refseqName)
-            outFileName = self.inputFileName+".shortH.fa_aln"
-            #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName))
-            
-            self._log.info("Copy file path %s " % self.cpyFileName)
-            print("Copy file path %s " % self.cpyFileName)
-            cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName)
-            self._log.debug("Running : %s" % cmd)
-            process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-            output = process.communicate()
-            self._log.debug("Output:\n%s" % output[0])
-            
-            if process.returncode != 0:
-                self._logAndRaise("ERROR when launching '%s'" % cmd)
-                
-            cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat"
-            os.system(cmd)
-            
-        else:
-            self._logAndRaise("Only one sequence available")
-            cmd = "echo empty"
-            
-        self._renameHeaders()
-        
-        for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]:
-            os.remove(fileName)
-        self._log.info("END LaunchRefAlign")
-        return 0
-        
-
-if __name__ == "__main__":
-    iLaunchRefAlign = LaunchRefAlign()
-    iLaunchRefAlign.setAttributesFromCmdLine()
-    iLaunchRefAlign.run()

--- a/commons/launcher/LaunchRefalign_old.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-
-import pyRepet.launcher.programLauncher
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-def help():
-    print
-    print "usage: launchRefalign.py [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (refseq is first, format='fasta')"
-    print "     -r: keep the reference sequence"
-    print "     -o: name of the output file (default=inFileName+'.fa_aln')"
-    print "     -v: verbose (default=0)"
-    print
-
-
-def main():
-    """
-    Launch 'refalign' to build a master-slave multiple sequence alignment.
-    """
-    inFileName = ""
-    keepRefseq = False
-    outFileName = ""
-    verbose = 0
-    try:
-        opts,args=getopt.getopt(sys.argv[1:],"hi:ro:v:")
-    except getopt.GetoptError, err:
-            print str(err); help(); sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-r":
-            keepRefseq = True
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-    if inFileName == "":
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-        
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    if verbose > 0:
-        print "build a multiple alignment from '%s'..." % ( inFileName )
-        sys.stdout.flush()
-        
-    if outFileName == "":
-        outFileName = "%s.fa_aln" % ( inFileName )
-        
-    csh = ChangeSequenceHeaders()
-    csh.setInputFile( inFileName )
-    csh.setFormat( "fasta" )
-    csh.setStep( 1 )
-    csh.setPrefix( "seq" )
-    csh.setLinkFile(  inFileName+".shortHlink" )
-    csh.setOutputFile( inFileName+".shortH" )
-    csh.setVerbosityLevel( verbose - 1 )
-    csh.run()
-    
-    bsDB = BioseqDB( inFileName+".shortH" )
-    bsDB.upCase()
-    bsDB.save( inFileName+".shortHtmp" )
-    del bsDB
-    os.rename( inFileName+".shortHtmp", inFileName+".shortH" )
-    
-    pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" )
-    if keepRefseq:
-        pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", refseqName="seq1", verbose=verbose )
-    else:
-        pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", verbose=verbose )
-        
-    csh.setInputFile( inFileName+".shortH.fa_aln" )
-    csh.setFormat( "fasta" )
-    csh.setStep( 2 )
-    csh.setLinkFile(  inFileName+".shortHlink" )
-    csh.setOutputFile(  outFileName )
-    csh.setVerbosityLevel( verbose - 1 )
-    csh.run()
-    
-    for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.fa_aln" ]:
-            os.remove( f )
-            
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/launcher/LaunchRepeatMasker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-  
-class LaunchRepeatMasker(object):
-
-    def __init__(self,queryFileName="", libFileName ="",sensitivity="", engine="wu", cutOff=225, outputDir = ".",verbosity=0):
-        self._queryFileName = queryFileName
-        self._libFileName = libFileName
-        self._engine = engine
-        self._sensitivity = sensitivity
-        self._cutOff = cutOff
-        self._outputDir = outputDir
-        self._verbosity = verbosity
-         
-    def setAttributesFromCmdLine(self):
-        description = "LaunchRepeatMasker runs the RepeatMasker program  ."    
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-q", "--query", dest="queryFileName", default = None,  action="store", type="string", help="input query file [compulsory] [format: fasta]")
-        parser.add_option("-l", "--libFileName", dest="libFileName", default = None,  action="store", type="string", help="custom library [optional]")  
-        parser.add_option("-n", "--outputDir", dest="outputDir", default=".", action="store", type="string", help="outputDir (default : current directory) [optional] ")  
-        parser.add_option("-c", "--cutOff", dest="cutOff", default=225, action="store", type="int", help="Sets cutoff score for masking repeats when using -lib (default 225) [optional] ")
-        parser.add_option("-e", "--engine", dest="engine", default = "wu",  action="store", type="string", help="engine  [optional] ")    
-        parser.add_option("-u", "--sensitivity", dest="sensitivity", default = "",  action="store", type="string", help="sensitivity  can be s, q, qq[optional] ")    
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")    
-
-        (options, args) = parser.parse_args()
-        self._setAttributesFromOptions(options)
-
-    def _setAttributesFromOptions(self, options):
-        self._queryFileName = options.queryFileName
-        self._libFileName = options.libFileName
-        self._outputDir = options.outputDir
-        self._engine = options.engine
-        self._sensitivity = options.sensitivity
-        self._cutOff = options.cutOff
-        self._verbosity = options.verbosity
-        
-    def checkOptions(self):       
-        if self._queryFileName != "":
-            if not FileUtils.isRessourceExists(self._queryFileName):
-                raise Exception("ERROR: Query file: %s does not exist!" % self._queryFileName)
-        else:
-            raise Exception("ERROR: No specified --query option!")
-                                
-    def run(self):
-        if not CheckerUtils.isExecutableInUserPath("RepeatMasker") :
-            print "ERROR: RepeatMasker must be in your path"
-        else:
-            self.checkOptions()
-            
-            engine = ""
-            if self._engine == "wu":
-                engine = "-e wublast"
-            elif self._engine == "cm":
-                engine = "-e crossmatch"
-            sensitivity = ""
-            if self._sensitivity:
-                sensitivity = "-%s" % self._sensitivity     
-            libFileName = ""
-            if self._libFileName != "":
-                libFileName = "-lib %s" % self._libFileName
-
-            cmd = "RepeatMasker %s -dir %s -pa 1 -gccalc -no_is -nolow %s %s %s" % (self._queryFileName,self._outputDir,engine,sensitivity,libFileName)
-            cmd = cmd.split() 
-            
-            if self._verbosity>0:
-                print("Running RepeatMasker with following commands : %s" %cmd)
-            
-            process = subprocess.Popen(cmd, stdout=subprocess.PIPE,stderr = subprocess.PIPE)
-#            process.wait()
-            output= process.communicate()
-            if self._verbosity>0:
-                print("".join(output))
-            return process.returncode
-            
-if __name__ == "__main__":
-    iLaunchRepeatMasker = LaunchRepeatMasker()
-    iLaunchRepeatMasker.setAttributesFromCmdLine()
-    iLaunchRepeatMasker.run()
\ No newline at end of file

--- a/commons/launcher/LaunchTRF.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules
-from commons.core.checker.ConfigChecker import ConfigChecker
-import subprocess
-import glob
-import os
-
-LOG_DEPTH = "repet.launchers"
-
-class LaunchTRF(object):
-    
-    def __init__(self, inFileName = "", outFileName = "", maxPeriod=15, doClean = False, verbosity = 0):
-        self.inFileName = inFileName
-        self.setOutFileName(outFileName)
-        self.maxPeriod=maxPeriod
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch TRF to detect micro-satellites in sequences."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
-        epilog += "\n\t"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--in",      dest = "inFileName", action = "store",       type = "string", help = "input file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.TRF.set]", default = "")
-        parser.add_option("-m", "--maxPeriod",  dest = "maxPeriod",     action = "store",       type = "int",    help = " maximum period size to report  [default: 15]", default = 15)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setInFileName(options.inFileName)
-        self.setOutFileName(options.outFileName)
-        self.maxPeriod = options.maxPeriod
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-                
-    def setInFileName(self, inFileName):
-        self.inFileName = inFileName
-        
-    def setOutFileName(self, outFileName):
-        if outFileName == "":
-            self._outFileName = "%s.TRF.set" % self.inFileName
-        else:
-            self._outFileName = outFileName
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self.inFileName == "":
-            self._logAndRaise("ERROR: Missing input file name")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    
-    def _launchTRF(self):
-        cmd = "trf %s 2 3 5 80 10 20 %d -h -d" % (self.inFileName, self.maxPeriod)
-        self._log.debug("Running : %s" % cmd)
-        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        output = process.communicate()
-        self._log.debug("Output:\n%s" % output[0])
-        
-    def _parseTRF(self):
-        self._log.debug("Parsing TRF output")
-        with open( "%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod),'r') as inFile:
-            with open(self._outFileName,'w') as outFile:
-                nbPatterns = 0
-                nbInSeq = 0
-                for line in inFile.readlines():
-                    if line == "":
-                        break
-                    data = line.split(" ")
-                    if len(data) > 1 and "Sequence:" in data[0]:
-                        nbInSeq += 1
-                        seqName = data[1][:-1]
-                    if len(data) < 14:
-                        continue
-                    nbPatterns += 1
-                    consensus = data[13]
-                    copyNb = int( float(data[3]) + 0.5 )
-                    start = data[0]
-                    end = data[1]
-                    outFile.write( "%i\t(%s)%i\t%s\t%s\t%s\n" % ( nbPatterns, consensus, copyNb, seqName, start, end ) )
-        self._log.debug("Finished Parsing TRF output")
-    
-    def _clean(self):
-        try:
-            os.remove("%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod))
-        except:pass
-        
-
-    def run(self):
-        """
-        Launch TRF to detect micro-satellites in sequences.
-        """
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START Launch")
-        self._log.debug("Input file name: %s" % self.inFileName)
-        
-        self._launchTRF()
-        self._parseTRF()
-        
-        if self._doClean:
-            self._log.warning("Files will be cleaned")
-            self._clean()
-        self._log.info("END Launch")
-  
-if __name__ == "__main__":
-    iLaunchTRF = LaunchTRF()
-    iLaunchTRF.setAttributesFromCmdLine()
-    iLaunchTRF.run()        
-

--- a/commons/launcher/LaunchTallymer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,328 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Launch Tallymer's sub programs, generate map file, and convert output to gff and wig, as well as visual (RPlot) data
-"""
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import shutil
-import subprocess
-import time
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.LoggerFactory import LoggerFactory
-from SMART.Java.Python.convertTranscriptFile import ConvertTranscriptFile
-from commons.core.seq.BioseqUtils import BioseqUtils
-from commons.core.seq.BioseqDB import BioseqDB
-from Tallymer_pipe.PlotBenchMarkGFFFiles import PlotBenchMarkGFFFiles
-
-LOG_DEPTH = "repet.tools"
-
-
-class LaunchTallymer(object):
-    """
-    Launch Tallymer's sub programs, generate map file, and convert output to
-    gff and wig, as well as visual (RPlot) data
-    """
-    
-    _lValidFormats = ["gff", "gff3", "wig", "bed", "map"]
-    
-    def __init__(self, inputFasta="", indexationFasta=None, merSize=20, minOccs=4, outputFormats="gff", nLargestScaffoldsToPlot=0, clean=False, verbosity=0):
-        self.inputFasta = inputFasta
-        self.indexationFasta = indexationFasta if indexationFasta != None else inputFasta 
-        self.merSize = merSize
-        self.minOccs = minOccs
-        self.outputFormats = outputFormats
-        self.nLargestScaffoldsToPlot = nLargestScaffoldsToPlot
-        self.doClean = clean
-        self.verbosity = verbosity
-        
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-        self._workdir = os.path.join(os.getcwd(), "launchTallymer_%s" % time.strftime("%Y%m%d%H%M%S"))
-        self._tmpSearchFileName = None
-        self._tmpMapFileName = None
-        self._tmpStatFileName = None   
-        self._tmpPngFileName = None
-        self._plot_data = {}
-        self._plot_data2 = {}
-        
-    def setAttributesFromCmdLine(self):
-        description = "Generates stats from the results of the tallymer search ."    
-        parser = RepetOptionParser(description=description)
-        parser.add_option("-i", "--inputFasta", dest="inputFasta", default = "",  action="store", type="string", help="input fasta file [compulsory] [format: fasta]")
-        parser.add_option("-u", "--indexationFasta", dest="indexationFasta", default = "",  action="store", type="string", help="input indexation fasta file used to generate kmer index (defaults to input fasta)[optional] [format: fasta]")
-        parser.add_option("-s", "--merSize", dest="merSize", default = 20,  action="store", type="int", help="input merSize [optional][default:20]")
-        parser.add_option("-m", "--minOccs", dest="minOccs", default = 4,  action="store", type="int", help="input minimal kmer occurence count [default:4]")
-        parser.add_option("-f", "--outputFormats", dest="outputFormats", default = "gff",  action="store", type="string", help="comma separated list of output file formats (can  be %s) [optional] [default:gff]" % ", ".join(self._lValidFormats))
-        parser.add_option("-n", "--nLargestScaffoldsToPlot",default = 0, type="int", action="store", dest = "nLargestScaffoldsToPlot", help = "generate graph of Kmer repartition along the input sequence for the n biggest scaffolds")
-        parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true")
-        parser.add_option("-v", "--verbosity", dest="verbosity", default = 1,  action="store", type="int", help="verbosity [optional] ")
-        options, args = parser.parse_args()
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.inputFasta = options.inputFasta
-        self.indexationFasta = options.indexationFasta if options.indexationFasta != "" else options.inputFasta
-        self.merSize = options.merSize
-        self.minOccs = options.minOccs
-        self.outputFormats = options.outputFormats
-        self.nLargestScaffoldsToPlot = options.nLargestScaffoldsToPlot
-        self.doClean = options.clean
-        self.verbosity = options.verbosity
-        
-    def _checkOptions(self):
-        if self.inputFasta == "":
-            self._logAndRaise("Error: missing input fasta file")
-        if self.merSize < 1:
-            self._logAndRaise("Error: invalid kmer size '%i'; must be a positive integer" % self.merSize)
-            
-        self.outputFormats = self.outputFormats.lower().split(',')
-        sOutFormats = set(self.outputFormats)
-        sValidFormats = set(self._lValidFormats)
-        lInvalidFormats = list(sOutFormats - sValidFormats)
-        self.outputFormats = list(sValidFormats.intersection(sOutFormats))
-        if lInvalidFormats:
-            self._log.warning("Warning: ignoring invalid formats: <%s>" % " ".join(lInvalidFormats))
-        if not self.outputFormats:
-            self._logAndRaise("Error: no valid output formats specified")
-
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def clean(self):
-        try:
-            shutil.rmtree(self._workdir)
-        except Exception as inst: 
-            self._log.error(inst)
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self.verbosity)
-        self._checkOptions()
-        self._log.debug("Input fasta file: %s; K-mer size: %s; Output formats: %s; Cleaning: %s" % (self.inputFasta, self.merSize, str(self.outputFormats), self.doClean))
-        try:
-            os.makedirs(self._workdir)
-        except:pass
-        
-        srcPath = os.path.abspath(self.inputFasta)
-        dstPath = os.path.join(self._workdir,os.path.basename(self.inputFasta))
-        os.symlink(srcPath, dstPath)
-        
-        if (self.indexationFasta !=  self.inputFasta):
-            srcPath = os.path.abspath(self.indexationFasta)
-            dstPath = os.path.join(self._workdir,os.path.basename(self.indexationFasta))
-            try:
-                os.symlink(srcPath, dstPath)
-            except OSError as inst:
-                pass
-        
-        os.chdir(self._workdir)
-        
-        if (self.indexationFasta !=  self.inputFasta):
-            self.indexationFasta = os.path.basename(self.indexationFasta)
-        else:
-            self.indexationFasta = os.path.basename(self.inputFasta)
-        self.inputFasta = os.path.basename(self.inputFasta)
-        
-        self._tmpSearchFileName = "%s.tallymer" % os.path.splitext(os.path.basename(self.inputFasta))[0]
-        self._tmpMapFileName = "%s_tmp.map" % self._tmpSearchFileName
-        self._tmpStatFileName = "%s.stat" % self._tmpSearchFileName
-        self._tmpPngFileName = "%s.png" % self._tmpSearchFileName
-        
-        
-            
-        
-        
-        self._runTallymerSearch()
-        self._convertTallymerToMap()
-        self._writeOutputFiles()
-            
-        if self.nLargestScaffoldsToPlot > 0:
-            self._doPlot()
-            shutil.copy2(self._tmpPngFileName, "../.")
-        
-        shutil.copy2(self._tmpStatFileName, "../.")
-        os.chdir("..")
-        
-        if self.doClean:
-            self.clean()
-
-    def _runTallymerSearch(self):
-        self._log.info("Starting to run tallymer search of sequence %s " % (self.inputFasta))
-        self._indexInputFastaFile()
-        self._countAndIndexKmersForGivenK()
-        self._searchKmersListInTallymerIndex()
-        self._log.info("Finished running tallymer scan of sequence %s " % (self.inputFasta))
-        
-    def _convertTallymerToMap(self):
-        self._log.info("Starting to run tallymer search to map conversion")
-        totalNbOcc, dKmer2Occ, self._plot_data, self._plot_data2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(self.inputFasta, self._tmpSearchFileName, self._tmpMapFileName)
-        self._log.debug("totalNbOcc=%i" % totalNbOcc)
-        self._writeOccurencesNbAndFrequencyOfKmers(totalNbOcc, dKmer2Occ)        
-        self._log.info("Finished tallymer search to map conversion")
-    
-    def _doPlot(self):
-        iBioseqDB = BioseqDB()
-        iBioseqDB.load(self.inputFasta)
-        largest_seqsDb = iBioseqDB.bestLength(self.nLargestScaffoldsToPlot)
-        
-        for seq in largest_seqsDb.db:
-            headerCleaned = seq.header.replace(" ", "_")
-            shortFastaName = "%s_%s" % (os.path.basename(self.inputFasta),headerCleaned)
-            data = self._plot_data2[seq.header]
-            gffPlotter = PlotBenchMarkGFFFiles(yLabel="Number of Kmer Occurences", maxLength=1, title="Kmer repartition along the input sequence: %s; MerSize: %i" % (shortFastaName, self.merSize) )
-            gffPlotter.setOutFileName("%s_%s.png" % (self._tmpSearchFileName, headerCleaned))
-            gffPlotter._title = "Mers along the input sequence: %s MerSize: %i" % (shortFastaName, self.merSize) 
-            gffPlotter._xLabel = "Coordinates along the input sequence (%s)" % shortFastaName
-            gffPlotter._rawData = data
-            gffPlotter.run()
-
-    def _indexInputFastaFile(self):
-        self._log.debug("index the input fasta file: get an enhanced suffix array.")
-        cmd = "gt suffixerator -dna -pl -tis -suf -lcp -v -db %s -indexname %s.reads" % (self.indexationFasta, self.indexationFasta)
-        process = subprocess.Popen(cmd.split(' '),stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._log.debug("Running suffixerator with following params %s" % cmd)
-        output = process.communicate()
-        self._log.debug("Suffixerator Output:\n%s" % output[0])
-        if process.returncode != 0:
-            self._logAndRaise("Error in generating enhanced suffix array in %s" % self.indexationFasta)
-
-    def _countAndIndexKmersForGivenK(self):
-        self._log.debug("Counting and indexing k-mers for k = %i " % self.merSize)
-        cmd = "gt tallymer mkindex -mersize %i -minocc %i -indexname %s.tyr-reads -counts -pl -esa %s.reads" % (self.merSize, self.minOccs, self.indexationFasta, self.indexationFasta)
-        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._log.debug("Running tallymer mkindex with following params %s" % cmd)
-        output = process.communicate()
-        self._log.debug("Tallymer mkindex Output:\n%s" % output[0])
-        if process.returncode != 0:
-            self._logAndRaise("Error in indexing kmers in %s.reads" % self.indexationFasta)
-
-    def _searchKmersListInTallymerIndex(self):
-        self._log.debug("Searching list of kmers in tallymer-index ")
-        cmd = "gt tallymer search -output qseqnum qpos counts sequence -tyr %s.tyr-reads -q %s" % (self.indexationFasta, self.inputFasta)
-        process = subprocess.Popen(cmd.split(' '),stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._log.debug("Running tallymer search with following params %s" % cmd)
-        output = process.communicate()
-        self._log.debug("Tallymer search Output:\n%s" % output[0])
-        if process.returncode != 0:
-            self._logAndRaise("Error in searching for kmers in %s.tyr-reads" % self.indexationFasta)
-        tmpOutputFile = open(self._tmpSearchFileName,'w')
-        tmpOutputFile.write(output[0])
-        tmpOutputFile.close()
-
-    def _writeOccurencesNbAndFrequencyOfKmers(self, totalNbOcc, dKmer2Occ):
-        with open(self._tmpStatFileName, "w") as statFile:
-            statFile.write("kmer\tocc\tfreq\n")
-            for kmer in dKmer2Occ.keys():
-                statFile.write("%s\t%i\t%.10f\n" % (kmer, dKmer2Occ[kmer], dKmer2Occ[kmer] / float(totalNbOcc)))
-
-    def _writeOutputFiles(self):
-        for format in self.outputFormats:
-            self._log.info("Generating %s file" % format)
-            outputFileName = "%s.tallymer.%s" % (os.path.splitext(self.inputFasta)[0], format)
-            try:
-                iConvertTranscriptFile = ConvertTranscriptFile(inputFileName=self._tmpMapFileName, name="Tallymer",\
-                         inputFormat="map", outputFileName=outputFileName, outputFormat=format,feature= "Match", featurePart="Match-part", verbosity=0) #self.verbosity
-                iConvertTranscriptFile.run()
-            except Exception as inst:
-                self._log.error("Error: %s - Failed to generate %s format ouput, skipping" % (inst, format))
-            shutil.copy2(outputFileName, "../.")
-
-
-class ConvertUtils(object):
-    
-    def convertTallymerFormatIntoMapFormatAndGenerateData(fastaFileName, searchFileName, mapFileName):
-        dIndex2NameLengthList = ConvertUtils._createDictOfNameLengthAccordingToSeqOrder(fastaFileName)
-        plotData = {}
-        plotData2 = {}
-        with open(searchFileName, "r") as talFile:
-            with open(mapFileName, "w") as mapFile:
-                totalNbOcc = 0
-                dKmer2Occ = {}
-                line = talFile.readline()
-                while line:
-                    data = line[:-1].split("\t")
-                    name = "%s_%s" % (data[3], data[2])
-                    nbOccs = int(data[2])
-                    chrname = dIndex2NameLengthList[int(data[0])][0]
-                    if data[1][0] == "+":
-                        start = int(data[1][1:]) + 1
-                        end = start + len(data[3])
-                    elif data[1][0] == "-":
-                        start_revcomp = int(data[1][1:])
-                        start = dIndex2NameLengthList[int(data[0])][1] - start_revcomp - 1
-                        end = end - len(data[3]) + 1
-                    mapLine = "%s\t%s\t%s\t%s\t%i\n" % (name, chrname, start, end, nbOccs)
-                    mapFile.write(mapLine)
-                    
-                    if plotData2.get(chrname,None) is None:
-                        plotData2[chrname] = {}
-                    if plotData2[chrname].get(start, None) is None:
-                        plotData2[chrname][start]=0
-                    plotData2[chrname][start] += nbOccs
-                    
-                    totalNbOcc += 1
-                    if dKmer2Occ.has_key(data[3]):
-                        dKmer2Occ[data[3]] += 1
-                    else:
-                        dKmer2Occ[data[3]] = 1
-                    plotData[start] = nbOccs
-                    line = talFile.readline()
-        return totalNbOcc, dKmer2Occ, plotData, plotData2
-    
-    convertTallymerFormatIntoMapFormatAndGenerateData = staticmethod(convertTallymerFormatIntoMapFormatAndGenerateData)
-    
-    def _createDictOfNameLengthAccordingToSeqOrder(fastaFileName):
-        with open(fastaFileName) as fastaFile:
-            line = fastaFile.readline()
-            i = 0
-            length = 0
-            dIndex2Name = {}
-            while line:
-                if line[0] == ">":
-                    dIndex2Name[i] = [line[1:-1]]
-                    if i > 0:
-                        dIndex2Name[i - 1].append(length)
-                        length = 0
-                    i += 1
-                else:
-                    length += len(line[:-1])
-                line = fastaFile.readline()
-            dIndex2Name[i - 1].append(length)
-        return dIndex2Name
-    
-    _createDictOfNameLengthAccordingToSeqOrder = staticmethod(_createDictOfNameLengthAccordingToSeqOrder)
-
-if __name__ == "__main__":
-    iLaunchTallymer = LaunchTallymer()
-    iLaunchTallymer.setAttributesFromCmdLine()
-    iLaunchTallymer.run()        
\ No newline at end of file

--- a/commons/launcher/MafftClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch MafftProgramLauncher on several files in parallel on a cluster.
-
-
-from pyRepet.launcher.AbstractClusterLauncher import *
-from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
-
-
-class MafftClusterLauncher( AbstractClusterLauncher ):
-    """
-    Launch Mafft on several files in parallel on a cluster.
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractClusterLauncher.__init__( self )
-        AbstractClusterLauncher.setAcronym( self, "Mafft" )
-        
-        self._cmdLineSpecificOptions = "p:"
-        
-        self._exeWrapper = "MafftProgramLauncher.py"
-        self._prgLauncher = None
-        self._prgLauncher = self.getProgramLauncherInstance()
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -p: parameters for 'mafft' (default='--auto')"
-        return string
-    
-    
-    def getProgramParameters( self ):
-        return self._prgLauncher.getProgramParameters()
-    
-    
-    def getProgramLauncherInstance( self ):
-        if self._prgLauncher == None:
-            self._prgLauncher = MafftProgramLauncher()
-            self._prgLauncher.setInputFile( GENERIC_IN_FILE )
-            self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
-            self._prgLauncher.setClean()
-            self._prgLauncher.setVerbosityLevel( 1 )
-            self._prgLauncher.setListFilesToKeep()
-            self._prgLauncher.setListFilesToRemove()
-        return self._prgLauncher
-    
-    
-if __name__ == "__main__":
-    i = MafftClusterLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/MafftProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,188 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch Mafft (multiple alignment).
-#
-# options:
-#      -h: this help
-#      -i: name of the input file (format='fasta')
-#      -p: parameters for 'mafft' (default='--auto')
-#      -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import os
-import sys
-import getopt
-import exceptions
-
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-from pyRepet.seq.fastaDB import *
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-class MafftProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch Mafft (multiple alignment).
-    """
-    
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "mafft"
-        self._formatInFile = "fasta"
-        self._prgParam = "--auto"
-        self._cmdLineSpecificOptions = "p:o:"
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -p: parameters for '%s' (default='--auto')" % ( self.getProgramName() )
-        string += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
-        return string
-    
-    
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        """
-        Set a specific attribute from the command-line arguments.
-        """
-        if o == "-p":
-            self.setProgramParameters( a )
-        elif o == "-o":
-            self.setOutputFile( a )
-            
-            
-    def checkSpecificAttributes( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-            
-            
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for MafftClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        
-        
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        self._prgCmdLine += " %s" % ( self.getProgramParameters() )
-        if self.getVerbosityLevel() == 0 and "--quiet" not in self._prgCmdLine:
-            self._prgCmdLine += " --quiet"
-        self._prgCmdLine += " %s.shortH" % ( self.getInputFile() )
-        self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() )
-        if self._verbose < 2:
-            self._prgCmdLine += " 2> /dev/null"
-            
-            
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        
-        
-    def setListFilesToRemove( self ):
-        """
-        Set the list of files to remove.
-        """
-        self.appendFileToRemove( "%s.shortH" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.shortHlink" % ( self.getInputFile() ) )
-        
-        
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 )
-        
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile( self.getInputFile() )
-        csh.setFormat( "fasta" )
-        csh.setStep( 1 )
-        csh.setPrefix( "seq" )
-        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
-        csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) )
-        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
-        csh.run()
-        
-        bsDB = BioseqDB( "%s.shortH" % ( self.getInputFile() ) )
-        bsDB.upCase()
-        bsDB.save( "%s.shortHtmp" % ( self.getInputFile() ) )
-        del bsDB
-        os.rename( "%s.shortHtmp" % ( self.getInputFile() ),
-                   "%s.shortH" % ( self.getInputFile() ) )
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
-            print string
-            sys.exit(1)
-            
-        csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
-        csh.setFormat( "fasta" )
-        csh.setStep( 2 )
-        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
-        csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
-        csh.run()
-        
-        absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        outFileHandler = open( self.getOutputFile(), "w" )
-        for header in lInitHeaders:
-            bs = absDB.fetch( header )
-            bs.upCase()
-            bs.write( outFileHandler )
-        outFileHandler.close()
-        os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = MafftProgramLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/MapClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch MapProgramLauncher.py on several files in parallel on a cluster.
-
-
-import os
-import sys
-import getopt
-import exceptions
-
-from pyRepet.launcher.AbstractClusterLauncher import *
-from commons.launcher.MapProgramLauncher import MapProgramLauncher
-
-
-class MapClusterLauncher( AbstractClusterLauncher ):
-    """
-    Launch Map on several files in parallel on a cluster.
-    """
-    
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractClusterLauncher.__init__( self )
-        AbstractClusterLauncher.setAcronym( self, "Map" )
-        
-        self._cmdLineSpecificOptions = "s:m:O:e:"
-        
-        self._exeWrapper = "MapProgramLauncher.py"
-        self._prgLauncher = None
-        self._prgLauncher = self.getProgramLauncherInstance()
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() )
-        string += "\n     -m: penalty for a mismatch (default='%i')" % ( self.getMismatchPenalty() )
-        string += "\n     -O: penalty for a gap openning (default='%i')" % ( self.getGapOpenPenalty() )
-        string += "\n     -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() )
-        return string
-    
-    
-    def getGapSize( self ):
-        return self._prgLauncher.getGapSize()
-        
-        
-    def getMismatchPenalty( self ):
-        return self._prgLauncher.getMismatchPenalty()
-        
-        
-    def getGapOpenPenalty( self ):
-        return self._prgLauncher.getGapOpenPenalty()
-        
-        
-    def getGapExtendPenalty( self ):
-        return self._prgLauncher.getGapExtendPenalty()
-    
-    
-    def getProgramLauncherInstance( self ):
-        if self._prgLauncher == None:
-            self._prgLauncher = MapProgramLauncher()
-            self._prgLauncher.setInputFile( GENERIC_IN_FILE )
-            self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
-            #TESt de SATannot verifier si clean est a vrai
-            #self._prgLauncher.setClean()
-            self._prgLauncher.setVerbosityLevel( 1 )
-            self._prgLauncher.setListFilesToKeep()
-            self._prgLauncher.setListFilesToRemove()
-        return self._prgLauncher
-    
-    
-if __name__ == "__main__":
-    i = MapClusterLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/MapProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,251 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch Map (multiple alignment).
-#
-# options:
-#      -h: this help
-#      -i: name of the input file (format='fasta')
-#      -s: size above which a gap is not penalized anymore (default='50')
-#      -m: penalty for a mismatch (default='-8')
-#      -O: penalty for a gap opening (default='16')
-#      -e: penalty for a gap extension (default='4')
-#      -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import sys
-import os
-
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-class MapProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch Map (multiple alignment).
-    """
-    
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "rpt_map"
-        self._formatInFile = "fasta"
-        self._cmdLineSpecificOptions = "s:m:O:e:o:"
-        self._gapSize = 50
-        self._mismatchPenalty = -8
-        self._gapOpenPenalty = 16
-        self._gapExtendPenalty = 4
-        self._outFile = ""
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() )
-        string += "\n     -m: penalty for a mismatch (default='%i', match=10)" % ( self.getMismatchPenalty() )
-        string += "\n     -O: penalty for a gap opening (default='%i')" % ( self.getGapOpenPenalty() )
-        string += "\n     -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() )
-        string += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
-        return string
-    
-    
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        """
-        Set a specific attribute from the command-line arguments.
-        """
-        if o == "-s":
-            self.setGapSize( a )
-        elif o == "-m":
-            self.setMismatchPenalty( a )
-        elif o == "-O":
-            self.setGapOpenPenalty( a )
-        elif o == "-e":
-            self.setGapExtendPenalty( a )
-        elif o == "-o":
-            self.setOutputFile( a )
-
-                        
-    def setGapSize( self, arg ):
-        self._gapSize = int(arg)
-        
-        
-    def setMismatchPenalty( self, arg ):
-        self._mismatchPenalty = int(arg)
-        
-        
-    def setGapOpenPenalty( self, arg ):
-        self._gapOpenPenalty = int(arg)
-        
-        
-    def setGapExtendPenalty( self, arg ):
-        self._gapExtendPenalty = int(arg)
-        
-        
-    def getGapSize( self ):
-        return self._gapSize
-        
-        
-    def getMismatchPenalty( self ):
-        return self._mismatchPenalty
-        
-        
-    def getGapOpenPenalty( self ):
-        return self._gapOpenPenalty
-        
-        
-    def getGapExtendPenalty( self ):
-        return self._gapExtendPenalty
-        
-        
-    def checkSpecificAttributes( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        if self.getGapSize() <= 0:
-            string = "ERROR: gap size should be > 0"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getMismatchPenalty() >= 0:
-            string = "ERROR: mismatch penalty should be < 0"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getGapOpenPenalty() < 0:
-            string = "ERROR: gap opening penalty should be >= 0"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getGapExtendPenalty() < 0:
-            string = "ERROR: gap extension penalty should be >= 0"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-            
-            
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for MapClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        self._wrpCmdLine += " -s %i" % ( self.getGapSize() )
-        self._wrpCmdLine += " -m %i" % ( self.getMismatchPenalty() )
-        self._wrpCmdLine += " -O %i" % ( self.getGapOpenPenalty() )
-        self._wrpCmdLine += " -e %i" % ( self.getGapExtendPenalty() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        
-        
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        self._prgCmdLine += " %s.shortH" % ( self.getInputFile() )
-        self._prgCmdLine += " %i" % ( self.getGapSize() )
-        self._prgCmdLine += " %i" % ( self.getMismatchPenalty() )
-        self._prgCmdLine += " %i" % ( self.getGapOpenPenalty() )
-        self._prgCmdLine += " %i" % ( self.getGapExtendPenalty() )
-        self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() )
-        
-        
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        
-        
-    def setListFilesToRemove( self ):
-        """
-        Set the list of files to remove.
-        """
-        self.appendFileToRemove( "%s.shortH" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.shortHlink" % ( self.getInputFile() ) )
-        
-        
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        self._summary += "\ngap size: %i" % ( self.getGapSize() )
-        self._summary += "\nmismatch penalty: %i" % ( self.getMismatchPenalty() )
-        self._summary += "\ngap openning penalty: %i" % ( self.getGapOpenPenalty() )
-        self._summary += "\ngap extension penalty: %i" % ( self.getGapExtendPenalty() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 )
-        
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile( self.getInputFile() )
-        csh.setFormat( "fasta" )
-        csh.setStep( 1 )
-        csh.setPrefix( "seq" )
-        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
-        csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) )
-        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
-        csh.run()
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        returnStatus = os.system( cmd )
-        if returnStatus != 0:
-            string = "ERROR: program '%s' returned status '%i'" % ( self.getProgramName(), returnStatus )
-            print string
-            sys.exit(1)
-            
-        csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
-        csh.setFormat( "fasta" )
-        csh.setStep( 2 )
-        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
-        csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
-        csh.run()
-        
-        absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        outFileHandler = open( self.getOutputFile(), "w" )
-        for header in lInitHeaders:
-            bs = absDB.fetch( header )
-            bs.upCase()
-            bs.write( outFileHandler )
-        outFileHandler.close()
-        if self.getClean():
-            os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = MapProgramLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/NWalignProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch NWalign (pairwise alignment).
-#
-# options:
-#      -h: this help
-#      -i: name of the input file (queries, format='fasta')
-#      -s: name of the subject file (format='fasta')
-#      -p: parameters for 'NWalign' (default='-d 2')
-#      -o: name of the output file (format='align', default=inFile+'.align')
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import os
-import sys
-
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.core.coord.AlignUtils import AlignUtils
-
-
-class NWalignProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch NWalign (pairwise alignment).
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "NWalign"
-        self._formatInFile = "fasta"
-        self._sbjFile = ""
-        self._prgParam = ""
-        self._cmdLineSpecificOptions = "s:p:o:"
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (format='fasta')"
-        string += "\n     -p: parameters for '%s'" % ( self.getProgramName() )
-        string += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        return string
-    
-    
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        """
-        Set a specific attribute from the command-line arguments.
-        """
-        if o =="-s":
-            self.setSubjectFile( a )
-        elif o == "-p":
-            self.setProgramParameters( a )
-        elif o == "-o":
-            self.setOutputFile( a )
-            
-            
-    def setSubjectFile( self, arg ):
-        self._sbjFile = arg
-        
-        
-    def getSubjectFile( self ):
-        return self._sbjFile
-    
-    
-    def checkSpecificAttributes( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        if self._sbjFile == "":
-            string = "ERROR: missing subject file (-s)"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-            
-            
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for NWalignClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
-        if self.getProgramParameters() != "":
-            self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        
-        
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        if self.getProgramParameters() != "":
-            self._prgCmdLine += " %s" % ( self.getProgramParameters() )
-        self._prgCmdLine += " -o %s.afa" % ( self.getInputFile() )
-        self._prgCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        self._prgCmdLine += " %s" % ( self.getSubjectFile() )
-        self._prgCmdLine += " %s" % ( self.getInputFile() )
-        
-        
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.afa" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        
-        
-    def postprocess( self ):
-        absDB = AlignedBioseqDB( "%s.afa" % ( self.getInputFile() ) )
-        lHeaders = absDB.getHeaderList()
-        queryHeader = lHeaders[0]
-        subjectHeader = lHeaders[1]
-        queryLength = absDB.fetch( queryHeader ).getLength()
-        subjectLength = absDB.fetch( subjectHeader ).getLength()
-        lAligns = absDB.getAlignList( queryHeader, subjectHeader )
-        for i in lAligns:
-            if "re-oriented" in i.getQueryName():
-                i.setQueryName( queryHeader.replace(" re-oriented","") )
-                start = i.getQueryStart()
-                end = i.getQueryEnd()
-                i.setQueryStart( queryLength - end + 1 )
-                i.setQueryEnd( queryLength - start + 1 )
-            if "re-oriented" in i.getSubjectName():
-                i.setSubjectName( subjectHeader.replace(" re-oriented","") )
-                start = i.getSubjectStart()
-                end = i.getSubjectEnd()
-                i.setSubjectEnd( subjectLength - end + 1 )
-                i.setSubjectStart( subjectLength - start + 1 )
-            if not i.isQueryOnDirectStrand():
-                i.reverse()
-        AlignUtils.writeListInFile( lAligns, self.getOutputFile() )
-        os.remove( "%s.afa" % ( self.getInputFile() ) )
-        
-        
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
-        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
-            print string
-            sys.exit(1)
-            
-        self.postprocess()
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = NWalignProgramLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/RepeatMaskerClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch RepeatMaskerProgramLauncher on several files in parallel on a cluster.
-
-
-import os
-import sys
-import getopt
-import exceptions
-
-from pyRepet.launcher.AbstractClusterLauncher import *
-from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
-
-
-class RepeatMaskerClusterLauncher( AbstractClusterLauncher ):
-    """
-    Launch RepeatMasker on several files in parallel on a cluster.
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractClusterLauncher.__init__( self )
-        AbstractClusterLauncher.setAcronym( self, "RM" )
-        
-        self._cmdLineSpecificOptions = "s:n:gbl"
-        
-        self._exeWrapper = "RepeatMaskerProgramLauncher.py"
-        self._prgLauncher = RepeatMaskerProgramLauncher()
-        self._prgLauncher.setInputFile( GENERIC_IN_FILE )
-        self._prgLauncher.setOutputFile( GENERIC_IN_FILE )
-        self._prgLauncher.setClean()
-        self._prgLauncher.setVerbosityLevel( 1 )
-        self._prgLauncher.setListFilesToKeep()
-        self._prgLauncher.setListFilesToRemove()
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (repeats, format='fasta')"
-        string += "\n     -n: nb of processors to use in parallel (default=1)"
-        string += "\n     -g: calculate the GC content"
-        string += "\n     -b: skip bacterial insertion element check"
-        string += "\n     -l: mask low-complexity DNA or simple repeats"
-        return string
-    
-    
-    def getSubjectFile( self ):
-        return self._prgLauncher.getSubjectFile()
-    
-    
-    def getNbProcessors( self ):
-        return self._prgLauncher.getNbProcessors()
-    
-    
-    def getCalculateGCcontent( self ):
-        return self._prgLauncher.getCalculateGCcontent()
-    
-    
-    def getSkipBacterialIsCheck( self ):
-        return self._prgLauncher.getSkipBacterialIsCheck()
-    
-    
-    def getMaskSsr( self ):
-        return self._prgLauncher.getMaskSsr()
-    
-    
-if __name__ == "__main__":
-    i = RepeatMaskerClusterLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/RepeatMaskerProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,286 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch RepeatMasker (pairwise alignment for repeat detection).
-
-
-import os
-import sys
-
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-
-
-class RepeatMaskerProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch RepeatMasker (pairwise alignment for repeat detection).
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "RepeatMasker"
-        self._formatInFile = "fasta"
-        self._sbjFile = ""
-        self._nbProc = 1
-        self._calcGc = False
-        self._skipIs = False
-        self._maskSsr = True
-        self._onlySsr = False
-        self._cmdLineSpecificOptions = "s:n:gblmo:"
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (repeats, format='fasta')"
-        string += "\n     -n: nb of processors to use in parallel (default='%i')" % ( self.getNbProcessors() )
-        string += "\n     -g: calculate the GC content"
-        string += "\n     -b: skip bacterial insertion element check"
-        string += "\n     -l: does not mask low-complexity DNA or simple repeats"
-        string += "\n     -m: only masks low complex/simple repeats (no interspersed repeats)"
-        string += "\n     -o: name of the output file"
-        string += "\n         with -s: format='align', default=inFile+'.cat.align')"
-        string += "\n         with -m: format='path', default=inFile+'.cat.path')"
-        return string
-    
-    
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        """
-        Set a specific attribute from the command-line arguments.
-        """
-        if o =="-s":
-            self.setSubjectFile( a )
-        elif o == "-n":
-            self.setNbProcessors( a )
-        elif o == "-g":
-            self.setCalculateGCcontent()
-        elif o == "-b":
-            self.setSkipBacterialIsCheck()
-        elif o == "-l":
-            self.unsetMaskSsr()
-        elif o == "-m":
-            self.setOnlySsr()
-        elif o == "-o":
-            self.setOutputFile( a )
-            
-            
-    def setSubjectFile( self, arg ):
-        self._sbjFile = arg
-        
-        
-    def setNbProcessors( self, arg ):
-        self._nbProc = int(arg)
-        
-        
-    def setCalculateGCcontent( self ):
-        self._calcGc = True
-        
-        
-    def setSkipBacterialIsCheck( self ):
-        self._skipIs = True
-        
-        
-    def unsetMaskSsr( self ):
-        self._maskSsr = False
-        
-        
-    def setOnlySsr( self ):
-        self._onlySsr = True
-        
-        
-    def getSubjectFile( self ):
-        return self._sbjFile
-    
-    
-    def getNbProcessors( self ):
-        return self._nbProc
-    
-    
-    def getCalculateGCcontent( self ):
-        return self._calcGc
-    
-    
-    def getSkipBacterialIsCheck( self ):
-        return self._skipIs
-    
-    
-    def getMaskSsr( self ):
-        return self._maskSsr
-    
-    
-    def getOnlySsr( self ):
-        return self._onlySsr
-    
-    
-    def checkSpecificAttributes( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        if ( self.getSubjectFile() == "" and not self.getOnlySsr() ) \
-               or ( self.getSubjectFile() != "" and self.getOnlySsr() ):
-            string = "ERROR: need to specify -s or -m"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getOutputFile() == "":
-            if not self.getOnlySsr():
-                self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) )
-            else:
-                self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) )
-                
-                
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for RepeatMaskerClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        if self.getSubjectFile() != "":
-            self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
-        self._wrpCmdLine += " -n %i"  %( self.getNbProcessors() )
-        if self.getCalculateGCcontent():
-            self._wrpCmdLine += " -g"
-        if self.getSkipBacterialIsCheck():
-            self._wrpCmdLine += " -b"
-        if not self.getMaskSsr():
-            self._wrpCmdLine += " -l"
-        if self.getOnlySsr():
-            self._wrpCmdLine += " -m"
-        if self.getOutputFile() != "":
-            self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        if self.getVerbosityLevel() != 0:
-            self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-            
-            
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        self._prgCmdLine += " -dir ."
-        self._prgCmdLine += " -pa %i" % ( self.getNbProcessors() )
-        if self.getCalculateGCcontent():
-            self._prgCmdLine += " -gccalc"
-        if self.getSkipBacterialIsCheck():
-            self._prgCmdLine += " -no_is"
-        if self.getMaskSsr():
-            self._prgCmdLine += " -nolow"
-        if self.getOnlySsr():
-            self._prgCmdLine += " -int"
-        if self.getSubjectFile() != "":
-            self._prgCmdLine += " -lib %s" % ( self.getSubjectFile() )
-        self._prgCmdLine += " %s" % ( self.getInputFile() )
-        
-        
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            if not self.getOnlySsr():
-                self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) )
-            else:
-                self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        self.appendFileToKeep( "%s.cat" % ( self.getInputFile() ) )
-        
-        
-    def setListFilesToRemove( self ):
-        """
-        Set the list of files to remove.
-        """
-        self.appendFileToRemove( "%s.stderr" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.tbl" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.ori.out" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.masked" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.out" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.log" % ( self.getInputFile() ) )
-        self.appendFileToRemove( "%s.ref" % ( self.getInputFile() ) )
-        
-        
-    def convertCatIntoAlign( self ):
-        """
-        Convert a 'cat' file into the 'align' format.
-        """
-        cmd = os.environ["REPET_PATH"] + "/bin/RMcat2align.py"
-        cmd += " -i %s.cat" % ( self.getInputFile() )
-        cmd += " -o %s.cat.align" % ( self.getInputFile() )
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR while converting 'cat' file into 'align' format"
-            print string
-            sys.exit(1)
-            
-            
-    def convertCatIntoPath( self ):
-        """
-        Convert a 'cat' file into the 'path' format.
-        """
-        cmd = os.environ["REPET_PATH"] + "/bin/RMcat2path.py"
-        cmd += " -i %s.cat" % ( self.getInputFile() )
-        cmd += " -o %s.cat.path" % ( self.getInputFile() )
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR while converting 'cat' file into 'path' format"
-            print string
-            sys.exit(1)
-            
-            
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        if self.getSubjectFile() != "":
-            self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
-        self._summary += "\nnb processors: %i" % ( self.getNbProcessors() )
-        if self.getCalculateGCcontent():
-            self._summary += "\ncalculate the GC content"
-        if self.getSkipBacterialIsCheck():
-            self._summary += "\nskip bacterial insertion element check"
-        if self.getMaskSsr():
-            self._summary += "\nmask low-complexity DNA or simple repeats"
-        if self.getOnlySsr():
-            self._summary = "\nonly masks low complex/simple repeats (no interspersed repeats)"
-        if self.getOutputFile() == "":
-            if not self.getMaskSsr():
-                self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) )
-            else:
-                self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
-            print string
-            sys.exit(1)
-            
-        if not self.getOnlySsr():
-            self.convertCatIntoAlign()
-        else:
-            self.convertCatIntoPath()
-            
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = RepeatMaskerProgramLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/YassClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch YassProgramLauncher on several files in parallel on a cluster.
-
-
-from pyRepet.launcher.AbstractClusterLauncher import *
-from commons.core.coord.AlignUtils import AlignUtils
-from commons.launcher.YassProgramLauncher import YassProgramLauncher
-from commons.tools import srptBlasterMatcher
-
-
-class YassClusterLauncher( AbstractClusterLauncher ):
-    """
-    Launch Yass on several files in parallel on a cluster.
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractClusterLauncher.__init__( self )
-        AbstractClusterLauncher.setAcronym( self, "Yass" )
-        
-        self._cmdLineSpecificOptions = "s:p:A"
-        
-        self._exeWrapper = "YassProgramLauncher.py"
-        self._prgLauncher = None
-        self._prgLauncher = self.getProgramLauncherInstance()
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (format='fasta')"
-        string += "\n     -p: parameters for 'yass'"
-        string += "\n     -Z: concatenate output files"
-        string += "\n     -A: same sequences (all-by-all)"
-        return string
-    
-    
-    def getSubjectFile( self ):
-        return self._prgLauncher.getSubjectFile()
-    
-    
-    def getProgramParameters( self ):
-        return self._prgLauncher.getProgramParameters()
-    
-    
-    def getProgramLauncherInstance( self ):
-        if self._prgLauncher == None:
-            self._prgLauncher = YassProgramLauncher()
-            self._prgLauncher.setInputFile( GENERIC_IN_FILE )
-            self._prgLauncher.setClean()
-            self._prgLauncher.setVerbosityLevel( 1 )
-            self._prgLauncher.setListFilesToKeep()
-            self._prgLauncher.setListFilesToRemove()
-        return self._prgLauncher
-    
-    
-    def processOutputFile( self, tmpFile, outFile ):
-        sortFile = "%s.sort" % ( tmpFile )
-        AlignUtils.sortAlignFile( tmpFile, sortFile )
-        if self._prgLauncher.getAllByAll():
-            srptBlasterMatcher.filterRedundantMatches( sortFile,
-                                                                  outFile )
-            os.remove( sortFile )
-        else:
-            os.rename( sortFile, outFile )
-            
-            
-if __name__ == "__main__":
-    i = YassClusterLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/YassProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,195 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Launch Yass (pairwise alignment).
-#
-# options:
-#      -h: this help
-#      -i: name of the input file (queries, format='fasta')
-#      -s: name of the subject file (format='fasta')
-#      -p: parameters for 'yass' (default='-d 2')
-#      -o: name of the output file (format='align', default=inFile+'.align')
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import os
-import sys
-
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-
-
-class YassProgramLauncher( AbstractProgramLauncher ):
-    """
-    Launch Yass (pairwise alignment).
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        AbstractProgramLauncher.__init__( self )
-        self._prgName = "yass"
-        self._formatInFile = "fasta"
-        self._sbjFile = ""
-        self._prgParam = ""
-        self._allByAll = False
-        self._cmdLineSpecificOptions = "s:p:Ao:"
-        
-        
-    def getSpecificHelpAsString( self ):
-        """
-        Return the specific help as a string.
-        """
-        string = ""
-        string += "\nspecific options:"
-        string += "\n     -s: name of the subject file (format='fasta')"
-        string += "\n     -p: parameters for '%s'" % ( self.getProgramName() )
-        string += "\n     -A: same sequences (all-by-all)"
-        string += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        return string
-    
-    
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        """
-        Set a specific attribute from the command-line arguments.
-        """
-        if o =="-s":
-            self.setSubjectFile( a )
-        elif o == "-p":
-            self.setProgramParameters( a )
-        elif o == "-A":
-            self.setAllByAll()
-        elif o == "-o":
-            self.setOutputFile( a )
-            
-            
-    def setSubjectFile( self, arg ):
-        self._sbjFile = arg
-        
-        
-    def getSubjectFile( self ):
-        return self._sbjFile
-    
-    
-    def setAllByAll( self ):
-        self._allByAll = True
-        
-        
-    def getAllByAll( self ):
-        return self._allByAll
-    
-    
-    def checkSpecificAttributes( self ):
-        """
-        Check the specific attributes before running the program.
-        """
-        if self._sbjFile == "":
-            string = "ERROR: missing subject file (-s)"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-            
-            
-    def setWrapperCommandLine( self ):
-        """
-        Set the command-line of the wrapper.
-        Required for YassClusterLauncher.
-        """
-        self._wrpCmdLine = self.getWrapperName()
-        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
-        self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
-        if self.getProgramParameters() != "":
-            self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
-        if self.getAllByAll():
-            self._wrpCmdLine += " -A"
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
-        if self.getClean():
-            self._wrpCmdLine += " -c"
-        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
-        
-        
-    def setProgramCommandLine( self ):
-        """
-        Set the command-line of the program.
-        """
-        self._prgCmdLine = self.getProgramName()
-        self._prgCmdLine += " -d 2"
-        if self.getProgramParameters() != "":
-            self._prgCmdLine += " %s" % ( self.getProgramParameters() )
-        self._prgCmdLine += " -o %s.blast" % ( self.getInputFile() )
-        self._prgCmdLine += " %s" % ( self.getInputFile() )
-        self._prgCmdLine += " %s" % ( self.getSubjectFile() )
-        
-        
-    def setListFilesToKeep( self ):
-        """
-        Set the list of files to keep.
-        """
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self.appendFileToKeep( self.getOutputFile() )
-        
-        
-    def setListFilesToRemove( self ):
-        """
-        Set the list of files to remove.
-        """
-        pass
-    
-    
-    def convertBlastIntoAlign( self ):
-        """
-        Convert a 'blast' file into the 'align' format.
-        """
-        cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py"
-        cmd += " -i %s.blast" % ( self.getInputFile() )
-        cmd += " -o %s" % ( self.getOutputFile() )
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR while converting 'blast' file into 'align' format"
-            print string
-            sys.exit(1)
-            
-            
-    def setSummary( self ):
-        self._summary = "input file: %s" % ( self.getInputFile() )
-        self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
-        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
-        if self.getAllByAll():
-            self._summary += "\nall-by-all"
-        if self.getOutputFile() == "":
-            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
-        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
-        
-        
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        self.setProgramCommandLine()
-        cmd = self.getProgramCommandLine()
-        if self.getVerbosityLevel() > 0:
-            print "LAUNCH: %s" % ( cmd )
-            sys.stdout.flush()
-        exitStatus = os.system( cmd )
-        if exitStatus != 0:
-            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
-            print string
-            sys.exit(1)
-            
-        self.convertBlastIntoAlign()
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = YassProgramLauncher()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/launcher/launchBlasterMatcherPerQuery.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,196 +0,0 @@
-#!/usr/bin/env python
-
-"""
-This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards.
-"""
-
-import os
-import sys
-import getopt
-import exceptions
-import logging
-import ConfigParser
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-import pyRepet.launcher.programLauncher
-import pyRepet.seq.fastaDB
-
-#-----------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the list of the command-line options.
-    """
-
-    print
-    print "usage:",sys.argv[0]," [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -q: fasta filename of the queries"
-    print "     -s: fasta filename of the subjects (same as queries if not specified)"
-    print "     -Q: queue name on the cluster"
-    print "     -d: absolute path to the temporary directory"
-    print "     -C: configuration file"
-    print "     -n: max. number of jobs (default=10,given a min. of 1 query per job)"
-    print "     -m: mix of Blaster and/or Matcher"
-    print "         1: launch Blaster only"
-    print "         2: launch Matcher only (on '*.align' query files)"
-    print "         3: launch Blaster+Matcher in the same job (default)"
-    print "     -B: parameters for Blaster (e.g. \"-a -n tblastx\")"
-    print "     -M: parameters for Matcher (e.g. \"-j\")"
-    print "     -Z: collect all the results into a single file (format 'align', 'path' or 'tab')"
-    print "     -c: clean"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-#-----------------------------------------------------------------------------
-
-def main():
-
-    """
-    This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards.
-    """
-
-    qryFileName = ""
-    sbjFileName = ""
-    queue = ""
-    tmpDir = ""
-    configFileName = ""
-    maxNbJobs = 10
-    minQryPerJob = 1
-    mix = "3"
-    paramBlaster = ""
-    paramMatcher = ""
-    collectFormat = ""
-    clean = False
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hq:s:Q:d:C:n:m:B:M:Z:cv:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-q":
-            qryFileName = a 
-        elif o == "-s":
-            sbjFileName = a
-        elif o == "-Q":
-            queue = a
-        elif o == "-d":
-            tmpDir = a
-        elif o == "-C":
-            configFileName = a
-        elif o == "-n":
-            maxNbJobs = int(a)
-        elif o == "-m":
-            mix = a
-        elif o == "-B":
-            paramBlaster = a
-        elif o == "-M":
-            paramMatcher = a
-        elif o == "-Z":
-            collectFormat = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if qryFileName == "" or configFileName == "" or collectFormat == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    if not os.path.exists( qryFileName ):
-        print "*** Error: query file '%s' doesn't exist" % ( qryFileName )
-        sys.exit(1)
-    if sbjFileName != "":
-        if not os.path.exists( sbjFileName ):
-            print "*** Error: subject file '%s' doesn't exist" % ( sbjFileName )
-            sys.exit(1)
-    else:
-        sbjFileName = qryFileName
-
-    pL = pyRepet.launcher.programLauncher.programLauncher()
-
-    nbSeqQry = pyRepet.seq.fastaDB.dbSize( qryFileName )
-    qryPerJob = nbSeqQry / float(maxNbJobs)
-
-    # split the input query file in single files into a new directory
-    prg = os.environ["REPET_PATH"] + "/bin/dbSplit.py"
-    cmd = prg
-    cmd += " -i %s" % ( qryFileName )
-    if qryPerJob <= 1.0:
-        cmd += " -n %i" % ( minQryPerJob )
-    else:
-        cmd += " -n %i" % ( qryPerJob + 1 )
-    cmd += " -d"
-    pL.launch( prg, cmd )
-
-    # prepare the subject databank
-    if sbjFileName != qryFileName:
-        prg = "blaster"
-        cmd = prg
-        cmd += " -q %s" % ( sbjFileName )
-        cmd += " -P"
-        pL.launch( prg, cmd )
-
-    # launch Blaster+Matcher in parallel
-    prg = "srptBlasterMatcher.py"
-    cmd = prg
-    cmd += " -g %s_vs_%s" % ( qryFileName, sbjFileName )
-    cmd += " -q %s/batches" % ( os.getcwd() )
-    cmd += " -s %s/%s" % ( os.getcwd(), sbjFileName )
-    cmd += " -Q '%s'" % ( queue )
-    if tmpDir != "":
-        cmd += " -d %s" % ( tmpDir )
-    cmd += " -m %s" % ( mix )
-    if paramBlaster != "":
-        cmd += " -B \"%s\"" % ( paramBlaster )
-    if paramMatcher != "":
-        cmd += " -M \"%s\"" % ( paramMatcher )
-    cmd += " -Z %s" % ( collectFormat )
-    cmd += " -C %s" % ( configFileName )
-    if clean == True:
-        cmd += " -c"
-    cmd += " -v %i" % ( verbose - 1 )
-    pL.launch( prg, cmd )
-
-    suffix = ""
-    if mix in ["2","3"]:
-        if "-a" in paramMatcher:
-            suffix = "match.%s" % ( collectFormat )
-        else:
-            suffix = "clean_match.%s" % ( collectFormat )
-        os.system( "mv %s_vs_%s.%s %s_vs_%s.align.%s" % ( qryFileName, sbjFileName, collectFormat, qryFileName, sbjFileName, suffix ) )
-
-    # clean
-    if clean == True:
-        prg = "rm"
-        cmd = prg
-        cmd += " -rf batches formatdb.log %s_cut* %s.Nstretch.map" % ( sbjFileName, sbjFileName )
-        pL.launch( prg, cmd )
-
-    if verbose > 0:
-        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-#----------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/launcher/launchMafft.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-#!/usr/bin/env python
-
-# DEPRECATED
-
-import user, os, sys, getopt, exceptions
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-import pyRepet.launcher.programLauncher
-import pyRepet.seq.fastaDB
-from pyRepet.seq.BioseqDB import *
-
-#------------------------------------------------------------------------------
-
-def help():
-
-    print
-    print "DEPRECATED"
-    print
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='fasta')"
-    print "     -o: name of the output file (default=inFileName+'.fa_aln')"
-    print "     -v: verbose (default=0/1)"
-    print
-
-#------------------------------------------------------------------------------
-
-def main():
-    
-    """
-    This program launches MAFFT to build a multiple sequence alignment.
-    """
-
-    inFileName = ""
-    outFileName = ""
-    verbose = 0
-    
-    try:
-        opts,args=getopt.getopt(sys.argv[1:],"hi:o:v:")
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-            
-    if inFileName == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-        
-    if verbose > 0:
-        print "beginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    if verbose > 0:
-        print "build a multiple alignment from '%s'..." % ( inFileName )
-        sys.stdout.flush()
-        
-    pyRepet.seq.fastaDB.shortenSeqHeaders( inFileName )
-    
-    bsDB = BioseqDB( inFileName+".shortH" )
-    bsDB.upCase()
-    bsDB.save( inFileName+".shortHtmp" )
-    del bsDB
-    os.rename( inFileName+".shortHtmp", inFileName+".shortH" )
-    
-    pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" )
-    pL.launchMafft( outFileName=inFileName+".shortH.fa_aln", verbose=verbose )
-    
-    pyRepet.seq.fastaDB.retrieveInitSeqHeaders( inFileName+".shortH.fa_aln",
-                                                inFileName+".shortHlink",
-                                                inFileName+".shortH.fa_aln.initH",
-                                                verbose-1 )
-    
-    if outFileName == "":
-        outFileName = "%s.fa_aln" % ( inFileName )
-    os.system( "mv %s.shortH.fa_aln.initH %s" % ( inFileName, outFileName ) )
-    
-    for f in [inFileName+".shortH",inFileName+".shortH.fa_aln",inFileName+".shortHlink"]:
-        os.remove( f )
-        
-    if verbose > 0:
-        print "%s finished successfully" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    return 0
-
-#------------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/launcher/launchMreps.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-#!/usr/bin/env python
-
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.core.parsing.MrepsToSet import MrepsToSet
-import subprocess
-import os
-import sys
-import getopt
-
-def help():
-    """
-    Give the list of the command-line options.
-    """
-    print
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='fasta')"
-    print "     -o: name of the output file (default=inFileName+'.Mreps.set')"
-    print "     -f: error filter (default=1.0)"
-    print "     -c: clean"
-    print "     -v: verbosity level (default=0/1)"
-    print
-
-def main():
-    """
-    Launch Mreps.
-    """
-    inFileName = ""
-    outFileName = ""
-    errorFilter = 1.0
-    clean = False
-    verbose = 0
-
-    try:
-        opts=getopt.getopt(sys.argv[1:],"hi:o:f:cv:")[0]
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-f":
-            errorFilter = float(a)
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if inFileName == "":
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "beginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    # Mreps 2.5 doesn't fully support IUPAC nomenclature
-    if verbose > 0:
-        print "* check IUPAC symbols"; sys.stdout.flush()
-    tmpInFileName = "%s.tmp%i" % ( inFileName, os.getpid() )
-    if os.path.exists( tmpInFileName ):
-        os.system( "rm -f %s" % ( tmpInFileName ) )
-    bsDB = BioseqDB( inFileName )
-    for bs in bsDB.db:
-        if verbose > 0:
-            print bs.header; sys.stdout.flush()
-        bs.partialIUPAC()
-        onlyN = True
-        for nt in ["A","T","G","C"]:
-            if nt in bs.sequence:
-                onlyN = False
-        if onlyN == True:
-            if verbose > 0:
-                print "** Warning: only Ns"; sys.stdout.flush()
-        else:
-            bsDB.save( tmpInFileName )
-
-    if not os.path.exists( tmpInFileName ):
-        sys.exit(0)
-
-    if verbose > 0:
-        print "* remove N stretches"; sys.stdout.flush()
-    prg = os.environ["REPET_PATH"] + "/bin/cutterDB"
-    cmd = prg
-    cmd += " -l 200000"
-    cmd += " -o 0"
-    cmd += " -w 11"
-    cmd += " %s" % ( tmpInFileName )
-    if verbose > 0:
-        print cmd; sys.stdout.flush()
-    log = os.system( cmd )
-    if log != 0:
-        print "ERROR: %s returned %i" % ( prg, log )
-        sys.exit(1)
-
-    # launch Mreps on the input file
-    MrepsOutFileName = "%s.Mreps.xml" % ( tmpInFileName )
-    prg = "mreps"
-    cmd = prg
-    cmd += " -res 3"
-    cmd += " -exp 3.0"
-    cmd += " -maxsize 50"
-    cmd += " -xmloutput %s" % MrepsOutFileName
-    cmd += " -fasta %s_cut" % tmpInFileName
-    process = subprocess.Popen(cmd, shell = True)
-    process.communicate()
-    if process.returncode != 0:
-        raise Exception("ERROR when launching '%s'" % cmd)
-
-    if outFileName == "":
-        outFileName = inFileName + ".Mreps.set"
-
-    # parse Mreps results in xml format
-    iMrepsToSet = MrepsToSet(inFileName, MrepsOutFileName, outFileName, errorFilter)
-    iMrepsToSet.run()
-    if clean:
-        iMrepsToSet.clean()
-
-    # remove temporary input filename
-    os.remove(tmpInFileName)
-    os.remove("%s_cut" % tmpInFileName)
-    os.remove("%s.Nstretch.map" % tmpInFileName)
-
-    if verbose > 0:
-        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == '__main__':
-    main()

--- a/commons/launcher/launchPhyML.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-
-from pyRepet.launcher.programLauncher import programLauncher
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-def help():
-    print
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (aligned fasta)"
-    print "     -c: clean"
-    print "     -v: verbose (default=0)"
-    print
-    
-    
-def main():
-    
-    inFileName = ""
-    clean = False
-    verbose = 0
-    try:
-        opts,args=getopt.getopt(sys.argv[1:],"hi:cv:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help(); sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help(); sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-    if inFileName == "":
-        print "ERROR: missing compulsory options"
-        help(); sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    csh = ChangeSequenceHeaders()
-    csh.setInputFile( inFileName )
-    csh.setFormat( "fasta" )
-    csh.setStep( 1 )
-    csh.setPrefix( "seq" )
-    csh.setLinkFile( inFileName+".shortHlink" )
-    csh.setOutputFile( inFileName+".shortH" )
-    csh.run()
-    
-    pL = programLauncher( inFileName+".shortH" )
-    
-    pL.launchSreformat( outFormat="phylip", outFileName=inFileName+".shortH.phylip", verbose=verbose )
-    
-    pL.reset( inFileName+".shortH.phylip" )
-    
-    pL.launchPhyML( verbose=verbose )
-    
-    csh.setInputFile( inFileName+".shortH.phylip_phyml_tree.txt" )
-    csh.setFormat( "newick" )
-    csh.setStep( 2 )
-    csh.setLinkFile( inFileName+".shortHlink" )
-    csh.setOutputFile( inFileName+"_phyml.newick" )
-    csh.run()
-    
-    if clean:
-        for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.phylip",
-                   inFileName+".shortH.phylip_phyml_lk.txt", inFileName+".shortH.phylip_phyml_tree.txt" ]:
-            os.remove( f )
-        os.system( "mv %s.shortH.phylip_phyml_stat.txt %s_phyml.txt" % ( inFileName, inFileName ) )
-
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/launcher/launchPrank.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-
-from pyRepet.launcher.programLauncher import programLauncher
-
-
-def help():
-    print
-    print "usage: launchPrank.py [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format=fasta)"
-    print "     -o: name of the output file (format=aligned fasta, default='inFileName'+fa_aln)"
-    print "     -P: Prank's parameters"
-    print "     -c: clean"
-    print "     -v: verbose (default=0/1)"
-    print
-
-
-def main():
-    """
-    Launch PRANK.
-    """
-    inFileName = ""
-    outFileName = ""
-    parameters = ""
-    clean = False
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hi:o:P:cv:" )
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-P":
-            parameters = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if inFileName == "":
-        print "ERROR: missing input file (-i)"
-        help()
-        sys.exit(1)
-
-    if not os.path.exists( inFileName ):
-        print "ERROR: can't find file '%s'" % ( inFileName )
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    if outFileName == "":
-        outFileName = "%s.fa_aln" % ( inFileName )
-
-    pL = programLauncher( inFileName )
-    returnStatus = pL.launchPrank( outFileName, parameters, "yes", verbose )
-    if returnStatus != 0:
-        print "ERROR: launchPrank() returned '%i'" % ( returnStatus )
-        sys.exit(1)
-
-    if verbose > 0:
-        print "END %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/launcher/launchTCoffee.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import exceptions
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-from pyRepet.launcher.programLauncher import programLauncher
-
-
-def help():
-    print
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='fasta')"
-    print "     -P: parameters"
-    print "     -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)"
-    print "     -c: clean"
-    print "     -v: verbosity level (default=0/1)"
-    print
-
-
-def main():
-
-    inFileName = ""
-    parameters = ""
-    outFileName = ""
-    clean = False
-    verbose = 0
-    
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:P:o:cv:")
-    except getopt.GetoptError, err:
-        print str(err); help(); sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help(); sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-P":
-            parameters = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = "yes"
-            
-    if inFileName == "" and parameters == "":
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-        
-    if outFileName == "":
-        outFileName = "%s.fa_aln" % ( inFileName )
-        
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    pL = programLauncher( inFileName )
-    pL.launchTcoffee( outFileName, parameters )
-    
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-    
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/launcher/launchTEclass.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import glob
-import shutil
-
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='fasta')"
-    print "     -o: name of the output file (format='map', default=inFileName+'.map')"
-    print "     -c: clean"
-    print "     -v: verbosity level (default=0/1)"
-    print
-
-def parseFastaFileFromTEclass( inFile, outFile, verbose=0 ):
-    tmpHandler = open( inFile, "r" )
-    outHandler = open( outFile, "w" )
-    dClassif2Count = {}
-    header = ""
-    classif = ""
-    while True:
-        line = tmpHandler.readline()
-        if line == "":
-            break
-        if line[0] == ">":
-            header = line[1:].split("|")[0]
-            classif = line[1:-1].split(": ")[1].split("|")[0]
-            if not dClassif2Count.has_key( classif ):
-                dClassif2Count[ classif ] = 0
-            dClassif2Count[ classif ] += 1
-        else:
-            seqLength = len(line[:-1])
-            outHandler.write( "%s\t%s\t%i\t%i\n" % ( classif, header, 1, seqLength ) )
-    tmpHandler.close()
-    outHandler.close()
-    if verbose > 0:
-        for classif in dClassif2Count.keys():
-            print "%s: %i sequences" % ( classif, dClassif2Count[ classif ] )
-            sys.stdout.flush()
-            
-            
-def main():
-    """
-    Launch TEclass to classify TE sequences.
-    """
-    inFileName = ""
-    outFileName = ""
-    clean = False
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hi:o:cv:" )
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-            
-    if inFileName == "":
-        print "ERROR: missing input file (-i)"
-        help()
-        sys.exit(1)
-    if not os.path.exists( inFileName ):
-        print "ERROR: can't find input file '%s'" % ( inFileName )
-        help()
-        sys.exit(1)
-    if outFileName == "":
-        outFileName = "%s.TEclass.map" % ( inFileName )
-        
-    if verbose > 0:
-        print "START %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-        
-    if verbose > 0:
-        print "launch TEclass..."
-        sys.stdout.flush()
-    prg = "test_consensi_2.1.pl"
-    cmd = prg
-    cmd += " %s" % ( inFileName )
-    returnValue = os.system( cmd )
-    if returnValue != 0:
-        print "ERROR: '%s' returned %i" % ( prg, returnValue )
-        sys.exit(1)
-        
-    lOut1 = glob.glob( "%s_*" % ( inFileName ) )
-    outDir = ""
-    for i in lOut1:
-        if os.path.isdir( i ):
-            lOut2 = glob.glob( "%s/*" % ( i ) )
-            if len(lOut2) == 4 and "%s/%s.lib" % ( i, inFileName ) in lOut2:
-                outDir = i
-                break
-    if outDir == "":
-        print "ERROR: can't find output directory"
-        sys.exit(1)
-    os.chdir( outDir )
-    
-    if verbose > 0:
-        print "parse the results..."
-        sys.stdout.flush()
-    parseFastaFileFromTEclass( "%s.lib" % ( inFileName ),
-                               outFileName,
-                               verbose )
-    os.system( "mv %s .." % ( outFileName ) )
-    os.chdir( ".." )
-    
-    if clean:
-        if verbose > 0:
-            print "clean the temporary files..."
-            sys.stdout.flush()
-        shutil.rmtree( outDir )
-        
-    if verbose > 0:
-        print "END %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-        
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/launcher/tests/MockDataBankForBlat.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,299 +0,0 @@
-class MockDataBankForBlat(object):
-	
-	def write(self, inFileName):
-		f = open(inFileName, 'w')
-		f.write('>Vein_ctg_2286\n')
-		f.write('AGCAAAAaCGTATTTTCTAAGCTAAAATTTAGCGTAGAAGCTTGGACTCGCTtATTTTTT\n')
-		f.write('ATCCTAGGAATTAGTAGAATCTCTCTATAAATATTTATTTTTTATCCGCGCAAAGCTAGG\n')
-		f.write('AAACTATAGAATCTTATATATTAGTATATTCTAGCGATTATCTAGAGATTGTaGGGGGGG\n')
-		f.write('ggAAAGGTAGTAATAGGCGTGTAAGAGAGATAAAGAGTTtATCTTAGAATCTCCCTACGC\n')
-		f.write('CAAGCGAGATTCCTAAGGTAAGAATCCTAAGGTAAAGAATCTAAGCGAGAATTTAGAATC\n')
-		f.write('ACGTGCTCGCTTCCTACTACCGTAATTTTACGGTTATAGAGTACGACAGTTCCTATATAT\n')
-		f.write('AACCTATACTTATAACAACGAATATAaTATAAGACGTTAATTTGATTTTTTACCGTGTTA\n')
-		f.write('CTTATAATAAGGTGTCCCAAAGTTGTTCGAATTTTTTTTGTCCAAGATTGAATACGGTGT\n')
-		f.write('TGGTCATGTGATAGTATTTTCACGGTATTTAAACGGAAATTTTACCTACGGCCCCCcGCC\n')
-		f.write('TATGTACATCATGAGGATGCACGATGGAGATGAAATGCTTCGTTTCATACTGAGTGGCCG\n')
-		f.write('ATTGATGGACGCGTGAACGTCAAAGTAACTTCCATTTGTTTCCTGTCGTTGTCCGGTAGC\n')
-		f.write('CTGGCAAATAGTGACATGTTTGATGTCTTTGGAACAGGGTGGAAACTTTTTTTGGGTtGC\n')
-		f.write('AAATCGTCAAGAGTCACGTGTCCACACAGTGGCGCAAGTGGGGGCTTAAAATGGTGGACT\n')
-		f.write('TGCGCGAGGGCGATTTCTTTTCTTCCCCAACCACAATCTATCGTGATCAAAGAAGCACCC\n')
-		f.write('ATCCGGTTGTTGAGGTATGCCAGCCAGCATCCAATGATGCGCTCAAACAACAACTAACTC\n')
-		f.write('TCATACAGATCGCCATGCAGATTTTCGTGAAGACCCTCACGGGCAAGACTATCACCCTcG\n')
-		f.write('AGGTGGAGTCCTCCGACACCATTGACAATGTCAAGACCAAGATTCAGGGTACGTGGCCTC\n')
-		f.write('GCGCAAGCATTTGTAACCATCTTCTAACCCTCTGCCGTAGACAAGGAAGgAATCCCCCCA\n')
-		f.write('GACCAGCAGCGCTTGATCTTCGCCGGCAAGCAGCTCGAAGATGGACGCACCCTATCGGAC\n')
-		f.write('TACAACATCCAGAAGGAGTCGACCCTCCACCTCGTCCTCCGACTCCGTGGTGGTATGGCC\n')
-		f.write('AAGAaGCGCAAGAAGAAGGTCTACACCACCCcAAAGAaGATCAAGCACAAGCGCAAGAaG\n')
-		f.write('ACCAAGTTGGCTGTCcTCAAGTACTACAAGGTGGATGGCGATGGAAAgaTCGAGcGCcTC\n')
-		f.write('CGACGAGAGTGCCcAGCTGACGAGTGTGGTgCCGGTgTCTTCATGGCTGCCATGCACAAC\n')
-		f.write('CGtcAATACTGCGGAAAGTGCCACCTCACCtACGTTTTCGACGAGAGCAAGTAGACGGTT\n')
-		f.write('CTGGAAAGCATACAATGACAACCATGATTATGCTGTGGGATGATGGATGCTGAACAAAGG\n')
-		f.write('GAGGGAATAGCGACGGACACCGCGTTCTGTAGCTACACAATCAAGCAAAACCTTCACCTC\n')
-		f.write('GATAGCGGGCCTCGATCCATGTACTATCTTATGATATGTGACATTGAATGTGCGAGTGTT\n')
-		f.write('CATTATTCTTTCGCCGTAGCTTCGTTCTCTCTGTGTTCACCCAACCTCCAAGAATCCCGA\n')
-		f.write('CAGTTTCTGGCGATGTTCAAGAATGATATTGCCAGAAATTTATCGGTACCGAACCCTAGA\n')
-		f.write('TAAAAGGATGGGTTCGGAGTTAACGTAATTTCGAAGGGCAGATGCCATGTGCTTGGGTGC\n')
-		f.write('CGCGTTACGAGAATTACTATGATGGTGCTGTGTATCTTCACAATGGCAACATGGCAGAAC\n')
-		f.write('AACGCCAAGAAGTTTCTCCAATGTCAACCCAAGGTCTCCGGACGAATCTAGATGCACCCT\n')
-		f.write('GACTGCATCGTTATCGGTCATGCAAAAGCACGCCTAATGTGCAGCGTGATGACAAGGTGG\n')
-		f.write('AAAaGGAGGCAAATGCTGGTCTAGTGTCTTGTGGCAGAAGTCAGAGTCACGATGAGCAAG\n')
-		f.write('CATGGCGCATGAGGGTTGCCTCCGCAAGCATCCGACAGAGTAGAGACAGAGAAAACACCA\n')
-		f.write('CAGCAAAAGATGTCACGGCACTCTCGATTCGCTTGTGACGGCCAAGTCTAGGTCCAGGTC\n')
-		f.write('CAGGTCCAGGATACGGATACAAGGCGAATGTGGACACCCCAGCCTCCCGATTAGGGAACT\n')
-		f.write('ATACAGCGGGCTGGGTTTATGAATAATGAATCCAATTGCAGCATGAGATCATAGCGTTTG\n')
-		f.write('TCTAAGAGGCTTTTTGCTACTGTACATGGCGATTGGCGAGTGTTGGGGGTTAGGTGAGAC\n')
-		f.write('GGTCTTGGCTGGCAACCCTGTGAGCGCAAAGATGGAGAAGGGAATGGCAGGCGATCAGGA\n')
-		f.write('CGATTGTTTCATGGATGAGCAATGGGCATCTCAAaGAAACACGGATCGTTTCTGATGGAC\n')
-		f.write('AGACGGGCCAAGACTGACCAAGCATTTGTGAAATTGGGACAGGAGAAGGGATGGTGGCTT\n')
-		f.write('CGACGTGCTGCAGCTGCATACTGTGTAGCTGCGTGTTGATAGCTGCACAACTGCATTGGC\n')
-		f.write('TCGACCAGACACATTCCCGGAGCGTTATGCATCCAGCGCCTGATTCGCTTGGGACTTGGG\n')
-		f.write('TCGCGACTCGCGAGAGAATTGGTACTCGTAGTCGGTACCTAAGCTGCACCTTGTCCCCGA\n')
-		f.write('AGTAGACTGTCGAGACTGTATAGtAGAGGTCGAGGTATATTCTATGCTATACTGTACATT\n')
-		f.write('ATTGAAGTGCTCCCATCATATCACCAACCCTCCCGCCTCGTCTTCCATGTCcGTTTCCGC\n')
-		f.write('CTTCACATTTCAAAAAGTCGTTGAGTGGTCCTAGTGCTCAATTAAATTGCTTACCAGAGC\n')
-		f.write('GTCAGAGCTCTCCTGGAGTCCTGGCAAAAGCCAaaGCTCAACGACCAATTGCCCCATCCT\n')
-		f.write('CTCTCCTACCGAGTACTCCGTACCGCTCATCTCGTCAACCACCACCGCAGACAACAATCG\n')
-		f.write('CACCACTTCTCCAGCGCGTCCACTGAACTCAGGTCTCGCTGTGGTTGCGCAGTATTGCCT\n')
-		f.write('GTCGGACCCATCTCGCGCGCGCTACTGTCATTCCAACTCCCGGATCTTTCGGCCACAAAT\n')
-		f.write('TGGTCCGTGGCCTGCTCGTCACTCTCCGTCACCATCAAAACTCAACAGGCCGCCTTCACC\n')
-		f.write('TCACCAAAGTCACCCTTCCTACCACCACCGCGACCACCGCGACCACCACCACCACCTACA\n')
-		f.write('ATGTCGCCCACGCTGCCCTCGTTCGACTTCGCCACTACCAGAGGGAAGCGGTCGCGGATG\n')
-		f.write('CCTTCGTTCGCGCCGGCCCTTCCGGACGGACTTTCACACCTACCAAACATGCGATACATC\n')
-		f.write('ATTCCTCGCCAGGTGAGAAGGAGATGGAGAGCAACAAAGGGCAGACTACGTGTTGGACAG\n')
-		f.write('TCACCTGCTTCGAATGTCTTTAGACTGCAGACTTCTTGGTCGCCCACCGACACAATAGCT\n')
-		f.write('GCAcTGCGCACGCATCAGTGGTCATTGTATGACTTTCAGTACTTGGGACTGGCAATTCTG\n')
-		f.write('GGCATTTTCTGCTTGAGCATTATGGAgACTCcAGGTCCTATGGTTAAGACGTTCGGCGCT\n')
-		f.write('ACCGCACTCTTGCTATCTCTTTGTTTtCCCGTTACAAGTCAATTCTGGCTCCCAACGTTA\n')
-		f.write('CCCGTTGTAGGCTGGATCATTCTGTTCTTCTCCTGCAGGTACGTACACCCTTGCTTAATT\n')
-		f.write('TCTAATCGACCATTTCCAACTCGATACTAACACGCGTTTCTTTGTAGATTCATCGATGGC\n')
-		f.write('GCATATCGTCCTTCCATCCACGTCCGCGTTCTCCCTGCCCTAGAAAACATATTTTACGGC\n')
-		f.write('GCCAATCTCAGCAACATCCTATCTAGCCaCAAAAaTTCCTTCCTCGAtGTCCTCGCATGG\n')
-		f.write('CTACCATATGGCATCACCCACTTTGGAGCGCCCTTCGTCGTTTCAATCATCATGTTCATC\n')
-		f.write('TGGGGACCTCCAGGGATCGTCCCGACCTTTGCCCGCGCTTTTGGTTACaTGAACATTGCA\n')
-		f.write('GGTGTTCTCATCCAaCTGCTGTTTCCATGCTCTCCACCGTGGTATGAAAATCTATACGGT\n')
-		f.write('TTGGTGCCTGCAAACTACAGCATCCCGGGCTCACCGGCGGGTTTGGCGGCTGTGGACAAG\n')
-		f.write('CTCTTTGGGGTCGACATGTACACTACAGCGTTCACCGGCTCTCCCCAGGTTTTCGGCGCC\n')
-		f.write('TTCCCATCTTTACACTCCGCCAACGCCACCGTCGAGGCTCTCTTCATGAGCTTTGTTTTC\n')
-		f.write('CCAAAGCTTGCACCCCTATTCATTGCTTACACGCTTTGGCTTTGGTGGGCAACTATGTAC\n')
-		f.write('CTGTCGCACCACTACGCTGTAGATCTCGTTGGCGGAAGTCTTCTCGCTGGCATTGCTTTT\n')
-		f.write('TATATTGCTAAAGCAAAGTTCCTCCCACGCATGCAACCCGACAAGGAATTTCGATGGGAT\n')
-		f.write('TACGACTACCTTGAGATTGGCGAATCTCAGGACAATTATTCAGCCAAGGATGGCACTGGG\n')
-		f.write('TTTTACGAAGAGTTTCAGACCGGCGTATCTGATGACGAATGGACCGTTGGCTCAAGTTCC\n')
-		f.write('AGCATCTCGTCCAGAAGTAGAAGCCCTTCCAACACCAACAGATCCTCTAGCGAAACATCA\n')
-		f.write('ATGTGGGAAGGTGAAACCCTGGCCTCGACTtCCGACACCGAACAACGAAGCAGGTAGTAC\n')
-		f.write('CAGCAAaTTAAtctCAACATCCTCGCcTtCCCcGCGACCCAAGCTACATTCTCAaCcAAC\n')
-		f.write('CTGGTTCcTCGATTTTtCGTATCGGTACCCTTGTTGTTCACACGGGACACAATCACGTCA\n')
-		f.write('ACATTGGGCGGAGTTTTGCATCTCTGCATTTGCATGTCACATCTGCAGttagg\n')
-		f.write('>Vein_ctg_2288\n')
-		f.write('GCTGACTTGATATGGAGACAATAACGCAAGGCTGACCGACTGACtGTTTGATtATGTGCA\n')
-		f.write('GGAaTAAAAATACAAAATTGGAATTCGCAAGAGGACAAACAAAACTCTTTTGAACAGCTG\n')
-		f.write('TAGAGATCCACAAAAGATTACAGACCGACCCGGTAATCTGAGACGCTCAGCCTGCAACAC\n')
-		f.write('TTCACCCGTACGAAACAATGGAAACCTGGGCAGACGAATGAGAGGAAGTGGATATTCGCG\n')
-		f.write('GAGTAATTTACATCGAGAAACATTCAGCCACCAGATCCATGATCGTGAAACGCCAAAGGT\n')
-		f.write('CGAAATGGGTTAGCTGGAAGAGGGCGTTTTTGTGGAGAGTCGTCGACGACAACAATGGAT\n')
-		f.write('CCACAGCTTTCTATCAATTCAGTAATCCAACAGTAGCAGCTGACCTAAACATGGCCAGCT\n')
-		f.write('ATAGATCGATCAATATATCCAAGCTTCAGATACCTCCCGAcTCCGCCGGACGATATGGAG\n')
-		f.write('AGCGCACGTCGTGCAAGCTACGCACTTGATGCCCGAGAACGAGAAGGAAAGGAACCGACA\n')
-		f.write('ATGTAAACACCGAACGGATTACACTCAACTACATTAGTaTAAAAAATCGCCAGAGCGACG\n')
-		f.write('TCGTAAACCCCTCAATATGCCATAACAACGCGCCCCGACCTGGTATAAAACTGCCAAATT\n')
-		f.write('TCCCATAAACACCACCCCATCGCACGAATGTCCTCCTGCGCAACAGGATAAAAGAGGCCT\n')
-		f.write('TACCGAGCATCCACGTACCTCTCCCCCTTGTCCACACCCCcAACCTCCCTCTTCTCCTTC\n')
-		f.write('CTCGCCCCcACAAGCGCAAGCCCCGCCAACACCAACCCAACAACATCCGTCAAGAAAATA\n')
-		f.write('GGAATCAACATCCACCTCCAAGCCTCCATATTCCGAACCTTGTTCCTAAACGTCTTCTTC\n')
-		f.write('AAGCTCTCCTCGATGGGAAGCTTGAGGACGGCTTTGTACCATGTTTCTGGCGTCCAGCGA\n')
-		f.write('TGGTCTGGGTAGGGTTCTCCTGCGCGAAGGAGGGAGGGCGTGATTtGTTTGTGCTTGGTT\n')
-		f.write('TGGGAGGTTACGGTGAAGGTGAAGATGAGGGCGGAGAGTGTGAAGAGCGTTGCTAGTGTA\n')
-		f.write('AGGAGGATTGTCAGGACCAGGACGAGGGTCGGTGTACTCTATTCACAAACACATATTAGC\n')
-		f.write('CTGATATCGGAAGAACATTCGATACAGGAAGCGAGGGAGCGATACATAcTTTtCCCTTTT\n')
-		f.write('tGTATCGGAAGGCAATGAACATGCCCAGGAGACCTAGGAAAAACCCATAACCGGCCACGC\n')
-		f.write('CGTTAGATGTGTGGCCTTGATCGAGCCAGATGTGGGCTGGGAGTGCTTTCATCTGGATGC\n')
-		f.write('TCTCGCTTGACGACACTTGAACGGAATAACCAGGCCCGTATTTTTGGACGTGCAGGAAAC\n')
-		f.write('CGACCATGGAACTTATGAGGCCTAGATTCGTGATGGAGAGTGCACTCAGCACGAATTGCG\n')
-		f.write('AGACGAAAAGGGGGAGgAGTAACATGATTCCTGGTGTGATTGCTAGGTGTGTAGTGTACT\n')
-		f.write('CTGAGGAATAAAAGAGTATGTAATAGCCAAATTCCAAAATATTAGGGCGTTTGGAATGGA\n')
-		f.write('CGTGGAACGAGGAACGATGAaCAAAGAGAAGAATAAGCGTCCCGTCGAGATCACAAACAT\n')
-		f.write('CCCGCGCCGCCTTGTTTCTCTATCTATACGAACACACACACACATACATACCTCAGCCGC\n')
-		f.write('AAGGGAACCGCATTGGCAAAGCTTGTGCAAAATATGCATGGTTGCCGGTAGGTATGTAAG\n')
-		f.write('ACGCGCAGCAGCGGCACACAAGAGTCAAGACACATCTTGTCCAAAAGCCCCGGCCACATG\n')
-		f.write('GAATGCAGATTCGTTGGCACCCTCTCAGCACGGATATGTGTATCCATTACCGTTATCGGT\n')
-		f.write('TTTCGGGTTAGTGCTGACTGATGCGATTTTTTACATGCTGAGAGTGTGGGTATTAGGAAG\n')
-		f.write('CAGTATGTATGTAATCATGCTGCGGTCTACGGTCTGCGGGTCGGTCAGGCTGAGGCTGAG\n')
-		f.write('ACATTCACCGCTTGGTATCTTGATCATGATAATGTTTGTTGCTGCGCAGAGGATAGCGAT\n')
-		f.write('TGACCAGTGTTTGTATGTATTAACCATGATTGAAGCTTTTTTTTTCATTGCCAATTTTCT\n')
-		f.write('GGTTGTCGAGTTCGGCCCAAGCTTTtGTCTTGTGGATGGAACGTTTTCAGCTCCTGTTCA\n')
-		f.write('GATCGGGCAAAGGCCGGGTTTTGAATGTTGGGGTGTGGCATTTCGCTATTTGGTGGGGTT\n')
-		f.write('GTGCAGACTGCATAAAGAGTGATTACTACAACTGTTTGCATGTGGAGCTGTGTGACCAGT\n')
-		f.write('TTGTATGCACAGAATCTTTCAAAATGGCATAATCACTGCCATAGGAGGTTCGATTCGATG\n')
-		f.write('GAACCTTTGCAGGGACAGTCTTCCTTCTCGAATATCGAGTTCAGTATTTGGGGCGTCTTT\n')
-		f.write('GCTCATCTTCGTTGGCATCGTCTTTGCAAATTGTGATCAGTTGCCTTTGCACCTGCGTGC\n')
-		f.write('CTTACAAGTCCCCGTTGCTGGTTCGAATTATTTCATGTCTGATAGGATCCTTGACATTGA\n')
-		f.write('TGTGTTCGGGCAATAGCTTGGAGTAAGCACAGAATGCTGGAACGTCTACAGGGTAATTAT\n')
-		f.write('GAATACGCAAAGTGGAACGAGGCATGTCACAAACCAGCTGGTGCGACAGTAGGATGGACA\n')
-		f.write('ATTCCATCGAAACTCACGGGGAAAGGCCAAAAGGGACGGCATCACGGTGTCACACATCGG\n')
-		f.write('GGAGCGGCATCTCCAGGAGAATATGCCAGCAGCATTCCTGCTTTGCCATGCTCTGCTCAT\n')
-		f.write('GCCTCATGCATAGCGGCATGAATTGGTCTGTTCAGTCTGGgTAAATTGTATTCGGTTTGA\n')
-		f.write('CTACAGTTTACACCATCCTCAGCCACCACGCTGAAAGAGCCCCGGTTTGGGAAGCCCTAA\n')
-		f.write('TGCCATATCCTtCCTTTTGTCATGATTCTTGGTATAATGCGTGTGTATCTAACCGACCAA\n')
-		f.write('TTGGACGACTCCACCGGCGTCCTTAAtCTTTTtCTCGGCCTCTGCGGAGAAGtATCGGGC\n')
-		f.write('GCGAACGACGAGTGGGATTTctGGGAGACGACCCTTTCCGAGGACCTTGGAGTAACCGAA\n')
-		f.write('GGAGAGCTTTtCAAAGATTAGCGATTGCGATGGAATCGGCGCGTAGAGATACGTACGAGG\n')
-		f.write('TCGAGGACTGGAGCGGTGTCGGACTTCTTGTTTGAGAGGTACTTCTCACGCTGCTCGAGA\n')
-		f.write('GGAACGAGGGACCAAAGCTGTACTGGTTAGTAGCGGTACAATTTGAATTGGACTGCAGAA\n')
-		f.write('CTGACCTTGTCCAAGTTGATGGTTGGCTTCCAGAAGTGGTTGCCTTGCTTGTGGAAGTAT\n')
-		f.write('CGCATACCGACCTTTCCGAAGTAACCTGGATGGTATTTATCCATGTTGGTTCTGTGGTGG\n')
-		f.write('TGCTGACCACCAGCGAGACCACGACCACCGGGATGCTTGCGGCTATGCGACTGTTAGCCA\n')
-		f.write('ATGCCCTCTGATTCAATTAAGCCCAGTCCTGTAGGCGCTCTTCTTTCAAGTAGCAGTGAG\n')
-		f.write('TGTGGGCGAGAGCATTCGCAAAGCTGAAGAATTCCTCCCACACTGACTGCAATCGCGAAA\n')
-		f.write('TTTCGAAGATCCATTCGACATCGAGGAGAGGGTTATTGCTGAGGGCGTAACATACTGCTT\n')
-		f.write('GCCGACACGACCGTGACCGGCAGAGACGTGACCGCGGTGCTTGCGGGTGTTCGATAATCT\n')
-		f.write('GGTAGGCATCTTGGATGTGAAGGTGCTTGTCGTTGCTTCGGGATGGGAGATAGCGCGAAG\n')
-		f.write('TTTCGATATTCTCGTCTCTGTGTAGCGAGATTTTCCCGACGCCAATATAATAGTGACGCT\n')
-		f.write('AGCCGCGTCGGGAACTCTGATCATGTGACCACATCGGACTACCAaGAAGTTGGAAATGAT\n')
-		f.write('TGATTTGATTCATCTTGGTTCAAATTTACTTTGAAGCAAGATCTAATGATTCTAATCCCT\n')
-		f.write('CTTCTTACAAATGGAAGTGCCCAATATCAACGCTCATTTTCCACCACGGAATGTCGAGCC\n')
-		f.write('CCAGAGTCCAACCGAAGCCAGACAGAGACCACAATCTTCCAGTTCAAGATCAAACCAaCG\n')
-		f.write('CAGTTCAATCTCTCCGCGCACAAACAATACcATAAACCCGAATAAAGGGTGTACCAATTG\n')
-		f.write('ACTAACCAATCGCAGCCCGCTCAAATCCAATCGGCCCTCTCTCCCCACATCTCCAGCCTC\n')
-		f.write('GGTATCATGGCAAAGaTATCACCGTCGGCCTAAGAACcTtGAAATGCCGGGGAATAaaCC\n')
-		f.write('ACCGCCGCATAAGCATTCCAACTCTTAAGAACTGCATTTGTGAAAACCaTATCCATCTAT\n')
-		f.write('CTCATTCCCCGCTCCAGCACTCTCACAGTCCTTTAAaTACTTCTGCGCGCGCAAGTCTCT\n')
-		f.write('GTCTTCTAAGCTCATCCCCTCCACCTTACCTCGTACTTCTACCGAAGCAATCCACAATGT\n')
-		f.write('CAAAACAACTCTCCACAAAGGAAGTCGCAGAACACAAGTCCGTCGAAGAGGGTCTCTGGA\n')
-		f.write('TCATAATCGACAACGAAGTCTACGACGTCACAAAATTCATCGACGAACACCCCGGCGGTG\n')
-		f.write('TCAAGATCCTAAAGCGCGTCGCTGGAAAGGATGCCAGCAAGCAATTCTGGAAGGTGAGAG\n')
-		f.write('ATAATCCTCTTTCCCCCCAGACGTTCTGTAGTTGTAACTAACCCcGCTCGTGTTCATAGT\n')
-		f.write('ACCACAGCGACAACGTCCTAAAAAAGTACAAGCCAAAACTCAAAATCGGAAaCGTAAAGG\n')
-		f.write('AAGACGCCAAaCTATAAAACCCCCGCGCACACACAAGGAGAAACATTGAAGAGTGGAGGA\n')
-		f.write('TATGACACGAGTACAAGGCAGGCAGGCAGGCAGGCGGgCGGGCGGTCAGGCAGGCACGAG\n')
-		f.write('GCCGTCCAGCGTTATACCGGCATGATGAGAGAACGGCATTGCATATACACCCACCAGTAA\n')
-		f.write('TCTTGTCTACCTTGGGGGGgTTATATAGACGCATGCATAGATGAGCGGAGCGTACTAGTT\n')
-		f.write('TTACTTGCAGCAGACACTGCTGAACATCATCATTTTGGATACTTCACTTTCAATTCGTTG\n')
-		f.write('GTTTGGGCTACTTTACTCCTTTGCGGAAAGGAAGTGATTGGTCAATGTAGAATCAAGGAG\n')
-		f.write('CCATTCCAAATTTCCGTTGTTCCAATCCTGATGCTTTCATGAATGGCAATCGGCTGAAGT\n')
-		f.write('TTTCAGGGCGAAGAGTATTGATTCGTGGGATAGACAACCCCAACTTCACCACAAAGGAAA\n')
-		f.write('GGAGAAACAGAACCAATGGACAAAAACAACGGGGAGAGTGGTCATAAAAAGCACAATGGT\n')
-		f.write('ATCAATTACTAAAAGCAATAGtGACGAtCGAATTtCCCTCCCAAACTCATATtCTGAGTT\n')
-		f.write('CCCACAGCCGTGATCCCAAACGCCACGACATTGAGAAaTGAAAAGTCAGACAAGCAACGC\n')
-		f.write('CATCGGGGTgTCCGAATCAATAAGAAGAAAaTAAAGGAATAAAGCAACGCAACGCGACAT\n')
-		f.write('TCCATCGTATTGGTTCAACCATTCTCACAATGCCCAGTACCATGTCCGCTAATCACCGAG\n')
-		f.write('ATGGATGTTTCCCCAAACTCGCATCCAGCCGTGCTGGCCTCGACATAAATgCTTGATAGG\n')
-		f.write('ATCGCATAGTTGCGGCAGTCTCACTTTTGTGCTCTTGGGTCGTCGTCCGAGGTCGCAGTT\n')
-		f.write('GTTTTGTATCTGAAAACCCCGCAGGGAGGGCCCTCAAAAGCTGTCGATTCGGACAGCCCA\n')
-		f.write('TGGGATTTGTACCACCAAGATCATTCGCGCCACTCTGAGCAGACCTCTCATTGTCATTTG\n')
-		f.write('AAGATTTGGGACCAGACTGGCAGGAAATCACAGCACTTGTAAGCTGAGTGGgCGAGTGGA\n')
-		f.write('GAGAATTGACACCATTTGCAGGCTGAGTAGGCGCACCATTGACCACCAGGCCTTGTTGGG\n')
-		f.write('ATTGTCCGCCTCTCTGTATATGATCCGTtACCCGCTTGCAGCGCCCATCGTCCATCGTCT\n')
-		f.write('GAAGTTGGAGCTTGATATTTGCTGGCATGGTCGCAAGAACATGACTAGGTAGGTGgCTTG\n')
-		f.write('CAACGACATCCGCACTTCTCAAaaCTGGTTTGGGCTTACTGCCGAATCCATCAGGGCGCT\n')
-		f.write('TTTGAGCAATGCTTTGATTGCCATCTGAAGAGTCGAAACCAGAACTGCGCAAAACATGAA\n')
-		f.write('TGAGCAACGATAATTCTAACGAGACGTAGAGCTTTGTGGGCTGTTTTTTTAGTAGATGGT\n')
-		f.write('GAGATGGAAATGATATTTGGCTGATGAACCGAAACGCCCCAAAATTGTGGGTCTCCGCAT\n')
-		f.write('GGAGACTTACGACTTGAGGAGTTGGGCGTCCAACCTCTTCAAATCGCT\n')
-		f.write('>Vein_ctg_5197\n')
-		f.write('AAACCATTTGTACAGTCCTAGCCTCCTCTTCAAGAACCAGACGCTAAACAAGCCGACGAA\n')
-		f.write('GAGTACTAAAGCACCACGCGTCATCTGGTAGATAGACGCGGCCACAAACAACAAGCCCAC\n')
-		f.write('ATTCATAAGCGTAGTGCCTATGATATCGCAGATCGCTGGCAGAGCTAGATAtGTCACTTT\n')
-		f.write('CCAGCCTCCCAAAGTCGCTCTTCCATCGTGTGTAAGtGTGAGAGAGgTCGCTAGCGGATC\n')
-		f.write('GTCCGAGTATGCATCAtcGTCATCGTCTTCGGGCTCTTCATTGTTAACGAGTAAAGGATC\n')
-		f.write('GGGGGCGGAGGAAGGGATGGAGAAGTAGCCGGCCTGCTTCCCTCGTCGTTCCTGGATACG\n')
-		f.write('TCTGTAGAGAGAGTGTGCTCCGACAACGAGCCAGCAGCCcATCTcGCCCATGAACaTTTG\n')
-		f.write('CAGCGTTTGTATGACtGGTTGTTCGAAGTGTcTCCTGTtCTTTGGGTTGGTAGCTTTGCA\n')
-		f.write('GTTGCCAGTACaTTGCATGtCCTTTCGCGATCCAGTCAGTTAAGGCCTCATATCAGCTAG\n')
-		f.write('CAGGAGACAACCATACCTGGTACTTCGTGAGCAGAGTATTACACACTCCCGTCGTCAACA\n')
-		f.write('TCATAGCCaCCAAAAACGGAATCACCGCCTTCACGGCcATGGCTGCGTGCGAGGCCGGAG\n')
-		f.write('CTCAACGAGCTCAAGGCAGGGGATGGGAGAGCTTCGggCAGGCCTATAAGACGCAAGCTG\n')
-		f.write('ATGAATAGTTGTCAGTGATATTGGAGGTACTTTAGCTGGAGGAGAGCTGTTGGGTATTTT\n')
-		f.write('CAGTGTTTGAAGGTAGGCACTATAGAAGCTCGTCGCGTGATGGTGATTCAGACAGGGTCT\n')
-		f.write('GTGATAAGTAACGACCTCGGGAGGTCCGTTCACAAGCTACGATAGTACCGATTTACCAGT\n')
-		f.write('GCTTGGCACTGTTGGCAGACATCGCGGTCGCGAAAGACGAACGCATGAGGCATCTGATTA\n')
-		f.write('CAGCGAGCACGCTAGGAAAGATATGAGTGTGGGATTCTCCACACAAAAAGTGGCACAGTA\n')
-		f.write('TCAGTCATAACACATCGCTTCTATTGTTTGTTTGAACTCGCAGAAGTGAAATCTAGAGTC\n')
-		f.write('CCCAGGAGCAGACTCCTTCGCATAACCGTTCCTTCGTGAGCCGCATTAACACATGGAAAG\n')
-		f.write('AAGTTGACCGGCTATTTTtGCATACTTTGACGAACGTCGAACCATGCCCCATGAGAAAAA\n')
-		f.write('AAAaaCaGATGCAGTGGATATATTGAAGACCTGAGAATGCAAaGAtAACTTTGCGGgAGA\n')
-		f.write('GGTTCCTACCCGACGTTTCCATCAGAAAACCCATTCCGCTAATCACCCTCATCGAACTAT\n')
-		f.write('GGGTCGTGGAGCATCTACTTCTTGGCACCAGCCTtGACGGCAGCCTTGGTAACCTTACCG\n')
-		f.write('GCTTTGTCGACCTTGACGACGCTCTTGATGACACCGACAGCGACAGTCTGTCTCATGTCA\n')
-		f.write('CGGACAGCGAAACGTCCGAGTGGTGGGTAGTCAgTGAAAGCCTCAACaCACATtGgCTTG\n')
-		f.write('GAaGgAAtcATCTTGACAaTGGCGGCGTCACCAGACTtGATGAACTTGGGGCTGGTTTCG\n')
-		f.write('GTGGCTTtACCAGTACGGCGATCGATCTtCTCCAAAAGCTCAGCAAACTTGCAAGCAATG\n')
-		f.write('TGGGCAGTGTGGCAATCcAAGACTGGAGCGTAACCAGCACcGACCTGACCTGGGTGGTTG\n')
-		f.write('AGGACGATGACCTGGGCGTTGAAGGACTCGGCACCCTTTGGAGGGTCGTTCTTGGAGTCA\n')
-		f.write('CCGGCGACGTtACCACGACGAATTTCCTTGACGGAAACGTTCTTGACGTTGAATCCGACG\n')
-		f.write('TTGTCACCTGGGAGACCCTCAACGAGCTGCTCGTGGTGCATCTCGACGGACTTGACTTCA\n')
-		f.write('GTGGTGACACCAGCTGGGGCGAaGGTAACGACCATACcGGCCTTGATGACACCGGTCTCG\n')
-		f.write('ACACGACCGACTGGCACTGTTCCAATACCACCGATCTTGTAGACATCCTGGAGAGGAAGA\n')
-		f.write('CGgAGGGgCTTGTCGGATGgACGGGATGGTGGgTCGATGGCATCAATGGCCTCGAGGAGG\n')
-		f.write('GtCTTTCCGGTGACCTTGGACTtGGTCTCCTTCTCCCAACCCTTGTACCATGGGCAGTTG\n')
-		f.write('CTGGAGTTGTCGATCATGTTGTCACCGTTGAAACCGGAGATTGGCACGAATGGGACGTGC\n')
-		f.write('TTTGGGTTGTAACCAACCTTCTTGATGAAGGAGGATGTCTCCTTGATGATTTCGTTGAAT\n')
-		f.write('CGCTCCTCGGACCACTTGGTGGTGTCCATCTTGTTGATGGCGACGATGAGCTGCTTGACA\n')
-		f.write('CCcAAGGTGTAGGCGAGCAGGGCGTGCTCACGAGTCTGACCATCCTTGGAGATACCAGCC\n')
-		f.write('TCGAACTCACCAGTACCAGCGGCAAtGATGAGAATGGCGCAATCAGCCTGGGAGGTACCA\n')
-		f.write('GTGATCATGTTCTTGATGAAATCaCGGTgACCgtGGGgCGTCAATGACGGTGAC\n')
-		f.write('>Vein_ctg_10638\n')
-		f.write('AGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCA\n')
-		f.write('GAGCACTGGGCAGAAATCACATTGCGTCAACACCACTTTCTGGCCATCGCAATGCTATGT\n')
-		f.write('TTTAATTAGACAGTCAGATTCCCCTTGTCCGTACCAGTTCTAAGTTGGTTGTTAAGCGTA\n')
-		f.write('GACTGGGTTCCCTTGGTTGTAGACCAAGAAGATGAAAGAACAGAGTTGCCCCCATTCTCT\n')
-		f.write('CTTCCTCAAGGTCAATACCAAGGGTCCATTTCTACCCAACCCTTAGAGCCAATCCTTATT\n')
-		f.write('CCGAAGTTACGGATCTATTTTGCCGACTTCCCTTATCTACATTGTTCTATCAACTAGAGG\n')
-		f.write('CTTTTCACCTTGGAGACCTGCTGCGGTTATGAGTACGACTAGGCGAGAAAATTATTCTTT\n')
-		f.write('CCCTTGGATTTTCAAGGATCGTTATGAATGCACCGGACACAGCAAAAaGTACTGTGCTCT\n')
-		f.write('ACCAGCAGATAAACCTTTTCTCCTGCTAAACAGATTTCAAGGTTTATACTAACTGTCAAA\n')
-		f.write('AAGAAAAGATAACTCTTCCCGGGACCCATACTGATGTCTCCAAGTTCAATCGCGTTGCCG\n')
-		f.write('CAAAAAATCCTCGTCCTAGTACCGGAATATTAACCGGTTTCCCTTTCGATAGGCGGCCCA\n')
-		f.write('AAAATTGGGCGCTTTGAAAAAACGGAACTTCCCTATCTCTTAGGATCGACTAACCCTGGA\n')
-		f.write('CCAACTGATGTTCTCCAGGAACCTTTCTCCACTTCAGTCTTCAAAGTTCTCATTTGAATA\n')
-		f.write('TTTGCTACTACCACCAAGATCTGCACTAGAGGCTGTTTCACTCCGGTTCACACCAAGAGC\n')
-		f.write('TTCTTAACAGTTTATAAAAACCTCCACGCCTGCCTACTCGTTATTGCTTCGCTTTTACAA\n')
-		f.write('TAACGGCAGAGTATGGGTAACACGCTTAAGCGCCATCCATTTTCAGGGctAGTTCATTCG\n')
-		f.write('GCAGGTGAGTTGTTACACACTCCTTAGCGGATTCCGACTTCCATGGCCACCGTCCTGCTG\n')
-		f.write('TCTAGATGAACTAACACCTTTTGTGGTGTCTGATGAGCGTGTATTCCGGCACCTTAACTC\n')
-		f.write('TGCGTTCGGTTCATCCCGCATCGCCAGTTCTGCTTACCAAAAaTGGCCCACTAGAAACTC\n')
-		f.write('TGCATTCAATGACCTGCTTCAATTAAGCAAACAGGTCGTCTTACATATTTAAAGTTTGAG\n')
-		f.write('AGTGGTTGAAGGGCGTTTAGCCCCCCGAGACCCCAATCATTCGCTTTACCACATAAAACT\n')
-		f.write('GCGTATAAGTTTCTGCTATCCTGAGGGAAACTTCGGCAGGAACCAGCTACTAGATGGTTC\n')
-		f.write('GATTAGtCTTTcGCCCCTATaCCCAAATTTGACGATCGATTTGCACGTCAGAATCGCTAC\n')
-		f.write('GAGCCTCCACCAGAGTTTCCTCTGGCTTCACCCTATTCAGGCATAGTTCACCATCTTTCG\n')
-		f.write('GGTCCCATCATTAGTGCTTTGTCTCGGTCAATTCAGTATAAAACGTCAGCGCCGGACGAT\n')
-		f.write('ACTGCCTCCTTAATGGATTCGTATCAATCAGTTTCCTTACGCATATGGGTTTGGCACCCA\n')
-		f.write('AATACTCGCACTAATGGTGGACTCCTTGGTCCGTGTTTCAAGACGGGTCATTTAGAGTCA\n')
-		f.write('TTAAGCCAACAACCTAAGCGAATAGAAGTATAACCAAAAAGATCAACCTTGATACCGTAG\n')
-		f.write('TACCTCAGAAAACCTTCCTGGAAAACTCGCCAATAAGCATTCGCTGCGTTCCTCAATCCA\n')
-		f.write('ACCCAAGGTATTTTCTAAGGGACTATAACACCCACAAGTGGGCCACATTTCCCCTAGTTT\n')
-		f.write('TTTCCCTCAAGTCAAATTGTCGTTGGCAGGCATAGCCTGCAAGTGCATCCAGGCCGAAGC\n')
-		f.write('CTAGATTGATTACAGACAAGCCAGTCTGGCTCCAAACGGTTCCCTTTTAACAATTTCACA\n')
-		f.write('TACTGTTTAACTCTCTTTTCAAAGTTCTTTTCATCTTTCCCTCACGGTACTTGTTCGCTA\n')
-		f.write('TCGGTTTCTCGCCAATATTTAGCTTTAGGTGAGATTTACCACCCAATTTAGGCTGCATTC\n')
-		f.write('CCAAACAACCTGACTCTTTGAAAGCGTATCACAAAAGGCAAATGCTCAAGCCAAAGACGG\n')
-		f.write('GATTCTCACCCTCTATGATGCCCTGTTCCAAAGGACTTATTTACTCGGCTTGCCTGGAAA\n')
-		f.write('ACACTTCTACAGTCTACAATCCGGTTTAGCTAGGCCAAACAGGTTCCAACTTTGAGCTCT\n')
-		f.write('TTCCTCTTCACTCGCCGTTACTAGGGAAATCATTGTTATTTTCTTTTCCTCCGCTTATTG\n')
-		f.write('ATATGCTTAAGTTCAGCGGGTAATCCCACCTGACTTCAGATCATAGTTTGAAAGTTACTG\n')
-		f.write('GATTATACTCTTGTACTTTACTTCCTGGGCGAACCAAAAAAAAaGATCCTGAGACCAGCG\n')
-		f.write('TAATATTCCTGCCTAGCAAGCCAGACAGAAAATCACACACATTTTAGGTGCTCACTGTAA\n')
-		f.write('TAAAACAGCGATGCGACCCATCACCACATAAACAAATGTTATGTGTGGGTTTGTGATGAT\n')
-		f.write('ACTGAAGCAGGCGTACTCTATAGAAAAACCAT\n')
-		f.write('>Vein_ctg_10639\n')
-		f.write('ACAAACAGACAAACAGACAAACAGACAAACAGACAAACAGACAAACAGAGAGGCAGACAA\n')
-		f.write('ACAGAGAGGCAGACAAGCAGACAAACTTAACATAATGCTTGCATACAAGTATCCTTGAAG\n')
-		f.write('ATCAGAAGCCAAGTGTCAAACTGCTAAAACTGAATTACATAAGTGAATCTAGATAAAGAA\n')
-		f.write('TCACATGTGGGGGAAGAACATTAAACTAATACTGTTTACATAAAAAAAAaGCAAAAAAAA\n')
-		f.write('ATAATATTTAATTTGTATAGCTGAAAGTGTTCCCGTAAGGAACAAATTCAATGACAAGGG\n')
-		f.write('CTTAATCTCAGTACATCGTAGCAACAAAGGCTACTCTAGTACTTACAATACCCCGTCCAT\n')
-		f.write('TTCATGTCGTCTGCATGCGATTTATCACTTTGATCATTTGCATTATCATCACAGGGTAGT\n')
-		f.write('GAATCACAGCATTTCCGCTGCAAAGCCTATCCCGCAAGTAAGGTTTTCAAGCCGAAGCTT\n')
-		f.write('TATTTGTACACAACTAGTACAATCAAAGCACAGTAGTATCGCTTCCAGCATGGATTCTGA\n')
-		f.write('CTTAGAGGCGTTCAGCCATTATCCAGCAGATGGTAGCTTCGCGGCATTGGCCTTTCAACC\n')
-		f.write('AGCCGCAAATACCAATTATCTGAATGAAGGGTTCCTCTCGTACTAACTTCAATTACTGTT\n')
-		f.write('GCGATACCAATACCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGC\n')
-		f.write('TCACGTTCCCTATTAGTGGGTGAACAATCCAACACTTAATGAATTCTGCTTCATTATGAT\n')
-		f.write('AGGAAGAGCCGACATCGAAGAATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACA\n')
-		f.write('AGCCAGTTATCCCTGTGGTAACTTTTCTGGCACCTCTAGCCTCAAATCTTGAGATTCTAA\n')
-		f.write('AGGATCGATAGGCCACACTTTCATGGTTTGTATTCACACTGAAAATCAAAATCAAGGGGA\n')
-		f.write('CTTTTACCCTTTTATTCTACAGGAGATTTCTGTTCTCCTTGAGTCCCCCTTAGGACACCT\n')
-		f.write('GCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACTTGACAATGTCAATAA\n')
-		f.write('CATGGGTCGCACCCTAATGGATGCTTAAAGCTAGAAGGTGAGTCTTGCGACTCAATCCCA\n')
-		f.write('CTTAATTATTTAAGTAAAAAAaCAATAGA\n')
-		f.close() 

--- a/commons/launcher/tests/MockESTBankForBlat.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5996 +0,0 @@
-class MockESTBankForBlat(object):
-	
-	def write(self, inFileName):
-		f = open(inFileName, 'w')
-		f.write(">gi|226792376|gb|GO546081.1|GO546081 Mdas9010M17_e784.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850886.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("GTTTCACGCTCTTCCTCAGCTTCATCAACCTCCGAACCCTAAATTCCCAAATGGCCTCCTCGCCGGACCA\n")
-		f.write("CCACATCAACGGCGACACCAAAACCCACATCTCCAAAAAACCTAAACTTTCCCCAAATTTCATCACTGCC\n")
-		f.write("GCCGAAATCGCCGCCGAATTCTCCCACCACGACCCGAACGTCGCCCGGATCAACAACGGCAGCTTCGGCT\n")
-		f.write("CCTGCCCCGCCTCCTTGATCGAAGCCCAGCGGCGGTGGCAGCTCAAAAACCTCGCCCAGCCCGACCATTT\n")
-		f.write("CTACGTCAACGAGCTCAAGAAGGGAATCCACCGTTCCAGAACCATTATCAAGGAGCTCATCAATGCGGAC\n")
-		f.write("CATGTCAACGAGGTCTCACTCGTCGACAACGCCACCACCGCCGCCGCCATCGTGCTTCAGCAGACGGC\n")
-		f.write("\n")
-		f.write(">gi|226792375|gb|GO546080.1|GO546080 Mdas9010J22_e767.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTCCCATTAAAGAATTATAAAAGATCAATACATAGAGAAATAAGAGAGGGACATATATATTGTCA\n")
-		f.write("CATATACTGGCTAGATATATATATATCTAGCTAGCTACTTGACAGTTATTTGTACGTAATTACTTGACAA\n")
-		f.write("TTAAAAGAAGAAGAAGCAAAGAAAAGTGAACAAGACAAAGATGGAAGTAAGACCATGAGGGTGGAAGTGC\n")
-		f.write("ATTCTCAAATGAACCGATTTAGAAAAATAAGGTGGCGGGGGACTGTAAGGATTTACAGGATAAAGGCTTG\n")
-		f.write("GTGGTACTATAGAGGGCGCAAATGGA\n")
-		f.write("\n")
-		f.write(">gi|226792374|gb|GO546079.1|GO546079 Mdas9010L17_e779.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG35782.1|AF280060_1 tonneau 1 [Oryza sativa], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTCAGTTACTAATTTATATTTCAAGAAATCAATCAAAAAGCACTCCAACAAAGCACTA\n")
-		f.write("AATCAAATCAAAATAGGGTATAATCTTACATAACATGCCTATCATTTGCGGGTGAAATACACAAAATCAA\n")
-		f.write("ATACCGTGCAGTTATACAAAGGTTGTCATCGTGCAGCTACATCTGGTCAGCCCTGCCGTCATCCTCACTA\n")
-		f.write("ATTCCATCTCCTGCGTGCCGCCAAAATGTTGTTAAATTGCGAGCTTTTCTATCCAACTGGAGGTTTTCCA\n")
-		f.write("TCGCACTTGAAGCTCGAATGACATCCTCTGGACTTTCATCACTGTCGTATCTATAGCTGTAGTCATCTTT\n")
-		f.write("CCTGTAGCCAGACATGGAGGACCCACCTCTTCGATCAAATGACTGGGAAGATGCACCAGGCCTTCCTAGT\n")
-		f.write("GGAGGTAGCCCACCAGCAACAGATGATGAAGAAGGTCTTCTCATATTGCGAGAATCTAAATTGGACAGGG\n")
-		f.write("ATTCTGTTTCTGAAGTCGTTAGCCTCCTTCCGGTACCCCTTGATTGAGATAGATTCTCAAATTTCAAAAA\n")
-		f.write("TCCTTCAAGCACATCCAAAAGCAAAGGACCACTATCTCCATTTCGGTTAAGATCATATCCATTCTTGCTA\n")
-		f.write("CTAAAGTCCTTCAACTCAGCTTTCCAAGAATCCTTTT\n")
-		f.write("\n")
-		f.write(">gi|226792373|gb|GO546078.1|GO546078 Mdas9010H22_e754.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n")
-		f.write("AAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGACTGCTTTGAA\n")
-		f.write("GCAGTCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGGCGCACCGTC\n")
-		f.write("AAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCTCCGAGCAAA\n")
-		f.write("CTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATCTGCAGACCC\n")
-		f.write("CGAGACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGTGCACTGGGA\n")
-		f.write("TGCGTCTTCACAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGAGGCTGTCTGGTTCAAGGCTGGAT\n")
-		f.write("CGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGGCACCCAAACCTTATCCATGCTCAGAGCATCTT\n")
-		f.write("GGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGGATACAGAGTTGGAGGAGGAACCACT\n")
-		f.write("CGGTGAAGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCCCTTGGACTTGCTGATGATCCCGAA\n")
-		f.write("GCTTTTGCTGAACTGAAGGT\n")
-		f.write("\n")
-		f.write(">gi|226792372|gb|GO546077.1|GO546077 Mdas9010K23_e774.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187130.1| ribose 5-phosphate isomerase -related [Arabidopsis thaliana] gb|AAF04905.1|AC011437_20 putative ribose 5-phosphate isomerase [Arabidopsis thaliana] gb|AAG51427.1|AC009465_27 putative ribose 5-phosphate isomerase; 91580-90750 [Arabi, mRNA sequence\n")
-		f.write("TTTTTTTGAAGCACGAAGGTAATTCATTTCACATTATTTCACAATTCACAATTCCATCATTCTTTAGTAT\n")
-		f.write("CATTAGTATACCACTGAGTCGAAACCGCAATGCTCAACAAACAATAAGACTATCGAATGCAGAATTTTCG\n")
-		f.write("ACAAATTTCCCATTTCGCCAATCTAAAATTACACCAAAGCAGCTAAATTTCACCAGTAAATACTGAACAA\n")
-		f.write("CAAGCAGCAAGTACCAAAACCCCCCAAAAATATGGAAAAAAACAGAGTACTAATGGAGATTCCAAATACT\n")
-		f.write("CACCACCACCGGAGAACCCGAAAAAAGCCAATCACTTGGTCTTCACATCCACTCCATCCGTGCCCGCAAT\n")
-		f.write("GATCACCGCCGTCGCCATGTCCAAGAACAACCCATGTTCCACAACCCCTTCAAATTTCAAAATCTCCTTC\n")
-		f.write("CCTGCCGCCGGCCCGTCTTTAATCGGAGTCTGGAAGTACAAATCCACAATGTAATTGAAGTTATCAGCCA\n")
-		f.write("CATACGGCTTCCCGTCGCCGTCGATCC\n")
-		f.write("\n")
-		f.write(">gi|226792371|gb|GO546076.1|GO546076 Mdas9010F21_e739.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n")
-		f.write("TCACTGAAGTTGCATTTTAATGAAATCAAATTACAAGAAGCACAAATTATACTCACATAGTCATCATCAT\n")
-		f.write("GATCTTAAATACATTGCAAATTACACAAATCAATATCATGATCATATGTCATAAACTTGCTTGCCGGTGA\n")
-		f.write("ACTTGACCTCAATTGGGTTGACATTCTTCCCAATCGACCTAAAGTTCTGGCCAACCCCTTGGCGCCCAGG\n")
-		f.write("GTTCACCTTCTCAGGGTACACACCATCCTTGGGGTGCAAGTATTGGACCTCCCCGTTAGGGAAAACCCTG\n")
-		f.write("TAAAACTGGTACTTAATCTTGTACTTTGACCTCAGCCTTGTCCCAAGAACCAAGCACTGCTCTTTCCTAA\n")
-		f.write("CCAGTTTCAACAAGTTAGGACCCTCCCTCATGATGGCTGCTCCGCCGGTCGGCATCTCAAAAATCTGCTC\n")
-		f.write("CTTTGGTGACTCCCATGTGATCACGTAAAACTCTTCCTCCTGCGCTTTCCTCAACAGCCCGCCGGTGCTG\n")
-		f.write("CCGCCAAAGATCGGCGAGGGAGTTGGTGGGTCCAGCTCGGG\n")
-		f.write("\n")
-		f.write(">gi|226792370|gb|GO545820.1|GO545820 Mdas9004G01_e277.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192425.1| 4-coumarate:CoA ligase (4-coumaroyl-CoA synthase) family [Arabidopsis thaliana] pir|H85064 4-coumarate-CoA ligase-like protein [imported] - Arabidopsis thaliana emb|CAB81058.1| 4-coumarate--CoA ligase-like protein [Arabidopsis tha, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTACTGTAGAAGAAGACTGTATACTCCATATGGTAAAATGATATACCTCTGC\n")
-		f.write("CCTTTTCGGGCAAGAATGCTAGATCCACCGAAAAGTACGTATACTCGTTATGGTGAAATGAAAAATATAA\n")
-		f.write("ATAATTTGCATTAAAAGCAACGTACTGAGGTTGTTGCTATTTTTCTTTTTGGGTATAGGAGTTTCTATAT\n")
-		f.write("GGACATAATGAAACTGCTCTTCTTTATTTAAATCCAAAAACTTACTGCTCAGATTGTTGAAGAGAATCGT\n")
-		f.write("AGAGAGTTGGTACTAAGAGCTACGTCCTGCTCTTCTTCCCTATAAAGAATGGCAGCACAGCTGAATATCG\n")
-		f.write("TAACATACCTGCAACTTTAAAACAAGCGTACGGAACTTGTAGTGTTCCTACAAGCCTTCCCGATAAAGCA\n")
-		f.write("AACATCGCATCAATGAGGAGCCATGATACAATTTCATATTTTCGACCGCACTTTCTCGATGAGCTCTCTT\n")
-		f.write("CTGAGGATTTTGCCCGATGCTGACTTGGGGACACTGTTTATGAATGATACTCTTCGTAGTCGTTTGAAAG\n")
-		f.write("ATGCAACTTGACTAGCAATAAAGCTCTTGACATCTTCTTCAGTTAGAGAACTATTTGGCGTACGTACACA\n")
-		f.write("ATATGCAGCGGGGACCTCACCAGCTTCAGCATCAGGG\n")
-		f.write("\n")
-		f.write(">gi|226792369|gb|GO545819.1|GO545819 Mdas9003M23_e232.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTGTGAAGAATTTCTAGTTTTGAGGATTCTAGAAAACTGAATGTAG\n")
-		f.write("AATTTATAGCCCAACAGTTACATCAACAAGTATTCTGTGGCTTTTATATCTCAGTTCAATGTTTCCAGCT\n")
-		f.write("ATAGATTGGCTAGCTCATGCTGGTTGAGATGGTGTTGTCTCTTTCTCTTATGAATAAAATAATTCTTTGT\n")
-		f.write("GCCGATGTGTTGCCTCAACCACAGCACGTACGGCATCGAAGTCAACATTGGGGCCGACATCGGTGGCCTT\n")
-		f.write("GAGCACTCGAATGCTCAAATTCTGATTAACCTTGCCGATGATTTCAGCAGCATGACCAACCGTCAGATGT\n")
-		f.write("GCTTCAGGATTAAATTGTAGCGTTACAGCACCATCGCTGTCCAA\n")
-		f.write("\n")
-		f.write(">gi|226792368|gb|GO545818.1|GO545818 Mdas9003L19_e221.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T02087 gag/pol polyprotein - maize retrotransposon Hopscotch gb|AAA57005.1| copia-like retrotransposon Hopscotch polyprotein, mRNA sequence\n")
-		f.write("TCGAGAAACAAATATTTTTCCAATTTGGAGATCATAAAGACGATGCCATTTTTGCCTATAAAGGTATCCA\n")
-		f.write("AGGAATATGCATTGGGAGGCACATGCATCAAATTTGGTGAGTCGTTTATCATCTGTGGAGCTTATGGTGG\n")
-		f.write("ATGGTGAACGGGTATGTTTAGCTAAAGGGCAAACTGAACAATAATTAATTTCAGAAAACTGAATGTCTTT\n")
-		f.write("TACATATGCTTGCATTAATCGGAAATGTTTATCGGAAAGGTGCCCAAGGCGTTCATGCCAAAGGCAGGAA\n")
-		f.write("ATAGCGGACTTGCTGACAAAATTGCAGATAGCCTCCATAGTAACAATGTTGAGATAGTAGAGTCATCCCC\n")
-		f.write("TTTCAGTTCTCGTCCCAATCATCATCCCCAAGCATTGGTCCTGTAACACAAATAGGTTTTTAGCAAAAAA\n")
-		f.write("GGCAATGTAGTCCGAGTGTTGGACAAGTTTAGCGACGGATATTAGATTCAATTGGAATGAAGGAACACAT\n")
-		f.write("AAGACATTACGAATGGTCAAATTGGGAGAGAATTTGACACTCCCTACGTGTGTAACAGTAGCACTCATGC\n")
-		f.write("CATTTGGTAATTGTATGGTTCGATTTTGTATTAATGAGCACGTAATAAGTAGGGCAGGAGAGTACACTAT\n")
-		f.write("ATGATCAGTTGCTCCTGTGTCCAAGATCCAAGCTACGTCTTTCCAAAGAGCGAAGCCACGAAAAGATTTA\n")
-		f.write("CCTGAGAGACTA\n")
-		f.write("\n")
-		f.write(">gi|226792367|gb|GO545817.1|GO545817 Mdas9004B15_e260.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24059|MT3_MALDO Metallothionein-like protein type 3 pir|T17015 metallothionein-like protein AMT2 - apple tree gb|AAC23698.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n")
-		f.write("CAAAATACCATTCAAGCGAAAACCCTAATTTAAACACATCTTCAGCTCCAAGTTCTTAAGTTTATCTTCA\n")
-		f.write("ACATGTCGGGCAAGTGCGGCAACTGCGATTGTGCTGACAGCTCCCAGTGCGTGAAGAAGGGAAACGGCTA\n")
-		f.write("CGACTTGGTGATCGTGGAGACTGAGAACCGCTCCATGGACACCGTCGTCGTGGACGCTCCTGCAGCCGAG\n")
-		f.write("AACGACGGAAAGTGCAAGTGTGGCACAACCTGCCCATGTGTGAACTGCACCTGTGGTCAGTAAGCCCAGA\n")
-		f.write("TAACCAAATTAAAGATGTGATTAATAAAAGTGTCATATTAATTAAGGGATTATAGACCCTTAATTAATGA\n")
-		f.write("AAAGTGTTTGTGGGATAAAATAACGTTGTGGCTTTGTCTCTTGTTTGCTTATAGTATTTGAGTCTGTCGA\n")
-		f.write("GTGACATGTTGTACGTCTGTGAAAACATGTCACTCATATGTTTGTGTTTCTGTGATTGTGTCATGTAATG\n")
-		f.write("GCCATGTTCATGGCCCTTTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792366|gb|GO545816.1|GO545816 Mdas9004B22_e262.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10129.1| hypothetical protein [Cicer arietinum], mRNA sequence\n")
-		f.write("AATTAGGGTTTCTAGCTCCTCCTCCTTATCTCTCGATTTACCAGACGGCATGGGAGGAGGCAACGGTCAG\n")
-		f.write("AAGGCCAAGATGGCCCGCGAGAAGAACTTGGAGAAGCAGAAAGCTGTCGGCAAGGGAAGTCAGCTTAAAA\n")
-		f.write("CAAACGAGAAAGCCATGTCAATCCAGTGTAAGGTGTGTATGCAAGCATTTATGTGCACCACATCGGAAGT\n")
-		f.write("GAAATGCAGGGAGCATGCTGAGGCAAAGCATCCCAAGTCTGATGTCTACGCTTGTTTCCCTCATCTCAAG\n")
-		f.write("AAATGAAAGAACATTTGGTAAGAAGTCACAGGGACAAATTGTGAACGTCGTGGCCCTTTATATTAAAGCC\n")
-		f.write("TGGAATGAATTTACCGAGTTCTTCTAGAGCGATAGCTATTTAATACTGCTTGTGGAGTTGTTTTTGTGTG\n")
-		f.write("TATGTGGTGTGTGTGAGTGAGGGAGAAAGAAAGAGATGTATCTCCTTGTTGAACCGAAACTCGGTCTTAA\n")
-		f.write("ATGATTGTGAATGTTGTTGGTGTAACTCTTGAAAAGAGTTTGTTTCATGGAACCTTGGTTCACTGCGTTG\n")
-		f.write("TGTCGTCTGTACGGGTTGAGTGTCGAGTTTGTGGAACTGCTGTTTGTCTGGCAACTCCGAGGCAAATTCA\n")
-		f.write("CACCAAACCTTGCCTCTTTGGTAATTAATTTGTGTGTCGAAGGTTCTGTTAAAA\n")
-		f.write("\n")
-		f.write(">gi|226792365|gb|GO545815.1|GO545815 Mdas9004A17_e252.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33652.1| carbonic anhydrase prf|1710354A carbonic anhydrase, mRNA sequence\n")
-		f.write("GAAGGAACCAACCTGGATCTCCGTTTATTATTTTTTCGCAAACGATTACAATCTCAAGGAAATTATACGA\n")
-		f.write("TTACATTTGCAACGACGCTGCAGATGAAATTAAGAAGGAAATTACAAACAGGAAGCAATTGAGTTGCATG\n")
-		f.write("GGAATGTGATTGCGATCATACGGAGAAGATGGGGTTGAGGCTGAAATCAACATCCCAGAGCTCGAAACGT\n")
-		f.write("CCGTTGACAAAGTCATAGTATCCTCCCTTGATTGCTAGGGTTTTCTTCAGCAAACCCTCTCTCACAAACG\n")
-		f.write("GATAGCTCAGCAGGTTTCCGATCGATACATTCACCGCCTCCTTTTCACAGTGGCCGCAGAGATCAGCGAA\n")
-		f.write("AGGAGCATCGGCACCATGATCTGCCTTCACCTTCTTCCCTGCCGGCGATGCGATACCAATCCAGTCTTCT\n")
-		f.write("ATGAAGTCAGTGCCAAGGGTAGACCCATCTTCTGGAATCGACAAGAGCGCCTTGATTCCTCCACAGGCGC\n")
-		f.write("TGTGCCCAATCACCACTATGTATGAAACCTTGAGATGCAAGACAGCATACTCAACGGCCGCCCCAGTTCC\n")
-		f.write("AGCGTATTTAGTC\n")
-		f.write("\n")
-		f.write(">gi|226792355|gb|GO546075.1|GO546075 Mdas9010C10_e729.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCTAGTTTTTTTTTTTTTTTTTTCTTGGAAAGCAGTCACCATATCGGAAAAATACTGCTGCTTGTGTGAT\n")
-		f.write("CATATAAATGTTATTAAATAATCAAGTGA\n")
-		f.write("\n")
-		f.write(">gi|226792354|gb|GO546074.1|GO546074 Mdas9010K17_e772.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GTAAGTAAATATAAAATACCACTTGAAAATTTCCCCAGTTGACTTACAAATAACATCCCACTTGATTTTC\n")
-		f.write("ATTGCTACCAAAAATCACAGAATTTTGCCTTATAGGGCAAACTTGCCATTAGTTATAACCAAATTGAATA\n")
-		f.write("AAACAAAAAAAACAACTTGCTAACCCTGTTTTGAAAAAAAAAAATGGAAATAGGGATGGAAACCCAAGCA\n")
-		f.write("CCTAAAAAAATGAAA\n")
-		f.write("\n")
-		f.write(">gi|226792353|gb|GO546073.1|GO546073 Mdas9010D09_e734.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCAC\n")
-		f.write("AATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAG\n")
-		f.write("CGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTA\n")
-		f.write("GGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTC\n")
-		f.write("CACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCT\n")
-		f.write("CCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTC\n")
-		f.write("GGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACACCTGCATG\n")
-		f.write("CATTGCACTCTTCCTCCATTGCTTGCAATAGAGGTAATGTCATTGCTTTTTCTGGTGACAGGGAAAGCTG\n")
-		f.write("AGGAGGACTTGAGGCCGGTGAATGGAGCAACCATTCTGGCTTGAGCGGGGGCGGAAACTGTAGCCACGGC\n")
-		f.write("ACCGGAGGAAATCATGGAGGAAGCCATTGCTCTCTCTCTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792352|gb|GO546072.1|GO546072 Mdas9010N19_e792.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL18930.1|AF429389_1 hydroxymethylglutaryl coenzyme A synthase [Hevea brasiliensis], mRNA sequence\n")
-		f.write("ATTTTTTACGCTGACAATACTTAGCTGCCAATCAAACTATTGGCTTTTAACATACAAACTTAGGGAGGCC\n")
-		f.write("AGCATGTTCTGTTTTACGAGTTAGAACTGGCATCTAGCTACATAAATCTCAACTTAACCATGTGACCGGC\n")
-		f.write("TTGAATTACGTCCATCAGTGACCGTTGGCAACCACACCGTTGGCATTGGTGGTGGCGGCCGCATCCTTCT\n")
-		f.write("TGGCATAGAATCTACGGTACTTAGAGTCGACTTCGGTAAGATAGTATGTGCCTGGAAGTAGAAGGCTAAT\n")
-		f.write("GTCCTGGTTGGTCACAAAGTCTTTGCCTCCATACCTGTGCTCCATGATCTTCATCACTTCAACAAACTTC\n")
-		f.write("TCGGGAGGGAACTCATGTCTTGCCTTCAACTTCTCTCCAACATTCATCATGGCTGCGATGTTCTCCAAGC\n")
-		f.write("TAAAGGGCTGTTGACCAGCATTGAGACGCAATGAGAACATGGTTGCAGTTGAGCCACTTCCATAAGAGAA\n")
-		f.write("CAGTATCACCCGCTTGCCATCCAAGGAGCTGTGCTTGTTGTGGAGGAGGGATACAAATGCCGCATAAAGA\n")
-		f.write("GATGCAGTGTACATGTTTCCCACTTGCTTTGGTACCAAAGTTGTTGGTACAACCCTTAC\n")
-		f.write("\n")
-		f.write(">gi|226792351|gb|GO546071.1|GO546071 Mdas9010O08_e797.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S14305 chlorophyll a/b-binding protein (cab-11) - tomato, mRNA sequence\n")
-		f.write("TTTTCTTGACTTAATTCAGGTGGGGAAAACAATGGCAACAGTCACAACTCAGGCCTCGGCCGCCGTTTTC\n")
-		f.write("CGGCCATGCGTCAACTCGAAATCGAGGTTCCTTTCGGGTTCTTCTAGTAAGTTAAATAGGGAAGTGGCTT\n")
-		f.write("TTAGGCCTATGGCTTCTCCTCCTGCTTCTTCTTTTAAAGTTGAGGCTAAGAAGGGTGAGTGGTTACCTGG\n")
-		f.write("CTTGCCTTCACCAGACTACCTCACCGGCAGCCTTCCTGGTGACAATGGATTTGATCCTCTGGCACTTGCT\n")
-		f.write("GAGGACCCAGAGAACTTAAGGTGGTATATCCAAGCTGATCTTGTCAATGGCAGATGGGCAATGTTGGGCG\n")
-		f.write("TTGTTGGGATGCTATTGCCTGATGTGTTCACCATCATTGGGATCCTTATCTTTTCCTTTTGTCATG\n")
-		f.write("\n")
-		f.write(">gi|226792350|gb|GO546070.1|GO546070 Mdas9010L11_e778.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTACATTAACTACGATTACAATATCCTCCAACTACACAAACGGCCAACATATTTGACAAACGTTGAAAAC\n")
-		f.write("AATTGAG\n")
-		f.write("\n")
-		f.write(">gi|226792349|gb|GO546069.1|GO546069 Mdas9010J21_e766.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTAATGAAAAATCAGAGTTGTATCATATATAACCAGATTGTTGTACAG\n")
-		f.write("CACAGACCATCAACGAAGCTGCAGAGTTGTCAACACATCTTTTATTCTCGACATTTCATCTCCTGTCACG\n")
-		f.write("ATAGCACACCATCCGCGGTTGCAATTTTATCTGAGGATACAAATTTCTTCATATGTTTTGTCTTGATTCT\n")
-		f.write("GTGCTACCCATAAAAATTTCTCCTTGTCATGGGTTGCGAAATCTGGTGGTGCACATGAATATAGAACATG\n")
-		f.write("ATTAACATTCAATCCATGACCAACATTCTTATTTAGTCCAGAACATCGAACGAGGCCATACAAACAAGCT\n")
-		f.write("CTTTGAAATTCCAAGAGGAATCGAGAGTGACCTCCAAATATAGAAATAAAGGGAAAGGCTACCCAATAAC\n")
-		f.write("TAATTTGACCACAGTAAAGAAAATAACTAACAGACTTATTCCCTTGAAACAAAAAACAAGCAGCCTTGTC\n")
-		f.write("AGCCAACGAATCATAACCCAAAGTCTGTAGAGTACTGATGGAAAATCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792348|gb|GO546068.1|GO546068 Mdas9010I09_e759.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10284.1| chlorophyll a/b binding protein [Cicer arietinum], mRNA sequence\n")
-		f.write("TTTTTTTTTTTCAGACACATATTGTAGCACATAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATT\n")
-		f.write("TACATCACCGACAACAATACAAACGAAAGTACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGT\n")
-		f.write("TTGTGGCGTAGTTCCAGGCATTGTTGGCGACTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCC\n")
-		f.write("CTTTCCGGTGACGATGGCCTGGACAAAGAATCCGAACATGGAGAACATGCCAACCTTCCATTCTTGAGCT\n")
-		f.write("CCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGG\n")
-		f.write("GTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAAC\n")
-		f.write("ACAACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGA\n")
-		f.write("GACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCG\n")
-		f.write("GGACAAGAGCTCGGGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGC\n")
-		f.write("TCACGGTTCTTGGCGAAGGTCTCTG\n")
-		f.write("\n")
-		f.write(">gi|226792347|gb|GO545814.1|GO545814 Mdas9003N22_e235.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB01236.1| gene_id:MDJ14.23 unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTTGTCTATCAAAGTGATCATAAATCTACAAGCATTTAGAACATATTTAGTCGACTAATTAT\n")
-		f.write("TGATAATTACAATTATTTACAGATTGAATGGGGAATTGCCCCAAAGATGACTGGGAGATTTGAACTGAAT\n")
-		f.write("TTACAGCTATCTATTTTAGCAGAGAATTCCTATGCCTTTAGTTGCTGATATCAAAGTATTTCGGATCGGA\n")
-		f.write("AGGAAAGTGATATTCCACATGTAACTTGCCCTCATCAGCATCCGTCTGGCGTTGAGGGAACACGACCCTC\n")
-		f.write("AAATCATTATACAAGTAGAAGCGCCTCCCCCCTTCGACATCGATACTGTTTGTCGCTTGTCCAGATGATG\n")
-		f.write("GATCTAACTTGCATCTCTGGACTGACCTCGAACATTTCTTAGGAAATAGGCATGAGAAACGAAGGTGAAG\n")
-		f.write("AGCATAACGCAGAACGCCAGCACCAGCAGTTTTCTTGCTCGTCTTTAAAGGGCTACGCACCCTACTTTCA\n")
-		f.write("CTAATCTCACTGGTCTTTTCAGACGTACAAAGGCTACAATCACTGGGTTCACTGTGATAACAGGCCTTTG\n")
-		f.write("TGCGTTCTCCCTCTCTTTGGTACTGATTAACTACATCCTTAAACTCGTTTGAGTCCGCATCATTGTC\n")
-		f.write("\n")
-		f.write(">gi|226792346|gb|GO545813.1|GO545813 Mdas9003P22_e248.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTGCTACTATAATAGCTCTCCAATTGCAATATATATATTCAAATTATCCTCACAACTGTAACATGCTCTA\n")
-		f.write("TTTACTAACTGGACATATTCCCTCTATG\n")
-		f.write("\n")
-		f.write(">gi|226792345|gb|GO545812.1|GO545812 Mdas9004H08_e282.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198322.1| GDSL-motif lipase/hydrolase protein [Arabidopsis thaliana] gb|AAM64916.1| putative GDSL-motif lipase/acylhydrolase [Arabidopsis thaliana] gb|AAO42146.1| unknown protein [Arabidopsis thaliana] gb|AAO50514.1| unknown protein [Arabid, mRNA sequence\n")
-		f.write("TTTCACGACACAAGGAAAATTATAATAAATGGGCAATACTAACGAAGACACATTGAGAAACTGAAGAAAG\n")
-		f.write("TCTTATGATAGAAAAACAAACACACCCCTTGTAGTTCTAGAACTAGTTCTAGGTCTTAGAGTCCAAGGCC\n")
-		f.write("AAAATAGTGCTGAGGTTCATTGGATTCATGTACTTGTTGGACCCAGTAAGGATTTGCTGCGCAATAATTC\n")
-		f.write("TGCTTGCCTTCTCAGAAGGATGGAATGCATCCCAAAACGCGTACAAATCTCTATTTGGGCACAAGTTGGA\n")
-		f.write("GGCAATTGTGCAGAGTCCGATCCCATTGTAGGGTCCTTGGCCACAGCAAGCTATCTTTGAAGTCACAAAT\n")
-		f.write("CCATAAGCTTGAGGATTGGAGATAAAATCCATGTGCATTTGAAATGCATTTGCAGCAACAAATACATCTG\n")
-		f.write("AGCCAATTTGGCCATTCAGGCTGTTGATCATATCGACTAGCTGTGGGTTAAATAAAGAAGCAGCTCGCTG\n")
-		f.write("CAGCTCCACCGCACATTCGCCTCTTCTGCTGCGCTGAGCCAACTCTGCTGGAGCACACCCTAGTGGCCCT\n")
-		f.write("GTGCCTGTCACCAAAACCTTACGAGCTCCTAATTCATACAGCCTGCTAGAACTTTGCGATACTCGGAGAT\n")
-		f.write("GAGGTAGACGACATAGTCCGGGAGAGAGAATTG\n")
-		f.write("\n")
-		f.write(">gi|226792344|gb|GO545811.1|GO545811 Mdas9003P14_e245.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T12041 cysteine proteinase (EC 3.4.22.-) 3 precursor - kidney bean emb|CAB17076.1| cysteine proteinase precursor [Phaseolus vulgaris], mRNA sequence\n")
-		f.write("AAACATGCGGCCGTACCGATCATCGCCGGTCGTGGCGATCCTCCTCCTCCTCACGATCTTCACCGTCTCA\n")
-		f.write("TCGGCCCTCGACATGTCGATCATCTCCTACGACAGCAACAACCACGTCGGAGACAGCAAGTCGTCGGGCA\n")
-		f.write("GCTGGAGGACAGACGATGAGGTGATGTCGATATACGAGGGGTGGCTGGCGGAGCACGGAAAGGCATACAA\n")
-		f.write("CGCTTTGGGAGAGAAGGAGAGAAGGTTCCAGATCTTCAAGGACAACCTTAGGTACATCGACGAACAAAAC\n")
-		f.write("TCCAAGAACCTCAGCTACAAGCTCGGTCTGAACAGGTTCGCCGATCTGTCGAACGAGGAGTACCGGAACA\n")
-		f.write("CTTACCTCGGCGCCAAGACTCGCGCGCAGATGAAGCGGGTGTCCAACAGGAACACCAAGAGCGACCGGTA\n")
-		f.write("CGCGCCACGTGTCGGCGATTCGTTGCCCGACTCCGTTGATTGGAGGAAGGAGGGCGCGGTGAGTCCAGTC\n")
-		f.write("AAAGACCAAGGCAGCTGCGGGAGTTGCTGGGCATTCTCAACTATCTCCGCCGTGGAAGGTATCAATAAGC\n")
-		f.write("TAGTCACCGGAGATCTCATCTCCCTATCTGAGCAGGAGCTGGTAGACTGCGATAGAACGTACAATGAA\n")
-		f.write("\n")
-		f.write(">gi|226792343|gb|GO545810.1|GO545810 Mdas9004J05_e291.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187574.1| 60S ribosomal protein L4/L1 (RPL4A) [Arabidopsis thaliana] sp|Q9SF40|RL4B_ARATH 60S ribosomal protein L4-2 (L1) gb|AAF23293.1|AC016661_18 putative 60S ribosomal protein L1 [Arabidopsis thaliana] gb|AAL09727.1| AT3g09630/F11F8_22 [, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGTCACGAACGAAACTAGATTGATAAACTAAGCTACAAATATGA\n")
-		f.write("ATCCAGTGCCCGTTATACAAAATCTCCAACCAGATCGAACGGAGGAAAAACACCTTGAAACTTGCTTGTT\n")
-		f.write("AAACTCATTTCCCTGCAACTTATCATTCATAACTCAAAAGTAAACAAAAGACACAGATAAACACCACAAC\n")
-		f.write("AAAATAAACTAACAAAGGCAATGTCTTGTAAAATTTTAAAGCAATAAACTAAATCACTGGGCTACACCGA\n")
-		f.write("GCCACTTTGTGAAGTTGTCGAATTCTGTGTAATCGCTGTCAGAAATCATAGTTTTGTACCAAGCCTTTCC\n")
-		f.write("AGCTGCCTTGATGGCGGTAGCTTCCTCCTTAGTAATGGGCTTTCTCTTCTTGTCAAGCTTCTCCTTCTTG\n")
-		f.write("GCCTTCACGCGCTGCTCCTCAGCCAAAAGTGACATTCTCCTCGCTGTCTTAACATAGGGGTTCAACTTGA\n")
-		f.write("GCAGTGTGTTGAGATTTTTGAGAGGGTTTTTCTTCATTGGAGCTCTCTTGGCATCCTTCTTGATTGGCCT\n")
-		f.write("GACAACAGATTGAACTTCATCAGAGTTGATGATCCTCGCCAAGTCAGCATTGACCATCTTCGACCTCGGC\n")
-		f.write("AGCACATATCCCTTCTTCTTCTCCGAGGGCTTGTCAAACGACCCGTAAATTGAG\n")
-		f.write("\n")
-		f.write(">gi|226792342|gb|GO545809.1|GO545809 Mdas9004B06_e256.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TTTTCAAGATAAAGTTAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAG\n")
-		f.write("CTTAAAGATCATCTATTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGG\n")
-		f.write("CCCAGGCATTGTTGGTAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGAC\n")
-		f.write("AATGGCCTGCACAAAGAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTA\n")
-		f.write("AGCTCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGT\n")
-		f.write("CAGTGATCTCACCAAGGGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGT\n")
-		f.write("TGCCCAGATTGCTAGAATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCG\n")
-		f.write("CTGAAGATTTGAGCTCCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCT\n")
-		f.write("CCGGGAAAACACAGCCCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTC\n")
-		f.write("\n")
-		f.write(">gi|226792333|gb|GO546067.1|GO546067 Mdas9010O09_e798.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK38744.1| carotenoid 9,10-9',10' cleavage dioxygenase [Phaseolus vulgaris], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAATCAACATAATTAAGATGGTATAGGTATTGCTATGTGACCCAC\n")
-		f.write("TGATTCTTTTTGTTCAAAGTAATTAAAACACCATCCGGTAGTTTAAACACAGAGGTGTATACATTATTTA\n")
-		f.write("TTGGTGTACATGTGGAGTAGACCGCCTACACGACAACAGGTTCAGTTTACGCTGGCGTGCCTTCCCCTTG\n")
-		f.write("TACGTTCTAACAATGATGAATAATTTTAGAGCTTTGCTTGTTCTTGCAGTTGCTCCTCTGTCACGAAGAA\n")
-		f.write("GGCATGGAAACCATATGGAACTCTGTGTGGCAATTCCACGACTGCAACGGGCTCTGATGACATTGTCTTT\n")
-		f.write("GCATCAACTACATGAACTGCTGATTTTCCAGTGTTCTCGTCATGAACAAAGAGTATTAAGTAGCCATCAT\n")
-		f.write("CTTCTTCAGAAGTAACGCCAGGAATACGAGGGACAAAAATAGCTTCAGAACCAAATCTGCCAGGTCCCAG\n")
-		f.write("GTCATAGAGGCCTTGGACATTTCCTCCAACCTCAATTTTTGTTTTTCCGACCTCTGGTTCAGCATGCAAA\n")
-		f.write("TCAAACTTGGCTACCCCTGTAACCTTG\n")
-		f.write("\n")
-		f.write(">gi|226792332|gb|GO546066.1|GO546066 Mdas9010M20_e786.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD31838.1| putative quinone oxidoreductase [Cicer arietinum], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTTCAGTAATAAAAACTGTTTATTCAATAATAAAACTTGTTACAACAATT\n")
-		f.write("AAATTTGACAAAGCAAATTATCCTTTACAAAAACACGAAATTGCAAATTGAAAACTGGACTGAAAATCAA\n")
-		f.write("GAACAAAAAAAATGAAAGTATGGAACACTCAACAGCGATCGTATAATTGATCATCATAATTAGGCAAATC\n")
-		f.write("CCTTAAGCTTCTTTGCGATGCCAGCAAAGTACTTTCCCTGGTGGCTAGCTGTTTCTAGTTCTAAATCAAA\n")
-		f.write("AGGTTGTCTTGTGCCATCCCCAGCATAAGTTCCCGCACCATAGGGGCTTCCACCCTTGACCTGCTCCATC\n")
-		f.write("TCGAACATGCCAGCTCCACTCGTGTATCCGATAGGCACAAAAAGCATTCCGTGGTGAACAAGCTGAGTAA\n")
-		f.write("TGGTCGTCAAGGGGGTAGTCTCTTGTCCACCACCTTGAGATCCAGTGCTGTAAAAAATTCCAGCGGGCTT\n")
-		f.write("GCCAGCAAGTGCTTGAGTTCTCCATAAGCCTCCAGTTGAATCGAAAAATGCTTTAAACTGTGCAGCCATC\n")
-		f.write("ATTCCAAATCTGGTAGGGAAACCGAAAATTATCCCATCAGCCTCCACAAGTTCCTCAGGTGAAATTACAG\n")
-		f.write("GCACTTCACTCTTTGGTGGTGCACCCATTTTTCCAAGAACTTCTGCTGGCAGCGTTTCTGGTACC\n")
-		f.write("\n")
-		f.write(">gi|226792331|gb|GO546065.1|GO546065 Mdas9011C01_e819.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191781.1| serine/threonine protein kinase, putative [Arabidopsis thaliana] pir|T48014 serine/threonine protein kinase-like protein - Arabidopsis thaliana emb|CAB71882.1| serine/threonine protein kinase-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTAAAACATGAAATACCACCTTGCATTATGAACAAATCAAATACACCGCAAATAATGAAGCAATATA\n")
-		f.write("GTACATCTCTTTCAAAAAGAGGAAAAAAAGAAGAAAACGAAGCATATAGAACATTGTGCAAACAATATAC\n")
-		f.write("CACCAGACCACCCTCAGAACTCTATCCCCTTTTGTTACAATAATTGCATGCTGAATTACTTATACATGCA\n")
-		f.write("CACATGCCACACCTTCAGAGGCAAAGGGAGAGACAGAGGGAGATTGAGAGATTCACAAGTTTGGTGATTC\n")
-		f.write("ACCAGCAGGTCCATGACGAGCATTTAACAGGGGTTGGAGGGCTTTAACAACAATGCTCATGTTTGGGCGG\n")
-		f.write("AAATCAGCCTCATATTGCACGCACAAGGCAGCAACTGCAGCCATCTTTGCAACCGCCTTTGGTGGGTACT\n")
-		f.write("CTCCTCCAAGTCTTGAATCAATACACTGCCTAACTTTGTCTTCACTAAGCTTTGGTGTAGCCCATGTTAC\n")
-		f.write("TAGACTCTGCTGTCCCCGTGGTAATGTATGATCAACAGGTTTTCGTCCAGTCAAAAGCTCAAGCAGGACA\n")
-		f.write("ACACCAAAACTGTAAACATCACTCTTGGCATTCAACTGTCCTGTCATTGCATATTCAGGGGCATGATAGC\n")
-		f.write("CAAAAGTTCCTAGCACACGAGTGGAGTGAAGACGTGCTGC\n")
-		f.write("\n")
-		f.write(">gi|226792330|gb|GO546064.1|GO546064 Mdas9011C14_e822.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC32136.1| YGL010w-like protein [Picea mariana], mRNA sequence\n")
-		f.write("CTAATTTTCTCGGAAAATTCTCAAATGGGGAAGACCGGACTGTTTGATCTCGAAAAGCACTTTGCTTTCT\n")
-		f.write("ATGGAGCTTACCACAGCAACCCGGTCAACATAGCGATTCATATGCTCTTCGTCTGGCCTATCCTCTTCAC\n")
-		f.write("CGCTCTGCTCATCCTTTACTTCACGCCCTCGCTGCTCAGTTTTGGGGTTTCGGTGTTTGGTAACGACGTC\n")
-		f.write("GCTCTGCCTTTCAACGTCGGCCTGCTGTTGACTATAATCTATTCGGCGTTTTACATCTGTTTGGACGCAA\n")
-		f.write("AAGCTGGCTCCTTGGGTGCTCTGCTCTGCGTAATTTGCTGGGTTGGTAGCTGTTTCCTTGGAACCCTACT\n")
-		f.write("CGGATTTTCCATCTCTTGGAAGGTTGTTCTGGTGGCTCAGATAGTGTGTTGGACTGGACAATTTATCGGC\n")
-		f.write("CATGGAGTCTTTGAGAAAAGGGCACCAGCTTTGTTGGACAATCTTGCACAAGCCTTTATCATGGCTCCCT\n")
-		f.write("TCTTTGTTCTGTTAGAGGCTCTGCAGATCTTCTTCGGGTACGAACCGTACCCCGGGTTTCAAGCAATTGT\n")
-		f.write("TCAAGCAAAGATTGATGCTGAAATCAGTGAATGGCAAGAGAATAAGAAGAAACTGATCTCCTAATCTGTA\n")
-		f.write("ACTGGATTTACTTTTACTGTAATATCTGGGGTGTGGTTAAAAGCAATACCAAAGCTTTTATCTGTAAACA\n")
-		f.write("TGT\n")
-		f.write("\n")
-		f.write(">gi|226792329|gb|GO546063.1|GO546063 Mdas9010N01_e787.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568147.1| coatomer delta subunit (delta-coat protein) (delta-COP) [Arabidopsis thaliana] gb|AAK96656.1| coatomer delta subunit (delta-coat protein) (delta-COP) [Arabidopsis thaliana] gb|AAM47945.1| coatomer delta subunit (delta-coat protein), mRNA sequence\n")
-		f.write("ACGAATAGGCATCCACTTTTATTATTAACATTCCTTGGGGGGGAAGGGGATAGTATCAAATAACATGAAA\n")
-		f.write("GAATGCACATCTATAGCATCCAAATTCTGGCAGGCTTCCCTTCATCTCAAATTTAATGGGAATTAAAACA\n")
-		f.write("CCACAAAATGAAAACTCCTGGTTTTCGAATTCAATCCATATCCAAAAAGGTTGCAGATCCACACACCCCA\n")
-		f.write("AACCAATCACACCACTTGGTAATTCTCCGTCACCAACTGCGTTCTTTGAGAAAACTTGGGAGCGGCTCCA\n")
-		f.write("CCTTGCAGAGGTATAATGTTCAAAACCTTCAGGTCACTGAATGTCTCAGTGGCAGCGAAGCGCACAGAAA\n")
-		f.write("TGGGGAAAAATACAGATGGGTCTGCTGGGGGAACAACAAACTCCATTGATCCACTGCGGTTCGAGTTATC\n")
-		f.write("TACGAGAAGTATGGACCACTCCAACATTGAATTCCTAGCATCGTATCTCCATTCACCTTCAATCTGGTTT\n")
-		f.write("ACACGTGGAGCCTCTCTCGCAGCTGGGAGAGGTACAGAGATAACAACATTTCTCAGATCAAACATCTCTG\n")
-		f.write("AAGCCTCATACTCAATGTTGACATAAGTTTCATTCCCGGAAACAGTGGGCCAACAGTTGATTGTCAGGGG\n")
-		f.write("CACCATTGACTCATCTGAAGTCTGCATTCTCCATCTCAAAAGACCAACAC\n")
-		f.write("\n")
-		f.write(">gi|226792328|gb|GO546062.1|GO546062 Mdas9010O18_e800.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P54260|GCST_SOLTU Aminomethyltransferase, mitochondrial precursor (Glycine cleavage system T protein) (GCVT) pir|S59948 aminomethyltransferase (EC 2.1.2.10) precursor - potato emb|CAA81081.1| T-protein [Solanum tuberosum], mRNA sequence\n")
-		f.write("TCGAGTTGCTTGAGTATTACCTCAGCGCCAAGAAAGCCGCCCTCTGCCCTTCTTCTCTTCCCTATGGCCC\n")
-		f.write("ATGTGAGTCCAGCCTCCACAGGTGTTGTGTGTTGCTCCATGTCATTGCCATATAAACACAACCCAGCTTC\n")
-		f.write("CAGTCGGAGACTGTCACGAGCACCCAGACCTGTCAGCCTCACCTTCCCCTCGGATTTCTCCAAGATTGCC\n")
-		f.write("TTGGCAAGATCCACTGCATTCTCATCAGGAACCGAGATTTCAAATCCACAAACAATGTAGCATACACGAC\n")
-		f.write("ATGAGTGATTACAGTTCGATAAAAAGAAGCAAGTCTACTTGAAGAAGTAAGGAAGGTTAACAACATAGAG\n")
-		f.write("GAGGAAGTAGGCCCAAGTGACACCCGAAATGCCTCCGAAGAAGAAGCCGCCGGTGAATTTAGACCATCCC\n")
-		f.write("TCCGCGGTTTGAAGCTGGTCGGGCTCCTTCTTCCTGCCAGTCAATGTCAAAGCGGGCGCGGAGGACGGCT\n")
-		f.write("CTCCTTCCTTGAAGGAGGAAATTCCATAGATTGTCAAGCACAGGGTTTAGGATGACCACAAGACCAGCAG\n")
-		f.write("CAGCCAAGGAGCCAGCTCCCCAGCATAAAGGGGTGTTCCTCAATGGGCCAGTCTTGACAAACGGGCCTAC\n")
-		f.write("CAGAAAGAAAACCGTGGGCCAGGCCCACCTCAAATACCCCTGAGAAGTGGGCTGAC\n")
-		f.write("\n")
-		f.write(">gi|226792327|gb|GO545808.1|GO545808 Mdas9004B24_e263.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO85557.1| photosystem I subunit XI [Nicotiana attenuata], mRNA sequence\n")
-		f.write("TTGGAGACTCCAGTGACATCAAGCCCTTTGATTGCCTGGTACTTGTCCAACCTCCCAGCCTACAGGACAG\n")
-		f.write("CAGTCAGCCCACTTCTCAAGGGTATTGAGGTGGGCCTGGCCCACGGTTTCCTTCTGGTAGGCCCGTTTGT\n")
-		f.write("CAAGACTGGCCCATTGAGGAACACCCCCTATGCTGGGGGAGCTGGCTCCTTGGCTGCTGCTGGTCTTGTG\n")
-		f.write("GTCATCCTAACCCTGTGCTTGACAATCTATGGAATTTCCTCCTTCAAGGAAGGAGAGCCGTCCTCCGCGC\n")
-		f.write("CCGCTTTGACATTGACTGGCAGGAAGAAGGAGCCCGACCAGCTTCAAACCGCGGAGGGATGGTCTAAATT\n")
-		f.write("CACCGGCGGCTTCTTCTTCGGAGGCATTTCGGGTGTCACTTGTGCCTACTTCCTCCTCTATGTTGTTAAC\n")
-		f.write("CTTCCTTACTTCTTCAAGTAGACTTGCTTCTTTTTATCGAACTGTAATCACTCATGTCGTGTATGCTACA\n")
-		f.write("TTGTTTGTGCCTCGCGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792326|gb|GO545807.1|GO545807 Mdas9003M08_e227.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07086 acid phosphatase (EC 3.1.3.-) - soybean emb|CAA11075.1| acid phosphatase [Glycine max], mRNA sequence\n")
-		f.write("AGGAGTATTACTCTTCCTTCTTGCCATATTTTTCTCAACAACTCAAGCTTATGAGCCACTTATAAACCAC\n")
-		f.write("CATATCCATCTCCTCAGGCCGAAATCCGGGGCGGGTGGCAGCAGCGTTCCCGGCGTGTCTTGCCTGAGTT\n")
-		f.write("GGCGTTTGGGGGTGGAAGTTAGGAACATTATCAACTGGAAGACTGTTCCGGCACAGTGTGAAAGCTACGT\n")
-		f.write("TGGGCACTACATGCTTGGGCACCAGTACAGGAAGGACTCAAAAGCGGTCACTGATGTGGCTTGGCTCTAT\n")
-		f.write("GCTAAGAGCCTCAATCTTACAAAGGATGGCAAGAACGTTTGGGTCTTTGATATCGATGAAACTACACTCT\n")
-		f.write("CTAATCTACCGTATTATGCTCGTCATGGATTCGGGACCGAGGTATACAATTCCACTTCATTCAATGAATG\n")
-		f.write("GGTGTTGGAAGGCACAGCCCCAGCTTTGCCCGAGAGTCTTCAGCTGTACAAGAAATTGTTGAAACTTGGA\n")
-		f.write("GTCAAGGTCGTGTTCATAACAGGTAGAGGAGAAGATCAGAGAAGTGTCACAATCGCCAATCTCAAAAATG\n")
-		f.write("TCGGATATCACACCTGGGAGAAGCTTGTCTTAAAGGGATCAGCTTATTCTGGGAAGACATCGTACGAGTA\n")
-		f.write("\n")
-		f.write(">gi|226792325|gb|GO545806.1|GO545806 Mdas9004D04_e268.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P50694|TLP_PRUAV Thaumatin-like protein precursor gb|AAB38064.1| thaumatin-like protein precursor, mRNA sequence\n")
-		f.write("GGGAATGCAAGAGTATTATTCTTTATTTATTTCATTGAAATTATTACAAATTCATGACAATACTAAGCGT\n")
-		f.write("CAAAATTCATAAAGTTTATTTCTCCTTTAGTATGATATAAAGGGATATTACATAATATCCTTTCTAGTTC\n")
-		f.write("TATTTTTAGGGTGATGGACAGAATGTAATAACGTAGTTTGGTCCACCGCTGCATGTAAAGGTGCTGTTGA\n")
-		f.write("CATCATCATAAGCGTAGCTATAAGCCTGAGGGCACTGGTCCTCAAAGATCTTAGAGTAGTCTGTGGGTGG\n")
-		f.write("ACATGTAGCTGGTGTGTCATTAGGAGGAGTGCAGCAGTATTGTGGTTGATTAAATTGTGTACACGCACTC\n")
-		f.write("TTGCATGCAATTACGCTCCCATCGGACCCCTTCACTTGCAGCTCAGCTGGGCAAACAGCGTTGACGTTGG\n")
-		f.write("CGGGGCAAGAAGAGGTCTGGCAGTCGCCCGTGCCGCCTTGTGGGGCAACAGACACGGGCAAGTTGAAGCC\n")
-		f.write("ATCAACAAGACTTACGTCGTAGAAATCTTGGCCTCCGTTTGCGACAATATTTATTTCGACTAGGCTTGCT\n")
-		f.write("GGTGGAACTGCTCCGTTACCGTTGCATGTGACTTGGCCAGAGCTACACTCTGCTGTGGCACAACTGAACT\n")
-		f.write("TTCCTGAAGCGTCAGTGGAGCATCCGGTTCGGCCCCAGAAGCGGCCTTTCCATGGGACTGGAGTG\n")
-		f.write("\n")
-		f.write(">gi|226792324|gb|GO545805.1|GO545805 Mdas9004F09_e274.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179752.1| 40S ribosomal protein S25 (RPS25B) [Arabidopsis thaliana] sp|Q9SIK2|R25A_ARATH 40S ribosomal protein S25-1 pir|H84602 40S ribosomal protein S25 [imported] - Arabidopsis thaliana gb|AAD23647.1| 40S ribosomal protein S25 [Arabidops, mRNA sequence\n")
-		f.write("TAAAATTGTAGATTAAACAAAATCGACGCTAAATAGTCTGAAACGACATATAACGATACCCGAAACGACA\n")
-		f.write("ATTAAACACGAAAGAGCAAAGAGACCTAGGTGTTGGTAGCCCTGGTGTAGATCTGCTGGCTGGCGTGGGC\n")
-		f.write("AGAGACCATCCTAATCGAGCCTCTAGCCATCAACTCCCTGATGGCCTTCCTGGCCAGGGAACCGTTGATC\n")
-		f.write("CTGAGACGGTCGGAGAGAATGGATGGTGTGATGAGCTTGTACTTGGGGGCCTCAGTGAGGAGCTTGTCGT\n")
-		f.write("AGGTGCCCTGGTCGAAGAGCACCATGTTGTTCACCTTCTCCTTCTGCTTTCCCTTGCTCCACTTCTTCTT\n")
-		f.write("CTTCTGCTTGCCTCCTCCGGACTTCGCCGGCTTCGACGACGGCGGCGGTGCCTTGTCCTTCTTCGGCGCC\n")
-		f.write("ATGATCGGATTACAGCGACAGGGAAGGGAGGAGAGAGGAGGAGAGAGGGAGGGATCGGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792323|gb|GO545804.1|GO545804 Mdas9003O06_e237.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO85557.1| photosystem I subunit XI [Nicotiana attenuata], mRNA sequence\n")
-		f.write("CAACTGTGTCTGTGTATCTTCTGCAGTTGGTGCAAAAGTGATGGCCTCAGCTTCTCCAATGGCCAGCCAG\n")
-		f.write("CTTAAATCCAACTTCACCTCTCCGATCACCACCAGACCTGCCTTGTTTTCTCCCAAAGGCCTCTCTGCCT\n")
-		f.write("CCCCACTCAGGCTCTTCCCTTCCAAGAGACTCTCTTCCTTCTCCATCAAGGCTGTCCAATCTGACAAGCA\n")
-		f.write("AAATTTCCAAGTGATTCAACCCATCAACGGAGATCCTTTCATTGGAAGCTTGGAGACTCCAGTGACATCA\n")
-		f.write("AGCCCTTTGATTGCCTGGTACTTGTCCAACCTCCCAGCCTACAGGACAGCGGTCAGCCCACTTCTCAGGG\n")
-		f.write("GTATTGAGGTGGGCCTGGCCCACGGTTTCCTTCTGGTAGGCCCGTTTGTCAAGACTGGCCCATTGAGGAA\n")
-		f.write("CACCCCCTATGCTGGGGGAGCTGGCTCCTTGGCTGCTGCTGGTCTTGTGGTCATCCTAACCTTGTGCTTG\n")
-		f.write("ACAATCTATGGAATTTCCTCCTTCAAGGAAGGAGAGCCGTCCTCCGCGCCTGCTTTGACATTAACTGGTC\n")
-		f.write("GGAAGAAGGAGC\n")
-		f.write("\n")
-		f.write(">gi|226792322|gb|GO545803.1|GO545803 Mdas9004J23_e295.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P27608|AROF_TOBAC Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (Phospho-2-keto-3-deoxyheptonate aldolase 1) (DAHP synthetase 1) (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1) gb|AAA34068.1| 3-deoxy-D-arabino-hept, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGTCAAAATCATACGCATTATTCAATTTATTTTTGCTTCCCTTCAA\n")
-		f.write("AGTTCAAAGTCTCCAACCATCACTTCCAGTATATACGTACAACACACAACATAAATTATCACTAAACACC\n")
-		f.write("AGTGACGTATTAACACAGTGCAGTTTTGAAAAGATGAATAAAATAACTTCCAGGGTTCTTAACCCTTGAG\n")
-		f.write("ACCATTCTACAGACCTAAAGCGGCAAGCGGGTTCTGTGACTTGATCCTTCTTTTCCTGAGGCGCTCGGCA\n")
-		f.write("ATGATAAAGGCGAGCTCAAGAGATTGTGAGGCGTTGAGCCTTGGGTCGCAGTGAGTGTGGTAGCGTGAGC\n")
-		f.write("TAAGGTCGTCGAATGTCACAGTGCGTGAACCTCCAATGCATTCCGTCACATTCTGGCCTGTCATCTCTAG\n")
-		f.write("ATGAACACCACCTGGGTGGCTTCCTTCTTGCTCGTGTACATCAAAGAACGCTCTCACCTCCGCCCTTATG\n")
-		f.write("GCATCAAAAGGACGTGTTTTGAGGCCGCAGGGAGCCTTAATGGTGTTTCCATGCATTGGGTCACTGACCC\n")
-		f.write("ATGTGACAATCTGTCCAGCCCTGCGG\n")
-		f.write("\n")
-		f.write(">gi|226792314|gb|GO546061.1|GO546061 Mdas9010N21_e794.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n")
-		f.write("GAGAATTCGTGTGCTTGGGAGTCCCTGATGATTAATTATTAAATAAACCAAGATTTTACCATGACTGCAA\n")
-		f.write("TTTTAGAGAGACGCGAAAGCGAAAGCCTATGGGGTCGCTTTTGTAACTGGATAACCAGCACTGAAAACCG\n")
-		f.write("TCTTTACATTGGATGGTTTGGTGTTTTGATGATCCCTACTTTATTGACCGCAACTTCTGTATTTATTATT\n")
-		f.write("GCTTTCATTGCTGCACCTCCGGTAGATATTGATGGTATTCGTGAACCTGTTTCTGGATCTTTACTTTATG\n")
-		f.write("GAAACAATATTATTTCTGGTGCCATTATTCCTACTTCTGCAGCTATAGGTTTGCACTTTTACCCTATATG\n")
-		f.write("GGAAGCGGCTTCCGTTGATGAATGGTTATACAATGGTGGTCCTTATGAGCTAATTGTTCTACACTTCTTA\n")
-		f.write("CTTGGTGTAGCTTGCTACATGGGTCGTGAGTGGGAACTTAGTTTCCGTCTGGGTATGCGCC\n")
-		f.write("\n")
-		f.write(">gi|226792313|gb|GO546060.1|GO546060 Mdas9010O06_e796.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAN62336.1|AF506028_3 CTV.2 [Poncirus trifoliata], mRNA sequence\n")
-		f.write("TGCAAATCTCAGACTGCGGTGTCGTATTAATCCTTCTGCTTATCTTCCTGCTAATGTTAGCCCTCCGCTT\n")
-		f.write("CCCCTTTGCAACAGTTCTAACGTACAGCCCCTTGTTATTGCGGCGCATCCACAAGAAGCAAATCAGTTTG\n")
-		f.write("CATTAGGACTATCGGATGGTGCTGTTCACGTCTTTGAGCCCCTTGAATCTGAAGGCAAATGGGGTGTGGC\n")
-		f.write("TCCACCTGTTGAAAATGGTTCAGCAAGCAGTGCGCCGGCTACTCAAGTTGGAACTTCAGGTTCAGATCAA\n")
-		f.write("GCTCAGAGATGATCAAGAGGCTGGCAGAGCACAAGTTCTTTTACATGCTTTGCTTGCTGGCCTATTCCAA\n")
-		f.write("ATACAGTTTGTGTTCTTCATGCAGTGTAATTTAATCAAGGAAGGATGTGCAGATATGTATATTTAACAAG\n")
-		f.write("TTGGTTCAGAATCTCAAGTAAGGTA\n")
-		f.write("\n")
-		f.write(">gi|226792312|gb|GO546059.1|GO546059 Mdas9010C05_e728.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTGAAACTTTGAAAGCATATATATTTATGAATGTTTAATGGTACATGCTCATACACCTCACATTTAACA\n")
-		f.write("TTTGAAAATAATTACAAACTAAGCAAAACAAGTAATTAGTTTTTGCATCAAAAAGTGTCAAGTATGTTTG\n")
-		f.write("ATGCATTGTGTAAGATAAAGCCGAACACAGCTGACAAATATGTCAATATAGCTCAGCTTTATCCACACAT\n")
-		f.write("TATTTTAAGAAATACTATGGTAAAAACCATAAGCATCTGAAAGAGTAATGGCAGTGGACTCGCTCCGCCG\n")
-		f.write("GCTTGTGTCCTTCACTTTGTTGAAGTTTTTCGAGCCATTGCCGCCTTCAGTTTCTCCTCCCTTCTCACCC\n")
-		f.write("CCGCGCTGTTGCTTGAGAAAGATTTTGGAATCCAGTCCTGAGATTAAAAGAATGGATGACTGGAATATGC\n")
-		f.write("TCAACCGCCTGACGATCTTCACCATCCCTTTGAAGCTTGGCAATGAGTACAGTGGGCATGTCATGGAGAA\n")
-		f.write("ACAGTTCCTCGAGTTCCCGTAGACCCTCCATGCCGAGTGGAGGTAAATTCAAACTCTTACAATTGGACAG\n")
-		f.write("GGTTACCTTCTTAAGATTANGCATTGCTCCAGACTCAACTTTCATGGTATGTAGTTGATCAAATTGTTTG\n")
-		f.write("ATACTTAATATCTTTAGCTTCATGAACGTTTTAGCCTCAGATTCTAACACTTGTCCGGTATAATAGCAAA\n")
-		f.write("CCAAATGAAGCTCCATCATATTCGGCAATGCTT\n")
-		f.write("\n")
-		f.write(">gi|226792311|gb|GO546058.1|GO546058 Mdas9010C19_e731.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93111|HMA1_CUCSA Glutamyl-tRNA reductase 1, chloroplast precursor (GluTR) pir|T10186 glutamyl-tRNA reductase (EC 1.2.1.-) - cucumber dbj|BAA08910.1| glutamyl-tRNA reductase [Cucumis sativus], mRNA sequence\n")
-		f.write("TTTAATTACTTTTTTTGAGAGTATTACTGATATCTCATATTTTCCATATGTTGCCGAACAGCCACTTACG\n")
-		f.write("AACATGTGGTGGTAGACATATAAATCACTCCCACAGAAAAATCATGTTACTGTGTCTTTCACCAGTGAAT\n")
-		f.write("GAATTGCAAGATCCCCCAGCCGGGACCACCACAATTTGTCTATCGAGTTGAAGATTACACCAGACTGAAC\n")
-		f.write("ACCAAAATGACAATGTGAGGATGTTTTCCCCTTATTCGAGTATGAGGAACTCCAGGTGTCATGAGAGATA\n")
-		f.write("TTTGACATTGTACCTTTAGTTCTGGGTTTGTTCCACCTTACCTCGAATTTTCTGTTCCCATACGGATCTC\n")
-		f.write("TCCGTCTCGAGGCTGAACATTCTGTTAATAGCGTGCATGTTCTCAATGGTCTCACTCAGAGTTCGACTAT\n")
-		f.write("CTCTCCCATCACATCTTAGATGATG\n")
-		f.write("\n")
-		f.write(">gi|226792310|gb|GO546057.1|GO546057 Mdas9010I08_e758.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCATTTCGAATGGAACGTTTAATATAAATTGCTTGTTTACCAAAAA\n")
-		f.write("AGACATCAAGGATTTGATCCTTGTATTAGTGAATATACAAGAAAAATCCTACGAGTAACCAGGGAGGGCG\n")
-		f.write("TTAAAGCGCTGTACAACCGGTAAAGATTAGCAACGAGGCAGTTAGGAGTTGAGAGGGCGGCCTACTTAAT\n")
-		f.write("GTTTTAGCCGCTGGCGTTTATCCTGATGCCTGGAAAATGTTGGACTGCAAATTAAGTCAGGAGAAACAGA\n")
-		f.write("AAATTGATTTGGGCAACATGTCCATAAAGAATCTCCCCTAATTGCACTGGCACTACAACCGACTCAATAA\n")
-		f.write("TTCAAGAAACTCCACTGGTTCTTCATTTTCTTTAACAATCTTAATGATTGTGTCCTTTGGCAGACCCATT\n")
-		f.write("TGAACAAGAACATGAAAACCAACTTGATCCCAGTCACTCTCTTCTACATCAGTTCTCTCTCTTCCACTAT\n")
-		f.write("CTAGTTGAATGGAAAACTTATCACTGTTGAAAAATCTCCCCACCCAGAGGTACAAAACCCGGTCTTTACT\n")
-		f.write("TTTTCCAAAATCTGTATTTGGTGAGAAAATAGTGTAAGCAGCTTTAGAATCTAGTTCCCTCACACCAAAT\n")
-		f.write("GTCGCAATCTTCTCTAAACTGGGCCAACGGCACACAAAAGGTTGGATAAAATTGCATTGCGCTGGACAAC\n")
-		f.write("TT\n")
-		f.write("\n")
-		f.write(">gi|226792309|gb|GO546056.1|GO546056 Mdas9010P01_e803.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177574.1| dolichyl-phosphate mannosyltransferase polypeptide 2 -related [Arabidopsis thaliana] pir|A96772 hypothetical protein F1M20.2 [imported] - Arabidopsis thaliana gb|AAG52357.1|AC011765_9 putative dolichyl-phosphate mannosyltransferas, mRNA sequence\n")
-		f.write("TTTTTTTAACAAGGTAATCAGTATCTGATCATTTCAGACACACTTGGATTCGGCTCCAAGGAAATGAAAA\n")
-		f.write("GAAACTAAAAGTGGGGGAAATACTGTCATCAAGCTTTCTTCTTTTTGGATTTTAACATGACAAATCCAAT\n")
-		f.write("GAAAATGCATAAAAAGCAGAGAAGCACCATGCCAGCAAACACAGGTATTAGTATGGCGTACTCTTGTGGG\n")
-		f.write("AGGAAATACCGGTGGATGAAGTGATCGTTGTTTACAAACGGCAGGATAATCACCCAAAATGTGTAATAAG\n")
-		f.write("TGAATATTGACAAACTGATGTAGGATAACAGAAATCCAACGGCCTTGTCCGCCAATTCCATTGTCGTGAT\n")
-		f.write("GTTTGTGGCTTCTGGTACCTGTAAATGGGGGAGAGGGACGATATGGCTACTGAGATGGTCTGCCTCGTGC\n")
-		f.write("CGAA\n")
-		f.write("\n")
-		f.write(">gi|226792308|gb|GO545802.1|GO545802 Mdas9004F21_e276.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175036.1| histidine decarboxylase -related [Arabidopsis thaliana] pir|E96500 probable histidine decarboxylase [imported] - Arabidopsis thaliana gb|AAF63121.1|AC009526_6 Putative histidine decarboxylase [Arabidopsis thaliana] gb|AAK25943.1|, mRNA sequence\n")
-		f.write("TGCAGCTCGGCCACCTCTCGACCGTTCGATCTTTCAACATTACAAATTTCATGGATCACGAGAACGGAGC\n")
-		f.write("TGTGGCGGTGGAGATGCTATCCGATGATTTCGATCCCACGGCTGTGGTTGCGGAGCCTTTGCCTCCGGTT\n")
-		f.write("GTAACCAGCACCGACGACTGCGATCTCCTCGGAAAATTGGCCGAAGACCGCAAAGGTAGCCGGGAGAAAC\n")
-		f.write("AGATGGTTCTCGGCCGGAACGTGCACACCACGTGCCTCGCCGTGACGGAGCCCGAATCCAACGACGATTT\n")
-		f.write("CACCGGCGATAAGGAGGCGTACATGGCCAGCGTCCTCGCCCGCTACCGCAAAACCCTCATCGAGAGGACC\n")
-		f.write("AAGCACCATCTGGGTTATCCTTACAATTTGGACTTCGACTATGGTGCTCTGACGCAGCTTCAGCATTTCT\n")
-		f.write("CCATCAACAATTTGGGCGATCCGTTTATCGAGAGCAACTACGGTGTCCATTCAAGGCAGTTCGAGGGTCG\n")
-		f.write("GTGTTCTCGATTGGTTTGCTCGGTTGTGGGAGATTGAGA\n")
-		f.write("\n")
-		f.write(">gi|226792307|gb|GO545801.1|GO545801 Mdas9003I20_e214.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAN03474.1| syntaxin [Glycine max], mRNA sequence\n")
-		f.write("GGCGAGGATTTTTCTCATTGGCAAGCGGGACCCCACCCTAGCTGTGGCCTCCGGCATTTTCCAGATCGGC\n")
-		f.write("ACCGCCGTATCCACCTTCCAGAGGCTCGTCAACACCGTCGGCTCCCCCAAAGACACGCCGGATCTCCGCG\n")
-		f.write("AATAGCTGCACAAGACAAGACTACAGTATCGGGCAATTGGTAGAAGGATACTTCATAAAAACTGACTCTA\n")
-		f.write("GTCAGTGAAAGAGATCATCAGACCGAAGTTAATGCAAGCCAGAAGATTACAGATGCTAAACTTGCAAAAG\n")
-		f.write("ATTTTCAAGCGGTGCTTAGAGAATTTCAGAAAGCTCAACGACTTGCAGCTGAGAGGGAAACAACATATGC\n")
-		f.write("TCCTTTTGTTCCTCACGCAGTTCTTCCGACAAGTTACACCGCTAGCGAGATAGATGTAAACTCAGACAAA\n")
-		f.write("AGTCTGGAACAGCGTGCTCTCCTTGTGGAATCTAGAAGACAAGAGGTCTTGCTACTGGACAATAGATTGC\n")
-		f.write("TTTCAATGAGGCTATCATCGAGGAAAGAGAACAGGGAATACAAGAGATCCAGCAGCAAATTGGTGAAGTG\n")
-		f.write("AATGAGATTTTTAAAGATCTTGCTATACTGGTTCATGAACAACGAACAATGATTGATGACATTGGCTCCA\n")
-		f.write("ATATTGAGAGTGCTCATGCTGCTACTGGGCAGGCAAA\n")
-		f.write("\n")
-		f.write(">gi|226792306|gb|GO545800.1|GO545800 Mdas9004H09_e283.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P49313|ROC1_NICPL 30 kDa ribonucleoprotein, chloroplast precursor (CP-RBP30) pir|S26203 RNA-binding protein 30 - curled-leaved tobacco emb|CAA46234.1| RNA binding protein 30 [Nicotiana plumbaginifolia], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAATGATTTTGATGTACCAAATCTATAAACTGTCAAAACAAGTTGATC\n")
-		f.write("ACAATCAGTTCCTTAACTGGGCCAAGTCACTCGGAATATAAATCTTACAACTCTCAAAACAGTCTTCTCT\n")
-		f.write("GCTCTTGTCCATCTACAGGCAGATGTAAAAAAACCACCACTACCGCTCACAAAGCCAACCATGGCGCAAG\n")
-		f.write("GCAGCATGATCTTGTCACTAACCGCTCCTAAAAATCTGAAATGAGTATCAGCAGATATTATGATCCTAAA\n")
-		f.write("TGCAAACGGAAAGAAAAGAAACCCATCAAGTATTCTGTTGGCCAATGACTCTGCAAAGTTTACATTTAAA\n")
-		f.write("ACTGACGCCTCGGCCTAGGTTCTGCCGCAGACACTCGGATAGATCTTCCATTTAAGTCAACTCCATCCAA\n")
-		f.write("TGATTCAATGGCACTGTTCATTTCATCAGCAGTATCATAAGTTACAAAACCGAAACCCCTCGATCTGCCA\n")
-		f.write("CTGTCCCTGTCAAAAACTACCTTGGCTTCCAAAACCTTTCCTTGCTCACTAAACAAGTTCTCAAGAGCCA\n")
-		f.write("AATTGTCAACACCCCATGCAAGGTTACCCACGTAAAGGCGGTTGTTAGAGTCATAACCACCACCACCTCT\n")
-		f.write("GGGACCTCTGGCACCTCTGAAAGAGGAAT\n")
-		f.write("\n")
-		f.write(">gi|226792305|gb|GO545799.1|GO545799 Mdas9004D05_e269.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTACCCGCCGCTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGACC\n")
-		f.write("ATCGACATGAGCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAGGCGTCG\n")
-		f.write("CTTCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGC\n")
-		f.write("TTTTCAACCAAGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTG\n")
-		f.write("CGACGCTGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATT\n")
-		f.write("GGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATC\n")
-		f.write("AAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACC\n")
-		f.write("TCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAA\n")
-		f.write("ATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTANG\n")
-		f.write("ACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACA\n")
-		f.write("\n")
-		f.write(">gi|226792304|gb|GO545798.1|GO545798 Mdas9004G02_e278.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTAGAAAACGATATAGACAATATAAAATTTCAAGATACACACGATGTGGAAGTACATATAGAAA\n")
-		f.write("CGATGAACTAGCGCATAATTTGTACTAGCTAGCTCGATCCCTCTTCCCTTAGCAAACAGCTTTATAAAGC\n")
-		f.write("TAGCAGTGGAAGAGCTAGCTAGATTAATACTATAACAACAAAAGGACAACTAGCTAGGGCATTTGTTTCC\n")
-		f.write("CATACATATATGTGTTCAAGCATGACATTTGACGGGCTAACCAGTCCCATAATAACGCTTATTATTGATC\n")
-		f.write("GGTTTACCGGTAGAAGTACGAGTACCATATACTTCTGTGATGGTTATCCCACCAAAGATTCTCGCTGCCT\n")
-		f.write("CATCAGAATTGATGAGCTTGTTATAATTATTAGGCCTCTGAAGGTTCTGTCGAGGTCCATGATTCTCCAT\n")
-		f.write("GTTGGCTGCAGTCGCCAGTCGTGGGTATCCTTGGTTATCATGATCACCGGTTGAAAGAGGTGTATTAGGA\n")
-		f.write("TGAAGAGAAGAGACTTGACTCGCCTGTCGTGGGTATCCTTGGTAATCATGATCACCGGTTGGAAAAGTTG\n")
-		f.write("TATCAGGATGAAGAGAAGAAATTTGACTCCCCATGTTAGCGAGAAATTCCAAATAATGAACTAGGACAAG\n")
-		f.write("TTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792303|gb|GO545797.1|GO545797 Mdas9004B01_e254.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD13683.1| major allergen Mal d 1 [Malus x domestica], mRNA sequence\n")
-		f.write("TTTTTTTTTTGCAAGTGAGACATTAACTGATTTCATTATATTTATAGATAATACACTTACAGTCTGCAAC\n")
-		f.write("TTTTTTTTCAAACAAATACATAAAGGGCAACCAGAAGATGATCACAACCATAAACTTATTTTTCAAAGCC\n")
-		f.write("AAAGTGCTCAAAACCATGGCTACTTTGGGCTGACTAGAAAAAGCATACAAAGAAAAGCCACACAACCTTC\n")
-		f.write("GACTGAAGGGTGACACCCAAAATACCATAGAAACATATTAATTTAGTTGTATGCGTCGGGGTGGCCCTTG\n")
-		f.write("AGGTAGCTCTCAATAAGCTTGAACAAACCATGAGCCTTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGA\n")
-		f.write("TCTCAACATCACCCTTGGTGTGGTAGTGGCTGATACTCTTGATGATGGAACCACTTCCAGATGCCACCAA\n")
-		f.write("CTTGGTCTCGTAAGAGACCTTCTCAATGGTGTCTGTCAAAGCATCTCCTTCAATCAAAGTGTAGGCGTAT\n")
-		f.write("GAGTAGTTTGCTTCGTCAACCGAGTCGATCTTGTGCTTCACGTAGCCGTATTGGCTGCCTTCACCAAAAG\n")
-		f.write("TGATCTTCTTGATGGTTCCAGGGCCACCGTCTCCTTCAAGGATCTCAGCATGCTTGATTGCCTGGGGTGC\n")
-		f.write("AATCTTGGGGATGAGGTTATCAG\n")
-		f.write("\n")
-		f.write(">gi|226792302|gb|GO545796.1|GO545796 Mdas9004D23_e271.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF73132.1|AF149017_1 homogentisate 1,2-dioxygenase [Lycopersicon esculentum], mRNA sequence\n")
-		f.write("TTTTTTTTGAAGGCCTATACCACTAGCACTGGTGTGGTGATTATTATTATTTTGCAAATTTAAGTATATA\n")
-		f.write("ATAGGCATCTGTTTACATGTAAAGAAACTTTGGGGGCCCATACGAATCCGGGGCACCTTTTGCACACCCT\n")
-		f.write("CAAGGCCGGCTCAGGTGCTTTAATACAGAAGTGGATACAAATAAGCATATTTGGTACACTTAACACTTTT\n")
-		f.write("TATAGTACTATGTACTCAGTAGGATTGTATTTGCTTAGTCTTTGTATGAACTATAGTTTCCATTCGTCTA\n")
-		f.write("AAGCAGCCACGGCAGTCTCCACTTTAATCCTCTTTCTTCCCATTCTGGACATCTCCGTCTTCAGCATTCA\n")
-		f.write("TCCTTCCACGCGTAAAATGTGATTTCAGTCCAGTCCAGCACTGGTAATAATCACGATCGATGACTGGAGA\n")
-		f.write("CTCGAGAGCCCATGTGCATACTCTGGGGATTAAACACGATTCAAACATAAAAGCCAAAGTATCGGTGATT\n")
-		f.write("CTGAATGGTCCTGCCTCATTTCCACGCGCAATGGTAGCCTCATATGTTTTGGTATCAGGACCATGGGGAG\n")
-		f.write("TCATGCAGCTATGAAGGCTTGCACCACCAG\n")
-		f.write("\n")
-		f.write(">gi|226792293|gb|GO546055.1|GO546055 Mdas9010K09_e770.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GGGGGCCTTCCCCGGGCAGCGAACGTTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAAT\n")
-		f.write("TAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGT\n")
-		f.write("CAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAA\n")
-		f.write("TGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCC\n")
-		f.write("AGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACT\n")
-		f.write("CTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGTATAAGTGGGAGCCTCGCGGCGAAATTGAAATAC\n")
-		f.write("CACTACTTTTAACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCATCGCCCCTCTTTTTGGAACCA\n")
-		f.write("AGGCCCGCTCGCGGGCCGATCCGGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCT\n")
-		f.write("GTTAAAAGATAACGCAGGTGTCCTAAAATGAGCTCAACGAGAACAGAAATC\n")
-		f.write("\n")
-		f.write(">gi|226792292|gb|GO546054.1|GO546054 Mdas9010G23_e750.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB90634.1| protein phosphatase 2C (PP2C) [Fagus sylvatica], mRNA sequence\n")
-		f.write("TCACTTGTCACAAGAGCACAATGCCTGTATAGAATCTGTGAGACAGGAGCTGCAGTCTTTGCACCCTGAT\n")
-		f.write("GATCCACATATCGTTGTTTTGAAACATAATGTATGGCGTGTGAAAGGCCTAATACAGATATCTAGATCTA\n")
-		f.write("TTGGTGATGTGTATTTGAAAAAGGCTGAATTTAACAGGGAGCCTTTGTATTCCAAGTTTCCTCTTCCGGA\n")
-		f.write("CCCTATCCAAAGACCAATTTTGAACGCTGATCCAGCAATTTCAGTGATCCCATTGCAGCCACACCATCAA\n")
-		f.write("TTTATTATATTTGCATCTGATGGGCTATGGGAACACCTCACCAATCAGGAAGCAGTGGACATAGTTCAAA\n")
-		f.write("AACATCCACGAAGTGGAAGTGCAAAAAGGCTGGTGAAAACCGCCCTGCAAGAAGCAGCAAAAAAGAGAGA\n")
-		f.write("AATGAGGTATTCGGACTTGAAGAAGATTGACCGCGGGGTTCGCCGCCATTTCCATGATGACATAACCGTG\n")
-		f.write("ATTGTTGTGTTTATTGACTCAAACCTTGTGAGCAAGGCTAGTTCTGTCAAGGGCCCAAATCTATCGGTGA\n")
-		f.write("GAGGAGGTGGAATCAACCTGCCTCCTAACACTCTGGCTCCATACGCCTCGGCCACGGAAGCTGGCAATAC\n")
-		f.write("CTGATTAAACTGTATCTCTCATGTGTGTTCTGTTGCAC\n")
-		f.write("\n")
-		f.write(">gi|226792291|gb|GO546053.1|GO546053 Mdas9010J19_e765.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO63778.1| unknown [Populus tremuloides], mRNA sequence\n")
-		f.write("TTTTTTTTTATTAATGAAATTGCTAAGACAGCTGATTTTCATTCACTGATTATTCGAGTAAATACTATGT\n")
-		f.write("AAAAGAAATACAAAGTAATACATCAAAAATACCTCAAAGACTTCTGGATCATGGAAAATTCAAGACCAAC\n")
-		f.write("CACAATATTTTAACCAAAATTTTATCCCAATTTCAACCACTGTACATATGATTTCTCTCCTTGAAAAAAC\n")
-		f.write("ACCGTATCAACTGAATTTTGCCAACCATTTAGCAAATGACACAAGCATTGGGATCCTCTTCTGAACTTCT\n")
-		f.write("TACGTAATAATACGCAGGCATTGGAGGATAAAGTGCTGGGTAGGCCTTCATAAGCTCAAGCATTTCGTCC\n")
-		f.write("TTTGGATCTTTCTTCTTCGGCTCCTCCTTCTTCGGCTCCTCTTTCTTCTTCTCCTCCTTTGCCGGTCCGA\n")
-		f.write("CTGAGACTATCTCCGTCCGGCAAAGCTTCCTCAATCTTCCCACCAAATGCACGGGATCTATGTCCCCTGT\n")
-		f.write("GGCCGTCAACTTCTTGTCCTTCATATCCATAGAAATTGAATCAAGGCCTTCAAGCCCCGAGACGGCCCTC\n")
-		f.write("ATGACTTTCTTCTTACACTTCTCGACGTATAATTCCAATTTCAACACTACTTTCTTCATTTTTCTGTGCA\n")
-		f.write("GCTTG\n")
-		f.write("\n")
-		f.write(">gi|226792290|gb|GO546052.1|GO546052 Mdas9010M15_e783.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC55114.1| S-adenosylmethionine decarboxylase [Malus x domestica], mRNA sequence\n")
-		f.write("TGACGGCCATTTTGGCAAGCTTGGTTTGGCAAGCAAGGCATATGTTATGGGAAGCCCTGACAAAACTCAG\n")
-		f.write("AAATGGCATATTTACTCTGCATCGGCGGAGTTGGCAAGCTTATTTTGGGGTTCACGCCAATCAGGCCCTA\n")
-		f.write("CATACACTCTGGAGATGTGCATGACTGGTTTAGACAGGAAGAGGGCTTCTGTCTTTTACAAATCCGACGC\n")
-		f.write("AAGTTCAGCTGCTGGTATGACCGTAGAATCCGGCATCAGGAACATCCTCCCGCAGTCCGATATATGTGA\n")
-		f.write("\n")
-		f.write(">gi|226792289|gb|GO546051.1|GO546051 Mdas9011B22_e817.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("AAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTAT\n")
-		f.write("TGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGGT\n")
-		f.write("AACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAG\n")
-		f.write("AAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCT\n")
-		f.write("CTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAAG\n")
-		f.write("GGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAGA\n")
-		f.write("ATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCTC\n")
-		f.write("CGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGCC\n")
-		f.write("CAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTT\n")
-		f.write("\n")
-		f.write(">gi|226792288|gb|GO546050.1|GO546050 Mdas9010G22_e749.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTGTTTAATACACTGAGAAATATATTCTATGGCTTAAATTGTGCCACTTGTCAAAGGATTG\n")
-		f.write("GAATGTTAGTTACTCAAATTCGTTAGTGAGCTGGTATTATCTACAAATTAATACATACTAAAAAAAGGGG\n")
-		f.write("ATATCACAATCTTCAATTCTACGTTGACGTATTAACTTAAATGAGATTGAAACTTTACACTTCTTGGAGC\n")
-		f.write("ACTATTTTGATTCTCATCAAGGTTGATCACTCTAATGAAGGGCCTTCCTCCTTTGTGTGCATGCTCCATC\n")
-		f.write("TCTAAAGACCAAGAACACCCTTCATAGATTTTCGGTTGCACCTAGCCTTGTCAAGAGTAGGTTGCCTACT\n")
-		f.write("TACTTCATCTCCAACAAAGATCAAACCGTCGTATTTCAGCCTCAGAACTAACGTAAGGATGGAGGAGGAG\n")
-		f.write("CAAGAGTGTTAAACTAGGACACACTCAAAAGAGATGGATGGCTTTGGATGTGTTTAATAAGTGAT\n")
-		f.write("\n")
-		f.write(">gi|226792287|gb|GO546049.1|GO546049 Mdas9010N22_e795.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198367.2| adenylate kinase -related protein [Arabidopsis thaliana] gb|AAL49859.1| putative adenylate kinase [Arabidopsis thaliana] gb|AAM91697.1| putative adenylate kinase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGAATGTGGAACGTTATTCAATTTAGTAGGAATTCCCCTCCAGTTATCCTCAACTGAAGACGGATTT\n")
-		f.write("GAGCTACTCCAACTTTTTCCTAATTTGATCTTCATTTCTTTATCTTTCTGCACTTGCGATAGTATAGAGT\n")
-		f.write("CTATTACTTCGAAAACAACATCCTTCGAATGGTTTCCATCGATCTTTTTCATGATATTCGAGTATGCGGC\n")
-		f.write("TGAGATTGAATCTGCATTTTTCTTGTATATTTCAAGACGCGACTTCACTTTTTCCTCGGTGTCATCAGGA\n")
-		f.write("CGAGTAATAAGTCTTGCTTTAATCTCCTGATTCTCCGGAGGGAAACTTTTTATATGGTAGATCTTCCCTG\n")
-		f.write("TAACTGGGTCTAGCCTTCTTCCAACACATCTGTCGATTAGAGTTTCATCAGGAACATCTAACACAATGTA\n")
-		f.write("CACATCTGGTATAATCTTCAATTTTTGCAGACTTTGCGCTTGGTTAAAACTCCGCGGATATCCATCAAGA\n")
-		f.write("AGCCACCCTTTTTCCTTCGCATCATCGCGTGATAACCGTGCTGTCACCATCGCTGTCACGACTTCATCGG\n")
-		f.write("GGACCAGACGACCGGCATTCATGAACTCTTTGGCCTTGTTTCCAATTTCCGTCCCGGAATGACACTTCAG\n")
-		f.write("CTCTGAGAAGGTCCCCCGTTGATATGT\n")
-		f.write("\n")
-		f.write(">gi|226792286|gb|GO545795.1|GO545795 Mdas9003L23_e224.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568299.1| 30S ribosomal protein S13, chloroplast precursor (CS13) [Arabidopsis thaliana] sp|P42732|RR13_ARATH 30S ribosomal protein S13, chloroplast precursor (CS13) pir|S59594 ribosomal protein S13 precursor, chloroplast - Arabidopsis thal, mRNA sequence\n")
-		f.write("TTTTTTTGTAAATAATTTCAGCAAGTTCATCACTTCTGATTAAATTTCATAGCATTCCAAGTAGTCAAGA\n")
-		f.write("ATCTACTGCAGTGTGACCAAGTGATTAGACAACATTTCCTTCTCAACATTTGACAATCCTATGAATAAAA\n")
-		f.write("CTGTGATCAAACAGGTACACCGACATTCACCTCTCCCAGACCCTGTGTAAAGCGGGAGCCTTGTGCACTG\n")
-		f.write("GGTACGACCTTATACATTGATGATCCCAACTACATTTCCAAAGGTGAGGGCACAGCTCAACGAAGCAAAA\n")
-		f.write("GCGATCAGAACAATTGTAGTTAATACTAAAACACAAAACCAGACAAAGGAATTCATTACCAATTACAAAA\n")
-		f.write("AGAGTCGAAAACCCATTCAATTACTTAACGGGCCTTTTTCTTTCCAGCAACAGTGACCCTCTTACCCTTC\n")
-		f.write("AGGGTCCTAGTGTTGTTCTTGGTGCGCTGTCCTCTGCAAGGCAATCCCTGGCTGTGGCGTATGCCTCTGT\n")
-		f.write("AGCACTGAATCTCCTTGAGTCTCCTTATATTCAAGGCATTGAACCTCCTCAAATCCCCTTCAATCATGTA\n")
-		f.write("CTTGGAGACTTCATCTCGGATAATGGTGAGCTCTTCTTCCGAAAAATCTTTGGTGATTTTGTTCT\n")
-		f.write("\n")
-		f.write(">gi|226792285|gb|GO545794.1|GO545794 Mdas9003H05_e208.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TACCATTCCATGATATTATTAGTTTTTTGGGAAATACATGCATGAGTTTTTACTATTTACTATTTACATG\n")
-		f.write("CACAACAAGATGAAGTAAATGCAGATAGGCTAGTCAACCCTGCATGAACTCCCATTAAATAGCTAATCAA\n")
-		f.write("AGGCCTTGAGACGTTAGATCGCCATCTGACGAGGATTCGGAGATGCTACACTTGATACTTTCCAGCAGTG\n")
-		f.write("GGCTGAGTAGATATGGTGGTGTATTCATCTGCCAAGTATTCTCGCTAGTACCAGTAGTGGTAGCAGTGCA\n")
-		f.write("CTCAAAGTCGATGCTGCTTGGTTGGTACCCGACATTGATAGATTTATGATGATGATCGGCTGCGCCTAGG\n")
-		f.write("TGTCCATTTTGTTGATCGAATGCTCTCACCGTTGCATGAGGATGATGGTTCGGATATTGCTCCACTACAT\n")
-		f.write("GATCCCCTTGTGTCAATAAAGCAGTCTCATTCAACATTGCATCGACCACTTCCAACGAATTCCAGTTTAC\n")
-		f.write("ATAGGCTTCCCTTGCTAAATTCTCAATGTAGGTCCTATTGATATTGCTGAGGTCTCGAATGGGGAAATTT\n")
-		f.write("TGGCCATTAACCACGGCCCTCAACACTTGACATATAGGATTTAGGAAAATCAAGAAATGAGAACCGCGAA\n")
-		f.write("ATATGAACATTTTGTTACCCATCACGCAGGTTTTGGCGTGCTTTACTGTCACTCCC\n")
-		f.write("\n")
-		f.write(">gi|226792284|gb|GO545793.1|GO545793 Mdas9004A01_e249.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n")
-		f.write("TTTTTTTATGATAAGCTCACATGCCATTGCATACACTAATCCTTTGATCCCATCACAATCTTTACAAGCT\n")
-		f.write("TAAGCAGTACATATCATGATTCAGATAATTAATCATGGTCTACTGATTAAAAAACCAAACATGATATGCA\n")
-		f.write("CATAAAGATACTTCTCTAAGAAGAGAAGGCGTCAATAATGGTGGTGTGGAGCGGGTCACTCAAATGGGTA\n")
-		f.write("GCCCAGTTGTTAAGTGGTCCCTTCCCGGTGACGGCGGCTTGCACGGCAAACCCCAGAAACGCAACCATGG\n")
-		f.write("CGAGGCGGGCGTGCTTGATTTCGGCCAGCTGAAGAGTGGCCTTCTTTTCCGGGTCAGCAGCAAGGCCCAA\n")
-		f.write("CGGGTCGAAGAACTTGCCACCCGGGTACAACCTCTTTTCCGGGTCGAGCTCGGCGTTCCTCTGGAACTCG\n")
-		f.write("ATGTAGCCAATCACTAGAACTTCGATCCAGATCAACGTGGTTAGTGAGAAAGGGAGTGGTTGACCCAAGT\n")
-		f.write("AGGACGACCCTTCGATGAGCTCCACCTTTCCGGCGTCTTGCCATGTGATCCCGGTGACGGACTCGACAGT\n")
-		f.write("GAGAGCACCGAGCGTGGCGAGCATGGCCCACCTTCCATGAATCAGCTCGCACTCCCTAAACCTCTGCAGC\n")
-		f.write("CCAAACACCTCCGAGTAAGGCT\n")
-		f.write("\n")
-		f.write(">gi|226792283|gb|GO545792.1|GO545792 Mdas9003M19_e231.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GCAAGATAAATCTCTTTACTTCTTAGATATCGAGGAAATTAGATTATGCAGATACATACATGATATATCT\n")
-		f.write("GAATCGGAAAATCTGTAAGGCTTTCAAATTAAAATTTACAGATGGGCATAAAATCTCTTTAGCTTAGTCA\n")
-		f.write("TACGTAATTGAATCATATGCTGTTTCCTGCCATATAGAGTTGTACACATGCTCCTCTTCTATGCCAACTC\n")
-		f.write("CATTATAATAAACATGAGAATAATCACGAACCCATTCACAATGATCTTTTGGACAATTATCCATCTGATC\n")
-		f.write("ATACTCACAAGAATCCGCATACCAATTCATGCCATTACTTGGTGAGCAAGCCACCTGATCCATTTCAAAC\n")
-		f.write("CATCCCAACGGATCGCAATCATCTGATGAAGGTGATCGTAAGCAATCCTGACCGTCCAAGCCTCCTACGA\n")
-		f.write("TGTTCCACAAGTTACTATCTTCCAAATCTTCGATGGTGATCCATTCAGTCTGTGTTACTCGAATCATTGC\n")
-		f.write("GGTCCATGGTTGTTTTGATTATTTCTGCCTCTAGAGATTGGATCACACTGTTTAATCTCTCCTCATCTCG\n")
-		f.write("ATCTTCCTCCTGCCATTCTTCTAGCAACGACATGAGAATGG\n")
-		f.write("\n")
-		f.write(">gi|226792282|gb|GO545791.1|GO545791 Mdas9003O20_e241.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAGGGTTATGAATTGAAATCAAATCTTGTATTTGATCTCGTTTTT\n")
-		f.write("TTTTTTTATTATATTACATAAGCATTACATACATAAGAGGGGCAATACACGATCGCCTCCTTCGCTACAA\n")
-		f.write("GCATGCTACTACTAATAACCCAGTACGTACTATAATTAATTTAGCTTATACCCACATTCTAGGGCATAGT\n")
-		f.write("TGACAAGGTCTTTGATCTCCTCTTTAGAAATGGTCCCGTCACGGTTGGCATCTGCATGACCCAAAGCTCT\n")
-		f.write("CCTCGCCCTGAAACCACCCCAACGCGACCCGAGCTTTTTGAAGGCTGCCTTCACCTCCTCTTTGGACAGC\n")
-		f.write("ATGCCGTCGCCGTCCAAGTCAAAACTATTGAAGAGATTCACCACCTGCTCCCTAGTCCATGGAACACCGG\n")
-		f.write("TTGGCTCCTTATAAATGACATCCCTAACCATGATACTATATAGATATATATAGTGATCTTGAAATTTTCT\n")
-		f.write("TCTGTGTTTTGTTCTACACACTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792281|gb|GO545790.1|GO545790 Mdas9004E19_e273.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188937.1| expressed protein [Arabidopsis thaliana] dbj|BAB03045.1| gene_id:F5N5.17 pir|G71408 similar to unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TGTTATTAACACTTACCCTCCAAACTTTATATATTAAAAAAAAAAAATACACTTGTGAGGAGTGTAAATT\n")
-		f.write("GAAATTTTTTGAGTACCAATAATACTTCTCTAAAAAAAATGATTGTCAAAAATTAAATTAAAAAGTGGGG\n")
-		f.write("GCCCCACAACCTTCAAATCACCGAATCCACCTTCTTTTCTAACATCTCCCCAATCAGTCTGGAAATCTCA\n")
-		f.write("AATTCCGATCTGAAATCGAGGTCCAAACTGTTGTTGCAGTTTTCATTGAAGCAGTTGCAGCGGTTCTGGC\n")
-		f.write("TACACCTCGTCACAGCCAATGATTGCTTTTCGTTGCTTTCCTCGATGAAATTCTGAACCATCTTTGTCAA\n")
-		f.write("AAACATGGAGCTCGGCTCGAACTCGGCTGATCCTCCGCCGTCCCCGTCCCCGTCATCTTTGTTGAAATGC\n")
-		f.write("AGCTCTTTGATTCCAATTCCACCGTTGGGCTTCTCCGTGGCCACCGAGCTTTTCAATACATTCGTGAGCT\n")
-		f.write("TAATCGAATTTCCCTCATTTCCACAAAGTTAAAGCTTCCTCTTGAGCTTAATAAAAAAATCAAGCTTGAT\n")
-		f.write("TCTCTACCTATTATACAATCAATTTTCTCTCCCAATCAATT\n")
-		f.write("\n")
-		f.write(">gi|226792280|gb|GO545789.1|GO545789 Mdas9004J06_e292.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB40142.1| plasma membrane intrinsic protein 1-1 [Pyrus communis], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGGGGTGAAATAAAGGTTGGTGTTATTTCTGAATTGAAAAATA\n")
-		f.write("CACAAATTCACAGCCACAGGATACAAAGGAAATGAGCACTCACATCAGACGGACGGGATTGGTGGGGCCT\n")
-		f.write("CTCCCTAAAAAAGAAGGAACAGAGGGCCCCTTGATTCTTGAGACATATCCATCAACACACATGCCTTTTG\n")
-		f.write("CTTGCTCATATCACAATAAATTTAACAGCTTAATCCCTTAATTACGTACAAAATACGCTTAAAACAACAA\n")
-		f.write("GCATTACAGATGAAAAATAACACAAACTTGATCGAAGATTGGCTTGAAAGACGATCATAAAACCGATTTA\n")
-		f.write("AGACGTAATTAACAGTAATCACTTGGACTTGAAAGGGATGGCCCTGATCACAACCACGTGGTACAAAGCT\n")
-		f.write("GCAAGTGCTGCCCCAATGAACGGTCCAACCCAGAATATCCAGTGGTCATCCCAGGCATGCCGCTTGTTGT\n")
-		f.write("AGATGATGGCAGCGCCGAGACTCCTGGCTGGGTTGATGCCAGTTCCGGTGACGGGGATGGTGGCCAAGTG\n")
-		f.write("CACCAAGAACACGGCGAACCCAATTGGCAACGGAGCCAAAATCGGAACGTGGGAGTCTC\n")
-		f.write("\n")
-		f.write(">gi|226792272|gb|GO546048.1|GO546048 Mdas9010P15_e808.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192772.1| light-harvesting chlorophyll a/b binding protein [Arabidopsis thaliana] sp|Q9XF89|CB26_ARATH Chlorophyll A/B-binding protein CP26, chloroplast precursor (Light-harvesting complex II protein 5) (LHCB5) (LHCIIc) pir|T04049 chlorophy, mRNA sequence\n")
-		f.write("TTTTTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCAATTTGATATACAATGCTTTTAATTTTGATT\n")
-		f.write("GGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGAGCTCTTTCGATAGATCCACCAATGACAGTA\n")
-		f.write("AGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATAGGTTTTCGACAGGACCTTCTCCGGTGACAT\n")
-		f.write("ACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAGTCTTCCGTTCTTAATCTCCTTCACCTTTAG\n")
-		f.write("CAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGGTCAAAAGGACCACCTGGGTGAAGCTTGTCC\n")
-		f.write("TCCAATTCCAGACCGTTAGTGATTCTGTA\n")
-		f.write("\n")
-		f.write(">gi|226792271|gb|GO546047.1|GO546047 Mdas9011C03_e820.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTGCAAACCAGTTTTGCTTATTTAGGCATCGGCTAACATCCAATAAAAGGTACAGACATTAA\n")
-		f.write("CCCAAATCGAATACTGCAATACTAAATTCACATTGTAAACACCCACCAATCTGCTCATTTACTGCAGAAC\n")
-		f.write("AATGCATTCTTGTGTCTCACCAACCATAGCAGCGCGGGAGCTTTTGTTAATGGTAGCGTCGACTTCTTCA\n")
-		f.write("TGAGAACGAGGCTTAACTTCTGGATCCTCCGGCAAATTTTCATTCCCATTTATTACCGGAAGCAATACGT\n")
-		f.write("TCGAAAATAAGAGCATTCACTTCTTGGAACCTCTCTTCAGAAAGGGAAACCTCTGCCAG\n")
-		f.write("\n")
-		f.write(">gi|226792270|gb|GO546046.1|GO546046 Mdas9010J15_e764.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197427.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("ACAAAATTGTGAAAATTTGATTACACGGCTGAAAGATCCAATATTATACTTAATAAACTTTTAATTATTA\n")
-		f.write("ATAATCCAACTTAAGTAGCCACCCAAAAGGGCTCCCAATACTTTAACAATCCTTTCTTCTCACACTCACC\n")
-		f.write("GCCACCTTCTTTGCACCTGCTTGGCCTTTCAAACTTTTCTATTCCATCTTTACCCCTAACATTCAAACTA\n")
-		f.write("TTCCCATCCACCTCCTCACCCTCTATCAAACACACATTTGAACTATTCCCTTCTTCTTCTTCTTCTTCTT\n")
-		f.write("CTTCCTCTTCCTCCTCCTTATCGCCTTCTAATTGTTCTACCAATTCTTCTTCTGTATTTTCTCCCACCAC\n")
-		f.write("TTCTTGATCTTGCTCTTCTGTTTCCTCCTCAATTATGTCATTTTCACACCCTTCATTGTATTCTTGAATG\n")
-		f.write("GCTGCTGCTTCTTCCTCTGAGTCAAAACTGGGAGTAAAGGTTTTTGAAAGGCACAATCGAAGGCGGCCAT\n")
-		f.write("TGCTTCTTTCAGCTTGGAAGCATGAATGACTTAAAGGGGCCTTGACAGCTTTGATGATCAGCCTCCCATC\n")
-		f.write("TTCCCTGTGAGGCCTAAAGGGTAGAGAATCCTCGCCGCTTA\n")
-		f.write("\n")
-		f.write(">gi|226792269|gb|GO546045.1|GO546045 Mdas9011B15_e816.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB91757.1| putative 60S ribosomal protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("CGACATCCAGTTTTAGGGTTTCCTTCTTCAGGAAGTTTTTTCGCAGCGAGGACAAAGATCTAACTAACCA\n")
-		f.write("TGAGTAAGCTTTCAAGTGATGGGCTGAGGGAGGCCATTTCTCAGATTAAGACAAATTCTGAGACAAAGAA\n")
-		f.write("GAGGAAGTTCACTGAGACGGTTGAGCTTCAGATTGGTCTGAAGAACTATGACCCACAAAAGGACAAGCGT\n")
-		f.write("TTCAGCGGTTCTGTCAGGCTTCCACATATCCCTCGCCCTAAGATGAGGGTTTGCATGCTTGGAGATGCTC\n")
-		f.write("AGCATGTTGAAGAGGCAGAGAAGATGGGTTTGGACTACATGGACGTTGAGAGCTTGAAAAAGCTTAACAA\n")
-		f.write("GAACAAGAAACTTGTTAAGAAGCTTGCCAAGAAATACCATGCATTTTTGGCTTCTGAAGCTGTCATTAAG\n")
-		f.write("CAGATTCCTCGTCTTCTTGGCCCTGGTCTTAACAAGGCAGGTAAGTTCCCAACCTTGGCGAGTCATCAGG\n")
-		f.write("AATCTCTGGAGGCAAAACTTAACGAGACCCAA\n")
-		f.write("\n")
-		f.write(">gi|226792268|gb|GO546044.1|GO546044 Mdas9010P11_e807.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_200125.1| cyclic nucleotide-regulated ion channel (CNGC1) [Arabidopsis thaliana] pir|T51354 cyclic nucleotide-regulated ion channel 1 [validated] - Arabidopsis thaliana emb|CAA76178.1| putative cyclic nucleotide-regulated ion channel [Arabi, mRNA sequence\n")
-		f.write("ATCGACTTCTTGCAAATAATCCACTGTGGAACAAAATATTTATAATTTCATGTGTGATTGCTGTGTCACT\n")
-		f.write("GGACCCTTTGTTCTTTTACATTCCAATCATCGATCAAGACAACAAGTGCCTTGGAATGGACAAAAAACTG\n")
-		f.write("AAGAATGTAACTCTTGTTTTGCGACTGCTCACAGATCT\n")
-		f.write("\n")
-		f.write(">gi|226792267|gb|GO546043.1|GO546043 Mdas9010L02_e776.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n")
-		f.write("TCGAGAAGCTTCAGATAGATTATCTGGATCTCTACCTGGTTCACTACCCAATGCCCACAAAGCACAATGC\n")
-		f.write("AATTGGTAAAACTGCCAGTCTTTTGGGCGAGGATAAGGTGTTGGACATCGATGTAACAATTTCCCTTCAA\n")
-		f.write("CAAACCTGGGAGGGCATGGAAAAGACCGTCTCTTTGGGCTTAGTTCGCAGCATTGGTCTCAGCAACTATG\n")
-		f.write("AGCTCTTTCTAACTAGAGATTGCTTGGCTTACTCCAAAATAAAGCCTGCTGTGAGCCAATTTGAAACCCA\n")
-		f.write("CCCCTATTTCCAGCGCGACTCTCTCGTCAAATTCTGTATGAAACACGGCGTTCTTCCCACAGCTCACACC\n")
-		f.write("CCTCTCGGAGGTGCTGCTGCCAACAAGGATATGTTTGGTTCTGTTTCACCTTTGGATGATCCAGTTCTCA\n")
-		f.write("ATGATGTGGCTAAGAAATACGGAAAGAGCGTGGCACAAATCTGTCTGAGGTGGGGAATTCAGAGGAAAAC\n")
-		f.write("AGCAGTGATTCCAAAATCATCGAAAATTCAGCGATTGAAAGAGAATTTGGAGGTTCTTGAATTCCAGCTG\n")
-		f.write("AGCGATGAAGACATGCAGCTCATCTACAGTATCGACAGGAAGTATCGTACCAGTCTACCTTCCAAGACTT\n")
-		f.write("GGGGCTTA\n")
-		f.write("\n")
-		f.write(">gi|226792266|gb|GO545788.1|GO545788 Mdas9003G21_e205.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGAAAAGTTGTGTAAATTGTCCCAATGGAAAGTGGACCAAAGGGTTCTTGGGGCATTAGAGGGCACA\n")
-		f.write("GGGTTAGATAATCTATATACTTTAGCAACTATTGTTGGTAGAAATGCCCATGACAATAGCATGATAGATG\n")
-		f.write("CTCTTGTTAGGCATTATGATGTTAGAGATAGGTGTTTTAAGATTAATAATCAAAATTTATTTTTCGGATT\n")
-		f.write("AGAAGATGTGCTTTTAATCACTGGGCTTCCAGTAGAAGGGACCCCGGTGATAAAGTCAACAACAAACATT\n")
-		f.write("CATGCCCTTGAAAACTTGTTAGGGGGAGTGCCTGAAAGTGAGTTGAAGGATAAATCAAATGCTGTGAACC\n")
-		f.write("TTAGTTGGTTACAAAAAGAGTTTGAGCATGTACCTGAAAATGTAGATGCCGATAGATTTTCCTGTCATGT\n")
-		f.write("TAGAGGATTTGTCCTCTACATATTAGGCACGGTAATGGTTCCCAGTTTAGACCATGTGCACGTGAATCTG\n")
-		f.write("GGCTACTTGGGCTGCATGTCCGAGATAGGTGAGATAAAGAAGTATGCATGGGGAGTTGCA\n")
-		f.write("\n")
-		f.write(">gi|226792265|gb|GO545787.1|GO545787 Mdas9003N07_e234.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196452.1| expressed protein [Arabidopsis thaliana] emb|CAC08335.1| putative protein [Arabidopsis thaliana] gb|AAM63112.1| unknown [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTCATGAAATTGACATGATTGATATTATAAACCCAGGCAAAAAAAGGGTAAAAC\n")
-		f.write("TAAAACCTTGAGGAAAATAAAAACACATGTAGAAGCTAATTACCGGAGATGAGCCAGCTCTCGTTAATTT\n")
-		f.write("GCTCATCCCCAAATTACAAAACACGTCTTGCTAATTGCTAATGTGCTGCCTGCATTTTCTAGTTGTGGGA\n")
-		f.write("CTGGTTGTGGTTGGCAATGGAAAGGGCCTTGTGAAGATTTCTGAAAGCTTTCTCGTAGCGCAAGAATCCC\n")
-		f.write("ATGAACCAGAAGTCGAAATCATCGTGGGTAACTATTTCAATGTACTTCTGTTGTGGTTTGTTGACATTCT\n")
-		f.write("CGCTTTGGTTCACTGTTTTGATCTTCCTTATTGGTATCCGAACTTTGTAATGCGTTCTGAGGAGTTGCAG\n")
-		f.write("TTGTCCAGCAGCAGCAGGACCAGAAGCAGGAGGAGAAGGGAGAGTGATGGGTCTTTCGCTGCAAAAAGCA\n")
-		f.write("AGCTTTTGGGTAGAAATGAAAAGGAGGCCAGGAATGGGACCGGCGGTGGTGGATAGGTAGCATTGGGAGG\n")
-		f.write("CCTTCAAGAGCTCTTCTCCTTGGCTGACACCGAATATCTGTTTAAAAATATTGGCCCTCCCACCCTCTTG\n")
-		f.write("AA\n")
-		f.write("\n")
-		f.write(">gi|226792264|gb|GO545786.1|GO545786 Mdas9003K17_e220.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172258.1| histone H2B, putative [Arabidopsis thaliana] pir|D86213 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF75074.1|AC007583_10 Strong similarity to histone H2B like protein from Arabidopsis thaliana gb|Y07745. ESTs gb|R8, mRNA sequence\n")
-		f.write("TTTTTTTTTTTGTTTTTTTTTTTTAGGTAAATCGTACTTTCATTTAGAATTTAAACCGCAATAGCACAAT\n")
-		f.write("ATCAGTACTTAATACTTACATAATCAAAAGCATTAAAACCCATAAACCCCTAACCCTAACCCTAATTCCT\n")
-		f.write("TCACAACCAATCTCAAACCCAAATCCACAGAATTAAACACATTAACCCTAACTCTTCAAGAGCTAGTAAA\n")
-		f.write("CTTAGTCACCGCCTTAGTCCCCTCAGACACCGCATGCTTAGCAAGCTCACCAGGCAGCACCAATCTCACA\n")
-		f.write("GCAGTCTGGATCTCCCGGGAAGTAATCGTCGGCTTCTTGTTGTACCTCGCGAGCCTGGATGACTCCTGGG\n")
-		f.write("CGAGCTTCTCGAAGATGTCGTTGATGAAGCTGTTCATGATTCCCATGGCCTTGCTGGAGATCCCGATGTC\n")
-		f.write("AGGGTGGACCTGCTTCAGCACCTTGAAGATGTAGATCTTGTAGGTCTCCACGCTCTTCTTCGATCTCTTC\n")
-		f.write("TTCTTCTTGTCTCCGGCGGCGGCTCCGGCCTCCTTCGGGAGCTTCTTCCCGGCCTTAGGCTTCTTCTCGG\n")
-		f.write("GCGGGGGCTTTCTCCGCCACGGCGGACTTCTTTTCCTCCGCGGGCTTCTTCTCGGCGGGGCTCTTCTCAG\n")
-		f.write("CT\n")
-		f.write("\n")
-		f.write(">gi|226792263|gb|GO545785.1|GO545785 Mdas9004B14_e259.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP47161.1|AF514908_1 dehydration responsive element binding protein [Glycine max], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTGGCCATAAAATTCAAAGACTATAATTTCAAGAAAAGAAACATTACTGATTGCCCTT\n")
-		f.write("CAGTTGGTTTGTTGTTACAATTGAGAAACTATATCAAATTACCAATCGAAACGGAATTCTTGTGATTCCA\n")
-		f.write("TTTCCTGATCGGACCCAATAAACCCTTCTCTGTATTTTTACTTTATTGCACACCTAAATACCTACTCATA\n")
-		f.write("ACAATAAACAGCTGGTGATCGGTCGGCCTTCTCAATTAACTTTCATCGGAGTTTTCTGGGTCGGGGTACT\n")
-		f.write("CATTTAAGTCGGGCTTCAAAGAGCCACCCCGGCTCAACGTTGTTTTGGACTGCGACGTCGGCGATGAGCG\n")
-		f.write("GAGAGCGGTTTGAACAGCGTCGACCTTAGCCCCGACCTCCGTAGCTTTCTTCCGTATCGAAGCCGCCGAC\n")
-		f.write("ATGTCGTGGAGCTGCTGGCCGTCGTCTTGGAATACAAGTTCCGGGAAGTTGAGGCGGGCAGAAGGGCCTC\n")
-		f.write("GAAGATAGAAAACGGCGGTGTCGTAAGCTCGGGCGGCAGCCATGGGGGTCGTGTAGGAGCCGAGCCAAAT\n")
-		f.write("TCGAGAGCGCTTGTTGGGTTCTCGAATCTCCGCCACCCACTTCCCCCACTTCCTC\n")
-		f.write("\n")
-		f.write(">gi|226792262|gb|GO545784.1|GO545784 Mdas9004I10_e289.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188060.1| glycolate oxidase -related [Arabidopsis thaliana] ref|NP_850584.1| glycolate oxidase -related [Arabidopsis thaliana] sp|Q9LRR9|GOX2_ARATH Probable (S)-2-hydroxy-acid oxidase, peroxisomal 2 (Glycolate oxidase 2) (GOX 2) (Short chain, mRNA sequence\n")
-		f.write("TTTTTATCCATGGAAATATTATCTCACCATCCAGTAATCAGTATCATTACAGAAAACGCAGAAATAATAA\n")
-		f.write("GGAATCCAAGAACAAAGGTTTATCCACCGCTGTTCATTTGAATGTTTCTATAACCTTGGCTGATGGCGAG\n")
-		f.write("GGCGAGGAGCGTCCCAGTCAGTCACAATGTGATCGCGGGTGATCTCTTTGAGCGAACGGCATCCACTTAA\n")
-		f.write("TGTCATGGTTAGCTCAAACTCTTCGCGCAGCATTTGGAGTACCTTTCTAATGCCAGCCTCTCCTTCAGCC\n")
-		f.write("GCGAGAGAGAACACCACAGGGCGCCCAATAAATATGCCAGAGGCACCCAAAGCTAATGCTTTGAAGACAT\n")
-		f.write("CTGTTCCTCGACGAACACCACCATCCAAGAAAACAGGAATGCGTCCTTGTGCACCTTTAACAACCTCTTC\n")
-		f.write("GAGGGCCATGATAGTCGAAGGGACGTAATCAAGTTGGCGAGCTCCATGGTTGGACACAATAATCCCAGCT\n")
-		f.write("GCTCCAGCTTGTACTGCAATCCTTGCATCTTCGGCAGTGAGAACACCCTTAACTAGGATAGGCAGTGAAG\n")
-		f.write("TGATTGTCTGAAGCCACTGCACATCCTTCCAGCTAAGAGAACGATCGATTTGACCAGCAACGTATGAAGC\n")
-		f.write("AAGTCCAGAGTCAGCAGCTTTGTCATCTTTCCGAGG\n")
-		f.write("\n")
-		f.write(">gi|226792261|gb|GO545783.1|GO545783 Mdas9004E14_e272.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC24587.1| AP2 domain containing protein [Prunus armeniaca], mRNA sequence\n")
-		f.write("TTTTACACGAAACGAAAATGGCATGGCCTTTTGGTAATTCCGTCATCCTCAAAGGTCAGATTGTCATACA\n")
-		f.write("GATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTACAAACACCAAGTCAAAAGTACATAGAACTG\n")
-		f.write("AAAACCAAACAATGCAAAATCTGATGGCCTCTTGTAAAAAGGAAGACCGAAATAAATTTAAACAAGTACA\n")
-		f.write("GAATTATGAGGTTTCAGTATCATCATAACTCACACAATTTCATCGTTACAAACATGAAAGTTCAGAAACC\n")
-		f.write("ACAAGTTCTTTGGACGAGAAAGTGGACCCATTACCTATACGATCTCCATACGCCATTAGCTACGGCTTAA\n")
-		f.write("ATGCTCCCCCGTACAAGCCTTATCCATGTCAACAGCTTGCACAGATGTACTCCAACCCGAAACACATCAT\n")
-		f.write("GTAGCTTTATTTACATAAACTGGAAAGCTGGGGTAAGGTTCATCTCTCAGAAAGTTCCTCCAACAATTGC\n")
-		f.write("GGGCAGATCGTCAAAGGTCCATAGGTCCCCCGGATTACCACCATCCTGAGTTGCGTCTCCGTTAAGGAAG\n")
-		f.write("GCGTCCACTGAAGCATCCCAGCTCCCATCAAGATATGGGGTCTGAAAGTACTTCATCTCAAAAGCTGAGA\n")
-		f.write("GCTCATCAGAC\n")
-		f.write("\n")
-		f.write(">gi|226792254|gb|GO546042.1|GO546042 Mdas9011B07_e815.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S28827 chlorophyll a/b-binding protein type I - common tobacco emb|CAA45523.1| photosystem I light-harvesting chlorophyll a/b-binding protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("GCTGTGGCATCGCCACTACTGCCTTCCCTTCAGTCCTCTCATCCTCCAAGTCTAAATTTGCGACCAGCGC\n")
-		f.write("AGTCCAGCTCCCAAGTATTGGTGCCAATGCCTCCTCCAGGTTCTCCATGTCCGCCGAGTGGATGCCCGGC\n")
-		f.write("GAGCCCCGCCCTCCTTACCTCGACGGCTCTGCCCCCGGTGACTTTGGATTTGACCCACTTCGGCTAGGAG\n")
-		f.write("AAGTGCCAGAGAACTTAGAGAGGTTCAAGGAGTCCGAGCTCATTCACTGCAGATGGGCAATGCTTGCTGT\n")
-		f.write("TCCAGGGATTCTAGTACCAGAGGCTTTGGGATTGGGCAACTGGGTAAAAGCACAGGAGTGGGCTGCCGTT\n")
-		f.write("CCAGGAGGCCAAGCCACCTACTTAGGCAACCCAGTTCCATGGGGCACTTTGCCTACAATTTTGGTCATCG\n")
-		f.write("AATTCCTTTCCATTGCCTTTGTAGAACACCAACGCAGCATGGAGAAGGACCCTGAGAAGAAGAAGTACCC\n")
-		f.write("TGGTGGCGCTTTTGACCCCTTGGGCTACTCCAAGGACCCCAAGAAGTTCGAGGAATACAAAGTCAAAGAG\n")
-		f.write("GTCAAAAATGGCCGGCTTGCGTTGTTGGC\n")
-		f.write("\n")
-		f.write(">gi|226792253|gb|GO546041.1|GO546041 Mdas9010G14_e745.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTCTTTTTTTTTTGGTTGAGATTAGTGAAATTGCTTTCATACCGAATTTTATCAATAAGCTAG\n")
-		f.write("TAGATGCTACAAGTACCTATAACTTTCTATCATGTGCCTTAATTCTAAAAAAACCTTGACGCCAACCTTT\n")
-		f.write("GAGCACAGGGTGACTTCAATATTTTTCACCTTCAGCAGTTCCATTGTGTTTCGGTAACTGAGTACCATAT\n")
-		f.write("AGGCTACCATAGCCTGTGTCATGCTCGCCCTCTGTCTCTGTCTGTCTAGCATCAAGCGTATTTTTGGTTG\n")
-		f.write("TTTCCGCGCTTGGAAAAATCG\n")
-		f.write("\n")
-		f.write(">gi|226792252|gb|GO546040.1|GO546040 Mdas9010M10_e782.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATTATTGTTGTCCAATACTTGGTACCAAATTTACCTCACCGACAACTATACAAACGAAAGTACAAGACAA\n")
-		f.write("CTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGAGGCGTATT\n")
-		f.write("\n")
-		f.write(">gi|226792251|gb|GO546039.1|GO546039 Mdas9010J03_e761.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO61490.1| arm repeat-containing protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAATATATAAATGTCTATACTACCAAGACAATGGGGGCATAACATC\n")
-		f.write("AACAATTCCAAATACAAATTTGTCATCATAATCATGCCTAGCCGGACTTACAGGTATGCTATTAACTTTT\n")
-		f.write("TCTTCCCACATTCACGTAGGTATTTTACAAATCAGACGTACAAATCTTCTATCCATCGTTTGTTATTCTG\n")
-		f.write("TCTTCTCTTGTCTATGGTTTCTGAAGTAGCTAAGGAGTGTCTGTGCCTTTTCTTTTGCCCTAGGGGTGCC\n")
-		f.write("GGATTGTGACAATACCACTAATGGTGGGACAGCTCCTTCTTGGAGGACCTGACTGCAATATCTATTACTG\n")
-		f.write("TTTGTGCAGAGCTGTAAAAGAGCAGCAGCAGCGTTCTCCTTCCCTCTTGGAGAACCCAACTCAACAACCT\n")
-		f.write("CGACAAGAACAGGGATCCCACCCTCCTGACCAATTGCTGTCCTTCCCTCGGGAATTGTCGAAAGATTAGC\n")
-		f.write("CAAAACAGCAACTGCCTTGTCAACCATTCCAGCTGCAGGGTCCATCAACTCCACTAGGTACTTTACAGCA\n")
-		f.write("CCAGCTTGAACAATTCGACCCTTGTTCTCATGAAAAATTGACAAATTAAACAAAGCTGTGGCTGCATCTT\n")
-		f.write("TCCTCCCTCTGGGACTCCCATTCCC\n")
-		f.write("\n")
-		f.write(">gi|226792250|gb|GO546038.1|GO546038 Mdas9011A18_e814.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191019.1| histone H2A.F/Z [Arabidopsis thaliana] pir|T47615 histone H2A.F/Z - Arabidopsis thaliana emb|CAA73155.1| histone H2A.F/Z [Arabidopsis thaliana] emb|CAB77576.1| histone H2A.F/Z [Arabidopsis thaliana] gb|AAM64788.1| histone H2A.F/, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGCTTATAAAAGTCGAATCATATAAATAAAGACAGAGAATACCAG\n")
-		f.write("GTTAAACTATCCAACAAAACACATAAAGATGAACAAACATACAGATAATGGTTCAAAGGGACAAGCACTA\n")
-		f.write("GATTGCCCATATGTACTACTAAATCCAGCTAACCTAAACAGCTACTAAAACACGAGAAATAAACAGTCAT\n")
-		f.write("AATATTAAACAACACCATCAGTTAATACCCGTTTGACTCATCAGATCTGAATTACTCCTTGGAAGTCTTG\n")
-		f.write("TTGATGAGGGACTTGTGGATGTGGGGGATGACACCACCGCCAGCAATGGTTCCCTTGATCAGAGTGTCCA\n")
-		f.write("GCTCCTCATCTCCCCTGATGGCTAGTTGCAGATGCCTGGGTGTGATTCTCTTGACCTTGAGATCCTTGCT\n")
-		f.write("AGCATTCCCGGCCAACTCAAGAACCTCAGCAGTTAGGTACTCGAGGATTGAGGCCAAGTACACAGCAGCA\n")
-		f.write("GTGGCGCCAACACGGCCATGAGCAGCAATTCGCTGTTTCAGCTGCCTATGAATTCGACCCACCGGAAACT\n")
-		f.write("GGATACCAGCGCGAGATGAACGAGAAACAGGCCTCTTCTTGTCCTTCTCCTTTTCTTTGTCCTTGTTAGC\n")
-		f.write("CCGCTGTGGGTATTCGCTGCAATAAGCCCCTTCCCGCCTTTGCCCGCCA\n")
-		f.write("\n")
-		f.write(">gi|226792249|gb|GO546037.1|GO546037 Mdas9010F06_e738.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TCTCATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGG\n")
-		f.write("GACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACC\n")
-		f.write("ACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACA\n")
-		f.write("ACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGA\n")
-		f.write("TGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTC\n")
-		f.write("GGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGG\n")
-		f.write("TTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGT\n")
-		f.write("AGTCAACTTCCTTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAG\n")
-		f.write("TCCAAGTGGAGGCCACACCTGCATGCATTGCACTCTTCCTCCATTG\n")
-		f.write("\n")
-		f.write(">gi|226792248|gb|GO545782.1|GO545782 Mdas9004H05_e281.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q42434|BIP_SPIOL Luminal binding protein precursor (BiP) (78 kDa glucose-regulated protein homolog) (GRP 78) gb|AAA21808.1| ER-lumenal protein gb|AAA21806.1| ER-lumenal protein, mRNA sequence\n")
-		f.write("GAGTCCGATGAGAAGGAAAAGATTGAGACCGCGACAAAGGAAGCCCTCGAGTGGTTGGATGACAACCAGA\n")
-		f.write("CCGCCGAGAAGGAAGACTATGACGAGAAGCTCAAGGAGGTTGAAGCCGTGTGCAACCCCATAATCTCAGC\n")
-		f.write("CGTCTACCAGAGGTCAGGAGGTGCCCCGGGTGGTGCCAGAGCCTCGGAGGAGGACGATGAGTCACATGAC\n")
-		f.write("GAGCTTTAAAAGAGTAGTTTATTTCATTTTCATCGAACACGGTTGGAAGCAGTGAGGAGAGAGAGGGGTT\n")
-		f.write("ATAGGTTTAGGGGAAGAAGACTTTTACTGTAATTTTTCCGATGGGAATAGAAGAAGCTGAGGGAGACGAA\n")
-		f.write("TTTCGACTCTCTCGGCTTATCGGGTCTTTTTGTTAGAACGTGTAATTTCATTATTTTGATAAAAAAAACA\n")
-		f.write("CAGTTTCAA\n")
-		f.write("\n")
-		f.write(">gi|226792247|gb|GO545781.1|GO545781 Mdas9004I24_e290.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187919.1| chloroplast 30S ribosomal protein S10, putative [Arabidopsis thaliana] dbj|BAB01403.1| unnamed protein product [Arabidopsis thaliana] gb|AAK60293.1|AF385700_1 AT3g13120/MJG19_6 [Arabidopsis thaliana] gb|AAL16207.1|AF428438_1 AT3g1, mRNA sequence\n")
-		f.write("TTTTTAAAGTGAAATGAATCCTAGACATGGAGAATAATCGAAAAGATACACAATGCGGAACTAATATGCA\n")
-		f.write("ACAAGGATATCAAATAATGTCGAAAGAGGAACTCTTTATCTCTATTCTTCAACTGAGATCCAAGGGCAGA\n")
-		f.write("AATTGCTTACAATTGCTTACAAAATACACAAAAGAAATGAATTTCAGGAAAGGATCAAAATGCATTCGAT\n")
-		f.write("AAGCGTAATCCTGCAGTCATTCAGCCTCTACAAAATAAACGTGAACCTTTGTAATCTCTTTCCCATGTTC\n")
-		f.write("TTCAAAGAAAACACCTAAGCTGCTGCCCTGCTTCTTCACAGTTTGACCTCCACATCAACTCCAGCAGGAA\n")
-		f.write("GGTCAAGTTGCATTAAGGAATCTATTGTTTGTGCAGTTGGGTATAGAATATCAATGAGGCGTTGGTGGGT\n")
-		f.write("ACGAATCTCAAAATGGAACCTTGCATCCTTGTGGACATGGGGAGATTTGAGAACACAGTAGATTCGCTTT\n")
-		f.write("TTAGTTGGCAAGGGTACAGGACCCATTGTTTTCGCATTCGTGTTCCTAGCAGCATCCATTATCTGCTTGC\n")
-		f.write("AGGAATCTTCTATNCATGGCACAAAGTAAGACCTCAGTTTAATCCTGATTTTCTGCTTGAGTGAGGCCTT\n")
-		f.write("ATCTCCATCTTCACCAATACTGAGTGATGAAGTACTCGG\n")
-		f.write("\n")
-		f.write(">gi|226792246|gb|GO545780.1|GO545780 Mdas9003G22_e206.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S16294 chlorophyll a/b-binding protein type I precursor - tomato, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCA\n")
-		f.write("ATTTGATATACAATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGA\n")
-		f.write("GCTCTTTCGATAGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATA\n")
-		f.write("GGTTTTCGACAGGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAG\n")
-		f.write("TCTTCCGTTCTTAATCTCCTTCACCTTTAGCAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGG\n")
-		f.write("TCAAAAGGACCACCTGGGTGAAGCTTGTCCTCCAATTCCAAACCGTTAGTGATTCTGTAGTATTCAGCTC\n")
-		f.write("CACCAAGAAGAACAACCTCAGCAACAACAGCGAAGATAAGATTAATCGGTATGTTCTTCCCAAAGTAATT\n")
-		f.write("CAGTGTGTTCCCATCAAGGAGTAGAGCTCCTGTCTTGAACCAAACAGCCTCAGGGCCGCAGTTAGCTCCA\n")
-		f.write("AATTTGTTGAAGGCCTCTGGAATGATGAATCCGGCTGCACCAAGCATGGCCCACCGAGCGTGGATCAGCT\n")
-		f.write("CATATGCTTGGTATTTGCTGAAGTTTTCTGGCTTCTTGCCTAGGCCAAAAGGA\n")
-		f.write("\n")
-		f.write(">gi|226792245|gb|GO545779.1|GO545779 Mdas9004D14_e270.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198099.1| seryl-tRNA synthetase [Arabidopsis thaliana] sp|Q39230|SYS_ARATH Seryl-tRNA synthetase (Serine--tRNA ligase) (SerRS) pir|S71293 serine-tRNA ligase (EC 6.1.1.11) - Arabidopsis thaliana emb|CAA94388.1| seryl-tRNA Synthetase [Arabid, mRNA sequence\n")
-		f.write("TTTTTTAAATCAGCTCTGTTAAACATTACGTAATTAAGGTTTCTTGCGGCGCAAGCATACTCCTCATCAG\n")
-		f.write("ATATAACTGTGCATATCAGAAATCATAAGGCAAAATATGAATCTTGTAGGACAAACCAAAACAAAACAAG\n")
-		f.write("TTGATCTGAATATATTTAATTCATTACATCAAAGATGAAGACATGGAATTTGGGTTTCAGGGTTTCTCAA\n")
-		f.write("AACAATCATCAGAAGAGTTTACGCACGCCATGTATCATGAACTTCTCTTGTTAATCTATTCTTCATTAAA\n")
-		f.write("GACTGAAAAAATTACGAATTTTAGGCCTTCGATTTCTTCCCTTTGACTTCAGGGGCTGGTTTGGCCTTGA\n")
-		f.write("ATGGTAAGAACTCCTTTCCACCCATGAAGGGTTGAAGAACTTTCGGTACGTTTACACCCTCTTCAGTCTG\n")
-		f.write("GTAGTTCTCGAGAATGCAGCATACAGTTCTCTCACTCGCTGTAAGAGTCGAGTTCAATAAGTGAACATAT\n")
-		f.write("TGCTTTGTCTGCTCGTTGCTCTTTTTCTGCCCATATCGAATTTCTAACTTTCTTGACTGGTAGTCCGTAC\n")
-		f.write("AGTTTGAACAACACACCAGCTCTCTGTATGTCTGAGATGCAAGATACCATCCGTTCAGATCATACTTCTT\n")
-		f.write("TGCTGCGGCATCATTCAAAGCACCAGAGACGATGGACACAATATGATATGCGAGCCCTAACGCTTGATAA\n")
-		f.write("AAT\n")
-		f.write("\n")
-		f.write(">gi|226792244|gb|GO545778.1|GO545778 Mdas9003O19_e240.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192721.1| expressed protein [Arabidopsis thaliana] pir|T04031 hypothetical protein F17A8.180 - Arabidopsis thaliana emb|CAB39650.1| putative protein [Arabidopsis thaliana] emb|CAB78106.1| putative protein [Arabidopsis thaliana] gb|AAL6703, mRNA sequence\n")
-		f.write("CAGGGATAATATTTCAACATTAAAAGCAATGCCTAATAGAAACACAACGGTTTTTGGTAAAACAAAACGA\n")
-		f.write("AACAAAAAGCAATACAAAAAAGATGCTTACAGAAGATGGAGAAGACCAAGCTATTCTCAAACAAGACAGC\n")
-		f.write("AAAAGTAAATTAAATTGATTGCATTTACCGCTTCCATGTTGTGCCGTCTTCCCTTATGGAATTGCACCAG\n")
-		f.write("AGAGCAGCTTTGTATTGTCGTGGTTCTTCCAAAGACTTTTGACACCGTCCCATGGGAAATACTTGGATGA\n")
-		f.write("ACCAACTGAACGCTTTCAGTAGGTAGAGTCATGACCAGGACTATCTGCATGCATGTCCATCGAGGTATCA\n")
-		f.write("TTGGAACTTGGAGGATTAGCATCCCGGTTTGGGTGGAGAAAGCTAGGTTCATTGTTTCGGGCTCCATTTC\n")
-		f.write("CAGATGGCAGAACTGCTCCTGGATAATATCCATCTTGAGAAATGTGATAGTGCTGAAGACTCTGGCGAAC\n")
-		f.write("AGGGCTCGACAAAGCATTTGAGAAGACCGAATTCTTAGATTGATGATCGCACTGCTCAGAACGAATTCCC\n")
-		f.write("TGCCCAGTAAATTGTTGGGACAGATGAACCAGAAGT\n")
-		f.write("\n")
-		f.write(">gi|226792236|gb|GO546036.1|GO546036 Mdas9010N20_e793.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTCTTGGGGTCGCAGTCAGGGGAACAAGCAGTGGAGGTCGGATTCAAGTAACCAGTGGAATGGAGCACA\n")
-		f.write("CTATGGAGGACAGGGTTATGGCGGGTATGGACATGCTGTGCCACAGGGTGAGGACCTGAGCATGCACACC\n")
-		f.write("GCAGCTGCGGTTAACGGGGCTTCTTAACAGGGCTGTCGCAGTTGCCAACAGCGTGTAAACTGAACTTACA\n")
-		f.write("AAAGTGGCATTTTAGATATAGTTTATCAATGCCTTTAATTGAAGTAGGGTCGATTTAGCTAAATATGTAA\n")
-		f.write("TGTGAGGAATTTTTGATACCGGATTTAGCAGCCCTTGTGTGAGATGAATACTTGTGTCTATGCCTGGCAA\n")
-		f.write("TCTTGGAATCAACAGGAATTCTTTTGACCCGGAAAATACGTTTATACCGA\n")
-		f.write("\n")
-		f.write(">gi|226792235|gb|GO546035.1|GO546035 Mdas9010O21_e801.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172650.1| aminomethyltransferase-related precursor protein [Arabidopsis thaliana] ref|NP_849646.1| aminomethyltransferase-related precursor protein [Arabidopsis thaliana] sp|O65396|GCST_ARATH Aminomethyltransferase, mitochondrial precursor (, mRNA sequence\n")
-		f.write("AACCCAGCTTCCACCCCGAAACTGTCACTAGCACCCAGACCTGACAGCCTCACCTTCCCCTCGGATTTCT\n")
-		f.write("CACAGATTGCCTAGGCAAGATCCACTGCATTCTCATCAGGAACCGAGATTTCAAATCCACAAACAATGTA\n")
-		f.write("GCATACACGACATGAGTGATTAC\n")
-		f.write("\n")
-		f.write(">gi|226792234|gb|GO546034.1|GO546034 Mdas9011B24_e818.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P07030|PLAS_SILPR Plastocyanin, chloroplast precursor emb|CAA26709.1| precursor [Silene latifolia subsp. alba], mRNA sequence\n")
-		f.write("TTGCTAGAACACATTCAATCAACTACATACAATGGCCTTCGTCAACCCCGCCGCGGTCGCTATCCCATCA\n")
-		f.write("TTCACCGGACTTAAATCCGCCGGCGCAGCCAAGGTTAACGCTGCAGCTAAGGTCTCAGCCTCCCCAAGGC\n")
-		f.write("AGATGTGCATCGTCAAGTCATCCCTCAAGGATGTTGGTGTGGCCGTTGCCGCCACTGCCGCCAGTGCTAT\n")
-		f.write("CCTCGCCAGTAATGCCATGGCCATTGAGGTCTTGCTAGGCAGCGATGACGGTGGCTTAGCCTTTGTCCCC\n")
-		f.write("AACAGCTTCTCCATCGCCCCCGGTGAGAAGATTGTGTTCAAGAACAATGCTGGATTCCCACACAACGTTT\n")
-		f.write("TGTTTGACGAGGACGAGGTTCCCAGCGGTGTGGATGCTGGAAAAATCTCGATGAGCGAGGAGGACCTCCT\n")
-		f.write("GAATGCCCCCGGGGAAACCTACGCCATCACCTTGACCGAAAAAGGTTCATACTCTTTCTACTGCTCTCCT\n")
-		f.write("CACCAGGGAGCTGGCATGGTCGGCAAAGTTACCGTTAACTAATTCAGTTGTCTGATTAATAATAT\n")
-		f.write("\n")
-		f.write(">gi|226792233|gb|GO546033.1|GO546033 Mdas9010M04_e781.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78526.1|AF195234_1 metallothionein-like protein [Pyrus pyrifolia], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTGATGAAAAATAAGATGGTAATTAACAGAGCCATAGCATGTATTCTAATATTTGC\n")
-		f.write("ATATAAATCAAAGGGCCATGAACATGGCCATTACATGACACAATCACAGAAACACAAACATATGAGTGAC\n")
-		f.write("ATGTTTTCACAGACGTACAACATGTCACTCGACAGACTCAAATACTATAAGCAAACAAGAGACAAAGCCA\n")
-		f.write("CAACGTTATTTTATCCCACAAACACTTTTCATTAATTAAGGGTCTATAATCCCTTAATTAATATGACACT\n")
-		f.write("TTTATTAATCACATCTTTAATTTGGTTATCTGGGCTTACTGACCACAGGTGCAGTTCACACATGGGCAGG\n")
-		f.write("TTGCGCCACACTTGCACTTTCCGTCGTTCTCGGCTGCAGGAGCGTCCACGACGACGGTGTCCATGGCGCG\n")
-		f.write("GTTCTCATTCTCCACGATCACCAAGT\n")
-		f.write("\n")
-		f.write(">gi|226792232|gb|GO546032.1|GO546032 Mdas9010J06_e762.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T12317 26S proteasome regulatory subunit S5A - common ice plant gb|AAC19402.1| 26S proteasome regulatory subunit S5A [Mesembryanthemum crystallinum], mRNA sequence\n")
-		f.write("TCGGGGAAGAGGATGATGGGAAGCCAGAGAAGCTGGAGGCCCTTCTGTCTGCAGTTAATAATAATGACAG\n")
-		f.write("CAGTCATATAGTACATGTCCCCCCCGGTCCAAATGCTCTCTCAGATGTTCTCATAAGTACACCTGTATTT\n")
-		f.write("ACTGGTGACGGAGAAGGAGGAAGTGGTTTTGCAGTGGCTGCCGCAGCAGCAACTGCTGCTGCTATTGGTG\n")
-		f.write("GCTCTGGGTATGACTT\n")
-		f.write("\n")
-		f.write(">gi|226792231|gb|GO546031.1|GO546031 Mdas9010K13_e771.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM63765.1| unknown [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTGGTTAGAATATGCTTATGCAAAGTTGCAAACAACATGAAGAATGTTCACATCCTTATGAACAATGCTG\n")
-		f.write("CGAGATATTTACGTATACAGATAGATGCTTCAAAAACCGGCCACGAGTTCTTATCTTAAACAACATTACT\n")
-		f.write("TTTCGGGTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTAGCTTTAATCTTCAGTGTCAAAGCCTCT\n")
-		f.write("CTGTCTGGTTTGTAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAGCCAATTCCTACAAGCTCAAGAA\n")
-		f.write("CACCAGGAACTAAAGGAAGCCTATCAATTGCCGAAATCAGTCCAGTGGAGCCCCATAGTGCAGCAGCACC\n")
-		f.write("AGCTACTGCAAGTGAAGAAACTGCATATTTATCTTCCACTTTCTCCCAAGCTTCTTGAACGGTCTTCAC\n")
-		f.write("\n")
-		f.write(">gi|226792230|gb|GO546030.1|GO546030 Mdas9010P21_e809.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n")
-		f.write("ACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACATACATACATACATACATAGATGGCATG\n")
-		f.write("CTAAAAAAAAACCAAATAGCACCCATTAATTGAAAAGGACATTTAACCACTCAACTATTGTAGCGATATT\n")
-		f.write("GTTGAAATTAAGCATCACACTCTCACTGATCACACCACATGATAACTAGTAAAAACACAACATTGCATAT\n")
-		f.write("GTAGTCAAAAAATGATGTTCCACAATCCACATAAATCTAAAAGTGGTGGTGCTTCTTCTTTCCATAAGCC\n")
-		f.write("TCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATGGAAGGCAAATCCACCCGAACCAACTG\n")
-		f.write("CAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCATGCTCTGGGTCTTTCTTTTCATTGTG\n")
-		f.write("CTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCTACACCGGCCTCGCCGAGGTGCTCGAGATGCTTGTGG\n")
-		f.write("TGCTTCTCCTCCT\n")
-		f.write("\n")
-		f.write(">gi|226792229|gb|GO545777.1|GO545777 Mdas9003K16_e219.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566036.1| protease inhibitor/seed storage/lipid transfer protein (LTP) family [Arabidopsis thaliana] pir|D84887 probable proline-rich protein [imported] - Arabidopsis thaliana gb|AAB82643.1| expressed protein [Arabidopsis thaliana] gb|AAL1, mRNA sequence\n")
-		f.write("CAGTGATATCCCCTTTTGTAGTAGTGTGAATAATCAATAATACAAAAACCATCAATGCTCAATGACTGAA\n")
-		f.write("AAGATAATAAGTTCACAATCCAAAGGGAAACACAAGAAACACAAGAAAATGTTCCTTGGAGGGAACACTT\n")
-		f.write("TACATATCAATTACACTTTGAAGGAAACATGCACAATGCATTAATGCAGCCAAAGATTAGTGCCCTTTGT\n")
-		f.write("ATTTTTATTCACACAAAGCTGTGTAAGGGCAGGTACTTACGTAGTATGCAGATGAGAAGATCATCGTGCA\n")
-		f.write("TGTCTCTAAGAGCATTGGAAGCCATTCGGGACAGACTTGCCACAGTAATTCAAAAGCAAGCTCAAGGAGA\n")
-		f.write("CTGGCACGTCAAGATTGATGCCCAAAACGTTGGCCTTAATTGCAGTGCAAAGGCACACAGCAGCTTCAAG\n")
-		f.write("ATCGGCAAGTCCACCAATGAGGCTACAGCATGGGGTCTTTGGTGGGGTCCCCACAACAATGGTCACCAAG\n")
-		f.write("TCATTTAACAAGTCGCCACATACCCCTAGCTTAAGGGTGTCCTTAGGGCAAGAAGCTTTAGCTGGAGGGT\n")
-		f.write("TTTGGGGGCTAGCGGGGGTTGCAGGAGGAGGACATTTAGGGGTTTTCGGGGGTGGTGGTGGTGGACATTT\n")
-		f.write("AGAAGCATGATGGTTTGCACTGACTGT\n")
-		f.write("\n")
-		f.write(">gi|226792228|gb|GO545776.1|GO545776 Mdas9004J18_e293.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTCCAGTCTCTCCGCGTCTTAAAAAACCCTAGATTCCCGAAAGAACACAGAGTTCGAAACCCTATCAACA\n")
-		f.write("ATGGCAGTCTCAAAGGCATCCTCCGTCATCGCTCTCATGGCGGTCCTCTTCGCCGTCCTCTCCGCCATCG\n")
-		f.write("GCGCGGCCCAGGAGTCTCCGGCTCCCAGCCCAACCTCCCCCGCCGCATCCATCTCCCCCTCGTTCGTCTC\n")
-		f.write("CGCCCTCTTCGCCGCCGTCACCGCTCTGGCCTTCGGATCTGCGCTCAGGGTTTGAGGTCGCGGTTGCTGC\n")
-		f.write("TTGTCTGGATGTGGCTGTGTAGAGCGGTTTGGGATTTTGTGATTCGTTTTGTTTGGTAGCGAGTGTCGTT\n")
-		f.write("TTAGTAGGTGGTGGTCATGGATCTATAGGGATTTCGTTTACATATGATGGATTTTATTATTATATTATTG\n")
-		f.write("CTACTGTGATGGATTTCTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792227|gb|GO545775.1|GO545775 Mdas9004F13_e275.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ACGGATGGTACACCACGTGTTTTTATATAAGTGGTGGAAAATTGCATTTTTTAATACATATATCTCACCA\n")
-		f.write("TTTATATAACGACATGTAATATACCATGTATTCCGATCATATTGAAAAATCTCTAGTAGATGGGCTTTTC\n")
-		f.write("CCATCACATGACTCTAATCCACGTAACCACGGCCATCCATGTGGGTCCACCTCCCAAAAATCACATGGGC\n")
-		f.write("AGAAAAGAAAAAAGTTGAAAGGTCCACCATCCTAAATTGGGCCCATGTTATTGAATCACATGGCCCAACC\n")
-		f.write("AACAGCAACTCAGTTAGTTTGGAAATCTCAAAGAAACATTAAAAACCACTATTTTTTTACACTAAATCAT\n")
-		f.write("ATAGCACAGCATTGAAATCTCACCAAATTATAAAACGCAATTTTGCAATCTGTTGGAACATTCCAACTCC\n")
-		f.write("TACACTGGAACATTTCAACCCCAAGCGCTGCCGCACTCAAGATCGTCAAGTTCATAGACAAATCCTTCTA\n")
-		f.write("CAACCCACATGCCATCTATTACAAAGGTCCCAAGATAAAAGGGGTACATAGTACAAATTCTATGAACCAG\n")
-		f.write("AAGACCTGTTACTGTGCTTCACTGGATTCGCGCTTTGATGCTTCCTTGATTTCGTCCCCGGCATCATCCG\n")
-		f.write("TGATATC\n")
-		f.write("\n")
-		f.write(">gi|226792226|gb|GO545774.1|GO545774 Mdas9004C13_e265.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172536.1| expressed protein [Arabidopsis thaliana] gb|AAN41360.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTGAAAAATCAATCATAACGTTGTTATGTGCAAGTCTAAATGCCATAGCTGCTTCAGAAGAAC\n")
-		f.write("AATCATCTAGGGCAGCTAATTACAAATGGAAGCCTGAACCATCAAAATTTATCCTTTATCCAGGCCAAAA\n")
-		f.write("AAATCATTAATCTGTGGTGCCGCGGTGGCACCATGTAGCCTGGGATTTACAAACGCAGTTCTCATCCGCT\n")
-		f.write("TCCTCATCTCTCGTTCTGATAAGACTCCGGAAATGCTCTTGACAACAGCAAGTTCTTTATCCTAATAATT\n")
-		f.write("AGAGCGAAGACGCCGTAGCATGGGAGATGCATCAATCCAACCCCAAGATACCATAAGGGAGCATACGAGG\n")
-		f.write("ATGACAGGTCGAGAAATGGATCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226792225|gb|GO545773.1|GO545773 Mdas9003L22_e223.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12372|PSAD_LYCES Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) pir|S00449 photosystem I chain II precursor - tomato gb|AAA34185.1| photosystem I subunit II protein precursor prf|160151, mRNA sequence\n")
-		f.write("CACAAACCAACCACAACTCTCTCTCTCTCTCTTTCCTCTCTCTAGTTCCTCATGGCCATGGCAACACAAG\n")
-		f.write("CCAGCCTCTTCACCCCAACTCCCTCAGCCCCAAAGACCACTGCTGACCGTACAACCACCCCATGGAAGCA\n")
-		f.write("ATCAGTCTCCTCCTCCTTCATGGCCCCCAAGCCACTCAAGCTCTCCACCGCAAGAACGATGAGGATCAAT\n")
-		f.write("GCCTCCGCTGAGGAAAAAACCGTGACCCCCACAAAGGAGGCCCCGGTAGGCTTCACCCCACCCGAGCTGG\n")
-		f.write("ACCCAACAACACCCTCACCGATCTTCGGTGGCAGCACTGGCGGGCTGTTGAGGAAAGCGCAGGAGGAAGA\n")
-		f.write("GTTTTACGTGATCACATGGGAGTCACCAAAGGAGCAGATATTTGAGATGCCGACTGGCGGAGCTGCCATC\n")
-		f.write("ATGAGGGAGGGTCCTAACTTGCTGAAACTGGCCAGGAAAGAGCAGTGCTTGGCTCTTGGAACTAGGCTTA\n")
-		f.write("GGTCCAAGTACAAGATTAAGTACCAGTTTTACAGGGTTTTCCCTAACGGGGAGGTCCAATACTTGCACCC\n")
-		f.write("CAAGGATGGTGTGTACCCTGAGAAGGTGAACCCTGGGCGCCAAGGGGTTGGCCAGAACT\n")
-		f.write("\n")
-		f.write(">gi|226792224|gb|GO545772.1|GO545772 Mdas9004G04_e279.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n")
-		f.write("TTTTTTTTTGGGATGATGAAACCTACAAAATATATAACATTTCGTTGTGGAAATTGCTTGGAAATGTCAA\n")
-		f.write("AAGCTAGATAAAATTGAAGCTAAGAGAGTTCAAGTTTGACACCAAATTGCAAAAATAAGTTCAGACCACC\n")
-		f.write("ACATAATTTCTATTTTCTATCACTCGATAATGGATTGAATAACGCCAGCTCCAACAGTCTTCCCTCCTTC\n")
-		f.write("TCTGATAGCAAACCTCATCCCCTGCTCACACGCCACCGGAACAATCAGCTCGACAACAATCTTAACGCGA\n")
-		f.write("TCGCCAGGCATCACCATCTTCGACTCCTCATCCTTGTCGTTCATAATCGAAGTCACCTTCCCGGTGACAT\n")
-		f.write("CAGTGGTCCTCATGTAAAACTGAGGCCTGTAACCCGAAAAGAACGGCGAATGCCTCCCCCCCTCTTCCTT\n")
-		f.write("CTTCAGCACATACACAATGGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTTTGGCCAAAACCATC\n")
-		f.write("CCTCTCTGGATGTCAATCTTCTGAATACCCCTAAGCAACAACCCCACATTGTCACCAGCCATGGCATCAT\n")
-		f.write("CAAGAATTTTCTGAGACATTTCGACACCGGTGACAGTTGTGTTCCTGGTGTCCTTCAAGCCAACAATGTC\n")
-		f.write("GACGGTGTCTCCGACCT\n")
-		f.write("\n")
-		f.write(">gi|226791953|gb|GO546029.1|GO546029 Mdas9010L01_e775.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA04664.1| hypothetical protein [Citrus x paradisi], mRNA sequence\n")
-		f.write("GTCGATCTGAGTAGAGTTTGCAAGATGGAGAGCTTGAACAGCTTTTGGCAATTGGGTGATGAGCTCCGAG\n")
-		f.write("GGCAGTCAAAAGTCGCAGAAGATCACAAATGGTTAATGGCTGCTTCAAAATTGGCTGAGCAGACAAGGGT\n")
-		f.write("AAAGGGCGAGCGTATGAATAACCTTGATCTTTCAAAGGGCCCAGCTGAACAAAGGGCAAGGGATAAATTT\n")
-		f.write("GGGTTCCAGGAAGATAACAAATTTGAAGGCCAATACTTTAACATGCTGAGCTTGGATTCTAAAGTAAATG\n")
-		f.write("AAAATGTGAGCAAAAGTTCCTTCACGAATGGTATTTATAACATGAATGCAGTTTACCAGAAGAACAATGC\n")
-		f.write("AAGCATTGTGGGAAACATGACTGG\n")
-		f.write("\n")
-		f.write(">gi|226791952|gb|GO546028.1|GO546028 Mdas9011A09_e811.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177142.1| expressed protein [Arabidopsis thaliana] ref|NP_849870.1| expressed protein [Arabidopsis thaliana] pir|F96720 unknown protein, 58197-59415 [imported] - Arabidopsis thaliana gb|AAG52556.1|AC010675_4 unknown protein; 58197-59415 [A, mRNA sequence\n")
-		f.write("GCAAATATTTTGATTAACTTGTAGACTATATTACAAAGTTGAAGCATCACCCTTCAGTTTCAAAAAGCCA\n")
-		f.write("AAACAAGCATAGAAAACTCACACTGAAAATTATATACGTGACGATACGTCCAATAATTCAACAATAAAAT\n")
-		f.write("TAACCACGCTGTTTTAGATCCTAAATCACACCCAAATTCGAGTCTAGCGTAACCGCGCTAACAAACCATC\n")
-		f.write("GGAAGCTTAAAGATGCCGAGCCTCCCACTACTTACCATGTAACGGCATTACACCCGACTTCCTTGAAGGA\n")
-		f.write("GGCCGTCTCTTATCTGTGAAGAGATATCTTTCACAGCACCGGGTCCGTGCGGGATGAAAACCGAGTTGGA\n")
-		f.write("CTTTGAGGACGCACCGACGTCCTTCAATGTGTCGAAGTACTGGGTCACCATAA\n")
-		f.write("\n")
-		f.write(">gi|226791951|gb|GO546027.1|GO546027 Mdas9010I01_e756.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564093.1| expressed protein [Arabidopsis thaliana] gb|AAK59521.1| unknown protein [Arabidopsis thaliana] gb|AAL15188.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTGCAGAGACCAACAAGTGCCATTACATTGCTAGTAAGTTTTACCTATGCTCTATACATACA\n")
-		f.write("TATAATTATTTACTATATTCACAAGCTTTTTACATCATATATTCATATATATATATATATAAGAAAAGCG\n")
-		f.write("GAGATGCGCGGCGGATTGCGGGTGTAGCCGATGAGCTGATCAAACTTCCAAGAATGCTGTTTATGTACAG\n")
-		f.write("TTTTAAATCCCTACGGGCGATCCGTTCATGCCAAGTTCTTTCTAACACGAAGTTGGAAGAACTTGGCCCT\n")
-		f.write("CCATTGAGCAGCATCTCTATAGCGTTCCTCCACTGCCGCAATAAGCATGGTGCGCACAAGAATAAACTCC\n")
-		f.write("TTCCTTTCAACACATGGTTGACCATTTGGCCGATCCAGTTGAGTAAATAATAATCCATCTGAAGGGCCTT\n")
-		f.write("GAGTGGAAAACTTTCCAGATTCGATAACTTTCATTCCATCACTGTATGCCAGGTACTTGTTGACCTGTAT\n")
-		f.write("GGGAACCTTGCACCGTACAGCAATGTTGATGGCGTCTGAAGGTCGAAGGTCGAAGCTGACACACTCTGTC\n")
-		f.write("TCACTACCTGCCTTTCTGAGGTATAGCTGAGCAAAATACGCCTCAT\n")
-		f.write("\n")
-		f.write(">gi|226791950|gb|GO546026.1|GO546026 Mdas9011A16_e813.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTGACATAAACCTTATTCTTCATAAAGCAAAAATAACAAAATACAAGAAA\n")
-		f.write("AGAGGGAGGGATATACACCTTACCCCTCTTGAACAAGAAAATACAAGAAAAAGAGAAGGGGAGACATAGA\n")
-		f.write("CTTTACCCCTATTAAAAAATAAAATACAATAAAAAGAGAGGGGCGAACATAGGACCAAACCCCTCTAAAA\n")
-		f.write("TAAAACTTAAAAGGTAAGAACCTGCAAGACAAGATATGGTTCGATCGGTTTAATGCGCACCCCTATTTTT\n")
-		f.write("TTTTTCCATGCCCCGGAAAAGGTACGGTCTTATAGTGCACCGGTTCCTCTTCCTTTGCCACAACATGCAG\n")
-		f.write("ATGCGACCTACTGATGATCTTTTCTGCTACATTGTGCTTTGGTTTTTCAGAAACATTGGCAAAGACTAAT\n")
-		f.write("TTGGATGAGAACAATAGCAATAGGATGATGGAAATCATGTAAACAAAGTTGGCCTTGTGAACCATATTGT\n")
-		f.write("ATGATCAGCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791949|gb|GO546025.1|GO546025 Mdas9010N10_e788.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P54260|GCST_SOLTU Aminomethyltransferase, mitochondrial precursor (Glycine cleavage system T protein) (GCVT) pir|S59948 aminomethyltransferase (EC 2.1.2.10) precursor - potato emb|CAA81081.1| T-protein [Solanum tuberosum], mRNA sequence\n")
-		f.write("AAGCCGCCCTCTGCCCTTCTTCTCTTCCCTATGGCCCATGTGAGTCCGTCCTCCACAGGTGTTGTGAGTT\n")
-		f.write("GCTCCATGTCATTGACGTATAAGCACAACCCAGCTTCCAGTCGGAGACTGTTACGAACACCCAGACCTGG\n")
-		f.write("CAGCCTCACCTTCCCCTCGGATTTCTCACAGATTGCCTTGGCAAGATCCACTGC\n")
-		f.write("\n")
-		f.write(">gi|226791948|gb|GO546024.1|GO546024 Mdas9010P08_e806.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_114288.1| cytochrome b6/f complex subunit IV [Triticum aestivum] sp|P12119|PETD_WHEAT Cytochrome B6-F complex subunit 4 (17 kDa polypeptide) dbj|BAB47064.1| sytochrome b/f complex subunit 4 [Triticum aestivum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTCTAAAGTTTTGTCTAAACAGATAAAAATTCGTTTTGAATCTTGAATC\n")
-		f.write("TTTAGCACAATCCATATATTCCGAATAGGTCCAAAATTAAATTGAATAGATGTATCTAGGGAAAATTCAC\n")
-		f.write("TTTGAAGCGACTATTCCCTAGATACACACGTCATAATATACTTTTTTTTATTTCACAGTTGAATCGATTT\n")
-		f.write("AAAAAAGACCTAAAGTTAAGGACTTATCAATAGGTAGTGTTGCTCCAATACCCAACCAAAGGGCTACTAC\n")
-		f.write("AGTACCAATCAAAAAGACGGTTGTCGCTACGGGACGACGAAATGGATTTTGGAATTTATTAACATTCTCC\n")
-		f.write("AAAAAAGGTACTGTTAATAATCCCGCAGGTACTGAAACCATTAAAAGAACGCCCAATAACTTATTTGGCA\n")
-		f.write("CTGTACGAAGTATTTGAAATACGGGAAAGAAATACCATTCAGGCAATATTTCCAAAGGAGTTGCAAATGG\n")
-		f.write("ATCCGCGGGTTCACCAATCATTGATGGTTCTAGAACCGCTAAGCCTACGTTACATGCAATAGTACCTAAA\n")
-		f.write("ATTACTACTGGAAAAATATATAAAAGATCGTTTGGCCATGCGGGCTCTCCGTAATAATTATGACCCATCC\n")
-		f.write("CTTTAGCCAATTTAGCTCTTAACACAGGATCGTTCAAGTCAGGTTTTTTTGTTACTCCCATAATCCAT\n")
-		f.write("\n")
-		f.write(">gi|226791921|gb|GO546023.1|GO546023 Mdas9007M09_e535.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCCAGTTTTTTTTTTTTTTTTTTTTTGGATATCAAGGAGAATTAAATTTATTCAATTTCCATACAAAGAA\n")
-		f.write("AATGAATTAATGCAGGAACAACATTTGTGCACATTGAGAATGAAATTAACTAATTAACTTACTATCCCCT\n")
-		f.write("ACTGCAAATTTCACAACTATGCTCAAAACAGATTTTGTAACCAATATCCCAAAAAAGGGGCAAAAGGAAA\n")
-		f.write("GAAAAAAAAACTTTTGTATGGTATACTGCAGCGTTATCTGTGTAACCGAACTCAACCTAGCTACCTCCTT\n")
-		f.write("GTACACTTGGAAAACCCAAACCAACAGTAGCCTTCGAACTCCTGTTAAATCTCAGATTTATCAGCGGAGT\n")
-		f.write("AAACCAAATGCAAAATCCGCTCTTAACCGACAAAGCCTCGACAAACTGAGTTAAATAAAAAAAAAATACG\n")
-		f.write("ATGATCTGAACAAAGATCGCACCCAGACCGCACCAAAAATTGGTCGGAAAGCCGATGACAATTGGGGAGA\n")
-		f.write("AACGATTTACAGAGATGCAAAACTTGTCTCAAAACAGAGAACCCAAACAAACTCCCCAGAAAAAAATAAC\n")
-		f.write("ACGACGATCTTGGCGATGAATATTTTGCAAGACGAAAAACACAGGATTTCAAACGAGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791920|gb|GO546022.1|GO546022 Mdas9007I12_e518.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGGACGTAAATTCTAAATTGCATTACAAAAGGCGCTACTTTTTACACT\n")
-		f.write("TCTACAGCGGTTAGCAGCTTTAATTACCCTCCAAAAACTCCAACTCATGAAAAACCCAACGCCTAAAAAT\n")
-		f.write("TGGCCAAAATCTTTGATTAGAGAAACCTTTTCCTTCCTCTTTTGCTATTTAACTCTTTACTACTTCTCCA\n")
-		f.write("TTCACTTGGCTCTTGTGGACGAGAAATTTTCATTGTGCCGGAAACATAACCCGATATACCAAATGTCATA\n")
-		f.write("ATACAATTGATTGAAAGCTTAAAAAAAAATCCCAACCAATGGTATTACAACACTTGGTGTACCAAATCGT\n")
-		f.write("GTTCCCGACCGACTGAAAAACCTCCCGTTGTTGAAGGGGGTTTTTTTCTCTTTCTTTTTTTTCACCCCTC\n")
-		f.write("CTTACTTTTTACCTTTTTTTTCTTTGTTACTTCATTTCTCTCCCAATTTGAAGAGGGAAAATTACAAGTG\n")
-		f.write("AAACAAAAAATAACCGACTCAAAGTTACCGACTAGAAAGTAGTTAAGTGAGCAGGGGAAAGAGTGTGTCA\n")
-		f.write("CACCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791919|gb|GO546021.1|GO546021 Mdas9008A08_e556.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P58419|NU4C_OENHO NAD(P)H-quinone oxidoreductase chain 4, chloroplast (NAD(P)H dehydrogenase, chain 4) (NADH-plastoquinone oxidoreductase chain 4), mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTATAATCATTCCAATAGCCATTACAAAAGTAAAATATTTGTCACTA\n")
-		f.write("TAAGATATTTTTTACTAGCATGTATTCCAAAAATAAAACACTAACAATTCATCAACAAAACAGCTCATGC\n")
-		f.write("CCGGTGATGCAAGAGAAGGCATTGGCATAATAGTTATCAAACGGGTCCTAAAGATTTCAGACGCTTTTTT\n")
-		f.write("GTTTGATGGAACACGAAATTATACCAACTATTCCACATATCACTTGTCAAACTACACTAAACTGGCTTGT\n")
-		f.write("CACAGTGTGTATGCGGTAATGCTGCAAACCGCGACATAACTCGGGAACTGAAACCACTTCCCTATATACA\n")
-		f.write("GCAAATGCTAGTTCACAGTAACTGTAATCTAGCTCGTGTATCCACTCGTGAAAAATAATAGGAAATGTCT\n")
-		f.write("ATGTAGTTCCATGAACCAGCATAACTTAATGAAATGAAACTCACTGGCTATCAGGCTTGCCCGAGCATTT\n")
-		f.write("CTTGCTCCAAACAACCGAACCTGCTTTTCGCTCCCCTCGCTTTCTCTTGTTTCTATGAAAACTTACATCT\n")
-		f.write("GAAGCCAAGCATGACTCTAGAGTCGATTGCTCCTGAGGAAGAGCAGCTT\n")
-		f.write("\n")
-		f.write(">gi|226791918|gb|GO546020.1|GO546020 Mdas9007K24_e528.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564931.1| expressed protein [Arabidopsis thaliana] pir|A96709 unknown protein, 35272-36292 [imported] - Arabidopsis thaliana gb|AAG52398.1|AC011915_12 unknown protein; 35272-36292 [Arabidopsis thaliana] gb|AAM65154.1| unknown [Arabidopsis, mRNA sequence\n")
-		f.write("TCCAGCTTTTTTTTTTTTTTTTTTTTTGACTAAAACACAAATGCTTTATTTACACACTAAACGACTGTTT\n")
-		f.write("AAATCGACTCAACAGCGGCTTCAATTTATACAGATTCGCTTCGCAAGCCGCTCTATGAAACTCCGAAACA\n")
-		f.write("CCTAAATGGAAACACAACGAAAATTTTCCCACAGTACTCTTTTTACTTTTTACAATACAAGAGGGTCGTA\n")
-		f.write("AACACTCCTAGACACGATCGATGAACCCGTTTATTATTTGGTTAACATCTCATTTACTTACACGACACTG\n")
-		f.write("ACATTTCATTTACACAAATCCCTCGTACATATATACACAAGGTAGAAGGATCGTCGTAGTCTTCTCGTGC\n")
-		f.write("TGAAAATTTCAAAATTTCCTCACAGTGCTATCAAAGTAATGTGGTTGGCTATATCAAACTTTAAGCTCAG\n")
-		f.write("TCTGTTCCTATGTACCTTCATCGATTGAATTGGGATCTCATGCCAGGGTAGGGATACTGCAATTACGTCG\n")
-		f.write("ATCCCTGTCCAGGCAATCAAACCCCTCGATCCTCACTGCTGGTTTGCTCCCGAAACTGGCCCGAGCATAG\n")
-		f.write("CCTCCTTTCCTAGCAGATGATGAAGGAGACGATGAAAGGCCCATTGCGGGAGCGGTTGGCGACAGTGGTG\n")
-		f.write("ACAATGG\n")
-		f.write("\n")
-		f.write(">gi|226791917|gb|GO546019.1|GO546019 Mdas9008A19_e559.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAAACCATGTACTTCAAACCGAATTTAAAGTTATTGAAAAGGAACA\n")
-		f.write("CTACCAATCTAACTGATTGGATATAAATTGACCGTGTTTACAGTTGAAACGTTGCAAAAAGGATGATAAG\n")
-		f.write("TTTTACTTCCAAGACAACTACTCTTTTTTTGATAAACATGCTCCCTA\n")
-		f.write("\n")
-		f.write(">gi|226791916|gb|GO546018.1|GO546018 Mdas9007E02_e499.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29790|ATPG_TOBAC ATP synthase gamma chain, chloroplast precursor pir|PWNTG H+-transporting two-sector ATPase (EC 3.6.3.14) gamma chain precursor, chloroplast - common tobacco emb|CAA45152.1| ATP synthase (gamma subunit) [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCCTTAATTACATGATTAGCAGTATTATTAACTATGATGGAAAAA\n")
-		f.write("AATGACATACAATATATATATATGTGGAATGCTCTCTTTTGTTCTCATTTGTGCACACAAAGTTTATTGG\n")
-		f.write("CAGCTGAAAATTACAATGGAAGTGTTAAGTCTGCAAATTTAAAACAATTGGCACAACTCAAAGTGGAGGA\n")
-		f.write("AAAAACAAGTACCATGTTGTTCTTTGAATCGTCTAAACTAAAGCGTTGGCACCCGAAACAATCTCCAAAA\n")
-		f.write("TCTCTCCGGTGATTTTTGCCTGGCGCTGCCGATTGTAGGTCTGCGACAAGGTTTTCTTCAGCTCCACAGC\n")
-		f.write("GTTATCGGTTGCATTGCTCATAGCGGTCATCCTAGCAGCGAGCTCACTGGCTAGAGACTCCTGCAATGCC\n")
-		f.write("CTCAAAATCTGACTGTTGAGGTACAAGGGCAGCAAAGCGTCGAGAATCTGAACCGGATCCTGCTCAAACT\n")
-		f.write("GCAAAACCGGTGTGAAATCCACGGTCTGCGTCTTGATGACATCTCTCTCCACTGTCAATTTCCCTTCCTT\n")
-		f.write("TGTTGTCAGCCTGAAGAACTCATCATCCACGGCGTCCACACAAACGCCATTGATGTCGCAAATCTCTCCT\n")
-		f.write("TTTGGCGAGAGTGGAAGCAGGGTGTGA\n")
-		f.write("\n")
-		f.write(">gi|226791894|gb|GO546017.1|GO546017 Mdas9007P13_e550.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB62573.1| P0454H12.5 [Oryza sativa (japonica cultivar-group)] dbj|BAB64826.1| B1148D12.11 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCTGCAAGTAAAGGGCTTAGATATTGACTCGAACTCTTCACGAAAA\n")
-		f.write("ATGGCGACGTATATGAGTTTTCGAGTTTAATCTCCAGTAGTAACAAAAAATATGACATAAAAGTTTATGA\n")
-		f.write("GAACCAAAAATTTATGTACCAACAAGTTATCCACATCTAGTGATTGTTCCATTCGCCTTTCACATTCAAT\n")
-		f.write("CAAGAAACAAGGGAAGAAGACGTACAAGTAATGTGCATTTGGGTAGGTCGAATTCCCGACTTGCAAGATA\n")
-		f.write("GAAGGATCAATCACTGTGTTTGGCCTTTGAAACAGTTTTGATCAAACCTTTGGTAATCTTCCAAAACCAA\n")
-		f.write("ATGAGATTCATCATAGACAACATTGGAGGCACCAGGAGCAAGCTGTAAAATCCTAAAGGGAAGATTGTCT\n")
-		f.write("TGACTTGATCGAAATGGATAAACATGTGGACGAAAAAGTAAATGAACAAAAGAATCCTTGCAACCAGCCG\n")
-		f.write("CCCGAGGAACAATGCTACGCCATTGAAGATGTACAGGTTAGAGTTCTTCTTACCAGCAACATCCAAATAC\n")
-		f.write("CATCTCATGTTTACGAGAGGAGTCGTGCTCT\n")
-		f.write("\n")
-		f.write(">gi|226791893|gb|GO546016.1|GO546016 Mdas9007K23_e527.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB03143.1| ankyrin-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TACCCTCTGATGGAGTTTATACATATTACCTTCTGATGGGATTTATACAGATATCTCCGAAAGATAATAA\n")
-		f.write("AAATAAATTACATCATTCGGGTGGGGTGTTTATTCTTTGCTTTTGCAGTGTTTTTCTGCTGCCCTCTTCC\n")
-		f.write("TGTATCTTCACCTGGTAGACAGAAGGAATCATAATGATATGAAAATCTTTGATTTTCTTCTTTTCTCTTT\n")
-		f.write("TCCTTTTCCTTTTCACTTTTGCTTTGCACCTCTGTCTTTGCTTTTCTCCAGACATCATTGTTTTTCTCTT\n")
-		f.write("TGTCTTTGTCTCGGCATGGGTCAGGCAAATTATTGAAACAAATGGGAAATTATAATCTTTCCCTTGAAGC\n")
-		f.write("TCCGTGTTGTTATGCCGCCCCGTCACCTGCTTCATGTACTTCTTCTTCTTCGCCTGGTCAATCCGTTTTC\n")
-		f.write("CTGAGTTAGAAAACACTAAAGTCGGCGAGTTGGAAGTCAGAGACGACTGGCGAGTTGGAAGTCAGAGACG\n")
-		f.write("ACGTGGAAGTCAGAGACGACGAATTGGAAAGCACCAAAGCCGACGCTGACGCAATGGAAGATGGAGACGG\n")
-		f.write("CGATGACGATGGCTCGGCCAGAGGGTTTTGGCTCGGCTGTGCAGATGAAAGATGGTAGTGCAGAGCCCGT\n")
-		f.write("TTGTGATGGCTGGTAATGCAAAGCACATTCCTC\n")
-		f.write("\n")
-		f.write(">gi|226791892|gb|GO546015.1|GO546015 Mdas9007L11_e530.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92380.1| P0512C01.35 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGGTGAAACTGAACTGTATTGGGAATATACTTCTACAATCTAAACACC\n")
-		f.write("TTCTGTAATTTATTGGGGAAGCAAATCAAATACAACGAAGGGGAAGAAAAAATGCACAACAGGGAACTTT\n")
-		f.write("GCTAGTGGCAGTTTCATCTCTCACACCAACAAGGTCCGACCTCGGCCATTCTGACCAGTTATCGACTTGA\n")
-		f.write("AAGTGGCTTACAAAAGCTCCAAAACAAGGGCAGATGCACCTCCTCCACCGTTGCAAATACCAGCAGCACC\n")
-		f.write("GTATTTCCCGTTCTTCTGCTTCAGTACCCCTAAAAGGGTGACCAAGATACGAGCTCCACTGCAACCAAGA\n")
-		f.write("GGATGTCCCCCTCGTGCCGAATTCGGCACGAGGGTCATCCCTCTCCCAAACCCTAAAGCGCTACCTCAAG\n")
-		f.write("AAACCGTGGGAGATAACCGGTCCGTGCGCGGATCCGGAGTACAAATTGGCCGTACCCGGCGCGCTCGAGT\n")
-		f.write("ACCGGCTCGAGTGCCCTGCCACCACCAAGGTCCAGGCGTGCGTGCCCACCTCCAACCCGGAAACCGTTTA\n")
-		f.write("CGATATCAAGTATTTCGCCCGCGACCAGCGGCGCAAC\n")
-		f.write("\n")
-		f.write(">gi|226791891|gb|GO546014.1|GO546014 Mdas9008E07_e580.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191320.1| adenylosuccinate synthetase [Arabidopsis thaliana] sp|Q96529|PURA_ARATH Adenylosuccinate synthetase, chloroplast precursor (IMP--aspartate ligase) (AdSS) (AMPSase) pir|T06759 adenylosuccinate synthase (EC 6.3.4.4) - Arabidopsis th, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAATGGAGACAAAAGTGAATGCGATTGATTTTCTCACACATAAATTG\n")
-		f.write("TCATATTAATGTGAGATGAGCCTAGGCATCTGTTACCTGCTATCAAATAATAGTATAGCCCATAACTAAT\n")
-		f.write("ACATGAAAACTACGATAACGACCGACCCCGAGTACTCTGACCTCAATTCATTCCAACAAATTCATACCCT\n")
-		f.write("AGTAATCCATGCATTACAACAAGCAATCCTAAACACAACATAGATTTCTTGTGGCCGCCTCGGGTGGAAA\n")
-		f.write("ATGTGTTGAATCAAACTGTGTCTTGAAAATTACTTCTAATCCGAAAAATCAACTCAAGTATCAAGGGAAA\n")
-		f.write("ATCGAGATTACTATTTGTAAATCAGTGCATCGCGTCCAGGCCCTACACCAATGTAATGGACGGGTACACC\n")
-		f.write("AAGAAGTTCTTCTATCGTTTCCACATATTGACGTGCGGCCTGCGGAAGGTCGGAGTAATTTCTGACAGAA\n")
-		f.write("GAAATATCCGATTCCCATCCGGGCAATTCTTCATAGTCGACCTCTAATTGCTCAAGATCACGAAGGTCTG\n")
-		f.write("AAGGGAACGATTTAATCGGTGTACCATCCTTCTGTTTATAGGCAACACCCAACTGAATTTTGGGAAGATC\n")
-		f.write("AGACAAAACATCAAGTTTGGTGAGATTGAGAGAAGAAAATCCATTGATCTGACAGCAA\n")
-		f.write("\n")
-		f.write(">gi|226791890|gb|GO546013.1|GO546013 Mdas9008A06_e555.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_173710.1| expressed protein [Arabidopsis thaliana] pir|G86363 F19G10.8 protein - Arabidopsis thaliana gb|AAB72164.1| unknown protein [Arabidopsis thaliana] gb|AAL49950.1| At1g22970/F19G10_8 [Arabidopsis thaliana] gb|AAM70551.1| At1g22970/, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTACCGGAAAAACATAGCTTTATTGATTGATATTTCAGAAACA\n")
-		f.write("AAACAAAGAGGTCTTTATATAGAGAAAGACCAAAGCAAACCCTAGACTAAAACCCTAAACCAAATCCTAA\n")
-		f.write("ACAAACTCAAATACTTAATGGGCAAGTAACTAATCCTTGGCCCGCAAGATAACAACCTAAATTCCAAACT\n")
-		f.write("AAATTCCAACAATATGGACACAAGAAGCCAGCATAGGCCCTGCACCGACTGTACTCCCATGTGATAGCAG\n")
-		f.write("AAGAAAACCTTGCAGGGTATTGAAGTAGGAAACCATGTTTTCTTCAAGTGCTCTAACTTGCGGTGTTTCT\n")
-		f.write("CCTCCGGTCCAAAGCATTCCAAAAATGGTGGCTTGTTTGGAGACTTGATCGCCCATCTTTGTGACCTCCA\n")
-		f.write("CCCAGCTCACCTTCTCAAGTTTTGAAGGTGCAGTTTGATCCAACACCTGGAAGGTCTCGTGGACGGTGTT\n")
-		f.write("GAGGTGGTGATTGAGAGTTCGAGTCAGTTGGTCACTCTCGGCTCGGCCCATCGCTCGGCGTTTGACGGAA\n")
-		f.write("GGAATTGCAGCTGCAGCAGTGGCGTTTGACGAGGGACTCGGCCCACTGTCCATCACTCGGATTTTTTTTT\n")
-		f.write("ACTATTTTTCCACGACTGGCAATGAAGTGAGAGATGGCC\n")
-		f.write("\n")
-		f.write(">gi|226791860|gb|GO546012.1|GO546012 Mdas9007F15_e504.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAACTTCGTAACTCATTCTATTTGTGCATATTTCTTGCAAAGCTAT\n")
-		f.write("GAACAACAGCAGAGATTTCGTGTATGCACCAAG\n")
-		f.write("\n")
-		f.write(">gi|226791859|gb|GO546011.1|GO546011 Mdas9007L14_e531.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187796.1| amino acid transporter family [Arabidopsis thaliana] gb|AAF23206.1|AC016795_19 putative amino acid transporter protein [Arabidopsis thaliana] gb|AAP37661.1| At3g11900 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGATTTCTGCATCATTGGGCTGAAGAATATTATACACTGGTGGTAC\n")
-		f.write("ATCGAATATTGGAATCCAGATACAGATTAAAGTTCTTCTGCTTCCCCATTGTACAGTTTGTATTCATGTA\n")
-		f.write("TCTCTTACTTGTAAAGTACTAATTACGACAAGCGATTCAAACGCCAACTACGGCATTGTAAGCGCCGTAT\n")
-		f.write("GCGGCAAAAAGCATTCCGCAAAATAATATGCAACAATCCAAGGTTCTTTGCCACAATTTTAGGGAAGAAC\n")
-		f.write("CCAACAATGCTAAGTGAAATGAAGCAGGTAGAACAAATGAGATCAGTGCACATACAGTACTTCCCACGAG\n")
-		f.write("CGACGCAAATACTGCAAACCCTGGAACGCACGAGGCCAAGACGGCCAGTATGATCACCACTATTGCTCGA\n")
-		f.write("CTCACGTACACTGCAAACCTTCCTAGAGGCGGCATCGTTGAATAATCGTCATTGTCATCATGAGCTTTCT\n")
-		f.write("GAAACCATTTGCCTTTTACCAACTTCCCTTCTATGATCTCGTTTATCGGGTGTAGCATGATATGGGAGGG\n")
-		f.write("TAAATATTAGCCCCAAGCACAAACCAATCTGAACCACCATGGCAGACCAA\n")
-		f.write("\n")
-		f.write(">gi|226791858|gb|GO546010.1|GO546010 Mdas9007E17_e501.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191612.1| GATA zinc finger protein [Arabidopsis thaliana] pir|T47864 GATA transcription factor 4 - Arabidopsis thaliana emb|CAA74002.1| homologous to GATA-binding transcription factors [Arabidopsis thaliana] emb|CAB81839.1| GATA transcript, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAATTAATACATTTTCTTTTAATTAATTAAATATCCAAAATAGTAATG\n")
-		f.write("GAAATTAATTTCAACTTTTTTCTTTGCCTCAAAAACAAAAAATTCCCATTGTTTATGGTCAAATTTCCAC\n")
-		f.write("ACGGCCCATCAACTGAGAGACCGCCACGTGTTCCACACGTCAGCAAACTCGAAACTCGTCGCGGTGAAGA\n")
-		f.write("TAGAATTGCTGCTGATGCGGACGGTGTTGCTGTGGTTGCTCTTGCGGTGCCTGCTGCTGAGAAGCCTCCT\n")
-		f.write("TCTGGCGACGGAGCTCCAGAACCTTCCGGTGCGAGTTCGAGTGCTGAGTCAGCACGAAGGTCGGACTCGC\n")
-		f.write("CGCCGGCCGGTACTCGGGCACGAGCCGACCCGACTTGTACCGGACCCCGCACGCGTTGCAGAGAGTCTTG\n")
-		f.write("GGGCCCATCGGTCCTGCCCGCCACTGCGGCGTCTTCTCCGAGGCGCAGTGCGTGCACCTGAGCGGTGAAG\n")
-		f.write("GGGACGCTTCCGACGGCTCTCTCTTAGGCCTGTTGGGCCTC\n")
-		f.write("\n")
-		f.write(">gi|226791857|gb|GO546009.1|GO546009 Mdas9008C11_e569.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAATTTCTTACAAAAAAGTTGGCATCAAATAATCCATGTCCCACCCACATTTGGGTGATTTTAAAAAACT\n")
-		f.write("TATTTTAATTATCTTTTTACAAAAGATAAGCTTAATAACCAATACACAGCAATACATGGTTCTGTTCATT\n")
-		f.write("GAGTTCCCCATTTGCCTGCTACTTAAAATACGTTTGAAGATCCAACCCCAAGACCAAAAATACCAAACGA\n")
-		f.write("AATCGGAAAAAAAGCAAATTACCTGTCAACAACTACCGGTAAGCATATAGCAGTAGGTACCCCATGGCTT\n")
-		f.write("CAATTGTTCAACATTCCTCCACCCCCCCATCGTTTTGTTCCATCATTGTCCCCCTAATTTTTCAACAGAA\n")
-		f.write("AACTAATGCAGGAACCCCGCTGTATTCGGCTACATCAAATCTACATCGGCAGCACAATGTAAATAACAGG\n")
-		f.write("GGAGGGAGAAGGCCAACAAATTTCTGAAGAAATGAATTCCTCTCAATTTACAGGCCT\n")
-		f.write("\n")
-		f.write(">gi|226791856|gb|GO546008.1|GO546008 Mdas9007G24_e510.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568305.1| mannosyltransferase, putative [Arabidopsis thaliana] gb|AAK91470.1| AT5g14850/T9L3_150 [Arabidopsis thaliana] gb|AAM52236.1| AT5g14850/T9L3_150 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("ACATTTTCAAACCACATCACTAAAGGGGTCAAAACTGATATCATGTTTAACCATGACAGCCTATCCATGC\n")
-		f.write("TCACAGGCTGTATCCAGTTGAAAAATCAAGTTTAACACAACATAAATAGACACACAAAAACGCAGGAAAA\n")
-		f.write("ACAACAAAAACAAAGCATTTAATAAAATCCGGGGTTAATGAATGGAAAAAAATTTGTTACATACTAATTG\n")
-		f.write("GCGGTCTGAAATTGGAATCTGCTGAAGCGGGCATGTCTCCAATAAACCCCCATGCTCTGGCCATTCACTC\n")
-		f.write("CATTCATCAAGACATAAAGTCAATAAATTCTTCCAGCCCATCATACTGGAATGGTTCTAGTTGCACATAC\n")
-		f.write("AATAATCAGTCGCCTGTCAAACCGTACACAACAACTGACGCTTGCAAATCACGGTCCACTTTGAAGTGCG\n")
-		f.write("CATGGAAAAACCTTTTTATCTTTTTGAAAGAATGTGAAATCAAAAAAGCCCTCAACTGTTTTTCTTCCGA\n")
-		f.write("ATCAAATACTACAATGTGACTAGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791855|gb|GO546007.1|GO546007 Mdas9008D01_e573.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191593.1| palmitoyl protein thioesterase precursor, putative [Arabidopsis thaliana] ref|NP_850728.1| palmitoyl protein thioesterase precursor, putative [Arabidopsis thaliana] pir|T49229 palmitoyl-protein thioesterase-like protein F27H5.130, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAGTAATGGTCCGAAAGGTGGAAGATATAAAAGTACAATAAAGTTG\n")
-		f.write("GGAGTCATGTACATACTCTACAACGTAGAGTCTCCGTAAAATTACTTAACAAAGTACAACATCAATGATT\n")
-		f.write("ACGAAACAATATGGCAGCCGGCAGCCGGCAGCCGGCAGCCGGCAATCGTAAAAGGAATTGTCACTCACTC\n")
-		f.write("TCCCTTCTCCAATGGTGCAAAAAATAAACAGACATAACAAGTCCCGTTCGACTATAGTGCATAGAGTAGT\n")
-		f.write("AAGAATATACGTAGTAGCGATCATTTCAGAGCGTTCTTGTGTATATTTCGTGTTACCTTTAAACCCCGAA\n")
-		f.write("ACTCACATTACACGACCCTCAGCACCACCTTCTGATGCTCACCGAGTCCAACAAGATCCAAGTAGTTGTT\n")
-		f.write("CCAGATTAACGAAAGTGTCGTTGGAAATGAAGGCTCTGCTATCTTGTGCTGCGTTGAGTCTTCGTCTTCC\n")
-		f.write("AAGTATGGCACAATGTACGTTTTCATGTCGCTTCGAGAGATCTGCAGATGGCCCCCCGACACATTTATGA\n")
-		f.write("ACTTAACTTTTCCAGCTTCGTCCAAGGTTTTCAAACCAATCCAGTCTTCAGTGTACAACATGGTCTCTTG\n")
-		f.write("CGCAGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791828|gb|GO546006.1|GO546006 Mdas9008C21_e572.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTCATAATTATCATCTATTTGTACTATCTCTTTAATAAAAATAGGATCC\n")
-		f.write("GCCAATATATAGGGATTCCATCTCTATTAATAAAACGATACAAATAAATGATGAAAATAGCATTTTTGCA\n")
-		f.write("GCAAATATTACTCCAAAGTTTCCCCAAGTCAAAGTAAAAAATCCAAAAACCCAAAGAAATAACCACAAGA\n")
-		f.write("TATACCGGTGGAAAATTTAATACAAATACCACGCAGATATTATAAATAGTTATTGAAACTTCACCTTCAA\n")
-		f.write("CCCGTTAAACCCACGCTGTGAAGCACGACGGTCTCCACCGTGAGGCCGGGCCCAAATCCGAAAAGCACAC\n")
-		f.write("CCCACTCCTTTCCCTCCCCGGTCGTTTTGAGTCCTTTCTCGGAGGACTTCCTCCTGACCTCGTCCGAAAT\n")
-		f.write("AAAAAGCACACAAGCACTCGACATGTTACCGTAATCCGACAACACTTGCCTTGTTGCTTCTAGTTTCTCC\n")
-		f.write("GGCTTCAATGCCAACTTGGCCTCTACTTGGT\n")
-		f.write("\n")
-		f.write(">gi|226791827|gb|GO546005.1|GO546005 Mdas9007H11_e512.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850250.1| expressed protein [Arabidopsis thaliana] gb|AAL67023.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTCCATTTCTTTTATTGGAGCTACATATGAAGATTATGAATGATACACCTGAAAAAGATTTCTTTAAT\n")
-		f.write("ACACAACACTATTTCTCCCAGTCTTAATATGGATGCAGTCCTCTTCGTTTCTATTCATGTAGGTAAGTTA\n")
-		f.write("GGAACTAATTCGTTTGTCAAATACTTTCCCATGCTACTCGTCTTTGTATTTCCTTTGACAGATACATGTA\n")
-		f.write("CACGTATCGCTCGGTTTCTCTTACGGTGGTGGGTGATCGTCCTCACGGGTTTGAGGAGGGATAGGTCTCC\n")
-		f.write("AACCTGGTTTCTCATCCCAGTACATGTCATAGTATATGTGACCAGGAGTGTGTTCGGCCACACAACACCA\n")
-		f.write("TATACCAACATACCGCTTCGCACGATTCCTGAATTTCTCTTCCCTTGCCTTGTCGGTGAAACCTGGGAAT\n")
-		f.write("GCATCTTGCATAGAAGAAAACTGAATTACTTTTACATCCTTGAACGAGGAGAATACTGTCTTGAACGTTT\n")
-		f.write("CTTCGTTGCTTCTCTTTGGAAATCTGAGTGCTCCTGAAGGGGTGGTAGTATTTGAAGCAATGCAGTCTCG\n")
-		f.write("CGTTCCTTGTTGACAAAGCTGGACATCAAGCCATGATTCTTTCACCTGTTTTGGCATCAATGGATTGTCA\n")
-		f.write("AAGAATGAGTATTCTCTAATACCGATTGGGGGCCCAAATAT\n")
-		f.write("\n")
-		f.write(">gi|226791826|gb|GO546004.1|GO546004 Mdas9008B14_e564.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGCAGACAAAATATATAAAATATATGTATAGGTATAAAACAG\n")
-		f.write("AAATAGTAAACCCAGCATCCTACCAATTTATTTACATAAAAGGTTCAAACCATAATCATTGTCAATCGCC\n")
-		f.write("GTCACAAACAGTTTGCAGCAAACTCCACATTAGCCAACCGTTAAACGAGGAGAAAGATTGATTCCTTACC\n")
-		f.write("ACGCATCTTTATCAAAAGTTGCATTTATAGAATGACACACTTGGTTTCACCTCTTTTACGAAGCTCCTCC\n")
-		f.write("TCTGCTTTCATTAAATGTTCTCGAAGCTTTCGAATTTCATCATCAGACTTCAGCTGAGCCTGTTGAGCAT\n")
-		f.write("TCTCTTCTGCTCTCAGACGTGCAGCTTGTTCATCTGCCAACTGTTGCTCAAGCCTCATAGTGGTCTCTCT\n")
-		f.write("TAACTTTGACTCGACCATCTCAGTAATCCGCTTAAGCTGCTCGTCATGTGCACGCTGCATCTGATCCTTC\n")
-		f.write("AATTCAGATATTTCTCGTTTGGAATACCCCTTCAAGGAGTTGACCTCTTCTTGTTGATCACGAAGTTTAA\n")
-		f.write("TGGCCCCTTTCTTCACTTCAGCAAATATCTCATCTGTGTACGGTCGCCCACCATTTTGTGATATG\n")
-		f.write("\n")
-		f.write(">gi|226791825|gb|GO546003.1|GO546003 Mdas9007P19_e553.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196647.1| CBS domain containing protein [Arabidopsis thaliana] sp|Q9LEV3|UMP3_ARATH Protein At5g10860, mitochondrial precursor pir|T50795 hypothetical protein T30N20_130 - Arabidopsis thaliana emb|CAB96841.1| putative protein [Arabidopsis, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGTGAAAAAGAAATAAAAATTAGTACCATACTTACACGAATATGTGA\n")
-		f.write("ACGTGTGAACGTGCGTGATACAAAACGCACTACCATCTACCAGAGAGAGAGAGGATTTAAGCAAAAACAG\n")
-		f.write("AACGTACACTGCTTATTGTTAGGTACTTGACAGTCCCAAAGGTTTGTAATTAGACAGTGATTGGAAGTAC\n")
-		f.write("AGAACCAAACAACAACAACAACCGGAGATGCACAAACGAACACACAATACATACAAGCACTCGGGCTTAT\n")
-		f.write("TTCTGTTTGTCATTCCGGCGTGTCAACTAAAACAGCGTCTCACGTCTTCGTCATCATCATTATCTAGTAA\n")
-		f.write("CCACCTTGAATAAAAGCATTCAAGCGGTCTAGCTCCTCCCGGTGCTCGCTCACCACAGCACGAACCACGT\n")
-		f.write("CACCGATGGACACCATTCCAATCATTCCCCCGTTGTCTATTACTGGAATGTGCCTGATTCGGTTATCCGT\n")
-		f.write("CATAAGTTGCATTGCCCGCAAAACTTTGGTGTCAGGGGTGACAGTGATAAGCTTGTTCTCCTCAGTCATG\n")
-		f.write("ATATCCCCAACCTTTGTTGACTTGGATGATCTTCCCTGAACTATGATCTTCCTGAGATAATCTCTCTCTG\n")
-		f.write("TTATGATTCCTGCAAGAGACTTTTGCACTCCGGGTTTCACAACAACTAAAGCTCCAACATTGTGCTGGG\n")
-		f.write("\n")
-		f.write(">gi|226791824|gb|GO546002.1|GO546002 Mdas9007H05_e511.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568870.1| SKP1 interacting partner 1 (SKIP1) [Arabidopsis thaliana] dbj|BAB08860.1| contains similarity to N7-like protein gene_id:MTI20.16 [Arabidopsis thaliana] gb|AAG21976.1| SKP1 interacting partner 1 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTACAAAGAGAAAAGCATTAATACATGGTTTATACATGAACTCCATACA\n")
-		f.write("ATTTGACTTATTGGCGTTACCGAACAAGGTTTTCGATAAGTAGAAGTGAAAGAGATACAGAACCTTTTGT\n")
-		f.write("AAAGAGCTCCACACACCAGCATATACAATATGCTTTTCCCACAATTGATCAGAGCAACACAACACGGTCA\n")
-		f.write("TACATGTCTTATGTCCGAGCTTAACAGACTAGATTCTGAAAACATCTGTCTGGAATCGCTCGTCATACAA\n")
-		f.write("CCTCCAATGGCCATACCTCTCCGAATGGAAGACTGACCGTGGAATGTAGAAGTTTGGCTTTTTAATCTCC\n")
-		f.write("TTCAAATTCTTCAGATTGCATGTTGTGTTCTCAATATCCCGGCTAGTCAAGTTCACACACCCAAATAAAT\n")
-		f.write("CCAAGTACTCGAGATTTGGACATCCTACAGGTATCAAAGTAAACCCTTTAGCCGATACCTTTGAGAACCG\n")
-		f.write("AAGTTCAAGGTGCTCCAAATTTGGCATAGATTTGCCAATTGCAGCAGCTTCTGAATTTCCATCCTGAGGG\n")
-		f.write("CAAGTTTTTAAGTACTCATCTGGAACAACTCCAGTGTATTCGGATGGATCTAACCAGTTCAGCATATTCC\n")
-		f.write("GCTTTCAGATTTTCAGATTT\n")
-		f.write("\n")
-		f.write(">gi|226791823|gb|GO546001.1|GO546001 Mdas9007N23_e544.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATCGCTCCAATAAAAACCACATTACATTTTGCAACTAAATACAGATGCAGTTACTCAAGCTACATCCAAT\n")
-		f.write("TACATCATGGATACAAATTAAAGTTCGACATTTATTAAATTAAGCTATCTATTTAGCTGCTCCTTCAATT\n")
-		f.write("AATTATCACAAAAAAAAAAAAAAACTTTTGGGTACCCAAATCAACAAAATGGGTCGGACCCACGACAATC\n")
-		f.write("AAGAAATTGCAGGAGGAACCCATTACACAAATTGCATTCAAAATACCAAAAATTGAGGGAAAAAAACATC\n")
-		f.write("AACGAAATTGAGAGGAGGGATCGGAGGATCAACCTGCATTCGAATCAATGCCGGTGTCTAGAGAGAGAAA\n")
-		f.write("AAATCGGATGCAATCTTGAAAATGAGGAAGCAAAGGAACGCGAAAAAGATCGAGAGGAAGAGGTAATCCA\n")
-		f.write("CGAAGACGAAGAACTCGGTGGAGCCGTGGCTCCTCTTCTTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791795|gb|GO546000.1|GO546000 Mdas9008B02_e561.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB89355.1| ubiquitin-conjugating enzyme OsUBC5b [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGACTTCCACCCGAATATCAATAGCAATGGAAGCATTTGTCTTGACATCCTAAAAGAGCAATGGAGCCC\n")
-		f.write("AGCACTTACTATCTCTAAGGTATTGCTCTCAATCTGCTCATTGCTGACTGACCCAAATCCTGATGACCCT\n")
-		f.write("CTCGTGCCGGAGATCGCCCATATGTACAAAACTGATCGAGCCAAGTACGAATCCACTGCACGTATCTGGA\n")
-		f.write("CTCACAAATATGCAATGGGTTGAAGAAGTCTTTTCCGCCAAATGTAGAGTTTGTATTTGGGGGGAGGGGG\n")
-		f.write("ACAGGTTCGGGGCTTTTCAATTGAGGAAGAACAGTTTCCTTAATTATATCAAAAAAAGAAGGGTATGAAT\n")
-		f.write("GGGATGTAATTCTGGCTTTACCAGAACTTTAATTTCTTGTTTGATGTTGTTCCTTCCAGATTTCTAGACA\n")
-		f.write("GAAACTTAAGTGTTCAAGTTTTAATTCCATCGACTGAGGAATCGGTGTTGATTTTTCATCTGCCATTTCT\n")
-		f.write("TGTTGTGTCTTGAAAGATTGAGAAATGTATAAATCCAATGAACTGCTATGTTTGCTATTTACTCTTCCAA\n")
-		f.write("TAAATTGTTCTTGCAAAAAAACAAA\n")
-		f.write("\n")
-		f.write(">gi|226791794|gb|GO545999.1|GO545999 Mdas9007N14_e542.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAACAATTACAAATTTCAAATTTCAATTTTTAATTTAAAAAATATAG\n")
-		f.write("TAACTTACATTATTACATTAATGTCAGGGACCTCAATCAAAAACTAAAAACTAACAAGGTTTCAATCAAA\n")
-		f.write("GAATATTGATAGTTAGGGACCGCATCCAAAGTGTCCCTTTTAAATAACATCATTTAATCAAATACAAGAG\n")
-		f.write("AGGGTATGAATCTGTTCCACTTATTTTAGCCGATCCAATCAAATATAATCTGT\n")
-		f.write("\n")
-		f.write(">gi|226791793|gb|GO545998.1|GO545998 Mdas9007M06_e534.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTAACTACATGAAGAAACAATTATGTTACAAAACCCTTACATAATTA\n")
-		f.write("TGCAGCAGTCTCGCAATCATATAACTCTCTCCCCCTTTCAATTACAAAGAATTAATACATCAACAGGTAC\n")
-		f.write("CTAACCTATATACTTAAATATTTAGCTCACAGAACACACTTGTATGAAACTTGACTTTGTGGTAAATTAG\n")
-		f.write("GAAGGAAATTTGAAAAGAGATATCGAGAACGAAAGGGCCCCATTTTCTCCCAAGTTCCACATTCCTCTCC\n")
-		f.write("CCATTTCTGCTCAGTTTCCCCCTCCCCTTCCTAGTGCAGGCACTCCTCCTCATCATGTCTGGCTCCGCCA\n")
-		f.write("CTCCAAACCGATGACTTCGGAATGTTAGAGCTTAGTTAGGTAATTAACTAAGTAGCATCAGAGGATGAGA\n")
-		f.write("GAAGGGGTTCATGTTCCCTTCCTTCTTCCAACTGTTCGCCATCTGAAATCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791792|gb|GO545997.1|GO545997 Mdas9007G21_e509.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196186.1| signal recognition particle receptor beta subunit-related protein [Arabidopsis thaliana] dbj|BAB09661.1| signal recognition particle receptor beta subunit-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("GCATCCCAAATGCAATGAGCCATAATCACTTGGAACATCTTTTAACTTACAAGAAATTACCACAAATTCA\n")
-		f.write("TGAAATGGGATCAAATATCCTACGACTTTACGTTATCTCTGATAAATTGCTCCACCTGGGAAATTTCACC\n")
-		f.write("ACCAAGGCCAGAAGCTTCTCCAACTGTAACTTTGTTTTGACACTGCAAAAATGCAAATCGTTCTCCAGGT\n")
-		f.write("GCTCCGAGTGTAAACTCATTTGTAATATCAGCTGTTGATACTGCACTTCTTGATGCTCGTAATTTGTCAA\n")
-		f.write("TTTCCTTCTCCAATTGTTTTCGAATAAATTCCTTGCTATGTGCAGTCACTTTGTCTGTCTTATTGCAGAA\n")
-		f.write("AATAAGAACTGGAATTTTCTTCCTCACCACACTCGCCTTGGTCAAAATATCATACAGGTACTCTGAAGCA\n")
-		f.write("GCACGGCAATTTGGTAAGAATTCCACAGCATCAACCACAAACACTATACCAGCAGCTTGAGGGAGGAAAT\n")
-		f.write("CATCTAGTTTGGCTCTAAGGCGAGAATGCCCGGGAACATCAATAACATGAATAGGATTTAGCTTTCCATT\n")
-		f.write("CTTTGATTTTTCAGAATGAAGCACAAAAGTTCCCTCATTTGGTTCCATAGATGTGACAG\n")
-		f.write("\n")
-		f.write(">gi|226791791|gb|GO545996.1|GO545996 Mdas9007E08_e500.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566716.1| protein kinase, putative [Arabidopsis thaliana] dbj|BAB01250.1| kinase-like protein [Arabidopsis thaliana] gb|AAK59509.1| unknown protein [Arabidopsis thaliana] gb|AAL34187.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TGGAAAAGCTTGATTTCCCTACTAATTTACAATAAGAATGAAGAAGGAACCCCAAACAACAATATGGCTT\n")
-		f.write("TTCAAAAACGCTGTTTGTGCATTATTCAAAAATGAAAAGTGATTATTCAAAGACTGACTGCTGCCTGCAG\n")
-		f.write("TCTAGCGCTGAACTGGTAAACTGGTTTTAATATGCAATGCACAGTCTGTAAAGCTATATTACACCAAACA\n")
-		f.write("AAGAAGGTTATGGACCGCGAGGTGTGCCGAAACAAAAACAGCCGGTTGACTGGTCTTCAGGTATCATGCC\n")
-		f.write("CCCTCCCTTGCTCGTATCTATTGCGTACAACAGTTTCACAACCTCTTCCATTTCAGGGCGTTTATCCGGG\n")
-		f.write("CTTGCATCCCAGCATTTTCGCATGACGCTAGCCAATGTGCTCGGACAACATCTTGGGATTTCTGGTCGTA\n")
-		f.write("AATTCTGTCGCACTACTGCAGATGAAACATCAGCAAAACTTAAATTAAGATAAGGCATGTCGCAACAATA\n")
-		f.write("GATTTCCCATAAGCAAATACCAAAACTATAGACA\n")
-		f.write("\n")
-		f.write(">gi|226791790|gb|GO545995.1|GO545995 Mdas9007K19_e526.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|H71447 trehalose-6-phosphate synthase homolog DL4920W - Arabidopsis thaliana emb|CAB10557.1| trehalose-6-phosphate synthase like protein [Arabidopsis thaliana] emb|CAB78780.1| trehalose-6-phosphate synthase like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGAAGGCCAACATTAAGATACGAGAAAATTTTACAATTTCGCT\n")
-		f.write("ACTCACACACTAGTCACTGCATAATAACAGAACGGGGTTTCAATGAATAATCTATTTACTTTTCTAAAGT\n")
-		f.write("AAGTACTCGCTGAAAAAGTTGCCCTGCAGCGCTTTTGGCCGACTGCTCCGAAGCATTGGCCAGCCCCTGT\n")
-		f.write("AACATTCTCAAAATCTCAGTTGTGTCTTCCAGGTAGTACTTGGCCTTGCTGGGCTTCTGACCGACGGTGC\n")
-		f.write("AAGCAAACACTTCAGCCACCGGAGAGAGAGAGTCCCTTGAACTCATTATCGCCTCAAACATGTCTTCGTC\n")
-		f.write("GGACCTGTCATCCCCAATACACAGAACAAAATCTGGAAGCATTGCTTTCTGTTTCATTGCTACGAGGAGA\n")
-		f.write("CGTTCTGCTACAAGGCCTTTGTTGACACCCTGAGGTTTAACTTCTACAATGTGCTGACCACTCTTGACAG\n")
-		f.write("ACACTGGCTCATTGGCAAGAACACTTTCCAGGTGATCTAGAAGCTCCTTAGCCTGACAAAAGCCAAAATC\n")
-		f.write("TGGATCTGCGTATTGATAATTCCAAACAAGAGCACTTTCTTTG\n")
-		f.write("\n")
-		f.write(">gi|226791762|gb|GO545994.1|GO545994 Mdas9007K12_e524.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CAGGAGGTACTCTCTTGGCTTTCTTAATTCAAAAGTAATAAAGTAGTCAAAAAAGTAGTCAATAAAGTCC\n")
-		f.write("TCAATAAAGGTTCCCAAGTACTACAGTAAATGCCACTAAACAAAGTAAAATCCCTAAAAAACATGATTTC\n")
-		f.write("CCTGCCATCCAATCCAACCGCGGGTTGTAAATTTTCCATCCCCCCCCCCTGCTCTGGATTTCCTCTTCTG\n")
-		f.write("CCCTCTTGGTACCAGGCCTTCGCTTCATGTTCTCTTTCCCTTGAGGGTCTTAAAACTCTTTAAAAAAAAA\n")
-		f.write("CTGAAAACCCCCTTCAGGGGAGCTTTCCTTCCTTCTTTAAAGTTCCAAAGTTCAAAAAAAACATCCCCCC\n")
-		f.write("CCCTTGGATTGGAATCATTAAGTTCTTTC\n")
-		f.write("\n")
-		f.write(">gi|226791761|gb|GO545993.1|GO545993 Mdas9007C18_e496.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567082.2| serine/threonine protein kinase, putative [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTTGCAAACAACATTCAGTGAAAAATATATCCACCTCACAATC\n")
-		f.write("CAACCCCCAAGTCAATTCATGGCGAAAAAATTAGACATACAGCACTCAGCAATGACATGAAACTGGCCAA\n")
-		f.write("ACCAATCCTACACATCCAATCTCATATATGAAATGTAAAAAAATGAAACTATATATAATGTTTACGATGA\n")
-		f.write("AATCAGCGGGAGGCAGTTGAAAGCAGAGTGTTTCAAGGACGCAGAAATTCCAGCACAAGGAAAGACTGAG\n")
-		f.write("GCCCTTGCCTTCAAGACTCCGGAGCTGCTGCTGGTGGCTTCAGAAGCGGTTGAAGAGCCTTCACAACAAT\n")
-		f.write("GCTCATATTTGGCCGGAATTCAGATTCATATTGCACACACAGTGCTGCAACGGCTGCCAGCTTCGCGACC\n")
-		f.write("CCCTTAGCAGGATAATCCTTTAGCTTTGGATCAACACATTGTTTAACTTTGTCTTCGCTCAATCTTGGAG\n")
-		f.write("TAGCCCAAGTAACAAGACTCTGCTGTCCACGAGGCATTGTATGATCAACAGGTTTCCTCCCGGTCAGAAG\n")
-		f.write("TTCTAGTAGAACCACTCCAAAGCTGTACACATCACTCTTCTGTGTCAATTGGCCTGTCATTGCATACTCT\n")
-		f.write("GGGGCATGATAACCAAATGTTCCCAAAAATCGAGTAGAATGAAGACGAGCAGCCATATCAGGAGCCTGA\n")
-		f.write("\n")
-		f.write(">gi|226791760|gb|GO545992.1|GO545992 Mdas9007L07_e529.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGGACAACTCAATTTATTTAGACCGGGTCATAATGTTACACACT\n")
-		f.write("GAAATTCACTCGAGCATCTCGCGCACATTAGATGCTCGACAATAACATGAATTGAAAGACGTTAACACAA\n")
-		f.write("CAGAGTTCATAATTACAGCTCAAGAACAATATATTGTATCCCGGATTGGGGTTCGATAAACCCACTCATT\n")
-		f.write("TCTTCCCGCTTTTCTTGAGCCCAGAACCTCCGAAGGACCCTTTCTGTTGTGCCTTGGCTCTAAGCTCCTT\n")
-		f.write("CAGTGCCTTTTCCTCCTCTTTCTTCTTCTGAAGGTTGGCCAAATCGGACTCGTCGTACTCCTTCTTGTCG\n")
-		f.write("GCCTTGGGTGCCTTCAAGGGCT\n")
-		f.write("\n")
-		f.write(">gi|226791759|gb|GO545991.1|GO545991 Mdas9007H16_e514.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568754.1| expressed protein [Arabidopsis thaliana] ref|NP_851167.1| expressed protein [Arabidopsis thaliana] gb|AAK92812.1| unknown protein [Arabidopsis thaliana] gb|AAM14150.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("GGGAGTCGCTACGTTTGGAGCTCCAAGGAGTCCGAATATTCCTCCGCTGATCATCTCGTTGTCATGGTCC\n")
-		f.write("ATGGAATCATGGGAACTGCCGCGGATTGGAAGTTTGGGGCGGAGCAATTTGTTAAAACACTTCCAGACAA\n")
-		f.write("AGTTATTGTTCATTGTAGTGAACGGAATGGCTCTAGGCTGACTCTAGATGGTGTGGATGTAATGGGGGAG\n")
-		f.write("CGATTGGCAGAGGAGGTTATCGAACTGACTCGAAAAAAACCTAATCTACGAAAGATCTCATTTATTGGAC\n")
-		f.write("ATTCTGTTGGAGGATTAGTGGCAAGATATGCAATTGGGAGGCTATATAGACCCGGTCCCCCTAAAAGTGA\n")
-		f.write("CAATACGGAACCTAAAAGTGAGAATACGGAACATTCATCTCCTGATGGATGTGAAGAGGATGCAAGGAGT\n")
-		f.write("ACATTAGCTGGCTTGGAGCCTTTGAACTTTATTACTGTTGCCACGCCTCATCTTGGATCAAGGGGTAACA\n")
-		f.write("AGCAGGTGCCATTTCTCTTTGGTGTACCTGCCTTTGAAAGACTTGCTAGTGCGGTTATTCATTTGATATT\n")
-		f.write("TAGGAGAACAGGTCGGCATCTTTTTCTTAATGATGACGATGATGGGAAGCCCTCACTG\n")
-		f.write("\n")
-		f.write(">gi|226791758|gb|GO545990.1|GO545990 Mdas9008A20_e560.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB89355.1| ubiquitin-conjugating enzyme OsUBC5b [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("ACGTCTTCCACCCGAATATCAATAGCAATGGAAGCATTTGTCTTGACATCCTAAAAGAGCAATGGAGCCC\n")
-		f.write("AGCACTTACTATCTCTAAGGTATTGCTCTCAATCTGCTCATTGCTGACTGACCCAAATCCTGATGACCCT\n")
-		f.write("CTCGTGCCGGAGATCGCCCATATGTACAAAACTGATCGAGCCAAGTACGAATCCACTGCACGTATCTGGA\n")
-		f.write("CTCAGAAATATGCAATGGGTTGAAGAAGTCTTTTCAGCCAAATGTAGAGTTTGTATTTGGGGGGAGGGGG\n")
-		f.write("ACAGGTTCGGGGCTTTTCAATTGAGGAAGAACAGTTTCCTTAATTATATCAAAAAAAGAAGGGTATGAAT\n")
-		f.write("GGGATGTAATTCTGGCTTTACCAGAACTTTAATTTCTTGTTTGATGTTGTTCCTTCCAGATTTCTAGACA\n")
-		f.write("GAAACTTAAGTGTTCAAGTTTTAATTCCATCGACTGAGGAATCGGTGTTGATTTTTCATCTGCCATTTCT\n")
-		f.write("TGTTGTGTCTTGAAAGATTGAGAAATGTATAAATCCAATGAACTGCTATGTTTGCTATTTACTCTTCCAA\n")
-		f.write("TAAATTGTTCTTGTAAAAAA\n")
-		f.write("\n")
-		f.write(">gi|226791757|gb|GO545989.1|GO545989 Mdas9007D02_e497.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567082.2| serine/threonine protein kinase, putative [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTTGCAAACAACATTCAGTGAAAAATATATCCACCTCACAATC\n")
-		f.write("CAACCCCCAAGTCAATTCATGGCGAAAAAATTAGACATACAGCACTCAGCAATGACATGAAACTGGCCAA\n")
-		f.write("ACCAATCCTACACATCCAATCTCATATATGAAATGTAAAAAAATGAAACTATATATAATGTTTACGATGA\n")
-		f.write("AATCAGCGGGAGGCAGTTGAAAGCAGAGTGTTTCAAGGACGCAGAAATTCCAGCACAAGGAAAGACTGAG\n")
-		f.write("GCCCTTGCCTTCAAGACTCCGGAGCTGCTGCTGGTGGCTTCAGAAGCGGTTGAAGAGCCTTCACAACAAT\n")
-		f.write("GCTCATATTTGGCCGGAATTCAGATTCATATTGCACACACAGTGCTGCAACGGCTGCCAGCTTCGCGACC\n")
-		f.write("CCCTTAGCAGGATAATCCTTTAGCTTTGGATCAACACATTGTTTAACTTTGTCTTCGCTCAATCTTGGAG\n")
-		f.write("TAGCCCAAGTAACAAGACTCTGCTGTCCACGAGGCATTGTATGATCAAAAGGTTTCCTCCCGGGCAGAAA\n")
-		f.write("TTCTAGTAGAACCACTCCCAAGCTGTACACATCACTCTTCTGTGTCAATTGG\n")
-		f.write("\n")
-		f.write(">gi|226791756|gb|GO545988.1|GO545988 Mdas9007J16_e521.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_194589.2| calmodulin-binding protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAGATTATAACTCAATATATTTTCAAGAGAAGGAAGGATACTTC\n")
-		f.write("AACATTTTTCGTATTCTAATGTATTCACTTCTTTGTATCATTTCAAAATACATATATATAACTTACAAAC\n")
-		f.write("CACTTTCTGATTCTATCATACATGGTTTACAAGGTGCAACAAATCGAGGTGGTCATCGAAAGGGTTCGAT\n")
-		f.write("CGGCGCATGTTCTTCAAAAAAAGCTGCTGCCTCAAAGCACTCGGCTGTTTCTAGCGTTGATGCCCTCGCA\n")
-		f.write("TCAACTTTGTACAGCAGCCCCAGATTGTACCAAGCAGAGGGGTTTCCTCTGTCAAGTCGTAGTGCATCCA\n")
-		f.write("TGAGAAAGCTTCTAACGACTGGTAGAGATTGGCCACCGAACTGTCTGAGTATACAGGCAGTGGATATCAA\n")
-		f.write("GCTTGGGACGTGGGTAGGTTCGACATCTAATGCCTTCCTGAATGATTCCAAAGCTTCTTGCTGGAGACCC\n")
-		f.write("TTGGCTTCGTAGAGTAAACCTGTAGAGTGCCATCTGGAAGCAGAATGAGGATTGATGCTCTGGGATTTTG\n")
-		f.write("AAAGGCAGACCTCAGCATCCCGCCATTGGGACAAGCTTGTATATAAATTAGCTAAAT\n")
-		f.write("\n")
-		f.write(">gi|226791728|gb|GO545987.1|GO545987 Mdas9007C14_e495.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566740.1| expressed protein [Arabidopsis thaliana] dbj|BAB01857.1| dbj|BAA85220.1 gene_id:MYM9.15 similar to unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CATGCTAATCATACATGATCTAGTACAACATTTCAAAACAAGGGTTCTCAAATATACATTCATACCCAAA\n")
-		f.write("ACACCCCCATCACAATACACCTTTAACATTTAACAGATTTGAATGAAATCAGCAGTTCCATTCTCTCCAA\n")
-		f.write("ACTAGGGTTCCACATCCTGTAATTATATCAAGTTTCCATGTCAATTACCTCTTGCACATCTTGTGATGAC\n")
-		f.write("CTCACACCCTCTGTTGTAAGGATTCGCCGCCGCAGCGTGACAATTGTAATAAGAAGCCCCTGGTTTTCCA\n")
-		f.write("CAGGGAACCAAGTCCCTGTTGAGAGTCCCATAACTTATGTACTTCTTCTGCATTGCCAGAATTCTCCTGC\n")
-		f.write("TGCTCTCTGACTCCATCTCTGGCTCTGTCAAGCACTCCCCAATCTTCTTGCTGCAGACGCTTCTTCCCCC\n")
-		f.write("CATGGCAGCCTCGATTTCGCTTCCTTTGAGTGGATGATTCAGGTCAAGAACTGAAACCCCATTGCAGATT\n")
-		f.write("GAGAAGTGGATGTGGATT\n")
-		f.write("\n")
-		f.write(">gi|226791727|gb|GO545986.1|GO545986 Mdas9007D21_e498.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAACTTTGAAGACATACTCAATAATATCAGTCAAACTAGGCAAAGT\n")
-		f.write("GAACACCTAAAGCTCTACCTTGAAAATAACCTGATTATCTATCTACATCAAGACAGGCAACAAACAGACC\n")
-		f.write("CGAAAGACGATGAAAGAGTAGAAGTGTCATTGTAAATTCCAGAATTATAAAAAGGTCGTACCCAGTGCAC\n")
-		f.write("AAGGCTCCCGCTTTACGCAAGGTCTGGGAGAGGTGAATGTCGGCTAGCCTTACCCCCATTTATGGAGAGG\n")
-		f.write("CTGCTCCCCAGTCTCGAACCCGAGACCTACCGCTCATGCGCGAAGGCACTTGTCATTGTAAATTCCAGAA\n")
-		f.write("TTATGAGGAAA\n")
-		f.write("\n")
-		f.write(">gi|226791726|gb|GO545985.1|GO545985 Mdas9007A14_e487.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_199600.1| NADH dehydrogenase 10.5K chain-related protein [Arabidopsis thaliana] dbj|BAB11336.1| NADH dehydrogenase 10.5K chain-like protein [Arabidopsis thaliana] gb|AAL38780.1| putative NADH dehydrogenase 10.5K chain [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("AATTTGTTCTTAATGGAAGATGGAAAATACATGAATTATTCAAACTACAACACACGCATTACTGCGTAAG\n")
-		f.write("CAACCCAAATAATCATCTTACACAAAAAACGCCTGATCTAAATAAAGGGCAGGCGATCAAAGGAATAAAT\n")
-		f.write("TTCCCGTGAAGGTAAATTTATTTCATTTCACACTGTCGATTATCAGGCTTTTAAAGACTCCCCAACTTTA\n")
-		f.write("ACAAGTTCCTCTAGTGCCTTCGAAATCTGTGGCTCTGTTAAACCTTCCAATCGAACGCCCCTCTCAACAC\n")
-		f.write("CCATGTCATATCTAGCCCACAACTGAGGTTCAATCCCTCTGCATTCACGAATCAAGATGGGCAATTTGGG\n")
-		f.write("GTTCGCACTCTTCAAATCCTTGTAATTCTTCTCCACAAATGTTCTGGTGGATGCGCTTGAAGGGGACGAT\n")
-		f.write("TGGCAAAGCAAAACCCTAATCTCCTTCAAGTTCTGAGATAGCTTCCCTCTCCATGCCATTTTCTCCCTCC\n")
-		f.write("CCCTCTCTCTCTCTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791725|gb|GO545984.1|GO545984 Mdas9007K14_e525.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTATATAAAAAGCAAAGAGAGACATACAAAAAAATTATGAAGGAAAAAAAAAACAAGTGCTTGGTCCAT\n")
-		f.write("GAAATCGTTCGTTCATATAATTCTTGTACCACTGAACTGTCCCCTCTTCCACCGGCGCTTCGGCCTAACT\n")
-		f.write("TCGGATATAAAAGTTCCAAGGGGAGCACAACCCGATGATCGTATTGTGACACAAGGCCAACCGACAATAA\n")
-		f.write("CAAAAAGGCAGCTGGCATAAGGCCAATTCCTTCTAGCAGGAATGAAACAACAAAAAGGCAGCTGGCATAA\n")
-		f.write("TGCCAATTCCTTCTAGCAGGAACGAAAACACAACAACAAATGGCGACCAAAACAAATGAAACCTAAATTC\n")
-		f.write("TCAACTGTGCACAACCATAAACGCTTCCTTTGCACCGTGTCATTGGAGCAGCCTGGCGCCAAGTTGGTCT\n")
-		f.write("TTCACCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791724|gb|GO545983.1|GO545983 Mdas9007A17_e488.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTACAATTAAAACATTCCAATTTCTTCACTAAAATGCAACACTTTA\n")
-		f.write("CATGAGAACAAGCTAGGAAACCATAAAAATGAAAAAAGAAAAGTGAAAGAAAAGGAGACTCTTAGAACTA\n")
-		f.write("CTTAGAGATCTGCCTAAAGCATATTATAAGACATATTCGATCCAATTGACAGGGCTACGGGCGTTACAAT\n")
-		f.write("CGTTTTACTTTATCACCACATATCCGA\n")
-		f.write("\n")
-		f.write(">gi|226791723|gb|GO545982.1|GO545982 Mdas9007P05_e547.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATACTAATGGGGCAGGAAAAACCACCTTTTATCCTTTTAACCATTTAAAAACGGCATTCATGCAAATAAC\n")
-		f.write("TCCAGTATTGATACAATCAAATGCGATTCCGGCAACGGAAGTTGAAAATTCAAAAGCCGAAACTGCTCGT\n")
-		f.write("TGTCCCTTCACTAAACAAAAAAAATCAATTGTCGTCCTCCTTTAACTCAAAAACTATAATAAACATTGAT\n")
-		f.write("TTGAGTCCTGGTAAATACAAATGGGAATTCAAGTGTGACCGCTACAGAACAAACATTCTGGTTTCCACAA\n")
-		f.write("CCTTCTCCTCCTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791722|gb|GO545981.1|GO545981 Mdas9007F21_e505.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179548.1| senescence-associated protein- related [Arabidopsis thaliana] pir|E84578 probable senescence-associated protein 5 [imported] - Arabidopsis thaliana gb|AAD10165.1| putative senescence-associated protein 5 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAAACTTAGTTTCCTACTAGAATTTCACTGCCTGTCAATCATCTAT\n")
-		f.write("CCATCCATAAAGTCCAGATAGAAAAAGAACATACGAATATGTACACTGACTACACTAGTCACAAACAAAG\n")
-		f.write("ACTCATCGAAAGTCATCAAAAGATAAGAAATTGAAAACAAACAGACGGTTTGTTGTGTTTGGATACTGGT\n")
-		f.write("TAAGCCCGACCCTGCTTGTTCCGGCGGAAGAGTTCCTCCGTTTGGGCGTTCTTGAAGGCGCTACAGGCGA\n")
-		f.write("CGAGATAGACGCAGATGAGGATCACCACAGCCACAATAAGGATGACATTGACCCTCCTCCATTCTTTCCT\n")
-		f.write("CAGGTTCCCCAAAAGTCCAGCCCTGCAGGAATTGCAGTTGTAGCACAAGAGGTTTTGGTCATTGTTCCAT\n")
-		f.write("ATCAAGCAGTCCGGGTCAGCTCCTGGGTTCACTGGGTTTATCCACAGTGTTGGATTCACATAGTTGTATC\n")
-		f.write("CACACATTGTTGGAGGTTCACAACATCCTGACTGAAGGGGAGAGATGTGAGCATAGAGGAACTGATCAGC\n")
-		f.write("TGACATGTATTGTTGTGTAAGCTTANGGCAAGTATCAGACTCAGCCAAACAAGTCCTTATTTTCTGCCAA\n")
-		f.write("GTCGAAGAGTAAGTAACATAGTCCCTCAGCCACTTGGAAAACCCTTTCAGCCGGT\n")
-		f.write("\n")
-		f.write(">gi|226791460|gb|GO545771.1|GO545771 Mdas9004H11_e284.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG16977.1|AF184076_1 ACC synthase [Prunus armeniaca], mRNA sequence\n")
-		f.write("GAATGAATGAACAATATTTCAACTGTGCGATTTACAGGTTTCGGAAATTTTCCGAATTCGTTCCATAACA\n")
-		f.write("ACCGGAATATCTTTTTCAGTCAACGTTGTAAAACAAAACCGAAACCATCCGGGTTCAATACAATGACATG\n")
-		f.write("ATGAACCGGGAGTTACATTTAGCTTAGCTACATTCAACAACCTATCCCAGAGCTCAAGCTCCCCTTTCTC\n")
-		f.write("GCTGTAAGAGCGGATTAACCCGCTCATGTCAGCCCAACAGCTGAAACCCCCATTGCTCTTTGTGCACTCA\n")
-		f.write("ATGCCCAATTGCTTCAAACCTGTCACAAATTTTAGGTACATTGCACGGAGCCTTTCCCTACTAGTATCAA\n")
-		f.write("TGAACTTCCGGATAAATTTGGTGTCTGAAAGCATAGAGATGAGCAACCGTTGGGATGGGGAGGAAATGGA\n")
-		f.write("CGAGAACCTTGTCAACTTTTTAGCGGCAGCCAGAACATTCTTGTTATAGGAGTAGATAGCGCCAGCCCTA\n")
-		f.write("AAACCTGGAAGAGAGAGGTCTTTCGATAGACCATATACTATATGAACTCTGTTCTGGTCCAGATCTTCCA\n")
-		f.write("ATTCAACAATTTCTGCCATGCTTACAAACTCTTCACTAC\n")
-		f.write("\n")
-		f.write(">gi|226791459|gb|GO545770.1|GO545770 Mdas9004C19_e267.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S68805 pectin acetylesterase (EC 3.1.1.-) precursor - mung bean emb|CAA67728.1| pectinacetylesterase precursor [Vigna radiata], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTCTTATTGAATTTTTACCTTCAATTTACACAATCACACTCCTAGAAT\n")
-		f.write("AACTTTATTCGCAACACCATACAAGATGCCCGCTACCACTTTCAAATCAAAGCTCAAAAGAATAAATATT\n")
-		f.write("ACCCAGAACCATAAGTACGTAGGCCATTACATCAATAGGGTTTAGGTCATATAGCTCATAAAAACCATAT\n")
-		f.write("TTTCGACATAATGAAATTAATCTTCCTGATTGTTTGAGTCAAATTCACGGTTTTTGCAAGTGGGATTGCA\n")
-		f.write("CGGGTAAGGGCAATCAAACTTTTTGAACGCAGTGCGGTCGTAATACCAGTCTCCAACTGCCTTTGCAATT\n")
-		f.write("GTCGTCTTGCTCAACATAGGAGAGTCAGCTGCCAGCCATGTCTCCTGCGTTCCAATTTGGCAGTGGGCAA\n")
-		f.write("AGCAAGAGTCTATGAACGCTCCATGAGATGAAGAAATCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791458|gb|GO545769.1|GO545769 Mdas9003H06_e209.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("GTTCAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACACTACAAACAAAAGTACA\n")
-		f.write("AAACAATTCCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACCGG\n")
-		f.write("GTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAATCCA\n")
-		f.write("AACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGT\n")
-		f.write("CATCGGCAAGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCGAGGGGTCC\n")
-		f.write("GCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTC\n")
-		f.write("TGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCT\n")
-		f.write("TGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGGGAAAACGCATCCAAGAGC\n")
-		f.write("TCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTGGCGAAGGTCTCTGGGTCAGCT\n")
-		f.write("GAGAGTCCGGCGGTGTCCCAGCCGTAGTCACCGGGGA\n")
-		f.write("\n")
-		f.write(">gi|226791457|gb|GO545768.1|GO545768 Mdas9003G16_e204.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF86906.1|AF223358_1 triose phosphate/phosphate translocator precursor [Mesembryanthemum crystallinum], mRNA sequence\n")
-		f.write("TTTTTTTTTTAACAAAAAACATGATAGAGAAGTAATTAAAACATTATCTAGAATCTCATGAGACCATTAC\n")
-		f.write("AAATTAGAATGTCTTCGTACTCTCAATCAATGGGGAAAAAAAAAGGGCAGGGGGGGGGGGCGGCGGAGGA\n")
-		f.write("GGAAAAGAAACAAACTATGACATAGATAACAGATACTCAATTTGCAATTTCTTCTGAAGGGAATTTACAA\n")
-		f.write("AATTTACAATGCATGGTTCCCTCCATGTCCGTTCTTCGTTCCGTCTCATGCCGCTTTTCCTTGTCGTTTC\n")
-		f.write("TCTTCTTCTATCTTGGCCTTGAGGTAAGAGTAGATTGCCACTCCTGCAATTGCAATGGCAGTTCCAATAC\n")
-		f.write("CGGTTTGTGTTGAAATCTTGTTACCAAAGATCACGATCGAGAAGCCAATCACAAACACACGCTTCAGCAC\n")
-		f.write("GTTTCCAACTGCGTGCGTAAGAGGCGCCACTCTCTCCAGGGTGTTGGTGGCCAACTGGTTATAGAGATGG\n")
-		f.write("TAAAACAATCCAACCCAGAAGAGGTCGGTGACGAACTTGACAAGTCCTACTTTAGCAATTGCATCATTGA\n")
-		f.write("AGCCATACTTGATCAGTTGAGGTCCCTCTAAGATGAGAGCGGGTGGAATGCAGACAATGAGTGCAATGAT\n")
-		f.write("TGAAATATAAGCATAGAGATTTGTACTATCCATATCAGTCATGGCTTTCTTTGAATAGATACTCCTGTAA\n")
-		f.write("GTGAAGGAGATA\n")
-		f.write("\n")
-		f.write(">gi|226791456|gb|GO545767.1|GO545767 Mdas9003G14_e203.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD40837.1| OSJNBa0086B14.9 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTAACAACAAACTAAACTAGATTAGACGAAATATTGTTCAATAGTGAG\n")
-		f.write("GCTGCAGACAACCAAATGAACAAAAAAACGCAAATTAAACACATCTAGGTCCTTCATATTCTACGAAACA\n")
-		f.write("AACCAACCAAAAGCAGCAGCCGCAGATCTTAAAAGGAGTTTTGCCTATAACCATAATATCTGACCACATC\n")
-		f.write("TTGTCCCCAACCCTAACCTCCTATATCATCCTATCACAAAAAAACACCACCTTCTGTCCGCAAAAGCATT\n")
-		f.write("ATACATATCAGTCTTCAATCCCGTCTGCAGCCACCCCACAATTAACCCCGCTCCATTGCAAGGCAGGCGG\n")
-		f.write("GTTGCTTAGGCACGCTCACCCCTGATCCTCCTGGCAAGCTGGATATCCTTCGGCATGATGGTAACCCGCT\n")
-		f.write("TGGCATGGATAGCGCAAAGGTTGGTGTCCTCAAACAGACCCACCAGGTAAGCCTCAGCAGCCTCCTGCAG\n")
-		f.write("TGCCAGCACTGCATGGCTCTGGAAACGCAGATCAGTCTTGAAGTCCTGAGCAATTTCACGAACAAGCCTC\n")
-		f.write("TGGAATGGCAACTTCCTGATCAACAGCTCAGTA\n")
-		f.write("\n")
-		f.write(">gi|226791455|gb|GO545766.1|GO545766 Mdas9004B19_e261.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86339 protein F2D10.18 [imported] - Arabidopsis thaliana gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTATAACGAAGGCAAACTGAAATTCATTGAACATAAGGAGGATCATTAAGTACAGAAATGACGA\n")
-		f.write("CATTGGAATCGCGGGGAGAAGACGATCCTGAAACTGAATCCGATTTTGTTTTTGTGTTTTCCTAAAAACT\n")
-		f.write("AACCCCTAAAACAAAAGGTAGAGAGCCAGCAACTTATCCCATAGTGAAGAAAAGGTGCAGGCAGGCCTTT\n")
-		f.write("CAATTATCTTCTAAGCAACCCTACACATATCGCTTCTCCCCCTCCATTCAATTCCCGTTGCTCTACTCAT\n")
-		f.write("CGTCGTCTTCCTCCTCGCCGCTCTCGTCCTCATCCTCATCATCATCATCATTTACCTCAGACTTGGACTT\n")
-		f.write("GTCAGACTCTTCTTCGTCAGCTTCATTAGGTCCTTCAGCTAATTGCTTGTTGTATGCCTGAATGTTCTTG\n")
-		f.write("TTATACTCAACCTTCCTCTTATCTGCCTTGGCTTGATAAGGAGCTTTCTCAGCATCTGACAACGATTTCC\n")
-		f.write("ATTTCTCACCGCCAGCCTTACCGACAGCAGCAACCGACTTGTTGTTTGGATGATCCTTCTTGTACTTCTC\n")
-		f.write("TCTGAACTCCTCCATGAAGACGAAGAAGGCACTCGCAGGCCTCTTCGGCTTGTTCGGATCCTTTCCGGCT\n")
-		f.write("TTCTTCGCCGGCTTCTTGCTCGCTCCG\n")
-		f.write("\n")
-		f.write(">gi|226791454|gb|GO545765.1|GO545765 Mdas9003J01_e215.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAAGGAAAAACGGGGGCCGGGGCACCCCGGCCAATTTAATTTTTTTTTTTTGGGAAAAAATTGGGCGGG\n")
-		f.write("ATAAAACCCCCGCAAAACCCCCCCCCCTTTTTTTAAAAACCCCCCAAATTTCCAGTAATTTTAAAACCCC\n")
-		f.write("CCTTTCCATTTTCCCCCCCGAAAAGGGGGCCAAACCCAAAAAAAAAAAAAAAAAGGCCCCCCCAAAAGGA\n")
-		f.write("ACCCCCAAAAAAACCCCAAACCACCCCCCGAAAAACTTCTGCCCCAACCCCCCCCCCCCAAAAAAAACCC\n")
-		f.write("CCCCCCCCCCCGGAAAATCCCCCCAC\n")
-		f.write("\n")
-		f.write(">gi|226791448|gb|GO545764.1|GO545764 Mdas9003P03_e242.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD28640.2| geranylgeranyl hydrogenase [Glycine max], mRNA sequence\n")
-		f.write("AACGTATTATTAGTTTAAGATACTATTACAATGATATTTTGAAGGAGAAATTTTACAACGATTCTAAAAC\n")
-		f.write("AATGACGGACATAGAAATTTATATATGCTAGATCTCATTACACAAACTTGGAATTTCCACTCAAATCTGT\n")
-		f.write("TGAATTCAAAGAGTTCATTCCTCGTTACATGAGGAAAAACAAAAAATTACACAAACAACAAGGCTTCCTC\n")
-		f.write("CTTTCATACAGTAATTTTCTCCATCTCCCTCCTGAGTGCATTAGCCCTAACCAAGCTCCCAATGGTATTC\n")
-		f.write("ACAGCCAACTTCAAATCCTCCCACGGATTCCCCGGCACCACCCTCTTGTACAAGTAGCTATCGAACGTCA\n")
-		f.write("TCTTCTGCACGTACTCATCCGCACACATCTCCACGAACGCTTCCCTCGCGGGGTTCGACCTATAGAACAC\n")
-		f.write("CTTCTGCAACACATCCAACACCTTGTAAGTAGGCCAATAGGTCTTGTCCCACTTCTCCAAGTACGTCCTC\n")
-		f.write("AAGTCCGCCTCATTCACCATCCTCTTCCCATTCTCCGACCCCTCAACTATCGCCTCGGCACACATCCTGC\n")
-		f.write("CACTCTTTGCTGCAAAGTAGATGCCTTCACCAGAACACTTTGTTACGTACCCTGCTGCATCACCAACGAG\n")
-		f.write("TGCTACTCTGCCCGCCAACCTTCGTGGGCCGGG\n")
-		f.write("\n")
-		f.write(">gi|226791447|gb|GO545763.1|GO545763 Mdas9004C18_e266.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL49750.1|AF452012_1 aquaporin-like protein [Petunia x hybrida], mRNA sequence\n")
-		f.write("TTTTTTTTTAGCGTAAAAAGGTAGATTAAGGTAGAGAGAGGAGAGAAGACATTGTAATCATAAAAAGAAA\n")
-		f.write("ACACCACTACTCATGAACAATAATTAATGAACATAATTAAAGTTAAGTAATTAGATTATAAATAGAGAAC\n")
-		f.write("CCAGAAAGATTGAAAGATCATCATCCATCCTCTCAATACACACACTAACAAACAGAGAACAAAATATCAA\n")
-		f.write("CAGAACATTAATGTAGCTTTCTTTTCTTCAATCTTTGTTTTAGTTGGTTGGGTTGCTGCGGAAGGATCCC\n")
-		f.write("AACGCCTTGAGCGCCGCCGCCCTCAGAATGTACTGGTGGTACGCCGCTGCAGCCAGTGCTCCCACAAATG\n")
-		f.write("GTCCGACCCAGAAGATCCAGTGGTCATCCCAGATTTTATCGTTGTTGTAGATCACAGCAGCGCCGAAACT\n")
-		f.write("CCTTGCTGGGTTGATTCCAGTTCCAGTAATGGGGATTGTTGCGAGGTGCACAATAAACACAGCAAACCCA\n")
-		f.write("ATGGGCAGTGGAGCCAAAACAGGGACGTGGGAGTCGCGTGCGCTCCTCTTGGGGTCGGTGGCCGAGAAGA\n")
-		f.write("CGGTGTAGACGAGGACGAAGGTGCCGATGATCTCAGCTCCCAGAGCTGTGCCCTTGCTGTAGCCACTAGC\n")
-		f.write("CACAGAGTTGGCGCCGCCGCCGA\n")
-		f.write("\n")
-		f.write(">gi|226791446|gb|GO545762.1|GO545762 Mdas9003B18_e180.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTCTTTAATAACTCATTTATTAAGTACCAAAAAAAATACAAGGGCCGTT\n")
-		f.write("TATTATATTTTCCTTTGCAAGGCCTAATGCAAAGGGCGAATAATGAAGTTTTCAAACTAGCAGATAGATG\n")
-		f.write("AGCTTCTGGAAAATTATATGAAGCTCAGTTTATTGTAAGTAAGATTCACGATAGTTTCCATTTCGCTTCC\n")
-		f.write("GTTGAACAGCCTTGGAAGAAGTTGCGGAGGCAGCAATTCGAAGGTTTTTGAATGGCACGCTTATGCATAC\n")
-		f.write("ACGTCTAAGCCCCAAGTCTTGGAAGGTAGACTGGTACGATACTTCCTGTCGATACTGTAGATGAGCTGCA\n")
-		f.write("TGTCTTCATCGCTCAGCTGGAATTCAAGAACCTCCAAATTCTCTTTCAATCGCTGAATTTTCGATGATTT\n")
-		f.write("TGGAATCACTGCTGTTTTCCTCTGAATTCCCCACCTCAGACAGATTTGTGCCACGCTCTTTCCGTATTTC\n")
-		f.write("TTAGCCACATCATTGAGAACTGGATCATCCAAAGGTGAA\n")
-		f.write("\n")
-		f.write(">gi|226791445|gb|GO545761.1|GO545761 Mdas9003B06_e177.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P16059|PSBP_PEA Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|JS0771 photosystem II oxygen-evolving comp, mRNA sequence\n")
-		f.write("TTTTAGAGAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAAATAAATT\n")
-		f.write("CTTATGCAACACTGAAAGAACTTGCAGTGCTCTCTACAAACTTCCTTGCTCCTTTGAACCACCTCTTGTC\n")
-		f.write("TCCGGCTTGTGCCTTTAGAATGTAGAGCTTGCCGTCTTTCACGGTGGCTGTGATAATCTGGTGCTTGCCT\n")
-		f.write("CCTTCATCTCCGTCGGCTGTCCTTGTCAACACAGATACCTAGTAGTACTGCTTTCCGTCAATCACTCGAC\n")
-		f.write("TACAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCACCCTCGGATTCATTCTTGCC\n")
-		f.write("AAAGTAGGATTGTTTGCCTAGCAAGTAGTCCACCTTCGCGAGGAATTCCTCGGGGGAGCCATAGTCGGCG\n")
-		f.write("ATGGATTTCATGTCGGTTAAGGTGATTGTGACGGACACATTGCTGTTGCTGTCGAAGTTGTCCTCGTACC\n")
-		f.write("TAAGAACTTGACCATGGAAC\n")
-		f.write("\n")
-		f.write(">gi|226791444|gb|GO545760.1|GO545760 Mdas9011H23_e848.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_680161.1| No apical meristem (NAM) protein family [Arabidopsis thaliana] emb|CAC35884.1| ATAF2 protein [Arabidopsis thaliana] gb|AAL87335.1| unknown protein [Arabidopsis thaliana] gb|AAM91696.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CAGAAATGGCACTTTACGGAGAGAAAGAATGGTATTTCTTTTCGCCAAGGGACAGAAAATATCCAAACGG\n")
-		f.write("TTCAAGGCCGAACCGGGCAGCCGGAACCGGGTACTGGAAGGCGACCGGGGCTGACAAGCACATTGGAAAA\n")
-		f.write("CCCAAGGCACTCGGGATTAAAAAGGCACTCGTGTTCTACGCTGGTAAAGCCCCCAAAGGAATCAAAACCA\n")
-		f.write("ATTGGATCATGCACGAGTACCGCCTCGCCAATGTCGACCGGTCCGCCGCCGCTGCCAAGAAAAATCAAAA\n")
-		f.write("CCTGAGGGTACGTCCGTCTTTCCATTACCCTTTTTCTCTTTTACCATTATACCCTTGGACCCACACACGT\n")
-		f.write("CATTGACCGTGGACCATATTTTGTAATTTGACTAAAATATAAATGCATTTATTATTTCGACGGTCAGCTC\n")
-		f.write("AGATGTGCAATCTAAAAGAAAGAATATCATATCTAATTATATTTTACATATTATAAGATGAATGTATTAA\n")
-		f.write("GTAAATTCATGTACCTTTTTCGGTCTCTCAAATTTTGATCATGTCATCAATGCCTCTTAAGAATGCATGT\n")
-		f.write("TGTAACTTCTGGTAGATTAAATTAGAATATCGCTTTCGAAAAATAAATGAATCCGGCTTCAAATATTTTA\n")
-		f.write("ATCTCAATTTTGTTTAATTACTCAGAGTGCTTATCGTTCTAAATTGATGTTTATGTAATGCAGCTTGATG\n")
-		f.write("ATTGGGTACTATGCCGCATATACAACAAG\n")
-		f.write("\n")
-		f.write(">gi|226791443|gb|GO545759.1|GO545759 Mdas9011M20_e875.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAATTAAAGAATTATAAAAGATCAATACATAGAGAAATAAGAGAGGGACATATATATTGTCACATATACT\n")
-		f.write("GGCTAGATATATATTTATCTAGCTAGCTACTTGACAGTTATTTGTACGTAATTACTTGACAATTAAAAGA\n")
-		f.write("AGAAGAAGCAAAGAAAAGTGAACAAGACAAAGATGGAAGTAAGACCATGAGGGTGGAAGTGCATTCTCAA\n")
-		f.write("ATGAACCGATTTAGAAAAATAAGGTGGCGGGGGACTGTAAGGATTTACAGGATAAAGGCTTGGTGGTACT\n")
-		f.write("ATAGAGGGCGCAAATGGAGGCCGATTCGGGATTAATGAGGGAACATCTGCCGCGGGAGGAGAGGACGAGG\n")
-		f.write("ATCCGCAAGTGTCTTGACACGGAGGCCTCACAGGTGGTGGTGGTTGAGGTTGAGGGTGGGTGGTGGACAT\n")
-		f.write("TCACGGAGAGCTGGTGGTGGTGAAGAAGGAGGCGCAGGAGGTGGTGGGCATTCAATGATAACCGGTGGTG\n")
-		f.write("GCGGCAATGGTGGTGGTGAAGAAGGAGTCGCAGGAGGTGGTGGGCATTCAATGATAACTGGTGGTGGTGG\n")
-		f.write("CGATGGTGGAGGTAGAGATGGCGCGGGGCATGGGTTGGGGCACTCATTGCA\n")
-		f.write("\n")
-		f.write(">gi|226791435|gb|GO545758.1|GO545758 Mdas9011H02_e843.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n")
-		f.write("CCACTAGGGACGACCGGATCGGTGTTTGCACCGGAATCTTCAAGCCTGATAATGTGTCCCAGGAAGATGT\n")
-		f.write("TGTCAAGATTGTTGACACATTCCCCGGTCAATCCATTGATTTCTTCGGTGCCCTAAGGGCTCGAGTTTAT\n")
-		f.write("GACGATGAAGTGAGGAAGTGGATTTCCGGTGTTGGAATTGACGGGATTGGGAAGAAGCTTGTGAACTCAA\n")
-		f.write("AAGAAGGTCCCCCGACTTTCGATCAACCTAAGATGACTCTGGAGAAGCTCCTTCACTACGGACAAATGCT\n")
-		f.write("TGTTCAGGAGCAGGACAATGTGAAGAGAGTCCAACTGGCTGACAAGTACTTGGCCGATGCAGCCCTTGGA\n")
-		f.write("GATGCAAACCAGGACTCCATTAACCGAGGAGAATTCTATGGAAAGGCAGCCCAACAAGTTAATGTACCAG\n")
-		f.write("TCCCAGAAGGCTGCACTGATCGAACAGCTGCAAACTTCAACCCAGCAGCAAGGAGTGACGACGGTAGCTG\n")
-		f.write("TCAGTACGAGTAATTGGAGCTGAAGAAAATAAATATTCTGTTTGCTGGGTTATTGATATTTTCTTTGTAA\n")
-		f.write("TTTGCGCTTGTATTTCTATGGAAATTCTTGCAATTATTTTGTTTTAATTATTAAACAAGCTATTGATACT\n")
-		f.write("CCGGCTATTGAACAGTCGATAAGAACATAATGTTATGTTGTTGAGAATATGTTGTCATTGTCGCAAACAA\n")
-		f.write("AACTTCACAACATGTTATCAATACATTCATG\n")
-		f.write("\n")
-		f.write(">gi|226791434|gb|GO545757.1|GO545757 Mdas9011N23_e879.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T02946 hypothetical protein 3 - common tobacco chloroplast gb|AAA84680.1| unknown protein prf|1102209C ORF 3, mRNA sequence\n")
-		f.write("TTTTTTTTCAAGAATTCTTCTTACTTTAATACATAATACATAGGTCATCGATTCAGCATTGGATAAAAAA\n")
-		f.write("GATAAAACGTGGGATGAAATACCCATTTTTTCCAATCAAATAACGGATTCAAATCATTTTATCGACATGA\n")
-		f.write("GTGTTTTATATCGAAAAAAAATTCCAACTATTTGTTTTGAAACCATTTCTGTCTTAACTTATTAACTAAC\n")
-		f.write("ATAGTAGTAGAAAGAATACCATGCTGCATCTGAACTTCAAACGGTTTAGCTTTAACCCTGTTAATGGTTT\n")
-		f.write("ACATTATTGGTTGATAGAGAATCAAAGTAGATTTACCAATGAATCGCGAAATGCTATGGTTCTTCAATTT\n")
-		f.write("TTTTTTCAGAAGAAATTCGCGGAATCATGCACCTTTTTTTTTCGCGTTATAACGAAAAAATGCAGTTGGT\n")
-		f.write("CGTATCCAGCCTATTCTTGAAATAAACAACTCGCACACACTCCCTTTCCAAAAAAAATCAACACACCAAG\n")
-		f.write("CACTACGCTTAGATTTATTAGATTTGTTGCTAAAATATCGGTATTAAACCCGAAACTCCCGGCGGATGGC\n")
-		f.write("CAATAACCCAAGGAAAGGAAAGAATCGGTTACATTTTTCATATGATATCCTCTTTCTTATAGATAGACTA\n")
-		f.write("ATTATTTTATTTATATTATTTTTGTATTATTTTTATTATGAATTTCCCTATTTCTAAATAGAATATACTA\n")
-		f.write("AATAGAGTCAAAAAATA\n")
-		f.write("\n")
-		f.write(">gi|226791433|gb|GO545756.1|GO545756 Mdas9011C24_e824.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566564.1| expressed protein [Arabidopsis thaliana] dbj|BAA94980.1| gb|AAF26101.1 gene_id:K14A17.9 similar to unknown protein [Arabidopsis thaliana] gb|AAK55691.1|AF378888_1 AT3g17020/K14A17_14 [Arabidopsis thaliana] gb|AAK91493.1| AT3g17020, mRNA sequence\n")
-		f.write("TTTTCCGGTAAGCGAATCACCATCTCGGACTACCAGTTGAATTCACATGTATACGGTAGCAAATGCATGT\n")
-		f.write("AACGTAGCGATATACGCACATCAAATTTGTCCAACTTCAACATACCGCAACAAACAGTTGAAACCTTAAT\n")
-		f.write("TTAACTAGATCTTATTAAGATAAAAACTAGATCTTGTGCAAACTAAAAGGCTCAGTTGCAGGTAAGGAAG\n")
-		f.write("CAATTGACGCATTGCACTTATTTACCCAGCACGCATTGAGGACAAAGGATTTAGCTGGCATGGGACTCAG\n")
-		f.write("AACTAGTCTTGACGACAGTAACTGGGCACGAAGCATTATTTACGATATGGTTGCTGACACTGCCCATTAT\n")
-		f.write("AACCCTCTTAAGCTTGCCAAGGCCTCTGTTTCCAATAACAAGGAAGCTCAAGGGGGTCTTGTCAATTGCC\n")
-		f.write("TCGAGAATCTTCTCACGGGCATCGCCCCAGTAGATCTTCATCACCACCGTAACCTCTTTCTGCGTCGCAG\n")
-		f.write("TGTCGGCGATGTCGATGGTTTCAGCGTCAGGCGTCACTCCATATTTCTTCATGATGGTGGGATCAGAAAA\n")
-		f.write("CTCCTTCACAGGAATCAAAGGTGAACCGGTGACGCCCCACAGCTGCATCTCTCCCTGCTCGTAGTTCTCT\n")
-		f.write("TCAGGCCG\n")
-		f.write("\n")
-		f.write(">gi|226791432|gb|GO545755.1|GO545755 Mdas9011N11_e878.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGGAGGTAGAAGGGACTTGCAGACGAGAGAGAAGGACTTTTCTGGTAAATGGGGTCGTCGTCTAGGT\n")
-		f.write("GGTCAAGGACGGCGTGGAAGATCTCGTCGGTGAAGAATATCGAATGGGGTTGTTCATGGCGGCGGTGAGG\n")
-		f.write("CTGAGCTTTTTTCATGGGAGTGAGTTTCCTGCCTGAGTCGATAAGAGTTTGAAGGCGACAAACTAAATTA\n")
-		f.write("ACAGAAAACGGTGGATTTGGGGGAGACGGAAGGATATCCAGAATGTCAAATTACGATAATGTCCTTGTTG\n")
-		f.write("ACCATCGACTCTATTCTTTCTTATCAGGGGAAGTAAGCATACGCGAAACAAGAAATTTTTAGTTGTGACG\n")
-		f.write("GAAATACAATTGATATATTACGAGTTTTAATACGAATTATGAAAAATTTTACTTTTTAAATTATTAACTT\n")
-		f.write("TTTAACATATATATTTCACCGTTTGTTTAGTGACGTGATGTACCATCCGATATACCGATAATGGAAAATT\n")
-		f.write("TGAGCTCCAACACATAGAACGAAAAAGTCCATCATAATTAATTAACAAATTCGTATTTAGTGAGTTGAAC\n")
-		f.write("CTTTTACTTATAAATAATAAAAAAAAAGAAATATCGAAGAGATTGTAACGTAAATGTCAAGGTTACGCAT\n")
-		f.write("\n")
-		f.write(">gi|226791431|gb|GO545754.1|GO545754 Mdas9011D03_e825.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTATATCAACCATGTAGTCATTTAGCAAGTAGGAAAAGCTCACATGCCA\n")
-		f.write("TTGCATACACTAATCCTTTGATCCCATCACAATCTTTACAAGCTTAAGCAGTACATATCATGATTCAGAT\n")
-		f.write("AATTAATCATGGTCTACTGATTAAAAAACCAAACATGATATGCACATAAAGATACTTCTCTAAGAAGAGA\n")
-		f.write("AGGCGTCAATAATGGTGGTGTGGAGCGGGTCACTCAAATGGGTAGCCCAGTTGTTAAGTGGTCCCTTCCC\n")
-		f.write("GGTGACGGCGGCTTGCACGGCAAACCCCAGAAACGCAACCATGGCGAGGCGGGCGTGCTTGATTTCGGCC\n")
-		f.write("AGCTGAAGAGTGGCCTTCTTTTCCGGGTCAGCAGCAAGGCCCAACGGGTCGAAGAACTTGCCACCCGGGT\n")
-		f.write("ACAACCTCTTTTCCGGGTCGAGCTCGGCGTTCCTCTGGAACTCGATGTAGCCAATCACTAGAACTTCGAT\n")
-		f.write("CCAGATCAACGTGGTTAGTGAGAAAGGGAAGTGGTTGACCCAAGTAGGACGACCCTTCGATGAGCTCCAC\n")
-		f.write("CTTTCCGGCGTCTTGCCATGTGATCCCGGTGACGGACTCGACAGTGAGAGCACCGAGCGTGGCGAGCATG\n")
-		f.write("GCCCACCTTCCATGAATCAGCTCGCACTCCCTAAACCTCTG\n")
-		f.write("\n")
-		f.write(">gi|226791430|gb|GO545753.1|GO545753 Mdas9011D18_e828.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CAAAAAATCCCCCCTGAATTTTTGCCTGTCAGGAAGGGGCAAAAATAATTTCA\n")
-		f.write("\n")
-		f.write(">gi|226791429|gb|GO545752.1|GO545752 Mdas9003E01_e190.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n")
-		f.write("TTTAAATAAGGATATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAA\n")
-		f.write("ATTCGAAAACAAAAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGA\n")
-		f.write("AACCCTAATCAAGGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTACGTACAA\n")
-		f.write("CAACAATATTAATTACGACGAAGAAACATGATGAAACATGAACAACAACAACAACAACAACAACTTAGTA\n")
-		f.write("GCCTGCAGGCTTGTAGGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGG\n")
-		f.write("ATGAAGGCGTTGGGATAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATC\n")
-		f.write("CGAACATGGGCAGCTTCCACATTGTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791423|gb|GO545751.1|GO545751 Mdas9003F15_e199.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46293|RS16_GOSHI 40S RIBOSOMAL PROTEIN S16 pir|S41193 ribosomal protein S16 protein - upland cotton emb|CAA53567.1| RS16 protein, 40S subunit [Gossypium hirsutum], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTAGCAAAATAAACTAGTAATTAATTGAAGCATGTCATACTTAATATGGTAACCATT\n")
-		f.write("CAATATCCAACATACTCAAAAACAACAACAAAGTCTCGATGATCAAAATTCTGGAAAATTATAAAATACC\n")
-		f.write("CATTTAACTTCCAACTTCTTAAAACAAAGTCAATAACCCTTAAACCATAAACCGAAACGAAGAAGCTAAA\n")
-		f.write("CCTGTCCATCTTTCGCCTTCCATTTGCCCCAAATCAACGGTAAGACTTCTGGAATCTAGCACGAGCACCA\n")
-		f.write("CGACCGCCGAACTTCTTGGGCTCGCAGCGCCTCGGATCAGCAACAAGGAGGGTCCTGTCATACCTGACCA\n")
-		f.write("GAATGTCCTTAATCTCCTTCTTGCTCTGCTCATCCACATATTTCTGGTAAAAAGCGACGAGAGCTTTGGC\n")
-		f.write("GATGCTCTGGCGGATGGCGTAGATCTGGGAGATGTGACCGCCTCCCTTGACGCGGATGCGCATGTCGACA\n")
-		f.write("CCGGCGAAGCGCTGTCGTCCGAGGAGTAGGATGGGTTCGTAGGCCTTGAAGCGGAGGATCTCGGGCTCGA\n")
-		f.write("CGAGCTCGATTGGGCAGCCATTGATCTTGATGAGGCCACGGCCGCGCTTGCAGTATGTGACAGCGACAGC\n")
-		f.write("GGTCTTCTTGCGGCCAAAACACTGCACTGACTCGATTGCGGGAGTCGCCATTGCTA\n")
-		f.write("\n")
-		f.write(">gi|226791422|gb|GO545750.1|GO545750 Mdas9011M01_e870.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB40974.1| isopentenyl diphosphate isomerase 2 [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TTTTTTCGGTCAAGAAAAAACTGAAAACGCCTTACGAGTCCAAACTTATTGGAACAGGAAAAAAACACCA\n")
-		f.write("ACTATAATAAAACCACAATCAAAGTTTCCCAGCAGACTCGATTTAAGTCAACCTGTGGATGGTTTTCATG\n")
-		f.write("TCAGCAGCTTCCTTGATGGTGTTTTTCTCAACATGGTCCCACCACTTGAACAAGAAGTTGTCCACCACGA\n")
-		f.write("GCCTGAACCAAGGCGACAGCTTCAGACCTTCCTCCCCGGCATCTGCCTTCCTCAACAGCTCTTTCAGCTG\n")
-		f.write("CTCCTGGTTTACGTACTTGATATCAGCTACCTCGTCAGGGTTCGGATGCACATTAACATCACGTACAGTG\n")
-		f.write("AAGAGAAGGTAATCAAGTTCATGTTCTCCCCACTTGCCATCAGAAGGTGCCTTGTACAGCATGCGACCCA\n")
-		f.write("ACGGGATAAACTGATCAACTGGCACATCTTCAGCAGGAATACCGAGTTCATCCAAAAGCTTCCTTTGAGC\n")
-		f.write("AGCATTTCTTACCCCAAGAGAGTTCTCATCAATAAGCTCGGATTCACGATACAGCGGATGGCTGCAACAG\n")
-		f.write("GTGTTTGTCCACACAAGTGGAAAT\n")
-		f.write("\n")
-		f.write(">gi|226791421|gb|GO545749.1|GO545749 Mdas9003A08_e171.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_180375.1| glycosyltransferase family [Arabidopsis thaliana] pir|E84680 probable glucosyltransferase [imported] - Arabidopsis thaliana gb|AAC98458.1| putative glucosyltransferase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTATGTTAATTGAGAGGTTGCTTAATTAACATTCCCAAATAATTGGAGTTGTGCAACAAACGTGCATAA\n")
-		f.write("TAGAGTTGCGGAACCAAAGGAAAAAGCGCACATATAAATTCTAGATGTGTTACATTTCTAGTATTTCGGC\n")
-		f.write("CTTTTACATCGCTAATGAAGCGTCTTATGGCAGCCAGTCAATGAGATGATGAAGAAGAAACCACATGATG\n")
-		f.write("GCAATATGGAAGTCACATTTCGTGTCTGAAATTTTTTTCCTTCACATTTACTAATGAATTGAGATAAGTT\n")
-		f.write("CTTTTGTGATGACCCATTTAGAGCCACTGCATCCTCCAATGTTTGTGTTGCTTTCATGACCTTCTTCTGC\n")
-		f.write("AAACCGTCACCCGATTTTCCACATATCAGAACGGTTGATCTTCTCTGCTACCTCCACCCTTCTAACTGGT\n")
-		f.write("TTAACCCGATCACAAAGATTGAGTCCAATGCCCCAATCATCAACTACTAGTTTCCTATTAGTGATTTGGT\n")
-		f.write("CAGCCACTAGAGGAAAACATAGCATGGGAACACCACACCGCATACTTTCCAGTATAGAATTCCATCCACA\n")
-		f.write("ATGCGTTAAGAACCCTCCTACTGCTGGATGTGAAAGCACCTNCATCTGAGAGCACCATGGCACCATCAAC\n")
-		f.write("CCTCTATCTTT\n")
-		f.write("\n")
-		f.write(">gi|226791420|gb|GO545748.1|GO545748 Mdas9003F11_e196.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q42954|KPYC_TOBAC Pyruvate kinase, cytosolic isozyme pir|S41379 pyruvate kinase (EC 2.7.1.40), cytosolic - common tobacco emb|CAA82628.1| pyruvate kinase [Nicotiana tabacum], mRNA sequence\n")
-		f.write("ATGCATTGTTCAGCAAACGATCCTATTAGTAAACGTATTGCATAAAGTCCCATATCGCAATATCGGCAAA\n")
-		f.write("TTATGTAGCTATCAAAGCCTGCCCATCACATACACTGATGACGGCGGTAAATGTAAATGTTTTCGCATCC\n")
-		f.write("AAAAACACATATTAAACGAGCCAAGTCAAAATCATAAGCATTGTCATTGGCTAATTTTGAAAACGCCAAA\n")
-		f.write("AAGGAAAGGATGAACATCACTTCACGGTCAAAATCTTGATCACTGATGCAGTTCCATCACGGTGCAAAGC\n")
-		f.write("CACAACAGCATCTCCGTTCTTGCAAAGCCCCTTTGTCTTGGCATGTTGAAGGGCAAAGTCCAGTGCTTCT\n")
-		f.write("TCGGTCGTCTCTGCATGAAAGGCCCTAAAAAATCCCGCGCTTAAAACTGGAACCAACCCACGGAAAATCA\n")
-		f.write("AACTATCCTTGCTGGAGCTTCATCACTGCATGACCAGTCAAATGAATCTGTCTTGATCTCGGGGACAACA\n")
-		f.write("ACAGACAGTATAGGCATGCCAGGTCTGTACTTGGCCACCAGCTTTGCAGTACTTCCTCCTCTGGTTAGGA\n")
-		f.write("CCAATATAAGAGCTGCTTTGGACGAGTTG\n")
-		f.write("\n")
-		f.write(">gi|226791419|gb|GO545747.1|GO545747 Mdas9003E06_e191.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P24922|IF52_NICPL Eukaryotic translation initiation factor 5A-2 (eIF-5A) (eIF-4D) pir|S21059 translation initiation factor eIF-5A.2 [similarity] - curled-leaved tobacco emb|CAA45104.1| eukaryotic initiation factor 5A (2) [Nicotiana plumbaginifo, mRNA sequence\n")
-		f.write("TAGCAGAAACTAAGAGAAAACCCAAGGGGGACAGAGAAGCTCGGTCATCAACTTCGGAGGCAGAGAGATG\n")
-		f.write("TCGGACGAGGAGCACCAGTTCGAATCCAAGGCCGACGCCGGCGCATCTAAGACCTATCCCCAGCAGGCTG\n")
-		f.write("GTACCATCCGCAAGAATGGCTACATCGTCATCAAGGCCAGACCTTGCAAGGTTGTTGAAGTCTCCACCTC\n")
-		f.write("CCAAACTGGAAAGCACGGTCACGCTAAGTGCCACTTTGTGGCAATTGATATTTTCAATGGAAAGAAGCTT\n")
-		f.write("GAAGATATTGTTCCTTCGTCCCACAATTGTGATGTTCCCCATGTCAGCCGTACTGACTACCAGCTGATTG\n")
-		f.write("ATATCTCTGAGGATGGCTTTGTGAGTCTTTTGACTGAAAATGGAAACACCAAGGATGATCTGAGGCTTCC\n")
-		f.write("CACTGACGACAGTCTGCTTACCCAGATCAAGGACGGGTTTAATGATGGAAAGGATCTTGTGGTGACCGTC\n")
-		f.write("ATGTCTGCCATGGGTGAGGAGCACATCTGTGCCCTCACGGACATTGGTCCGAAGAATTAAGTATGATGCT\n")
-		f.write("GTATCAGTAGCTCTAGCTGATGGCACGACCTTCTTTGCTTT\n")
-		f.write("\n")
-		f.write(">gi|226791411|gb|GO545746.1|GO545746 Mdas9011O12_e881.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q41229|PSE2_NICSY Photosystem I reaction center subunit IV B, chloroplast precursor (PSI-E B) pir|T16963 photosystem I chain PSI-E, isoform b - wood tobacco gb|AAB31705.1| photosystem I subunit PSI-E [Nicotiana sylvestris], mRNA sequence\n")
-		f.write("CTAGAGTGACCAACAGCAGCACAGAAATCTCACACATGGCTAGCTGTGGCATGGCATCAGCTGCCTCAGG\n")
-		f.write("CTTTGTGGTAGCACCAAACGTTGCAACCACCAACTCAGGCTCAGCTTCCAGCCGGAGTAGCATGCTGTTT\n")
-		f.write("TTCCCTTCAAAACCCAACACCAACACCAGAAGCAATGCCAGGTTTGTGATCAGGGCAGCTGAAGAAGCCG\n")
-		f.write("CTGCGCCTCCGGCCGCCACCACGACTGCACCAGAGGGGGCAGCTACCCCTAAGCCTAAGCCACCACCAAT\n")
-		f.write("TGGACCCAAGAGAGGCACTAAGGTGAAGATTCTTAGGAGGGAATCCTACTGGTTCAAAGGCATTGGATCT\n")
-		f.write("GTTGTGGCTGTGGATCAGGATCCGAATACCCGTTACCCTGTCGTGGTCCGATTCAACAAAGTTAACTATG\n")
-		f.write("CCAATGTGTCCACAAATAACTATGCTTTGGACGAGATTGAAGAAGTTAAATGAGTTTGTAGTAGCACTGT\n")
-		f.write("AAATTGTAATCTTAATTAAATTGTCCTTCTCTCAGTTTCTTCCTTACTTGTTGGTGCCCTTTATTTGTGT\n")
-		f.write("ATCAAAACCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791410|gb|GO545745.1|GO545745 Mdas9011J12_e853.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q43517|FER1_LYCES Ferredoxin I, chloroplast precursor pir|T07175 ferredoxin [2Fe-2S] I precursor, chloroplast - tomato emb|CAA99756.1| ferredoxin-I [Lycopersicon esculentum], mRNA sequence\n")
-		f.write("TTTTTTTTCAACAGAGAGAGATTCATACAAGGGTGAGTTTACAAGATACAATGATCTCCATACCACAAAT\n")
-		f.write("GAGAGTACAAAAACATTAAGCAACTCATATAATTAGAAACAAGACAACCTTAACCCGAAACAAACTAAAG\n")
-		f.write("CCAGATCCAACCAGCCAGCAGCCATCAAAACATGACATCATCATGAGAAAGCTCAAAAGCACTTAACCAG\n")
-		f.write("TAAGCTCCTCTTCCTTGTGGGTCTCAAGTGTGACGTCAGACGACGGATAAGCCACACAAGTGAGCACAAA\n")
-		f.write("TCCACCGTCCATCTGCTCATCATCCAAAAAGCTCTGGTCCGACTGATCCACACCCCCACTCACAACTTTG\n")
-		f.write("CCGGCGCACGAGGAGCAAGACCCTGCCCTGCATGAGTAGGGAAGGTCAATCCCGGCCTCCTCCGCCGCGT\n")
-		f.write("CGAGAATGTACACGTCGTCGGGGCACTCAAACTCTTGTGGCCCTTCTGGTGTGAGCAGCTTCACCTTGTA\n")
-		f.write("GGCAGCCATCGCCACACGCCCTCCGCGGTTGGCCTTGAGCCCGAAAAGGGCCTGACCGACGTTGGGGGAT\n")
-		f.write("AACCGCAGGCTGGTCATCGGCTGGCCGCGGATGAAGGAGGTGCTGACCATGGTGCCTGAGAGAGCTGTGG\n")
-		f.write("CTGCCATGTTTGTTGGTTTGCTTTGGTTGCAAGGCTTTTTCCTCGTGCCG\n")
-		f.write("\n")
-		f.write(">gi|226791409|gb|GO545744.1|GO545744 Mdas9011C19_e823.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86459 Hypothetical 55.6 kDa protein - Arabidopsis thaliana gb|AAG26075.1|AC069299_1 hypothetical protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTCTAATAATATCAATATATTACGTGAAGAAAAAACCTTACATACGATACGACATATTATTATTAACA\n")
-		f.write("CACCACTGTAAATCCATTTCATAATTCATTTTCCTTTTTATTGTCCTCACGAAAACTAAGCCATCAGTCA\n")
-		f.write("CGTGGCATTATTTCCCACCGAAACCTTATTGCTAGGGTTTTGCCTCATTACTTGCAGAGATCTAGTGGAG\n")
-		f.write("CACCACAGAGACAATCATTCCCCAGAAACGCCGAAGCACCAAACTTGGTGGCCGGAAGCGGTCCGCAAAG\n")
-		f.write("ATGATTGTGGCTGACGTTCAGTCTCTCCAGCCCTGAAACTCCACTCGGCACCTTCCCGAAAACCAAATTC\n")
-		f.write("CTCGACAAGTCCAAATACTTCAACGTCTTCACAATCCTCAACTTCTCCAAATCAAACTTCAACTTATTCC\n")
-		f.write("CAGAAGCCCAAAACCCCACCAAGAAATCGGTCCTGTTCAGCAGCCCGACTGGACTCCCCGAAATCTCGTT\n")
-		f.write("CTCTGATAAATCGATGTAATCGTAGAAATACGTCTCCGCCGGCTTCCAGTCGTCCAATTTCAACTTGATC\n")
-		f.write("CCACACTTTGCGAGCTTCAGAGAGTAGATGATCGGCGACGACGTCACCCATTTTGGAATTTGCTTCAGAT\n")
-		f.write("GGAAGCTGTTGTACGACAAATCCAGGGACTCGATGCCT\n")
-		f.write("\n")
-		f.write(">gi|226791408|gb|GO545743.1|GO545743 Mdas9003D02_e186.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F96755 hypothetical protein F3N23.22 [imported] - Arabidopsis thaliana gb|AAD55649.1|AC008017_22 Hypothetical protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTAAGAACAAAATTGCTTCACATTTCTGCCATCTCTTACATTAAATGT\n")
-		f.write("GAATTTAAACAATCTCAAGGAAAGTAAATACTCTCCAATACTATACATCTACCTCATTGCGACTTCTTGA\n")
-		f.write("CATTACCAAACGTCATCCTCTCTCCAGAAATGCTCCTCAAGAGCTGTTTAGAACACATGTTCTCAGCTGT\n")
-		f.write("TGTCGCGTTTTTCACACGGTTGGCTTTTACCCAAGCAGGTTCCTCGGGAACAAAGCGGGAGAATCCAAAT\n")
-		f.write("TTGATCAACAAGAGAACATGTTCCATAACCAGAATTGCAGCCAGGCCAGGCTCTATCTTCCATTTGCCCT\n")
-		f.write("CTTCATCATATAACCATACAAGAAGTGCGCAGTTGGTGCATATAGACATAACTACAAGAAACTGAAATAT\n")
-		f.write("GTTAAGCCAAGCTCCAATTGTTGTGGAAAAGCGTGGAGTTGGTCTGCGCAACATGGCAAGAAGCTTCAAT\n")
-		f.write("GCATCCGCCCTAATTTCAGTGATGTTGTTCAAAATTGCAAAGGCAAAAGCAAGGGGGAATGCACAAGCAA\n")
-		f.write("ACATCATGATCATTCCAAACTGCAATGCCACCTCAAGAAAGTCATCAAACAGCCCATCTTCCAGTTCCAT\n")
-		f.write("GCCAATGCTAGCGGAATATGAAGGCTTCAGGTACTCTTTCTCTACCCTAGAAGCAAACCGAATCTTCCCT\n")
-		f.write("GTCGTTGAACCTTTTTCACACTTTTT\n")
-		f.write("\n")
-		f.write(">gi|226791407|gb|GO545742.1|GO545742 Mdas9003A06_e170.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("GGAAACCCTAGCTTGGTCCATGCACAGAGCATCTTGGCCATCTGGGCTACCCAAGTGGTGTTGATGGGCG\n")
-		f.write("CAGTTGAGGGATACAGAATTGCCGGCGGACCCCTCGGAGAGGTGACCGACCCTCTTTACCCCGGAGGAAG\n")
-		f.write("CTTCGACCCGTTGGGCCTTGCCGATGACCCAGAAGCCTTTGCTGAGCTCAAGGTGAAGGAGCTCAAGAAT\n")
-		f.write("GGAAGGTTGGCCATGTTCTCCATGTTTGGATTCTTTGTCCAGGCCATCGTCACCGGAAAGGGACCATTGG\n")
-		f.write("AGAACCTTGCCGACCACCTTGCCGACCCGGTCGCCAACAATGCCTGGAACTATGCCACAAACTTCGTTCC\n")
-		f.write("CGGAAAGTGAGAGCTCGGAATTGTTTTGTACTTTTGTTTGTAGTGTTGTCGGTGATGTAAATTTGGTACC\n")
-		f.write("AAGTAATGGACAACAATTGAT\n")
-		f.write("\n")
-		f.write(">gi|226791406|gb|GO545741.1|GO545741 Mdas9011L22_e869.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T17007 major allergen Mal d1 - apple tree emb|CAA96537.1| major allergen Mal d1 [Malus x domestica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTGGACATTAAACTTTTTATTATTATAGTAATTTTATTCAAACAAAGGTAGCAAT\n")
-		f.write("ACCCTTAGTAAGTTAGTATTTTTCCAACTAAAGCATCACTGAATGAAAAAAACATAAGAAACTTGAACTT\n")
-		f.write("ATGCCATGAAGACAACAAGGGTAACACACAAATTACATGTATCGATAACATCAGATTTAGTTGTAGGCAT\n")
-		f.write("CAGGGTTGGCCACGAGGTAGGCTTCAAGAAGCTTGAAGAGACCGGAAGCCTTCTCTTTGCCAGCCTTAAC\n")
-		f.write("ATGCTCTTCCTTGATCTCAACATCACCCTTAGCATGGTAGTGGCTAGTGGTTTTGATGATGGATCCTCCA\n")
-		f.write("TCAGGAGATGCGATCAATTTGGTCTCATAAGTGATCTTCTCAAGCTTGTCAGACAAGGTATCTCCTTCAA\n")
-		f.write("TCATAGAGTAACTGTATGTAAAGTTGTCTTTGTCAATCCCATTGACCCTTTGCTTAACATACCCGTATTG\n")
-		f.write("GCTGCCTTCACCAAAGGTAACTTTCTTGATGGTTCCAACACCTCCATCGCCTTCGATGATTTCAGTGCTT\n")
-		f.write("TTAATTGCTTGTGGAGCAATCTTCGGGATGAGGTTATCGCCATCAAGGATAAAAGCCTTGAACAATCTAG\n")
-		f.write("GTGCAGGGATGACAGAGGTGAACTCGGTTTCATATGTGAAAACACCCATGATGAACTTTGGATTTGGAAA\n")
-		f.write("ATGA\n")
-		f.write("\n")
-		f.write(">gi|226791399|gb|GO545740.1|GO545740 Mdas9003F16_e200.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGGATCTGAACCATGTAACCTCTTAATTTCAGACACATATTGTAGCAC\n")
-		f.write("ATAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATTTACATCACCGACAACAATACAAACGAAAGT\n")
-		f.write("ACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTGGCGA\n")
-		f.write("CTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAA\n")
-		f.write("TCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCT\n")
-		f.write("GGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTACGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGG\n")
-		f.write("GTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAGAT\n")
-		f.write("GCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGAGACCGCCCTCGCTGAA\n")
-		f.write("\n")
-		f.write(">gi|226791398|gb|GO545739.1|GO545739 Mdas9011K09_e860.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P10708|CB12_LYCES Chlorophyll A-B binding protein 7, chloroplast precursor (LHCI type II CAB-7) pir|S07408 chlorophyll a/b-binding protein type II (cab-7) - tomato emb|CAA32197.1| chlorophyll a/b-binding protein [Lycopersicon esculentum] gb|AA, mRNA sequence\n")
-		f.write("ATAAGTTTGTAGGTCACCAGCTGATTTCATACATATTGGAACGAAGGTTCCAAAGAGATTTTTGTACACA\n")
-		f.write("AGCACATCAAATTACAAGTTTTTAGTCCTACAAATTTCCCTTGGAACAACACAATACTTCTCAGCCTCTT\n")
-		f.write("TTCCCGGATCGATGACAACGTTGCTCCTTCTCCTCCCGCACTTGAAAGCCCCAGTTAGAATTCTCCTTCG\n")
-		f.write("TTCCTCACTTGGGGGAGAAAGAAGCGAAAATGGTGGCATGGCCGGGATCAGCGAGGTGAGCGAAGAGGTT\n")
-		f.write("GTCGATGGGGCCAGTCCCAGTGTAAATGTGTTGAAACCAAGCCCCCATCACAGCCAACATAGCTAGCCTT\n")
-		f.write("CCGTTCTTAATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGT\n")
-		f.write("CGAACCAGAGCCCTCCCGGGTACCCTACATCTGTCCCGGTGAGCTTGTTGTTGGGGAAGATTGGGTCGGT\n")
-		f.write("GTTAACGGAGCCGGGCTTGAGGATGTCGGCCCATCTCCTCCCCTCGGCCCACCCGATCAAAACAAGCTCA\n")
-		f.write("ACGACGAAGAGAGTGGTGGTGTCTGTGAAGTACTCTTGCTCTCCGGCTGTGTACCATGACGGGGTGTTTA\n")
-		f.write("GAATG\n")
-		f.write("\n")
-		f.write(">gi|226791397|gb|GO545738.1|GO545738 Mdas9011D09_e826.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196073.1| beta-ketoacyl-CoA synthase family [Arabidopsis thaliana] pir|T48449 fatty acid elongase-like protein - Arabidopsis thaliana emb|CAB85559.1| fatty acid elongase-like protein [Arabidopsis thaliana] dbj|BAC41850.1| putative fatty ac, mRNA sequence\n")
-		f.write("TTCTAAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACATGGTGGATCCTGA\n")
-		f.write("TGGCAACGTGTTTGCTGGCTCTTTTCTATGGTTTCTCCTGCCTCTGTAAGTTACTTCTCAGAAGGAGAGA\n")
-		f.write("CCAGGCATGCTATCTGCTGGCCTACGAGTGCCACATGCCACCAGACGACCTGAAGCTCAGCACTGATTCA\n")
-		f.write("TGCGTGAAAATCGTCTTGCGGAACAGGAATCTAGGACTGGAAGAATTCAGGTTTCTCTTGAAAACTATTA\n")
-		f.write("CCCATTCGGGCATTGGCGAGGAAACTTACTGCGCAAGAAACATCATCCAAGGCCGACAAGAAACTGCAAC\n")
-		f.write("CCTAGAAGATGAACTTGCGGAGATGGATGGCATCATCTTTGACGTGCTGGACAAGCTTTTCGCTCGGGCT\n")
-		f.write("ACCTCAATTTCTCCGTCGCAAATCGACATTCTTGTCGTCAATGTGTCGATGTTCTCCCCTGCACCCTCCC\n")
-		f.write("TATCTTCACGTATAGTGAATCGTTACTAGATGAGGGACGACATCAAGAGCTTCAACCTCTCGGGAATGGG\n")
-		f.write("CTGCAGTGCGACCCTCATTGCCATTGACGTTGTACAACACTTGTTCAAGTCTCACAAGAATGCGAATGCC\n")
-		f.write("ATCGTTGTAAGCACGGACTCGTTGGCTCCTCATTGGTATTGCGGCGTAGAAAAATCCA\n")
-		f.write("\n")
-		f.write(">gi|226791396|gb|GO545737.1|GO545737 Mdas9011H05_e844.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09756|CB23_SOYBN Chlorophyll A-B binding protein 3, chloroplast precursor (LHCII type I CAB-3) (LHCP) pir|S01962 chlorophyll a/b-binding protein 3 precursor - soybean emb|CAA31419.1| chlorophyll a/b binding preprotein (AA - 32 to 231) [Glycine, mRNA sequence\n")
-		f.write("TTCTATCTGTTGTTGTCCATTACTTGGTACCGAATTTACATCAGCGCGACAACACTACCACAAAAGTACA\n")
-		f.write("AAACCGTTCCCAGCTCTCACTTTCCGGGAGACGAAGTTTGTGGCATAGCTTCGCAGCTTTGATTGGCGAT\n")
-		f.write("CGGGTCCGCCCGGTGGTCCGCAAGGTTCTCCCCTGGTCCCTTTCCGGTGACCATGGCCTGGACCAGGAAT\n")
-		f.write("CCACCACATGGAGAACTTGGCCTACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCATAGGCTTCT\n")
-		f.write("GGGTCATCGGCTACGGCCAGCGGGTCGAATCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCCAGGG\n")
-		f.write("GTCCGCCGGCCAGTCTGGATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGAT\n")
-		f.write("GCTCTGTGCATGGACCGTCCTGGGGTTTCCCTTGTAGTCTAGACCGCCCTCGCTGAAGATCTGGGCTCCG\n")
-		f.write("GCCTTGAACCACACTGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGG\n")
-		f.write("\n")
-		f.write(">gi|226791395|gb|GO545736.1|GO545736 Mdas9011E17_e832.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA80688.1| chlorophyll a/b-binding protein, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTAGTTCAAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACA\n")
-		f.write("CTACAAACAAAAGTACAAAACAATTCCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAG\n")
-		f.write("GCATTGTTGGCGACCGGGTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGG\n")
-		f.write("CCTGGACAAAGAATCCAAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTC\n")
-		f.write("AGCAAAGGCTTCTGGGTCATCGGCAAGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTC\n")
-		f.write("ACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCC\n")
-		f.write("AGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAA\n")
-		f.write("GATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGGG\n")
-		f.write("AAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGGAGTGGATCACTTCGAGCTCACGGTTCTTGGGC\n")
-		f.write("GAAGGTCTCTGGGTCAGCTGAGAGTCCGGGCGGTGTCCCAGCCGTAGT\n")
-		f.write("\n")
-		f.write(">gi|226791388|gb|GO545735.1|GO545735 Mdas9011K14_e861.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTGAGAAGATGAGTACCACTGGAACTGGCTTTAGCAACCACGCTTTCACCATGCCCGGCGGTCTCCAAG\n")
-		f.write("TAAATGAGCAAACTAGCAAGAACAACACCCCATGCAACTTCCAGATGCCTCTGCACTACCCAAGGTACCA\n")
-		f.write("GAAGAGTGACTATGAGAGCATGCCTGAATGGAAACTGGACTGCCTTATGAAGCAGTACGGCCTCCCACTC\n")
-		f.write("ATTGGGGATGTCAACCAGAAGAGGAAGTTTGCCATGGGAGCCTTCCTTTGGCCTTCACAATACGAATGAG\n")
-		f.write("AAACCCTAGCTAGTAGCTTAATTGCTACGATTTCTAATAATATTCTACATATATATGGTATTACAAAAGA\n")
-		f.write("CTACTGGCATGCATGTATATAGTGAAATAATATTAATTGCTTTTTAGTAGTATCCCTTATTTAAGTACTG\n")
-		f.write("TCTATCTGTATTCAGCAGTGTATTACTGTGTACTTTTGCTATTAATGGAATCAAAATAAGGGTTGTAATA\n")
-		f.write("TAAGGTATGTGTTATCTATTGTATTAACCCGTTGTTTATGTCTAAAAAAAAAAAAAAAAAACTCGCCTCG\n")
-		f.write("TGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791387|gb|GO545734.1|GO545734 Mdas9011L02_e866.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564644.1| senescence-associated protein -related [Arabidopsis thaliana] dbj|BAC43242.1| unknown protein [Arabidopsis thaliana] gb|AAO42971.1| At1g53885 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CCAATTACCACTCATTCCATTAATTTTTCTCCTGCTTTGCTTTTTTGCAGTGTCAATTAACAAGAGAATG\n")
-		f.write("AAAAAGATCAAAAGAGAAATTAAACTATATATATATATATATGCATATGTCTAAAGTACAAATATCTTTC\n")
-		f.write("TTTGATGTCTGGTTTTCTCCTGTTGCAGATGTACATCTTCAAAAACATTAGTGTTGCGAGAGCCACGCCT\n")
-		f.write("ACTAGTGTTAGCATTACTACTCTTAGTAAGGCTGCAACGATATAGGCCACGCCTATAGGATGTTATCATT\n")
-		f.write("TGCTTGGTAGAAGCCTCTAATTCCTTCATGTCATCAATAACAATCTGTCTGTTCCTGCACTCTATGCTGC\n")
-		f.write("AAAAACCTAAATCACCTCTGTACATGTAGACCTCTCTATCAAGGCTTAATCCCTTGGTGCATAAGTGACA\n")
-		f.write("TGTTTTAAGAAAGCAAGAGAATTGCTCGAGGGAGCTGCAGGTTGTGGATTGGCTCAGTCTTAATGCAGAT\n")
-		f.write("TTCTCAATGATATTTGTCTTATTTCTTTGTGAATTCTGTACAAGGATTCCCAATCCAACAGCCACTGAGC\n")
-		f.write("TCCCATGGCTGGTTTTATCACTGATGCCCAGCTTATGGGCAGCTGGC\n")
-		f.write("\n")
-		f.write(">gi|226791386|gb|GO545733.1|GO545733 Mdas9003B21_e181.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGTTTACATACAAGCAGGTAGCTTAAAGATCATCTA\n")
-		f.write("TTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCCAGGCATTGTTGG\n")
-		f.write("TAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAA\n")
-		f.write("GAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCC\n")
-		f.write("TCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAA\n")
-		f.write("GGGGTCCTCCGGCAATGCGGTAACCCTCAACAGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAG\n")
-		f.write("AATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCT\n")
-		f.write("CCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGC\n")
-		f.write("CCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACG\n")
-		f.write("\n")
-		f.write(">gi|226791385|gb|GO545732.1|GO545732 Mdas9011O24_e884.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09755|CB22_SOYBN Chlorophyll A-B binding protein 2, chloroplast precursor (LHCII type I CAB-2) (LHCP) pir|S01961 chlorophyll a/b-binding protein 2 precursor - soybean emb|CAA31418.1| chlorophyll a/b binding preprotein (AA -33 to 223) [Glycine, mRNA sequence\n")
-		f.write("TTTTTTTTTAGTTCAAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACACTACAA\n")
-		f.write("ACAAAAGTACAAAACAATTCCGAGCTCTCACTTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATT\n")
-		f.write("GTTGGCGACCGGGTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTTCCGGTGACGATGGCCTG\n")
-		f.write("GACAAAGAATCCAAACATGGAGAACATGGCCAACCTTCCATTTCTTGAGCTCCTTCACCTTGAGCTCAGC\n")
-		f.write("AAAGGCTTCTGGGTCATCGGCAAGGCCCAACGGGTCGAAGCTTTCCTCCGGGGTAAAGAGGGTCGGTCAC\n")
-		f.write("CTTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCA\n")
-		f.write("GATGGCCAAGAAGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAA\n")
-		f.write("AACTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACC\n")
-		f.write("\n")
-		f.write(">gi|226791384|gb|GO545731.1|GO545731 Mdas9003F01_e195.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTCGAGTTGAAATGAACTTACTATTGACCATAAATTGAGACAACCAAGAATCACAA\n")
-		f.write("TCAAGTACATCACAATCAAGTACAAATACGGGCTTCCAACTGGAACCCGAGTTCTAAAACCCTCACAAAC\n")
-		f.write("ATTTCAGCAGACAGCACAAACCCATTCTTAGCATAGAGCATTAAGTATAGTCTTATCGTCAATAACACCA\n")
-		f.write("AGAACAAACCCATCATTACCATCTTTTCTATACACCACGAATGACAAAAAACCCGACCAAGCAAGCTAAC\n")
-		f.write("ACATCAAGCGACTACTATGACGATGGAGGCAGTGAGGAAGGCGACGAACGAATGAAGATGATGAGGAAAT\n")
-		f.write("ACATCATAGTGGCTTTGGTGAATAAACACCATTTGAAATAATACTCAAAACTTCTCATATAACTCCATAA\n")
-		f.write("CACTGGGCAATTCAAAGCATAGCATGGTCAAAACTAAGGCTCCACAATTATCTTTCCGGTAGCATGGCCA\n")
-		f.write("TCCATGGCTTTAGCCCAAG\n")
-		f.write("\n")
-		f.write(">gi|226791383|gb|GO545730.1|GO545730 Mdas9003A22_e175.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAAAATATATATTTTTAAAGAGGACTGAACCCAGTCAAAGCTCCGGCTAGGCCCTCAAGCCCAAATTAT\n")
-		f.write("ATTACTTGAAAAAACATAAAACGGGTGGGGCAAAGTGTAAACCCCGACAATCAAAAGTAAAATCATATAC\n")
-		f.write("AACCACTCTAAGCAAAACTCCATGAAATTTCAACCTTCAACAAATCATCTTCAATAATTTCATGATCACA\n")
-		f.write("AAACTCCTCACCAACATTTTGCAACCCTTCACCAACATTTTGTAAATGGAGGACCGGCTTTGAATGAATT\n")
-		f.write("AATTTAATTCATAAACTGTTACTGTTTGACAAAAGGCTTCTGCAGGTTCCCAAGTAAAATCACTCCTCCG\n")
-		f.write("GTGAATCTCCAAAAAAGTCAAAGTTTGCATATGCATTTTGAAAGTCTTCTTCAGCTATGTACCTGCTTTT\n")
-		f.write("TGGTTACTACAATATACTTCAGCAACTTTGGCTACTGCAAGGCCCATGCCGATGTCCTCCACCACAACAC\n")
-		f.write("AATTGTTTGCAGCTTGAATTTT\n")
-		f.write("\n")
-		f.write(">gi|226791382|gb|GO545729.1|GO545729 Mdas9011K15_e862.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09756|CB23_SOYBN Chlorophyll A-B binding protein 3, chloroplast precursor (LHCII type I CAB-3) (LHCP) pir|S01962 chlorophyll a/b-binding protein 3 precursor - soybean emb|CAA31419.1| chlorophyll a/b binding preprotein (AA - 32 to 231) [Glycine, mRNA sequence\n")
-		f.write("TCGAGATTTGTTTTGCAATGGCAGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCCGTGCA\n")
-		f.write("ACTTTCCCCGGGAGCCACCGAGCTTTTTGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCAAAAAA\n")
-		f.write("GTCTCCTCTGGCAGCCCATGGTACGGCCCTGACAGAGTCAAGTACTTGGGGCCATTCACCGGTGAGCCCC\n")
-		f.write("CAAGCTACCTCACCGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCCGGACTCTCAGCTGACCCAGA\n")
-		f.write("GACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCTCGGAGCTCTTGGATGC\n")
-		f.write("GTTTTCCCAGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAAGCCGTGTGGTTCAAGGCCGGAGCCC\n")
-		f.write("AGATCTTCAGCGAGGGCGGTCTCGACTACTTGGGAAACCCTAGCTTGGTCCATGCACAGAGCATCTTGGC\n")
-		f.write("CATCTGGGCTACCCAAGTGGTGTTGATGGGCGCAGTTGAGGGATACAGAATTGCCGGCGGCCCCCTCGGA\n")
-		f.write("GAGGTGACCGACCCACTTTACCCCGGCGGAAGCTTCGACCCATTGGGTCTTGCCGACGA\n")
-		f.write("\n")
-		f.write(">gi|226791376|gb|GO545728.1|GO545728 Mdas9003B15_e179.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566796.2| glyceraldehyde 3-phosphate dehydrogenase A subunit (GapA) [Arabidopsis thaliana] sp|P25856|G3PA_ARATH Glyceraldehyde 3-phosphate dehydrogenase A, chloroplast precursor (NADP-dependent glyceraldehydephosphate dehydrogenase subunit A), mRNA sequence\n")
-		f.write("TTTTTTACAAGATTCTCATTATTAATCAGAAAAGAAGAATAAAAGAAAAAGAAAGAAAAGTAGAAATTAT\n")
-		f.write("AAACGCAGAACGGTAAAAGAAAACCAAAAAACATGGATCTGGCCGCCGGGAATGACAAGTTGGAGGAGGA\n")
-		f.write("GGAGGAGCTAATTTGAATTTTGAAATGATGATCACTTCCAGTTGTTGGCGACAATGTCAGCCAAATCAAC\n")
-		f.write("AACCCTTTGGGAGTAACCCCACTCGTTGTCGTACCAAGCAATGACCTTGACCATGTCATCGCCCATTACC\n")
-		f.write("ATTGTCAATGAAGAGTCGACTGTGGAGGAGACATCTGTGCACCTAAAGTCGACTGAGACAAGGGGCTCGT\n")
-		f.write("CACAAACAGAAAGGATACCTGCAAGCTCCTTCTCGGCGCTGTCTCTGAAAGCAGCGTTCACCTCTTCTGC\n")
-		f.write("AAAGGTCTTCTTAGTTACTTGGACAACAAGGTCCACCACCGACACGTTTGGGGTGGGCACACGCAGGGCA\n")
-		f.write("ATGCCATTTAGCTTGCCCTTCAGACTTGGAAGGACTAGGGCCACGGCCTTTGCTGCACCAGTGGAGGTGG\n")
-		f.write("GAACGATGTTGAGAGCAGCAGCCCGT\n")
-		f.write("\n")
-		f.write(">gi|226791375|gb|GO545727.1|GO545727 Mdas9011E16_e831.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|EAA30389.1| hypothetical protein [Neurospora crassa], mRNA sequence\n")
-		f.write("TTTCATCATCATCATCGTCATCTATCATTAATACTAACTGAAGTGAAGAATTTATATACATGTATGATTC\n")
-		f.write("CGATGTTCGGAGAATTGTGTCTTTGTATTTCTGCAATTCATATCTCCAAATATTTGCTGTGTTTCCTTAG\n")
-		f.write("AGTTTCTGCATAGCAACGATGTCAGATGATTGGACGAAATCTTCGAAACCCTCAATCTCTTCTTGTAATT\n")
-		f.write("CGGATAGACCAACTTTGTCATCTTCGATGACTAAATTGATTTGAAGCTTCTTGATACCAAAGCCGACAGG\n")
-		f.write("TACTTGTTTGGATGCTCCCCAAACGAGACCATCTTTCTCGATTCCTCGAACAGAAGCTTCAAGAGCTTTC\n")
-		f.write("ATATCAGTTTCATCATCCCAAGGCTTGACGTACATCGTGACAACAGACTTGGCAGCAGGCTTAACTTTGC\n")
-		f.write("CTTCTTTCTTCTTTTTATATTCAGCAAGCCGCTCATTTCGTAACTTCTCAGCTTCAGCGTCTTCCTCTTC\n")
-		f.write("GTCATCACTTCCGAAAAGGTCTATGTCGTCGTCTTCCTCCTCTTTTTTGACATCTTTTGCGAGGTTCAAG\n")
-		f.write("GTAACATCGGAGGCTTCAGGTCCATAAATCGAGTATTCAACTGAAGCATCACCGGGAATGCTAGAGAATT\n")
-		f.write("CATTGGCGTATGAACCAATATGCTTGTACCATCTAGCTGCGCTGGGGAACTTCTCTGTATCTGGGGCTGA\n")
-		f.write("TTGAAGGGCTTTAAATG\n")
-		f.write("\n")
-		f.write(">gi|226791374|gb|GO545726.1|GO545726 Mdas9011F11_e837.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCCTCACCATCCGTCGCAAGCGGCTGAGCTTGGTGGACAACTGGGTGGTGTACGACGGAGAAACCGAGGT\n")
-		f.write("GAATCCGCGGTTCTGCGCGACGAAGCACGTGAACATCCTCAAGAACAAGTGCTTGGCGCACATGACCTCA\n")
-		f.write("GCCAACAGCTGCAAAGGTAGTGGCTCGTCGAAAAACTACGACAACAAGAACGCGGTGTTTTATCAGATGG\n")
-		f.write("AAGGGTCGTACGCGACGCGGTGCTGCGCGGTGTACGACAGCAAAAGGAGGAGGGTGGCCGAGATCAAGAT\n")
-		f.write("GAAGGAGGCAGTGGGCGGAGTGGCGTTGGGAGTCGACGTCTTCCGCCTCATCGTGCAGCCCGATATGGAC\n")
-		f.write("ACGGCGGTGGCCATGTCCCTCGTCATCTTGCTTGACCAGATGTACGGGACGTCGAGGCGGTAAAAAGTTC\n")
-		f.write("AAATTCCTTTTACTTCGTCACCCACCTTTTTCCCCTTGGTGGATTCACATCTCCTCCTCCTCTATAAATT\n")
-		f.write("CTATGTTCCAAATCTCTCTTTTTTGGTTTGATCTCGTCGATCTCTTGTTGTCTCTCCGATAATCCCACTT\n")
-		f.write("GCGTTTATCTTTTTTCTTTTTCTTTCCTTTTTTTCTTCTTCTTTTAAATCGGAAAAAATCAATGAAGCTT\n")
-		f.write("GGTTTTTTCCTTTTATATAAAAAAACCAGCTTCTTTAAGTGGGATGTATATATGACTTGGAAAAAACAAA\n")
-		f.write("GTTTA\n")
-		f.write("\n")
-		f.write(">gi|226791373|gb|GO545725.1|GO545725 Mdas9011P03_e885.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|JQ0956 myb-related protein 306 - garden snapdragon gb|AAB23528.1| Myb oncoprotein homolog {clone 306} [Antirrhinum majus=snapdragons, J1:522, flowers, Peptide, 316 aa], mRNA sequence\n")
-		f.write("TTTTTTCCAGAGCAAAAGCAGATACGTAAGTATGGATATACTTTAATTAATTTACACTTTTCTGTTTTTT\n")
-		f.write("GATTAAGGTGGTTTTATCTTTCTGCTTAGGCTAGTTGACAAAATAAAAGGAGTACTACAAGGATGGCTAG\n")
-		f.write("CTAGCTACAAAGCTCAAAAGCCTAATTCCAAAGAAATTAAACAAAAGAAACCCTAATTAAGTACTCGATC\n")
-		f.write("ATCTTTTGTTTTAAACAAAAGAAACCCTATTTATAGTACTTGATCTTGTTTTTTTTTTGTTTTTTTTTTC\n")
-		f.write("AAAACAAGCCTGCACCATTCTCCAATGATATGTTGATTAGGTCTTCGTGGGCATGAGGTGCAGCATCGTC\n")
-		f.write("AAGGAGCCACTTCTCCAGCAATGAGAGAGGGACTTGTCCCTCCAAATTGGGCTTGCTCTCATCCTGAAAC\n")
-		f.write("AGACAGCTTGCCTGATCTGCTATGAAATTTGCATTGTTCTCATCCACTGACATGGACTGAGACACATCCG\n")
-		f.write("ATGGGGATGAGTTGAAGCTGAACAACGAATCGAAAGCCTGATCCGGCGTGGTGGTTGCGCTGTGCGCCCC\n")
-		f.write("TTCACTAGAAGTGCTCATTGAACGACCTCTAGTAGTTGCAGTAGCGCCACCTTTGTTGTCGTTGTCGTTG\n")
-		f.write("TTGTTGTTTGTTGTGAAGGAAT\n")
-		f.write("\n")
-		f.write(">gi|226791372|gb|GO545724.1|GO545724 Mdas9011K16_e863.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB56850.1| catalase [Prunus persica], mRNA sequence\n")
-		f.write("TGACTACTTCCCATCAAGGTTTGATCCTGTTCGCCATGCTGAGACCTTCCCAATTCCTTCTAATATTTTC\n")
-		f.write("ACTGGAAAGCGTGAGAAGTGCGTCATTGAGAAGGAGAACAACTTCAAGCAACCTGGAGAGAGATACAGAT\n")
-		f.write("CTTGGGCACCCGACAGGCAAGAGCGATTCCTCCACCGATGGGTTGATGTCCTATCCGAACCTCGTGTCAC\n")
-		f.write("CCATGAAATTCGCAGCATTTGGATCTCATACTGGTCTCAGGCTGACCGATCCTTTGGTCAAAAACTGGCG\n")
-		f.write("TCTCGTCTTAACGTGAGGCCGAGCATTTGAGGGCGATGCCAATGCAAGATGTTTGAGTATCGTGATACTG\n")
-		f.write("TCATACTAAATTTCGCATGTAAGTGACACGTAGCCTCAATGTAATAAGTCCGAATCGTTCGTACTATGCA\n")
-		f.write("ACTCCAATGTAATCCCTGTTTGGTGCCAATTATCTCCTGTTAATGGATGTGATCTGGTTGCTGTTCGGGG\n")
-		f.write("TTGGCGGTGTTGTCTGAGGCGGCGATGCTCGGTGATGGATGACGTTTCCGGTGGCTGGCTTGGATCTCTG\n")
-		f.write("TCGGTGGAGGAGAT\n")
-		f.write("\n")
-		f.write(">gi|226791371|gb|GO545723.1|GO545723 Mdas9011M03_e871.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD28640.2| geranylgeranyl hydrogenase [Glycine max], mRNA sequence\n")
-		f.write("AGATACTATTACAATGATATTTTGAAGGAGAAATTTTACAACGATTCTAAAACAATGACGGACATAGAAA\n")
-		f.write("TTTATATATGCTAGATCTCATTACACAAACTTGGAATTTCCACTCAAATCTGTTGAATTCAAAGAGTTCA\n")
-		f.write("TTCCTCGTTACATGAGGAAAAACAAAAAATTACACAAACAACAAGGCTTCCTCCTTTCATACAGTAATTT\n")
-		f.write("TCTCCATCTCCCTCCTGAGTGCATTAGCCCTAACCAAGCTCCCAATGGTATTCACAGCCAACTTCAAATC\n")
-		f.write("CTCCCACGGATTCCCCGGCACCACCCTCTTGTACAAGTAGCTATCGAACGTCATCTTCTGCACGTACTCA\n")
-		f.write("TCCGCACACATCTCCACGAACGCTTCCCTCGCGGGGTTCGACCTATAGAACACCTTCTGCAACACATCCA\n")
-		f.write("ACACCTTGTAAGTAGGCCAATAGGTCTTGTCCCACTTCTCCAAGTACGTCCTCAAGTCCGCCTCATTCAC\n")
-		f.write("CATCCTCTTCCCATTCTCCGACCCCTCAACTATCGCCTCGGCACACATCCTGCCACTCTTTGCTGCAAAG\n")
-		f.write("TAGATGCCTTCACCAGAACACTTTGTTACGTACCCTGCTGCATCACCAACGAGTGCTACTCTGCCCGCC\n")
-		f.write("\n")
-		f.write(">gi|226791370|gb|GO545722.1|GO545722 Mdas9011K05_e859.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD33072.1|AF149251_1 secretory peroxidase [Nicotiana tabacum], mRNA sequence\n")
-		f.write("AGAAAACCATGGCTTCTTCTTCTTCTTCCAGAATTCTCTTCTTCTTCTTTGCTTTGCTTTCTCTCTCAGC\n")
-		f.write("AGTTTCTTGCTTTGCTGAGAGCAATGAGCAGGATCCAGGTCTTGTCGTGGACTTCTACAGGGACACGTGT\n")
-		f.write("CCTCAGGCTGAAGAGGTCATCAGAGAACAAGTTAAGCTTCTCTACAAGCGCCACAAGAACACCGCCTTCT\n")
-		f.write("CTTGGCTCAGAAACATCTTTCATGACTGTGCTGTCCAGTCATGTGATGCATCTCTGCTGCTGGACTCAAC\n")
-		f.write("AAGGAGATCGTTGTCTGAGAAGGAGATGGACAGGAGCTTCGGTATGAGAAACTTTAGGTACATTGAAGAG\n")
-		f.write("ATTAAAGAAGCTTTGGAGAGGGAGTGCCCTGGTGTTGTTTCCTGCTCAGATATTCTTGTCTTGTCTGCAA\n")
-		f.write("GAGAGGGTGTTGTTAGGCTAGGAGGCCCATTCATTCCTCTTAAAACTGGAAGAAGAGATGGAAGGAGAAG\n")
-		f.write("CAGAGCTGAGATCCTTGAGCAATACCTTCCTGACCACAATGAGAGCATGTCCGTTGTCCTTGAGAAGTTT\n")
-		f.write("GCTGACATGGGCATTGACACCCCCGGTGTGGTCGCCCTTCTAGGAGCTCACAGCGTTGGAAGAACACACT\n")
-		f.write("GTGTGAAGCTGGTGCACCGGTTGTACCCAGAGGTTGACCCTCAGCTCAACCCTGATCATGTCCCTCACAT\n")
-		f.write("GCTCAAGAAGTGCCCTGATGCTATCCCCGACCCCAAAG\n")
-		f.write("\n")
-		f.write(">gi|226791242|gb|GO545980.1|GO545980 Mdas9008A15_e557.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86339 protein F2D10.18 [imported] - Arabidopsis thaliana gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGACTAATCGATGATTAAATGCTTAATTGAAAATAAGTCACACACT\n")
-		f.write("AACTTGCATAATAAGAAACTAACGAAAGCGTTATGTTACGAAAGCAAACTGAAATTCATTGAACATAAGG\n")
-		f.write("AGGATCATTAATTACAAACACAACGAGTTGGGAATCAAGGGGAGCAGACAATCTTCAAACTTAATCCGAT\n")
-		f.write("TTTCGTTTGTGTTTTTCCTAAATCTAATCCCTAAAAGCAAAAGTAGAGAGCCAGCAACTTATCCATAGTG\n")
-		f.write("AACACGAAGTGCAGGCAGGCCTTTCAATTATCCTCTAAGCAACCCTACACACATTGCCTCTCCCCCTCCA\n")
-		f.write("TTTCGATTCCCCTACTCTCTACTCATCGTCATCTTCCTCCTCGCCGCTCTCATCCTCGTCTTCATCATCG\n")
-		f.write("TCATTTACCTCAGACTTGGACTTGTCAGACTCTTCTTCATCAGCTTCGTTATTTCCATCAGCTAATTGCT\n")
-		f.write("TGTTGTATGCCTGAATGTTCTTGTTATATTCTACCTTCCGCTTGTCTGCCTTGGCTTGATAGGGAGCTTT\n")
-		f.write("CTCGGCATCTGACAACGATTTCCATTTATCGCCAC\n")
-		f.write("\n")
-		f.write(">gi|226791241|gb|GO545979.1|GO545979 Mdas9007P01_e546.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD29671.1|AF126402_1 major allergen Mal d 1 [Malus x domestica] emb|CAD10375.1| allergen Mal d 1 [Malus x domestica], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGATTAAAAAGTAATTTCATTATATTTATAGAAGATAATACAC\n")
-		f.write("TCCGTTCAGTCTGCAACTTTTTTCCAAACAAAGACATCAATAGCAACAAGAAGATCATCACAACCATAAC\n")
-		f.write("ACTTATTTTTCAAGCCCAAACTGCCCAAACCATGGTTATTACTTTTGGCTGACGTGAAAAAAACATACAA\n")
-		f.write("AGAAAAGCCACACAACCTTCGACTGACCATATAGTAACGGTAACACCCAAAACACCATAGATACTTATGA\n")
-		f.write("TTAATTTAGTTGTATGCGTCGGGGTGGTCCTTAAGGTAGCTCTCAATAAGTTTGAACAAACCATGGGCCT\n")
-		f.write("TCTCTTTTCCAGCCTTGACGTGCTCTTCCTTGATTTCAATGTTTCCCTTGGTGTGGTAATGACTGATGCT\n")
-		f.write("CTTGATGGTGGAACCACTTCCACATGCCACCAACTTGGTCTCGTAAGATATTTTCTCGATGGTGTCTGTC\n")
-		f.write("AAAGCATCTCCTTCAATCAAAGTGTAGGAGTATGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791240|gb|GO545978.1|GO545978 Mdas9007L15_e532.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG13395.1|AF283006_1 cold acclimation protein WCOR413-like protein [Oryza sativa (japonica cultivar-group)] gb|AAP50941.1| putative cold acclimation protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGACTAGTTCTCTCTTTCTAGTAACTCTGTTCCTGTCTTCCCCTGTCCCTGTTCCTCTAGATGGCAA\n")
-		f.write("AAAAACAGAGCTACTTGAAGATGATGACTGAATCTGATGCCGCCGATTTGATCAGCAGCGATTTCAAAGA\n")
-		f.write("GCTCGGCGCTGCTGCTAAGAAGCTCGCCGGCCACGCCGTCCGCCTCGGCAGCTTGGGATTCGGAACTGCT\n")
-		f.write("TTTCTCAAATGGGTTGCTTCGTTTGCTGCAATCTATCTGTTGATCTTGGATCGAACAAACTGGAAATCGA\n")
-		f.write("ACATTCTTACAGGGCTATTGATCCCCTACATTTTCTTTACCCTTCCTTCAATATTGTTCAACATCTTCAG\n")
-		f.write("GGGAGAGATTGGAAAATGGATTGCTCTCGTTGGTGTTGTCTTACGGCTTTTCTTCCCTAAACGTTTCCCA\n")
-		f.write("GAGTGGCTGGAATTGCCCGCAGCGTTGATTCTTCTTATAGTGGTTGCTCCTAGTTTATTTGCGAACACTC\n")
-		f.write("TGAGAGGCGACTGGATTGGTGTTGTAATATGCCTTCTCATCGCCGGTTATTTGCTGCAAGAACACATCCG\n")
-		f.write("GGCAGCTGGTGGGTTCAGAGACGCTTTCACCAAAGCTGGTGGAATATCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791239|gb|GO545977.1|GO545977 Mdas9007P21_e554.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T09642 hypothetical protein precursor - alfalfa gb|AAB41813.1| unknown protein [Medicago sativa], mRNA sequence\n")
-		f.write("CATAGCCCACATTCAATATTACTTAAATCTGAAAACTTAAATAGCTTTCTGGTTGAAAATATAGCACTGC\n")
-		f.write("AGTCTGCAAACTTAAATAACAGTAACACATCTGCCCTCAGCAACGGCCAAATTTACAAAATGTCCGAATC\n")
-		f.write("ATATTACCCGTTGCACAATCTCTATAATGATGTTCTAGTCTTATGATGATTTAACCAAAAAAACTAGCAT\n")
-		f.write("TTAAGCAACAGGGGAGACCTTAACTTCATCTAGGATAGGGCCACAAAGAGCTCCATAGTCCTTGGTGTGG\n")
-		f.write("TAAAAGGAGCTGAAAAACGTGATTCTGGTCCTGATTGAAACCGCTTTGAAACTGAAACTGGCCTTCTTGA\n")
-		f.write("ACCCGCCTTTTCCTTTGGAGGCGAAGGGAACTTTGAGCGTGTCCTTGCCGGCAAATGCTTCAACCATCAT\n")
-		f.write("TGATCCTTGGCAGCCGTTTCTTGCATCACCGACGGTGAATGAGAGGCTGTAGAGCTTGTTGGGAACTGTT\n")
-		f.write("CTAATAATCTGGGCTATGGCGCTTTCTCTCCCCGCAACAAGCTCAACTGCGCCCTTTCCGACTGGAACAT\n")
-		f.write("TGAAGTGATTGGAATCG\n")
-		f.write("\n")
-		f.write(">gi|226791238|gb|GO545976.1|GO545976 Mdas9007C05_e494.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27880.2|AF139468_1 photosystem I reaction center subunit III [Vigna radiata], mRNA sequence\n")
-		f.write("CACAAGCATTTGGTACATTAATTCCAAGTAATTTTACAAATTATACAAAAAAATTAAAAACAAATAAAAA\n")
-		f.write("AAAAAACCTCAAACGTCCTTGGCAACAAGTTCACCATTCACTAACTCTCTGTAAGCACCCACAGGCCAGC\n")
-		f.write("TAAACCCTCTGAAAACCAAGCTAGTACCCAAAGGCACATCAATGATGATCTCCTTCTGTGTCGGCTTCTT\n")
-		f.write("ATCATCCCTAAGGGCAATCAAGTACCTCCTCCCAACCCACCCAATCCACCCAGCAATGTACAGGAACAAA\n")
-		f.write("ATACCAGGCGTGATAAACTCACCCCAGTGCCTCGGGTCACCGCTGACAATCAAAGGGGGGAGCCCATCCA\n")
-		f.write("ACCCACAAAGCAAACCCTGCTTGCCATAGTTGGAAAACCCCCTCTGAGTCTTCTCTATGGGGGCCTTGAT\n")
-		f.write("GGCTAGGGCGGGTGCACTGTCGGGTGCATAAAGCTTCAGTGAGGACTCGAGTTTTTTGATCTGCTGCTTC\n")
-		f.write("TCACGCTTGGCAAACTGCTTGGAGTCTTTGCATGGGGTGAGTCCCGAGATGTCACCAACTGCAGGCATGG\n")
-		f.write("GGGCCGAG\n")
-		f.write("\n")
-		f.write(">gi|226791237|gb|GO545975.1|GO545975 Mdas9007N06_e540.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|A85097 neutral invertase like protein [imported] - Arabidopsis thaliana emb|CAB78074.1| neutral invertase like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("GTTTATAGTTTATATTATTTTCAAATTAAAAACTCATTTGATAATACTAAACAAAAAGTATCTTCATCAC\n")
-		f.write("TTGATCTAACGCACATTTGAAAAAAAAAAAAGTATATGTGTTTAAATGCTTAATGTTCCACATTCCCACC\n")
-		f.write("AAATATTGACATACCCAAAGTGTTCGCATACAAAATCGAAATTAAAAGGTCCATGAAGCAAATCTTTTAA\n")
-		f.write("TAAGGGGTTTCATTTGCTCGTCCTCCTCCAATGCTATCATGCCCAAATGAAACGGGTCTTCCAGCATCAT\n")
-		f.write("CTTCGCCACCAAGTACCCCGCGATCGACCATGTCTGGTACTTCCGTGCCTGCTTCCCCATGAACCTCCCT\n")
-		f.write("AGCTTCCCATCATAGTACTCCGGCCACCCATCTTTCGACAACCGGCTTTCCGCCAGCTCGATCGCACGCC\n")
-		f.write("TTGCAATCTGTGGCCGGCCGGTCTTTATGCATGCCGCGGTTAACAACCACAGCAGTACTGGCCAAGAGCC\n")
-		f.write("TCCATTGTGGTAACTCCATCTAGTATTCTTTGGATCACAGCCAGTAACAATCCTCCACTCATGACTTTCA\n")
-		f.write("AATGCCGGATAGCAAATCTTCAAC\n")
-		f.write("\n")
-		f.write(">gi|226791217|gb|GO545974.1|GO545974 Mdas9007J24_e522.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T06386 probable malate dehydrogenase (EC 1.1.1.37) - garden pea gb|AAC28106.1| nodule-enhanced malate dehydrogenase [Pisum sativum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGCAATTGAAAAGTATGAATTCACATTCTTCGAATTTATTTTC\n")
-		f.write("GCATCAGAAGCTAGCCCTTGCATACACGCAAGATAGAAATACATGATATTCCTAAAAACTCATGATCGAC\n")
-		f.write("CAGCCAAGTTATTTCAAAACTGTCACTACAAGTTTCCGCCCGCAGAAGAAGGCTTCTATTCTTCAATCTA\n")
-		f.write("CAACAATAGAAGCAACTCTGTATTTCTTCCGAAAATAGCTTCAACATAGAACACTGAAAGGATACCGACT\n")
-		f.write("TCATTCTACAAAACTGAAAGTACTGATGCATTGCTAAATCTGCTAAAAAATATCTGTAAAGCATTCATTA\n")
-		f.write("GAATGAGGTAATAGAAGCTTCTGATAATAGCGACCTAAGCAGTCACGGTCTGCTTGTTGGCAAAAGCAAT\n")
-		f.write("ACCCTTCTCAATGCTGGCTTTCAGTTCCGGCTTGAGTGCTTCCAACGCCTTTTGCTCATATTATGTCAAA\n")
-		f.write("CCTTGGAGGTCAGACGGTATGAAAGCTTCAATTCCATTCCTTCCAAGCTTAACCCTTGATGCAAAGAATG\n")
-		f.write("GAAGCTCGGTCAG\n")
-		f.write("\n")
-		f.write(">gi|226791216|gb|GO545973.1|GO545973 Mdas9008C01_e568.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGATGAAACCTACAAGATATATAACATTTCAAGGTGGAAATTGC\n")
-		f.write("TTCCAAATGTCAAAAACCCGATAAAAATTGAAGCTGAGAGAGTTCAAGTTGGGCACCAAATTGCCAAAAC\n")
-		f.write("AAGTTGAGACCACCCCATAATTTGTATTTTCTATCACTCAATAATGGATTGAATAACACCAGCTCCAACA\n")
-		f.write("GTCTTCCCTCCTTCTCTGATGGCAAACCTCATCCCCTGCTCGCACGCCACCGGAACAATCAGCTCGACCA\n")
-		f.write("CAATCTTAACGCGATTGCCAGGCATCACCATCTTCGACTCCTCATCCTTATCGTTCATAATCGAAGTCAC\n")
-		f.write("CTTCCCGGTGACATCAGTAGTCCTCATGTAAAACTGCGGCCTGTAACCCGAAAAGAACGGTGAATGCCTT\n")
-		f.write("CCCCCCTCTTCCTTCTTCAACACATACACAATCGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTT\n")
-		f.write("TGGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791215|gb|GO545972.1|GO545972 Mdas9008B06_e562.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_186898.1| pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana] gb|AAF32456.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCGAACAAACGCTCTGCTACATTATCCTCGTGAAAGACATTACAA\n")
-		f.write("GATACAGTCTAACAAAGCCTAAGCAGCCACCGCCGTGGGAGCAGCACGTTCTCCAGATTTTGCAGAATAA\n")
-		f.write("AATAGATCCAACACATCAGCATGGTTGCGGATGTAGCCTGGACATTTGGAAAGGAAATTCTGTGCTTCAC\n")
-		f.write("TGTGCCGTCCAGCCTTGAAATAAGCTTCAAATACATTGAGGAAGACGGTGGTAGATGGAAACCTCCTTGA\n")
-		f.write("AGTCATCGCCTTCAGGAAAGCTAAAGCATCTTCACCTGTTCCAGACTTTGATACATACTCAACGAATGGA\n")
-		f.write("TCAATAAAAGGAGGGAATCCATGATTTTTCATCATACCCAGAATATTCAGAGCATCCTTGAATCCACCCT\n")
-		f.write("GAACCAATAACTTACTTATCAACAACTTGTATGTGGTATGCCATGGCTTGAGTTGCCCTTCATTGACCGA\n")
-		f.write("ATCATTGAGTAACTTGTATGCATCTATCGCACTGTTTTTTCTGCAATATGCATCTACTAATATATCAAAA\n")
-		f.write("GCATAACCAGCAGAGGCAGC\n")
-		f.write("\n")
-		f.write(">gi|226791214|gb|GO545971.1|GO545971 Mdas9007I09_e517.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566842.1| pectinesterase family [Arabidopsis thaliana] dbj|BAB01985.1| pectin methylesterase-like protein [Arabidopsis thaliana] gb|AAL49785.1| putative pectinesterase [Arabidopsis thaliana] gb|AAM20211.1| putative pectinesterase [Arabidops, mRNA sequence\n")
-		f.write("TCCAGTATTTTTTTTTTTTTTTTTTTTAAGGTCCAAAGGGAAAGGGGTTTTTTCATCACAAGAAAAGTAC\n")
-		f.write("CCACATTAACCATCCATGTTGCAGGCCAAAGATGAATACACATAACACAACAAGTTGATCTATATTATCC\n")
-		f.write("TGGACAAACCTAAAAGCCAAATCAAACGAATTCTTCAGCACAAGCAATTACATCTGATAAACGCTAAAAG\n")
-		f.write("TGACCGTGTAACGCCTCTTGCACCTTGAGAACACAGGATTTGAAATAGCTATGTTGCATATCTTATGCTT\n")
-		f.write("TCGTCGTAAAATGTTTTCAATATACTCGACTATCTTTGTTGGGATCATTCCCATGTTTTTAACTCCTAGG\n")
-		f.write("CAGAATACGGTATTCTTAGGGCCATTCTCTGAGCAAGCCAAGGCCTTCCTGGATCAGGATCAATGAAACG\n")
-		f.write("ATGCTGGAGGAACTGGTCTGCTTCCTCATCTACCAGCTCTCTTGCCCATGTCACCCGTTTTGATGGGCAA\n")
-		f.write("CTACCCGGTCCAAAATACCTGTATTCATAAAAGCAAGCAGTTCGTTCATTCTCTGTTTTACCCCAATTAT\n")
-		f.write("TCCATCCTAC\n")
-		f.write("\n")
-		f.write(">gi|226791213|gb|GO545970.1|GO545970 Mdas9008B18_e567.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P24226|HISX_BRAOC Histidinol dehydrogenase, chloroplast precursor (HDH) pir|A39358 histidinol dehydrogenase (EC 1.1.1.23) precursor, chloroplast [validated] - cabbage gb|AAA32991.1| histidinol dehydrogenase, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGCTTTTTTAGAATTCACTTGCATTTTCATAAAGATTAGTTTCAAAA\n")
-		f.write("ACACTTCCAAATGAACCCCAACGTTTATTGAAATTTGGGGAAAAAGAAGGAAAAAGGAATGCTTCAAAAG\n")
-		f.write("AAAGAAAACATTACCAACCTAGAACAAAGTTTAATGGTATTCCACCCACCAGTTTTGCTCTATAGTACAA\n")
-		f.write("CGATCAAAATTCAACCACCGCAGATTTTTCAATAGTAGCTGGTACATCCCCAAAAACGGCAATTTGCCCC\n")
-		f.write("AAAGGGGAGAACAAATTTGGCAAATGCTCTTGCTGCGAAAATCACCTTATGTTAGGACCTGCCGGGCTTC\n")
-		f.write("GATATCCTTAAGTCTAAGGGTTACAGCTCTCTTGTGCGCCTCTAGTCCCTCAACTTCGGCCATGGTAGCC\n")
-		f.write("ACATATGGGCCGAGCTTTTGCAAACCTTCCTCTGTCAAAGACTGCACTGTCATGTACTTGAGAAATGAGT\n")
-		f.write("CCAA\n")
-		f.write("\n")
-		f.write(">gi|226791191|gb|GO545969.1|GO545969 Mdas9007G16_e507.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191183.1| copper homeostasis factor (copper chaperone) (CCH) [Arabidopsis thaliana] pir|T47741 copper homeostasis factor [imported] - Arabidopsis thaliana gb|AAC33510.1| copper homeostasis factor [Arabidopsis thaliana] emb|CAB87423.1| copp, mRNA sequence\n")
-		f.write("CAACACACTGACTCTCTTCCATTTATTTATACAGGAATCATACAACAAGTTCAAAGAAAAACATTGGGGG\n")
-		f.write("TTTACAAACAAGTAAAAGTTTAACGAGGACTTAATAGTCTATGACGTTGGGGTTCACCGATGAAACACAT\n")
-		f.write("ATTAAACGACATTGAATAGGCAAAACACTAAGCTAAGCAGCACCCACAGTTTCTGCAGGCTTTGCTTCCG\n")
-		f.write("GTTCTGCTGGTGCCGGTGCTTCTGCTTCCCAATAAGCAGTTTTCTTGCCAGTTTTGGAAACAGTTTGCAG\n")
-		f.write("CACTGTCTCGGGTGGTAAATTGCTTTTCACTGTCACCTTCTGAGCGTCAAAATCTATGTCATATGATTCT\n")
-		f.write("ACACCTTCAAGTTTGCCAAAAACCCGTTTGACGGCCCCAACACAGCCTTGACACGACATACCAACCTTGA\n")
-		f.write("GGACCGTAGTAGTCTGTGACGCCATGTTAGGGTATTTGGGATTTCAAGAAAACTGAGGAAAAATTGAGAA\n")
-		f.write("ATTTTGTTATGGATTTGATTGGATGCTGTTGTGCATCTGGTCAAACCCAAATGGTCCTTTTATAACAGAG\n")
-		f.write("AATAAAAA\n")
-		f.write("\n")
-		f.write(">gi|226791190|gb|GO545968.1|GO545968 Mdas9008E01_e576.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564534.1| chorismate synthase (5-enolpyruvylshikimate-3-phosphate phospholyase), putative [Arabidopsis thaliana] gb|AAL09759.1| At1g48850/T24P22_3 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTCAATTGAATGAAATTTATTCAGTTTCAAAGTCTAAAACACATAATTCTGGGATTAACAGTACCTCCCC\n")
-		f.write("CGGATAAAAAAAAACCTTGTTTCACATATTTAAAAAAAATAACTGCAGTAATGATAATAAATAATAATTT\n")
-		f.write("TATTGGCTCGGAATTACTTCTACAGATTGAATGATTGAAAAAACTTATTTTTGAAAAAAAATGGTCCACA\n")
-		f.write("CACCTCACATATATTCCAGTCTGACAGCGTCTCACTAATTCTAACTTGCCGTTTCACACCAAACATGCGT\n")
-		f.write("TTCATGACGATGAATTTTCACTGTCCGAAACAAAACATAAATAATGCTATAAAACGTTTGTCAACCTTCA\n")
-		f.write("AATGTGCACACCAGCTGCCTCCGCTGCTTCAACCACTTGCGGCGGCACAGGGTCTTGTAAGTCAACCATT\n")
-		f.write("GGCTGTGGCACAAGGTCTTGTAAGTCGGGATTGATAGGAAACATGTGACACTGTGCAAAATCTGCCATTA\n")
-		f.write("GTTGGTCCACCAACGCA\n")
-		f.write("\n")
-		f.write(">gi|226791189|gb|GO545967.1|GO545967 Mdas9008H24_e600.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB87573.1| chlorophyll a/b binding protein of LHCII type I precursor [Panax ginseng], mRNA sequence\n")
-		f.write("ATCCCCAATGTTTACTATGGCTCTCTCATCCCCATTCACTGGGAAGGCCATTCCTCTTAACACACAGACA\n")
-		f.write("GAGTTCACAGCTGTCCAAGGAAATGGTAGGGTTTCTATGAGGAAGACGGGCAAAAAGCCTGCTGTCTCAT\n")
-		f.write("CAGGGAGCCCCTGGTACGGCCCTGATCGTGTCAAGTACCTCGGACCATTCTCCGGTGAGGCTCCATCTTA\n")
-		f.write("CCTAACCGGTGAATTCCCCGGTGACTACGGGAGGGACACTGCTGGGCTATCAACAGACCCCGAAACCTTT\n")
-		f.write("GCCAAGAACCGTGAACTTGAAGTCATTCACTCAAGATGGGCAATGCTTGGAGCTTTGGGC\n")
-		f.write("\n")
-		f.write(">gi|226791188|gb|GO545966.1|GO545966 Mdas9008H20_e599.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T51178 actin ACT2 [imported] - Striga asiatica gb|AAC49652.1| actin [Striga asiatica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTAGTCAATGATCACTGTGAACACAAATATATTCAGCAAAATTACAGATAATCCA\n")
-		f.write("GCGGCAAACCTACAAAGTCATCGTCCAGACATTTTAAGTAACATAAAGCGAAATAAAAACGGACAACAAA\n")
-		f.write("ACCAGAGAGCAAGAATGCAAGCAGCATTTTCTTTCCATTATCATCACTCCGCCTATCGTTGATTGTTCTC\n")
-		f.write("AGAAGCATTTCCTGTGCACGATTGAGGGACCGGATTCATCGTACTCAGCTTTGGCAATCCACATCTGCTG\n")
-		f.write("GAAGGTACTGAGGGAAGCTAAGATAGAGCCTCCGATCCAGACACTGTACTTTCTCTCTGGTGGGGCAACC\n")
-		f.write("ACCTTGATCTTCATGCTGCTTGGGGCCAATGCAGTAATTTCCTTGCTCATTCGGTCAGCAATTCCAGGGA\n")
-		f.write("ACATGGTTGAACCACCACTAAGAACAATGTTGCCATACAAATCCTTCCTGATATCGACATCGCATTTCAT\n")
-		f.write("TATGGAATTGTAAGTGGTCTCATGAATACCAGCAGCCTCCATTCCGATCATGGATGGTTGGAAGAGGACT\n")
-		f.write("TCTGGGCA\n")
-		f.write("\n")
-		f.write(">gi|226791187|gb|GO545965.1|GO545965 Mdas9008F01_e585.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172184.1| mitochondrial carrier protein family [Arabidopsis thaliana] gb|AAM98208.1| mitochondrial carrier protein, putative [Arabidopsis thaliana] gb|AAP42736.1| At1g07030 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CGATTTTCCTATTCGAACTCATTTTCCTGATTTTGAATCGCTTATTTTTTTTTTCGACAATTTTCTCCGC\n")
-		f.write("GAAGTTTGAACCCCATCTTGTACTACACCATTCACCATGGCGATTGACGCCTCCCCTGCATTCCAAACCG\n")
-		f.write("TCACTCAACCCCACGACTTCCGGCCAGAAATATCAGCATCCCCCTCCTCCGCCCATGACGGCCTAGAGTT\n")
-		f.write("CTGGCAGTTCATGATTGCCGGCTCCATAGCGGGCCTAGTTGAGCACATGGCTATGTTCCCAGTTGACACG\n")
-		f.write("CTCAAAACCCGCATGCAGATTTTTGGCGGGTCCTGTTCCGTTCAACCTATTGGCGTTAGACGGGCCCTTG\n")
-		f.write("GCTCGATTCTGAAGCTCGAAGGCCCCGCAGGGCTCTACCGCGGCATCGGCGCAATGGGGCTCGGAGCAGG\n")
-		f.write("ACCTGCCCATGCA\n")
-		f.write("\n")
-		f.write(">gi|226791167|gb|GO545964.1|GO545964 Mdas9008H06_e596.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565841.1| hydrolase, alpha/beta fold family [Arabidopsis thaliana] pir|H84778 hypothetical protein At2g36290 [imported] - Arabidopsis thaliana gb|AAD21437.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTACCAGCAACAATCCTAGTTTCACACAATTATTTCTCAAATCCAACTTTCAAAATTCAATCCCTAA\n")
-		f.write("GAAGCAACTGCATTATGATGCAACAATCTATAAACAGAGTTGGCCGGTACAAGATCTATCATACATACCA\n")
-		f.write("AACTGACTAACTGAAATTCAGTAACTCCGTATTGGAGAAATGCACAGAAAAGTTCACCCCGAGGTAGCTC\n")
-		f.write("GTTACGTAAGAGGAAATGTTTACTATCCGTCGGTTAAAAGTGCCTTGACAATGGTCTCGCACATCCCATC\n")
-		f.write("AGCAAGTGGCAACAAATGTCCAGCACCTGGTATCTCATGATAGTGGATCCATGGAAGCTGTTCAGCAATG\n")
-		f.write("TAGCGTTGCAGTAAAACGGGTACCATGCGATCTTCATCTCCATGCCACACGTGGACAGAAGCTTCATTGT\n")
-		f.write("TAGGGAATGGGTTTTCCAGTTCCAGAGGACTGAATTCCCAGGTCCCAAATCCAACATTCATGTCACGGTA\n")
-		f.write("AATGGACTCAAATTCTCCCTGCTGTCGTACCTGTCCCGCATATGGTTCTCTTTTTTGAAGCTTGGGCAGG\n")
-		f.write("ATTTCTTTGTCTTGGTCAGAAAGACAATCTATACTTCGAGCCAGAACACTTGAACCAGGAAACCATTTTT\n")
-		f.write("GAGTGTTCCAGA\n")
-		f.write("\n")
-		f.write(">gi|226791166|gb|GO545963.1|GO545963 Mdas9008P12_e635.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TAAAACACCAAATTCTAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGA\n")
-		f.write("CAGAGGTCTTGAAAGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACCAGA\n")
-		f.write("CTCATAGAGCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCT\n")
-		f.write("GCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAAGCTCCCTCTCCGGAATCGAACCCTAATTCTCCGTCA\n")
-		f.write("CCCGTCACCACCATGGTAGGCCACTATCCTACCATCGAAAGTTGATAGGGCAGATATTTGAATGATGCGT\n")
-		f.write("CGCCAGCACGATGGCTGT\n")
-		f.write("\n")
-		f.write(">gi|226791165|gb|GO545962.1|GO545962 Mdas9008K24_e611.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GCGTTTCAGACGTATAGTTGATTGCTTCAGAACAGACATATCTCAATGAGATAGAAGACGGAGAGCAGAC\n")
-		f.write("CAAGAGCGTAATGGTGGAGGTTAACGGTCTGTCCCTTCCTGTTGGGAAGAACTTTGCCATGTCTTGGCAA\n")
-		f.write("ATGGGGATCAAGGCTTGATTTGCTATACGATATGTGCCCTTTATTTTGAGCTAGCTAGTTTTGGTCCTCT\n")
-		f.write("AATTTACTTGTTCTGCAGCCATTCGGGCGGAAATAGTTGATGTCTTTAGAGTTATTATCGCGGTT\n")
-		f.write("\n")
-		f.write(">gi|226791164|gb|GO545961.1|GO545961 Mdas9008E17_e582.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGTACGTAAGTGTACTTTTATCATTTATTTCTATAATAAAATATCG\n")
-		f.write("GAAGCATCGCGATATGAATTACAAGGAGCTAACAGGGAAACAAATGACAGTAGTACTAGTTACATATATC\n")
-		f.write("TCGCAGACAAAGTACATACATAACATTAAGTATAACTTTGGTCAGAATATGCTTCTGCAAACAACATGAA\n")
-		f.write("GAATGTTCACTTCTTTTGCGGACAATGCTGCGAGATATTTACGTATGTAGATAGAAGCTTCAAAAACCGG\n")
-		f.write("CCACGATTTCATCTCATCTCAGCAGCAATACTTTTCGGTTTGTTCTAGCTGCTGCCGATTATATCTTTGT\n")
-		f.write("ATGTGCCCTTAATCTTCTGTGTCAAGGCTTCTCTGTCTGGTTTGAAAACAAGGTTCTTGTATGCAAACCA\n")
-		f.write("CCCAGTGTAACCAATTCCTACAAGCTCAAGAACACCAGGGACTAAAGGAAGCCTATCAATTGCCGAGATC\n")
-		f.write("ATTCCACTGAAGCCCCATACTGCAACAGCAACAGCTACTGCAAGTGAAGACACTGCATATTTATCTTCCA\n")
-		f.write("CTTTCTCCCAAGCTTCTTGAACTGTCTTCACAATCTCTGGGGGCTCAGCTGTTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791163|gb|GO545960.1|GO545960 Mdas9008H07_e597.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO42863.1| At2g36290 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTACCATCTACAATCCTAGTTTCACACAATTATTTCTCAAATCCAACTTTCAAAATTCAATCCCTAA\n")
-		f.write("GAAGCAACTGCATTATGATGCAACAATCTATAAACAGAGTTGGCCGGTACAAGATCTATCATACATACCA\n")
-		f.write("AACTGACTAACTGAAATTCAGTAACTCCGTATTGGAGAAATGCACAGAAAAGTTCACCCCGAGGTAGCTC\n")
-		f.write("GTTACGTAAGAGGAAATGTTTACTATCCGTCGGTTAAAAGTGCCTTGACAATGGTCTCGCACATCCCATC\n")
-		f.write("AGCAAGTGGCAACAAATGTCCAGCACCTGGTATCTCATGATAGTGGATCCATGGAAGCTGTTCAGCAATG\n")
-		f.write("TAGCGTTGCAGTAAAACGGGTACCATGCGATCTTCATCTCCATGCCACACGTGGACAGAAGCTTCATTGT\n")
-		f.write("TAGGGAATGGGTTTTCCAGTTCCAGAGGACTGAATTCCCAGGTCCCAAATCCAACATTCATGTCACGGTA\n")
-		f.write("AATGGA\n")
-		f.write("\n")
-		f.write(">gi|226791162|gb|GO545959.1|GO545959 Mdas9008O13_e631.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TGCAGAACGACTTAGGAAGAGAAGGATGGGAACTCAACGTTTGCCCTCGTTAAACCTCTAAACAAAACAT\n")
-		f.write("CGAAGTCGTGCATTATATCAAATGATTGGAAACCGTGGTGTATTCGGTAGAAAATAAAACTGGTATGGAT\n")
-		f.write("TATCCAGCAAACTGCATATTGCTCCACCTGCAGATTAGCGATCAGAGAGTCGAAACAGTTCAGAGAAACA\n")
-		f.write("GGATAAACGATGAGAAAGTTGAGCTCTGGATCGAAAAATGTCGAGTACTATATATATATTCCCAAGTTGT\n")
-		f.write("TTTTGGTTGTGCAGATTGGATTGCAAGGTGCTGGCGATCAAAGCTTGTACAATGCCATAATTTAATTTGT\n")
-		f.write("TGTATTTCGGATTTGAGTTTGTCTTATTTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791161|gb|GO545958.1|GO545958 Mdas9008F17_e591.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_173322.1| peptide transporter -related [Arabidopsis thaliana] pir|G86322 hypothetical protein F6A14.2 - Arabidopsis thaliana gb|AAF27093.1|AC011809_2 Similar to peptide transport proteins [Arabidopsis thaliana] gb|AAL49811.1| putative pept, mRNA sequence\n")
-		f.write("TCGAGTCCCTTTTTTTTTTTTTTTTATAATAATAATAATTATTATTATTATTGAAATCTCTAACATCTAA\n")
-		f.write("TACTAAAACAGGTTGATTCGATTTGATTGGATTTTATTTGCATATATACAGAGCCATGTTTAAGCATTTG\n")
-		f.write("TTGAACCTAACTGCACCTGATCAGTATCATATGGCTTCTCTTCAACGTTCACATTTGTGGCCTTGTAATG\n")
-		f.write("ATAACGTTGCGCACAAAACAGAAAGTAGGCAAAAGTCAGAACCCCAATCCCAGCCAATAGGAAGTAAAAG\n")
-		f.write("TACTCCAATCTCCCAGCATTGAGGTCAT\n")
-		f.write("\n")
-		f.write(">gi|226791141|gb|GO545957.1|GO545957 Mdas9008O11_e630.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAATGAATAGTATCATGATTGATTTTTTTGTGTAAAAATGTGGTTT\n")
-		f.write("TTCGTTAAAGTGAACAGTACCGTGAGCTTTTCGTTAAAGTTCCCCATAATATTTGAACTTGATCATGGAT\n")
-		f.write("AAAAGTCAAAACAATCACCATATGAAGGAGCAATTGCAGTAACCCTAGTTCTCAAGATAACCGAATTTAA\n")
-		f.write("CTGACAAACTGCATCTCTATGCTTTGAAATTCTAACATACGAACTAAATTAAATCTTTTCGGTTTATATT\n")
-		f.write("TTTCCGAAAATTCCTACTATTTGGGCTCCAATGGTGACTTGTCTATAATCCAGAACCTGTTTTTCTTCGT\n")
-		f.write("AATATATGGCTGCAACTTCCACATCCTGTTGTTTTTGCTGCGCCGGAATCCAGAATTCAGATACCCAGAT\n")
-		f.write("ATACTTGTAAGAAGTTGCATATCGGTTAGCAGCTAAAGACTACACTCTGTGTCCATATAGGAGGATCAAG\n")
-		f.write("AAAAGCCTGTTGTCTAGTCTGTGTGATCACGGAAGCGGATGATTTTGTTGATGAAGGATCTCTCACGGCG\n")
-		f.write("GTATATAACAAACGACGACATGCAGAAGCAAGCAAC\n")
-		f.write("\n")
-		f.write(">gi|226791140|gb|GO545956.1|GO545956 Mdas9008G12_e593.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P14278|CB24_LYCES Chlorophyll A-B binding protein 4, chloroplast precursor (LHCII type I CAB-4) (LHCP) pir|S10857 chlorophyll a/b-binding protein precursor - tomato gb|AAA34141.1| chlorophyll a/b-binding protein precursor, mRNA sequence\n")
-		f.write("TTTTATATTACTAAGGAGCTTGGGAGTTTTTTACTGCATACAGCGGTTTCAATACAAGCAGTTTCTAGTA\n")
-		f.write("AAATTGCATCAGAACTAATGGAGTCCACAACAAGAGAACCTCAACACAAGCAGTAAGTTCGGGTAATGTT\n")
-		f.write("ACAGATGAACGGCCATGGCTTGAGGTTTCTTCACTTTCCAGGGACGAAGTTGGTGGCGTAAGCCCATGCG\n")
-		f.write("TTGATGGCCACTGGGTCATCGATGTGGTCG\n")
-		f.write("\n")
-		f.write(">gi|226791139|gb|GO545955.1|GO545955 Mdas9008E21_e584.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTCATGAACATTAAATACTTGATGGGCACTGACAAAGTGCCAGAAAATACAACTAGAGACCCATATCTTG\n")
-		f.write("GTTACACCAGTTAATGATAAAGAAATGAAAATTCAATTCATACCCCCTGAAAAACATCTGTTTTCCTTTT\n")
-		f.write("ACCTTAGGAACAACTTCTGCATCCATCACACAACCACAAAGATCAACACACCCAAAAACAGTAAACACTA\n")
-		f.write("TCGAACTAACGGGATTAAGCTTCAAACTCCATGCCAGAAACGGGCAATCTCCTTATATCGCCGCTCCTGG\n")
-		f.write("ATTTGACGAAAGATAATTAGTGGAATTATCCCAGGTTAATGGTTCTGCTGTACCCAAGCTTCGCCACCTT\n")
-		f.write("CCCTCATGCACCGAAGGTAAACTAAAACTTAACCTCCCTTTTGCTCTATCCCCACCCGGAAAAATCGAGC\n")
-		f.write("TCCAACACCTTTGTTGGATTCTGCACTGAGAGTATAAAGATTCATTCAGGCCCAAGTGAACCCTCTGAAT\n")
-		f.write("AATTATGCTCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791138|gb|GO545954.1|GO545954 Mdas9008L04_e613.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTCCTTTTTTTTTTTTTTTAAATTAAGATATTTTAATGAACATGTATAACCAAATTTTTTATGCC\n")
-		f.write("AGGTAATATCTTACAGAAACAAAAGAAAATAATTTTCTTTTGTTCAATTCACAGTTTTCTTTTCCTTTTC\n")
-		f.write("TTTGCTTTCTGTCGAGTTTTACAACCTAATATGCACATCTGCGTGTCTAACACGTAAAAGGAAACAAAAC\n")
-		f.write("CCCATTTTACGCATGCAGCGGTCCCCGGCATGCCGCCAGAAACGTTTCTACAAAGCCGAAAGGGACTCGG\n")
-		f.write("TTCGCCACGAAACATCTGCAACGCCGCCCACCGGGTAATCAAACAAACCGTCTAAAGCCAGGTACTCCAC\n")
-		f.write("CCCACCAATATAATTGTTATTAGCAAATTCAGAGTCGCCACCGATTCCGAAGTCGAACGAGTCGTAACTC\n")
-		f.write("GGAATCATGTCGTTCTCGAACCCTACCATGCCATCCAATTCAACGGCCTCGGAGCCACTCGTGGTGAAAT\n")
-		f.write("CAGCAGCCTCGATTTTTCCCTCCTCACTTGCTCCATTGGTCGGTGGAAAACCAAGC\n")
-		f.write("\n")
-		f.write(">gi|226791137|gb|GO545953.1|GO545953 Mdas9008K16_e608.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29677|MPPA_SOLTU Mitochondrial processing peptidase alpha subunit, mitochondrial precursor (Alpha-MPP) (Ubiquinol-cytochrome C reductase subunit II) pir|S23558 ubiquinol-cytochrome-c reductase (EC 1.10.2.2) alpha chain precursor - potato emb|C, mRNA sequence\n")
-		f.write("TCGAGTTTTCTTTTTTTTTTTTTTTTTTGCCAAAACAAATCCTGGTATATGTAATTTGGATCAAATTAAT\n")
-		f.write("CCTTTCAAAATTTTATTTCGACAATTGCCAACAACGGCGAATAGCTCGGAAGCCGTGAGTAGTCATGCGA\n")
-		f.write("TTCAAAAAATTACAGCCAGCAGGAGGCATCCTCTCATTTTGCTTGGAACCTGCTGCTAATTGAGTCGTAA\n")
-		f.write("CCGGGTACATGTACAACATTGCCATATGTTGCCATTGTTAGCGGTGAAGAAATAATCTTCTGCGCGATTG\n")
-		f.write("TAGTAATATCTTTCAAGCTCACTTCTTCTACCGTCTTCAAGAAGTGCTCCACAGGTTTCCTCTCTCCGTA\n")
-		f.write("TGTCAAAACCTGCCTTCCTATATCCTCTGAATGCAATCATTCTAGATTCTAGAT\n")
-		f.write("\n")
-		f.write(">gi|226791136|gb|GO545952.1|GO545952 Mdas9008O15_e632.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190817.1| expressed protein [Arabidopsis thaliana] pir|T08450 hypothetical protein F22O6.130 - Arabidopsis thaliana emb|CAB43425.1| putative protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTCTTTTTTTTTTTTTTAAATAAATAAAACAAAGAAAATTATGAAAATTAAACCGACCACCAAT\n")
-		f.write("CTGTAACAGGAAAATCATGGATCATAATGTACATGTAGTTATACATAAAAGGAAAATCTTTTAATCTCCA\n")
-		f.write("ACCCTAAGAACTAAAAACATACTAAACAAAAAAAAGTTTCGAAAGAAGCAAACAGACACTTCAAAAGAAA\n")
-		f.write("AAACCATCAAACTATTTTTTGTTCCTTCCTCCCATTTTTTCACACCTCTTGAATTTTGAAAACAATGCGC\n")
-		f.write("CTATCGACAGATTCAAGAAGACCAATGTCATCAATCGATTGATACTCGGAACTATCATCGTCATCAAAGG\n")
-		f.write("AAATGTTCAAATCGAGAGACACACAAGGGCTTGTTTCCTCCAAAGCAGCAATATCCCTATTATCTTCTTC\n")
-		f.write("ATTTAGCCCTTCTGATAATTTTTGCTTGATAGGAGGAGAGCAAGCTCTTGATCTCGAGCTGAAGCTTTCG\n")
-		f.write("CAGCTCAAAATAATGATAGCATCTCCAAGACCAACTTCTTCGCCACTTGAATTGGTTATTCGTCCTCGTT\n")
-		f.write("CAATTGCTCTCTTAAACCCCATTTGAGAGCAGTAGTCCGCCTCG\n")
-		f.write("\n")
-		f.write(">gi|226791114|gb|GO545951.1|GO545951 Mdas9008H13_e598.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190146.1| senescence-associated protein family [Arabidopsis thaliana] pir|T47500 hypothetical protein F9K21.180 - Arabidopsis thaliana emb|CAB75489.1| putative protein [Arabidopsis thaliana] gb|AAK62405.1|AF386960_1 putative protein [Arabi, mRNA sequence\n")
-		f.write("TCGTGCCGCAATCATGGTGGTTTCTCTTGCTGGGTTCGCGGGTGCGTGCTACAGGAACACCTTCCTCATG\n")
-		f.write("TGGGTGTACCTGTTCGTCATGTTCTTCGTCATCGCCGCCCTCATCGGCTTCATTATCTTCGCCTACGCCG\n")
-		f.write("TCACTGACAAGGGCTCCGGGAGGTCGTTGACGAATAAGGGTTACAAGGACTACTACCTGCAGGACTATTC\n")
-		f.write("CGGCTGGCTGAAGGACCGCGTGGCGGATAATGGCTACTGGAGGAAGATTGCGTCTTGTGTGAGGGACTCA\n")
-		f.write("AAAGCTTGTCAAAAGATCGGGAGGAGTGTGAATGGTGTGCCTGAGACTGCTGACATGTTTTACAGCAGAA\n")
-		f.write("AGCTCAACTCTATCCAGTCTGGCTGCTGCAAGCCACCTACAGAATGTGGATATAGCTATGTGAACGAGAC\n")
-		f.write("CGTCTGGACCACCGGAGCAGGTTTTTCCGGGACCAGTACGGACTGCACACTGTGGAGCAATGACCAACAG\n")
-		f.write("CAAA\n")
-		f.write("\n")
-		f.write(">gi|226791113|gb|GO545950.1|GO545950 Mdas9008I03_e601.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27882.2|AF139470_1 chlorophyll a/b-binding protein CP24 precursor [Vigna radiata], mRNA sequence\n")
-		f.write("CCGTTGTTAACGGCATTTAAGTACCAATTAAATTGAAAAGGATAAAAAAAAATTGGGTAATTATTTATAT\n")
-		f.write("CTACATATTGAAAAGTAAATGCCAAATGGTTTACAACCCAAGGGCACCAAGGGGCGTCTTTCCTTGCCCA\n")
-		f.write("CCTTCAAAGTAAAAAATGAGCATACCCACCATACCAAGCCTTGCATGCTTAATCTCACCCAGTTTCAGTC\n")
-		f.write("TCTCCAACTTTTCCCTGTCTGGAACGTAAACCCCGTCCTGAATGGACCCGGCAAACCCCAAGGGGTCAAA\n")
-		f.write("AAACTTGCCACCCGGGTACCCTTGCTCTCCGGGGGAGTTGGCAAATTTCTCCAAGGTCTTGGACCAAGGT\n")
-		f.write("GTGGCCCACTCAACGGACTGGGACTCAGGGTTGTAAAAGTCCACCCATCTCTTGCTTTCCACCCATCCCA\n")
-		f.write("TGACCAAAACCTGAATGCCAAGCAGTG\n")
-		f.write("\n")
-		f.write(">gi|226791112|gb|GO545949.1|GO545949 Mdas9008K19_e610.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTGTTCTCGGAGTCTACAAACTTGGATTCAAGAGCAAACTACGACAATACACAACGTCAATGCATGACCG\n")
-		f.write("ATCTGGTAAATAGTAGAAGATCCAAAATAAAGCTGTAATGTTGGCAGACGAAGACATGTTTTACTCGAAG\n")
-		f.write("AACAAGAGGTTTGTACCAAAACAATTAGTAACTGATTGCACAGCCATACCCCATTTGATCGAAGAGAAAT\n")
-		f.write("GAGATGTACACATCGCACGCAACACCTTCTCACTATAAAAGGGGTTCGTCGTCACCGTCATCTTCCATAT\n")
-		f.write("TATAATCATCTTCATCATCATCAACATCAAAACCCTTATAATAATCATCATCACTAAAGTCCTCCTCCTC\n")
-		f.write("TTGTTCCTCCTCCTCTTCATTTTCATCTTCATCCTCACCTTCACCTTCTTTCTTTTCTTTTGTATCATTT\n")
-		f.write("TGGCCCTGACGCTGCTCGAGCTTTTCAAATAAATCCAACTTCTCCAGCCCTGAGTTAGGATTCCATCGAA\n")
-		f.write("CTCTCTTTCGACCTGGCTGCTGCACCCTTGAACCTCCGGTCAGTTCTTGAGGAAATCCCTTGAGCTCCAA\n")
-		f.write("TATACTAAAAAGAGAACCGCGTCTTATNCGTGGTTTTTGGCTTTGTTCTGTCAGAATATCTTTCTACATC\n")
-		f.write("TTCGTTTTGCCTCTCATTCGA\n")
-		f.write("\n")
-		f.write(">gi|226791111|gb|GO545948.1|GO545948 Mdas9008L16_e618.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_178536.1| GDSL-motif lipase/hydrolase protein [Arabidopsis thaliana] pir|A84459 probable GDSL-motif lipase/hydrolase [imported] - Arabidopsis thaliana gb|AAD25823.1| putative GDSL-motif lipase/hydrolase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTAAACCATTCAAATTCATAACTTATACCCAAACGCTGCCACAAATGTACTTTCACACAACATA\n")
-		f.write("TAATTGTTGTCTTGGGTCACTCAGAAATGGGTACAGGAATACGTACTAATATCACAGGCACCATAGGTCC\n")
-		f.write("ACAAGATCCTAGGCTTAATTCCATTTTTCTGCAAACAACATATTCTTCTACCAACACAGCATCGCGTAGA\n")
-		f.write("ATACATATATGATGACAAAGCATATATATGGCGCGTACATTTCTCTTGAATTTGAAGCTAATCAAAGGAA\n")
-		f.write("CTGGGCAAGTACTTTTTTCACCACATAATCAGAGATTATACGGTTTGCTTTTTCAGTAGGATGAAAGGCA\n")
-		f.write("TCCCAGAAAATGTATTTGCTTGCGTCTGTGCAAGTGAGCAAGTTGTTTCGATTGCATGCGTAGCCCATTT\n")
-		f.write("CAAACATTCCACTGGCACAACACGCCGCCGATGACACCTCGAATCCATAAAAAGAAGGCCTTCTTATCAT\n")
-		f.write("ATGCAGGAAAATGTAATATGGGTTTGAAAAAACCAATTTGATCCCAGGAAGCTGTTTATTCAGATTTGTA\n")
-		f.write("GTCAAGGTCTTCAGCTTGCCATTGAACTCTAAAGCCACA\n")
-		f.write("\n")
-		f.write(">gi|226791110|gb|GO545947.1|GO545947 Mdas9008K18_e609.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568487.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTACCTGCTAATTCGATATTCATACGCTAATGTGGTTTTAACGAGAACAACAACATTGCATTATCT\n")
-		f.write("GCTAATGCTACATAACGAGAACCTTTACAACTGTGGTCTGTGCAGCAATTCCTAATTCCTTGACTAAAAC\n")
-		f.write("TGAAGTTTCATGCCCTTTATACACGACACTCGACAGTACAATGATTTCATCGCTTTGAGAACACCACCAA\n")
-		f.write("GATCAACATGGACATAGACATCATGATTTTGAAACCGGAGGTTTCCCAAAAGTTTTGTCTTTCAGCAGCT\n")
-		f.write("GCAGCTCCACCACCACCCCGCTGTAACTGATCTTTGAGCTCTTTCAGAGCCTTGTCTCTCCGCTCACCCA\n")
-		f.write("TCCTTTGAAGCTTTCGTGTTTGAGCACGAGCTTCCTGGAGACAAAACTCTAATTTCAAGACCCTCTTTTT\n")
-		f.write("CAGTTCCTGATCAACGCGTCGTTGTTTCTCCAACTGTGATTCAAACTCCTTAGTTTTGAGCTTCCAATGA\n")
-		f.write("GCAGACATTACCCTGATTTCATCTT\n")
-		f.write("\n")
-		f.write(">gi|226791109|gb|GO545946.1|GO545946 Mdas9008E19_e583.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM64550.1| unknown [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGCACCCGTTTTCTCAACATTTCTGTTACATCTCTCACTTTGCTCTTCCTAAGGAGAGCTGAGATGGAG\n")
-		f.write("GATTGCAACAGAGGCCAAGACTATTTCTCTGCCCAAGACCATGAGTCAGCAGCTACCAACAAATATGGAG\n")
-		f.write("GACTTGCGCCAAAGAAGAAGCCTTTGATTTCAAAGGATCATGAACGTGCCTTCTTTGATTCAGCAGATTG\n")
-		f.write("GGCACTATGCAAGCAAGGTGCAGGGGTGAATCCGAAATCAACAGCAGCAGTGGAGACCTTACAACCAAAG\n")
-		f.write("CTCCAGAGAACTCCACACCAGCAGCTCCCCCCAAGGAGACCTGCTTGTACATCTGGCCATGAATGATATG\n")
-		f.write("CAGCCTCGGAGCATAGAGTCGTCGAGGGCTCAAAGTAGTTTGTTGTTTGAGAGGATTAATGTTGATGACA\n")
-		f.write("AAGCTATATATATAACAAGCATCGGAATTGGCTGAATGTAATAATTGTCAGTTAGTCTTTTTTTTATTTT\n")
-		f.write("TTATTTTTTTATTTTTAATAAG\n")
-		f.write("\n")
-		f.write(">gi|226791108|gb|GO545945.1|GO545945 Mdas9008K07_e607.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTTTTTTTAATAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCG\n")
-		f.write("ATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAG\n")
-		f.write("ACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCAC\n")
-		f.write("AATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAG\n")
-		f.write("CGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTA\n")
-		f.write("GGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTC\n")
-		f.write("CACATTGTCCAGTACCTTCCATCTTAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCT\n")
-		f.write("CCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCA\n")
-		f.write("\n")
-		f.write(">gi|226791089|gb|GO545944.1|GO545944 Mdas9008O06_e627.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_199223.1| casein kinase, putative [Arabidopsis thaliana] dbj|BAB10977.1| casein kinase I [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTGACTATGTGTTTCAGAGAAGTAAGTTGCAGTAGACACCGGATGCCTCTGCTTCCATAACTGCACCTG\n")
-		f.write("CTACCCCTGCAGCTTTACCCCCTGGACCATCTGCGTAAACATCAGACAGACCTACAGCATCGGGACGAGA\n")
-		f.write("TTTTCTAGAAAGACTCTCATGTGCGTTAGAGGCATTTTCTATAAGGAATAGTTCTGGTCATGGTTATGGC\n")
-		f.write("GATCACTCCAGACATAGGTCGACCGATGATGCGCCATCGTCCAAAGACGTCCAAACTGATTCAGAAAGGG\n")
-		f.write("CTCGTAGTTCATCTACAAGTGGCAGTAGTTCAAGGAGGCCAGTCATATCAAGCAGCCGGCCAAGCTCATC\n")
-		f.write("TGGTGAGCCCAGCGAGAGTCGGTCAAGCCGGCTGGTCTCAAGTAGTGGCCGCCTGTCCACCACCCAAAGG\n")
-		f.write("GTTCAACCTGGGTATGAACCCAGAACATCTTTCACCCGAGCATCCGCTGCAAGAGGTGGCCGTGATGACA\n")
-		f.write("CACTTCGGAGCTTTGAACTCCTTTCAATCGGCACAGGAAAGAGGAAGTAAGGTCTCAAGATT\n")
-		f.write("\n")
-		f.write(">gi|226791088|gb|GO545943.1|GO545943 Mdas9008F07_e588.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCTCAAAATACTAGAGCTAGACAAAGATAAACAACACGATAGAGAAACTTCTGCTTTACATGTACATTGA\n")
-		f.write("CATTTGCATGTGCAAAGCTCTCTTTCCTCCTTTCCTTTCTTTTCTTCCTCACCTTTCGAATCTTTCTCCT\n")
-		f.write("AAATTAAGGAGATTGTTGTTTTGTTGTTAGTGGTTGCCATCATCATCACATTGAAATCAACTTTAGTTAA\n")
-		f.write("TACTAGCCTCCTGCACGCGCTCACGGGCGTGCGGAAGGCCCTTTTGTAATTAAGGCATTCTACGTGCGAC\n")
-		f.write("TTAAATAATTTAAATGATAACAAAAGAGCGGTTGCTCTCTGATCTAATTGCAGACACAATCTGCAGAACC\n")
-		f.write("GTCTTCTATGGGATTTGAACTTGTGAAGTGTGAGGTGGAGACCTCTATTACAAAAATGTTACAACAGTAG\n")
-		f.write("ACAAAAAAGGCCAAAAATACCAAAAGCCGCACCTCCTATACTCCATGTGTGGACTCCAATTTTCAATCAC\n")
-		f.write("AATTCAAAATTCAAGAGGCCTGTACAGTGTTCAGATGTAGCAATCCTATGCAATCGGCCAAATGATGTGT\n")
-		f.write("GTCCTCTCAAAGATCTGGTTTGAGAGAGTGGGACACCATCGG\n")
-		f.write("\n")
-		f.write(">gi|226791087|gb|GO545942.1|GO545942 Mdas9008G21_e594.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM23005.1|AF502434_1 orcinol O-methyltransferase [Rosa hybrid cultivar] emb|CAD29459.1| orcinol O-methyltransferase [Rosa chinensis], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTAACAAAAAAGCACATCAATCCCAAACTGGTCCATAATCATATGGTATGCATTTT\n")
-		f.write("GACAGTACTTATTCAGCAATCAGCATCCACATAAATCATATATATCACATGGTTGCTTCTAACTTTCTAA\n")
-		f.write("AGAAAAACTTCAATGAGGGATCTCAAACCAAATATTGGTGTCACCTTGTAGCCGCTGAAACCAGCCTCCA\n")
-		f.write("GGAAGAGCTTTTTCCAGTCTTTCTCGCTCCTCTCTCTTCCAGTGACCACAACCATCATAAGCAGATCAAA\n")
-		f.write("CAAGAGCTTTGCTTCGGTTATTTCATGCTCATCTTTCTCTTCATTTATCACTATGTCTATGATTATAACT\n")
-		f.write("TTCCCTTGGCCATTGCTTGCAATTGCTTCCCTGCATTTCTTCAAAACCTTCAAGCATTCCTCATCGCTCA\n")
-		f.write("GAGCATGCAAAGTCAGCTTGAGGAAAACAGCATCCGCTGGAGGGATAACCTGGAACATGTCTCCTCCAAC\n")
-		f.write("AAACTTCAAATTCTCACTGTCTGGCAAATCAGCAACAACGTGTGGAAGTTCAAGAACTGTGCATTTCAGT\n")
-		f.write("TGAGGGAAAGCGTCACAGAGAATCCTAGCAACTTTTCCAGTCCCACCACCAACATCAACCAATGAACTCA\n")
-		f.write("AC\n")
-		f.write("\n")
-		f.write(">gi|226791086|gb|GO545941.1|GO545941 Mdas9008L07_e614.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T09544 phosphoprotein phosphatase (EC 3.1.3.16), catalytic beta chain - alfalfa emb|CAA05491.1| protein phosphatase 1, catalytic beta subunit [Medicago sativa], mRNA sequence\n")
-		f.write("TTTTTTTTTAACTAGAAGACCCAGAAAAATTTCCCGAATTTCATCACAGGCATCTGGCTGTTCTGACATT\n")
-		f.write("TTCCATGGCCTCGGAGAGACTAATAATTCATAGCAGCAAATTAGTGTACAAGGACGAAGAGAAGAAGATA\n")
-		f.write("CACAGCCTTCTACCTTCTAACCCAACTTTATACCATTCTGCATTATTTTCTAGTGATTACAGTGAAATTA\n")
-		f.write("AGTTGGCTCTCATGCTTCCCGATGGAACCCTTGGCTCGATCATGATACAAACCGGGCTTCGGCACCTTCC\n")
-		f.write("CTCTCCGCCAAATCAAACATCTTACCTGTGCATCATGGACCTGATTCCTGTAACAGTGTTCCCAGGCTTA\n")
-		f.write("GCTGTTGCTGTGCTCGCAAAAGCGCTAACTCCAGACGAAGTATTTCCAGGCTTAGCTGTAGTCATGCTCC\n")
-		f.write("CAAAATTGAATTTCGGCTTTTTATCTGCAGGTTTTAGTATTTGAAAAGAGCACATTAATGTCTCATCCAC\n")
-		f.write("ACTCATCATGGCACCGGCATTATCAAATTCCCCACAATAATTAGGTGCTGAAAATATCGTCACAAGTTGG\n")
-		f.write("CGGTTGGCAAATAACTCGTAGCCATCCTCCACAACCTGGTGAGCACGACAAACGAGATCCAAATCGTGCT\n")
-		f.write("TCTGAAGAAACTCCGTCACTGTGTCAAGACCAAATGTAAACGAAACTCCACGGTCGTTCCTTCCCCACCC\n")
-		f.write("TTGACATCTTTACT\n")
-		f.write("\n")
-		f.write(">gi|226791085|gb|GO545940.1|GO545940 Mdas9008I07_e602.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176897.1| glyoxal oxidase (glx1) -related [Arabidopsis thaliana] gb|AAG00252.1|AC002130_17 F1N21.11 [Arabidopsis thaliana] gb|AAO22637.1| putative glyoxal oxidase (glx1) [Arabidopsis thaliana] gb|AAO42437.1| putative glyoxal oxidase (glx1), mRNA sequence\n")
-		f.write("GAAACAAAATATCAATTAATGCTTTACGGTTCTTATCCACATTTAATTCATCCACGAACTTTCTAACCAA\n")
-		f.write("AAATTAAAATCATACATCAAGACACCAGATGTATCCAGCGCGCAACACTTGGCACGCCCTGATTGACCGC\n")
-		f.write("AAATGCCATGTAATAACCCGGCGGAGCAACCATCCCATTCGGCGGCGCCACACAGCTAATCCTGTAACGC\n")
-		f.write("CCCTCACCGTCCGGCACCGACGGCGTAACGGCCAGTTTGACCAGCCGCTGACCCTGCGAAAACGAATGCG\n")
-		f.write("TGGCAAAAGGCGCGTTCCCCAAATTAACCTCCACAACCCCCACCACGGACAGCGGAACCGACACCGTAAC\n")
-		f.write("GTCAAAACTCTCGCCGTAGCGCACCGTTTCGGGTATCCCCTCGAAAATGGGTCGGAGATTCGCCCGGTCC\n")
-		f.write("GGACTCAAATACTCGGGCGAAAACGCTTCGATTCGTAACTCCGTGGGAAACTCGGCGTCGAATCTGTAGA\n")
-		f.write("AATAATGCGGATTGCTTCCGGCGATTAATACCCGTCCATCGGGTAAGAGATTCGCGGTGGAGTGGTACAA\n")
-		f.write("TCGGGGCACGGT\n")
-		f.write("\n")
-		f.write(">gi|226791084|gb|GO545939.1|GO545939 Mdas9008N11_e625.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGAGCAATGTCAGGTAAGTAATCAGGCAAGGGGTTCCGGGCAGTCAGTTCCTGAATGGAAGCTTGAT\n")
-		f.write("TCCAAGTGTTGACTGATTGCTCTCTTTCTCATTGTCTTGCAGGTAAGAACAAGGTCAAAGGAAAAGACAG\n")
-		f.write("GGAAAAAGCATGATATGGGATACTCTTGCTCTTGTGTGGCTTGTTTGCAGAGGTATTATCGGGAGGAAAA\n")
-		f.write("TAAGCTGAGTATTTCGAAAGACTCTGCTGAGAGTGCCCTCTCGAATGTGAAGAAAAGTTGAGCATTTTTT\n")
-		f.write("TTTATTTGCGGGTTTGCCTGGCCGTGGAGGATGGAGGTCGACATATATAGAAGTCTCCCTAACAACAAGT\n")
-		f.write("AGTAATGCTATTCCTTTACCCTTCTTGATCATAGCAATGTAGTAGGAGCTGCAAGCTTCACATGTTTTAA\n")
-		f.write("CTTTGTCAGAACGCTTTGAAAAAGTGGTATGTGGTATCTGGAAAGCTGATGTTGCGTATAAAGATTGCAG\n")
-		f.write("ACAAGCTTTATCCCAGGAAATCTGGCTCTCGAAGTTTGGAGAGCGGTGTCTCTTCGGTTTTCGAACAAGC\n")
-		f.write("AATCCTGTCGGGGATCTGGC\n")
-		f.write("\n")
-		f.write(">gi|226791083|gb|GO545938.1|GO545938 Mdas9008O18_e633.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCAAACACATATTGTAGCACATAGTTCAAATTATTGTTGTCCAAT\n")
-		f.write("ACTTGGTACCAAATTTACATCACCGACAACAATACAAACGAAAGTACAAGACAACTCCTGAGCTCTCACT\n")
-		f.write("TTCCGGGAACAAAGTTTGTGGCGTATTTCCAGGCATTGTTGGCGACTGGGTCAGCGAGGTGGTCGGCAAG\n")
-		f.write("GTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGAACAAAGAATCCAAACATGGAGAACATGGCCAAC\n")
-		f.write("CTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGT\n")
-		f.write("CAAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTC\n")
-		f.write("AACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAAATGCTCTGTGCATGGACCAAGC\n")
-		f.write("\n")
-		f.write(">gi|226791063|gb|GO545937.1|GO545937 Mdas9008N16_e626.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n")
-		f.write("TTTTTTTCCTTTTTTTTTTTTTTTTTTTATTTTCTTTAATAACTCATTTATTAAGTACCAAAAAAAATAC\n")
-		f.write("AAGGGCCGTTTATTATATTTTCCTTTGCAAGGCCTAATGCAAAGGGCGAATAATGAAGTTTTCAAACTAA\n")
-		f.write("CAAATAAATGAGCTTCTGGAAAATTATATGAAGCTCAGTTTATTGTAAGTAAAATTCACGATAGTTTCCA\n")
-		f.write("TTTCGCTTCCGTTGAACAGCCTTGGAAAAAGTTGCGGAGGCAGCAATTCCAAGGTTTTTGAATGGCACGC\n")
-		f.write("TTATGCATACACGTCTAAGCCCCAAGTCTTGGAAGGTAAACTGGTACGATACTTCCTGTCAATACTGTAA\n")
-		f.write("ATGAGCTGCATGTCTTCATCCCTCAGCTGGAATTCAAGAACCTCCAAATTCTCTTTCAATCGCTGAATTT\n")
-		f.write("TCAATGATTTTGGAATCACTGCTGTTTTCCTCTGAATTCCCCACCTCAAACAGATTTGTGCCACGCTCTT\n")
-		f.write("TCCGTATTTCTTACCCACATCATTGAG\n")
-		f.write("\n")
-		f.write(">gi|226791062|gb|GO545936.1|GO545936 Mdas9008O07_e628.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_193170.1| casein kinase I (CKI1) [Arabidopsis thaliana] pir|C71405 probable casein kinase I - Arabidopsis thaliana emb|CAA55395.1| casein kinase I [Arabidopsis thaliana] emb|CAB10213.1| casein kinase I [Arabidopsis thaliana] emb|CAB78476., mRNA sequence\n")
-		f.write("TTTGACTATGTATTTGATTGGACTATATTGAAGTATCCGCAAATTGGCTCCAGTTCCAGAACACGACCAA\n")
-		f.write("GTACAAAACCAGCTTTAAACCCTGGACCATCTGCAGAAAGAACAGAAAGACCTACAGCAGTGGCACAAGA\n")
-		f.write("TTTTCGAGAAAGACTCTCAGGTGCAGTAGAGGCATTTTCTAGAAGGAATAGTTCTGGTCATGGTTATGGC\n")
-		f.write("GATCACTCCAGACATAGGTCGACCGATGATGCGCCATCGTCCAAAGACGTCCAAGCTGATTCAGAAAGGG\n")
-		f.write("CTCGTAGTTCATCTAGAAATGGCAGTAGTTCAAGGAGGCCAGTCATATCAAGCAGCCGGCCAAGCTCATC\n")
-		f.write("TGGTGAGCCCAGCGAGAGTCGGTCAAGCCGGCTGGTCTCAAGTAGTGGCCGCCTGTCCACCACCCAAAGG\n")
-		f.write("GTTCAACCTGGGTATGAACCCAAAACATCTTTCACCCGAGCATCCGCTGCAAGAGGTGGCCGTGATGACA\n")
-		f.write("CACTTCGGAGCTTTGAACTCCTTTCAATCGGCACAGGAAAGAGGAAGTAAGGTCTCAAGATTCCTTTTGT\n")
-		f.write("ATTATCTATCAAAGATATGTCTCGGCACTAAAATGGTTTTGGCACAGCTTACT\n")
-		f.write("\n")
-		f.write(">gi|226791061|gb|GO545935.1|GO545935 Mdas9008F10_e590.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n")
-		f.write("CTTGTATCCTTTTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCC\n")
-		f.write("GTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCA\n")
-		f.write("AACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGTACTTAGGCCCATTCTCCGGTGA\n")
-		f.write("GCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCTGGACTCTC\n")
-		f.write("\n")
-		f.write(">gi|226791060|gb|GO545934.1|GO545934 Mdas9008M21_e622.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P19950|R141_MAIZE 40S RIBOSOMAL PROTEIN S14 (CLONE MCH1) pir|A30097 ribosomal protein S14 (clone MCH1) - maize, mRNA sequence\n")
-		f.write("TTTTTTTTCTTTTTTTTTTTTTTTTTTAGACCAAAAGATACTTCATTGCAGACCAGAATAACAGTATAAA\n")
-		f.write("TAACAAAACAAAACTTAAAAGAGTAGCAGAACTCTTTCCGAATTAATTGGAAATAAAACTTTCGAAAAAC\n")
-		f.write("ATAGTAAAAAACTAGAGAGTTTCGAAACCGAAAGTAACAGCGCCTAATTTCGAAGTAACATAATCCAACT\n")
-		f.write("GAGGCACAGCGACCACCCTGACAAGCAGTTCTGACCAGATAAGAGGTGCAAAGCTTACAGCCTCCTTCCT\n")
-		f.write("CTCCTTCCACCCTTTCTACGGGGGCTGTCAGTTGGAATTGGAGTCACATCCTCTATACGACCAATTCTCA\n")
-		f.write("TTCCAGAACGAGCAAGAGCACGGAGGGCAGACTGGGCACCTGGACCAGGTGTTTTTGTTTTGTTCCCGCC\n")
-		f.write("AGTGGCACGGAGCTTAATATGAAGTGCAGTAATGCCCAATTCCTTGCATCTCTGCGCAACATCCTGTGCT\n")
-		f.write("GCAAGCATAGCAGCATATGGGGAAGACTCGTCCCTGTCAGCCTTCACCTTCATACCACCGGTGATACGAA\n")
-		f.write("CAAGGGTTTCTCTTCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226791059|gb|GO545933.1|GO545933 Mdas9008I21_e603.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197053.1| UDP-glucose dehydrogenase-related protein [Arabidopsis thaliana] pir|T51527 UDP-glucose dehydrogenase-like protein - Arabidopsis thaliana emb|CAC01748.1| UDP-glucose dehydrogenase-like protein [Arabidopsis thaliana] gb|AAL07049.1, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTATAATTTCCTGGTTTCTGATTTTATTACATTAATCTAAGAGAA\n")
-		f.write("TAACAAATTGAGATATATTCCACTAAACTGAGGACAAACTCAGGAACCGTATTAAGGGTACTATTACAAG\n")
-		f.write("TAAAATATGACGCAACATAACCCCCAACTTTAAGAAAGGTGAAATAACAAATTAATACAAGAAGATAAAA\n")
-		f.write("ATAAGGACGAATTAAGCATCCACTCTCAGTAACAAACTTCGGAACTGATAGAACTTTTACGCACAAGGGG\n")
-		f.write("ATCGATCTTCAAATTACTGTGCTTCTCTCCTCATCATCAAGTCTTTACGCCACAGCGGGCATGTCCTTGA\n")
-		f.write("GCCACTCGTCCAGGGGCTTTCCAATCGAGTAAACAATGAACCCAATTTGCCTCAGCTTCTCAGCATCCAC\n")
-		f.write("CACGTTCCTTCCATCGAACACAAATGCAGGCTTCTGCATCTGATCATAAATCTGTTGGTAATCAAGACTC\n")
-		f.write("TTGAACTCATCCCACTCGGTCAGGATGCAGATTCCGTGAGCATCCTTTGTTGCCGCATAAGCATCCCAGG\n")
-		f.write("CTACACCAACTTGCTTCACAGCAGGGGGGCTCTGAGGTTGAAGATGAATG\n")
-		f.write("\n")
-		f.write(">gi|226790978|gb|GO545721.1|GO545721 Mdas9011D23_e829.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568984.1| protease inhibitor/seed storage/lipid transfer protein (LTP) family [Arabidopsis thaliana] gb|AAL50083.1| AT5g64080/MHJ24_6 [Arabidopsis thaliana] gb|AAM10364.1| AT5g64080/MHJ24_6 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTGAGTTTTCACAATCCCACAAGAAAAAATGGGAGCAGCAACGACTCTGGTGGTGGTGATGGCGGTGCTG\n")
-		f.write("CTGTTTGGACTTGGGGACTGCGCGGCGCCGGCTCCTGCGGTGGACTGCTCGAGCCTGATCTTGAACATGG\n")
-		f.write("CGGACTGCTTGTCGTTTGTGTCGAATGGGAGCACGGACACGAAGCCTGCAGGGACTTGCTGCAGTGGCCT\n")
-		f.write("CAAGACTGTTCTCAAAGCCGACGCTTCCTGCCTCTGTGAGGCCTTCAAAAGCAGTGCTCAACTCGGCGTC\n")
-		f.write("GTTTTGAACATCACCAAGGCCATCTCCCTCCCCGCCGCTTGCAAAGTCTCCGCTCCGTCTGCCTCCAACT\n")
-		f.write("GTGGATTATCTCTCAGTCCTGCTGGTGCTCCTGGTGGAGCACCTACCTCGCCGGCACCTTCTCCAATGTC\n")
-		f.write("AGGTGCTGACATTGGTGGTGCACCAGCGTCGTCGACTACTGGAGGGAATGAGCAAACACCCGCTGCATCT\n")
-		f.write("CCTCAGGGAAGCTCAGGTTCTTTTATGCTCGCTAGTTCGGTTGGATCCCTACTTGTTGGTCTTGTAATTG\n")
-		f.write("CATCATTCCCTTGTTTCTGAGAGCCGAGTTTGGTGGTGCCATTTTTGTGAGTAGAGAGGGATGATGTGAT\n")
-		f.write("ATATGGCACTTATGTTTATTTTACCATTGGAGTTAGTTCATTCTGAG\n")
-		f.write("\n")
-		f.write(">gi|226790977|gb|GO545720.1|GO545720 Mdas9003B09_e178.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL38341.1| chlorophyll a/b-binding protein [Arabidopsis thaliana] gb|AAM47913.1| chlorophyll a/b-binding protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTGACAATTAAACAAAGGAGCTCGGTGGTTTTACTGGGTACAGCGATTTCAATACAAGCAGT\n")
-		f.write("TTCTAGTAAAATTAAATCGGAAACAGCCATGGATTTAGGTTTCTTCACTTTCCAGGGACAAAGTTGGTGG\n")
-		f.write("CGAAAGCCCATGCGTTGTTGGCCACTGGATCAGCAATGTGGTCAAAGAGGTTCTCGACTGGGCCCTTTCC\n")
-		f.write("TGTGACAATAGCCTGAACAAAGAATCCAAACATCGAGGTCATAGCCAGACGCCCGTTCTTAAGTTCCTTC\n")
-		f.write("ACCTTCAGTTCAGCAAAAGCTTCAGGATCATCAGCAAGTCCGAGTGGATCAAAGGCACCTCCTGGGTAAA\n")
-		f.write("GTGGGTCAAGTCCTTCGCCGAGTGGTCCTCCACCAACTCTGTATCCCTCAATGAATCCCATGAGCACAAC\n")
-		f.write("CTGGACAGCCCAGATAGCCAAGATGCTCTGAGCATGGATAAGGTTTGGGTTGCCAAGGTAGTCAAGGCCG\n")
-		f.write("CCCTCGGAGAAGATTTGAGATCCAGCCTTGAACCAAACTGCCTCGCCGAACTTGACCCCATTCTTTGACA\n")
-		f.write("AGATTTCTGGGAAGACGCATCCCAGTGCAC\n")
-		f.write("\n")
-		f.write(">gi|226790976|gb|GO545719.1|GO545719 Mdas9011H20_e847.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTA\n")
-		f.write("TTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGG\n")
-		f.write("TAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAA\n")
-		f.write("GAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCC\n")
-		f.write("TCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAA\n")
-		f.write("GGGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAG\n")
-		f.write("AATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCT\n")
-		f.write("CCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGC\n")
-		f.write("CCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGCAAAGGTTTCGGG\n")
-		f.write("GTCTGCTGATAGCCCAGCAGTGTCCCACCCGT\n")
-		f.write("\n")
-		f.write(">gi|226790975|gb|GO545718.1|GO545718 Mdas9011M23_e876.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564094.1| coronatine-induced protein 1 (CORI1) [Arabidopsis thaliana] sp|O22527|CLH1_ARATH Chlorophyllase 1 (AtCLH1) (Chlorophyll-chlorophyllido hydrolase 1) (Chlase 1) (Coronatine-induced protein 1) (CORI1) pir|E86329 coronatine-induced pr, mRNA sequence\n")
-		f.write("TTTTTTTTTGCTAGTACATGATTAATGAATTAGAAAAATTGAGATGGTGCTAGTACATATCAACCCCCAA\n")
-		f.write("ATTTCAGTACTTGAGCACATGCATTTGATGACTGAGCTGTTTATTCGAAAGTAACAATCTAGGATCCGAA\n")
-		f.write("ATAACCCTCGAAGAAAGCCTGAAAATAATCACTGACATTAACCACTGATAGGCCTTATAACCCCCTCTTT\n")
-		f.write("ATGTGCTAATATGTGCAGCTAATGTCAGTGACTATTATCAAGACAACCTTGAGCTTGAACTTATGCTCTA\n")
-		f.write("ATGAACTCCACAGGTTCAAGCTTTGCAGGAGAACTATCAGGATCACCAACAATGGCAACCAAATCCCTAT\n")
-		f.write("CATCACCATTCAAATAAGCATTCAGAAACGCCACAACAATCCCACCCACAGTCTTCCTCATTAGCTCCCT\n")
-		f.write("CGGTCCTGTCCCGTTTTTACACATGCACCCCGACACTGCCCCAACCATGCCCTGTGGATCGTCGTCCAAC\n")
-		f.write("ATGTCCATGTGACCATAGTCCTTCACAACAAAATGTGCACATGGAGGCTTGCACTCATAGAAGAAATCCT\n")
-		f.write("TGTGGTTCACGCCATCTGGGGCACAAGGTTTTGACATGCAAGCATTTTTACCTTCCGGTCCCAGGCCAGC\n")
-		f.write("GCCGATCACTATGACTGGAATCGAGAGGTC\n")
-		f.write("\n")
-		f.write(">gi|226790974|gb|GO545717.1|GO545717 Mdas9003A11_e173.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T05875 hypothetical protein T29A15.190 - Arabidopsis thaliana emb|CAB38282.1| hypothetical protein [Arabidopsis thaliana] emb|CAB81420.1| hypothetical protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTTTGACGGAATTCTGCAGTTCAGTTGATCGAAAAAGAGAAATGATGAAG\n")
-		f.write("ACATTACGGGCGGAAATCATCCGGTCGTTGTTATGTTTAGCATCATTACAAGAACATTCAATTTGAATCC\n")
-		f.write("GAATTCACAAGCTGTTAGTTATGATAAGAAATCAATGGCAAGCACGCACGCACTCAATTTATGAACAAAA\n")
-		f.write("CACGCTCCTTTGAAGGAACTTTCTTTCATACCGCCACCGGTGTTTCACTCTTCTTCTTCTTCTTCTGCAA\n")
-		f.write("CCGATGGCAGCCCCTCTTTGAACCACGCGTAAAGTCCGCCTTCTAAGTGGAAGACATTCGTATAACCGTT\n")
-		f.write("GAGGACGAGCAAGTAGGCTGCTATCAGTGATCTTGACTGTTGGCCTTCTGGGAGATTTTGGGTCGGTCTC\n")
-		f.write("ATCGTACCGCCGGCGGCGCAAGCCACTATTATCTTTGCCTTCTTATCTAGCTGCGATCCCACACTTGATA\n")
-		f.write("TGAACTCAGGGTTCTCTTCTGTGCCGGCAAAGATGCCGAAAAACGCGAAAGCAGCACGGCGGGCAATGTC\n")
-		f.write("CCACGCTGTCCACTCCTTTATAAGCCTGTATATTTGCACGTTAA\n")
-		f.write("\n")
-		f.write(">gi|226790973|gb|GO545716.1|GO545716 Mdas9011F04_e835.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n")
-		f.write("ACCGGATCGGTGTTTGCACCGGAATCTTCAAGCCTGATAATGTGTCCCAGGAAGATGTTGTCAAGATTGT\n")
-		f.write("TGACACATTCCCCGGTCAATCCATTGATTTCTTCGGTGCCCTAAGGGCTCGAGTTTATGACGATGAAGTG\n")
-		f.write("AGGAAGTGGATTTCCGGTGTTGGAATTGACGGGATTGGGAAGAAGCTTGTGAACTCAAAAGAAGGTCCCC\n")
-		f.write("CGACTTTCGATCAACCTAAGATGACTCTGGAGAAGCTCCTTCACTACGGACAAATGCTTGTTCAGGAGCA\n")
-		f.write("GGACAATGTGAAGAGAGTCCAACTGGCTGACAAGTACTTGGCCGATGCAGCCCTTGGAGATGCAAACCAG\n")
-		f.write("GACTCCATTAACCGAGGAGAATTCTATGGAAAGGCAGCCCAACAAGTTAATGTACCAGTCCCAGAAGGCT\n")
-		f.write("GCACTGATCGAACAGCTGCAAACTTCAACCCAGCAGCAAGGAGTGACGACGGTAGCTGTCAGTACGAGTA\n")
-		f.write("ATTGGAGCTGAAGAAAATAAATATTCTGTTTGCTGGGTTATTGATATTTTCTTTGTAATTTGCGCTTGTA\n")
-		f.write("TTTCTATGGAAATTCTTGCAATTATTTTGTTTTAATTATTAAACAAGCTATTGATACTCCGGCTATTGAA\n")
-		f.write("CAGTCGATAAGAACATAATGTTATGTTGTTGAGAATATGTTGTCATTGTCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790965|gb|GO545715.1|GO545715 Mdas9011J14_e854.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK38342.1| seven transmembrane protein Mlo6 [Zea mays], mRNA sequence\n")
-		f.write("TTATCACGATGCTGCTCGGGAGGCTAAAGATTCGAGGCTGGAAGCATTGGGAGGCAGAGACTTCAAGTGA\n")
-		f.write("TGACTATGAGTTTTCCAACGATCCTTCGAGATTCAGACTTACTCACCAGATATCATTTGTTAGAGCACAC\n")
-		f.write("ACCAGTTTCTGGACTAAGATTCCTTTCTTCTTTTATTTCGGATGCTTCTTTCGACAATTTTTTAGGTCTG\n")
-		f.write("TTAGTAAGGCTGACTACTTAACACTGCGCAATGGATTCATCACTGTCCATTTAGGTGCAGGAAGTAAATT\n")
-		f.write("TAACTTCCAAAAATATATCAAGAGATCATTAGAGGATGACTTCAAGGTCGTCGTTGGGGTTAGTCCTCTA\n")
-		f.write("TTGTGGGCATCATTTGTGATCTTTTTGCTCCTTAATGTTAAAGGATGGCAGGCACTCTTTTGGGCATCCT\n")
-		f.write("TGATCCCTCTCGTTATAATTTTACTCGTTGGAACAAAACTTCAGGCCATCCTGACTAAGATGGCCATTGA\n")
-		f.write("AATTGCAGAAAGGCATGCTGTGGTTCAAGGGATTCCTCTAGTACAAGGATCTGACAAATNATTTTTGGTT\n")
-		f.write("TGGTCGGCCTCAATTGATTCTTAATCTTATCCATTTCGCGCTGTTTCAGAACGCATTCCAAATTATATAC\n")
-		f.write("TTTTTC\n")
-		f.write("\n")
-		f.write(">gi|226790964|gb|GO545714.1|GO545714 Mdas9003C11_e183.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24058|MT2_MALDO Metallothionein-like protein type 2 pir|T17014 metallothionein-like protein AMT1 - apple tree gb|AAC23697.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n")
-		f.write("AGTTTTTCATTAATTTAATCAGAAACACATAATACGATCCACCAAGTTAACACAACATAAAAACACAAAT\n")
-		f.write("ACGACTACTGCATGTACAAAGCAAACAGACAACAAGCAGCCATAACCTAGGACCAGATCCCAGCCTAATA\n")
-		f.write("GGACGTGCAGCTCAAAAAAAGCCATGGCCACTTTATTCTAAAAACACGACCTTCGTAAATTTGGATCATG\n")
-		f.write("ATTCATGATTACGACACACACGCATACATATATTACTGCTAAACATACAAGCCCCGCGAATCTCTTGCTT\n")
-		f.write("CATCAAAAGGGGACATCTGTCCCTCTCACTTGCAGTTGCAGGGGTTGCAGGGGCAGTTGTCTCCGCACTT\n")
-		f.write("GCATCCGTTCTCGGCAGCAACTCCCATCTCAGATGCCTCCATGTGAGACTTCTGGGGAGCAACTCCCATG\n")
-		f.write("ACGAGGGTCTCAGTGGTGGACCCCTCCATGTAGCTCAGATCAGGAGCCATCCCACACCCGTTGCAGCCAC\n")
-		f.write("TGCCGCAGCTGCAGCCGGAC\n")
-		f.write("\n")
-		f.write(">gi|226790963|gb|GO545713.1|GO545713 Mdas9011D10_e827.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n")
-		f.write("TTTTTTTATTCGTCAATCCATATTTTACTCATCATTACATTGCCCAATCATGGCCCTTTTTTCATCAATA\n")
-		f.write("TTGCAGTAAACAACATGAAAGTAAGGGTCCTTCCTTGCACCAAGATAACCCCATGACGCCCACACACAAT\n")
-		f.write("ATCCAAAAAGCCAAATTCTAACCAGAAAAGGCGGAAACAATACATAAACGAAGCAAATAGATAAATCAAC\n")
-		f.write("ACCGATATTCATGTCATCAAGCACCCACACTGTGAAGCACAACGGTCTCAACAGTGAGGCCAGGCCCAAA\n")
-		f.write("TCCGAAGAGTACGCCCCACTCCAGTCCTTCTCCAGTTGTTTTGAGTCCTTTCTCACCACACTTCCTCCTC\n")
-		f.write("ACTTCGTCCAAAATAAACAAGACACACGCACTCGACATGTTGCCGTAATCACACAGCACTTGCCTTGTAG\n")
-		f.write("CTTCTAGTTTCTCCGGCTTAAGGGCCAACTTGGACTCTACTTGGTCCAGAATAGCAGGGCCACCTGGGTG\n")
-		f.write("TGCAATCCAGAAGAGCGAGTTCCAGTCTGAAATGCCTATAGGCTTGAAGGCCTCGTTAAGGCTCTTTTCG\n")
-		f.write("ATATTCTTGGAAATAAGCCCAGGAACGTCCTTGAGAATGTGAAATGTAAGCCCTACTTCACGGAGATGGC\n")
-		f.write("\n")
-		f.write(">gi|226790962|gb|GO545712.1|GO545712 Mdas9011J16_e855.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM62737.1| Quinone oxidoreductase-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTACTGGCCAATATGATACATGTCAAATATGACGCAAAACATGTTACAAAGAGATAAGG\n")
-		f.write("CAACATCATATGTTCATCTTTATGTACACAGCAAAAGATGGCTCAACTGTTTTCTGTTTTCCTTCTCATT\n")
-		f.write("CAATTGGATGTATGACTACCTTTCCGGTGGCCCGATTTGTTTCAAGGTAAGAGAAAGCCTCCACAAGCTT\n")
-		f.write("GGAGAAGGGGAAGGGCCCTTTGGGGTCTATCACAGGCTTCACCTTCCCAGTCTCTAAGTACGGGTTTAGT\n")
-		f.write("TTCTTCAGAACTGCTCCGTTGGAAGTAACCACGAATCTGAAACCCGGAGGTGTTACTGCACCTGTTAAGG\n")
-		f.write("CCACCACACTGCCCCCTTCTTTCACCACCTTCACTGCTTTGTCACATTGACCAATAGCATCATAGACGAC\n")
-		f.write("ATCAAAATTTTCCGGCAATTCTTCCAAGTTCTCCTTAGTGTAGTCGATCGCTAAATCAGCACCCAAGCTC\n")
-		f.write("TTCAATAACTCCAGCTTTCCAGTGCTTGAAGTGGCTGCTATTCGTGAAGCTCCAAATACATGTTTTGCTA\n")
-		f.write("GCTGAATCACTAGGCTTCCAACTCCACCAGCACCATTCAGAACAAGCAAAGATTTACCGGCAGACAACCC\n")
-		f.write("GGTCTTTTCAAGAC\n")
-		f.write("\n")
-		f.write(">gi|226790961|gb|GO545711.1|GO545711 Mdas9011J11_e852.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n")
-		f.write("AATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAAATTCGAAAACAAAAGAGATTGCCTCGAA\n")
-		f.write("AAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGAAACCCTAATCAAGGACAAACTTAAACAA\n")
-		f.write("ACCACCGAAACCCTTAGGCTAAGAGCCACAATGGTACGTACAACAACAATATTAATTACGACGAAGAAAC\n")
-		f.write("ATGATGAAACATGAACAACAACAACAACAACAACAACTTAGTAGCCTGCAGGCTTGTAGGCGATGAAACT\n")
-		f.write("GATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGGATGAAGGCGTTGGGATAGGCCTTCTTG\n")
-		f.write("GCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCC\n")
-		f.write("AGTACCTTCCATCGTAGTATCCTGGGGGATTTGTGGTTCTCACGGTACACAAATCCATGCTCCAACTCAA\n")
-		f.write("ATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAATCAACTTCCTTGGCCAAGGACTCGGAAGAGAG\n")
-		f.write("AGGAGGAAGGTAAGAAGAGGGTCTCGAACTTCTTCAATCCAAGTGGAGGCCACACCTGCATACATTGCAC\n")
-		f.write("TCTTCCTCCAT\n")
-		f.write("\n")
-		f.write(">gi|226790960|gb|GO545710.1|GO545710 Mdas9003A10_e172.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA06245.1| elongation factor 1-alpha (EF1-a) [Cicer arietinum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTAAGAACAAAGCAACGAACATAGAAATTTAATGCAAAACGATGTTAA\n")
-		f.write("AGAGACAAAGCGCAGAAGTTGCAGACATTAATACGAAATTGTCCAATAACCAACTACACGACTCATCTCA\n")
-		f.write("ATGTATAAAGCAACCAAAAACCATAACAAATAGCATACAACACAGCTTGCCGAGCAACCCGAATCGATTC\n")
-		f.write("TTGCCGCTCAGCTCCTCCAACAATCCTTGCAAGCAAAGTTAGAGGGCTACGATGTAAAACTCATAAAACT\n")
-		f.write("GTCCAAATAAACTACGAGAGTAGCGCAAAAATGGAAAATAAGCGACATTCGACAAAACTAATCCAGTTAA\n")
-		f.write("GGCCGGATGATAACACAACACACTTCATTTCTTCTTGGCTGCAGCCTTGGTCACCTTGGCACCGGTTGGC\n")
-		f.write("TCCTTCTTCTCCACACTCTTGATCACACCGACGGCAACCGTCTGACGCATGTCTCTCACAGCAAAGCGAC\n")
-		f.write("CAAGCGGTGGGTACTCAGAGAAGGTCTCGACGACCATGGGCTTGGTGGGAATCATCTTAACCATACCAGC\n")
-		f.write("GTCTCCATTCTTCAAGAACTTCGGTTCCTTCTCAAGCTCCTTACCAGATCGCCTGTCAATCTTGGTCAAG\n")
-		f.write("ATCTCAGC\n")
-		f.write("\n")
-		f.write(">gi|226790959|gb|GO545709.1|GO545709 Mdas9011M13_e874.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n")
-		f.write("AACCATGTAGTCATTTAGCAAGTAGGAAAAGCTCACATGCCATTGCATACACTAATCCTTTGATCCCATC\n")
-		f.write("ACAATCTTTACAAGCTTAAGCAGTACATATCATGATTCAAATAATTAATCATGGTCTACTGATTAAAAAA\n")
-		f.write("CCAAACATGATATGCACATAAAGATACTTCTCTAAAAAGAAAAGGCGTCAATAATGGTGGTGTGGAGCGG\n")
-		f.write("GTCACTCAAATGGGTAGCCCAGTTGTTAAGTGGTCCCTTCCCGGTGACGGCGGCTTGCACGGCAAACCCC\n")
-		f.write("AAAAACGCAACCATGGCGAGGCGGGCGTGCTTGATTTCGGCCAGCTGAAGAGTGGCCTTCTTTTCCGGGT\n")
-		f.write("CAGCAGCAAGGCCCAACGGGTCGAAAAACTTGCCACCCGGGTACAACCTCTTTTCCGGGTCGAGCTCGGC\n")
-		f.write("GTTCCTCTGGAACTCGATGTAGCCAATCACTAGAACTTCGATCCAGATCAACGTGGTTAGTGAGAAAGGG\n")
-		f.write("GAGTGGTTGACCCAAGTAGGACGACCCTTCGATGAGCTCCACCTTTCCGGCGTCTTGCCATGTGATCCCG\n")
-		f.write("GTGACGGACTCGACAGTGAGAGCACCGAGCGTGGCGAGCATGGCCCACCTTCCATGAATCAGCTCGCACT\n")
-		f.write("CCCTAAACCTCTG\n")
-		f.write("\n")
-		f.write(">gi|226790951|gb|GO545708.1|GO545708 Mdas9011I13_e850.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93338|GAPN_NICPL NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (Non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase) (Glyceraldehyde-3-phosphate dehydrogenase [NADP+]) (Triosephosphate dehydrogenase) gb|AAB47571.1| non-phospho, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTAATACAAGTCTCTCAGTTCTTATTGACCAAGTCTCCAACTTCATCAGGTAC\n")
-		f.write("AGAAGAGAAGCTTAAAGTTATTGCAGGAGCTTAAAACATCATGTAATAATCGCGTGATGCAGCCTTTCAA\n")
-		f.write("TAAGGGTATTGCCCATTATTCTCTTTTTCTCAACTCCATTTGTCCGACGATGACACATTTTTATAGTCTG\n")
-		f.write("CAGCCTAAAAATTCACTTACACATTTTACTAAATCCGCTACTACAACGACATTAAGTAGCTTCGATTACT\n")
-		f.write("ATATTATCACCCGATTCGTTATTAACACTGTCACTAACCCATGGTGTAAGAAGGGGTTGGCAAGTTGATT\n")
-		f.write("ACAGTGGTCTTGATCTTGGTCATCATGTTGATGCTGTTGGTGATTCCTTGTGAGCCAATTCCACTGTCCT\n")
-		f.write("TTATGCCCTGGAACGGAAAATGATCTGGTCCACGAGCAGGTGCGGAGTTTATTTGAACAGTTCCCGTCTC\n")
-		f.write("CATTGCATCACCAATCAAAATGGCCTTGTTGATGTCCTTTGTGAACACACAGCCCTGGAGGCCGAAATTA\n")
-		f.write("CTGGCATTGCAATGGGTGGATTCCTTCTTCTACCGTAGTAATCCTAATAACGGGCAAGACTGGACCGAAT\n")
-		f.write("GGCTCTTCCCACGCGATTCTCATAT\n")
-		f.write("\n")
-		f.write(">gi|226790950|gb|GO545707.1|GO545707 Mdas9011L09_e867.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF89961.1|AF200525_1 cellulose synthase-1 [Zea mays], mRNA sequence\n")
-		f.write("AGCAAACAATAAATACTTGACAACGGGGCAACATAACCGATACACAAGGCGTTCTCTCATTGTTCTTCCA\n")
-		f.write("CCCGACTCCCTTCTGAACGTGGAGACCATACGTAGAAGTTCAGTAGACGAATTTACCTGATTTCTTGTAT\n")
-		f.write("ATAGTATATACACACAGATGGCGTGGAGAGAGATGCCAGTTCCAAAAAATTAGTCCTTGAAACGAACTAA\n")
-		f.write("CAGTTGATGCCACATTGACCGTTTGTTGCAGCTTTTGTTTTGTCTGAAGTGAATGGGTCGATGCGCACCC\n")
-		f.write("ATAACAAGGAAAATATTGAAGCAAGAAGGATAGACCACACGATGACAATTGTAGGGGTACGATTTTGCCG\n")
-		f.write("ACCCAACAGACCCTTCAAGAATGGATACAGATGTGCTACGACCCATAAGGCGAAAAACAGTTTGCCAAAA\n")
-		f.write("AGTGGACCCCAAGATTGGTAACCGCTATTTATGGCATATGAAACACCGGCCACAATACCTACTATGTTCA\n")
-		f.write("CAAGAAGAACCGTGGTTGGAGGGATGAGCAGTGATGTCCATTTGAACACGTAGAGCTCAGCAAAATCCCC\n")
-		f.write("ATCCTCATCAGATGACTTTGACGTGACAGTGAAGTTGGTATCAATCCCAGCAAGAACTTTCAGGAGACCT\n")
-		f.write("TGGAAGACAGCGAAGAGATGAGCTGATGTTCCACAATGATCCAGAACTGTTCATTTCCCTCG\n")
-		f.write("\n")
-		f.write(">gi|226790949|gb|GO545706.1|GO545706 Mdas9011L14_e868.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAG\n")
-		f.write("TGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACA\n")
-		f.write("AACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACCACAACAACATTATTTATG\n")
-		f.write("AAAATTGTACAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGAC\n")
-		f.write("ATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAAC\n")
-		f.write("ACCTGAGAAGAGTCGGCGCATCCGAACATGGGCAGCTTCCACATT\n")
-		f.write("\n")
-		f.write(">gi|226790948|gb|GO545705.1|GO545705 Mdas9011J21_e857.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTT\n")
-		f.write("GAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAA\n")
-		f.write("CAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAA\n")
-		f.write("GAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGC\n")
-		f.write("TTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATT\n")
-		f.write("GGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGG\n")
-		f.write("CAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAAT\n")
-		f.write("CCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCA\n")
-		f.write("AGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACAC\n")
-		f.write("CTGCATGCAT\n")
-		f.write("\n")
-		f.write(">gi|226790947|gb|GO545704.1|GO545704 Mdas9011G20_e842.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177406.1| hydrolase, alpha/beta fold family [Arabidopsis thaliana] pir|G96750 unknown protein F28P22.19 [imported] - Arabidopsis thaliana gb|AAG51842.1|AC010926_5 unknown protein; 69438-68116 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CAAAAGTTGTGGAATGCTTTCTTCTTCTACCTCTCAACCGCATCAACAATTTTCCACACCCTCTTATCTT\n")
-		f.write("TTTTCTTCAAAACCAACTGGGATCTAGTGTTCTTCAAACTCCCAGATACTCTTGTAGCTTTATATTTCAG\n")
-		f.write("GCTATGTGGTCTCTCTCCTTGTACAATCGACGTTGACGACCAAACCACCGTGCACTTCTGGACTGCCAAC\n")
-		f.write("CACCGGCGCTTCGATAAACCCGGTCTCGTTCTGGTTCATGGCTACGGAGGCAATTCTCTGTGGCAGTTTG\n")
-		f.write("TGTGTCATGTGGGTGCCTTGTCCAGGAACTTCAACTTGTACGTGCCGGATTTGCTGTTCTTTGGGAAGTC\n")
-		f.write("TTACACGAACCGGTTGGACCGGAGCGAGGTATTCCAAGCGAAAAGTGTTGTGGACGGGTTGAAGAGATTG\n")
-		f.write("GGTGTGGACCGGTTCTCGGTTTACGGTCTGAGCTACGGTGGGTTTGTGGCGTATCGGATGGCTGAGATGT\n")
-		f.write("ATCCGGAGACGGTGGAGAAGGTTG\n")
-		f.write("\n")
-		f.write(">gi|226790946|gb|GO545703.1|GO545703 Mdas9003A20_e174.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTAGACGGAAACAAATTATAGTAGTACTAGTTACATGTATCTCGCAGACTAAGTACGTAC\n")
-		f.write("ATTACATTAATTAATAACCTTGGTTAGAATATGCTTATGCAAAGTTGCAAACAACATGAAGAATGTTCAC\n")
-		f.write("ATCCTTATGAACAATGCTGCGAGATATTTACGTATACAGATAGATGCTTCAAAAACCGGCCACGAGTTCT\n")
-		f.write("TATCTTAAACAACATTACTTTTCGGGTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTAGCTTTAAT\n")
-		f.write("CTTCAGTGTCAAAGCCTCTCTGTCTGGTTTGTAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAGCCA\n")
-		f.write("ATTCCTACAAGCTCAAGAACACCAGGAACTAAAGGAAGCCTATCAATTGCCGAAAGCAGTCCAGTGGAGC\n")
-		f.write("CCCATAGTGCAACAGCACCAGCTACTGCAAGTGAAGAAACTGCATATTTATCTTCCACTTTCTCCCAAGC\n")
-		f.write("TTCTTGAACGGTCTTCACAATCTCTGGCAGCTCAGTTACTGCAACTTCTGCTGGTGCTTCCCCTGTCGCC\n")
-		f.write("ATGGCCATGACATTGCGCGCNAACTTACGACAGTAGGCAGTGGTCTTCCCTGCGTGATTTTGAGAATGAA\n")
-		f.write("CTGGCGGTGGAGGAAGGGAAGGCAGGGTCACACATTGTGGTGATGAGGCA\n")
-		f.write("\n")
-		f.write(">gi|226790939|gb|GO545702.1|GO545702 Mdas9011F03_e834.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P87066|TBA_CANAL TUBULIN ALPHA CHAIN gb|AAB53194.1| alpha-tubulin, mRNA sequence\n")
-		f.write("CTGCAGTTCATAAAGTTTCAATTTTTATCAGAGAAAAGAGAGAGAGATGAGAGAAATCATAAGCATTCAT\n")
-		f.write("ATTGGGCAGGCTGGAATTCAGGTGGGCAATTCATGCTGGGAGCTCTACTGCCTCGAGCATGGAATTCAAC\n")
-		f.write("CTGATGGCCAGATGCCCAGTGATACCACAGTGGGCGGTGGCCACGATGCTTTCAACACCTTCTTCAGCGA\n")
-		f.write("GACTGGATCAGGCAAGCATGTCCCAAGAGCCATATTTGTTGATCTCGAACCAACTGTTATTGATGAAGTT\n")
-		f.write("AGGACTGGGTCTTACCGCCAACTCTTCCACCCTGAGCAGCTCATTTCTGGAAAGGAAGATGCTGCTAATA\n")
-		f.write("ATTTCGCAAGAGGACACTATACAGTTGGAAAGGAAATTGTAGATCTCTGTCTTGATCGAGTTAGGAAATT\n")
-		f.write("GGCCGATAATTGCACTGGTTTACAAGGATTTCTGGTGTTCAATGCTGTTGGTGGTGGTACTGGTTCTGGT\n")
-		f.write("TTGGGGTCCTTGCTCTTAGAACGCTTGTCGGTGGATTATGGAAAGAAGTCAAAGCTTGGGTTCACCATCT\n")
-		f.write("ATCCTTCTCCGCAGGTTTCAACAGCAGTTGTTGAGCCTTATAATAGTGTTCTCTCTACTCATGCCCTCCT\n")
-		f.write("TGAACACACAGATGTATCTGTGCTCTTGGACAATGAAGCTATCTATGATATTTGCAGGAGATCCCTAGAC\n")
-		f.write("ATCGAGAGA\n")
-		f.write("\n")
-		f.write(">gi|226790938|gb|GO545701.1|GO545701 Mdas9011J23_e858.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AATCGAAAACAGCAACAAAATAATTGCTGTAAAAATTTATTCATCGTATCAACTTTTCACACTTACATAT\n")
-		f.write("GTTTTTGCTGAAATTCTTTAAAACTAAAATATAAATCTGCGTACAATAAAACTTTGTTGTCTCTAAATCA\n")
-		f.write("TATTTACATCCCCACTTAAAAAGCTTGGCTTTTTATATAAAAGGAAAAAACAAAGCTTCATGGATTTTTT\n")
-		f.write("CGGAATTAAAAAAAAGGGAAAAAAGGAAGGGAAAAAACGATAAGCGTACGTGGGAATTTTGGAAAGACAA\n")
-		f.write("CAAAAGATCGACAAGATGACAAATTCAAACCCAAAACAAAAACAAAAAAAAAAAGATTTTGAGCAAAAAA\n")
-		f.write("TTTATGGAGGAGGAGGGGATGTGAATCCACCAAGGGGGAAAAGGTGGGTGACAAAGTTAAAAAAGTTTTT\n")
-		f.write("ATCTTTTACCGCCTTGACGTCCCGTACATCTGGTCAAGCAAAATGACGAGGGACATGGCCACCGACGTGT\n")
-		f.write("CCATATCGGGCTGCACGATGAGGCTGAAGACGTCAACTCCCAACGCTACTCCACCCACCGCCTCCTTCCT\n")
-		f.write("CTTGATCTCGGCCACCCTCCTCCTCTTGCTGT\n")
-		f.write("\n")
-		f.write(">gi|226790937|gb|GO545700.1|GO545700 Mdas9011N24_e880.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTATACACAAAATAATAATAATATATTATTAACATGAGATATCAATGTAG\n")
-		f.write("CAACATACAATAGATGCAATATAAAAATTTTCTCACTCATCATCACCACCATCTACTGTGTGTTTTATTC\n")
-		f.write("AGTAAGTAATAGTCCTTGTAACTAGGATGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC\n")
-		f.write("TCTATATTCCCTCTAAAAAAATAAGGCGTTATATCACAAGGTTGTGGGAGGCTATATATGTTTTTTTTTT\n")
-		f.write("TTTACAAAAAAAAATATAACCCCCTCAAATATATATATATACAGATAATACATAGATACTTTTAAAAAAA\n")
-		f.write("AAGAGAAAGAGAGAGAGATCTCTATTTTTTTACACGACACAAGTGAACTACACCCACACAAACACACATG\n")
-		f.write("GGGGGGGGGGGGCCCAACACCTAAAGAGCGCGCCTCTCTGTTTTAACACTTGGTGTGTGTCT\n")
-		f.write("\n")
-		f.write(">gi|226790936|gb|GO545699.1|GO545699 Mdas9011O23_e883.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TTTTTTAATTCAAATTATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACAATACAAACAA\n")
-		f.write("AAGTACGAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTG\n")
-		f.write("GCGACTGGGTCTGCAAGGTGGTCGGCAAGATTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAA\n")
-		f.write("AGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGC\n")
-		f.write("TTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCG\n")
-		f.write("AGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCA\n")
-		f.write("AGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGC\n")
-		f.write("TCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCGGGGAAAACGCAT\n")
-		f.write("CCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTTGGCGAGGGTCTCT\n")
-		f.write("GGGTCGGCTGAGAGTCCAGCGGTGT\n")
-		f.write("\n")
-		f.write(">gi|226790935|gb|GO545698.1|GO545698 Mdas9011H09_e845.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("GAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGCTCAAATCCACACTCAAACAAAAGGGA\n")
-		f.write("CTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTCCGGGAACAAAGTTTGTGGCATAGTTC\n")
-		f.write("CAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTACCGGTGACAA\n")
-		f.write("TGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAG\n")
-		f.write("CTCAGCAAAAGCTTCTGGGTCGTCGGCAAGACCCAATGGGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCG\n")
-		f.write("GTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAG\n")
-		f.write("CCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCT\n")
-		f.write("GAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCT\n")
-		f.write("GGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCAC\n")
-		f.write("\n")
-		f.write(">gi|226790934|gb|GO545697.1|GO545697 Mdas9003F14_e198.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S68465 L-ascorbate peroxidase (EC 1.11.1.11), cytosolic isoform - pepper, mRNA sequence\n")
-		f.write("TTTTTTTTTTTGAAATTACAGTATTATTTAATCAACGAGGATGATTACCAGCATTCCATCCAATTTAAAA\n")
-		f.write("ACATTCGTTCTTCAAATCGAACTAGAAGTCCCACTTCCTAAAATCTGATAAGATAAAAAAGAAAAGCACC\n")
-		f.write("AACTGCCTACAACCTCACAACCAAGAGGCATCCAAAAATACAAAAGAAAGGCGCACAGGCATTGGCTTCA\n")
-		f.write("TCCCTTGTAGTTCTCCAGCTCTGCTTAGGCCTCAGCAAACCCAAGCTCGGAGAGCTTCATGTGAGATTCA\n")
-		f.write("GTATAGTCAGCAAAGAAAGCATCTTCATCCGCAGCGTATTTTTCCACAAGAGGGCGGAAGACAGGGTCAT\n")
-		f.write("CCAGAAGAGCCTTGTCAGTTGGAAGCATTAGAAGACCTTCCTGGTCTCCACCAAGAAGCACCTTGAAGTA\n")
-		f.write("GGAGTTGTCAAAGATAAGGGGGTTGGGAGTCCAAGGTCCTTCAAATCCAGATCGCTCCTTGTGGCACCTT\n")
-		f.write("CCCAGGGTGTGACCACCGGAGAGAGTAACAATATCCTTGTCGCTGAGGCCCATGTTCTTGCAGAAGACAT\n")
-		f.write("CCCTCAAATGGTCATTACCCTTGGTAGCATCATGAAGACGGCCCTCTGGTGGTGGCACGGGGGCATCCGT\n")
-		f.write("\n")
-		f.write(">gi|226790933|gb|GO545696.1|GO545696 Mdas9011K18_e865.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S20941 protochlorophyllide reductase (EC 1.3.1.33) precursor - garden pea, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGCAGTTTGCAACAGAGGTGAGTGATTTTATTCTCATTTGTT\n")
-		f.write("ACTAACACTAGTCATCCACACGAGAAAAATTGTCTATGACAGTAGAGCATTTGATTTCAAAATCTGCACT\n")
-		f.write("CTACAAATGGACCTGATCTCGGGTGACATCCTCCGCCTCCGAGGTAAAACATCAAGTTTCTATACTCAGG\n")
-		f.write("CCAAACCCACAAGCTTCTCACTGACCTCCCACACCTTGCGAGCCTTCTCCGCATCACTAGCTTCTTGGGA\n")
-		f.write("CAGTTGGTTCTCGAAGGAAGCCGAATCCTTGTTCCAGCTCCAGTAGACTCCCGACTTTGTCAAGCTTGGG\n")
-		f.write("TCGCTCACAACCTGAGCAAGTCTCTTTCCGGCTTCTTCTTCTGAGACGTAGCCCTTGGTGATGTACTTTT\n")
-		f.write("GGAATGGAGGGAACAGAAGCCTGAACAAGGGAATGTGCTCCCTGAACAAACCAGTGGTGGCAATGCAGCC\n")
-		f.write("GGGGTAAAGGGAAGTAAATGTTATCCCGGTTTCCTCATGGTAGCGCCTGTGGAACTCTTGCATTGTGAGC\n")
-		f.write("ATGTTGCAGACTTTGCTGTCCTTGTAGGCCTTGGCACCGTCAAAGTCTCCACCATCGATCATGGCCGAGC\n")
-		f.write("TGTTTAGACCGTTTAAGCCTCCTGCAAGTCCCCTC\n")
-		f.write("\n")
-		f.write(">gi|226790925|gb|GO545695.1|GO545695 Mdas9011G11_e840.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTGAAGAGAATTTAGTATTTGTATTCAATTTATCACATTAGCCATCAAATAAAATTTTGACATATTATA\n")
-		f.write("TTTAACATATCATTGGGAGATGTTTTAAGTATTCAAAAGTCTCTTTGATTTTATTGAAAAAATGAAATAA\n")
-		f.write("AAAATAAAAAATAAAAAATATCGTTTTTTCGCCACCCCCATAGGCTAGGCGGACGCCTATCAAGCTGCCA\n")
-		f.write("ACACTCCTATAACTATAACGATGATGACCATCAAAGCGGTTAAGAATCCCAAAACTATCAGATCCTTCTT\n")
-		f.write("CTTCCTCCTTATCTGACTTTCCAGCTGCCTGCAATGTTGTGCCATTAAAGGAATGCGTTCTCGATCTCGA\n")
-		f.write("TCTCGATCTCTATCTCTCTCTCGGCCTCTCTCTCTATCCCAATCTCGGTCTTGATCATAATTGGCGGTGG\n")
-		f.write("TTGCGGGCGGTGCGGCGTCGGAGGAATGGCGTGAGGGGGTGAGACTGGAGAGGAAATGGTGCTGGTGGCG\n")
-		f.write("CCTTGGATCTTCGGTTTGTCCTTGACGGAGTTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790924|gb|GO545694.1|GO545694 Mdas9011M07_e872.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP03871.1| oxygen evolving complex 33 kDa photosystem II protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TTTTTTTTACGCATGTCAAATTTTGACGTATAATGATTTACCGTTAAAGAAGTTTGACTCCTTAAAAGAT\n")
-		f.write("AATGTACAAGAAAGATAATACATACAAGATAATAGGCATGATAATATACAAGAAGATAATGATCTGAGTG\n")
-		f.write("ATCTCAGTGCTTGTTGTTCAATTGGGTTACAAAGAGAGTTGAGCAACACCTTTTTAACTTATAGCAAAAT\n")
-		f.write("CTGAAACCCAGAATCACCATTAATACATAGAGGAAAACGAAACTAATCAAGCTGAGCATACCAAACTCCC\n")
-		f.write("TGGATTTTGACATCCTTTGGAGTCTTGGCTCCCAAGTCAGTGTCGGATGGCTGAAGGCTCTCGAACACCC\n")
-		f.write("CAATCAACTCACCAGTCTCAGGCTTGGTCTTTGTCACACTCAGTGTTATCTTCCCCTTCGATGCTGCTGT\n")
-		f.write("ATTCTTGGTGTTCTCCTTTGCCAGCTCCTCCTCGTCTCCTCTGCCTCCTGCCGGCAGTGCGACCGCATTG\n")
-		f.write("TCATAACCGGTGGATCCTCCTCTTCCCTTGGGGTCCAAGAAAGAGGATCCACGGTATGATGGTACTAGAA\n")
-		f.write("ACTCTCCCGTGAAATTTTCGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790923|gb|GO545693.1|GO545693 Mdas9003E12_e192.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n")
-		f.write("CAGGACTCCACTTTGATCCATGACCGCCATGCACACAGTCTCGAGCGTCGGAACTGTTAACCGGACTCCG\n")
-		f.write("GTGAGCCTGAACGGCTCCGGTTCCGGAAGCTCGGCCTTCTTGGGCACCACTTTGAAGAAAGCGACCTCAA\n")
-		f.write("GAGTCCCCTACCAAAAGATTGCATCTGCAGGCAAGTTAAAAATCAATGCGGAAGTCGACGAGAATAAGCA\n")
-		f.write("AACCAACAAGGACAGATGGAAAGGCCTTGCCTACGATATGTCCGATGACCAACAAGACATAACAAGAGGA\n")
-		f.write("AAGGGTTTGGTTGATTCTGTGTTCCAAGCTCCCCAGGGGAGTGGAACTCACTATGCTGTCATGAGCTCAT\n")
-		f.write("ACGAATACATCAGTACCGGACTTCGAGAGTACAACTTTGACAACAACATGGATGGGTTTTACATCGCTCC\n")
-		f.write("AGCTTTCATGGACAAGCTTGTGGTTCACATAACCAAAAACTTCATGAGCCTGCCTAACATTAAGATTCCT\n")
-		f.write("CTCATTCTTGGTATATGTGGAGGATAAGGTCAGGGAAAATCCTTCCAGTGTGAGCTTGTGTTTGCCAAGA\n")
-		f.write("TGGGAATTACCCCCATCATGATGAGTGCTGGAGAATTAGAAAGCGGGAATGCAGGAGAGCCCGCGAAACT\n")
-		f.write("GATCAGGGCAAAGTACCGTGAGGCTGCAGATATCATCAAGAAAGGAAAAATGTGT\n")
-		f.write("\n")
-		f.write(">gi|226790922|gb|GO545692.1|GO545692 Mdas9011F23_e839.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n")
-		f.write("TCAACACCACCAAAACTTCAAACAGAAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAG\n")
-		f.write("CATTTGCTGGCCAGACTGCTTTGAAGCAGTCCAGTGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGG\n")
-		f.write("CCGCTTCTCCATGCGGCGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAG\n")
-		f.write("TACTTGGGACCATTCTCCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGG\n")
-		f.write("ACACTGCTGGACTATCTGCAGACCCCGAAACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAG\n")
-		f.write("ATGGGCCATGCTTGGTGCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGC\n")
-		f.write("GAGGCTGTCTGGTTCAAGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGCAACCCAA\n")
-		f.write("ACCTTATCCATGCTCAGAGCATCTTGGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGG\n")
-		f.write("ATACAGAGTTGGAGGAGGACCACTCGGTGAGGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCC\n")
-		f.write("CTTGGACTTGCTGATGATCCCGAAGCTTTTGCTGAACTGAAAGTGAAGGAACTTAAGAAC\n")
-		f.write("\n")
-		f.write(">gi|226790921|gb|GO545691.1|GO545691 Mdas9011F06_e836.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF71695.1|AF198168_1 phospholipid transfer protein [Aerides japonica], mRNA sequence\n")
-		f.write("TTTTTTTTGTATAAAAGGGGATCATTTAATTATTAATAGATGGTAATGGATTACGTACAATCCTTATACA\n")
-		f.write("GAACGATTCGACCCTTCCAGATTATTAAGTTCCACAAAAGCATTGTGATTTAAACAACTAAGAGGTCTGT\n")
-		f.write("CTAGCTATATGGCTTCGAGGAATAGTCTTCTCGGAAGCTTTATTCTCCATTCTCCAATCCTCCTATGGAT\n")
-		f.write("TCAGCTTACCGCAGAGCAATTTGTAGAGGGGTAAACTTTGTAAGGACAAGGAGAGCCACAGACATCACCA\n")
-		f.write("AGAGTGTTAATCCGGTCATAATTAATCCCGGGGATTGCTGCAGCTCCTTCCTGAATGCAACTACAAGCAA\n")
-		f.write("TTCTCCGGTCCATCGTGGTGTTTTGTGCAGCATTCAGCTCTTTTATGCCTTTACAGCAATCTGGAGGCAC\n")
-		f.write("TGTGCCTCCAAACACTCCAAAGGGTATGCATGGAGTGAGCCAAGCTACCACTTCACCACAAGTTATGGTG\n")
-		f.write("GCATTACTGACAAAAGGAGCTATCACAAATAAGAACACTATTGCCACGATGACCGAAAACCTGGCCATGG\n")
-		f.write("TTAGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790920|gb|GO545690.1|GO545690 Mdas9003D19_e189.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAACCCAAATCATGTTTCTGAGGTTGCATTTTAATGAAATCAA\n")
-		f.write("ATTACAAGAAACACAAATTATACTCACATTGCCATCATGATTATAAATACAATGCAAATTACACAAATCA\n")
-		f.write("ATATTATCATCATATGTCATAGACTTGCTTGCCGGTGAACTTGACCTCAATCGGGCTGACATTCTTCCCA\n")
-		f.write("ATCGACCTGAAGTTCTGGCCAACCCCTTGGCGCCCAGGGTTCACCTTCTCAGGGTACACACCATCCTTGG\n")
-		f.write("GGTGCAAGTATTGGACCTCCCCGTTAGGGAAAACCCTGTAAAACTGGTACTTAATCTTGTACTTGGACCT\n")
-		f.write("AAGCCTAGTTCCAAGAGCCAAGCACTGCTCTTTCCTGGCCAGTTTCAGCAAGTTAGGACCCTCCCTCATG\n")
-		f.write("ATGGCAGCTCCGCCAGTCGGCATCTCAAATATCTGCTCCTTTGGTGACTCCCATGTGATCACGTAAAACT\n")
-		f.write("CTTCCTCCTGCGCTTTCCTCAACAGCCCGCCAGTGCTGCCACCGAAGATCGGTGAGAGGTGTTGTTGGGT\n")
-		f.write("CCAGCTCGGGGTGGGGTGAAGCCTACCGGGGCCTCCTTTGTGGGGGTCACGGTTTTTTCCTCAGCGGAGG\n")
-		f.write("CATTGATCCTCATCG\n")
-		f.write("\n")
-		f.write(">gi|226790912|gb|GO545689.1|GO545689 Mdas9011I24_e851.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTAGTACTAACAATAATAATTATTAATAATAACTTGTTTATTTAGTAAGTGAAATGCATTTCACATGACA\n")
-		f.write("ATTATGGCAACCTATTAAGATTAAGAGCCTGTTTAAGGAAGTTTAGCATGATAAAAGGACAGGCACTTTA\n")
-		f.write("TTTATTAGTACCGAGTAAGTTTGCCTGCCTGC\n")
-		f.write("\n")
-		f.write(">gi|226790911|gb|GO545688.1|GO545688 Mdas9011O19_e882.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12302|PSBP_SPIOL Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|S00005 photosystem II oxygen-evolving co, mRNA sequence\n")
-		f.write("TTTTAGAAGAAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAAATAAA\n")
-		f.write("TTTCTTATGCAACACTTGAAAGAACTTCGCAGCGCTCTCTACAAACTTTCCTTGCTCCTTTCGAACCACC\n")
-		f.write("TCTTCGTCTCCGGCTTGTGCCTTTAGAATCGTAGAGCTTCGCCGTCTTTTCACGGTGGCTCGTGATAAGC\n")
-		f.write("TCGGTGCTTCGCCTCCTTTCATTCTCCGTCGGCTCGTCCTTCGTCAACACAGATACGTAGTAGTACTGCT\n")
-		f.write("TTTCCGTCAATCACTCGACTAGAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCAC\n")
-		f.write("CCTCGGATTCAGTCTTGCCAAAGTAGGCTTGTTTTGCCTAGCAAGTAGTCCACCTTTCGCGAGGAATTCC\n")
-		f.write("TCGGGGGAGCCATAGTCGGCGATGGATTTTCTTTGTCGGTTAGGGTGATTTGTGACGGACACATTTGCTG\n")
-		f.write("TTGCTGTCGAAGTTGTCCTCGTACCTAAGAACTTGACCAGGGAACTCAACCTCTTTGCTAGGGTTCCATT\n")
-		f.write("TTGCAGGAATGGATAGCTT\n")
-		f.write("\n")
-		f.write(">gi|226790910|gb|GO545687.1|GO545687 Mdas9011E23_e833.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176352.1| 60S ribosomal protein L3 (RPL3B) [Arabidopsis thaliana] sp|P22738|RL3B_ARATH 60S ribosomal protein L3 pir|B96641 60s ribosomal protein L3 [imported] - Arabidopsis thaliana gb|AAD25547.1|AC005850_4 60s ribosomal protein L3 [Arabid, mRNA sequence\n")
-		f.write("AAAGCATTCAGCAAGTACTCAAAAAAGTATGAGAGCGAAGATGGGAAAAAAGACATCCAGGCTCAGTTGG\n")
-		f.write("AGAAAATGAAGAAATATTGCACTGTGATTCGTGTTTTAGCCCACACCCAGATTAGGAAAATGAAGGGATT\n")
-		f.write("GAAGCAGAAGAAAGCCCATCTGATGGAGATTCAAGTGAATGGTGGGGACATTGCAAAGAAGGTTGACTAT\n")
-		f.write("GCTTATAGCATGTTTGAGAAGCAGGTTCCTGTTGATGCTGTTTTCCAGAAAGATGAGATGATTGACATTA\n")
-		f.write("TTGGGGTTACTAAGGGGAAGGGTTATGAGGGTGTGGTGACTCGATGGGGCGTCACCCGTCTTCCACGTAA\n")
-		f.write("GACCCATCGTGGTCTACGTAAAGTAGCCTGTATTGGTGCCTGGCATCCAGCTAGGGTGTCGTTTACTGTT\n")
-		f.write("GCCAGGGCTGGGCAGAATGGTTACCACCATCGTACTGAGATGAACAAGAAGATTTACAAGCTCGGAAAGG\n")
-		f.write("CTGATCAAGAGTCGCACTCTGCAATGACTGAATTTGACAGGACTGAGAAGGATATTACCCCGATGGGAGG\n")
-		f.write("TTTCCCACACTACGGTGAAGTGAAGCAGGATTACCTTCTAATGAAAGGCTGCTGCGTGGGTCCTAAAAAG\n")
-		f.write("CGCGTTGTTACTTTGAGGCAGACGCTTCTGAAGCAAACATC\n")
-		f.write("\n")
-		f.write(">gi|226790909|gb|GO545686.1|GO545686 Mdas9003B05_e176.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGGGTTTGAGAGAGAAATGGGGGGAAACACAGAAATTTTGATAATTCCAGATGTGCCCTTTGCCGGT\n")
-		f.write("TTGCACTTAATAACAAAGAGAATGTGAATTATAACTGCCCAAGCTTGCCTTGTGGAGGCAGTTACGATTT\n")
-		f.write("GCATCTAGCAAATTGTGTAGGC\n")
-		f.write("\n")
-		f.write(">gi|226790908|gb|GO545685.1|GO545685 Mdas9011K17_e864.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("ATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGA\n")
-		f.write("AAACAAACGAGAGTGCCTCGAAAAAGGGACAGAAAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCC\n")
-		f.write("CTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAAC\n")
-		f.write("AACATTATTTATGAAAATTGTAAAACAACTTAAACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACT\n")
-		f.write("GCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTC\n")
-		f.write("CAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTT\n")
-		f.write("CCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGC\n")
-		f.write("AGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n")
-		f.write("\n")
-		f.write(">gi|226790907|gb|GO545684.1|GO545684 Mdas9003F12_e197.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175633.1| photosystem I subunit VI precursor [Arabidopsis thaliana] sp|Q9SUI6|PSH2_ARATH Photosystem I reaction center subunit VI-2, chloroplast precursor (PSI-H1) pir|C96562 photosystem I subunit VI precursor [imported] - Arabidopsis thali, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTAAAAATAATATCATGATCAAACAATAATCTATTAAAATATAAATAGTAGTTCCCAAAT\n")
-		f.write("ATCTTTAACATATTGCCAAATTTAGGGGTTTTAATTCTGCATTAAACGTACTTTACAATTACAAAATAGA\n")
-		f.write("GAAGCAATTACACATACATGAGGAAAAGCATGAGAAAATGAGGATTAAATCCCATATAAGAATTAGATCT\n")
-		f.write("TGCCACGTGGCCCCAACTTGGGTGGAAGTTGTGGGCCCTTCTTGATTGGTAGAATGTCATCGGAGGCAGT\n")
-		f.write("GGCACTAAGGTAGGCAATGGTGGAAGCTCCTCCCAATATCAAGAACTTGAGGAGTAAGCCTCTCTTGGTG\n")
-		f.write("AATGGAGCAGCAAATGTCTCAAAGAACTTGCTCTGAAGAGGGTTGTAAGGTGAGGGCGCATCCGAACCAT\n")
-		f.write("ACAAGTCCCACTTCCCGGTGGTGTTGCCCAGATCCTCAAGGTCAAAGTAGATGCTCTTGTCTCCGTACTT\n")
-		f.write("GGCCACCACAGCACCATTCCTGATGTTTTTGGTTCTGATGCTCTGGCGAGTGGGCTTCACAACGAGCTTT\n")
-		f.write("GTTCCGGTGAGGGAGCTTCCGCCGAGGCCGTTAATGGCTGCAGGTTGAACAGCTGCTAGGGTTGCCAAAG\n")
-		f.write("ATGCCATTGCCTAACAATAATATTGGTCTACTGCTACTCTTTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790899|gb|GO545683.1|GO545683 Mdas9011I02_e849.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188003.1| root hair defective 3 (RHD3) [Arabidopsis thaliana] gb|AAB58375.1| root hair defective 3 [Arabidopsis thaliana] gb|AAM12987.1| unknown protein [Arabidopsis thaliana] gb|AAM91201.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CACTTTTAGACTTTAAGAGATATAACCAAGTAACCCTAGAGTAGTCATCTATGAATGTAACAAAATACTT\n")
-		f.write("GTACCCATCAAATGACTCAACACGGGAAGGTCCCCAAATATCTGAGTGTACAACTTCAAAGGGTTTACTA\n")
-		f.write("GTTCTAGATTTAGAGGGTACAAAAGGTAGCCTAGTGGCTTTTGACATTTGACAGATCTCACACTCATGTG\n")
-		f.write("TGTTGGTACAATAATTTGGAAATAACTTAGACATTACTGGTTCGGAGGGATGAGCTAGGCGTTGGTGCCA\n")
-		f.write("AAGTTGATGCTTCTGGACATGGCTTAGGTTGGCAATGGGTTCCTTAACTTGATTGAACTCCTTTGAGAGG\n")
-		f.write("TAGTACAGACCATTTAAGAAAAAACCCTCACCAATCTTCTTTTGAGTGACTCGATCATATTTATCATCAC\n")
-		f.write("AATGTCGGATATTGCCATAGCAAATAGAGCGCTTTTTTTCTCGAATGCAGTATCATCCTGGCCTCTCTCA\n")
-		f.write("CTTCCATCAGTACCCTCAATATCCAAGGCGAGGGTGCAAGGCTCAACGCCAACACACTTGGCAATCCAAA\n")
-		f.write("TGCCCTTCGTTGTTTGGCTCCTCCTATCTGGATTCATCTCCTGAAACTTAGTGTCGAACAGATGGTTCAT\n")
-		f.write("CAAAGTGCTCTTTCCTCCACTCTGAGGACC\n")
-		f.write("\n")
-		f.write(">gi|226790898|gb|GO545682.1|GO545682 Mdas9011H14_e846.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26909.1|AF319165_1 dehydration-responsive protein RD22 [Prunus persica], mRNA sequence\n")
-		f.write("ACTGCGGAATCCATCCCATTTTCGTCCAACAAGCTGCCAGAAATCTTCAACCAATTTTCAGTGAAATCGG\n")
-		f.write("GTTCCGTGGAAGCGGATATAATCAAGGGTACAATTCAAGAGTGTGAGAATCCAGCCATTAGAGGAGAGGA\n")
-		f.write("GAAATATTGTGCTACCTCTTTGGAGTCCATGATTGACTTTAGCACTTCTAAGCTTGGAGGAGGAAATGTT\n")
-		f.write("CGAGCAATTTCGACAGAAGCCGGAAAAGGAGCTACATTGCAGAAGTACACAATAACTTCTGGAGTGAAGA\n")
-		f.write("AGTTGGCGGCGGATAAGTCGGTCGTGTGTCACAAGCAGAACTATCCCTATGCTGTCTTTTACTGCCATGC\n")
-		f.write("AACAAAAACAACAAGAGCTTATGTGGTGCCCCTGAAAGGTGCTGATGGGGTGAATGTTAAAGCAGTAGCA\n")
-		f.write("GTCTGCCATACAGACACATCGGAGTGGAACCCTAATCATTTGGCCTTCCAAGTTCTCAAAGTTAAGCCGG\n")
-		f.write("GAACTGTTCCGGTCTGCCATTTCCTTCCCAGTGATCATGTTGTCTGGGTTCCAAACCAGAAATCTACCTG\n")
-		f.write("ATTTGACTGATCAACCTTTGAGTTCTACGTATGATGATGTGATCAGCTCAATTAGCATAGTTTGAGTGGC\n")
-		f.write("AAGAGTTTGAAATTAAATCGACCGTCGATTACTTCTTATTGTCACTATGTATTTCAGCCTATATATATAC\n")
-		f.write("TCATAAATGAAAGCATACTATCGTGTGGACTTGTACCAAAA\n")
-		f.write("\n")
-		f.write(">gi|226790897|gb|GO545681.1|GO545681 Mdas9011F14_e838.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTAAACAAAATAATTGCAAGAATTTCCATAGAAATACAAGCGCAAATTACAA\n")
-		f.write("AGAAAATATCAATAACCCAGCAAACAGAATATTTATTTTCTTCAGCTCCAATTACTCGTACTGACAGCTA\n")
-		f.write("CCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCTGTTCGATCAGTGCAGCCTTCTGGGACTGGTA\n")
-		f.write("CATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTCGGTTAATGGAGTCCTGGTTTGCATCTCCAAG\n")
-		f.write("GGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGCTCCTGAACAAGCATT\n")
-		f.write("TGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGACCTTCTTTTGAGT\n")
-		f.write("TCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAATCCACTTCCTCACTTCATCGTCATAAAC\n")
-		f.write("TCGAGCCCTTAGGGCACCGAAGAAATCAATGGATTGACCGGGGAATGTGTCAACAATCTTGACAACATCT\n")
-		f.write("TCCTGGGACACATTATCAGGCTTGAAGATTCCGGTGCAACACCGA\n")
-		f.write("\n")
-		f.write(">gi|226790896|gb|GO545680.1|GO545680 Mdas9009E19_e666.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTCTACAAAAATTAAGAGACAGCAGAGAATTAAATAATGAATAATTACAGACGAAATAATGGTGGG\n")
-		f.write("TGAAGCATATTCATATGCCAAAAGTATATACCATACAAAATGGACAGCACGAAGAGACATTTTTCTTTTA\n")
-		f.write("GCCCCTTGTTTAATGGAATCTCAGTCGGTGGGCTCTCCATGTTCCTTACAATAATGGTTCAACAACTTCA\n")
-		f.write("ACCCTCTCATTCAAAATTATCTTCATCGTCACCACCACCCCCCGTCGCCACCGCCACTGTATCACTCTTG\n")
-		f.write("TAGCAGTTGTAGGAAATTTGTAACTTGAGCTCATTTGGCCGATTCCTCGAGTCCGAGTTTCCGGAAAATA\n")
-		f.write("AATGTATGAGCTAGTTATATGAAGTGTTTTTCTATTCATATGTACGGAGGCCTCATTGCTACGTGACAGG\n")
-		f.write("CCTCGCGTACATGTTTCAAGAGGAAGGTTCTATATAACTCACACGTAAAACTTCGTCCGAACTATATCCG\n")
-		f.write("ATGCCCTCATAGTGTCGTACCATTGGAGAATTCGGGGCTGTAATTATGTTGGGGGAGGACTATCTGCGTG\n")
-		f.write("CACTTCCCAAACACATCCTCCATACTTTTACGCGAGAGAGCATATGGTGGTGTTGAACTCCTACAAGGAG\n")
-		f.write("TGAGGGGGCTTGAGGAGTTAATGGCGGTGTGACTAACCATGCTTTACC\n")
-		f.write("\n")
-		f.write(">gi|226790895|gb|GO545679.1|GO545679 Mdas9009B16_e647.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P02300|H3_PEA Histone H3 pir|S04520 histone H3 (clone pH3c-1) - alfalfa pir|A26014 histone H3 - wheat emb|CAA31964.1| histone H3 (AA 1-136) [Medicago sativa] emb|CAA31965.1| histone H3 (AA 1-136) [Medicago sativa] emb|CAA25451.1| H3 histone, mRNA sequence\n")
-		f.write("CCGTTTCAGGCCGGGAACTGTGGCGCTGAGGGAAATCAGGAAGTACCAGAAGAGCACTGAGCTCCTGATC\n")
-		f.write("CGCAAGCTTCCGTTCCAGAGACTTGTGAGGGAGATCGCACAGGACTTCAAGACTGATCTGAGGTTCCAGA\n")
-		f.write("GCAGCGCGGTGTCGGCGCTCCAGGAGGCGGCGGAGGCGTACTTGGTGGGTCTGTTTGAGGACACCAACCT\n")
-		f.write("CTGCGCTATTCGTGCCAAGAGGGTCACCATAATGCCCAAGGACATCCAGCTTGCTCGCAGGATTAGGGGC\n")
-		f.write("GAGAGGGCTTAAGAATTCCTAAATCTTAGGGTTTTGAATTTCCGCACACTGTACTGGGATATTT\n")
-		f.write("\n")
-		f.write(">gi|226790894|gb|GO545678.1|GO545678 Mdas9009N02_e703.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_682039.1| ORF_ID:tlr1249 hypothetical protein [Thermosynechococcus elongatus BP-1] dbj|BAC08801.1| ORF_ID:tlr1249 hypothetical protein [Thermosynechococcus elongatus BP-1], mRNA sequence\n")
-		f.write("TTTTGAAAGAAAACTGCTGCTCTTATTTATTTGGATATTGTTGCCAACAATGTATGTATATTGCTGCGCT\n")
-		f.write("ATATGATTACTGGATTACAGTTTCAAAACTTGTTCTTCAGCTGCAGTGAGCCTACCAGCTGAAGCTCCTA\n")
-		f.write("ATGAATTGGAAATACTCCTCACTTCTGCAATCATTGCAACCACATCATTGAGCTTGTTCACGGCTGAGCC\n")
-		f.write("GATGCCCACACCAGCAGCTCCTGCTGCTATTGCCATTGGGGCTGTAACTGCACTCAGTCCGGATGAACAC\n")
-		f.write("ATTACCGGAATCTTGACAGCACGGGATATCGAATATGCTGCTGCCAATGTTGGTGTTGCCTTCTCGACCA\n")
-		f.write("AACCAAGAACACCTGATTTCGAAGGACTAGTACATTTTCCTCCTTCGGTTTGAATGATGTCAACACCTTC\n")
-		f.write("CTGCTCCAGCATCTCTGCAAGCTTGACCTGATCTGGAAGGCTTAGTGTATGAGGTACAGTGACTGATAAG\n")
-		f.write("GTCACAGATGGAAGAATCCTCTTGGTCTCCTTTGTCAGATTCAAAATCTGCTCCGAAGTGAAAACCACTC\n")
-		f.write("CCATCTCGTATAAGGAGTCATAGTTTCCAATCTCAACCATCAGTGCTCCTGCTTCAACCGCAGCTGGAAA\n")
-		f.write("TGCCGCTGGATCCACAG\n")
-		f.write("\n")
-		f.write(">gi|226790887|gb|GO545677.1|GO545677 Mdas9009D21_e660.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_563634.1| expressed protein [Arabidopsis thaliana] pir|G86148 T1N6.14 protein - Arabidopsis thaliana gb|AAF78406.1|AC009273_12 ESTs gb|Z27282, gb|T44732, gb|Z29911, gb|AI997176 and gb|AI395420 come from this gene. [Arabidopsis thaliana] gb, mRNA sequence\n")
-		f.write("TTTCAATTGGTCAATTCATTACATTTACATCCATTCTAATATTACAACGTCGGCTGATCCCTTTTGAAGA\n")
-		f.write("ATCAAGGTGAATAACCCATTCTAATGAAAACATTACATCCATTCCAATTGATCAAATCATCAATGAAATC\n")
-		f.write("CCCCCTTTTTCTATATAATGGCGTCGGATTAAAAATTTCTGCTAGCAATCACATTCTATGCTAACGGTAG\n")
-		f.write("GACTACAGAACTGTTTCTTTTCTGCCTTTAGCTCAAAATGACTCCTGTTATTCATCAGTCTGAACTGTTT\n")
-		f.write("CTTTGCTGCCATTAGCTCGAAATGACTCCTTTGTTATTCCATAGTAGACTGGTTCTTCGCCTACAAAGGT\n")
-		f.write("AATGAAATTCCAGCCAAAAGCAGACCCACCGACAATACATGTCCCTTGAGTCTGACCATCTTCAGCCTGC\n")
-		f.write("TGCTTCTCGCTGGATACACCAGTTGGAAACTTATTTTCTGATGGTTTTACAAAAGCCTTTGTATCTTGGG\n")
-		f.write("GCTTTTCACCTGGCACATTCTTACTTCTTGCTGCCGAAACTGTTTCTGCCGTCATCTGTTTGCATAGTTC\n")
-		f.write("CATCAGAAGTTT\n")
-		f.write("\n")
-		f.write(">gi|226790886|gb|GO545676.1|GO545676 Mdas9009I24_e686.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9M5Q1|FUT1_PEA Galactoside 2-alpha-L-fucosyltransferase (Xyloglucan alpha-(1,2)-fucosyltransferase) (PsFT1) gb|AAF62896.1|AF223643_1 xyloglucan fucosyltransferase [Pisum sativum], mRNA sequence\n")
-		f.write("TTTTTTTTTCCACTCCACGAATTTTTATTTTTGCTAACATGGAATAACGTTCGTGTATATGAAAAATTCC\n")
-		f.write("ATGGTATTCCTGATCAAACAGTTACCACAACGGTCATATATCACAAGCTACCAACCTAAAACTCATCCTA\n")
-		f.write("ACGATTGACCAGCTTAAGAACCCAACTCATATCCTCACAATGCCTCCCATGAAGAACCAATGCACCTGGG\n")
-		f.write("TCGATTCCTGTCTTGGCCTTGCAATCGTAAAAGGGAGGTGCGTGGAAGCAAGGCTCCATTGACATTGCTC\n")
-		f.write("GTCGACAAGGAGGATTGGGTGCTGTACTGTTCTCCGGTTTGTAAAGTATCCACGGTGTCAGCCCCCCAAG\n")
-		f.write("ACTCTGCGCGACATACCCAAATGTTGACCATGAGCTTGTGACCAACACATCTGTCAAGCTTAGTAGATAC\n")
-		f.write("ATTTCGGCCCATGCCTTGCGGTTGTGCGTATGCTTCTCAGTTTGATGATACTCCTCGTGACTCGGCTGGA\n")
-		f.write("AAATGCCAACCACCTCCCCTGTCACAGTAGGATGCTCCCAGTAC\n")
-		f.write("\n")
-		f.write(">gi|226790885|gb|GO545675.1|GO545675 Mdas9009J02_e688.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CAACATGGTATTAAAAATTTAAATTTCTGGTTAAAATATTTACCAGGGCGGAAGAACTTTTT\n")
-		f.write("\n")
-		f.write(">gi|226790884|gb|GO545674.1|GO545674 Mdas9009B14_e645.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA74434.1| similar to hsr203J [Lycopersicon esculentum], mRNA sequence\n")
-		f.write("TTTTTTAAAGATAAGAAGTTGCAATTTTTATTTTCATTACGAAAGTATATATATATAGTGGGTATGAAAC\n")
-		f.write("AAACGGACCCATAAATGGCCACACATAGTAACGTTATTAGCAACTACAAAGTCGATATCTTTTAGTGCTT\n")
-		f.write("GTTGACAAAGTCTTTGATCCCAGAAATTAGAGCCTCAGTTTGCGCAGCCGTTTGAGGATCCATATCCACC\n")
-		f.write("GCAATCTTGTTAAGATAAAAGCTATGACTCATCCCTGGACTAATCAGAAGCTCCACATCCTTCTTAGCCT\n")
-		f.write("TCTTCATAGCGTCATAGTATTCCATCTCAGTGTCTATTATCATGTCCATCTCACCAATACATAGAAGAAA\n")
-		f.write("CGGCGGCAGCTTCAGAGTATCCAAAGGCGGTGCTTCGGGGCCCATCGGACAAGTTATTGGATGGTCCTTG\n")
-		f.write("GTCGACCCCACTGGCAGTGCCAAGCTCAAAAACTTGTCCACCATGTCTAGGGTTAGCAAAGGTGACTCTG\n")
-		f.write("GCTGCTCCAACTCCGACCTACTCCTCACCGCTCGAACGAAGCCTGGGTGGATAGGAATCCCACCCGCTAG\n")
-		f.write("CCTTAACGGACTCAAATCCACCTTCCCTGCTCGAGCGGCAATTTCATGCACGAGATTTCCCCTCGTGCCG\n")
-		f.write("AA\n")
-		f.write("\n")
-		f.write(">gi|226790883|gb|GO545673.1|GO545673 Mdas9009J01_e687.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12301|PSBQ_SPIOL Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) pir|S00008 photosystem II oxygen-evolving complex protein 3 precursor - spinach, mRNA sequence\n")
-		f.write("CTAGCCACGGCTAGCCTGCCGGTGCTGCTGACCGTGTTCAAGCGTGACGAGCCACTTAGGTGGAGGCTGC\n")
-		f.write("CCTCCAAAACTGCCTGGGAGGAGCCGTGCATGCCAGCCACTGAAGCCATAGCTTGTGCCATTTCCTGAAC\n")
-		f.write("CTTCCTAACTTTCTGAGATAGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790882|gb|GO545672.1|GO545672 Mdas9009G20_e675.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTGCAGAGATGGCATCCATGACCATGACAGCTGCCTCATTCCTGACCGCAGGCTCAGCCTCAACCATCGC\n")
-		f.write("CAAACCTTCAACTTCCATGCCGCCGGAGCCTCTTCGTAGCCAAGGCCGCCGCCAGAGCCCCAGAGGGAG\n")
-		f.write("\n")
-		f.write(">gi|226790851|gb|GO546227.1|GO546227 Mdas9001C03_e12.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849433.1| expressed protein [Arabidopsis thaliana] pir|T09892 hypothetical protein T22A6.120 - Arabidopsis thaliana emb|CAB45064.1| putative protein [Arabidopsis thaliana] emb|CAB79339.1| putative protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("AAAAGGTAGAACCCTGCCCTGTTGTGAACTTGTGAAGGTCAAAAAATTCTACATTGCAAAAACAAATGAC\n")
-		f.write("ATCGGAGGTGAGAAATGAAATATACAACACTACTACAACAGCCTCGGCAACTCTCACAGTATCGAATACC\n")
-		f.write("CCCCCGTTCTTCCTCCCAGTACCAAACATCTGTACCATTTCATCTTTTTTCCCATTTTCTTCGACAACAC\n")
-		f.write("GCGGAATCCGCTACTGTCCCTCCAACTCTTCTTCGTCAGGTAATATTACAGTCAACAAAGAGTATTTCAC\n")
-		f.write("ACGGAGGGATATCCTGCCCTTCTCAACCACTAGCCTTGCCCCAGAAACAACCCAATAACCCGGAGTCTCC\n")
-		f.write("TGTGGCCCTCTTACCATCTCTGTTGTGTCAACGAATTTCCGAAGCTTCGGGGCTTGGATGGGTACCGGAG\n")
-		f.write("GACCTCCAGGGTAAACGGCGGAGTTTATGTTCACATCTGCAGGCCGTGGAGGTGGTTTCTGAGCTGTTGT\n")
-		f.write("AAAATGATGGCTGATTAGTGTTGATATGAGTCCGGAC\n")
-		f.write("\n")
-		f.write(">gi|226790850|gb|GO546226.1|GO546226 Mdas9001A12_e3.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC24588.1| late embryogenesis-like protein [Prunus armeniaca], mRNA sequence\n")
-		f.write("TCGAGAAAACTGGAGAAATCCCCATCCCTTACAAGCCTGATGTCGATGTTGAGAAGATCAGGTTTCAAAC\n")
-		f.write("CTTCTCCTTTGAGGAAACCGTTGCGGTCCTCCATTTGAAGCTGGAGAACATGAATGACTTTGACTTAGGC\n")
-		f.write("CTCAATGCTCTCGACTACGAGATTTGGCTGTGTGATGAGAGCATTGGGGGTGCAGAGCTCGCCAAGTCTG\n")
-		f.write("CCAATCTTACTAAAAAGGGCATTACTTATGTCGATGTTCCCATTACCTTCAGGCCTAAGGATTTCGGGTC\n")
-		f.write("TGCGCTCTGGGATATGATTCGGGGAAAGGGTACCGGCTACAGCATCAAAGGGAATATCAATGTGGACACG\n")
-		f.write("CCCTTTGGAGCCATGAAGTTGCCCATTGTCAAGGAGGGTGGTACTACACGCATCAAGAAGAACAAGGGAG\n")
-		f.write("ATGGCGGTGATGACGATGATGATGAGGATTAGAGAGGGATGTTGGGGTTGGGTTGACAAGCGAAACTAGT\n")
-		f.write("AGTTGTTGTCGTCTGTTTATCTGTACTGGTGTTTTGGAATAATAGATCAATATTAAGGCATGATTTCTGG\n")
-		f.write("TGGTAAGTTGAGCTGTTTTGGAGGAGAAATTGGTGTAATTGCTATGGTT\n")
-		f.write("\n")
-		f.write(">gi|226790849|gb|GO546225.1|GO546225 Mdas9001H15_e41.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTTGGGTAAACTCATATATTACAATTTAAAATAATGCCTCGTATCTCTTTCTTG\n")
-		f.write("\n")
-		f.write(">gi|226790834|gb|GO546224.1|GO546224 Mdas9001N19_e77.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO91861.1| TGB12K interacting protein 2 [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TCGAGTAGAAGTGCCACGCATTCCTTCCTGCCATAACCGGCTGCATAATGAAGTGCGGTGTTTTTGTTCT\n")
-		f.write("TATCAAGAGCATCGACTCTTGCTCCAGCCTCAAGAAGAGCTTGAGCACACTTCACCTCACCATATCCACA\n")
-		f.write("TGCAAAATGTAATGCTGTCCTCCCTTCTGAATCTTCCTCATCCTTGTCAGCACCAGATGCTAAGGCAGCT\n")
-		f.write("TTCAAACCCTCCACGTCACCAACACTAGCAGTGTGATGAACAATTGATTCATCCTCATTTCCGGCATCTT\n")
-		f.write("CTGCTTCTTCTGGTGCTTCAGTAGAAGTAGCTGCATCCCCAACTGCAAGACCCATTGCTTCTCCCAACTT\n")
-		f.write("CTGCAAAACATCTTTATCATTCCAGTATCTCATCATGGCAGCTGGACCACCAGTTTCTATTTCTTCCAAA\n")
-		f.write("ATAAGTTTCAAAGAAAGATCTTCTTTGATACGTGACATGCGTTCCTCAAGCTGATCTTTGTTCGAGGGAT\n")
-		f.write("TGGCGAAACTC\n")
-		f.write("\n")
-		f.write(">gi|226790833|gb|GO546223.1|GO546223 Mdas9001H24_e44.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565906.1| oxygen-evolving complex 25.6 kD protein, chloroplast precursor, putative [Arabidopsis thaliana] gb|AAK64145.1| unknown protein [Arabidopsis thaliana] gb|AAC27838.2| PsbP domain protein, putative [Arabidopsis thaliana] gb|AAM62853., mRNA sequence\n")
-		f.write("TTTTTTTGCAATAGACAGAATTTTTTTAGCAATATATACTTCTTACACTGTCATTGGAGATTGCATTGCT\n")
-		f.write("CCATGACATTGGATTTCAGATGTCAAGCATTCTGAAAGAGTCTGCTACCACTTTAAGCTGGTTGCGGTAT\n")
-		f.write("CTTTTCCACCGTCTTTCGTTTGCTCCGACAATCAGGGTGTAGTATCTCCCGTTTCCAATGGCTATGGTTG\n")
-		f.write("CGAATGAAGTGGTAGCAAAGTTTGGAGATTCAAGTCCATACTCAATGGTGTAATAATTTTTCCCATCTAT\n")
-		f.write("GTTTTTCTCCTCGACGCCAAATATAGTTGCATACTGGTTTGGTGCAGCAAGTTTATGCCTCACCAGATCG\n")
-		f.write("GTAACAACCTGTTCCATTGGACCCAAATCATGGATGTCAGTTTTATTTGTGGGTATAAATCTCACTCTAA\n")
-		f.write("CATTATGCAGCTGCATATATCTGTCCTTGAATGCAGAGTCATGTGCTCTAAACTCAAAGTCCCTCCAATC\n")
-		f.write("GTTGGGGTAGTAGTATGAATACCCATCTACTTTGTCGACGAAAGCTCGAAACTTTTCCGGTATTTCTTGA\n")
-		f.write("GCAAAGAGGGAATTTGCATGAAGTAGACTTGTGGTTAGTGCCCCAAATCCTAAAAGTAGAGGCCTTCTCT\n")
-		f.write("TGCAATGGCTTTCTTCAATGGAGGCTGACTCTCCTGAGGCAGTGATTGATT\n")
-		f.write("\n")
-		f.write(">gi|226790832|gb|GO546222.1|GO546222 Mdas9001H01_e37.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_027545.1| expressed protein [Arabidopsis thaliana] gb|AAD17426.2| expressed protein [Arabidopsis thaliana] gb|AAM65678.1| unknown [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTCCACATCAACAACTCTATCCATTCTGCACCAAGTCCCAGAAGGTCATGTTGGGGTATATTGGAGAGGA\n")
-		f.write("GGCGCTCTTCTGAAGACAATTACAGATCCAGGTTTTCATCTCAAGCTGCCTCTGGTCACCCATTTTGAAC\n")
-		f.write("CAGTTCAAGTGACCCTGCAGACTGATCAGGTGAGGGATATTCCATGTGGTACAAAAGGGGGTGTCATGAT\n")
-		f.write("CAATTTTGAGAAGATTGAGGTTGTAAACAGGCTTCGTAAGGATTTTGTGTACGAGACGCTTCTCAATTAC\n")
-		f.write("GGTATCCATTATGACAATACCTGGATATATGACAAATTCATCATGAGATCAATCAGTTCTGCACCTCACA\n")
-		f.write("TTCTCTTCAAGAAGTTTATATTGATGTGTTTGATCAGATTGATGAAAAGATGAAAGAAGCTCTTCAGGGT\n")
-		f.write("GACTGTACCCGTTATGCTCCGGGTATTGAAATCATCAATGTCCGTGTTACAAAGCCTACCATCCCAGAAA\n")
-		f.write("GTATAAGACGTAACTTTGAGCAAATGGAAGAGGAGCGCACCAAGGTCTTAATTGCTATAGAGAGACAGAG\n")
-		f.write("AGTAGTGGAGAAAGAGGCAGAAACCAAGAAGAAGATGGCTATCAGTGAGGCTGAGAAGAATGCCAATGTC\n")
-		f.write("AGTAAGA\n")
-		f.write("\n")
-		f.write(">gi|226790831|gb|GO546221.1|GO546221 Mdas9009O02_e709.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n")
-		f.write("TTTTTTTTGCATTATAAAACAGGAAAGCGCTCAATATATAAATGGTTTCACCTCGCACATTGTCTCTCGT\n")
-		f.write("GGCAATATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATACAATTCAT\n")
-		f.write("CAGACACAACTGAATTAGTTAACGGTAACTTTACCGACCATGCCAGCTCCCTGGTGAGGAGAGCAGTAGA\n")
-		f.write("AAGAGTATGAACCTTTTTCGGTCAAGGTGATGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGTCCTCCTC\n")
-		f.write("GCTCATCGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTTGTGTGGG\n")
-		f.write("AATCCAGCATTGTTCTTGAACACAATCTTCTCACCGGGGGCGACGGAGAAGCTGTTGGGGACGAAGGCCA\n")
-		f.write("AGCCCCCGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGCTGGCTGC\n")
-		f.write("GGTGGCGGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGGGGAGGCT\n")
-		f.write("GAGACCTTAACGGCAGCGCTAACCTTGGCTGCGCCGGAAGACTTGAGTC\n")
-		f.write("\n")
-		f.write(">gi|226790830|gb|GO546220.1|GO546220 Mdas9001C07_e14.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04011|AB20_PRUPE Auxin-binding protein ABP20 precursor gb|AAB51240.1| auxin-binding protein [Prunus persica], mRNA sequence\n")
-		f.write("TTTACCTTCAACAACAAAGCACACACAACAAAACTTCTACTACAAACATACAAAAATCAAACGAAGCAAT\n")
-		f.write("CTTCTACAACGAATCAAAACCACCACTGAAAGGAAACCGAAATGGGACGTTCAACACAACAAGAAAGATA\n")
-		f.write("CAATATTTAGTGATAATGCTGGCTGAAATTCAAAGATGAGAGAGCTTAATTACTAATTAGTACCACCAAG\n")
-		f.write("AGCGGCCTTCAGTTTCTTGATCTGAGCAACGTCAAGGAAAGTAGTCTGCGCTATCAGTTCCGTTGGTAAA\n")
-		f.write("TCATTTTTAAACAGCGCATAGTCCAGAATCTGCAGCCCCGGGCTTGGACTACTGAAGCTAACAAATGCAA\n")
-		f.write("GGGCCGTAGCCTCACCTCCATTCACTTGGAAGTGCAGTAACCCCTGAGGGAAAACCATAATGTCTCCCTT\n")
-		f.write("CTCAAGAGTTTGTAGATAAACTGTGTTCGCTGAGGAAACAAAGCCGGCGCAGATGGTCCCTTCGATGACA\n")
-		f.write("ATTAGGACTTCCGAACCTCCAGGGTGTGTGTGAAATGGGATGACTCCACCAACAGCCAGGTCTAGACGCG\n")
-		f.write("CAAGTGAAATGCCAAGGCCGTTGACACCAGGGAACTGAGCAGCAAATGCAGGGGTGACTGCAGC\n")
-		f.write("\n")
-		f.write(">gi|226790829|gb|GO546219.1|GO546219 Mdas9001P07_e85.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_683304.1| expressed protein [Arabidopsis thaliana] gb|AAG09546.1|AC011810_5 Unknown Protein [Arabidopsis thaliana] gb|AAO22631.1| unknown protein [Arabidopsis thaliana] gb|AAO42362.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTCTGTCGAGTTTTACAACCTAATATGCACATCTGCGTGTCTAACACGTAAAAGGAAACAAAACCCCAT\n")
-		f.write("TTTACGCATGCAGCGGTCCCCGGCATGCCGCCAGAAACGTTTCTACAAAGCCGAAAGGGACTCGGTTCGC\n")
-		f.write("CACGAAACATCTGCAACGCCGCCCCCCGGGTAATCAAACAAACCGTCTAAAGCCAGGTACTCCACCCCAC\n")
-		f.write("CAATATAATTGTTATTAGCAAATTCAGAGTCGCCACCGATTCCGAAGTCGAACGAGTCGTAACTCGGAAT\n")
-		f.write("CATGTCGTTCTCGAACCCTACCATGCCATCCAATTCAACGGCCTCGGAGCCACTCGTGGTGAAATCAGCA\n")
-		f.write("GCCTCGATTTTTCCCTCCTCACTTGCTCCATTGGTCGGTGGAAGACCAAGCTCGTCGTCAGAAGCTTCCA\n")
-		f.write("GAAGATAACCAAGTTCTGGCTGCGTCGACTGGCCTGAATCTGACGTGGCTTCAGACCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790813|gb|GO546218.1|GO546218 Mdas9001I06_e46.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTGAAGATATTTTTTTTTTCCAGTAATTTATAAATGCAAAGGTCGTATTACAAGGTAGCTGCATAAC\n")
-		f.write("AGCAGAATCAAACAAGTACAACAACACAACCCACAATTTCAAGATAATAAAGTTACAACAACCTCATTTC\n")
-		f.write("TCTCTCCATGTAGGACTTTATTCTATAGCTATTTATATGCTACTCATCTCTTATTTGGAAGGAAAAGTAG\n")
-		f.write("CTAGTCTAGTTTAGGGAACAGTGGGAGGTAACGGCTTCCCAAGGAATGGATGCGGAGGAAATGGCTTCTT\n")
-		f.write("GAATTTTGGAATCGGCTTCTTGAAGAATGGATGGGGAAACGGCTTCTTGTAAACTGGAACTGGGGGAAGA\n")
-		f.write("AGTGGCTTCTTGTAAACTGGAATTGGCGGAAGAAGTGGCTTCTTGGAAACTGGAATTGGCGGAAGAAGTG\n")
-		f.write("GCTTCTTGAATTTTGGAAGTGGAAG\n")
-		f.write("\n")
-		f.write(">gi|226790812|gb|GO546217.1|GO546217 Mdas9001D13_e21.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTGGACATATGAAACTTTACGTACGTGCTATATTTCACAAAATCGTGCTACATATGGTGAATGAACAA\n")
-		f.write("AACAGAGCCACATATATACACAACATATGTGATCATCTGACCTAATTGCATTACAATTTGCTATCAGAAT\n")
-		f.write("TCACACCAGAACAACAGCATTCATCACGTTTGTTCAGGCTAGAAATTCCAATCAACATTTCCGACATAGA\n")
-		f.write("TTCACAGCGAAAAAAAGGTCACACCTTTTAATGCTTTATGCTCTACTTCTTAACACCATCAGCATCTTTC\n")
-		f.write("TCTACGACTACATTGATCTTCTCATACTTGAGATCCACAGCCCTTGCAGGAAACACAGCAAGGTACACCA\n")
-		f.write("GAACAACAGAATTCATCACATTTTCGGGTTAGAGATCACAAACCAGATTTGCAACATACATTCACAGAAA\n")
-		f.write("AAAAAAATAAAGCCACGCCCTTAAAGACCTTACAGACCTTACGCTCTACTTCTTAACACCATTGGCA\n")
-		f.write("\n")
-		f.write(">gi|226790811|gb|GO546216.1|GO546216 Mdas9001K17_e63.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567934.1| aminotransferase family [Arabidopsis thaliana] gb|AAL08279.1| AT4g33680/T16L1_170 [Arabidopsis thaliana] gb|AAL38732.1| unknown protein [Arabidopsis thaliana] gb|AAM51321.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTGCAGCAGCTGAAAAATGATTTGCATTTCCTAAAGACATAGAAATAGAATCCACAACGTTGAACATA\n")
-		f.write("AATGGAGCAACTGTCGATTTTATCTTCGAATCAAAATATACTAGACAGCAGATACTAGCCTCGCGAGGCA\n")
-		f.write("GACACTCCGGCTCACTTGTATAATTGCTTGAACCTTTTGCAAGCTTCTAATACATTTTTCCGGTGACCAA\n")
-		f.write("ATGCGCTAACCCTGACGAAACCTTCACCCCCAAATCCGAAACCACTCCCAGGTGTGGTGACCACATGAGT\n")
-		f.write("CTTCTCAAGAATCTCGCTGAATACATCCCATGAGCTTCGGCCAGGGAAGTGCACCCACACATAGGGTGCA\n")
-		f.write("TTCTTCCCTCCATACACCTTAAAGCCAAGAGATTCAAATGTCTCCACTATTATTTCTGTATTTTCTTTGT\n")
-		f.write("AGAAACCAATCACCTCACGCATAGCCTTAAGGCCTTCTGGTGAAAGGCAAGCAAGACCACCAGCTTGGGA\n")
-		f.write("TATATTGGATGCACCATTGAAGCAAGTACAAACAATGCGGTTGAAGTCCTTGGCAACAGGGAATCCATCT\n")
-		f.write("GAAAAGAGCAATTGCTTTGGAACAACAGTCCACCCCAGACGAACTCCTGTGAATCCAGCATA\n")
-		f.write("\n")
-		f.write(">gi|226790810|gb|GO546215.1|GO546215 Mdas9001F06_e27.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA11705.1| elongation factor 1 alpha subunit [Malus x domestica], mRNA sequence\n")
-		f.write("AGACTGGTGTCATTAAGCCTGGTATGGTGGTGACTTTTGGCCCAACTGGGCTAACTACTGAGGTCAAGTC\n")
-		f.write("TGTTGAGATGCACCACGAAGCTATGCTGGAGGCCCTTCCAGGTGATAATGTTGGATTCAACGTGAAGAAT\n")
-		f.write("GTTGCTGTCAAGGATCTCAAGCGTGGTTATGTTGCTTCCAACTCCAAGGATGATCCTGCAAAGGAGGCTG\n")
-		f.write("CTAACTTTACCTCTCAGGTCATCATCATGAACCACCCCGGGCAGATTGGACAGGGATATGCACCAGTTCT\n")
-		f.write("CGACTGTCATACCTCCCACATTGCTGTCAAGTTTGCTGAGCTTGTGACAAAGATTGACAGGCGATCTGGC\n")
-		f.write("AAGGAGCTCGAGAAGGAGCCTAAGTTCTTGAAGAATGGTGATGCCGGATTTGTGAAGATGATTCCAACTA\n")
-		f.write("AGCCCATGGTTGTCGAGACCTTCTCTGAGTACCCACCACTCGGACGTTTTGCTGTGAGGGACATGCGCCA\n")
-		f.write("GACTGTTGCAGTTGGTGTCATCAAGAGCGTTGAGAAGAAGGATCCAACTGGAGCTAAGATCACCAAGGCC\n")
-		f.write("GCCGCTAAGAAGAAGTGAACCGC\n")
-		f.write("\n")
-		f.write(">gi|226790809|gb|GO546214.1|GO546214 Mdas9001F03_e26.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78526.1|AF195234_1 metallothionein-like protein [Pyrus pyrifolia], mRNA sequence\n")
-		f.write("TTTTATTCTAATATTTGCATATAAATCAAAGGGCCATGAACATTGGCCATTACATGACACAATCACAGAA\n")
-		f.write("ACACAAACATATGAGTGACATGTTTTCACAGACGTACAACATGTCACTCAACAGACTCAAATACTATAAG\n")
-		f.write("CAAACGAAAGACAAAGCCACAAAGTTATTTTTTCCCACAAACACTTTTCATTAATTAAGGGTCTATAATC\n")
-		f.write("CCTTAATTAATATGACACTTTTATTAATCACATCTTAATTTGGTTCTCTGGGCTTACTGACCACAGGTGC\n")
-		f.write("AGTTCACACATGGGCAGGTTGTGCCACACTTGCACTTTCCGTCGTTCTCGGCTGCGGGAGCGTCCACGAC\n")
-		f.write("GACGGTGTCCATGGAGCGGTTCTCAGTCTCCACGATCACCAAGTCGTACCCGTTTCCCTTTCTTCACGCA\n")
-		f.write("CTGGGAGGTGACATCACAATCGCAGTTTGCCGCAGTT\n")
-		f.write("\n")
-		f.write(">gi|226790808|gb|GO546213.1|GO546213 Mdas9001O06_e79.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK13030.1| ribonuclease-like PR-10a [Malus x domestica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTAACTGATTTCATTATATTTATAGATAATACACTTACAGTCTGCAACTTTTTTTTCA\n")
-		f.write("AACAAATACATCAAGGGCAACCAGAAGATGATCGCAACCATAAACTTATTTTTCAAAGCCAAAGTGCCCA\n")
-		f.write("AAACCATGGCTACTTTGGGCTGACTAGAAAAAGCATACAAAGAAAAGCCACACAACCTTCGACTGAAGGG\n")
-		f.write("TGACACCCAAAATACCATAGAAACATATTAATTTAGTTGTATGCGTCGGGGTGGCCCTTAAGGTAGCTCT\n")
-		f.write("CAATAAGCTTGAACAAACCATGAGCCTTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGATCTCAACATC\n")
-		f.write("ACCCTTGGTGTGGTAGTGGCTGATACTCTTGATGATGGAACCACTTCCAGATGCCACCAACTTGGTCTCG\n")
-		f.write("TAAGAGACCTTCTCAATGGTGTCTGTCAAAGCATCTCCTTCAATCAAAGTGTAGGCGTATGAGT\n")
-		f.write("\n")
-		f.write(">gi|226790807|gb|GO546212.1|GO546212 Mdas9001K06_e61.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL86484.1|AC077693_23 putative beta-phosphoglucomutase [Oryza sativa (japonica cultivar-group)] gb|AAP55088.1| putative beta-phosphoglucomutase [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAAAAGAAATACTATCACGTTGCTTTTATTCACGAGTCGTCAAA\n")
-		f.write("AGAAGAGTCATTTGACAACTGTGCTTGCTAATAAGCTTTTACTCGTATACAACAACAAGATTGAGAAGTC\n")
-		f.write("CGAATGCCTGAATAGCGTACCAGAACAGAATCATAATATATATAAGGTTATATATTACTGGGAGTTGGAG\n")
-		f.write("TTGCAATTGCAACTGTTATTGCCTCTGGTGTTGCCTCTGCCGTTGCCTCGGGCTTCTTCTCCAACTTTTC\n")
-		f.write("CAGTGCTTCCCACAATTTCGTGTCCTCAAAATCTTTAATAACGAAGGAGACTCCAGCGTTAATCAATGAC\n")
-		f.write("GTCCCAGGATTCCTTGTAGCTATACCAACAACTGGCATTCCAGCTGCTACTCCAGCTGTCGTTCCTGAAA\n")
-		f.write("CGGAATCCTCAAAGATAAAAGTATGCTCATGTGACACTTCAAGTGTTTCAAGAGCCTTCAAATAAGGGTC\n")
-		f.write("TGGAAATGGTTTTGCTCGATCACATTCATTTCCAATAACGAGAATTTCAAAGAAGTCTGTGAGCCCTAAT\n")
-		f.write("GATGATATCATTAGCTCCCCACTTGCTCGTGGAGAATTTGTCACTGCGGCCCGTCTCAAG\n")
-		f.write("\n")
-		f.write(">gi|226790793|gb|GO546211.1|GO546211 Mdas9001N16_e76.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78507.1|AF195204_1 carbonic anhydrase isoform 1 [Pyrus pyrifolia], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTACAAGCTCGAGGAAATTATAATTATTGCTGCAAAATATCGGTTACATTTGCAGACGT\n")
-		f.write("GCTTCCGGGGACATTGCAGATGAAATTAAGAAATAAATTAGAAGTACTTAATGATAATTAATTAGGAAGC\n")
-		f.write("AATTGAGTTGCATGGGAATTATGTGATTACGATCATACGGAGAAGTTGGGGTTGAGGCTAAAATCAACAT\n")
-		f.write("CCCAGAGCTCAAAATGTCCATTGATAAAGTCATAGTATCCTCCCTTGATTGCTAGGGTTTTCTTCAGCAA\n")
-		f.write("ACCATCTCTCACAAACGGATAGCTCAACAGGTTTCCGATCGATACATTCACCGCCTCCTTTTCGCAACGA\n")
-		f.write("CTGCATAGCTCAGGGAAAGGAGTATCAGGACCGTGATCTGCCT\n")
-		f.write("\n")
-		f.write(">gi|226790792|gb|GO546210.1|GO546210 Mdas9001C22_e18.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_178786.1| hypothetical protein [Arabidopsis thaliana] gb|AAM15495.1| hypothetical protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGAATGCCGTTACCACGTTTTTATTTGATAGGGGGGAGTATTGGCAGGGGGTTAAAACCGCCCTGGA\n")
-		f.write("TGAAGCGACCTCTCAGGGGGAGTATAACCGCCTACTGGATTTCGAAAATAGGGATCTCCGGATTCGGGAG\n")
-		f.write("CAGAGGCATTCGTGCTATTGCCTTTTCGAACAGGTGCTTTCTGAGCATCCGTCCTTGGCGGAAAGAGCCC\n")
-		f.write("CCTACGATCCTAAAGAAGTCTTTTTTGATTTCGTTTCCGAGGCGCGGAACGGGCTGGACGCCCATCACGA\n")
-		f.write("GTGGAGCCCTCGG\n")
-		f.write("\n")
-		f.write(">gi|226790791|gb|GO546209.1|GO546209 Mdas9001L09_e66.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB64207.1| elongation factor 1-alpha [Zea mays], mRNA sequence\n")
-		f.write("GACAAATCGCCTTTGTTCCCATCTCTGGGTTTGAGGGTGACAACATGATTGAGAGGTCCACCAACCTTGA\n")
-		f.write("CTGGTACAAGGGACCAACCCTTCTTGAGGCTCTTGACCTGATCAACGAGCCCAAGAGGCCCTCAGACAAG\n")
-		f.write("CCCCTCCGTCTTCCACTTCAGGATGTGTACAAGATCGGTGGTATTGGAACTGTGCCAGTGGGACGTGTTG\n")
-		f.write("AGACTGGTATCGTCAAGCCTGGTATGGTTGTGACTTTTGGGCCAACTGGTCTGACCACTGAAGTTAAGTC\n")
-		f.write("TGTTGAGATGCACCATGAGGCTCTTCAGGAGGCACTCCCCGGTGACAATGTCGGGTTCAATGTTAAGAAT\n")
-		f.write("GTAGCCGTGAAGGATCTCAAGCGTGGTTTCGTTGCATCCAACTCCAAGGATGACCCTGCCAAGGAGGCTG\n")
-		f.write("CCAACTTCACATCCCAAGTT\n")
-		f.write("\n")
-		f.write(">gi|226790790|gb|GO546208.1|GO546208 Mdas9001E14_e25.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCAAAACAAGCCGATAACATTAAGGAGGAGCAGAGTATATTAATGTGTATGAATCAACATCCAACCACTA\n")
-		f.write("GCCACAGATCCACATTTTCTGCCAAAATTAACACCAAATCCTCACTAAAAACACTTGACCCAACAGACAG\n")
-		f.write("AAAAAGAAGACGAAAAATTACTACACCAAAAGGAATCATCATCCACTTCATGTTGAATTCCAAAGATTGA\n")
-		f.write("AATCAAAGGAGATGACCCATAGAACCGAATACTTCCAAACACTCGAAACGAGTTTTTCATTCTTAGAAAC\n")
-		f.write("CACGACTCAATTAAGCAAAAACCAAACAGACCACCACCACAAGCACAGAGACGG\n")
-		f.write("\n")
-		f.write(">gi|226790789|gb|GO546207.1|GO546207 Mdas9009N19_e708.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850942.1| leucine-rich repeat transmembrane protein kinase, putative [Arabidopsis thaliana] gb|AAL32758.1| Unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGAGTTTGAAAATTACAGTAGCCTGAAGGGAACAAGGGGACTAACTAGTAGTAGTAGATACATACAT\n")
-		f.write("ATCGTGCAAAAAGTCCTGCAACTATTTTACATCCACAAAACTGCAAACATACATATCTATATAATCTAAA\n")
-		f.write("TGCAATAATCCGAGGCTCTGGCTAATATGTTACAGGCAATCTCAGCTCTCGTAATTGGGCTGCTTCGACC\n")
-		f.write("AATTAATTTTCAAAGCGCGGCAGGAGTCTTGATTAGTTTCAATTCTCTATACCCTTCACTAGTTCCATTT\n")
-		f.write("TCTTATTACCAGCGGCATCATCTTTGCCGATAACAATTTTGAGCAATTTAAACGTCTCGTGAGCCTCTTC\n")
-		f.write("TAGCATTTGAACCACACTTCTCATGGAGGGTCTTAGCTCCGGCAGCCTAGCCGTGCACAGAACTGCAATT\n")
-		f.write("CTTAACACCTTGATAGCCTCTTCCTTGTACACCTCTGGAATATATGAGTCCACCATACTTAATATGCTCT\n")
-		f.write("CTCTACTCTTGAGCATGCTGCTTACCCAGCTCACTATGTCCTTGTTCTCCCCGAACTCTGCCTCTATCGG\n")
-		f.write("CCTTTTCCCCGTCACTAGCTCCATTAGTACCACTCCAAAGCTGTACACATCACTCTTCTCGTTCACTTTG\n")
-		f.write("TACGTGTATCCATATTCAGGAGCAATGTAGCCATGTGTTCCGGCAATAACGTGAGTAGAGTCCTTGCCTG\n")
-		f.write("CAGTGGCCTGAACAATCTTGGCAAGCCCAAAATCCGCAATTCTCGGGCTCA\n")
-		f.write("\n")
-		f.write(">gi|226790788|gb|GO546206.1|GO546206 Mdas9001D22_e22.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188935.1| ADP-ribosylation factor, putative [Arabidopsis thaliana] dbj|BAB03042.1| contains similarity to ADP-ribosylation factor gene_id:F5N5.14 [Arabidopsis thaliana] gb|AAL36314.1| putative ADP-ribosylation factor [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCCGACACCACTTCCTGAACGATTAATCAAATATTTAACTCTAAAGGCGCTTCCTTTATCGCCTTGTCGC\n")
-		f.write("AAACACCGCTAAGCTTTCCCCATACGGATCGCAAAATTTCTGAAACCCCAAAGCTTTTGGGTGGATTCCT\n")
-		f.write("GATCCAAACCCAAAATTAATCTCGGGGGTTTCTCTTGGTTCCAATCCTCCGCTTCCCGAACCATCGGTAA\n")
-		f.write("CCGCCCTTCCCCGCCATCAACCGCCACCTCCTCCTCCTCCATCTTTCACCCTTCCGCCAATATCCAAATC\n")
-		f.write("CAGGGATTTTTGGGTTGGGGATAGAAGATGGGGGCATTCATTTCCAAGTTTTGGTTCATGTTGTTTCCTG\n")
-		f.write("CAAAAGAGTATAAGATAGTGGTAGTTGGGTTGGACAATGCTGGGAAGACCACTACTCTTTACAAATTACA\n")
-		f.write("CTTGGGAGAGGTTGTCACTACGAACCCAACTGTAGGCAGCAACGTCGAAGAGCTTGTCTACAAGAACATT\n")
-		f.write("CGATTCGAGGTATGGGATCTTGGTGGACAAGAAAGACTGAAGACTTCATGGGCAACATATTACCCGTGGA\n")
-		f.write("ACACATGCTAT\n")
-		f.write("\n")
-		f.write(">gi|226790774|gb|GO546205.1|GO546205 Mdas9001I24_e52.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTCGTTCCTATTCTTCTTTCTATTTCTGAGAAAAAGAGGGCTTTCAAAAT\n")
-		f.write("AAAGTAAAGGATTATTTCGTTTCGAATAGTTATTTATTAAATCGGTGGATAGGAGTATACTCTGGATCGG\n")
-		f.write("AATCGTGTCATGGGGAGTACTGCCTGATCATTTCTACCAACTTAAAGCCCCAATTAGTATTCTTTGTTTG\n")
-		f.write("TATATTATGTAAAAATGTCCTTTTGGAGAATTTACATAGTCTCCATTACTAATCCTTTCCATATGTTCGT\n")
-		f.write("GTTTCTAACCATCCACTCGTTTTTGCTCAATCCCCCGTTATGCTAATACATAAAAATGATAGTGAAAACT\n")
-		f.write("CAATACGGTTGATCTTTTGAACCCGCTTCAAGTCAGGATGACTAATCAACCAATCTTGGGGGAAACGGTC\n")
-		f.write("TCTTCTGTTTATGTTTATTTCCGCTTA\n")
-		f.write("\n")
-		f.write(">gi|226790773|gb|GO546204.1|GO546204 Mdas9001L07_e65.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n")
-		f.write("TATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAAATTCGAAAACAA\n")
-		f.write("AAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGAAACCCTAATCAA\n")
-		f.write("GGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTACGTACAACAACAATATTAA\n")
-		f.write("TTACGACGAAGAAACATGATGAAACATGAATAACAACAACAACAACAACTTAGTAGCCTGCAGGCTTGTA\n")
-		f.write("GGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGGATGAAGGCGTTGGGA\n")
-		f.write("TAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATCCGAACATGGGCAGCT\n")
-		f.write("TCCACATTGTCCAGTACCTTCCATCGTAGTATC\n")
-		f.write("\n")
-		f.write(">gi|226790772|gb|GO546203.1|GO546203 Mdas9001D03_e19.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n")
-		f.write("TCCAGCCCTCTTAGCACCGAAGAAATCAATGGATTGACCTGGGAATGTGTCAACAATCTTGACAACATCT\n")
-		f.write("TCATGGGACACATTGTCAGGCTTGAAGATTCCTGTGCAAACACCGATCCGGTCTTCCCTAGTGGGAGCCC\n")
-		f.write("AGTAGAACTTCTCCATACGACCGTCACGAATGAGAGGGGCATACAATGTGGAGAAATCGTTACCAGTGAC\n")
-		f.write("TATAATGGGGACTCTAGGATTCTCTTCCTTGTTGTACATACCAGGAAGCTGCACGTTTGTCGGGTTATCA\n")
-		f.write("GCAATGTTCATGAGGGTAGCATTCACCATCTGGTTGTTCACAGTGTACTGTGTGGTTCCACCCATCCTAC\n")
-		f.write("CGGCACCTGCATCGAGATCATTGATGAAGAGGGGACACATTTTTCCTTTCCTGATGATGTCCGCAGCCTC\n")
-		f.write("ACGGTACCCTTTGCCTTGATCAGGTTTCGCGG\n")
-		f.write("\n")
-		f.write(">gi|226790771|gb|GO546202.1|GO546202 Mdas9001F12_e28.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAACCTACAAGATATATAACATTTCATGGTGGAAATTGCTTCA\n")
-		f.write("AAATGTCAAAAACCAGATAAAAATTGAAGCTGAAAGAGTTCAAGTTGGGCACCAAATTGCAAAAACAAGT\n")
-		f.write("TGAGACCACCACATAATTTGTATTTTCTATCACTCAATAATGGATTGAATAACACCAGCTCCAACAGTCT\n")
-		f.write("TCCCTCCTTCTCTGATGGCAAACCTCATCCCCTGCTCGCACGCCACCGGAACAATCAGCTCGACCACAAT\n")
-		f.write("CTTAACGCGATCGCCAGGCATCACCATCTTCGACTCCTCATCCTTATCGTTCATAATCGAAGTCACCTTC\n")
-		f.write("CCGGTGACATCAGTAGTCCTCATGTAAAACTGCGGCCTGTAACCCGAAAAGAACGGTGAATGCCTTCCCC\n")
-		f.write("CCTCTTCCTTCTTCAACACATACACAATCGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTTTGGC\n")
-		f.write("CAACACCATCCCTCTCTGGATATCAATCTTCTGGATACCCCCTAAGCAACAACCCCACA\n")
-		f.write("\n")
-		f.write(">gi|226790770|gb|GO546201.1|GO546201 Mdas9001G07_e34.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF73016.1|AF262934_1 ubiquitin conjugating protein [Avicennia marina], mRNA sequence\n")
-		f.write("TCGACTCCTGCAAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAGGACCCGCCTGCAGGGATTA\n")
-		f.write("GTGGGGCGCCACAGGATAACAATATAATGTTGTGGAATGCTGTTATATTTGGTCCCGATGATACACCTTG\n")
-		f.write("GGATGGAGGCACATTTAAGTTGACTCTTCAGTTTACGGAGGATTATCCAAACAAACCACCAACAGTCCGG\n")
-		f.write("TTTGTTTCTAGAATGTTTCATCCAAATATTTATGCGGATGGAAGTATTTGTTTGGATATTTTACAGAATC\n")
-		f.write("AGTGGAGTCCTATATATGATGTGGCAGCTATACTCACGTCCATCCAGTCACTACTATGTGATCCCAACCC\n")
-		f.write("AAACTCTCCTGCAAATTCAGAAGCTGCTCGCATGTTTAGCGAGAACAAGCGTGAGTACAACCGAAGAGTG\n")
-		f.write("AGGGAAATCGTGGAACAGAGTTGGACAGCAGACTAACCCCGTCAGGGGG\n")
-		f.write("\n")
-		f.write(">gi|226790757|gb|GO546200.1|GO546200 Mdas9001I16_e48.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q43517|FER1_LYCES Ferredoxin I, chloroplast precursor pir|T07175 ferredoxin [2Fe-2S] I precursor, chloroplast - tomato emb|CAA99756.1| ferredoxin-I [Lycopersicon esculentum], mRNA sequence\n")
-		f.write("TTTTTTTTTTTCACTTCAAACAGAGAGAGATTCATACAAGGGTGAGTTTACAAGATACAATGATCTCCAT\n")
-		f.write("ACCACAAATGAGAGTACAAAAACATTAAGCAACTCATATAATTAGAAACAAGACAACCTTAACCCGAAAC\n")
-		f.write("AAACTAAAGCCAGATCCAACCAGCCAGCAGCCATCAAAACATGACATCATCATGAGAAAGCTCAAAAGCA\n")
-		f.write("CTTAACCAGTAAGCTCCTCTTCCTTGTGGGTCTCAAGTGTGACGTCAGACGACGGATAAGCCACACAAGT\n")
-		f.write("GAGCACAAATCCACCGTCCATCTGCTCATCATCCAAAAAGCTCTGGTCCGACTGATCCACACCCCCACTC\n")
-		f.write("ACAACTTTGCCGGCGCACGAGGAGCAAGACCCTGCCCTGCATGAGTAGGGAAGGTCAATCCCGGCCTCCT\n")
-		f.write("CCGCCGCGTCGAGAATGTACACGTCGTCGGGGCACTCAAACTCTTGTGGCCCTTCTGGTGTGAGCAGCTT\n")
-		f.write("CACCTTGTAGGCAGCCATCGCCACACGCCCTCCGCGGTTGGCCTTGAGCCCGAAAAGGGCCTGACCGACG\n")
-		f.write("TTGGGGGATAACCGCAGGCTGGTCATCGGCTGGCCGCG\n")
-		f.write("\n")
-		f.write(">gi|226790756|gb|GO546199.1|GO546199 Mdas9009P07_e713.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565494.1| expressed protein [Arabidopsis thaliana] pir|B84595 hypothetical protein At2g20940 [imported] - Arabidopsis thaliana gb|AAD29822.1| expressed protein [Arabidopsis thaliana] gb|AAM15213.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTCTGTAACATAAGTAATTGAGATCCGAATGAACCTAACAATCCTGTTCAAGCTAATCAGCATAACTTAC\n")
-		f.write("ATGATGAGATTTGCACAACACTTACATTATTAATGACAAAAAAGAACGGTATACGATCAAAGATCCAAAT\n")
-		f.write("CTGAATAGACGAAACAAAAATAACAATAACAATAATAAAAATCTCCTCACTGATTTGCTACGGGTGCGAT\n")
-		f.write("CACCACTCTTCTGCAATGCTTAAACTCAATCCACTTTCACTACTTTGTGCAAACTTTAGGATTCCATGTG\n")
-		f.write("ATGATTTTGTCGGTAATTACTATAACTTCCTTGGTTAATATAGTTCCGTTGCTCCCCAGGCAAAGATGTT\n")
-		f.write("CATAGACCGCCGGTCTTGATGAGCCTTCTCCTGGCCAAAAACCTAAACACGGGAGGAGTAAGCGCCAGAA\n")
-		f.write("TAATAGGAACCCGAATCGGAAACAGGGCCTTGTTGCAGAACAAAGCCAATGCCAGAGCACCACCAGTCGA\n")
-		f.write("AGCCGCGAGCTCAGCCGTCCGACTCCTCTCCTTCTCCACAACCACAGCCGTCGATTGCCCATTTTCCGAT\n")
-		f.write("ATGGGTCCGTCCCGAAACTCCGACCCATCGGAGATCACAGGTGGGTTCTCTGGGTTTTCGT\n")
-		f.write("\n")
-		f.write(">gi|226790755|gb|GO546198.1|GO546198 Mdas9001N22_e78.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|C71443 ribosomal protein L15.DL4730C, cytosolic - Arabidopsis thaliana emb|CAB10520.1| ribosomal protein [Arabidopsis thaliana] emb|CAB78742.1| ribosomal protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("AACCCTAGCCCCGACTGCCCAACCCTGCGCGTCGCAGCTCATTTCTGAACCGGCCATGGGGGCTTACAAG\n")
-		f.write("TACGTATCCGAGATATGGAGGAAGAAGCAGTCTGATGTGATGAGGTTCCTCCAGAGGGTCCGCTGCTGGG\n")
-		f.write("AGTATCGCCAGCATCCTTCGATTGTCCGAGTTACAAGACCCACACGCCCTGATAAGGCGCGTCGTTTGGG\n")
-		f.write("TTACAAGGCCAAGCAGGGTTATGTTGTTTACCGTGTCCGTGTGAGGCGTGGTGGCGCAAGAGGCCTGTTT\n")
-		f.write("CCAAGGGTATTGTATATGGAAAGCCCACAAACCAGGGTGTGACACAACTCAAGTTCCAGCGAAGCAAGAG\n")
-		f.write("GTCTGTTGCTGAGGAGCGTGCTGGGCGCAAGTTGGGAGGCCTCAGGGTTCTCAACTCATACTGGCTCAAT\n")
-		f.write("GAGGATTCGACCTACAAGTACTTTGAGGTCATCATGGTTGATGTTGCTCACAATGCCATCAGGAACGACC\n")
-		f.write("CAAGAATCAACTGGCTCTGCAACCCTGTTCACAAGCACAGAGAGCTTCGTGGTC\n")
-		f.write("\n")
-		f.write(">gi|226790754|gb|GO546197.1|GO546197 Mdas9001H11_e39.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_201433.1| GATA zinc finger protein [Arabidopsis thaliana] dbj|BAB10711.1| GATA-binding transcription factor-like protein [Arabidopsis thaliana] gb|AAM97115.1| GATA-binding transcription factor-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTACGAGACTTTTAATGTTGGATTTAATTCCTAACAAATTTTATCACAAGGTTTAAATACTAATTTTT\n")
-		f.write("TTTAGTATGGGGCCATCTTTCCACTACCGTAACAACACGGAGACCATTAATTGATAATACAAGAAAAAGT\n")
-		f.write("ATAGAGCTAAAACCTAAAATCATGGCTAAATTCTAAAAGCTTCCTAAAAGCCTAGTACTACCACCCACCA\n")
-		f.write("ACAAAAATGTACAACACAATTGGGTCCATCCCAATCAAGCCGGTTCAACTGCACTATTCTCTAACTTTAA\n")
-		f.write("AAACTCCGAATCATTCGGTTCAACCGCGGTTCGGGCTCGCCAACCTCTTTCCTCTTCCTCATCTCCAACA\n")
-		f.write("CTTTACGGTGACTATTCGAGTGGACATCACCAGAGAAAGTCGGGCTACAAGCCGGCCTATACTCCCCTCG\n")
-		f.write("TGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790753|gb|GO546196.1|GO546196 Mdas9001E02_e24.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T51616 chlorophyll a/b-binding protein [imported] - garden pea gb|AAF13731.1| PSI light-harvesting antenna chlorophyll a/b-binding protein [Pisum sativum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTAGTAGATGTAATGAGAATGATAATACTAATTGCCACCATGGTTCCT\n")
-		f.write("GTACACCGGTAAAACATTTTGTCTACATTGATGCTCACCATTTCACACTCACTCAAAGAACATTAATTCA\n")
-		f.write("TTGTTACAACATAAAAAAGAACAGAATTTCCATATTTTCTTCTTCCACTTTTCTTGCGTTGCAATGGATC\n")
-		f.write("TAGAAGCCTCTTAGGGTTTGGATAATGGTGTTATGCCATGGGTCTGAGAGGTGCTGCAACAGGTTGTCGA\n")
-		f.write("ACGGTCCTTTTCCGGTCACATTGTGTTGAACCACAAACCCTAGGAATGCCAACATTGCCAGTCTCCCATT\n")
-		f.write("GGCAAGTTCCTTCTCCTTGGCCTCGAGAGTCGGTGCGAAGTTGAGGGGGTTGAAGATGCCGCCTGGGTAA\n")
-		f.write("CCCACATCACCTGGGGGCAAGCTGTATTGCTTGAAGATGGGGTCTTGGTTCACACTTCCTGGGTTCTTGA\n")
-		f.write("\n")
-		f.write(">gi|226790739|gb|GO546195.1|GO546195 Mdas9001C19_e16.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S51658 light harvesting chlorophyll a protein precursor - Norway spruce emb|CAA57409.1| light harvesting chlorophyll a /b-binding protein Lhcb1*2-2 [Picea abies], mRNA sequence\n")
-		f.write("TCGTGCCGGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTATTGTAC\n")
-		f.write("ACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGGTAACAG\n")
-		f.write("GATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAGAAGCC\n")
-		f.write("GAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCCTCT\n")
-		f.write("\n")
-		f.write(">gi|226790738|gb|GO546194.1|GO546194 Mdas9001F23_e30.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTAGGGGTTTCGCTACAAAAAAAAAGAAAAATCCTTTCTTGTCGAAGGACCCTTGTCGCCAATATTTACA\n")
-		f.write("GTCTGGCGTAGACTCCAAAAGTTTCTAACTTCATGTTCACAGAATTACTTGACAATTTG\n")
-		f.write("\n")
-		f.write(">gi|226790737|gb|GO546193.1|GO546193 Mdas9001C12_e15.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM13846.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGGTGTTGGATGATTTTGAGTCCTCGATTCGGGAACTCTCTCTTTCCTTGATTGTTGAAATGCTTAA\n")
-		f.write("GAACCAGAAAGATGCAATGGAAGATTCTGTTGAGGTCGTAATTGAGAAGCTGCTTCATGTTACGAAGGAT\n")
-		f.write("GTCGTTCCCAAGGTTTCAAATGAATCCGAGCACTGCTTGAGTATCGTTTTGGCCCAGTATGATCCATTCA\n")
-		f.write("GATGTCTAAGCGTTATTGTCCCTCTGTTGGTAACTGAAGATGAGAAAACTCTTGTTACTTGCATCAACTG\n")
-		f.write("TTTGACAAAGCTTGTGGGCCGGCTTTCACAAGAGGAATTGATGGCTCAGTTGCCATCATTTTTGCCTGCA\n")
-		f.write("CTTTTCGA\n")
-		f.write("\n")
-		f.write(">gi|226790736|gb|GO546192.1|GO546192 Mdas9001K04_e60.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n")
-		f.write("AAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGACTGCTTTGAAGCAG\n")
-		f.write("TCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGGCGCACCGTCAAAA\n")
-		f.write("GTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCTCCGAGCAAACTCC\n")
-		f.write("GTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATCTGCAGACCCCGAG\n")
-		f.write("ACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGTGCACTGGGATGCG\n")
-		f.write("TCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGA\n")
-		f.write("\n")
-		f.write(">gi|226790735|gb|GO546191.1|GO546191 Mdas9001G22_e36.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAA\n")
-		f.write("CGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCA\n")
-		f.write("AATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTA\n")
-		f.write("TTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTG\n")
-		f.write("ACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCT\n")
-		f.write("TTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCAT\n")
-		f.write("AGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAAC\n")
-		f.write("CCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAAA\n")
-		f.write("\n")
-		f.write(">gi|226790734|gb|GO546190.1|GO546190 Mdas9001A20_e4.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n")
-		f.write("TTTCCTTCTACTTGTATCAAAATTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTCCCCAACCTTCG\n")
-		f.write("CCGGCAAAGCCGTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTGTCCATGAGGAA\n")
-		f.write("AACTGCTACCAAACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGTACTTAGGCCCA\n")
-		f.write("TTCTCCGGTGAGCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCTGGAC\n")
-		f.write("TCTCAGCCGACCCAGAGACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCT\n")
-		f.write("CGGAGCTCTTGGATGCGTTTTCCCCGAGCTCTTGTCCCGCAACGGC\n")
-		f.write("\n")
-		f.write(">gi|226790733|gb|GO546189.1|GO546189 Mdas9001B21_e10.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77603.1| plastidic aldolase [Nicotiana paniculata], mRNA sequence\n")
-		f.write("CTTTGCCAGAGGAGATAAGATTATATTAAACTTTGCTCTCTCACTAGGCTGCCACTCTTTGTAGCTAACA\n")
-		f.write("ATGGCTTCTGCATCTCTCCTCAAGTCTTCTCCGGTTCTCGACAAATCTGAGTGGGTGAAGGGTCAGACCC\n")
-		f.write("TCCGCCAGCCTTCCGCCTCTTCGGTCGTCAGATGCCTCCCCACTGCCCCGTCTGGTCTACCATTCGTGCC\n")
-		f.write("GGTTCCTATGCTGATGAGCTTGTTAAGACTGCTAAAACTGTTGCATCCCCAGGCCGTGGAATCTTGGCCA\n")
-		f.write("TGGACGAGTCCAATGCAACTTGTGGNCAGCGTCTTGCCTCAATCGGGTTAGAGAACACTGAGGCCAACCG\n")
-		f.write("CCAAGCCTACCGTACCCTCCTTGTGACTGCCCCTGGCCTTGGCCAGTACGTCTCAGGTGCCATTCTCTTC\n")
-		f.write("GAGGAGACTCTCTACCAATCCACCGTTGATGGAAAAAAGATCGTTGATGTGCTCGTTGAGNCAGGCATCG\n")
-		f.write("TCCCTGGGATTAAAGTCGACAAGGGTTTGGTGCCCCTAACGGGTTCCAACGATGAGTCATGGTGCCAAGG\n")
-		f.write("TCTTGACGGTCTTGCCTCTCGCACAGCTGCCTACTACCAGCAGGGAGCTCGTTTCGCCAAATGGCGTACC\n")
-		f.write("GTTGTGAGCATCCCCAATGGCCCATCAGCTCTTGCAGTAAAGGAAGCAGCATTGGGGTCTTGCCCGCTAC\n")
-		f.write("GCTT\n")
-		f.write("\n")
-		f.write(">gi|226790512|gb|GO545671.1|GO545671 Mdas9009F15_e669.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n")
-		f.write("CTACACTGTTTTTTCCTTCTACTTGTATCAAAATTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTC\n")
-		f.write("CCCAACCTTCGCCGGCCAAGCCGTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTG\n")
-		f.write("TCCATGAGGAAAACTGCTACCAAACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGT\n")
-		f.write("ACTTACGCCCATTCTCCAGTGAGCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGA\n")
-		f.write("CACCGCTGGACTCTCAGCCGACACAGACACCTTCGCCAAGAACCGTGAGCTCAAAGTGATCCACTCCAGA\n")
-		f.write("TGGGCCATGCACCGAGCTCTTGGATGCTTTTTCCACCGCAGCTCTTGTCCCGCAACGGCGTCATGTTCGG\n")
-		f.write("CGAGGCTGTGTGGTTCAAGGCCGGAGCCCAGATCTTCTCCGAGGGCGGTCTCAACTACT\n")
-		f.write("\n")
-		f.write(">gi|226790511|gb|GO545670.1|GO545670 Mdas9009C04_e650.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_084793.1| photosystem II protein D2 [Lotus japonicus] sp|Q9BBT0|PSBD_LOTJA Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein) dbj|BAB33191.1| PSII D2 protein [Lotus japonicus], mRNA sequence\n")
-		f.write("CTCGAACGTTCAGAAAATGCTATGAGGTGTTCGAAAATGGTTGAAGTAGTTGAATAGGAGGATCACTATG\n")
-		f.write("ACTATAGCCCTTGGTAAATTTACCAAAGACGAAAATGATTTATTTGATATTATGGATGACTGGTTACGGA\n")
-		f.write("GGGACCGCTTCGTTTTTGTAGGTTGGTCTGGCCTATTACTCTTTCCTTGTGCCTATTTCGCTTTACGGGG\n")
-		f.write("TTGGTTCTAAGGTACAACCTTTGTATCTTCATGGTATACC\n")
-		f.write("\n")
-		f.write(">gi|226790510|gb|GO545669.1|GO545669 Mdas9009K12_e691.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGCAAAATAAAACAAACAAAACATAACCTAACCTTCCAACATTTGCTACAGGGATTTCCAACGATAC\n")
-		f.write("ATAACATGCCAAAGATCATTATTCCCACAGATTTTAGTCATCCCTACTCTTGAGCATATACTTAATCATA\n")
-		f.write("GTTACCATTCACTAGCTCACATTTAATCGTTTAAAACAACATTATGGACGTAGTAACATGCCTTAGAGAA\n")
-		f.write("TCCACTCAATTCCTTACTGGATACACTCTTATTTTCACACAGATTTTCTAACTACTCTCCCTATACTAAG\n")
-		f.write("TATATGTGAGAAGATTGATGTAAACATGGAAACGAACACTCACACATGTTATAAAAGAAGCAATTTTCTG\n")
-		f.write("GAATGATTAAGCATTTATAGATATGATCTCATGAATGGAACGCTACTACTTAGATGCGAGAACCAGGGAC\n")
-		f.write("ACCATATGCTCAAACCAATCCCAAACTCCACATATTGAAATACATAACACTCAAGATAGAAGTTAAGGGT\n")
-		f.write("TGTAACGGGGCTTGGGGAATGGTTAACAAAGAAAGGATAGGGAAAACAAACGTTCTTCAAGCATTAGTAA\n")
-		f.write("GCAAAGTAGTAAATTTGAGACTTAGAATTCACTTAGATTGTAGAAATTAACTTTAAAACACAAAGGGAAG\n")
-		f.write("ATTTAAACAACTTCTTAGGGCCGAATTCATTGTTTTGGACCCTT\n")
-		f.write("\n")
-		f.write(">gi|226790509|gb|GO545668.1|GO545668 Mdas9009N14_e706.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T08089 chlorophyll a/b-binding protein type III Lhcb3.1 precursor - rape (fragment) emb|CAA43802.1| LHC II Type III chlorophyll a /b binding protein [Brassica napus], mRNA sequence\n")
-		f.write("CTTCTACACACTTCCAAGCTTCAACACAATTCCACGGATTACTTCATCACAAAACAAATCAAGTCAACTG\n")
-		f.write("AATTAAGTTGCGAAAGCTTGGAAAGTCATGGCAGCAGCTGCTAGCTCGAGCACTCTTCTAAGAACAACCC\n")
-		f.write("CATTTCTTGGCCAAAGCCGAGGACCAAGCTTCAACACTCTTAAGGATGTTGTGCCAATGGGAACTGGCAA\n")
-		f.write("ATACACCATGGGCAATGATTTGTGGTATGGACCGGACAGAGTGAAGTATTTGGGACCCTTTTCTGCTCAG\n")
-		f.write("ACTCCTTCGTACCTGAACGGAGAATTCCCCGGTGATTACGGATGGGACACCGCAGGGTTGTCAGCTGACC\n")
-		f.write("CCGAGGCCTTTGCTAAGAACAGGGCTCTTGAGGTGATCCATGGCCGGTGGGCTATGCTTGGAGCACTAGG\n")
-		f.write("CTGCATCACCCCAGAAGTTCTCGAGAAATGGGTGAGAGTGGACTTCAAAGAGCCAGTGTGGTTCAAAGCA\n")
-		f.write("GGAGCTCAAATCTTCTCCGAAGGCGGCCTCGACTATTTGGGTAACCCCAACTTAGTCCATGCTCAGAGCA\n")
-		f.write("TCCTAGCGGTGCTTGGGTTCCAAGTCATCCTCATGGGTCTCGTTGAAGGATTCCGCATCAATGGTCTTGA\n")
-		f.write("TGGTGTCGGAGAGGGCACAACCTCTACCCGGGTGGGCAATACTTC\n")
-		f.write("\n")
-		f.write(">gi|226790508|gb|GO545667.1|GO545667 Mdas9009K14_e692.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P23322|PSBO_LYCES Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving system of photosystem II) (OEC 33 kDa subunit) (33 kDa thylakoid membrane protein) pir|T06368 photosystem II oxygen-evolving co, mRNA sequence\n")
-		f.write("TTTTTTTTTACAAGAAAGATAATACATACAAGATAATAGGCATGATAATATACAAGAAGATAATGATCTG\n")
-		f.write("AGTGATCTCAGTGCTTGTTGTTCAATTGGGTTACAAAGAGAGTTGAGCAACACCTTTTTAACTTATAGCA\n")
-		f.write("AAATCTGAAACCCAGAATCACCATTAATACATAGAGGAAAACGAAACTAATCAAGCTGAGCATACCAAAC\n")
-		f.write("TCCCTGGATTTTGACATCCTTTGGAGTCTTGGCTCCCAAGTCAGTGTCGGAAGGCTGAAGGCTCTCGAAC\n")
-		f.write("ACCCCAATCAACTCACCAGTCTCAGGCTTGGTCTTTGTCACACTCAGTGTTATCTTCCCCTTCGATGCTG\n")
-		f.write("CTGTATTCTTGGTGTTCTCCTTTGCCAGCTCCTCCTCGTCTCCTCTGCCTCCTGCCGGCAGTGCGACCGC\n")
-		f.write("ATTGTCATAACCGGTGGATCCTCCTCTTCCCTTGGGGTCCAAGAAAGAGGATCCACGGTATGATGGTACT\n")
-		f.write("AGAAACTCTCCCGTGAAATTTTCGGGCTTGCCAGAGGCTACCAGCTGCTTGATGGTAAAGAGGAAGGGCA\n")
-		f.write("CGCGCTCGCCTCCCGGGAGCTGGACTGTCACTGCAGCGTAGTCAATTCCGTCTTTCTCTTCGAACTTGAT\n")
-		f.write("GGAGCCATCTGGAGCAACTTCGAAAGGTCCTTCGAT\n")
-		f.write("\n")
-		f.write(">gi|226790507|gb|GO545666.1|GO545666 Mdas9009E04_e664.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_051097.1| ribosomal protein L22 [Arabidopsis thaliana] sp|P56795|RK22_ARATH Chloroplast 50S ribosomal protein L22 dbj|BAA84424.1| ribosomal protein L22 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGCCCGGGGCTTTAATTTTTTCACAGTTGTGCCCTCGTTGACTTCGGCTTTACTAATGATTAAACTT\n")
-		f.write("GTTTCGTTCAAACCCTTATTGTGATTAGCATTTGCTGCTGCAGAATAAACCAATTTTAAAATGGCATAAC\n")
-		f.write("ATGCTCGATAAGGCATAAGTTCTAGTATCATAAGTGTTTCTTCATAGGACCGCCCACGAATTTGATCAAT\n")
-		f.write("TACTCTTCTCGCTTTGTGAGCAGACATACATATATGTTGACCTAAAGTGTATACTTCTGTATATTTCTTC\n")
-		f.write("ACCTTTCTCTTCTGTATCATAAGATTCACCTCTCATTAATGAACGATAAGCATCTATATTTTATTATTTT\n")
-		f.write("TTTATTAATTATTAACGACGGGATCTATTATCATTTTTCGCATGCCCCCGGAAATTTAGAGTAGGTGCAA\n")
-		f.write("ATTCTCCCAATTTATGTCCTACCATACGATCCGTTATATAAATAGGCAAATGCTCCTTTCCATTATGGAT\n")
-		f.write("AGCGATAGTATGCCCGATCATTGTCGGTATAATGGTAGACGCTCGGGACCAGGTTACTATTATTTCTTTT\n")
-		f.write("TCTGCTTTTGTGTTAAGTGTATTTATTTTTCTTAATAAATGATTTGC\n")
-		f.write("\n")
-		f.write(">gi|226790499|gb|GO545665.1|GO545665 Mdas9009L06_e696.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849293.1| expressed protein [Arabidopsis thaliana] gb|AAL91159.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("ACAGCTTATCTAGTCATAGAGGCGATACAGGGGATGGGAGAGAGTTTGTGCACGAAAACTGCGATTGCTA\n")
-		f.write("CTAAACTACTACTACCGGTTGACCGGTCATTAGCCAGAGCTCAGGGGAGCTCCAGGTTCCCGTCAACCGT\n")
-		f.write("GGAGTGGCTTCGGAATCAGAATTCAATTCGTCTTTAGAAGACCGATCATCCTTCACCTCATGCTCACAAA\n")
-		f.write("GCTTCGACTGATGATCACTCAGCTCGGCCTGCATATGTACATTTATACTCGCCATCCGGTCAAATGTTCT\n")
-		f.write("TCAAACCATCCTACCGTTTTCTTCTTCCTTTTCTCGTTTCATGCTCAAGCAAGCCTCAACACCGCCACCG\n")
-		f.write("CCATCAATGTTCCGGCTCTCAAGTAAATCTCGTTCATGCTTCTATCTACCCTTTTCATTATTTCCTCTTC\n")
-		f.write("TTGTAAACCTGGCTTCTTTGAATTCTTCCTGATTTGAACAACTGTGTCCCTCAGTTTATTCACCCCCCAA\n")
-		f.write("GAGAGCCAGACTAATGCAAATGCAACTCCGGTGTTCAAGAGTTTGGATGCACAAAGGGGTACCCTCCCAG\n")
-		f.write("AAGCTACTTTACAGAGGACAGAGAAAAGGACAGCCAAGCCAGTTCCAGCGATACCAGCAGAAAACTGGGT\n")
-		f.write("TAGGAGTTCCGGAA\n")
-		f.write("\n")
-		f.write(">gi|226790498|gb|GO545664.1|GO545664 Mdas9009C03_e649.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P08282|GLN1_PEA Glutamine synthetase nodule isozyme (Glutamate--ammonia ligase) (Cytosolic GS1) pir|AJPMQ1 glutamate-ammonia ligase (EC 6.3.1.2) beta, cytosolic - garden pea gb|AAA33669.1| glutamine synthetase (cytosolic GS1) (EC 6.3.1.2), mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGTCAAGAATTACAAGTAAAATGACATTAAAACCAACCAGCC\n")
-		f.write("CTTTGAAAAATACGGTTCATAGATGACACTTATTCAACACAATGGGCAGAATGATGAGGAATTGGAGCAA\n")
-		f.write("TTAACCACATCTTGGCACTTTTAATAGGGAAAATAGCAACGCAATACAATTTAAAGGACAAAGCTAATTC\n")
-		f.write("TAGTTTGTAGCTAAGGACACACAAGGATCTTTTAAACGGACCTGGCAAAACACATTTCCAGCCTCAATGA\n")
-		f.write("AAGACGGGACTTGGAACTGCACGGGTGTAAGTGCAGCGGTGTGTGCTCATGGCTTCAACAGAATGGTGGT\n")
-		f.write("TTCTGCCATCATAGAAGTGACAACATATGGATCCATGTTCCACGCAGGCCTCCTGTCCTCAAAATA\n")
-		f.write("\n")
-		f.write(">gi|226790497|gb|GO545663.1|GO545663 Mdas9009E03_e663.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04011|AB20_PRUPE Auxin-binding protein ABP20 precursor gb|AAB51240.1| auxin-binding protein [Prunus persica], mRNA sequence\n")
-		f.write("TTTTTTTTCAATAAATAGGGCATTTACCTTCAACAACAAAGCACACACAACAAAACTTCTACTACAAACA\n")
-		f.write("TACAAAAATCAAACGAAGCAATCTTCTACAACGAATCAAAACCACCACTGAAAGGAAACCGAAATGGGAC\n")
-		f.write("GTTCAACACAACAAGAAAGATACAATATTTAGTGATAATGCTGGCTGAAATTCAAAGATGAGAGAGCTTA\n")
-		f.write("ATTACTAATTAGTACCACCAAGAGCGGCCTTCAGTTTCTTGATCTGAGCAACGTCAAGGAAAGTAGTCTG\n")
-		f.write("CGCTATCAGTTCCGTTGGTAAATCATTTTTAAACAGCGCATAGTCCAGAATCTGCAGCCCCGGGCTTGGA\n")
-		f.write("CTACTGAAGCTAACAAATGCAAGGGCCGTAGCCTCACCTCCATTCACTTGGAAGTGCAGTAACCCCTGAG\n")
-		f.write("GGAAAACCATAATGTCTCCCTTCTCAAGAGTTTGTAGATAAACTGTGTTCGCTGAGGAAACAAAGCCGGC\n")
-		f.write("GCAGATGGTCCCTTCGATGACAATTAGGACTTCCGAACCTCCAGGGTGTGTGTGAAATGGGATGACTCCA\n")
-		f.write("CCAACAGCCAGGTCTAGACGCGCAAGTGAAATGCCAAGGCCGTTGACACCAGGGAACTGAGCAGCAAATG\n")
-		f.write("CAGGGGTGACTGCAGCTATGATGATGTTTGTAGTGTTGCCAGCAACACCTAGGCCCGAGAAAACAAAGTC\n")
-		f.write("ATCTACTTTAACATTTGCAG\n")
-		f.write("\n")
-		f.write(">gi|226790496|gb|GO545662.1|GO545662 Mdas9009I12_e684.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n")
-		f.write("TTTTTTAAGAGCACCTACTGCATAGTGTACATTACAATACAAGATTACATGACACCAATCCGACATAGGA\n")
-		f.write("AAACAACATTATTTTTTTTTTACCCTTAACATCCTTAAAAAGTGCTTCTCTCCTTCCTCCCTCCCCTCAA\n")
-		f.write("TTATAACCTAAAAGAAAATGACTTAAAATGTGTAAAAGCAACTTCCATCATCACTTCTAGCCGTTGGATC\n")
-		f.write("AAAGTTTTCTCAGTTGGATCAGTGCAACCTTCAGGAACTGGAACATTCACTAGCTGCGCTGCTAGGCCTC\n")
-		f.write("CCACAGGAGCTCTCTAAATATCAAGGATCTAACCATAGAAAGTTCCTGTATTCATAGCATCTGAGTTAGC\n")
-		f.write("ATCACCAAGAGCAGCCTCGCTCAAGTACTTATCAGCCAATTGAACTCTCTTCACATTCTCTTGCTCTTGG\n")
-		f.write("ACAAGCATGTTTCCGTACTCGAGGAGCTTTTCGATAGTCATCTTCGGCTGCTCGAAAGTTGGGGGTCCTT\n")
-		f.write("CCTTTGAGTTCACAAGCTTCTTCCCAATGCTATCCACGCCAACACCCGTAATCCACTTCCTCACTTCATC\n")
-		f.write("GTCGTAAACCCTAGCCCTCAAGGCACCAAAGAAATCAATAGATTGGCCTGGGGAAGGTGTCAACAAGCTT\n")
-		f.write("GACAATGTCTTCCTTAGCAAC\n")
-		f.write("\n")
-		f.write(">gi|226790495|gb|GO545661.1|GO545661 Mdas9009D24_e661.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("CTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAG\n")
-		f.write("AAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGC\n")
-		f.write("TAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGA\n")
-		f.write("GGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGG\n")
-		f.write("ATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACAT\n")
-		f.write("GGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGAATCCTGGGGATCTGTGGTTCTCACGGTACACG\n")
-		f.write("AATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGATGTAGTCAACTTCCTTGG\n")
-		f.write("CCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCA\n")
-		f.write("CACCTGCATGCATTGCACTCTTCCTCCATTGCTTGCAAT\n")
-		f.write("\n")
-		f.write(">gi|226790487|gb|GO545660.1|GO545660 Mdas9009D02_e655.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P17067|CAHC_PEA Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) pir|S10200 carbonate dehydratase (EC 4.2.1.1) precursor, chloroplast - garden pea emb|CAA36792.1| precursor peptide (AA -104 to 224) [Pisum sativum], mRNA sequence\n")
-		f.write("TCGAGTTTGCCCATCACATGTTCTGGATATGCAGCCGGGAGAGGCTTTTGTTGTCCGCACAGTTGCTAAC\n")
-		f.write("TTGGTCCCACCCTATGATAAGGTTAAATACGCTGGGACAGGGGCGGCCATTGAGTATGCTGTCTTGCATC\n")
-		f.write("TCACGGTTTCATACATACTGGTGATTGGGCACAGTGCCTGTGGAGGAATCAAGGCACTCTTGTCTATTCC\n")
-		f.write("AAAAGATGGGTCTACCCTCGGCACTGACGTCATATAAGACTGGATTCGTATTGGATCGCCGGCAACGAAC\n")
-		f.write("AAGGTGAAGGCAGATCACGGCCCTGATACTCCTTTCCCTGAACTATGCACTCGTTGCGAAAAGGAGGCGG\n")
-		f.write("TGAATGTATCGATCGGAAACCTGCTGAGCTATCCGTTTGCGATAGAGGGTTTGCTGAAGAAAACCCTATC\n")
-		f.write("AATCAAGGG\n")
-		f.write("\n")
-		f.write(">gi|226790486|gb|GO545659.1|GO545659 Mdas9009E02_e662.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q04960|DNJH_CUCSA DnaJ protein homolog (DNAJ-1) emb|CAA47925.1| cs DnaJ-1 [Cucumis sativus], mRNA sequence\n")
-		f.write("TTCAAATTGATGCTATGTTACGGTGTGCAAATTCGCCATTTTAACAGCAGAACAAAAGCAGCAGAACAAA\n")
-		f.write("TTCTTAGCATTCAACAACAGACCAACAGACCAAACCACGTTTAAGTAGAATAAGCATCTCCTTAACAGCT\n")
-		f.write("ATTGTTCCGAAGAAGTTTCGGATTCACACACCAAACCAGAAATAAACACTGGGAAGCTAGACCAACAGAC\n")
-		f.write("CACGGTGCCGATAACTTTTATTTTTCTCAAATAACTTCATAAAGCTTGCTTAATCTAATCATTGCTGAGC\n")
-		f.write("ACATTGGACCCTTTGGGCACCACCATGCATGTCCTCATCCTCGTCATATGCCTCTTGCGCATGTGCTTGC\n")
-		f.write("TTTCGACGCATTTCCTCCTCTATGTTTACATCATGCAGCGTGGTCTCCTCACATTCATCCAACTCCATGT\n")
-		f.write("CGGTAAGTTGTGCCGAAGTCCTGGGGGGAAGGACAGCCTCCAGGGCCTTGCACTGTTCTGGGTTCAGTGA\n")
-		f.write("GTCGGGGAACTCCACTGTGAAATGAATATATAACTTACCCTTCATGAATGGCCTCTGGTACATTGGCATG\n")
-		f.write("CCCTCATCGTTTATAGCCTTGAATTGATCAGGCTTTACAACTTCTCCAGGATGAGATTTAAT\n")
-		f.write("\n")
-		f.write(">gi|226790485|gb|GO545658.1|GO545658 Mdas9009C24_e654.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC16504.1| contains ESTs C26074(C11585),AU092275(C11585) unknown protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGGAATCGATGAAGCGAAGCTTTCCTTGCAATCGGAAGATCACAAACAACGGGTCGAGGGGATGGCT\n")
-		f.write("TGACGCCCTCCTGAATCGCTTGATTGCCAAAGTTAGGAAACATGTTGGAGCTCGGAGGAACTGAACTGCT\n")
-		f.write("GGAATTAACGGGACTCTTGCCCAAATGAGAGGCAAAGGCGTTGTTAGTCTTGGCCGGAGGTGAAGCCGGA\n")
-		f.write("GCGGTGTGGCTCTGAGAACTCTCCTTGCTTGCTAAGAGCATGACTTCCTTGGCCTTGTCCGCACGAAAAT\n")
-		f.write("CGTTGAACACGATTACTTGTCCACCATAAAAGATGGTCATTTGTGCCTTCTGAGGCTCTCCAGGGGCAGA\n")
-		f.write("TTTCTTCACACTAGAATCAGCCGTCATGGGGACCTCTTCTCTGGGAGTGGGGGCAGAGGGACCAAAACCA\n")
-		f.write("GCTTGTTGAGGAAACAAATCCATGGATTTGAAGTCTCTCACCGCCCGTTGGCATGTTCCGAGAATTTTCC\n")
-		f.write("ACAAATGGAAAGAAGTTCATGGGTGGGGCTTTCTGGACAAAACATCTCAGGTGTACCTCCCTTACATTGA\n")
-		f.write("TGCATGTTGTTGCAT\n")
-		f.write("\n")
-		f.write(">gi|226790484|gb|GO545657.1|GO545657 Mdas9009C22_e653.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27880.2|AF139468_1 photosystem I reaction center subunit III [Vigna radiata], mRNA sequence\n")
-		f.write("CACAAATAGAGGAAAAAAACCATGTCTCTCACAATTCCCACAAACCTTTCAAAACCCATGTTTCAGCCAA\n")
-		f.write("AACTTAGCTCCCCATTGGCCGCAAAGCTGCCAAGAACCGTGGTCTTCTGCTCTGCCTCCCCAAACCCTAA\n")
-		f.write("CCCTACCCCAGAGAAAATATCGACTGCATCGCCCATGCAGGCTTTCTCCACTGCACTCGCACTCTCCTCC\n")
-		f.write("ATCCTCATTGGCTCGGCCCCCATGCCTGCAGTTGCTGACATCTCGGGACTCACCCCATGCAAAGACTCCA\n")
-		f.write("AGCAGTTCGCCAAGCGTGAGAAGCAGCAGATCAAAAAACTCGAGTCCTCACTGAAGCTCTATGCACCCGA\n")
-		f.write("CAGTGCACCCGCCCTAGCCATCAAGGCCACCATAGAGAAGACTCAGAGGAGGTTTTCCAACTATGGCAAG\n")
-		f.write("CAGGGTTTGCTTTGTGGGTCGGATGGGCTCCCCCATTTGATTGTCAGCGGTGACCAGAGGCACTGGGGTG\n")
-		f.write("AGTTTATCACGCCTGGTATTTTGTTCCTGTACAT\n")
-		f.write("\n")
-		f.write(">gi|226790483|gb|GO545656.1|GO545656 Mdas9009H14_e681.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGGCCATCGACATGA\n")
-		f.write("GCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAGGCGTCGCTTCTAGCCC\n")
-		f.write("GGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGCTTTTCAACCA\n")
-		f.write("AGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTGCGACACTGTC\n")
-		f.write("ATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATTGGTGGGTGAA\n")
-		f.write("CAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAAC\n")
-		f.write("GTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCA\n")
-		f.write("AATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCA\n")
-		f.write("AACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAAGACACCTGCGT\n")
-		f.write("TATCTTTTAA\n")
-		f.write("\n")
-		f.write(">gi|226790482|gb|GO545655.1|GO545655 Mdas9009J24_e690.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|A84674 60S ribosomal protein L10A [imported] - Arabidopsis thaliana, mRNA sequence\n")
-		f.write("TAGACTTTCCTTCAAAATTTTCCAAAAGCATTCAACTAAAACAACAGAGTACACATTGTACTTTAACGAC\n")
-		f.write("GAAATCCAAGTTAATGAAAACAAAATATAACACTGAAACATATGCAATAAATGTCTTAGACAAAAAGTTT\n")
-		f.write("GCCGATGCTTCCTTCGCTTGGAAAGTCTCTGATAAAGATTATGAACTTACTAGATACGGATAGCTTTCCC\n")
-		f.write("CATCGTACTCTTCAAGTTCAAAGACCTCACATTCTGCCAATTCTTCTTCAACAGTGCAACTAAGAAATTG\n")
-		f.write("ACACTGACTTGCACATTCAGGAAAATCTGCTTCTCCTCCATAGCAAGATTGCCGACAGCAACACCCATGC\n")
-		f.write("AAAGAACCTTCTTAAGTTGGAACTTCATCATAACTTTGGTCTCGTTAAGTTTTGCCTCCACAGATTCCTG\n")
-		f.write("ATGACTCACCAAGGTTGGGAACTTACCTGCCTTATTAAGACCACGGCCAAAAAAAACGAGGAATCT\n")
-		f.write("\n")
-		f.write(">gi|226790481|gb|GO545654.1|GO545654 Mdas9009M11_e702.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ACTATGGCTACGCTCCAACTCACTCCCTCCCCTTCTCTCAACCTCCCAAATCAAATACGCACAAACACCA\n")
-		f.write("ATCTCTCCGCTTCATTCCAGCTCAATCTCCGGCCGCGCCACCGATCATGGCGGTCCT\n")
-		f.write("\n")
-		f.write(">gi|226790473|gb|GO545653.1|GO545653 Mdas9009K19_e693.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA88898.1| cysteine protease component of protease-inhibitor complex [Zea mays], mRNA sequence\n")
-		f.write("TTCCAGTTGTATAACTCCGATGTATTTACAGGACGTTGTGGGACGGCATTGGACCATGGTGTGACAGTTG\n")
-		f.write("TGGGATACGGCACAGACAAGGGGCTTGATTACTGGATAGTGAGAAACTCATGGGGTGCAAGCTGGGGAGA\n")
-		f.write("GAAGGGATACATCAGGATGCAGCGTAATCTGGGCAACACCGCTAATGGGATATGTGGAATTGCCATGGAG\n")
-		f.write("CCTTCTTACCCGATAAAGAAAGGCCAGAATCCCCCTAACCCCGGTCCTTCTCCTCCATCTCCGATAAAGC\n")
-		f.write("CCCCGTCAGTTTGTGACAACTACTACTCCTGCCCTGAGAGCAACACGTGCTGCTGCATCTACCAGTTTGG\n")
-		f.write("AAACTATTGCTTTGATTGGGGATGTTGTCCACTTGAAGGTGCCACCTGCTGTGATGACCATTACAGTTGC\n")
-		f.write("TGCCCAAGCGAATATCCTGTCTGCGATGTCAATGCCGGAGCTTGTTTGATGAGCAAGGGCAATCCCTTGG\n")
-		f.write("GAGTGAAGGCATTGAAGCGCACCCCCGCGAAACCCCACTGGGCTGTTGGTGGCGGAAAGAGCAGCAGTGC\n")
-		f.write("TTAAGCAAAACACTCAAGCCTCGATGCAGTGGTTTAACAAAAGCTAAGAAGGAAGAGACATCCAAGCATT\n")
-		f.write("ATTGATAATCTTCTC\n")
-		f.write("\n")
-		f.write(">gi|226790472|gb|GO545652.1|GO545652 Mdas9009L08_e698.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF02817.1|AC009400_13 unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGTTGGAGGAAACAAAGATATATTAAATGTTAGAAAACAAAAAAGTTA\n")
-		f.write("TACAAGTGATTAACTTACATTTGGAATTTTATAACTATTCACTGCCAAAATCTTCATAACTTACACCTTC\n")
-		f.write("TGAGACGGTGTCCAATCTGTTATTGTCCCCTTGATGTTCTCTGTCACGAGAATCCAGGAAGTTGTTATTA\n")
-		f.write("TCTGTAGCCAAGAAGGGTGATCTAGGATAGCTCTCCAGTATGTCTGAACTCTGAGAAAAGTCAGTTGCAA\n")
-		f.write("GATCCGAAAAGCTCAAGATTCGAGGAATCTGACCTAAAAGACCAAATGATGAACTGTCTGCATCAAGCAG\n")
-		f.write("AGATTCATTTAGGGACTGTGAATTGGACTCTACGCTATTGAATGCTGCAACAGAAGCATCTCCAATAGCG\n")
-		f.write("GGCCGGGTTTCCAGGATGTTTCCATCAGCACTAAACATGTACGAACTGCCTGAATATCCAACTTCTGATT\n")
-		f.write("TGACAATTCCCCCATTCATTCCATGCATCAGACCTATGTTGGAGATCTGGTTCGAAAGCATGTTTGGTTG\n")
-		f.write("GACATCAATCCTACCGGTATGAGCAGACATTTTACCAGCATTGTGCATACTGATGTGCAATGAAGATCCA\n")
-		f.write("CCATTAGTAAAAGCATTATGTAGGCAAGAACCAACTTGGTGGTGTATAATTTCTGTCTTCAGCGCTGTTC\n")
-		f.write("CTACATGC\n")
-		f.write("\n")
-		f.write(">gi|226790471|gb|GO545651.1|GO545651 Mdas9009K21_e694.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n")
-		f.write("TTTTTTTTTTATTCTCACAACATAACATTATGTTCTTATCGACTGTTCAATAGCCGGAGTATCAATAGCT\n")
-		f.write("TGTTTAATAATTAAAACGAAATAATCGCAAGAATTTCCATAGAAATACAAGCGCAAATTACAAAGAAAAT\n")
-		f.write("ATCAATAACCCAGCAAACAGAATATCTATTTTTCTTTCAGCTCCAATTCACTCGTACCGACAGCTACCGT\n")
-		f.write("CGTCACTCCTTCGCAGCTAGGGGTTCGAAAGTTTAGCAGCAGTTTCGATCAGTGCAGCCTTTCAGGGACA\n")
-		f.write("GGTACATTTAACTTAGTTGGGCTGCCTTTTCCATAGAATTTCTCCTCGGTTAATGGAGTCCTGGTTTGCA\n")
-		f.write("TCTCCAAGGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGCTCCTGA\n")
-		f.write("ACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGACCTT\n")
-		f.write("CTTTTGAGTTCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAATCCACTTCCTCACTTCATC\n")
-		f.write("GTCATAAACTCGAGCCCTTAGGGCACCGAAGAAATCAATGGATT\n")
-		f.write("\n")
-		f.write(">gi|226790470|gb|GO545650.1|GO545650 Mdas9009L07_e697.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTGAACAAAATTATATATGTCATTAAACCGAAATTATTGAACACAAATGCAGAGCAAGCCG\n")
-		f.write("TATTACATTGGTCTTAATGGATACAAATTCAGGTACATGCCAACAAATATTACCCTTGCTCCCTGCATGT\n")
-		f.write("CAAAAATGAAACAAAATTGAACATGCATTTTCACCACTCCCTTCCACACTCTTACAAACATGCATATGCT\n")
-		f.write("GATGACAACC\n")
-		f.write("\n")
-		f.write(">gi|226790469|gb|GO545649.1|GO545649 Mdas9009M03_e701.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_171617.1| pyruvate dehydrogenase E1 alpha subunit [Arabidopsis thaliana] gb|AAB86803.1| pyruvate dehydrogenase E1 alpha subunit [Arabidopsis thaliana] gb|AAK96625.1| At1g01090/T25K16_8 [Arabidopsis thaliana] gb|AAL36074.1| At1g01090/T25K16_, mRNA sequence\n")
-		f.write("TTTTTTTTCTAAAAGAACATGAACAAAATTGAAAAGATAAACAAACATATGTCCTGCTTTTACAGTAGAT\n")
-		f.write("AAAAGCTGATACAATCTTCTGACAAGTGACAAGTAGCTGCTAGCAGTAACTAAAAATTTAACGCCACGCA\n")
-		f.write("GGCATACCTAGGAACAGAGAGCTAGCACTAGTTGATTGCTAGAGGCTCCAACCAGCGGAGATTTAGACGT\n")
-		f.write("GAGCTGTGCCCTGAGTGAACTTAGGATCCTCACATCTGTAGCTGCCATCAGGCCCGATTCCAAAACCCTT\n")
-		f.write("GGGATCGGCAAACACATTCTCGAGCAGCTGGCTGCGAGGTGGAAGAGGACTCTCATCTGCAAACTCAACG\n")
-		f.write("GCATCCTCAACCACCTCGTCGATCTTCTTATGGATGGCCTTCAAGTCTTGTTCGGTCGCCAAATTGTTAT\n")
-		f.write("CAAGTATGTATTTCTTGAGGGCTGTGATGGGGTCTCTGGCAGCGTAGTGTGCCTTCTCAGCAGGGTCACG\n")
-		f.write("AAGCTCATCGGGATCAGCCAATGAGTGTCCTCTGAATCTGTATGTTTCACATTCCACCAAAGTTGGCCCT\n")
-		f.write("TCTCCTCTCCTGGCCCTTCCAATCGCCTCCTTTGCCACCTCCCTCACCTTCAGCACATCCATCCCATCCA\n")
-		f.write("CATGAACACCTGGCATACCGAATGCACGCC\n")
-		f.write("\n")
-		f.write(">gi|226790468|gb|GO545648.1|GO545648 Mdas9009F21_e671.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n")
-		f.write("TGGAACTTCAACAGCAGCTAGGTCTAGAGGGAAATTATGAGCATTACGTTCATGCATAACTTCCATACCA\n")
-		f.write("AGGTTAGCGCGGTTAATAATATCAGCCCAAGTATTAATTACACGACCTTGACTATCAACTACAGATTGAT\n")
-		f.write("TGAAATTAAAACCATTTAAGTTGAAAGCCATAGTGCTGATACCTAAAGCGGTGAACCAGATACCTACTAC\n")
-		f.write("AGGCCAAGCAGCTAGGAAGAAGTGTAAAGAACGAGAATTGTTGAAACTAGCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790461|gb|GO545647.1|GO545647 Mdas9009G05_e672.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n")
-		f.write("CTTGCCCGCTACGCTTCCATTGCTCAAGACAGCGGGTTGGTCCCAATTGTCGAGCCAGAGATCTTGCTTG\n")
-		f.write("ATGGTGAACACACCATTGAAAGGACTTTCGAAGTGGCCTTGAAGGTCTGGGCCGAGGTTTTCTTCTACCT\n")
-		f.write("AGCTGAGAACAACGTCTTGTTCGAGGGTATCCTCCTCAAGCCAAGCATGGTTACTCCTGGTGCTGAGGCC\n")
-		f.write("AAGGAAAGAGCCACCCCTCAACAGGTTGCTGACTACACCCTCAAGCTCCTCCACAGGAGAATCCCCCCAG\n")
-		f.write("CTGTCCCCGGAATCATGTTTTTGTCTGGTGGACAATCTGAAGTTGAGGCAACCCTGAACTTGAATGCGAT\n")
-		f.write("GAACCAATCACCAAACCCATGGCACGTGTCCTTCTCCTACGCCAGAGCTCTCCAAAATACCTGCCTGAAG\n")
-		f.write("ACATGGGGAGGCAGACCGGAGAACGTGAAGGCAGCTCAGGATGCTCTGCTCATCCGTGCCAAGGCCAACT\n")
-		f.write("CACTTGCACAGCTGGGCAAGTACACCGGAGAGGGAGAGTCAGAGGAGGCAAAGAAGGAATTGTTTGTCAA\n")
-		f.write("GGGCTATGTGTACTAAGTAATTTGTACCGACGCTGTAGATGATGAAGAACAAAGGGAAGATGATGATGTT\n")
-		f.write("GA\n")
-		f.write("\n")
-		f.write(">gi|226790460|gb|GO545646.1|GO545646 Mdas9009G10_e674.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB64530.1| polyphenol oxidase [Pyrus pyrifolia], mRNA sequence\n")
-		f.write("TCGAACAACCCATAATTTGCAAGGCGAGACCTTCTCATCGGAGGGCTAGGAATATACGGCGGATCAAAGA\n")
-		f.write("TGAGCGAAATCACAGGGAATTCCGGCGAATCGGCGGCCGCCGAGACTACTCCAAACAGGGTCGTCGAACT\n")
-		f.write("CAGTGAGTTACCGATCACTCTGGACTCGGTTATCAGCGTGATCGTGCCGCGGCCAAAGAAGTCTAGGACC\n")
-		f.write("AAGGCGGAAAAGGAAGCGGAAGAGGAGGTGCTGGCGATTCAGGGGATCGAGTTCGTAGCGGACGACACCG\n")
-		f.write("TGAAGTTCGACGTTCACGTGAACGATGACGAGGACGCGCTGAGTCGACCCGACAAGGCCGAGTTCGCCGG\n")
-		f.write("GAGCTTCGTGTATTTGCCGCACAAGCGGAAGGAGGTGAGGACGAGCCTCCGCCTTGGGATAACGGACTTG\n")
-		f.write("CTGGAGGACTTGGGCGCTGACGGCGACGACAGCATTAAGGTTACCTTGGTGCCTAAGTATATCATACGGC\n")
-		f.write("CCGTTACCGTCCGTCAGATAAAGATCGA\n")
-		f.write("\n")
-		f.write(">gi|226790459|gb|GO545645.1|GO545645 Mdas9009N05_e705.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190595.1| AP2 domain transcription factor, putative [Arabidopsis thaliana] pir|T45572 hypothetical protein F11C1.100 - Arabidopsis thaliana emb|CAB62305.1| putative protein [Arabidopsis thaliana] gb|AAK73937.1| AT3g50260/F11C1_100 [Arabido, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTCCGTCACAAAGGCCATAAAATTCAAAGACTATAATTTCAAGAAAAGAAACATT\n")
-		f.write("ACTGATTGCCCTTCAGTTGGTTTGTTGTTACAATTGAGAAACTATATCAAATTACCAATCGAAACGGAAT\n")
-		f.write("TCTTGTGATTCCATTTCCTGATCGGACCCAATAAACCCTTCTCTGTATTTTTACTTTATTGCACACCTAA\n")
-		f.write("ATACCTACTCATAACAATAAACAGCTGGTGATCGGTCGGCCTTCTCAATTAACTTTCATCGGAGTTTTCT\n")
-		f.write("GGGTCGGGGTACTCATTTAAGTCGGGCTTCAAAGAGCCACCCCGGCTCAACGTTGTTTTGGACTGCGACG\n")
-		f.write("TCGGCGATGAGCGGAGAGCGGTTTGAACAGCGTCGACCTTAGCCCCGACCTCCGTAGCTTTCTTCCGTAT\n")
-		f.write("CGAAGCCGCCGACATGTCGTGGAGCTGCTGGCCGTCCAAATTCATAACTTATACCCAAACGCTGCCACAA\n")
-		f.write("ATGTACTTTCACACAACATATAATTGTTGTCTTGGGTCACTCAGAAATGGGTACAGGAATACGTACTAAT\n")
-		f.write("ATCACAGGCACCATAGGTCCACAAGATCCTAGGCTTAATTCCATTTTTCTGCAAACAACATATTCTTCTA\n")
-		f.write("CCAA\n")
-		f.write("\n")
-		f.write(">gi|226790458|gb|GO545644.1|GO545644 Mdas9009B15_e646.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCGTCTAGTAGCTGGTTC\n")
-		f.write("CCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGTGAACGAGTTCTATCGGGTAAAGCCAATGATTAGAG\n")
-		f.write("GCATCGGGGGCGCAACGCCCTCGACCTATTCTCAAACTTTAAATAGGTAG\n")
-		f.write("\n")
-		f.write(">gi|226790457|gb|GO545643.1|GO545643 Mdas9009I03_e683.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n")
-		f.write("TTTTTTTTTTCTCTCATCACCAAGAAGTTTATTAACTTGCTAAAAGGTGCATAAAATGTTCAACAAAAAT\n")
-		f.write("AGTCTTTCATGGCTATAAAGCATTACACACATTAGAGATGCATGTCTGGTTCCTCCATTAACATCAACAT\n")
-		f.write("CATCATCTTCCCTTTGTTCTTCATCATCTACAGCGTCGGTACAAATTACTTAGTACACATAGCCCTTGAC\n")
-		f.write("AAACAATTCCTTCTTTGCCTCCTCTGACTCTCCCTCTCCGGTGTACTTGCCCAGCTGTGCAAGTGAGTTG\n")
-		f.write("GCCTTGGCACGGATGAGCAGAGCATCCTGAGCTGCCTTCACGTTCTCCGGTCTGCCTCCCCATGTCTTCA\n")
-		f.write("GGCAGGTATTTTGGAGAGCTCTGGCGTAGGAGAAGGACACGTGCCATGGGTTTGGTGATTGGTTCATCGC\n")
-		f.write("ATTCAAGTTCAGGGTTGCCTCAACTTCAGATTGTCCACCGGACAAAAACATGATTCCGGGGACAGCTGGG\n")
-		f.write("GGGATTCTCCTGTGGAGGAGCTTGAGGGTGTAGTCAGCAACCTGTTGAGGGGTGGCTCTTTCCTTGGCCT\n")
-		f.write("CAGCACCAGGAGTAACCATGCTTGGCTTGAGGAGGATACCCTCGAACAAGACGTTGTTCTCAGCTAGGTA\n")
-		f.write("GAAGAGAACCTCGGCCCAGACCTTCAAGGCCACTTCGA\n")
-		f.write("\n")
-		f.write(">gi|226790456|gb|GO545642.1|GO545642 Mdas9009A06_e639.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566245.1| expressed protein [Arabidopsis thaliana] gb|AAF27013.1|AC009177_3 unknown protein [Arabidopsis thaliana] gb|AAM62522.1| unknown [Arabidopsis thaliana] gb|AAO44023.1| At3g05070 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CGGGGAAAATACAAGAATACATTCAGTTTCCACAAAAGCACAGCAGAAAGTTTATCATCAATAATAAAAC\n")
-		f.write("TAAAAGAAGCTCACTTCCAAGTCGCTACTTGCATACAGGTGGAAGTCAACTCTATTCAACATGTTTAAAA\n")
-		f.write("GTGAGCGAGAACAATCTTCTCAAGTTTAATTCGAAAAACTTGGGTGATTTTCTTTCCTTTTTCCCCTTTT\n")
-		f.write("GTTTTTCCGTTGCCAAGGTTAAGAAAAATCAATTCTAGTCTTCACCATTTCTGCCATCTCCATCCAATTG\n")
-		f.write("CTTTTGCTTCTCCTGTTCCTCCATAAGTTTAAGCATTGCCTTTTGGGTTCGCTTTTCAAGCTTATCAAGC\n")
-		f.write("CTCTTCTGCACATCCCTGCGAAGTTCCCAGTTTGGTTTTTTAGGAACAATATTCACAAACGGGTCCTCTT\n")
-		f.write("TCTTCTCTGATGGAGGTGGTACTCCTGCAACAGGGTCTTCAAACTTTGGCAGCACTGGTGGAACAAGCTT\n")
-		f.write("TCCCTCCTGAAGCTGCTTATCATGAGGAACATAATTTCGGAATTTCATGTTGGTATTAGTTTCGTCACTA\n")
-		f.write("ATTGGATTGCTTTCATTAGTGTTATCGTGAACTTGTGCGGAATCCTCATCTG\n")
-		f.write("\n")
-		f.write(">gi|226790449|gb|GO545641.1|GO545641 Mdas9009G07_e673.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("TTTTTTTTTGTCCGAAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTT\n")
-		f.write("CCACGCTCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTC\n")
-		f.write("ACTTTCCGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGC\n")
-		f.write("AAGGTTCTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCC\n")
-		f.write("AACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAAGCTTCTGGGTCGTCGGCAAGACCCAATG\n")
-		f.write("GGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCC\n")
-		f.write("CTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTA\n")
-		f.write("GGGTTTCCCAAGTAGTCGAGACCGCCCTCACTGAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGC\n")
-		f.write("CGAACTTGACACC\n")
-		f.write("\n")
-		f.write(">gi|226790448|gb|GO545640.1|GO545640 Mdas9009L03_e695.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175633.1| photosystem I subunit VI precursor [Arabidopsis thaliana] sp|Q9SUI6|PSH2_ARATH Photosystem I reaction center subunit VI-2, chloroplast precursor (PSI-H1) pir|C96562 photosystem I subunit VI precursor [imported] - Arabidopsis thali, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGCCAAACTTAGGGGCTTTAATTCTGCATTACAGGTGCTTTACAAG\n")
-		f.write("TACAAAATAGAGAAACAATTACACACACATGATGAAAAGCTTGAGAAAATGAGGATTAAATCCCAAATAA\n")
-		f.write("AATTTAGATCTTGCCACGTGGGCCCAACTTGGGTGGAAGTTGTGGGCCCTTCTTGATTGGTAGAATGTCG\n")
-		f.write("TCGGAGGCAGTGGCACTAAGGTAGGCAATGGTGGAAGCTCCTCCCAATATCAAGAACTTGAGGAGTAAGC\n")
-		f.write("CTCTCTTGGTGAATGGAGCAGCAAATGTCTCAAAGAACTTGCTCTGAAGAGGGTTGTAAGGTGAGGGCGC\n")
-		f.write("ATCTGAACCGTACAAGTCCCACTTCCCGGTGGTGTTGCCCAGATCCTCAAGGTCAAAGTAGACGCTCTTG\n")
-		f.write("TCTCCGTACTTGGCCACCACAGCACCACTCCTGATGTTTTTCGTTCTGATGCTCTGGCGAGTGGGCTTCA\n")
-		f.write("CAACGAGCTTTGTTCCGGTGAGGGAGCTTCCGCCGAGGCCGTTAATGGTGGCCGGTTGAACGGCTGCTAG\n")
-		f.write("GGTTGCCAGAGATGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790447|gb|GO545639.1|GO545639 Mdas9009A18_e641.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564615.3| expressed protein [Arabidopsis thaliana] pir|H96569 unknown protein, 54928-56750 [imported] - Arabidopsis thaliana gb|AAG52277.1|AC019018_14 unknown protein; 54928-56750 [Arabidopsis thaliana] gb|AAK60317.1|AF385726_1 At1g52870/F, mRNA sequence\n")
-		f.write("TTTTTTTTAGTTACAAAATCTCATTCTTCTTACTCTTCTTTATGGCATTATTATTACAAGTATACAGTTT\n")
-		f.write("CTCCAAGCTACAACATGAGTTGCAGTACCTGTTGAAATTTACAGCTACTCCAATGAATATACATAGCACG\n")
-		f.write("AGATCGCCAGGGGGAGCTGACTGAATTTGAGAACGAATATAGAACACATTTGGCAGAAAAATTATTATTT\n")
-		f.write("GTATCGTATATGTTTGGTTAGGATAACCAATAATTGCTTGTCTCCCAAGCTGCATAGCTCATGCTGCTTC\n")
-		f.write("CTAGTATATTGTGGTCTGCACAGCCATTGAATGATGATCTCCCCTAACAACTACTTTCCTCGCAGTTCTC\n")
-		f.write("GTATAGAAATTTTGCGCTTCCAAACACTAATAGGGTGGAAACAGTGGTTATTGCGTTGGCTGTAGAAAAC\n")
-		f.write("CGTCTCAGTACCATGCTTTTCAGAATTTAGTCCTTTGAAGAACTGCTTGACGAAGAAGCAGAATCTGCAC\n")
-		f.write("CAGAAGATGCCTCGGATAAACTGGAATCTGCATTCTCATTTGAATAAGTTGAGAGAATAGTAACCCAAAT\n")
-		f.write("AAGCTCCACACAGTCCACCCAAAGAAGCCTTTGTTCAACAGGGATCAGGCCATACGTAACCACATGAGCA\n")
-		f.write("AATGGCCAAAGTTTCCATCCCGCTGTCAGCATTGGCACAAATGTAGCCCTCAATTCATCAAAAATCTTGG\n")
-		f.write("TTGGGGACTCAAAACGCAAGAACCCCAAAACCACAAAATAGATGCTGTTCCAAATCGCTG\n")
-		f.write("\n")
-		f.write(">gi|226790446|gb|GO545638.1|GO545638 Mdas9009H06_e678.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9MTP0|YCF3_OENHO Photosystem I assembly protein ycf3, mRNA sequence\n")
-		f.write("TCGAGAAAAAAAAATGGGATATATCTCTGAGAAATCTCATTCAATTAGATAGGGTAATTAAAAAATAGGA\n")
-		f.write("CACCAAAAGAATTTGACCGCTGAGCCGTATGAGGTCGGAAACTCTCAAGTACGGTTCTAAGGGAAGGAAT\n")
-		f.write("TTACCCCCCTATTCCGACCGGGGAGAACAGGCCGTTCAACAAGGAGATTCCGAAATTGCGGAGGCTTGGT\n")
-		f.write("TCGATCAAGCCGCCGAGTATTGGAAACAAGCAATAGCGCTTACTCCTGGTAATTATATTGAAGCACAGAA\n")
-		f.write("TTGGTTGAAGATTACAAGGCGTTTCGAATAAGAACAGTTTATTATTTAATTTAGATATTTAGTTTTATAG\n")
-		f.write("ATTTTTTATATTTGTTATAATTCATTTTCTAATTAATTGTTTGTTGTCCCTATCGAGGATCATTTCTCTG\n")
-		f.write("GGAAGAACCAATCAAAGAATTTCATTATATCCCTTCTAAGATCCTTCTATTTCGTCTGGTATTTCGTAGG\n")
-		f.write("AATAAACGATATATACAGATAAAGTGGAGAATCCATTTTTTTTTCTTCTATTAAAACTAATAAAAGAGAC\n")
-		f.write("CTTCGAATGACTAAATTTAAATACTGAGATGTCTCTTAGTAATGACTTCTCGCGAAATTTTGATTTGGAA\n")
-		f.write("TAGAGTACGGAATAGAGTAATATGTTCTATGTAAGACATAAAGTATAAAGTAGT\n")
-		f.write("\n")
-		f.write(">gi|226790445|gb|GO545637.1|GO545637 Mdas9009C06_e651.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTAGCAAAATGGAACTTAATTACTGCCAAGAAAGAGGAAGAGTTACATACTTCTAGCAGAACA\n")
-		f.write("ACCTGGATAACATAATTACTTCAAAGTTCAAACCCTCAAAATTCAAAGTAAAAAAAAAGAAAAACACCAG\n")
-		f.write("AAACAAATAACTTCCCTTAAGTAATTTCTTTCATCATACGGTCACAATCTGCCATCTCTCTCTCTCTCTC\n")
-		f.write("TCTCTTCCCCTTTCCCAAAAGCTGGTAGCTTTAATCGTACCCATTAAAAGAGTAGCTTGCAGAAGGTGAG\n")
-		f.write("CTTTCCTCTGGAGAATTGGTGTCACAGTTTGCTGCTGATCCTCCTGATGAACATGCTTGATTAGATCTGC\n")
-		f.write("CCCCAATCCCAAAGATACCGGCTTTGATACGACCTCTTTTTGGTGGCAAATTGGTCAAGTCCCTCCCTTT\n")
-		f.write("TCCTTTCCTCTTCACTGGGTTGCTGCTGCCGCCTTTGGTTTCCATTTTTTTTTTCCTCAGCTGAATTATG\n")
-		f.write("GTGGAAAAGAAAGAAATTGAGACAGAAGAGAGGAGTCGCAGAGGGCCAGATGGTAAAGTGAAGTAGAGAG\n")
-		f.write("GTCTCCACTGTACTATATATAGAGATATTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790444|gb|GO545636.1|GO545636 Mdas9009A09_e640.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n")
-		f.write("TTCAATATAACACGTTTTACTTCAACTACTCTCCCTACTAATCTATGGTAAAAATATCTCATATAAACGA\n")
-		f.write("AAAAACATATTAACCCAAATCATGTTTCTGAGGTTGCATTTTAATGAAATCAAATTACAAGAAACACAAA\n")
-		f.write("TTATACTCACATTGCCATCATGATTATAAATACAATGCAAATTACACAAATCAATATTATCATCATATGT\n")
-		f.write("CATAGACTTGCTTGCCGGTGAACTTGACCTCAATCGGGCTGACATTCTTCCCAATCGACCTGAAGTTCTG\n")
-		f.write("GCCAACCCCTTGGCGCCCAGGGTTCACCTTCTCAGGGTACACACCATCCTTGGGGTGCAAGTATTGGACC\n")
-		f.write("TCCCCGTTAGGGAAAACCCTGTAAAACTGGTACTTAATCTTGTACTTGGACCTAAGCCTAGTTCCAAGAG\n")
-		f.write("CCAAGCACTGCTCTTTCCTGGCCAGTTTCAGCAAGTTAGGACCCTCCCTCATGATGGCAGCTCCGCCAGT\n")
-		f.write("CGGCATCTCAAATATCTGCTCCTTTGGTGACTCCCATGTGATCACGTAAAACTCTTCCTCCTGCGCTTTC\n")
-		f.write("CTCAACAGCCCGCCACTGCTGCCACAGAACATCGGTG\n")
-		f.write("\n")
-		f.write(">gi|226790437|gb|GO545635.1|GO545635 Mdas9009F17_e670.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565671.1| expressed protein [Arabidopsis thaliana] pir|A84684 hypothetical protein At2g28370 [imported] - Arabidopsis thaliana gb|AAD20689.1| expressed protein [Arabidopsis thaliana] gb|AAK53025.1|AF375441_1 At2g28370/T1B3.11 [Arabidopsis, mRNA sequence\n")
-		f.write("TCGAGTGTTTTTTCCCATACACGCATTCATCGAGATGCCAGTGACCAGAAATTCAAGAGAAAAGATGGTA\n")
-		f.write("ACACAGCGAACCAGGATATGAAAGCCATCGCTGTAGCTGTTTCAAATTGGGCACAATGGTTGTGGGCACA\n")
-		f.write("GCTGCTAAGATCATTGTCAATAAGAACTGTGATGCCTGCAGAAGCACAAGCTGCAGCAAATGTAAGAGTG\n")
-		f.write("GATGTCACCCCATCACCAAGGGTGAACAAACACACAACTCGATGGTTCTGCAAGGAACGCCCAACTAGAA\n")
-		f.write("GGGCATAAACGTCAACAACGCCCAACGAGAAGCTCCACAAACACTGCAAACCAGTAGCTGCAACAAGGTA\n")
-		f.write("GCAAAACGCAGTGACGGAGGGGAAGTCAGAGGTGGTGGCCATGACGACGAGCGAGGCGGCGGAGAAGAAG\n")
-		f.write("AACTGGGCGAGGCGCAAGACGAGGCCGCCCGGGGTGCCGGGCATGCCAGGAAGATCCTTCATTCGGACCC\n")
-		f.write("GGGGTGGGTTCGGGCCGGCGCCGTCTGTGGTGGGTACATCTTCAACTGGGTGAACCGACCCATGGCTCAC\n")
-		f.write("GTTCATCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790436|gb|GO545634.1|GO545634 Mdas9009D16_e659.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192813.1| aldolase -related [Arabidopsis thaliana] pir|T01902 hypothetical protein T12H20.10 - Arabidopsis thaliana gb|AAC35519.1| similar to 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolases [Arabidopsis thaliana] emb|CAB81176.1| putative, mRNA sequence\n")
-		f.write("CCGATTCTCCTTTATAAGATAATAATATGAGTACGAAAATCACTCTGTGTATCTTTGCCTCCAATCCAAT\n")
-		f.write("CCTTCTAATTATTTAATTTGGCCGGCAATTTGACCTTCATTATGAAAACACCAATGGACTCAAAATTTAC\n")
-		f.write("AAATAAGCGAGTCCAAAATTCTAATTATTTTCGTCAATATTTCTCCCAGCCAAAAAAGACAGCTTTCAAC\n")
-		f.write("AATCTGCCTCTTCATTCGCTCCAGTACTTCTCATCAGCATCCTTCTCGTCCTCCCGCTCATCATCTGCAC\n")
-		f.write("CGTCCATCAAGCTCATCTTGAACCGCTTCACGTCCTCCACCGCCGCGCTCCTAAACAGCCCTACATCGAC\n")
-		f.write("GGCTCCCGACACCATGTGGTATCCACGTGTCCCCAAA\n")
-		f.write("\n")
-		f.write(">gi|226790435|gb|GO545633.1|GO545633 Mdas9009F08_e667.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9FVI1|ADF2_PETHY Actin-depolymerizing factor 2 (ADF 2) gb|AAG16974.1|AF183904_1 actin-depolymerizing factor 2 [Petunia x hybrida] gb|AAK72616.1| actin-depolymerizing factor 2 [Petunia x hybrida], mRNA sequence\n")
-		f.write("GCCATCGGAGGAGAGACCCCCTTTCCCTATATCTTCTCCTCCTTCTCCGTCGCCATCAGAGAACTAAACA\n")
-		f.write("GGCAGCAAAAATGGCCAACGCAGCATCTGGTATGGCTGTGCACGATGATTGCAAACTGAAGTTTTTGGAG\n")
-		f.write("CTTAAGGCAAAGAGGACCTACCGCTCCATAGTTTTCAAGATTGAGGAGAAGCAAAAGCAGGTTGTGGTGG\n")
-		f.write("AACATGTTGGTGAACCAGCAGAAACCTATGAGCAGTTCACTGAGAAGCTTCCTGCTGATGAATGCCGATA\n")
-		f.write("TGCTATTTTTGATTTTGACTTCCTTACACCAGAAGGTGTCCAGAAAAGTCGGATATTCTTCATTGCCTGG\n")
-		f.write("TCTCCTGATACATCAAGGGTGAGAAGCAAGATGATCTACGCAAGCTCCAAAGACAGATTCAAGAGAGAGC\n")
-		f.write("TCGATGGCATTCAGGTTGAGTTGCAAGCGACTGATCCTACTGAGATTGGTCTTGATGTCATTAAGAGCCG\n")
-		f.write("\n")
-		f.write(">gi|226790434|gb|GO545632.1|GO545632 Mdas9009A02_e638.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566596.1| expressed protein [Arabidopsis thaliana] dbj|BAB02017.1| emb|CAB36779.1 gene_id:MRC8.3 similar to unknown protein [Arabidopsis thaliana] gb|AAK96874.1| Unknown protein [Arabidopsis thaliana] gb|AAN15376.1| Unknown protein [Arabido, mRNA sequence\n")
-		f.write("TTTTTTTTTATCATGTCAATTGGTGAAATAGGCTGTGTTTTCGGCACACTAAAAAATTAACACTTTCCAA\n")
-		f.write("ATGAGAAAGAAGAACCAGAAGAAACCCTATTCAATTCTTCTTCTTCATTTTTGTGGAAATAGGAACAAAA\n")
-		f.write("GATGCAGCCTACAAGCTACAATAAATAAACAGAGACAGAAACTTCACAATTACATAGAAAAAGAACTTAC\n")
-		f.write("ATTGTAGAGACTGTGCAAGCATTTGGAGCAGCCACCAAGACCAGGAAACCAATTGCCATTGGCGCCGCTG\n")
-		f.write("CTCAAGCAATCTCTCTCCAACTTCTTCACCTTTTCATCCCCAACAAGCTTCCCTCTTTCGTTCTCCGAAA\n")
-		f.write("ACGCCTCGGGACAGCTCAAGGGGTGCAATCTTATCCCGCAATAGCAGTACACAACATCACAGGTCTCATT\n")
-		f.write("CGGCTTGATTAGCTCGATACCTCTGTTTTTCAGCGCCTTTCCCAAGTCCTGAACACAAGTTTCCGTGTCG\n")
-		f.write("TCCGGCAGCAGTGGCAAATCATAAGACTGACCGGCCACTGCTGAGCCCACCCTGCCTACTCTGCCGAGAG\n")
-		f.write("CGGTGTCAGAGTAGGCAGAGTAGAGCCACGAGGCCAGCGCAGGACAGCACCTGCTGCGCTGCAAGTGACC\n")
-		f.write("TGAGGCATCGCCTTTGGTGGCGGAGCATGCGGACTTTATGCCATG\n")
-		f.write("\n")
-		f.write(">gi|226790433|gb|GO545631.1|GO545631 Mdas9009M02_e700.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07014 phosphoglycerate kinase (EC 2.7.2.3) precursor, chloroplast - potato gb|AAC26785.1| phosphoglycerate kinase precursor [Solanum tuberosum], mRNA sequence\n")
-		f.write("TGAAAGGGTCGCAAAGAACAAAATTATTAGATTGCTCGGACGGCTGCGTTTGTCCCTCCCCGCCATCTCT\n")
-		f.write("TATGGAAACTTTATATAGACATAATGGGACCTTATACTGAAGGTAACATCAGACATTCACAACTCGAACT\n")
-		f.write("CACATCTTCCTACATGCCATTTCTCGTTTACAGACTCGAATGAAACACCAACACGGTGGGCAGGGAAAAA\n")
-		f.write("AACAAACAGGAAAAAAGATTGTTCTTACACAGGAACTGGTGTGGCTTCGTCAAGAGCAAGTACACCAGGA\n")
-		f.write("AGTTCTTTGCCTTCCAACAACTCCAAACTCGCACCACCACCAGTTGATATGTGGCTCATCACACTAGCGA\n")
-		f.write("CTCCTACTTTCTCCACGGCTGCAACAGAATCTCCACCTCCGATGATTGTTGTCACTCCCTTCCCACTAAG\n")
-		f.write("TTCCGCAAGCTTCTTTGCAACAGACTCTGTTCCTTCTGCGAACTTGTCAAACTCAAACACTCCCATCGGT\n")
-		f.write("CCATTCAACATTATGGTTTTAGTGGTATCCAGTGCAT\n")
-		f.write("\n")
-		f.write(">gi|226790426|gb|GO545630.1|GO545630 Mdas9009E13_e665.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACA\n")
-		f.write("CCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATT\n")
-		f.write("AAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCT\n")
-		f.write("TGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCC\n")
-		f.write("TGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATG\n")
-		f.write("AAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGA\n")
-		f.write("ACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTA\n")
-		f.write("CACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCC\n")
-		f.write("TTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGA\n")
-		f.write("GGCCACACCTGCATGCATTGC\n")
-		f.write("\n")
-		f.write(">gi|226790425|gb|GO545629.1|GO545629 Mdas9009C12_e652.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565301.1| expressed protein [Arabidopsis thaliana] gb|AAD17434.2| hypothetical protein [Arabidopsis thaliana] dbj|BAC42227.1| unknown protein [Arabidopsis thaliana] gb|AAO50598.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTGGTCGTGATCGTCTACTCATATTACATACGTATCCATGTCTTCAAATGAGAAGCTCCTACAAGT\n")
-		f.write("TTGATTTCTACTATTACTTGGAAATTAGGGTTTACACAAAGCATAAGCCAGTGGATATCAATCCTTGACG\n")
-		f.write("CCAGCCTCCTCCTTCAACATTGCGATGAACTTTGTCTTTCTCATCAGGTGTCATTCCCTCTGCCGAGCAA\n")
-		f.write("TCTCCAACTCCCCACTCTGCCCCCCGTATGCAGTACTTGTCTTGAATTTCTTTACTATTCTTTTCTTTGT\n")
-		f.write("TGAGCTTGGATTTTTCTAGTAGCTCCTTGAGTATTGGAGTTGATCTGAATCTTGCATCATTTTCTGCGTA\n")
-		f.write("CTTTTTCTGGTTTTCTTCGTTGAAGCGTTTGAGGAAGTCGATTTGAGGCATCTCAGGACCTGGAACTGAT\n")
-		f.write("TCAATTCCAGTCGATCCTGATAGTAATCCAGCACTAGCTGGATTTGAGCCGAGAAGAATGGCAGCTGAAG\n")
-		f.write("CAGCCAAAGAAAGAGAGGTTTGGAGAAGAACATGGCGGGGAGACGTCGGCGCCGGAGAAGAACTAGAACA\n")
-		f.write("AACTACTACTGGGGTAGGTCTTTTATGGACATCTAACTT\n")
-		f.write("\n")
-		f.write(">gi|226790424|gb|GO545628.1|GO545628 Mdas9009H07_e679.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK73147.1|AC079022_20 putative RING-H2 finger protein [Oryza sativa], mRNA sequence\n")
-		f.write("TTTTACACACTTAATTAAGAATTAAATTTCAAATTCTATAATCTTCATAACACGCAGAACCAAAGATGTT\n")
-		f.write("TTGCTACAAATTGAGCCAATTTTGTGCTGCTTTTTTTTATGAACACAGAACCCCAAACCGGCAAACTCGA\n")
-		f.write("AAGTTCTTCGAAACTCAATGCTATAATAATCAAAGTATTTACACTGATGAATATTTCAATAAATTAATAA\n")
-		f.write("ACAAAACAAAAAAAGAAGAAGAAGCCAAAACTGTGGTCTTTCTAATCATCCAACACCCACGCCCTCCTAC\n")
-		f.write("GCCGGTGTACGAACCGCCCAATCACCGAACTTGACTGACTTCTAGTCAAACCCGGCCCGGATTCAGATTC\n")
-		f.write("CGACCCGGACCTCGAAGACGATGAATTGGGACGTAATCGCCCCCAGAACGAAGCTATATTACGAAAAGCA\n")
-		f.write("CTCCGAATCCCGCGACTTTCGCTCCCTCTACTCCTCGATGCCCATAATACCCTTCTTGGAGCCCCGTTAC\n")
-		f.write("CATTGAACCCGCCGTCCATTTCTGTGTACACAACCGGTAATTCCCTCTCGCCGGGTCTTCTGCCGCCGGA\n")
-		f.write("GAATCTCCCCACGGCAAATCCGCCGCCGGGTAATCTCCAGATGGTCAAACCCATCGTCT\n")
-		f.write("\n")
-		f.write(">gi|226790423|gb|GO545627.1|GO545627 Mdas9009F13_e668.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191173.2| chloroplast lumen common protein family [Arabidopsis thaliana] gb|AAM13110.1| putative protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGCAATTTCAGCGCGATCAAAACAATTCCTGCTGCAGGTTCTGGCAGCAGAATACCACAGGAAATCA\n")
-		f.write("GCAACAGGAACTTCTCCCTCTCGTCGTATGTGCTGTCTTTCAGGATCAAGTAATATAACTACTTGGTTTT\n")
-		f.write("TCTTTTGCAACTTCTTTGAAATTCTGGCCGGCAGCCCAGTCCCTCTAATCCCATATTTAACATGGCTTGC\n")
-		f.write("ACCTGTCACCACCACTAGCATACCACTTGCTCCTCCATCCGCCATGGCCTTTAAAATAATCTGGGACATA\n")
-		f.write("GTATAATCCTCAACCACTCTTGCTTGTGCAGAAAGATACGAGCTTGGCCCAAAAGGAACAGATTGACTCC\n")
-		f.write("GGGAATTTGAATCAACTGGTGGTCTGCGTGTGATAGAAGTGAAGCCTGATATGAAGCCTGAACCCGCTGG\n")
-		f.write("AGGAGCATATGTTTTTCGATCAGCCTCTGAAAGCCCACTAATTCCCTCTGCTTGGACAGTCCTTAAAACC\n")
-		f.write("TTGAGTGGAGTTCCACAAGCCACTAGCCGAATTCCGTTATCCCGACAGTAACTCAGGAGAGGCTCATACT\n")
-		f.write("CCTGCCAGCGTTGAGGTGGCCAATGTGATGTGTAGGACTTCAAAGCTTCTCCATCTATGCTTTTGTCCAT\n")
-		f.write("GTACTGATT\n")
-		f.write("\n")
-		f.write(">gi|226790422|gb|GO545626.1|GO545626 Mdas9009L20_e699.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q05145|MDHP_MESCR Malate dehydrogenase [NADP], chloroplast precursor (NADP-MDH) pir|S33066 malate dehydrogenase (NADP) (EC 1.1.1.82) - common ice plant emb|CAA45270.1| malate dehydrogenase (NADP+) [Mesembryanthemum crystallinum], mRNA sequence\n")
-		f.write("TCGAATTTTTTTTTTTTTTTTTTACGGTTATTTGCAACTCAAACACATAAATTTAGACATAAATGTTCAG\n")
-		f.write("GATCTAGGCTGCACAGCAGAAACCTCAAAATTTAACGACTTTTACATTACTCCCTCTGGTTTATTTTCAT\n")
-		f.write("GCTCTTACTACATAAATGATGCTCCATTATTTGCCTCATGTGCTCTATGTGGTATCGTATCCTTCGTAAA\n")
-		f.write("AGTTCTCGAGACGTGGAACTTGTCTGCTGAGGATTACATCTCTCCAGGAAGCATAGTATCCTCGGGTAAA\n")
-		f.write("TCACACACAGCGATACCCTGCCCAGTAAGGTGAGCGACGCATCTTTTCTCAGCTAGTAATTCAGCTTCGC\n")
-		f.write("TCTTTTTTATTCGCTTGCGAAGATAGTCATCAAATTGTATGTCCTTTACAAGTTCATAGTCGCCGTCTCC\n")
-		f.write("TTTAGATCTGCATGGCATACTGAATACTAAATCCTCTGCTATACCATAGGGATTTCCATTTGTGTAAACT\n")
-		f.write("GCAGATGAAAACCAATCGCCCTCTGGGGTAGGAGTAATCAAAGACTTTATGGCATCTGCAATTGACATGG\n")
-		f.write("CAGTTGATGCAGCTGACGATCTTCCCCATTTCTTGATGAGCACACCTCCTCTCTTCTGGGATAGTTCGGT\n")
-		f.write("AAATTCTTC\n")
-		f.write("\n")
-		f.write(">gi|226790403|gb|GO545932.1|GO545932 Mdas9008L08_e615.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTGATGCTCGAAAAGTAGTAGAGCCAGACTTTTATCGCATTGAGAACCTACGAAAGAAGCTCCCAA\n")
-		f.write("ATGTTGTTGGTTCAGCATTTCCAACAATAATTAGAAGTTTGTCTTTACCGGTCTCAGTTGCTCCACCTCC\n")
-		f.write("CCTTATTTTGGGGTAATTTAATACAATTTTTTCTTGGATGGTGCTAACTGAGCAGCCTCTCCATAAATGG\n")
-		f.write("GGGTAAGGCTAGCCGACATTCACCTCTCCCAGACCCTGCGTAAAGCAGGAGCCTTGTGCACTGGGTACGA\n")
-		f.write("CCGACACACCTCTCTCAATTGTCGGCCGTTAGAACGAATAAATTGAAGAATATCAAGTATCAGAAATTAA\n")
-		f.write("TAAGAAATGTGTGGGAGATAAAAATGAGTGTGTAAATAGCATCATTTTTTTTAACCGAAACAGTAGCAAT\n")
-		f.write("TTCAATAAAATATATTATGCATGGTTTAGAAAAGGGAACAAAAAAAATTGGGAACTCAGATTTAAGCATG\n")
-		f.write("GTTTAGAAAAGGACTAAGTCACCACACCAGAGAATATTATTCACCACAATAGACTGAAAAAGCATAAAAA\n")
-		f.write("GGAAGTGAAGGGGGAGGAGGAAAGAGCAAATGTCTCTCCTTTCTCTTCCCTTTAGATGATTTTTGCCCC\n")
-		f.write("\n")
-		f.write(">gi|226790402|gb|GO545931.1|GO545931 Mdas9008L02_e612.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB41987.1| FtsZ-like protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("ATGAAAACGACGATGGCTGCATGGAAGAACCCGAACGAGCTAATCTGGACGACGTCGTCCTCAATTCCCG\n")
-		f.write("CAGCATTTCACCACCACAAGCCACTGCCTTCCCTCAGAACGTGCATTCCTCTGAGCAGCAAAAGAAGAAG\n")
-		f.write("CGCATGGAAGCGTCACCGTTTCGGGGTTGTCAGCTGTTCCTTTGCTCCCATGGAATCGGCCAAGATTAAG\n")
-		f.write("GTCGTTGGGGTCGGCGGAGGCGGCAACAATGCTGTTAATCGCATGATTGGCAGCGGTTTACATGGTGTTG\n")
-		f.write("ATTTCTATGCCATAAACACGGATTCTCAAGCGCTCTTGCAGTCTGCTGCCGAGTACCCGCTGCAGATTGG\n")
-		f.write("GGAGCTTTTGACTCGTGGGCTAGGTACTGGTGGGAATCCACTTTTGGGGGAGCAAGCGGCAGAAGAGTCA\n")
-		f.write("AAAGAGGCTATTTCTAATGCTCTA\n")
-		f.write("\n")
-		f.write(">gi|226790401|gb|GO545930.1|GO545930 Mdas9008E08_e581.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTGAATCAAGGCAGATATGGATTATTTTACGTCAATGGGACAATCCCATTCAAATATGCA\n")
-		f.write("ACTAAAAGAAGAAAAAAGTCGAAGTGTCCGAATAGAATATTGGGCTCAACAACTGTAAAACCCACAAAAG\n")
-		f.write("CAGCTTCTGCATCATTAACATATCTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTGCTTTTCT\n")
-		f.write("CACACATTGCAGGGAGGCCAACTTACAACCACACCAAGGAAAGGCCAAGAGCATCTAAGAGAGGCAAGAG\n")
-		f.write("TATGCCAAAGCTTTCTCCTCACTGAGCTCCTCTGCAGTTGCATCCAACTTCTTCCTCGAGAACTCGTCAA\n")
-		f.write("TAGAGAGTCCTTGAACAATCTTCCACTCCCCATGTTGGCAAGTGACTGGGAATGAGAAAATGAGACCAGA\n")
-		f.write("AGGTACATCGTATGAGCCGTCAGAGTAAACACCCATGGAAACCCAAGTGCCCTCCGGGGTTCCAAGTACC\n")
-		f.write("CAATCACGAATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGATGA\n")
-		f.write("TTGC\n")
-		f.write("\n")
-		f.write(">gi|226790400|gb|GO545929.1|GO545929 Mdas9008L22_e619.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATTCACATTAAAATTACCATACAACCCCAAAGCTACACGAGCAAAAGAAACAAGAAAAAATAAATTGAAC\n")
-		f.write("AAAACATGGAGCACATGTCTATATATAGCTTTTCATTTTCATTTGTAGA\n")
-		f.write("\n")
-		f.write(">gi|226790399|gb|GO545928.1|GO545928 Mdas9008P19_e637.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTGCATCCAAGTATCAATTCCAAACTGAACCCGCAGAATGAAATTCATCACTCTTTTGATCAGTCTATC\n")
-		f.write("TTTCGGTTTGACTCTGGCGGCGGGCGCGGTTGTCACTTGCGGCGATAGGGAATATAGTGAAAAGACATGT\n")
-		f.write("CTCACAACGTCTCGAATATGTAGGATATGACTTCAATCCACCAGATGGAGTTTTCGATGGTACCCGGCCT\n")
-		f.write("TATCAGAAGGTACCATTAACCGGTTATGATGGAGGTCGAGGTTCGTTGGATTATCTTATTGTCGACTCCT\n")
-		f.write("CCGATAATCTAGTTGGCGCCGTCACCTTCGCTTCAGGTGGAGGGTCATACACTATGTGCAGCGTCAGCTA\n")
-		f.write("ATTACAACCCATGACGGATAATTTATTTGGCCGTCGAGAGGAAACGGGATCAGACACATCTGATGGGATG\n")
-		f.write("ATGTGAGCATGATGCAGCAAAATTTGTGACGGCCTTAGACTACATGTACCAACACGACAGTCATTATCTA\n")
-		f.write("ATTATCTTTCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790398|gb|GO545927.1|GO545927 Mdas9008J20_e606.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK13030.1| ribonuclease-like PR-10a [Malus x domestica], mRNA sequence\n")
-		f.write("ATTAACTGATTTCATTATATTTAAAAATAAAACACTTACAGTCCGCAACTTTTTTTTCCAACAAATACAT\n")
-		f.write("AAAGGGCAACCAAAAAAAGATCACAACCATAAACTTATTTTTCAAAACCAAAATGCTCAAAACCATGGCT\n")
-		f.write("ACTTTGGGCTGACTAAAAAAAGCATACAAAAAAAAACCCCACAACCCTCCACTGAAGGGTGACACCCCAA\n")
-		f.write("ATACCATAAAAACATATTAATTTAATTGTATGCCTCCGGGTGGCCCTTGAAGTAACTCTCAATAAACTTG\n")
-		f.write("AACAAACCATGAACCCTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGATCTCAACATCACCCTTGGTGT\n")
-		f.write("GGTAATGGCTGAAACTCCTGAAGAAGGAACCACTTCCAAAAGCCACCAACTTGGTCTCGTAAGAAACCTT\n")
-		f.write("CTCAATGGTGTCTGTCAAAACATCTCCTTCAATCAAAGTGTAAGCGTAAGAATAGTTTGCTTCCTCAACC\n")
-		f.write("GAATCGATCTTGTGCTTCACGTAACTTTT\n")
-		f.write("\n")
-		f.write(">gi|226790397|gb|GO545926.1|GO545926 Mdas9008P05_e634.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTGAAATTAATGTACTCAAATTAATAAAGCTTCAAGGATCCATCATTTCATCCACCA\n")
-		f.write("ACAAAAAGGGCAGATTTTCCATCCATCCAGATGCGCACAGAAGCAATTTTGTGCATGAATATCATCATCG\n")
-		f.write("CTGCAGAGACAGTTTTGAGTTCCTTGACTCTTTTCAGTATATCATAAAACAGTCACAACCTAAAGCTTTT\n")
-		f.write("GAAGAATCGAAAACCGAAAAAAAAAAAGGGCAAACATTTCCAATCAGAGAATTCCATGAAGTGAGCTGCA\n")
-		f.write("AATATTGATGGTGATTCGATCTTTGATGAATATATATTCTCCCACATGTCCTGTTGCCGTTCCAAAATAA\n")
-		f.write("GTTTCCGTCCATGCACCGGTCCACCATTCCGGTCAGGTCATAAGGTGGTGCCTATTTCCTGCTCTCTCTA\n")
-		f.write("TCTTCTGGAAGTAAATGTAGCATTGGTCATCCTGCCATGTTGTTTCCCAACAGCATTTGAGCTCAGCCGG\n")
-		f.write("CCATTAGGCAAGCCTGAGCTTTGGGTACTGCTCATGCTTGATCTATCCAGAACTGCTCCATTTCCACCAT\n")
-		f.write("TCAAAAGTACAGATGACTGGCTTGGCCTAGTGTCAGGGCTGTTCAGTTCCCAAGAATCTTT\n")
-		f.write("\n")
-		f.write(">gi|226790396|gb|GO545925.1|GO545925 Mdas9004P19_e323.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191788.1| ADP-ribosylation factor [Arabidopsis thaliana] pir|T48021 ADP-ribosylation factor-like protein - Arabidopsis thaliana emb|CAB71889.1| ADP-ribosylation factor-like protein [Arabidopsis thaliana] gb|AAK49618.1|AF372902_1 AT3g62290/, mRNA sequence\n")
-		f.write("CAATAATCGAATTACAACTCAGAACAGAATTGTATCCAAAATCCAACCAAAAGAAATACAACCCGATTTA\n")
-		f.write("AAAAGGTCCTAGATGAAAACAGCATTCCCACAACAAATACAAGAAGCAGATTTAACAACAATTCAATCGT\n")
-		f.write("CTCAATAGCATAAAAAAAAAAAAAAAACAACTAGATAATATTCACCCCTGCATCCAGAATTTCCGGTCCA\n")
-		f.write("CAAAAAGACTCCTCGATACAATCACGCCTTGTTAGCAATGTTGTTGGAGAGCCAATCCAGCCCCTCGTAT\n")
-		f.write("AGACCCTCCCCGGATGTTGCACAAGTGCTCTGGATGTACCAGTGACGCTGTCTCAGAGAGTGGAGGCCAA\n")
-		f.write("GCTTATCAGTAATTTCAGCAGCATTCATTGCATTGGGAAGATCTTGTTTGTTAGCAAATACGAGCAACAC\n")
-		f.write("AGCATCACGCAGTTCATCCTCATTCAACATCCTATGTAATTCGTCCCTTGCCTCAACAACACGGTCTCTG\n")
-		f.write("TCATTGCTGTCCACAACAAAGATAAGACCCTGCGTGTTCTGGAAGTAGTGCCTCCACAATGGTCGGATCT\n")
-		f.write("TGTCCTGACCCCCGACATCCCAGACGGTGAAGCTGATGTTCTTGTACTCCACGGTCTCCACATTAAACCC\n")
-		f.write("\n")
-		f.write(">gi|226790371|gb|GO545924.1|GO545924 Mdas9005J02_e371.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB12722.1| gamma tonoplast intrinsic protein [Pyrus communis], mRNA sequence\n")
-		f.write("TTTTTTTTACAAAAGATAAATGGAATTTAGTGACACAACAGCGGAGAGCATGCAAAACAAATTACAAATC\n")
-		f.write("AACGATGGAGATCAACTCATGACGACAACGATCATGATCATGATTTTCTTGATGAAACGAAACACAAGAA\n")
-		f.write("CTCAAAGGTCCAAAACCCAGCATGCATGCAAATGTAATTAAATCTTATGACTCCTTAATTAAGCTTACTT\n")
-		f.write("AAGGCTTAATCAATTAGTAGTCAGTGGAGGGCAGTTGCTCGTGGCCGCTGTTGCCGATGAACACGAACTC\n")
-		f.write("GTAGATGACCCCGGCGATCCCGGCGCCGATCAAAGGCCCGGCCCAGTAGACCCAGTGGTTCTCCCAGCTC\n")
-		f.write("CAGCTCACCAACGCCGGCCCGAAAGAAACGGCCGGGTTCATGGACGCCCCGTCAAAAGCCCCACCCGCCA\n")
-		f.write("AAATGTTGGCGCCAACGATGAAACCAATCGCGATGGGCGCGATTGTCCCCACGCTCCCTTTCTTCGGGTC\n")
-		f.write("AATCGCGGTCGCGTAGACCGTGTAGACCAGTCCGAACGTCATCACGATCTCGAAAACGAACGCGTTCCAC\n")
-		f.write("ACTCCCACTCCCGGGGACAGGGAGAAAGCAACGGTAGTCTGGCCGTTGGTGACCAACT\n")
-		f.write("\n")
-		f.write(">gi|226790370|gb|GO545923.1|GO545923 Mdas9005M12_e381.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGGAAAAATCAGAAAAAGAAGAACATAATTTCGCGTGATGCAGATTTTTTGTTTTTTTTTTTTTTGG\n")
-		f.write("GTATGATGATATATTTTACACTAAGAGGAGGGGGAGTTCGATTAAGTCACACAATGGGCAACCTAATTTG\n")
-		f.write("GTATTGAATTATCCATCTACGAGATTCAAACCTAAAGCCTCTCATTTACAAGTGAAGAAGAATACTACCA\n")
-		f.write("GATCGTGAGTGACCGAGCGTTGTAGAGTATGCCATAAGAAAAATGAGCTATGCAAGAAATTGCGATCCTT\n")
-		f.write("GTTTCGTGCTCTATTTTTCAACGGTTACAAATATAATCTTGAGAGAGTAAAAGAAAAACTCGTATAATCA\n")
-		f.write("CTAAATTGTTACAACAATTTGTCACAAAAGAGAACATTTGTCACCAATTTGTGGCAGAAATTCTATCCTT\n")
-		f.write("TTCGTGAAGGAACTTAACACCAGCTGCTACTGCTAACAGAAAACAACGAGTAGAGCAACCACGACGACGA\n")
-		f.write("TCGAGCAAATTAAAGCCTGCACCTGTACGATTTTTCAGCACAAAGGGAAATAAAATGTCGATACTAACAT\n")
-		f.write("CAAAGGACAAAAATGGTAGGCAAAATCTGCATAATTTCTTACTGCAAAGGGATGTGGCATAATATC\n")
-		f.write("\n")
-		f.write(">gi|226790369|gb|GO545922.1|GO545922 Mdas9005I12_e368.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO33770.1| unknown [Oryza sativa (indica cultivar-group)], mRNA sequence\n")
-		f.write("CCAAAATCTCTCTCAAAGCTTGAAACTTTAAGCCTTTTGGTCCCAACCCATTTCCCAAGGGCGCGGTTTC\n")
-		f.write("CACCGGTTCTAGCCGGGAAAAGCTGACTTGGGTCGCCGGAGAGTTGAACCACCACCATGGACGTTGACTT\n")
-		f.write("GTGGGCTTCCAGGGTTCACGCAGCTAAGAGCCTCTCTGCTGCTCATGCTGCAAGGCTTCACTATGATAAT\n")
-		f.write("CATATGGGTTTGGAAGATTCTGAAGGAGATGACGACACAAAATCGTGTTTTCCATGCCCTTTCTGTTATG\n")
-		f.write("TGGATATTGAAGTCCCAGTGCTTTGCAGCCACTTGGAGGAAGAACACTGCTTTGACTTTAAAAATGCAGT\n")
-		f.write("TTGTCCTTTGTGCGCTGCGAATCTGGGGAAAGATGTAATTGGACATTTTATGGTGCACCATGGAAGCTCC\n")
-		f.write("TTCAAGCACAGGAGAAAATCTCAAAAATCCGGTTTGTGGACTGGTAGTTCAGCAATGCTGGGGAAGGCAC\n")
-		f.write("TGCTTAAACATGGAAGGACATATGCACAGGAAACTGCACCTGATCCTCTCCTCTCACCATTTATCTGCAA\n")
-		f.write("TATATCATTTTCAGACCCTACAGGTATCCCCGAAGATGTTTG\n")
-		f.write("\n")
-		f.write(">gi|226790368|gb|GO545921.1|GO545921 Mdas9005N15_e388.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_445525.1| hypothetical protein [Chlamydophila pneumoniae AR39] pir|G81516 hypothetical protein CP0988 [imported] - Chlamydophila pneumoniae (strain AR39), mRNA sequence\n")
-		f.write("CAACTTGTTCCGACCTAGGATAATAAGCTCATGAGCTTAGTCTTACTTCACCGTCGAGAAACGAAAGAAG\n")
-		f.write("ACTTCCATCTCCAAGTTTAACTCAGACGTAGCTCGCTTCTTTTTGGGTGTGAAGCAGTGTCAAACCAAAA\n")
-		f.write("TACCCAACAAGCATTAGCTCTCCCTGAAAAGGAGGTGATCCAGCCGCACCTTCCAGTACGGCTACCTTGT\n")
-		f.write("TACGACTTCACTCCAGTCACTAGCCCTGCCTTCGGCATCCCCCCCCTTGCGGTTAAGGTAACGACTTCGG\n")
-		f.write("GCATGGCCAGCTCCCATAGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGAATTCACCGCCGTATGGC\n")
-		f.write("TGACCGGCGATTACTAGCGATTCCGGCTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGGACGG\n")
-		f.write("GTTTTTGGAGTTAGCTCACCCTCGCGGGATCGCGACCCTTTGTCCCGGCCATTGTAGCACGTGTGTCGCC\n")
-		f.write("CAGGGCATAAGGGGCATGATGACTTGACGTCATCCTCACCTTCCTCCGGCTTATCACCGGCAGTCTGCTC\n")
-		f.write("AGGGTTCCAAACTCAACGGTGGCAACTAAACACGAGGGTTGCGCTCGTTGCGGGACTTAACCCAACACCT\n")
-		f.write("TACGGCACGAGCTGACGACAGCCATGCACCACCTGTG\n")
-		f.write("\n")
-		f.write(">gi|226790367|gb|GO545920.1|GO545920 Mdas9004L06_e303.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27882.2|AF139470_1 chlorophyll a/b-binding protein CP24 precursor [Vigna radiata], mRNA sequence\n")
-		f.write("CACTTAAGTATCTATTAAATTGAAAAGGATAAAAAAAAATTGTAATTAGTTATATCTACATATTGAAAAG\n")
-		f.write("TAAATGCCAAATGGTTTACAAGCCAAGAGCACCAAGGGGCGTCTTTCCTTGCCCAGCTTCAAAGTAGAAA\n")
-		f.write("ATGAGCATAGCCACCATAGCAAGCCTTGCATGCTTAATCTCAGCCAGTTTCAGTCTCTCCAACTTTTCAC\n")
-		f.write("TGTCTGGAACGTAAACCCCGTCCTGGATGGAGCCGGCGAAGCCCAAGGGGTCGAAGAACTTGCCACCCGG\n")
-		f.write("GTAGCCTTGCTCTCCGGTGGAGTTGGCGAAGTTCTCCGAGGTCTTGGACCAAGGTGTGGCCCACTCGACG\n")
-		f.write("GACTGGGACTCAGGGTTGTAGAAGTCCACCCATCTCTTGCTTTCCACCCATCCCATGAGCAAGAGCTGAG\n")
-		f.write("TGCCGAGCAGTGAGCCGAAGGAGAAGGGTGCGATGGCACTGGGGTCAGCTCCGGCTTCGAACCATGGGAT\n")
-		f.write("ACCACTCCAGGCCTGGCCAACAAAGATGCCAACGACTGCCGCCATTGCCCACCGGCCGTGGATGAGCTCC\n")
-		f.write("GCCTCTCTGTACCACTTGAGGAACGCCGGGTCCTTGCCTAGTCCTAGTGGGTCAAAACCGTAGTCACCTG\n")
-		f.write("GAAGCGAGCCATCGAGCCA\n")
-		f.write("\n")
-		f.write(">gi|226790366|gb|GO545919.1|GO545919 Mdas9005K11_e376.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC48323.1| 2-Cys peroxiredoxin [Pisum sativum], mRNA sequence\n")
-		f.write("CCCCATCTTACAAGTTTCTGATCAAATAAAATTACATAGGCTCACCCTGTTTCCATGATAAAATAAAAAG\n")
-		f.write("TGACAACAATGAAATTGTATGCTACTTGAATATGCTGAAAATCGGGCAAGTCCCATTGATTGGGGTTTAT\n")
-		f.write("TGTGACATGCAAATGCTCAAAATTACCAAGGATTGGAAAAAAAGGTTACACAAATACAAAACTCGTTTAC\n")
-		f.write("ACGTCCTATTTGAGTCCAACATGGACATGCAGTGTACTACCTCTATATTGCGGAAAAGTACTCTTTGCTG\n")
-		f.write("CCCTTGGGGTCTGGCTTCATGGACTTCTCCCCGGGCTTCCACCCTGCAGGGCAAACTTCATCGGGATTGT\n")
-		f.write("CCTGCACGTACTGCAAGGCCTGGAGCGTTCTCTTAGTCTCATCCACACTACGGCCAATGGCAAAATTGTT\n")
-		f.write("AATGGTGGAGTGTTGAATGACCCCTTCCTTGTCAATAATGAAAAGTCCTCTCAAAGCGATTCCCTGA\n")
-		f.write("\n")
-		f.write(">gi|226790365|gb|GO545918.1|GO545918 Mdas9005B21_e332.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04867|GLN1_ALNGL GLUTAMINE SYNTHETASE (GLUTAMATE--AMMONIA LIGASE) (GS(1)) emb|CAA69937.1| glutamate synthetase [Alnus glutinosa], mRNA sequence\n")
-		f.write("ATGCACTCAATTAACAAAAACAGCTAAAAAAAAAAAAAAAAGATGAGGCTTGCAATTTTCAAAAATTACA\n")
-		f.write("AGTGAAATGGCATTTAAACCAACCACCCCTTTGAAAAATATTATTCATATAAAAAACTTATTCAACACAA\n")
-		f.write("CGGGCAAAATGATGAGGCAATGAAGCAACAGCATAATAAAGTTTAAAGGACAAAGCCAACTCTAGTTTGA\n")
-		f.write("AGCTAAGGACCCACAAGGATCCATCCAAAAGGATCTGGTAAATCACATTTCCAACCTCAATGAAAAACAA\n")
-		f.write("TTACGTTGTCACAAAACTTATAAATGCACGCGTGTAGGTGTGGCTGCGTGTGCTTATGCCTTCAACAAAA\n")
-		f.write("GGGTGGTTTCTGCAATCATAAATGTGACAATGTATGGATCCATGTTCGATGCAGGCCTCCTGTCCTCGAA\n")
-		f.write("ATAGCCCTTGCCAGCTTGTTCTGTGTCTCTACCAACACGGATAGAAGCACCGCGGTTGGCTACACCCCAT\n")
-		f.write("TTGAATGTATTGATATCAACAGTTTCATGCCTTCCTGTCAAACGG\n")
-		f.write("\n")
-		f.write(">gi|226790336|gb|GO545917.1|GO545917 Mdas9005I04_e367.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCAATATCCACTGTTCTTAAACATTTCTTAACATGCTTAAGAGCAGAACAAACAATTGGCAACTGCCAAT\n")
-		f.write("ACACAAACATCTTATATAATCTTAGAACATATACATATAAACATTACAAGAACAACGATTCCATGGATAA\n")
-		f.write("ATTTTTCCATCCATGTTCCGATAATTAGCTATATATTACATTAGCAAGTCACTGAATCGTCGATCAGCCA\n")
-		f.write("CTAGAGATGTTACACCAACAACCCCCGGTCCTCCTCTTCGTTGTGGTCAGAAGCCGGAATCCTTGGATCT\n")
-		f.write("TAACATTCATAGGACTGCTAAACTTTAGTTAATAGATTCTGCTGTCTGCAAAAGCTTTATCGAACCAACT\n")
-		f.write("AACAAAATACGATGATCCAGCTAGATGCAGAATCACACACTCCTTTGCATCCAACAACCAAAGCCTAGCC\n")
-		f.write("CTCGTCGTACAAGAACCAGGCCAAAGCAGGATCTTAGTGCCACAATTATCAATACAACAGTAAATTACTA\n")
-		f.write("TAGCTACACAATCTTACAAACTGCAAACAATCCCTTCATTATTCTGGGAGTGTCAAGCTTAGGTTATATA\n")
-		f.write("TCATCGAGTGGTATAAGTCAATTTTATCAATTATCGGAGAGCACGAATTTA\n")
-		f.write("\n")
-		f.write(">gi|226790335|gb|GO545916.1|GO545916 Mdas9005N19_e390.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T15056 photosystem I chain IV - wood tobacco dbj|BAA07667.1| PSI-E subunit of photosystem I [Nicotiana sylvestris], mRNA sequence\n")
-		f.write("AGCACAGAAACAAATATGGCTAGCTGTGGCATCGCATCAGCTGCCTCAGGCTTTGTGGTAGCACCAAATG\n")
-		f.write("TTGCAACCACCAACGCAGGCTCAACTTCTAGCCGAAATAGCATGCTGTTTTTCCCATCAAAACCCAACAC\n")
-		f.write("CAACACCAGAAGCAATGCTAGGTTTGTGACGAGGTCAGCAGAGGAAGCCGCTGCTCCAACGGCAGCCACC\n")
-		f.write("AAGACTGCACCAGAGGGGGAAGCTACCCCTAAGCCTAAGCCACCACCAATTGGACCCAAGAGAGGCACTA\n")
-		f.write("AGGTGAAGATTCTGAGGAAGGAATCCTACTGGTTCAAAGGCATTGGATCTGTTGTAGCTGTGGATCAGGA\n")
-		f.write("TCCGAATACCCGTTACCCGGTCGTGGTCCGGTTCAACAAAGTTAACTATGCCAATGTGTCAACAAATAAC\n")
-		f.write("TATGCTTTGGACGAGATTGAAGAAGTTAAATGAGTTTGTAGTAGCACTGTAAATTGTAATCTTAATTACA\n")
-		f.write("TTCTCCTTCTATCAAAAAAAAAAAAAAAAAACCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790334|gb|GO545915.1|GO545915 Mdas9005B01_e327.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P10748|AROA_LYCES 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (5-enolpyruvylshikimate-3-phosphate synthase) (EPSP synthase) gb|AAA34136.1| 5-enolpyruvylshikimate-3-phosphate synthase precursor (EC 2.5.1.19), mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAACAGCAGAATTGCATTGCAAATTCTTTGAACCAAATACTTAA\n")
-		f.write("CAAACCGAGCAACGTATGCCTTTCTTGACATCAAGTTTGTCCCAAAGAAAGGTACAAAAAAAGACCCACG\n")
-		f.write("AACCAAATCATGAATCACCAATATTGAGTAGAATCAGATCACAAATATTAGAAACAATAACGAGCTCAAC\n")
-		f.write("TTGCAAAGACAAATCATCCAAAATTACAGGGGAATAAAGAGAAACTGAAACAAGTGTGGCTTCCATCTGC\n")
-		f.write("ACTTCTTTGGCTGTAGAGGCACAAGGACAATCCCTCTCTCTCCCTATCTACAGATAAATATATCTTATAA\n")
-		f.write("CCACTGTTCAATGCTTGGTAAACTTCCTGAGGACTTCAAAGTAATCGGGGAATGTTTTTCTGGTACAACC\n")
-		f.write("GGGATCCTTGATAGTAACTGGAACGTCTCCACAGGCAGCAAGAGAGAAAGCCATGGCCATTCGGTGGTCA\n")
-		f.write("TCATACGTGTCTATTGCAGTCAAGTTTAATTTTTCTGGCGGTGTGA\n")
-		f.write("\n")
-		f.write(">gi|226790333|gb|GO545914.1|GO545914 Mdas9005F15_e357.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TTTTTTTTCAGTTAAAATTCCCCATTGATGCATTTTTTGAAGCTTAATTTTACATACAAGTAGGTAGCTT\n")
-		f.write("AAAAATCATCTATTGTACACACTGATTAGGTGTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCC\n")
-		f.write("AAGCGTTGTTGGTAACAGGATCAGCCAGATGATCAGCAAGGTTCTCAATGGGGCCCTTTCCGGTGACAAT\n")
-		f.write("AGCCTGCACAAAGAAGCCGAACATTGAGAACATGGCAAGCCTTCCATTCTTGAGTTCTTTGACCTTAAGC\n")
-		f.write("TCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCTGGGTACAGTGGGTCGG\n")
-		f.write("TGATCTCACCAAGGGGTCCTCCGGCAATGCGGTAACCCTCAACAGCACCCATGAGAACCACCTGGGTTGC\n")
-		f.write("CCAGATTGCTAGAATGCTCTGTGCATGAACTAGGCTTGGGTTTCCAAGGTAATCGAGGCCACCTTCACTG\n")
-		f.write("AAGATTTGAGCTCCGGCTTTAAACCACACTGCTTCTCCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCG\n")
-		f.write("GGAAAACACAGCCCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGC\n")
-		f.write("AAAGGGTTCGGGGTCTGCTGATAGCCCAGCAGTGTCCCATCCGTAGTCACC\n")
-		f.write("\n")
-		f.write(">gi|226790332|gb|GO545913.1|GO545913 Mdas9005G12_e361.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACA\n")
-		f.write("CCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGT\n")
-		f.write("CTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTAC\n")
-		f.write("ATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAA\n")
-		f.write("CTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCT\n")
-		f.write("TGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGT\n")
-		f.write("CCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCA\n")
-		f.write("AATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTA\n")
-		f.write("\n")
-		f.write(">gi|226790331|gb|GO545912.1|GO545912 Mdas9004N12_e313.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTAGTTTCATCTTTTTTCATCATAAAAAGGATTTAAAATAGTTAGATGCCAAAGTGAAATAATTGT\n")
-		f.write("TAAAAGGAGTCGACCATATAAAGTTGACAATGAAATGAAGCAAAAGGGACCCGTTGTGAGTCATCGACAC\n")
-		f.write("GTACTCGCATGCGTGCCTCTCCATTTGTTAGGTAACATTAAAAAGTTAAAACAAAACAATCACTTGGTCC\n")
-		f.write("CCATTCCCCAGTCTCTCTCTCTCTTCCTTTTCAAAATTTGTGTTTATACACTGTACACATAGTTTTATTC\n")
-		f.write("CTCATCCTCTCATTTCACTGCTAGATATTTTTTAATTTTAAAATTTACATTTATACATTGTATAAATTTT\n")
-		f.write("AAAATTTAAACTTATTTAACGATAATAGATAATGATGAGGAAAAAACAATTCTTCCCCATAAAGGATGCA\n")
-		f.write("TAAGATTCAAAAGTCGCGCTGCAATATTATAGAGAAAAGAGTGTTAGTTATTATCCATGTGTACCCTCAA\n")
-		f.write("TTCTAAATTATTATAATTTTTTCTTTTAAAATAATTACTAGTTTGTTTCGATTTATCATTGGATTTT\n")
-		f.write("\n")
-		f.write(">gi|226790330|gb|GO545911.1|GO545911 Mdas9004P11_e321.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n")
-		f.write("CTGCATTGGTGGCCGTGGTGGCGCTGAGTGTTTTCCTGTGTGCCAGCAGCGACGGCGATTACTCGTCCAC\n")
-		f.write("CGTGGCGAAAGTGAAGATTGTGAGGGGGAAGAAGCTGTGCGACAAAGGGTGGGAGTGTAAAGGGTGGTCA\n")
-		f.write("AAATACTGTTGCAATCTCACCATCTCCGATTACTTCCAGACTTACCAGTTTGAGAATCTGTTCTCCAAGA\n")
-		f.write("GAAACACGCCGGTGGCGCATGCCGTTGGGTTTTGGGATTACCAGGCGTTTATCACCGCCGCGGCGCTTTT\n")
-		f.write("CGAGCCTCTTGGGTTTGGGACCACCGGTGGGAAGCTTATGCAGATGAAGGAGATCGCCGCCTTTCTTGGA\n")
-		f.write("CATGTCGGCAGCAAAACCTCCTGCGGTTACGGTGTGGCCACCGGAGGACCATACGCTTGGGGGCTTTGCT\n")
-		f.write("ACAACAGGGAAATGAGTCCCATGCAGTCATACTGTGATGACTATTACAAGTACATATATCCCTGCAGCCC\n")
-		f.write("TGGAGCTGAATACTATGGCCGTGGTGCTTTGCCTATCTACTGGAACTACAATTACGGTGCAGCTGGAGAC\n")
-		f.write("GCTTTGAAGGTGGATCTGTTGAACCATCCAGAATACATTGAGCAGAACGCTA\n")
-		f.write("\n")
-		f.write(">gi|226790306|gb|GO545910.1|GO545910 Mdas9005B05_e329.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGTTGCAAAACGAATAAATTTATTATCTATTTTTCAGTGGCATAACA\n")
-		f.write("AACGATAAGATTTTCTGTACTGTAATCAGTTACACAGCCAGACAATCGATAGAAGAAAAAAAATCAATAT\n")
-		f.write("TATCATGAGGATACACATTCTAAAATAACCCTAAATCATTATTGCCAACATAACAGAACGCTCTTGAGAA\n")
-		f.write("AGTGAACAAATATTACAAAGGTAACATCCCACTGCAACTATATATAACAAGCAACAACTTTTGAGTTACC\n")
-		f.write("TAAGATCCAATTGCTAGCACCATAACAGATGACTGTTATCTCGCATGTACAAGTCAAGACTCCTGGGGCG\n")
-		f.write("TCTCAAATCTCGTTGGAGTGTCAATCCCCATCATACAGCAAATGCCCGATATTAAGATTATAAGCAAAAC\n")
-		f.write("AATTCCAACTAGAAGTCCCTCTAGAAGAGATGATTTTAATAGACAAACTTCATCACAGGCCGTAGAATTG\n")
-		f.write("GCTGATGCATTTCCTGAACCACTTTCGGCCAGAAATCTTTCTAATTCTCGATGAGAAGGATATTGGATCG\n")
-		f.write("ACTTACTGGGATCTGAAACATATAGAACTCCAT\n")
-		f.write("\n")
-		f.write(">gi|226790305|gb|GO545909.1|GO545909 Mdas9005D21_e343.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP43511.1| oxygen-evolving enhancer protein 3 precursor [Pisum sativum], mRNA sequence\n")
-		f.write("TTTTTATTTAATATCACTAGATTTCCTCCAAATAGCATCCGAACAATTTGATCTCACAAACAGTCAAACA\n")
-		f.write("AAGCTCTTAAAAAGCCTTATACATCAAATACATTAATCCCTTTTAGGGTTTAACCAAGCTTTGCAAGAAC\n")
-		f.write("ATCATTGAGGGAAGATACGGTCGCGGCGTAGTACTTCTCTGCTTCCGGGGTGCTCTTGATCTTTGCTGCG\n")
-		f.write("TGGTCCAAGCCGTCAATGTCTTTGAAGAGCTTTCCAGCGAGTTCCTTGAGGGGCTCCTTCTCGGGTTTAG\n")
-		f.write("GTTTGGCAGAAATGACGGTCTTGAGGTCATAACGGAGATACGAGGATCTGAGACGAAGATCGTTCTGACG\n")
-		f.write("TAGGGCCATGCCTTTTTGTCAATGAACTCCTTGACAGCTACAATTTCCTTGGCTGACTCCTTCGCCCGCG\n")
-		f.write("CGGCAGCCTGAGCCGGAGTGAGTGGTTGGAGGAAGAACCTCTCCTTCAACGGCAGGTCAAGGTCTCTTGC\n")
-		f.write("CTCATCCGAGTTTAGGGTTCCAGGCAATCCTCCGGAGGGAGGTGGAGGAGGACCGATTTTGATGGGCTTA\n")
-		f.write("GCCTCGGCAAGCACAGCTTGAACAAATGACCCGGACGCCAAACCAACTGCGACGAGA\n")
-		f.write("\n")
-		f.write(">gi|226790304|gb|GO545908.1|GO545908 Mdas9004L22_e306.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192880.1| short-chain dehydrogenase/reductase family protein [Arabidopsis thaliana] pir|T10561 hypothetical protein F25E4.30 - Arabidopsis thaliana emb|CAB81242.1| putative protein [Arabidopsis thaliana] emb|CAB82146.1| putative protein [A, mRNA sequence\n")
-		f.write("TTTTGAGCAGTATAAGAAGACTATTCAGCTTGAAAGGATATTGTTCAACTTTTGAATTATAAGTTACAGC\n")
-		f.write("ATTCTTGGAGTCTATTATTCAAAAACAAACAACCACCACTACGCATTATCCCTGTAAATAGGGTTGGTTG\n")
-		f.write("TATGAATCTTATAACGACACAATGCAAAGGGCACTTTCTTAAGTCTTTATATAGAGTTTTAAGTTTTACA\n")
-		f.write("GAAGATCATTTAGTCAAATCCATGCTAAAATCCCATAGTTTCTTTGCCATCTCCACGTCTTGACCTTGTG\n")
-		f.write("GCCTTGGCTTGGATAGGTTACAGTCCGAGAAATATTCACCGGTCACCCCCTTGACTTGTGGATGCAGTGC\n")
-		f.write("CACGTAACACGTCGTTGCTGCTCCCTGCTGAACATTTTTAAGCACAGCTCTACCAAGCACGTTAACAAGC\n")
-		f.write("CCGTTAATAATGCTGTAATAACGAAACAGATTGGTAACAATTGCACCAGGGTGAAGCGAGTTTGCAGTAA\n")
-		f.write("TATCAGCTCCTTCTTCCTTTAAGCGTCTTGCAAGCTCATTAACAT\n")
-		f.write("\n")
-		f.write(">gi|226790303|gb|GO545907.1|GO545907 Mdas9005C13_e335.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCTAAACGGAACACGGGAATTTTATTGATAATAAAAAAAAATTTACTTCTAAACAAAGGGACATAAACCT\n")
-		f.write("AACCCCTCCTAAAACAAAAAAAAAGAAATACAAAAAAAAAAGGGGGACTTGCCCCTTACCCCTTTTGAGT\n")
-		f.write("GGCTTCCTAATCGAATCAAGTGCTCAAACAATAACATTGCGAACAATAATAAAAATTACATATTCACGGC\n")
-		f.write("CACACCCTTGTACTAGTGTGAAGGGACCCCCCAAGTAGGCACTACTTGTACTGGGGTTGCCATGTAATTG\n")
-		f.write("ACTGTCCCAGAATTTTCCAACCATCCAATCTCCTCGGGGTTCACCCC\n")
-		f.write("\n")
-		f.write(">gi|226790302|gb|GO545906.1|GO545906 Mdas9004P14_e322.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTACGAGAACAAAACGGTTCATATATTGCATATAACAACTTACACAGACGATG\n")
-		f.write("CATTTCGACGATGGAAAAGAATAGATTTCAAAACCCAGAAAGTAAATAACTTAAGTATGGCAACAAATCA\n")
-		f.write("ATCAACAGTTTACACATTCTCACAGATATGCATCTTCACGAGCGAGGTTCCAAGTAATCCATTAACATCT\n")
-		f.write("ACCTTCGACGCCTTTTTATTAATACTTCACCTTGTAGAGAAGACGGGTTTCGATTTTCCTTCTGAATTTC\n")
-		f.write("TAAGCTGATGGAAGAAGAAGATGGCTTTGATAGGGCAGGCAACCTAACACGATATAGATCTCAAGAAGAT\n")
-		f.write("GCAGTAACAGCAGGCTGGATTGGGTTAAATGCAACCTGCTCGGCACAAGTTAACACTTCATGAGGCCCTG\n")
-		f.write("CCTCGTCTCGGTTGACACCCATAAGGTCCAGGTAGTACTGGTAATGTGAAACGATGTTGTTCATGGCATC\n")
-		f.write("AATGTCACCCTTGCCACAAACTGATTCCCCATAAAGAATATTCATTGTAGTGCCCAATCCAGGAAACCGC\n")
-		f.write("TTACTCAAGGTATCGGTCTTGGTAGGCTTCCAGTCTCCAACAAATG\n")
-		f.write("\n")
-		f.write(">gi|226790301|gb|GO545905.1|GO545905 Mdas9005D09_e340.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF76226.1|AF272572_1 14-3-3 protein [Populus x canescens], mRNA sequence\n")
-		f.write("TCGAGTTCTCTTTTTTTTTTATTTTGAATACATGCTCCCCAATGTTATATCTGGTAAAAAAACAACACAA\n")
-		f.write("GCCATTGGAAATCTGAAGAAACAGTGAAGAAAAACACTAATTTTTAACACTAAATCATATAGCACAGCAC\n")
-		f.write("TCACAGCACTGAACCAAATTCTTCTCACCAATTATAAAACGCAATTTTGCGATCTGTTGGAACATTCCAA\n")
-		f.write("CCCTAGGCTGGAACATTTCAACCCTAAGCGCTGACGCGCTCAAGACCGTCAAGTTCATAGGCAAATCCTT\n")
-		f.write("CTACAACCCACATGGCATCTATTACAAAGGTCCCAAGATAAATGGGTACATAGTACAAATTCTACGAACC\n")
-		f.write("ACAAGCCTCGTTACTGCTGTGTTTCACTGGATTCGCGCTTTGATGCTTCCTTGATTTCGTCCCCAGCATC\n")
-		f.write("ATCCGTGATATCAGAAGTCCAGAGTGTCACATTGTCACGGAGGAGCTGCATGATCAAAGTGCTATCCTTG\n")
-		f.write("TAGGATTCCTCACCCAATGTGTCAAGCT\n")
-		f.write("\n")
-		f.write(">gi|226790275|gb|GO545904.1|GO545904 Mdas9005J14_e374.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTACTTGCAAGGAAACGATAGTATATTCCAAAATTAGCAGTTTACAGAGAAATATAAATATTGT\n")
-		f.write("TTTCAAGAAATTAATATGATTGCAAATGTAATAGGTCCATACATAGTGAGGTAGGATAAATGATGGAAGA\n")
-		f.write("CGCACTGAAATTTGAGGTCCATAGGTTGAGAAGAGTCCATAGCATTGATCCATATATGGATAGCTTGCAC\n")
-		f.write("AGATCACATGCTAGCTGAATCCGAACTCAAAATGACCACGATATTTTCCCAGCAATGATCACAAAGATAT\n")
-		f.write("TGATGCCTGGGACTTCTGTCCATCCCTGAAAACAATGGAATAATATACCCATTAAAAAACGTCACAAAAA\n")
-		f.write("GATTTACAGTAACTGTCCCAACTATTATAATTATATGGTTTTATTGGCATATTCAGACTTCAAAATAAAA\n")
-		f.write("GCTGGCAGTTTGCACTCGTAAACAATTTCTCTTTACAAAACTAAATAAATTGTAATGACCCAAGAAATCA\n")
-		f.write("AAATTTGATTAGGCATTAGAAACAATGTTACCTTTTGGAGAAAAGGATGCTCAACCAAATGGAAGCCCAA\n")
-		f.write("ATTTAAAACAGCAACTGAATGAAAATCTGACGTTATAAAATCCATAAGAAGCGTGTAATGCGTCTAATTT\n")
-		f.write("AAAAAGTCTCTCACACCTGTAATTGCACGTAACGGTT\n")
-		f.write("\n")
-		f.write(">gi|226790274|gb|GO545903.1|GO545903 Mdas9004L20_e305.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD21625.1| putative chlorophyll a/b-binding protein [Phalaenopsis sp. 'KCbutterfly'], mRNA sequence\n")
-		f.write("TTTTTTTAAGGAGCTTGGGAGTTTTTTACTGCATACAGCGGTTTCAATACAAGCAGTTTCTAGTAAAATT\n")
-		f.write("GCATCAGAACTAATGGAGTCCACAACAAGAGAACCTCAACACAAGCAGTAAGTTCGGGTAATGTTACAGA\n")
-		f.write("TGAACGGCCATGGCTTGAGGTTTCTTCACTTTCCAGGGACGAAGTTGGTGGCGTAAGCCCATGCGTTGTT\n")
-		f.write("GGCCACTGGGTCAGCGATGTGGTCGAAGAGGTTCTCCACCGGTCCCTTTCCAGTTACAATAGCCTGAACA\n")
-		f.write("AAGAATCCGAACATTGAGGTCATAGCCAGACGCCCGTTCTTAAGTTCCTTCACCTTCAGTTCAGCAAAAG\n")
-		f.write("CTTCGGGATCATCAGCAAGTCCAAGGGGGTCAAAGGCCCCTCCTGGGTAAAGTGGGTCTAGTCCCTCACC\n")
-		f.write("GAGTGGTCCTCCTCCAACTCTGTATCCCTCAATGAATCCCATGAGCACGACCTGGACAGCCCAGATTGCC\n")
-		f.write("AAGATGCTCTGAGCATGGATAAGGTTTGGGTTGCCAAGGTAGTCAAGGCCGCCCTCAGAGAAGATTTGCG\n")
-		f.write("ATCCAGCCTTGAACCAGACAGCCTCGCCGAACTTGACGCCATTCCTTGACAAGAATTTCTGGGAAGACGC\n")
-		f.write("ATCCCAGTG\n")
-		f.write("\n")
-		f.write(">gi|226790273|gb|GO545902.1|GO545902 Mdas9004N15_e315.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25754.1|AF334834_1 putative chaperon P13.9 [Castanea sativa], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAGTTGAAATTCGTAATCAAATTCGACCCGAAACAGCAAATTAACCG\n")
-		f.write("CCGTATAATATGAATCCCATAAATTTCCATCCATATACAATGTCACAAGACTATATCACTATGCATAGCC\n")
-		f.write("AATGTACACAAGTCCAAAGCTAGGAAGGTTGTGCAGCTAATGGTTTTTTTCATCATTCGGCCGTACTATC\n")
-		f.write("GGAAGTACTCATGAAACCTCCGAGAAACCCAGCTCCGTTGCAATTTCCGCACAACATCTCTTTTCTTCCA\n")
-		f.write("CCGCAGAGCCAGCACGAGTCACCGGCTTTAAACCGTCCACCGAAGAGATCAACAGAGTTCACTCCACTAC\n")
-		f.write("CTTTGCACTGTGAGCACAGAACATTTGCATCACAATCAGGGCAAATCATGCTGTTAGGTTTTACGCTTTC\n")
-		f.write("ATTGCTTTTCTCAGCCTTAGCTTTGAGCTGGTTAAATCTAGCGGCAGGAGAAATTTGCAGCAGCTTATCT\n")
-		f.write("ATTCGAACCAGCTTTTGAGTAGCGCTATGGTTGCCTGGTTCTGGGGTGATTTTCAAGGAACTTGAAGGTG\n")
-		f.write("CCAAGTACAAAGCATAAGCCATTGGAGAATGAGGAGGGAGCTAGCAAGTTATGATGAAAACTAGTTTGAA\n")
-		f.write("TG\n")
-		f.write("\n")
-		f.write(">gi|226790272|gb|GO545901.1|GO545901 Mdas9005B03_e328.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("AATTGTTGTCCTTTACTTGGTACCAAATTTACATCACCGACAACACTACAAACAAAAGTACAAAACAATT\n")
-		f.write("CCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACCGGGTCGGCAA\n")
-		f.write("GGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAATCCAAACATGGA\n")
-		f.write("GAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCATCGGCA\n")
-		f.write("AGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAA\n")
-		f.write("TTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATG\n")
-		f.write("GACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCAC\n")
-		f.write("ACGGGTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCT\n")
-		f.write("\n")
-		f.write(">gi|226790271|gb|GO545900.1|GO545900 Mdas9004K04_e298.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TGACCCAATCCATCAAGCATACAGTCCGAGTCTCCGAGTCTCGGGGAGATATGAATAGGG\n")
-		f.write("\n")
-		f.write(">gi|226790270|gb|GO545899.1|GO545899 Mdas9005G21_e363.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197001.1| seed maturation -related protein [Arabidopsis thaliana] pir|T51442 seed maturation-like protein - Arabidopsis thaliana emb|CAC01816.1| seed maturation-like protein [Arabidopsis thaliana] gb|AAM98229.1| seed maturation-like protei, mRNA sequence\n")
-		f.write("TTCGTCCATGGCGGCGACAGCTCGCGCCGTCATTCTCTCCCGCTTCACCGACCTGTCTCTCAAGCCTTCC\n")
-		f.write("CAGCCGCCGCCCCCGATTACCCGCCACCTCCTCGTCCGCCCCTTACTCCCCTCCTCCTTCCGGCGGCGTC\n")
-		f.write("GTTTGTCCGCCAGCTCGACTTCCGCCGTCCGATGCCTCATGTCCGGCGTCGACGGCGGCGGCGTGTCGGA\n")
-		f.write("CGAGTTCGTCTCGACTCGGAAGTCCGGCTTCGACCGCGGTTTCTCCGTGATTGCGAACATGCTCAAGAAA\n")
-		f.write("ATTGAGCCCCTCGACACCTCCGTTATCTCCAAGGGCGTTACGGATTCCGCCAGGGACTCCATGAAGCAGA\n")
-		f.write("CCATTTCTACTATGCTGGGGTTGCTCCCGTCCTATCAGTTCTCCGTCACCGTTAGGGTTTCCAAAGCCCC\n")
-		f.write("TCTCCATCGCCTCCTCACATCCTCGATAATCACCGGATATACACTGTGGAACGCGGAGTATCGGATATCG\n")
-		f.write("TTGATGAGGAATTTCGACAAATCCACGGAAAATTCTGTGCCGT\n")
-		f.write("\n")
-		f.write(">gi|226790269|gb|GO545898.1|GO545898 Mdas9005A07_e324.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S30151 polyubiquitin 6 - parsley emb|CAA45621.1| polyubiquitin [Petroselinum crispum] emb|CAA45622.1| polyubiquitin [Petroselinum crispum], mRNA sequence\n")
-		f.write("AAAACTAGAAATTATTTATTGATACCAAATTGAGTTTTGATGATTAAAAGTAAAGATAGAACAACCCATT\n")
-		f.write("CACCATCCCAAAGAACAAAACACGGTGGCAGACTGGCCACTCAACACAATTACACCACCATCAGAACCAA\n")
-		f.write("CATATCAAAACAAAACAAACCGAAACTAACTAACAAACTTTCTAGAAATCACCGCCACGGAGACGAAGAA\n")
-		f.write("CGAGATGGAGGGTAGACTCTTTCTGAATGTTGTAATCCGCAAGGGTACGACCATCCTCTAGCTGTTTCCC\n")
-		f.write("AGCGAAGATCAACCTCTGCTGGTCAGGTGGGATCCCCTCCTTGTCCTGAATCTTAGCTTTGACATTGTCA\n")
-		f.write("ATAGTGTCAGAGCTCTCAACCTCGAGAGTGATCGTCTTCCCTGTCAGTGTCTTCACAAAAATCTGCATAC\n")
-		f.write("CACCCCTCAATCGAAGAACCAAGTGCAAAGTTGACTCCTTTTGGATGTTGTAATCCGCGAGAGTCCTGCC\n")
-		f.write("ATCCTCCAATTGCTTACCAGCAAAAATTAATCTCTGCTGGTCTGGGGGGATTCCCTCCTTATCTTGGATC\n")
-		f.write("TTTGCCTTGACGTTATCGATCGTATCAGAACTTTCGACCTCCAGAGTAATTGTCTTCCCGGTCAGGGTTT\n")
-		f.write("TGACAAAGATCTGCATACCACCTCTCAATCGAAG\n")
-		f.write("\n")
-		f.write(">gi|226790245|gb|GO545897.1|GO545897 Mdas9005F17_e358.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TTTTGTCCGATAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGC\n")
-		f.write("TCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTC\n")
-		f.write("CGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTT\n")
-		f.write("CTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTT\n")
-		f.write("CCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAATGGGTCGA\n")
-		f.write("AGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAAC\n")
-		f.write("TGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTT\n")
-		f.write("CCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACT\n")
-		f.write("TAACACCGTTGCGGGACAAGAGCTCTGGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTG\n")
-		f.write("GATCACTTCGAGCTCACG\n")
-		f.write("\n")
-		f.write(">gi|226790244|gb|GO545896.1|GO545896 Mdas9005M13_e382.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTGATGAAAAAACAGGAAGGCGCTCAATATATAAATGGTTTCACCTCGCACATTGT\n")
-		f.write("CTCTCGTGGCAATATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATAC\n")
-		f.write("AATTCATCAGACACAACTGAATTAGTTAACGGTAACTTTACCGACCATGCCAGCTCCCTGGTGAGGAGAG\n")
-		f.write("CAGTAGAAAGAGTATGAACCTTTTTCGGTCAAGGTGACGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGT\n")
-		f.write("CCTCCTCGCTCATCGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTT\n")
-		f.write("GTGTGGGAATCCAGCATTGTTCTTGAACACAATCTTCTCGCCGGGGGCGACGGAGAAGCTGTTGGGGACG\n")
-		f.write("AAGGCCAAGCCCCCGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGC\n")
-		f.write("TGGCTGCGGTGGCGGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGG\n")
-		f.write("GCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790243|gb|GO545895.1|GO545895 Mdas9004M02_e308.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAATAAATTTCCTATTATTAAATTAATATATTGTATTGAATTAAATAC\n")
-		f.write("ATACTATTATTAAATTAATATATTGTATTGAATTAAATACATATTAGTTAATTAAATATTAAATAATATG\n")
-		f.write("AGACTCGAAATGAAAGTACCCTTCTCGCATACATTCCCCATTACGTTGTCGGAACAAAAATATTGCATGT\n")
-		f.write("ATCAATATGGATGGAAATATTTAGTACATGAAATATCGATTTGCTAGATATATAAATAGATATATAAGAT\n")
-		f.write("ATAACTAATAAAACGGATCTTGTGTTCTGGAATTGGAATCAAAGAAAGATATTTAAAATGGCTCGTATGT\n")
-		f.write("TGTGACTTGGAATAAATGTTTCCCGGTAAAGGAAGGGAATAGTAATTTATTCATTCCTAATTTATTCCTA\n")
-		f.write("TAGAACGTCTAGGAACAAGAAGATTAAATCGGATATATCGACAGATTCCCGCGTAGTCCAAAGAAAAAAA\n")
-		f.write("AGATCCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790242|gb|GO545894.1|GO545894 Mdas9005I19_e370.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB09799.1| hypothetical protein [Citrus x paradisi], mRNA sequence\n")
-		f.write("AGGGAAAATCCGTCGCTCCAAACGCCGAGATTTTGGAATGGCCGAAGAAGGACAAGCGCCGATTCCTCCA\n")
-		f.write("CGCCGTGTACCGCGTCGGCGATCTCGATCGCACCATCAAGTTTTATACGGAGGCTTTGGGGATGAAGCTG\n")
-		f.write("TTGAGGAAGAGGGACATTCCGGAGGAGAAATACTCGAATGCGTTTCTGGGATTTGGGCCCGAAGATTCTC\n")
-		f.write("ACTTCGTGGTTGAATTGACGTACAACTACGGAGTTTCTTCTTATGACATCGGCACTGGTTTCGGCCATTT\n")
-		f.write("CGCCATCGCTACTCCCGATGTTAAAAAACTGGTGGAAGATGTTCATGCCAAGGGTGGAAATGTGACGAGG\n")
-		f.write("GAGCCGGGCCCTGTGAAAGGCGGGACGAGCGTCATAGCCTTTGTGAAGGATCCTGATGGTTACACGTTTG\n")
-		f.write("AGATTATTCAGCGGCCCTCCACCCCTGAGCCACTTTGCCAAGTCATGCTCCGCGTTGGTGATCTCGAACG\n")
-		f.write("CTCTATCAAGTTCTATGAGAAGGCATTGGGGTTGAAGCTGTTGAGGACGATTGAGAGGCCCGAATACAAG\n")
-		f.write("TACACCATAGCCATTTTGGGATATGCAGAAGAAGACCA\n")
-		f.write("\n")
-		f.write(">gi|226790241|gb|GO545893.1|GO545893 Mdas9005E11_e347.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564507.1| expressed protein [Arabidopsis thaliana] pir|A96515 hypothetical protein F16N3.25 [imported] - Arabidopsis thaliana gb|AAD46039.1|AC007519_24 Similar to gb|X77136 HSR203J protein from Nicotiana tabacum and is a member of the PF|00, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCGCTTCTCTATAAATTAGAATAGTAAATTCCAATAAAGCGTACAA\n")
-		f.write("TAATCAAGAAAGGGATCAAAGTACAGCAATGAAGTGAGAATGATCACTCTAAAAACGAGTGGTCGAATTG\n")
-		f.write("CTGAAAAGAGCAAATTCAAATTGCAGGTTTTTATTGCTTATTACAGAACTAAAGACTTATTAAAACTACC\n")
-		f.write("ATTAATTTAGAAATATAGAACCCAATTTCAGGCATTTATATATCCTGGTTAAGGAAGGAAGCAATTTTCA\n")
-		f.write("TGAGCAAAGCCACAGCATTGTCTCCAACGGGATTGTTCAAATGGAATACATGGTCCTCCTCCTTAGACTC\n")
-		f.write("CACAACCTCCACATTTCCTCCCCACTCACTTTTCCTCAATAAATCACTATAATACCAACCTCTTTGCCTC\n")
-		f.write("AACGCATCTTGCTCAGCAACACAAACCAGCACTCTCTCTGCCCCTAATTTCGACAGCTTCGGATCCTTTC\n")
-		f.write("CCGGGTTTATAAGCAGGTCATCCGCTCCGCTAGTAGTCGGATAAGCGAACCGCCATATACCCTCAGCCCT\n")
-		f.write("TGCCCTATTCTCAACCACATCAGTCTCACCCTCAATTGGTTCTGACCCCCA\n")
-		f.write("\n")
-		f.write(">gi|226790240|gb|GO545892.1|GO545892 Mdas9004K11_e301.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TGTCTAAGGAAAAACTTCATTGAGCTTTTCAACAGTGAAATGAACCCAACAATGGATACACATATACAGA\n")
-		f.write("GTAAGCTGTTGCAAAACCATTTTAGTGCCGAGACATATCTTTGATAAATAATACAAAAGGAATCTTGAGA\n")
-		f.write("CCTTACTTCCTCTTTCCTGTGCCGATTGAAAGGAGTTCAAAGCTCCGAAGTGTGTCATCACGGCCACCTC\n")
-		f.write("TTGCAGCGGATGCTCGGGTGAAAGATGTTTTGGGTTCATACCCAGGTTGAAACCTTTGGGTGGTGGACAG\n")
-		f.write("GCGGCCACTACTTGAGACCAGCCGGCTTGACCGACTCTCACTGGGCTCACCAAATGAGCTTGGCCGGCTG\n")
-		f.write("CTTGATATGACTGGCCTCCTTGAACTACTGCCATTTCTAGATGAACTACGAGCCCTTTCTGAATCAGCTT\n")
-		f.write("GGACGTCTTTGGACGATGGCGCATCATCGGTCGACCTATGTCTGGAGTGATCGCCATAACCATGACCAGA\n")
-		f.write("ACTATTCCTTCTAGAAAATGCCTCTACTGCACCTGAGAGTCTTTCTCGAAAATCTTGTGCCACTGCTGGA\n")
-		f.write("GGTCTTTCTGTTCTTTCTGCAGATGGTCCAGGGTTT\n")
-		f.write("\n")
-		f.write(">gi|226790239|gb|GO545891.1|GO545891 Mdas9005F14_e356.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179547.1| cytidine deaminase -related [Arabidopsis thaliana] pir|T51733 cytidine deaminase (EC 3.5.4.5) [validated] - Arabidopsis thaliana emb|CAA06460.1| cytidine deaminase [Arabidopsis thaliana] emb|CAA06671.1| cytidine deaminase [Arabid, mRNA sequence\n")
-		f.write("CTCGCCCCCCTTTCCCTTCTCCAATTTCCAGGTAGGCGCCGAAGGGTACGGTTCTTCGGGTCGAATCTTC\n")
-		f.write("TTCGGCTTCAACCTCAATTTCCCGGGTCTCCCCCTCCATTACTCGGTCCACGCCAAGCATTTCCTTGTCA\n")
-		f.write("CCAACCTCTCATTCCAATCGAAATCCAAGCTCCAATACTTCCCCGTCTCCGCTGCCCCCGGCGGCCATTG\n")
-		f.write("CCGCCATTTCATCCAAAAATTCCGCGAACCCCAGAATATCCAAATCCTAATTACTTCGGGGAAATCCGGC\n")
-		f.write("AACAACAATTCCGGAATAACCGTTTTCAACCCGCTCCAACACTTACTCCCCCACCGGTTCGAACCCAAAA\n")
-		f.write("ACCTCCGGGAACAGGACTTCCCCTGGTTCTTAAAGCACCTCAAAAACGGCCGGTCTTTTTTAAGCAAAAC\n")
-		f.write("CAAAAATTTAACCAACAATTTAAAACTGATTGCGAATTTAAAACCCGCGGCTTTAAAGGCCCCAAAAAAT\n")
-		f.write("TCACACCCGCCTTACACCGGTTGCCCTTCGGGGGTGG\n")
-		f.write("\n")
-		f.write(">gi|226790212|gb|GO545890.1|GO545890 Mdas9005I02_e366.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n")
-		f.write("CTAGTATCACATTTGTTTTGCAATGGCAGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCC\n")
-		f.write("GTGCAACTTTCCCCGGGAGCCACCGAGCTTTTTGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCA\n")
-		f.write("AAAAAGTCTCCTCTGGCAGCCCATGGTACGGCCCTGACAGAGTCAAGTACTTGGGGCCATTCACCGGTGA\n")
-		f.write("GCCCCCAAGCTACCTCACCGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCCGGACTCTCAGCTGAC\n")
-		f.write("CCAGAGACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCTCGGAGCTCTTG\n")
-		f.write("GATGCGTTTTCCCAGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAAGCCGTGTGGTTCAAGGCCGG\n")
-		f.write("AGCCCAGATCTTCAGCGAGGGCGGTCTCGACTACTTGGGAAACCCTAGCTTGGTCCATGCCCAGAGCATC\n")
-		f.write("TTGGCCATCTGGGCCTACCCAAGTGGTGTTGATGGGCGC\n")
-		f.write("\n")
-		f.write(">gi|226790211|gb|GO545889.1|GO545889 Mdas9005A11_e325.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CGGCCCATGAACCGGGATTGGAAGCACAAAATGGGGGCCCCAACCTCTCCTCACAAAAAAAAAAAAAAAT\n")
-		f.write("TTCTAAAACCAAAGAAACAGGGTAATAAAATTTTGACACAAACCCCCCGGTAAAAAACACCCCTCCCCCC\n")
-		f.write("CTAAAAAAAACCCCCCGGGCCCCCCAAAAAAAAACTTTTAATTTTACCCCACCCTCAAATTTTTCTCCAA\n")
-		f.write("AAAAATCAACAACCCGAAAAGCCCCCAAAAACACCTTTTAAACCTTTTTTGACAGCCCCCTATCGGAAAA\n")
-		f.write("AAAAAAGAAATCCCCCATCAAAACCTAAAAAAGCAGCGCCTTAGAAAAAAAGAAAAAAAAAAA\n")
-		f.write("\n")
-		f.write(">gi|226790210|gb|GO545888.1|GO545888 Mdas9004O03_e318.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|B86212 protein F24B9.20 [imported] - Arabidopsis thaliana gb|AAF75084.1|AC007583_20 F24B9.20 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTAAGAAGCTGATTAGCTGAACACTGCAATAAGGTGTATAAGACAATTGCTTACAATTGCTAAAT\n")
-		f.write("TGAAGGAACATTGATTGATACGAGAAACTGATTTACGTTCTAATGAATGAAATCCATCAACTGAAACTTT\n")
-		f.write("ACATTCTAAAATATTAAGAGTGTCAATGCTGTGGTAACACCGGTCTCTTCTCCAACAACTCGTAATGCAC\n")
-		f.write("AATAAAATTATCCTTTCGGATAGTTTCAAAGGTATTGGGATCAAAGCAGTGATAAGATCCTCTCTCACAC\n")
-		f.write("GTGTTGGTCTTCACAAGTGGTTCCATGTTGGGTACTCTTATGAACCATAGGCGGTGTTCCTTGTGATAAA\n")
-		f.write("ACCAGCCTCTATTATTTAGTTCATTGGCAGCATATAATTGGGCCTCGTCTTTGGGCATGCTGTAAAAGAT\n")
-		f.write("ATAGAACAACGTTTCCACAGAAAACTTTGAAAAATACCCTTGATGTAGTACAGGCGGTTGTTTAGCATAG\n")
-		f.write("TAACATTGTGGAACAGTAAACTCTGGATCACCCTTAGCCGGCTCGTCAGACCATGGGGAACCAAAAGTCT\n")
-		f.write("TGTGAAGGTTTTCTGTTGAATTCAAGTTTAATCCAAGCGTTGTCAAATCAATTCCAAGTGCAAGAGATGT\n")
-		f.write("AAGATCAGGATCACTCATC\n")
-		f.write("\n")
-		f.write(">gi|226790209|gb|GO545887.1|GO545887 Mdas9005E03_e345.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849293.1| expressed protein [Arabidopsis thaliana] gb|AAL91159.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTCTATCCATTTTGATGAGCAGAAAGCAGAATGGGAAATTGGCAATCCTCTCTCTTAAAAGATCTGGCCC\n")
-		f.write("CGAGCTTCCGGATCTCCTGACGCAGTTTTCTGCCGCTATTGCTGGAACTGGCTTGGCTGTCCTCTTCTCT\n")
-		f.write("GTCCTCTGTAAAGTAGCTTCTGGGAGGGTACCCTTTTGTGCGTACAAACTCTTGAATACTGGAGTTGCAT\n")
-		f.write("TTGCATTAGTTTGGCTCTCTTGGGGGGTGAACAAACTGAGGGACACAATCGTTGAAACCAGCAAGAATTC\n")
-		f.write("ACAGAAGCGGGCTTTAAAAGAACAGGAAATCATGGAAAGGGTAGATAGAAGCGTGAAGGAGATTTACTTG\n")
-		f.write("AGAGCGGGAACATTGATGGCAGTGGCGGTGTTGAGGCTTGCTTGAGCATGAAATGAGAAGAGGAAAGAGA\n")
-		f.write("AAACGTAAAGATGGTTTGAAGAGCATCTGACCGGATGGTGAGTATAAATGTACATATGGTGTCCGATTTG\n")
-		f.write("GGTGATCGTCGGACAGATGAAGCTTGATGGGCATGAGGTGAAGGATCCTTCTTCGAAAGACATTGAATTC\n")
-		f.write("TGATTCCGAATCACTCCACTCCACGGCTGACGGGAACCGGAGCTCCCCTGAGCTCTGG\n")
-		f.write("\n")
-		f.write(">gi|226790208|gb|GO545886.1|GO545886 Mdas9004N04_e311.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n")
-		f.write("CTCGAGTTTTTTTTTTTTTTTTTTCAACAAAAATAGTCTTTCATGGCTATAAAGCATTACACACATTAAA\n")
-		f.write("GATGCATGTCTGGTTCCTCCATTAACATCAACATCATCATCTTCCCTTTGTTCTTCATCATCTACAGCGT\n")
-		f.write("CGGTACAAATTACTTAGTACACATAGCCCTTGACAAACAATTCCTTCTTTGCCTCCTCTGACTCTCCCTC\n")
-		f.write("TCCGGTGTACTTGCCCAGCTGTGCAAGTGAGTTGGCCTTGGCACGGATGAACAAAGCATCCTGAGCTGCC\n")
-		f.write("TTCACGTTCTCCGGTCTGCCTCCCCATGTCTTCAGGCAGGTATTTTGGAAAGCTCTGGCGTAGGAAAAGG\n")
-		f.write("ACACGTGCCATGGGTTTGGTGATTGGTTCATCGCATTCAAGTTCAGGGTTGCCTCAACTTCAAATTGTCC\n")
-		f.write("ACCGGACAAAAACATGATTCCGGGGACAGCTGGGGGGATTCTCCTGTGGAGGAGCTTGAGGGTGTAGTCA\n")
-		f.write("G\n")
-		f.write("\n")
-		f.write(">gi|226790207|gb|GO545885.1|GO545885 Mdas9005B07_e330.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CGGGACTGAGATTCGCCGCATTCACTCTGGTGAAAGGAAGTTGGAGAAACCAAGTGGGAATGTGGTTTTG\n")
-		f.write("GAGAGGCGTAAAAACTTGCCCCCAAACTATCGAATCCCATATAGGAAATTCCAACCCAGACCTCGTCTCA\n")
-		f.write("GACAACATGTCTAAAGAGGCCAAGGGAATCAACAACCAGATAAAGAGGAGAAAGGTAAGCTAGTAGGGTC\n")
-		f.write("ATTTTTGTCTTTTCGATGCGTGTTCTTCGTGTACATATTGGTATGAAATGCAGAAATCGAGTACTGTCTG\n")
-		f.write("TCTGTCTAATACACGACGAGAAGAAGAAGAAGAAAAATAGGCCCTACGTTTGACGGGTAGTGTTGGGCCT\n")
-		f.write("AGGGTGGTAATTAAACCGTAAGCCCGGCCCATTTCTTTTTCCAAGAATTTTTCTTTAAATTTTTTGCCTT\n")
-		f.write("CCCTCCTAAAAATTGGAAAATTGTTGTGTATTTTGGTAAAATGTATGTAGATTCCATTGAGAAAAATGTT\n")
-		f.write("GGCTACATCAGATAAATGTTCTTTTGTAAAAAAAAAAAAAAAAAAACTCGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790206|gb|GO545884.1|GO545884 Mdas9005E10_e346.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCATTCAACACCATCTTGAATC\n")
-		f.write("CGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAAT\n")
-		f.write("AGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCC\n")
-		f.write("ACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTA\n")
-		f.write("AGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGG\n")
-		f.write("TAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCT\n")
-		f.write("TCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATG\n")
-		f.write("CTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCC\n")
-		f.write("\n")
-		f.write(">gi|226790177|gb|GO545883.1|GO545883 Mdas9004K07_e299.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM66084.1| thioredoxin [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTAAACCTTGACGATTTTTCTACATCACGAGATTATACAAAATTACATACTTATGAATGTTTATGC\n")
-		f.write("TGGCTGAGGGAATTGAACACCCTGAAAGGGCTGTGGTATCAGCGGTGAAGCTGAAGAACCTACACATTGA\n")
-		f.write("CACAATCCAGCAAGCATACAGTCCGAGTCTCCGAGTCTCGGGGAGATATGAATATGGTTCCCTTTTATAG\n")
-		f.write("CGTACAATATATGCATTGGCACAAACACTAGCAGGAAAGCTTCCATAGCATATGAGGTCTTACCAATTAA\n")
-		f.write("AACTGCAAATGTAAAACACAAACTCTGATCTTAGACAGAGCGGCATTTCTCGACCTTTTTCTCGAGCTCA\n")
-		f.write("TCCTTTTTCGCTCCGATCACCCGATCCACTTCCTTCCCCTTCTTCAACAGGACGAACGTTGGCATTGCCT\n")
-		f.write("GCACACCGAATTCCCGCGCCACTTCAGATAGCTCGTCGACGTCGATCTTGGCGAACTGGACGTCGGTGAA\n")
-		f.write("CTTGGCGGCCATGGCGCGGATGGCGGGCTCTATGAACCGGCAGGGCCCGCACCACGACGCCGAGAAATCG\n")
-		f.write("ACCACCAGCAGCTGGGAGGATTCCTCATGGGTTTTCAAGTGAAGCTGCCATCTCTCCGACGAGTGAAACG\n")
-		f.write("ACGTCACTCCGGACTCCTCCCCTGCCGAGTCGTCTGCCGGCGCTCCGCCGGCGCCCATCAAGCTTGACAG\n")
-		f.write("AAGGGCCCCCCATCTCTCTCTCTCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790176|gb|GO545882.1|GO545882 Mdas9004O18_e319.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA33810.1| phi-1 [Nicotiana tabacum], mRNA sequence\n")
-		f.write("CTGAAAAACCTCTCCAAAATCTAATAATTTTTCAGAAGAAACAATGGGTTTGAATTCTAGTCAGTGGCTT\n")
-		f.write("ATGAAGCTGTTTGTTGTGGCCACCTTGTTCCAAGTTTCATTCGGTTCCAGCAGGTTGTTCCAAGTCTCGT\n")
-		f.write("TGGCAACAAGGAAGCTGAGCGAGCTTGTCCAAGACCAAACCCAGCTCCTCAAATACCACAACGGCCCTCT\n")
-		f.write("CCTCTCCGGTAAAATTGCCATCAACCTCATCTGGTACGGTAACTTTAAGCCCTCCCAGAAAGCCATTGTT\n")
-		f.write("TCCGATTTCGTCTCCTCCTTGTCCTCCTCCTCCCCTTCCAAAACCCCCCAACCCTCCGTCGCCGCCTGGT\n")
-		f.write("GGAAGACCACCGAGAAATACTACCACCTCACCTCCAACAAAAAGTCCTCCAACTCCCTCTCCCTCTCTCT\n")
-		f.write("GGGGAGACAGATTCTCGACCAAGGCTACTCCCTCGGCAAATCCCTCACCACCAAACAGATTGTCGCATTG\n")
-		f.write("GCCGCAAAGGGTGACCAAAAGAACGCCATCAACGTTGTCCTGACATCCGCCGACGTGGCTGTCGATGGCT\n")
-		f.write("TCTGTATGAACCGGTGCGGTACCCACGGGTCTGCATCCGGCTCTTCCAAGCAGGACACATCAAAGGCG\n")
-		f.write("\n")
-		f.write(">gi|226790175|gb|GO545881.1|GO545881 Mdas9005H12_e365.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTACGGATCTCATTGAATTATGAATTTCTCAATCAACACCCTCTTGAATCCGATTACCAC\n")
-		f.write("CAAATTCAAAAACAAACGACAGTGCCTCGAAAAGGGGACAGAGAATTAAAGAAACAAATACACAGTATGT\n")
-		f.write("CTTGAAAGCCCTATTCATCTACCAACTTGTTCAGACCACCTGGACCCTTGGCTAAGAGCCACATATGGTA\n")
-		f.write("CATACAAGAACAACATTATTTATGAAAATTGTGGAACAACTTAAACGCCTGCAGGCTTGTTTTCGATGTA\n")
-		f.write("GACTGATGCACTGCACTTGACGGACATTGTCCAATCCGATGATCCGGATGAACGATTGGGGGTAG\n")
-		f.write("\n")
-		f.write(">gi|226790174|gb|GO545880.1|GO545880 Mdas9005C09_e334.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197770.1| amino acid transporter family [Arabidopsis thaliana] dbj|BAB10054.1| amino acid transporter [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGGATGAATACATACATATATATATATATATGTGTATATTATATT\n")
-		f.write("CATTTGTTTATGGAGGATATTACAATATTCTTTGTACTTCCCTAGCTCAGTTTGGCACTTATAAGTCCTT\n")
-		f.write("CAACTGATCCAATCACACCCACAACTGTCACAATAAAGCAAGCTATACTAAATGTCCTCAGAACAACCCA\n")
-		f.write("TGTTTTTGTCCAAGCCCCAATTTTCTTCTGTACAAAGTACATTTCTACAGGGAAATATATGGCCAAAGGC\n")
-		f.write("CAAAAGTTCAAGGCCCCTAAAACTCCCAAAACCTGGTTGAAGTAAGGAAACATCATCGCAATTGCGGTAG\n")
-		f.write("TTGACACAACGTAAACAGTACGGAAACAAAGCCTGAAGGGATTCACTTGAAATCTCGGTAACAATGGGAC\n")
-		f.write("TTTGATAGAGTAAAAGTTGTTCACAAATCCACTGCTCGGGTATTTCTTCCTAGACCATCTCTCAGCAACT\n")
-		f.write("GCAAATACTGGTTGACTGAAGATCTGATATCCTCCCACCAAATGAAGAACAATGCAAGCATTGGCAAAAT\n")
-		f.write("CAATGAGCCAGTAGGGTTCGTAGAATCCAAATCCTGTACAGAGGTTCCCTGGCGTGTCATCCCCCAAGGC\n")
-		f.write("GGCATATT\n")
-		f.write("\n")
-		f.write(">gi|226790173|gb|GO545879.1|GO545879 Mdas9005A12_e326.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGGTATGAGGCATACATACCTTTGAACGCCACATGCGTGGCCATTTACCCCAGCATAGCACACTTGA\n")
-		f.write("TACCGAAGCCAAAGCCGAGGCACCCGGATTACAAGCCTACGAAGAACACGGGCAGGTTTTGCTGCTACCA\n")
-		f.write("CGAGCATAACAGCCGTGACGGTGAGAAGTGTATCACCCTTCGTGATCATATTAAAGCTTTGGCACATGAA\n")
-		f.write("GGAAAAATTGATCAATTCCTCATTCACCCTCCAAAGGGTAACCGTAACCAACGCCAGGTAAATGTGATAT\n")
-		f.write("ATTTCATAAGTGGTGGCACACCCATATCTAAATCTTCCAACAGGGCCATGAAAAATAGTGAACGAGTTTT\n")
-		f.write("AAGGTTTGGCCATCAAGTGTTTCACGTGAAAGACATCAAGGGAGGTAAGTATCAAAAGCCTAACTAGGAT\n")
-		f.write("CTAATATGTTTCTACCCTGAGGAAGAAAGATGTATCATCTACCCTTACAACGACCCACTGATCGTGGAAG\n")
-		f.write("CTCACATAGCCAACTTTAAAGTACGATAAATCTTGGTAGACACGGGGGCTTCAGTCAATATCATGTTTGC\n")
-		f.write("TGAAGCTTTTAGGGCACTTAATGTAGCTGAACACTTGCTCGACCGCTCGATTTCCCATCTGATAAGCTTC\n")
-		f.write("TCCGGTGATATCGTGCAACCTTTGGGGGGCATACACTTACCTTT\n")
-		f.write("\n")
-		f.write(">gi|226790172|gb|GO545878.1|GO545878 Mdas9005H09_e364.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTAGCCACTATAAATAATACATTAATATTTATTTTATGAACATGCGTAACAGGAG\n")
-		f.write("TAGGTATCAAATAATAATGCCGAAAACCAAAAACAAAAGACTACTAGCAAAAATTAAAAAAAAAAAAAAA\n")
-		f.write("CTGACTGAACAAGAACATATCTGAACCCGAT\n")
-		f.write("\n")
-		f.write(">gi|226790171|gb|GO545877.1|GO545877 Mdas9004O02_e317.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n")
-		f.write("TTAGAATCAAGGCAGATATGGATTATTTTACGTCAATGGGACAATCCCATTCAAATATGCAACTAAAAGA\n")
-		f.write("AGAAAAAAGTCGAAGTGTCCGAATAGAATATTGGGCTCAACAACTGTAAAACCCACAAAAGCAGCTTCTG\n")
-		f.write("CATCATTAACATATCTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTGCTTTTCTCACACATTG\n")
-		f.write("CAGGGAGGCCAACTTACAACCACACCAAGGAAAGGCCAAGAGCATCTAAGAGAGGCAAGAGTATGCCAAA\n")
-		f.write("GCTTTCTCCTCACTGAGCTCCTCTGCAGTTGCATCCAACTTCTTCCTCGAGAACTCGTCAATAGAGAGTC\n")
-		f.write("CTTGAACAATCTTCCACTCCCCATGTTGGCAAGTGACTGGGAATGAGAAAATGAGACCAGAAGGTACATC\n")
-		f.write("GTATGAGCCGTCAGAGTAAACACCCATGGAAACCCAAGTGCCCTCCGGGGTTCCAAGTACCCAATCACGA\n")
-		f.write("ATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGATGATTGCAGCAC\n")
-		f.write("CACGTTGTTGAACAGTGGAAATGAATTCTCCATTTCACCATGCATCATCAGCAACAAGCTCACGGACAC\n")
-		f.write("\n")
-		f.write(">gi|226790170|gb|GO545876.1|GO545876 Mdas9004O20_e320.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCTGTCTCATTCTTATTGAATCTTTTGAAAGCATCTCGGAACTTCCTGCATTTGCTTTATATTGCTACAT\n")
-		f.write("AATCACTTTCTATCAACTTTTCAAAGCAAGAGAATCTCACTTGTGAGATTCAGTGTTCACTTGTAGAGCC\n")
-		f.write("AACATTGATTAATACTAGTTAAAGTGATCGATCATTCACGTCCCAAGGCACAGGTGCAGG\n")
-		f.write("\n")
-		f.write(">gi|226790051|gb|GO546188.1|GO546188 Mdas9009O17_e711.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("AGTTCCCATGAAAAATCTGGAGTTGTGAACTGTAATAAAAAAATAATAAATATGACAGTAAATTGTATAA\n")
-		f.write("TCTAACTTCCATGGATGTACAAGTTTTCAAGATCAAGTTAAAATTCCCCATTGATGCATTTTTTGAAACT\n")
-		f.write("TAATTTTACATACAAGTAGGTAGCTTAAAAATCCTCTATTGTACACACTGATTAAGTGTCCTCCCTTCCC\n")
-		f.write("GGGCACCAAATTGGTGGCATAAACCCCAGCGTTGTTGGTAACAGGGTCAGCCAAAAGATCAGCAAGGTTC\n")
-		f.write("TCAATGGGGCCCTTTCCGGTGACAATAACCTGCACAAAAAAACCCAACATTGAAAACATGGCAAGCCTTC\n")
-		f.write("CATTCTTGAGTTCTTTGACCTTAAACTCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAA\n")
-		f.write("GCT\n")
-		f.write("\n")
-		f.write(">gi|226790050|gb|GO546187.1|GO546187 Mdas9001P02_e83.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD37374.1|AF145348_1 peroxidase [Glycine max], mRNA sequence\n")
-		f.write("TTTTTTTTCTATATAACCATCATCGTTGAAATCCATACATCAGCATACATGTTCAAAGTTCAAATCATCC\n")
-		f.write("ATCCATACATACACACATCCCGACATATCCACCATGCCCATCTCACCCAAAGAGAAGAAGCCAAAAGATA\n")
-		f.write("AAATCGAAACCCTAAATCAGACACAGTGCATCATGAACAAGGGCCACATGAACAACTGACCACATGCATG\n")
-		f.write("CCTTTTAACCCTAGCACTGACCAACTTCCATAAAAACAAAACATACATATTGGTTAAAAAAAAACCCTTT\n")
-		f.write("TATTATCCAGCAACTTGCCCCACACACATTTTCTCCCCTAATTACATAACTAAAGAAGAAAAGTGCTTCC\n")
-		f.write("TGACAAGGCTGCTTTTTGCTCTAGTCCCGGATCTTATTGGCAACATTGCACTGCTGTCGGATCTCGCCCT\n")
-		f.write("TGTTTCCGGTGAGAGGGTTGTTCTCGGAGAGAATGGTGAAGGCTCTCGAAAAC\n")
-		f.write("\n")
-		f.write(">gi|226790049|gb|GO546186.1|GO546186 Mdas9001G06_e33.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGCTGCTCCCGCGGCGAGAGCGGGCCGCCGCGTGCCGGCCGGGGGAAGGACCGGGAACGGTCCCCTC\n")
-		f.write("GGGGGCCTTCCCCGGGCAGCGAACGTTCAGCTCATAACTGGTACGGACAAGGGGAATCCGACTGTTTAAT\n")
-		f.write("TAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCCGTGCTCTGAATGT\n")
-		f.write("CAAAGTGAACAAATTCAACCAAGCGCGGGTAGACGGCGGGAGTAACTATGACTCTCCTACAGTACCCAAA\n")
-		f.write("TGCCTCGTCATCTAATTACTGAAGCGCATGAATGGATAAACGAC\n")
-		f.write("\n")
-		f.write(">gi|226790048|gb|GO546185.1|GO546185 Mdas9001J10_e56.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCTTTTTAATTTAGAGCAAAATCTGAGATCCCCGAATCACATTAATTTAATAC\n")
-		f.write("\n")
-		f.write(">gi|226790047|gb|GO546184.1|GO546184 Mdas9001H16_e42.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB64719.1| AKIN beta2 [Arabidopsis thaliana] gb|AAK25958.1|AF360248_1 putative kinase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTGCAAAAGCGGATGGATCAATGGTCATTAAGCAATGGAATTGTGTGAAAATACAATCCTGAAGTTTC\n")
-		f.write("ACCTGAAAAATTCTTCCTGAACATAAACCGACGCCATGGAAATGGCATTTGACTTTGAAATTGATATAAA\n")
-		f.write("ACTAACTACATAATGGGAACCGTGGAGTCCAGACAGACACTTTGTGTGTGTATGTTTTTTTATCTCTGCA\n")
-		f.write("AGGACTTGTAGAGAACCACTGTAACATACTTCGCTATAAACCTCTCTGTTGTACCGAGTGCCACCACAGA\n")
-		f.write("TGGTCCACTCTTCCCTCTCTGCATGTAAAGATGATTGAGTACCACATGTTGAGGTCTTGACAAAGGAGGC\n")
-		f.write("GGCATCTCCATGTAAGATGAAGGTGCATTCAGCAGTGTCATTTGTAGGTGTGGAGGAACCAATGGGGGCT\n")
-		f.write("CCTTCGCGAAATCTTCAGATCCAAGCTGCAGGTTGTTATAACTTGATTCCGGCGACTGGGGAGGTTTCAA\n")
-		f.write("ACCAGAAATGCTGCCGATGTCTTCTGGGACGTAATCCTGCAAGTCCAAAAGGTTGTAAGAATTGCCAGCA\n")
-		f.write("TCA\n")
-		f.write("\n")
-		f.write(">gi|226790046|gb|GO546183.1|GO546183 Mdas9001D24_e23.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P52765|NU3C_LUPLU NAD(P)H-quinone oxidoreductase chain 3, chloroplast (NAD(P)H dehydrogenase, chain 3) (NADH-plastoquinone oxidoreductase chain 3) gb|AAB86905.1| NADH-plastoquinone oxidoreductase [Lupinus luteus], mRNA sequence\n")
-		f.write("TTTTTTTTTTATTGTTTGATGACTATTCAAGAGCTAAGACCATTCCAATGCTCCTTTTCGCCATGCATAA\n")
-		f.write("ATTAAACCAACAATTAGGATAAGCACGAAAATTAAAGCTTCTATAAATACGGATACTCCCAATACATCGA\n")
-		f.write("AACTCATTGCCCATGGATAAAGAAAAACCGTTTCAACATCAAAAACAACAAAAACTAGAGCAAACATATA\n")
-		f.write("ATAACGGATTCTAAATTGTAACCAAGCATCCCCCATTGGTTCTATTCCCGATTCATAACTCGAAAGTTTT\n")
-		f.write("TCTGGTCCTTTGCTAATCGGGGCTAAAACTCCGGAAATTAGAAATGCCAAAATAGGAATAACACTTGATA\n")
-		f.write("CTATCAGAAATGCCCAGAAAAAATCATATTCGTAAAGCAGAAACATAGACGTACTCCTATTAATGTGGAA\n")
-		f.write("AATATACCGTACTAGTCGATTCGAATTAGAATAAATTGTAAAATAATCCATAACTGTTTAGTCAAAACAA\n")
-		f.write("CAATTTATTTTGATCGAACCGCCCAGTTTCTTTTGTTTGCTGCGGTACATGTCTTGTTTCAAGAAT\n")
-		f.write("\n")
-		f.write(">gi|226790045|gb|GO546182.1|GO546182 Mdas9001D05_e20.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL36317.1| unknown protein [Arabidopsis thaliana] gb|AAM20042.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("AAACATTAGCATTCACCATTTCATGAAAATTTCAAGTTGGAGTTTGGATTTAATCCAATCTATTACACAG\n")
-		f.write("ATTTCACACAATGAGATACAGAGCAAGTCTATTATCTGACTAGCGAGTACCAACGACGGAACACAAAAAA\n")
-		f.write("TACACCGAGGTGAAGACGAACATTTAGCATTAATAAGCTGGAGCCGGAACTTTAAAGTACGATCGACACA\n")
-		f.write("AAACCCAAATGTGGGGAAAATAAAACCCTAATAGAAACCTAACGATTGTATTTGTATCTTTCGTTGTCGA\n")
-		f.write("AGCGTCAAACACATCCAAAGAACTGTTCCAAGGATGGGGCGTTGAACACATTAGAAGCAGGTCGTTCTGT\n")
-		f.write("TCTGGTAGGAGAGATGTGAAGCTGATACTTGATGAACCTAGATAATTGAAATATGATGTCAGGATTTGTG\n")
-		f.write("TCGATATGCCAATCTGGTT\n")
-		f.write("\n")
-		f.write(">gi|226790032|gb|GO546181.1|GO546181 Mdas9001A11_e2.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTATGTAACCCTGCTTAACATTATCAGAGACAGCAACATAACACAGCAGAATTATAGATACTCGATGG\n")
-		f.write("AAACAAAAGATAGCACTCTGCCACAATAATAACCTCAAATAAACACATAGGAGCGCACCGATGGCCAGCC\n")
-		f.write("ATTATCCGTTCAAAGATCTAATAGACAAACTAAGCAGCTAAATGCTACAGAATTCTTAATTAGCAATTAC\n")
-		f.write("TAAAACCTTAAGCATGGTCTTTCTAGACATCAACACAAGCATCTCGACTTGCTATACCTGATCCAACGTT\n")
-		f.write("CTAATGGTCGGATGACTTTAAAGCCTCCAGAATCACCTTCGTCTGATCTCTCATTAACTCGGACCGCTTC\n")
-		f.write("ACAAAAAGCTCCAATTCCGCAACATGCAGCTTCCTCCATTTCTCCTTCAACTCAGCTCGCTTGGGCCCTC\n")
-		f.write("CAATCAACTCCAAACCCTGTTTCACCACACCCTCCGGCAACCCCAGCTTGCCGAAACCCTTGTCAAACCC\n")
-		f.write("AATCACCTCACTCAAACTTTCCGAAGAGCACGGGTTCAGACCAAAATCCACCTTCGCAGCCTCCTTTGGC\n")
-		f.write("GGCTCCGGTGAGCTCAAACTATCAGCTCTTATCGAAGCGAGAGTCTTGGTATTTCTAGCTTTCCCATTAG\n")
-		f.write("ACTTTGGCTGTTCAGACACCCCGCTGACACCACTCGACCCCTCCCCGCTACTGCTGCTACCCCAT\n")
-		f.write("\n")
-		f.write(">gi|226790031|gb|GO546180.1|GO546180 Mdas9009P23_e715.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK50586.1|AC084404_11 putative translation initiation factor [Oryza sativa], mRNA sequence\n")
-		f.write("TCGAGCAATCAAATTATTAGTTCTTGATGAATCTGATGAAATGTTGAGCAGAGGATTCAAGGATCAGATT\n")
-		f.write("TATGATGTCTACAGATATCTTCCTCCTGAGCTCCAGGTTTGCTTGATTTCTGCTACACTTCCTCATGAAA\n")
-		f.write("TTTTGGAGATGACCAACAAGTTTATGACTGAACCTGTAAGGATCCTTGTTAAACGTGATGAGTTGACGTT\n")
-		f.write("GGAGGGAATCAAGCAATTTTTCGTGGCTGTCGAAAGAGAGGAATGGAAGTTTGATACTCTTTGTGATCTA\n")
-		f.write("TATGATACCCTTACGATTACACAAGCTGTTATTTTCTGCAACACCAAGCGAAAGGTGGACTGGCTCACCG\n")
-		f.write("AAAAGATGAGGAGTAATAACTTTACTGTCTCTGCAATGCATGGAGATATGCCTCAGAAGGAAAGAGATGC\n")
-		f.write("TATTATGGCTGAGTTTCGTGGTGGTAATACTCGTGTCCTGATCACAACCGATGTTTGGGCCCGGGGCCTT\n")
-		f.write("GACGTTCAGCAGGTTTCTTTGGTTATCAATTATGATCTCCCAAACAATCGAGAGCTATACATTCATCGAA\n")
-		f.write("TTGGTCGTTCTGGACGTTTTGGGCGCAAGGGTGTGGCAATAAACTTTGTGAAAAGTGATGATATTAAGAT\n")
-		f.write("TCTAAGAGACATTGAGCAGTATTACAGTACGCAGATTGACGAAATGCCGATG\n")
-		f.write("\n")
-		f.write(">gi|226790030|gb|GO546179.1|GO546179 Mdas9001C04_e13.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567130.1| membrane protein -related [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTATTACAAAGTCATTTTTATTCATCACTAAAAGATGCTATTGGTGGCAAGAACAAATTTTCGAT\n")
-		f.write("AGCCATATAATGTCTTTGAATGAGCGGAACGGACTCAACAATTGCCTACCAAAACAAGAAGCAAGTATAC\n")
-		f.write("ATCATCTTAAGTGTGTTGTTTTTGGAAACCGAGAAGAAAGCCCCCATAGAAAAGGGGAAGTTGGGGTTTT\n")
-		f.write("ATTTTCTTAGAGATCAAGTCTACCAGCCAAGTACCACGAGTGCATAGCAAGGCTGCCAAATGCGAAGATG\n")
-		f.write("TTGGCAAGAGATGATAGCCCGTGAATCATACCAAACTTCTTATTCATGGCTGCCAGTTTTGGGTTTACCT\n")
-		f.write("TTGCAACTTGCACATTCTTTGACCATCCAACTTCTTCCCCAATGTTCTGCTCCCTCTCCACCTTATGCCT\n")
-		f.write("TTGCTTCATCATCTCGATGGTCATGGGAGTGAAGACGAAGAGATTGGTGAGATTGAATGCAAAGGCAGAG\n")
-		f.write("AGCAAAAAGCCGAGCTGGTACTTGTCGGCAACAGAGGAAGAGCTCCACGGATGCAAATACCCAAACGACC\n")
-		f.write("CAGCTGATACTGCAAGGCATATCCCCACCATCGTGAAGTACGCCGGAAACATCTTGCTCTGAAGATTCCC\n")
-		f.write("GAACTGATGCCGCGGAAGATTCTTTGACATGATGATGCCGCCTATG\n")
-		f.write("\n")
-		f.write(">gi|226790029|gb|GO546178.1|GO546178 Mdas9001M08_e69.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC77927.1| similar to chloroplast 50S ribosomal protein L31 [Medicago sativa], mRNA sequence\n")
-		f.write("ACAATGTAATTATGTAAATTAAATTAACAAAAAGGCAGGTATTAACGTAATAAACACAGATAGGCACTGA\n")
-		f.write("ATTCTACTCAATTTTCATGCTTCACCTATAATCTTACATTGAGTAAGCAAAGCATTGGCCTTTTCTACTT\n")
-		f.write("CTTCTTGCCCCCTTTACCGGCGGCGGCCTTGCGGCGGGAGGGCAAAACAATCTCTCCCTTGAGGACAGGA\n")
-		f.write("ATCCCCATGATCTGGGTGAACTCGCCGTACTTCTTCCTGAACTTCTCCACCTGGTCGTCCTCCACGAACA\n")
-		f.write("TGCCCGACCGGTTTCCGAAGTAAAAGGGGTGGTTGCCCGACCACACGTCCACCACGTACTCCTTCTGGGT\n")
-		f.write("CCCCCCCGGGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226790028|gb|GO546177.1|GO546177 Mdas9001L01_e64.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567980.1| protein kinase family [Arabidopsis thaliana] gb|AAL27496.1|AF439824_1 AT4g35230/F23E12_210 [Arabidopsis thaliana] gb|AAM98327.1| At4g35230/F23E12_210 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTGCAACAAAAGGCGTTTCTGTGTAAATACATTCTCAACGGTAAAGACAATTTGGATTCCCAGCTC\n")
-		f.write("AGATTTTATACAAATTACGTGTAGCCTCAACAACAATTGTCAACTGGCAATGGTAAATTATGGACTATCA\n")
-		f.write("CTCATTAGTTATTAAAGAGTTGATCCTCATGATCCCCGGCCTCCTCGCTGCTTCTTTTCTTCTAGCGCAG\n")
-		f.write("TCGCTTCGTTCAACATGTCAGCGGCATCCTTGTGCATGTCCAGCTTGGCTAGAGCAACTGACTGCATGTA\n")
-		f.write("GAAGGCTGTGGGCCACTCAGGATAGACACATTGCGCTTGCATTGCATCTCGAAGGGCAGCATCTGGTTGC\n")
-		f.write("TCATTTAACAGGTAGCATAAACTGCGTCGGGCAAAAACAGTTGGCGAAACCATAGTTCCAACATCTATGA\n")
-		f.write("ACTGGGAGTAACACTCAATGGCTGCTTTAAAATCTTTGTCCCGAAATGCATAATCCCCTCGTTTCCTTGC\n")
-		f.write("CTCCAACATGTCTCTCATCTGTTGAGTCCACTCTTGGAAAGATAACTCATTGGTTCCTTCATCATCTCTG\n")
-		f.write("TAGTGCGTCATAACCAAGATCTGATGGATTGCTGTGAG\n")
-		f.write("\n")
-		f.write(">gi|226790027|gb|GO546176.1|GO546176 Mdas9001J09_e55.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTACTATGCGGTTTTTATTATCAAAATAAACAGCAGGAACTTGTAAGGGAAAATTAGACACTCTCTTTAC\n")
-		f.write("AAATAACAGCAGAGATTATGCAGACTTAGCAACATGGAAACCCTAGCAACTCGGAACGAGCACACCCGAA\n")
-		f.write("CCCTAGCAACAGCGGAGATTCAACCACTATACTTAGATAGTCGCACATGCACTAGATTGCAACTCAGAAC\n")
-		f.write("AAACAACACCCAAAACCCTACGTGGAAACCCTAGACAGTTTCTTTTTTCCTTCCAGCCATGGCTAAACCG\n")
-		f.write("TCCGCAGAAAACATGTACATCTCATCGCATGCCGTGAAGAGGGCTCGCATCTCAAATCTCACGGATGAT\n")
-		f.write("\n")
-		f.write(">gi|226790026|gb|GO546175.1|GO546175 Mdas9009P04_e712.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n")
-		f.write("ACTCATTTATTAAGTACCAAAAAAAATACAAGGGCCGTTTATTATATTTTCCTTTGCAAGGCCTAATGCA\n")
-		f.write("AAGGGCAAATAATGAATTTTTCAAACTACCAAATAAATGACCTTCTGGAAAATTATATGAACCTCATTTT\n")
-		f.write("ATTGTAAGTAAAATTCACAAAATTTTCCATTTCCCTTCCGTTAAACACCCTTGAAAAAATTTGCGAAGGC\n")
-		f.write("ACCAATTCAAAGGTTTTTGAATGGCACGCTTATGCATACACGTCTAACCCCCAAGTCTTGAAAGGAAAAC\n")
-		f.write("TGGAACAATACTTCCTGTCAATACTGAAAATGACCTGCATGTCTTCATCCCTCACCTGGAATTCAAAAAC\n")
-		f.write("CTCCAAATTCTCTTTCAATCCCTAAATTTTCAATGATTTTGGAATCACTGCTGTTTTCCTCTGAATTCCC\n")
-		f.write("CACCTCAAACAAATTTGTGCCACGCTCTTTCCGTATTTCTTACCCCCATCATTGAAAACTGGATCATCCA\n")
-		f.write("AAGGTGAAACAAAACCAAACATATCCTTGTTGGCACCACCCCCTC\n")
-		f.write("\n")
-		f.write(">gi|226790011|gb|GO546174.1|GO546174 Mdas9001B10_e8.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTACCCGCCGCTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGACC\n")
-		f.write("ATCGACATGAGCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAAGCGTCG\n")
-		f.write("CTTCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGC\n")
-		f.write("TTTTCAACCAAGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTG\n")
-		f.write("CGACGCTGTCATCACTAGGGTA\n")
-		f.write("\n")
-		f.write(">gi|226790010|gb|GO546173.1|GO546173 Mdas9009N17_e707.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTTAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAA\n")
-		f.write("ATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTG\n")
-		f.write("AAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATAC\n")
-		f.write("AACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGACACTGA\n")
-		f.write("TGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGC\n")
-		f.write("CTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAG\n")
-		f.write("TACCTTCCATCATAGTATCCTGCGGATCTGTGGTTCTCACGGTACACGAA\n")
-		f.write("\n")
-		f.write(">gi|226790009|gb|GO546172.1|GO546172 Mdas9001L14_e67.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB87573.1| chlorophyll a/b binding protein of LHCII type I precursor [Panax ginseng], mRNA sequence\n")
-		f.write("TCAGCATCTCCTCTCTCTCTCTCTCTCTGTCTCTCAGCCTCTCTCTCTCATCCCCAATGGCAACTATGGC\n")
-		f.write("CCTCTCATCCCCATTCACTGGGAAGGCCATTCCTCTTAACACACAGACAGAGTTCTCAGCTGTCCAAGGA\n")
-		f.write("AATGGTAGGGTTTCTATGAGGAAGACGGGCAAAAAGCCTGCTGTCTCATCAGGGAGCCCCTGGTACGGCC\n")
-		f.write("CTGATCGTGTCAAGTACCTCGGACCATTCTCCGGTGAGGCTCCATCTTACCTAACCGGTGAATTCCCCGG\n")
-		f.write("TGACTACGGGTGGGACACTGCTGGGCTATCAGCAGACCCCGAAACCTTTGCCAAGAACCGTGAACTTGAA\n")
-		f.write("GTCATTCACTCAAGATGGGCAATGCTTGGTGCTTTGGGCTGTGTTTTCCCGGAGCTCCTCTCCAGGAACG\n")
-		f.write("GAGTCAAGTTTGGTGAAGCAGTGTGGTTCAAAGCCGGAGCTCAAATCTTCAGCGAAGGTGGCCTTGACTA\n")
-		f.write("CCTTGGAAACCCAAAGCCTGGTTCATGCACAGAGCATTCTAAGCAATCTGGGGCAACCCCAGGTGGGCCT\n")
-		f.write("CAAT\n")
-		f.write("\n")
-		f.write(">gi|226790008|gb|GO546171.1|GO546171 Mdas9001A24_e7.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AATGGTCGAAACGGACAGAAAACAAGAAAGAGGCCCCACAACAATGAAGCCCAAAAAAAAACACAGAACA\n")
-		f.write("ACCCACCGAGAAGCTTCTGCTCAAATCTCCTCCACCGACAGAGATCCAAGCCAGCCACCGGAAACGTCAT\n")
-		f.write("CCATCACCGAGCATCGCCGCCTCAGACAACACCGCCAACCCCGAACAGCAACCAGATCACATC\n")
-		f.write("\n")
-		f.write(">gi|226790007|gb|GO546170.1|GO546170 Mdas9001O20_e81.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GGCAAAAATTAAAATTTGGTTGGAAAACAATAATATCTTAAAAAGCAAAAATATTTGACTACTAAAAAAA\n")
-		f.write("CATAGGAAGAGGGGAATAAGGCCCTGAATTTACAAAAGGGCGGATTCGGCTCCCAATTCCCCCAACTTTT\n")
-		f.write("TTGCCATAAATTACAAAGGACTCTCCCTCTCTCTATCACCTTAACACATCCCTTGCTCTCCATGAAGGAT\n")
-		f.write("TAAAACCAAAACAAAAAGATTAAAACTAAATTTAAAAAACAGACGGCCCCGGCAGACACACCGACACCAA\n")
-		f.write("ACTAAAG\n")
-		f.write("\n")
-		f.write(">gi|226790006|gb|GO546169.1|GO546169 Mdas9001I10_e47.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO72532.1| aldehyde dehydrogenase 1 precursor [Lotus corniculatus], mRNA sequence\n")
-		f.write("TCCCACAAAACAGTATAACATCTTTCTATCACCACAAACTAGTCAACTTCTTTCGATTACGGATTACAGA\n")
-		f.write("CAGACTTTTTGTATCTTTATTATTTGAAACCACACAGATCGGAGCATATGGTTCGGTCGAGAGATTTTAC\n")
-		f.write("AGCCATGCCGGATTCTTCAAAGGAGTGACAACAGCCTTCACCTGCAAGTAGTTGTGAAGGCTGTAGATTC\n")
-		f.write("CCTTTTCTCTGCCTATTCCACTCATCTTGTATCCGCCAAAAGGAATCGCAGCATCAAACACGTCGAAGCA\n")
-		f.write("GTTCACCCAGACTGTCCCAGCCCTCAATGCCCGTGTCAAGTAGTTGGCGGTGTTAATGTTCTTTGTGAAT\n")
-		f.write("ACTCCGGCAGCTAGACCATAGCGCGTTGCGTTTGCCCTTCGTACCACTTCATCGAGCTCCTTGAATTTCA\n")
-		f.write("\n")
-		f.write(">gi|226790005|gb|GO546168.1|GO546168 Mdas9001N03_e74.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AGACCGACTTCCCTTCTCTCTCTCTCTCTCTCTCTCTTCTCTTTCTCTCTCTAAAATCTCAGACACCAGA\n")
-		f.write("AGTGAACTGCTGCTGCTGCTGCTGCCCCCGCCGCCGCCGCCGCCGCCGCCGCCGTATACATATAAATGTA\n")
-		f.write("TCCCACAAACTCATCCTCCTCGCCTCAAAAGCCCATGGCCCCGAGACCAAGCACAACGGGCCTGACCCGC\n")
-		f.write("TACGGCTCCGCCCCGGGATCCCTCCTAAACTCAGCCGTGGACTCCGTCATGGGAGCCGCCGCCGACCGCG\n")
-		f.write("AATTCTCATCCCTCCGACCGCAGCACCTACGAGGCCACTACTTCTCCGGAGACGGTGGCGGCGACTCTCC\n")
-		f.write("CTCCCTCACTGGCTCCGAGTCCAGCTTCAAAGTCAACTCATCCAACGGCAGCCACAGGGACACCAGCACC\n")
-		f.write("ACCAAGCCATTGCTCCAATCGCACGGACGGAACGAGATTGGATCTTC\n")
-		f.write("\n")
-		f.write(">gi|226790004|gb|GO546167.1|GO546167 Mdas9001H13_e40.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCGGATTTTATATTCCTTTTTTATAACTGCAGAGACGGAGAGATTTACAAGACTACCCCTACAGACCAAC\n")
-		f.write("TAGACTCTCTTCCTCTCTAAACTCTCTCACTTCCTTCCTCTGCGAGCTGGAGCTTTCCTCGCCGGCGACT\n")
-		f.write("TCACGCTCCGCGCAGGAGCCTTCTTCGGAGCCGACGCTTTCTTAGGGGCAGGCCGGGGGGTCGGAGCTTT\n")
-		f.write("CCTTCCGGGAGACGACCTCGTCAGCGTCCTCGACACCTTGGCTGGCTTCTCCTTTGGCTTCGGCTTCGGA\n")
-		f.write("GCAGCCGCCTTGGGCTTGGCAGCAGCAGCTTTTGGCTTGGCGGCCGCGGGTTTAGGCTTGGCGGCGGGTT\n")
-		f.write("TAGGCTTGGCAGCAGGCTTAGACTTAACCGGAGCAGCCGCTTTGGGCTTCGGAACAGCAGCTTTTGGCTT\n")
-		f.write("ATCTGCGGGCTTTG\n")
-		f.write("\n")
-		f.write(">gi|226790003|gb|GO546166.1|GO546166 Mdas9001I19_e50.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAACACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACAT\n")
-		f.write("ACATACATACATACATAGATGGCATGCTAAAAGAAAACCAGATAGCACCCATTAATTGAAAAGGACATTT\n")
-		f.write("AACCACTCAACTATTGTAGCGATATTGTTGAGATTAAGCATCACACTCTCACTGATCACACCACATGATA\n")
-		f.write("ACTAGTAAAAACACAACATTGCATATGTAGTCAAAAGATGATGTTCCACAATCCACATAGATCTAGAAGT\n")
-		f.write("GGTGGTGCTTCTTCTTTCCATAAGCCTCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATG\n")
-		f.write("GAAGGCAAATCCACCCGAACCAACTGCAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCA\n")
-		f.write("TGCTCTGGGTCTTTCTTTTCATTGTGCTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCTACACCGGCCT\n")
-		f.write("CGCCGAGGTGCTCGAGA\n")
-		f.write("\n")
-		f.write(">gi|226789990|gb|GO546165.1|GO546165 Mdas9001G03_e32.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTTGAATCCGAACCGTGCACTTGTAGAATACATTTGAAAGTAGTGTGAAAACGAACAGAAGCCTAATTCG\n")
-		f.write("TTATGAGCAAACGATAACCCGCTGGGCCAGACAACCGAAAAAGAATGAAAGAAAACCCTAACTTGTATTA\n")
-		f.write("TACACAAACAATAAGCCCTTGCCATACAAAACACACATTTTTACACTCACTCTCTCAAACCAATCTTATT\n")
-		f.write("GAAAGCTCATTCTTGTTGGATCATCTTGAAACACCGTCACGACTCA\n")
-		f.write("\n")
-		f.write(">gi|226789989|gb|GO546164.1|GO546164 Mdas9001K13_e62.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB64115.1| putative aspartate aminotransferase [Oryza sativa (japonica cultivar-group)] dbj|BAB86539.1| putative aspartate aminotransferase [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("CAACAAAACAAACACCCCTTTGTTTACTTTACGGTTAAATACAACGCCAAAAAAATTATTTTCCACCTTC\n")
-		f.write("CCAACATGACCAACTTATTCGTACCTTCAACTCAAATACTAAAATACGGATTTACCCCAAGTAAAACAGG\n")
-		f.write("GGCAAAACCAAAAACATTTTAGTTAGTAACACCGGCCACAGGCTTTAATTCAACAAAAGCTTTCTTAATT\n")
-		f.write("CCCCCCACACCTGCCTGTACGGGGGGAAGGGATGCTGCGAAGGAAATTCGAATGCACGTGTCATCCCCAA\n")
-		f.write("AGGCATCCCCCGGAACTAGGGCAACCTGACCCTTGTCAAGTAGGTAACGGCATAGGGACTCTGAATTCTC\n")
-		f.write("AATTTTACCAAATCCTTCACCCTCGGTTCCATAGTAAGCGCTGAAATCTACAAAAAAATAAAAAGCTCCC\n")
-		f.write("CTGGGTTCTGAAATCTTGACACCGGAAAGTTCGCCAAAGCTTTTGACCAAAAAATCCCGTCGCTCCCGGA\n")
-		f.write("ATGCTTTCACCATAACAAAAACGGCCTCCCCACCA\n")
-		f.write("\n")
-		f.write(">gi|226789988|gb|GO546163.1|GO546163 Mdas9001N13_e75.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_683478.1| RRM-containing RNA-binding protein -related [Arabidopsis thaliana] dbj|BAC41896.1| unknown protein [Arabidopsis thaliana] gb|AAO63346.1| At1g67325 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CACCGTTGTTTCTGCTAGGGCAACTTGCCTTCCTCTCTGGCATTCGAACCCGGACTCTCATATCTCGCCG\n")
-		f.write("CCGATATGTCTCAGGTTGACAACAGAAATTCTTCAGCAGCCAAGCGTGCTAGAACCGATGGTAGTCGAAG\n")
-		f.write("GGAAGATGATTGGACCTGCCCTAGCTGTGGGAATGATAATTTTTCATTTAGAACGACTTGCAATATGCGT\n")
-		f.write("AATTGCACTCAGCCGAGGCCTGCAGATCATAACTCAAAACCCGCTGCTAAGCCTTTCCCAGCCCCACAGG\n")
-		f.write("GTTACACATCTGCTCCTCCTTATCTGGGCTCTGCTGCACCCTCTTCAATGTATCTTGGTGTGCCACCCTA\n")
-		f.write("TGGTTCTTCTATCTTCAATGGATCATCCATTCCTCCCTATGATGTCCCATTTTCAGGGGGATCAGCATAT\n")
-		f.write("CATTACAACTACGGCAGCCGCCTCTCTACGGGCAGCCCCTACAGACCTCTGCATTTGTCTGGACCAACAC\n")
-		f.write("CCATATT\n")
-		f.write("\n")
-		f.write(">gi|226789987|gb|GO546162.1|GO546162 Mdas9001O10_e80.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566406.1| ethylene-responsive protein -related [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTCTTCACGACGAGGACAGGGCAATTGGCGTGCTGAACACAGTAGTCGCTGACACTACCAAGAATTGCC\n")
-		f.write("CTTTTGATTTTTCCGAGCCCACGCTCGCCTACAACTAGCAGCTTGATGCCGTGTTTTTTGACAGCATCAC\n")
-		f.write("GTATGGCTTCTTTCGGATCTCCAACTTCTGTGACTGTCTCAGCATTTACCCCACGACTAGCACAGATCTG\n")
-		f.write("TTTAGCTTTCTCCAACAGTGCCAACGCAAACTTCCTTTGATTTTCTTGGGAAGAGTTAACAAACTCCTGA\n")
-		f.write("CTGGAAGACATAGGACAGTACATGCGAGCAGCGCCGAGCGACGCCGAGAAGGTGATGTTGCCCCTCTTGC\n")
-		f.write("CGAA\n")
-		f.write("\n")
-		f.write(">gi|226789986|gb|GO546161.1|GO546161 Mdas9001P03_e84.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK93649.2| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTACATTGGCAATCTACGGCACGCTTTATTTCACCATTTCGTTCTGCACATTACAAGCCAATA\n")
-		f.write("AACTTCGGTTCTACATAAGAGGTTTTGCATCCAATTACACTGATAGAAAGGTAAACTCATATATCTGCTA\n")
-		f.write("ATTGCTTGCTCACGGTGCATATTAAGCTTTAAGCAATTTATTGGCCTTTTTCACCCAAACATCGTAAATA\n")
-		f.write("TCGTCTGCGAAGAGAACAAAGTGCACCTCCTTTAGGCCATCCGCAAACTCCTTAATTGTGGATATAGATA\n")
-		f.write("CTGTGGCTGCTTCATCATACGGATATCCATACACACCACAAGAAATAGCAGGAAACGCGATATGCTGAAG\n")
-		f.write("GTTGTTTGATTTGGCTAAGGTCAAGCTATTCCTGTACGCAGCACTCAGAAAGGTTTCCGGGTTGCTGCCA\n")
-		f.write("GAACGGTACACGGGTCCAACAGTATGAATTACATGAGATGCAGGCAACTTAAAACCCGGGGTGATCCTTG\n")
-		f.write("CTTCTCCGGTGGGACAGCGAACACGTGGCCTGACTTCTGGGACACTATAGCATGCTTGCAGAAGATCTGG\n")
-		f.write("GCCAGCAGCCCTATGTATAGCTCCATCTGCACCACCACCTCCAAGCATCCCCTC\n")
-		f.write("\n")
-		f.write(">gi|226789985|gb|GO546160.1|GO546160 Mdas9001L22_e68.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n")
-		f.write("TTTTTTTTTAGGTCGCCAGCTGATTTCATACATATTGGAATGAAGGTTCCAAATAGATTTTTGTACACAA\n")
-		f.write("GGCAAGCAGATAAAATTACAAGTTTTTAGTCCTACAAACGTTGCCCCTTCTCCTCCCGCACTTGAATCCC\n")
-		f.write("AATTAGAATTCTCCTTCTTTCCTCACTTCGGGGAAAAAGAAGCAAAAATGGTGGCATGGCCGGGATCGGC\n")
-		f.write("GAGGTGAGCGAAGAGGTTGTCAATGGGGCCAGTCCCAGTGTAAATGTGTTGGAACCAAGCTCCCATCACA\n")
-		f.write("GCCAACATAGCCAGCCTTCCGTTCTTGATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGC\n")
-		f.write("TTCCCCATCCAAGTGGGTCGAACCAGAG\n")
-		f.write("\n")
-		f.write(">gi|226789972|gb|GO546159.1|GO546159 Mdas9001H05_e38.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTCCCCCCACGGTTTTTTAAACCAAATTCAAAACCAACACCTGTACTTCGGAA\n")
-		f.write("TTTCCAAACCAGGGTTAATTTATTTATCCAAAAAAAAAAAAAAAAAAAAAACCTTTTTACCAGGGTTCTA\n")
-		f.write("CAAGGATATAAGGCCCTATTTGGTTTTTCACATTTAATGGCCAAAAATTTCAAAACAAAAAATGGTTTCA\n")
-		f.write("ATAGAACAAAAATAATTTCAAAACAAATGGCACCCAATTTCATTTCCTGGGAACAAAATCAATAAACACT\n")
-		f.write("TCCTCTTCAAAAACACTGCATACCCAAAAAACCCAACCCTTGCCGCCCCTAAATTGAATTTCTCAACTTC\n")
-		f.write("TTTGTACAAAAAACCAAAGGAAACCATAATTTGAAACCTCACACTTCACGTGCAAAAGGCCCCTACCCCC\n")
-		f.write("CTTCAGGCAAACACTTTGTTTCGTTCACCTGGAAACTTTGGGGGCAACCTTTCCTTGAAACCTATCACCT\n")
-		f.write("TATTCAAGGCCCCGATGTAGGCCTTG\n")
-		f.write("\n")
-		f.write(">gi|226789971|gb|GO546158.1|GO546158 Mdas9002D15_e108.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40519|PSBR_TOBAC Photosystem II 10 kDa polypeptide, chloroplast precursor (PII10) pir|S32021 photosystem II 10K protein - common tobacco emb|CAA49693.1| NtpII10 [Nicotiana tabacum], mRNA sequence\n")
-		f.write("CCAGCTCAATATTACACCCATCAAATTGAATCCATGCCAAAACAATTACAATTAAGGTTTGCACAAAATA\n")
-		f.write("TTTCTTTAATGTTCTTGTTTACGGCAACTAATTGGGACAGGCTACATAAATTACAACAACAAAAGAATAA\n")
-		f.write("TCAATAATTTTACTGTGACAAAACACTTGTGTTGTAAACAAAAAGGGCACCCCCTGCAAAAATGCCAAAA\n")
-		f.write("AAGGTAACTGCCCAAATGGCCAAGCCAGTAAAACCCCCAACATAAACATCACCAAATGGAACCCACTCAT\n")
-		f.write("CTTTGTTGTAAATGGGACTGTATCCATCAACATTAACACCGTACTTGTCTACAAACTGGTAAACACCCTT\n")
-		f.write("TCCCGTAAGCTTCCTCCCGGAAGCATCAACACCGTTCCTCAACTCCATGCCGCCACCAGTTCCATATGGG\n")
-		f.write("GTGGCAGTCTTGATTTTCTTGACGCCACTGGCTTGCACCTTGAATGAAACAAAAGACCTGGAAAGAGAGG\n")
-		f.write("GAAGGCCTCTCACTGCTGACTTCTGAA\n")
-		f.write("\n")
-		f.write(">gi|226789970|gb|GO546157.1|GO546157 Mdas9010B13_e722.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n")
-		f.write("AACACCACCAAAACTTCAAACAGAAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCA\n")
-		f.write("TTTGCTGGCCAGACTGCTTTGAAGCAGTCCAGTGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCC\n")
-		f.write("GCTTCTCCATGCGGCGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTA\n")
-		f.write("CTTGGGACCATTCTCCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGAC\n")
-		f.write("ACTGCTGGACTATCTGCAGACCCCGAAACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGAT\n")
-		f.write("GGGCCATGCTTGGTGCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGA\n")
-		f.write("GGCTGTCTGGTTCAAGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCT\n")
-		f.write("\n")
-		f.write(">gi|226789969|gb|GO546156.1|GO546156 Mdas9002B06_e94.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("CTTGGTACCAAATTTACATCACCGACAACAATACAAACAAAAGTACGAGACAACTCCTGAGCTCTCACTT\n")
-		f.write("TCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTGGCGACTGGGTCTGCAAGGTGGTCGGCAAGA\n")
-		f.write("TTCTCCAATGGTACCTTTCCGGTGACGATGGCCTGGACAAAGAATCCGAACATGGAGAACATGGCCAACC\n")
-		f.write("TTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGTC\n")
-		f.write("GAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCA\n")
-		f.write("ACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGT\n")
-		f.write("TTCCCAAGTAATCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACAGCCTCGCCGAA\n")
-		f.write("CTTGACAC\n")
-		f.write("\n")
-		f.write(">gi|226789968|gb|GO546155.1|GO546155 Mdas9002I06_e129.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86149 hypothetical protein T1N6.22 - Arabidopsis thaliana gb|AAF78417.1|AC009273_23 Contains similarity to a retinal short-chain dehydrogenase/reductase retSDR4 from Homo sapiens gb|AF126782. It contains a short chain dehydrogenase PF|00106 do, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTTTGTCACCTAAAACAAGAGATTTATAATTGAAACTTCATTAAAACTTG\n")
-		f.write("ACATATATTTTTATTAAGAACACATTGTGCTTAAGAGTACATGTCACATGTGCATATAGATATATTAAGA\n")
-		f.write("GACGAAAAATAGACCAATTATTTCACAATTTCAAATTTTCATTCCAAGGTTGACAATTCAGTCTGTTCGA\n")
-		f.write("AAAAAAGGCCAGAAACTCCATTATCAGGCAGCAAAGCCAGCTTCACAGGACCTTTTGCAGCTTCTTCAGT\n")
-		f.write("TGTGAAGACTCCAGTGTGATTGTTCATGTCCGTGTCAGTAAAACCCGGACACACGGCGTTGATAGCAATT\n")
-		f.write("TTGTTGGAATACTTCTTAGCCAAAACTCTTGTATAAGCATTCAGAGCGGCTTTGGATACAGTGTAGGCAG\n")
-		f.write("AGAAATTGGTTGGCCAGCTTTTGGCTTCAACCA\n")
-		f.write("\n")
-		f.write(">gi|226789967|gb|GO546154.1|GO546154 Mdas9002B04_e93.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565889.1| expressed protein [Arabidopsis thaliana] gb|AAC28759.2| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTCAAACTAAATTTTTGACATGAAATTGCAATTAACAAATGATTGTCTTCCCATGAAAATAAAGGC\n")
-		f.write("TTAGGTACATTGATACGTCCGGAAAATAAACAAAATTAACTGAAGAAAGTATAAATCTTGTTACAGGCAC\n")
-		f.write("ATCCATGATGGGCGAGGGTCAGCACGATTCCAAGCACAGCCTACGACATCCAGCTCAAAATTTGATCGGA\n")
-		f.write("CACGAAGGACAACTTCGTCGTGCTAAGAATCACCCTTCAGTTCATCTGAATCTGAGTCACTTGCATTATA\n")
-		f.write("ACCTGGCTGCTTATCACTAACTTTCCAAACCGAAGATCGAGTCCTCGAGGCTCTTGTAATCCATACTTCT\n")
-		f.write("TCCCATGTGGTCATCTCTGGGGACGCCATAACCGGTGTAATACATCTGTCCCCACCAAAAACCTGCATGT\n")
-		f.write("TAATATCGCCAGCTTTGGCCTCCTTGAGCGTGTCCTTGAACCACCGC\n")
-		f.write("\n")
-		f.write(">gi|226789952|gb|GO546153.1|GO546153 Mdas9002J04_e135.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTCCAATGCCACTTAGCTGATTGCCTCCACAAACACAGGGAGGAGGAGAAGGCAGACGTCTCCAATGGCG\n")
-		f.write("GTTTTGGCTCATGGGTTTTATCTACCCCCACCCACACGGACACCCAAATCGTCAAATCGGAAACTTGTTG\n")
-		f.write("GGTATTCGAGCTCTATCATTGTCAGACGCAGATTGCTGACGGACGGGAACGAATGCGTGCAGGTTTCCGA\n")
-		f.write("ACTCTTCACTCCCAAGACTTTCAGGATCAGAAGCTTTTATGAGGAGGATGCAGGAAATAATGAGGTTGAA\n")
-		f.write("ATATCTAAAGACATTCTGGATGGGGAAGATGGGATTTCGGATGATCTGCTTGAAAATGTTGTGAATACTG\n")
-		f.write("AAATTAGTACAGAAAATT\n")
-		f.write("\n")
-		f.write(">gi|226789951|gb|GO546152.1|GO546152 Mdas9002I12_e130.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("GCAGAGAGAGATAGCAATGGCTTCCTCCATGATTTCCTCCGGTACCGTGGCTACAGTTTCCGCCCCCGCT\n")
-		f.write("CAAGCCAGAATGGTTGCTCCATTCACCGGCCTCAAGTCCTCCTCAGCTTTCCCTGTCACCAGAAAAAGCA\n")
-		f.write("ATGACATTACCTCTATTGCAAGCAATGGAGGAAGAGTGCAATGCATGCAGGTGTGGCCTCCACTTGGACT\n")
-		f.write("GAAGAAGTTCGAGACCCTCTCTTACCTTCCTCCCCTTTCTACCGAGTCCTTGGCCAAGGAAGTTGACTAC\n")
-		f.write("CTCCTCCGCAAAAACTGGGTTCCCTGCTTGGAATTTGAGTTGGAGCATGGATTCGTGTACCGTGAGAACC\n")
-		f.write("ACAGATCCCCAGGATACTATGATGGAAGGTACTGGACAATGTGGAAGCTGCCCATGTTCGGATGCACCGA\n")
-		f.write("CTCTTCCCAGGTGATGAAAGAGCTG\n")
-		f.write("\n")
-		f.write(">gi|226789950|gb|GO546151.1|GO546151 Mdas9002F08_e116.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK55780.1|AC079038_14 Putative 40S ribosomal protein; contains C-terminal domain [Oryza sativa], mRNA sequence\n")
-		f.write("TCGCCGAGCTGAACGAGGTTCTGACCAGAGAGCTGGCGGAGGACGGCTACTCCGGCGTCGAAGTTAGGGT\n")
-		f.write("CACCCCTGTCCGGACTGAAATCATCATCCGAGCCACTCGCACTCAGAACGTCCTTGGCGAGAAGGGAAGA\n")
-		f.write("AGGATTAGGGAGCTGACATCTATTGTTCAGAAGCGGTTCAAGTTCCCGGAGAACAGCGTCGAGCTCTATG\n")
-		f.write("CTGAGAAGGTGAACAACAGAGGACTCTGTGCCATTGCTCAGGCTGAGTCTCTTCGTTACAAGCTCCTCGG\n")
-		f.write("AGGCCTTGCTGTTCGCAGGGCTTGCTATGGTGTGTTGAGATTTGTCATGGAGAGTGGTGCAAAGGGATGT\n")
-		f.write("GAGG\n")
-		f.write("\n")
-		f.write(">gi|226789949|gb|GO546150.1|GO546150 Mdas9002G22_e123.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTATTTTGCGTCTCTATGCCATTGATGTTCAAATATGCAACTGAAAAAGAA\n")
-		f.write("AAAACAGTCAAAGCGTCCACATATAATAATGGGCTCAACAACTGTAAAACCCACAAAAGCAGCTTATGCA\n")
-		f.write("TCATTAACAGATTTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTAATTCCGTTTTTCACACAT\n")
-		f.write("TGCAGGGAGGCCAAACTTACAACCACACAAAGGAATGGACGAGAGCATCTAAGAGAGGCAAGAGTATGCC\n")
-		f.write("AAAGCTTTCTCCTCACTAAGCTCATCTGCAGTTGCATCCAACTTCTTCCTCGAAAACTCGTCAATAGAGA\n")
-		f.write("GTCCTTGAACAATCTTCCACTCTCCATTTTGGCAAGTGACTGGGAATGAAAAAATGAGACCCGAAGGTAC\n")
-		f.write("ATTGTATGAGCCGTCTGAGTAGACACCCATGGAAACCCAAGTGCCCTCTGGGGTTCCAAGTACCCAATCA\n")
-		f.write("CGAATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGAATGATTGCA\n")
-		f.write("GCACCACGTTGTTGAACAGTGGA\n")
-		f.write("\n")
-		f.write(">gi|226789948|gb|GO546149.1|GO546149 Mdas9002C13_e101.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P17067|CAHC_PEA Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) pir|S10200 carbonate dehydratase (EC 4.2.1.1) precursor, chloroplast - garden pea emb|CAA36792.1| precursor peptide (AA -104 to 224) [Pisum sativum], mRNA sequence\n")
-		f.write("TCGAGTTTGCCCATCACATGTTCTGGATATGCAGCCGGGAGAGGCTTTTGTTGTCCGCACAGTTGCTAAC\n")
-		f.write("TTGGTCCCACCCTATGATAAGGTTAAATACGCTGGGACTGGGGCGGCCATTGAGTATGCTGTCTTGCATC\n")
-		f.write("TCAAGGTTTCATACATAGTGGTGATTGGGCACAGTGCCTGTGGAGGAATCAAGGCACTCTTGTCTATTCC\n")
-		f.write("AGAAGATGGGTCTACCCTCGGCACTGACGTCATAAAAGACTGGATTCGTATCGCATCTCCGGCAGCGAAG\n")
-		f.write("AAGGTGAAGGCAGATCACGGTCCTGATACTCCTTTCCCTGAACTATGCAGTCGTTGCGAAAAGGAGGCGG\n")
-		f.write("TGAATGTATCGATCGGAAACCTGCTGAGCTATCCGTTTGTGAGAGATGGTTTGCTGAAGAAAACCCTAGC\n")
-		f.write("AATCAAGGGAGGATACTATGACTTTATCAATGGACATTTTGAGCTCTGGGATGTTGATTTCAGCCTCAAC\n")
-		f.write("CCCAACTTCTCCGTATGATCGTAATCACATAATTCCCATGCAACTCAATTGCTTCCTAATTAATTATCAT\n")
-		f.write("TAAGTACTTCTAATTTATTTCTTAATTTCATCTGCAATGTCCCCGGAAGCACGTCTG\n")
-		f.write("\n")
-		f.write(">gi|226789947|gb|GO546148.1|GO546148 Mdas9002C03_e98.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA93004.1| nonclathrin coat protein zeta2-COP [Glycine max], mRNA sequence\n")
-		f.write("CGGAAACTCCGTGTTATTGAAAGTTTATAGCTCAATCAAAACAACATCGCATATGGTACACAATTAATTA\n")
-		f.write("CAAACGGAATCTCGAACATCCCCGTGAGTTCATATGGCATTCAATTCATCAAAATATGTAAACGTATATA\n")
-		f.write("TCTCGAATACTAAACCTTTGGCATCAACTGTTCCAATGTCCAAATTAACCGAGTTCTGCAAAAGTAATCA\n")
-		f.write("AACTTGATAATATCGCAGCATCTGATGAAACAAAAACATATAAAACTGATGTCCTCTCTCCTTGCTTTTC\n")
-		f.write("CTCTTTCAACACATCATTTAAGGAGTTGTCTCGCTAGATGTTCGCGGGCAGTTGCCAATGCTTGACTTAT\n")
-		f.write("TGTCTGCTCGGACAACGGAGCTCCAGCATCAATACTGTGACTTGCAACCTTACTTGCTATAACATTTGAA\n")
-		f.write("TCGGTCTCAAAAAAAATACCTCCGTCAACAATTTCATCAAGGCATAATAAAATGAAATCCAAATTTTCAA\n")
-		f.write("GTGCCTCCTTCTTGT\n")
-		f.write("\n")
-		f.write(">gi|226789946|gb|GO546147.1|GO546147 Mdas9002N08_e153.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("TTTTTTTTTTGTCCGAAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTT\n")
-		f.write("TCCACGCTCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACT\n")
-		f.write("CACTTTCCGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGG\n")
-		f.write("CAAGGTTCTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGC\n")
-		f.write("CAACCTTCAATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAAT\n")
-		f.write("GGGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATC\n")
-		f.write("CCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCT\n")
-		f.write("AAGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAAC\n")
-		f.write("\n")
-		f.write(">gi|226789932|gb|GO546146.1|GO546146 Mdas9002M20_e151.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10766.1| cyclophilin [Pseudotsuga menziesii], mRNA sequence\n")
-		f.write("TTTGAACAAAAGGATCCTTCATCTTAAGTCAGAAGTCGGAACAATATACTGTATTAGAATTACACCCATA\n")
-		f.write("GAATGCTTTTATGGGAAAATTAAGATTCTATTGGTTACAAGAGTTTTTATAGTTAACCATCAATAGGCGG\n")
-		f.write("CTTACAAACTCGGGTTTTACATCTCTCCGCATTCAGCAATAACACAGGCTAGTTTAGGGCGATTGTTGGG\n")
-		f.write("TCCCGTAGCCACATTCTCAATCTTCCTAACAACCAAGAGACCATCTCCAAGCACTCTCCCGAACACAACA\n")
-		f.write("TGTTTATTGTCAAGCCAGTCACATTTCGCGCACGTGATAAAGAACTGGCTCCCATTTGTATTTGGTCCAC\n")
-		f.write("TATTTGCCATTGACAATAGGCCGGGACCAGTGTGTTTGGCATCAAAAGTCTCATCATCAAACTTAAGTCC\n")
-		f.write("ATAGATGGAAACACATCCACTACCATCACCCTTGAGAAAATCACCAGCTTGAATCATGAAATCCTTAATC\n")
-		f.write("ACCCTGTGGAACTGGCACCCCTTGTACCCAACTGGCAATCCAGCTTTTCTGTACTCGCCGGTGCAGAATT\n")
-		f.write("GCCTGAAATTCTCGGCGGTTTTGGGGGC\n")
-		f.write("\n")
-		f.write(">gi|226789931|gb|GO546145.1|GO546145 Mdas9002I14_e132.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD37374.1|AF145348_1 peroxidase [Glycine max], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCATCAATAATTATTGAAATTCATACATCATAATACATTTTAAAA\n")
-		f.write("GTTCAAACCATCCATAAATACATACACACATCCCGACATCCATCCACCATGTCCATCTCACCCCAAGAGA\n")
-		f.write("AGAAGCCAAAAGATACAACGAAACCCTGCATCACAAGCAGTGCATCACGAACAAGGGCAAACATGTACAA\n")
-		f.write("CAAACCACATACCCTTTAACCCTAGCACTGACCAACTTCCATAAAAACAAAACATACATCTAGGTGAAAA\n")
-		f.write("AAATAAAGCATCTTATTATCCAGCAACTTGTCGCACACAATTTCTCCATTAGTTGCATAACTTAAAAAAA\n")
-		f.write("TAAGTGCTTCTTGGAAAAGCTGCTTTTTTCTAGTCGCGGATCTTGTTGGCAACATTGCACTGCTGTCGGA\n")
-		f.write("TCTCGCCCTTGTTTCCAGTGAGAGGGTTGTTCTCGGAGAGAATGGTGAAGGCTCTCGAAAACTCCTTGAA\n")
-		f.write("GAAGTAGTCTTGGCTCTTGGCCAT\n")
-		f.write("\n")
-		f.write(">gi|226789930|gb|GO546144.1|GO546144 Mdas9002F24_e118.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("GCATTCAAAGCTCTTAAAAAGCGTTATACATCAGGTACATTAATCCCTTTAAGGGTTTTAACCAAGCTTT\n")
-		f.write("TGAAGACCCT\n")
-		f.write("\n")
-		f.write(">gi|226789929|gb|GO546143.1|GO546143 Mdas9002K02_e140.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO88964.1| sorbitol transporter [Malus x domestica], mRNA sequence\n")
-		f.write("GTCGGGTTCTTCTCGACTGGGATTGGGCCCATTGCCTGGGTTTACAGCTCTGAGATCTTCCCATTGAGGC\n")
-		f.write("TGCGGGCTCAAGGGTGTGGTATGGGAGTGGCCGTGAATAGGGTGATGAGTGGCGTGCTCTCAATGACTTT\n")
-		f.write("CATTTCGTTGTATAAGGCCATCACAATGGGTGGTGCCTTCTTCCTTTATGCGGCAATTGGCGCTGTTGGT\n")
-		f.write("TGGATCTTCTTTTTCACAATGCTCCCGGAAACACAAGGCAGAACCCTTGAAGACATGGAGGTCTTGTTTG\n")
-		f.write("GTAAATTCCACAAGTGGAGAAAAGCCAATAAACTGCTCGAAAAGGAAAGGCAAGTTGCTCGTGGTGATGG\n")
-		f.write("TGGCACCAGTGATCCGGACAACAGGGTGAACCTCTTGGCTTAGTGAGCGAATATAAACAACTAGTAGAAC\n")
-		f.write("TGCAGAACAATCTCTTGAATTATAAAAATATTTATTGTACGCACCGGTTATATATGAGGGTGATTCCGCC\n")
-		f.write("CAT\n")
-		f.write("\n")
-		f.write(">gi|226789928|gb|GO546142.1|GO546142 Mdas9002N20_e156.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n")
-		f.write("TTTTTTTTTATCAATAGCTTGTTTAATAATTAAAACAAAATAATTGCAAGAATTTCCATAGAAATACAAG\n")
-		f.write("CGCAAATTACAAAGAAAATATCAATAACCCAGCAAACAGAATATTTATTTTCTTCAGCTCCAATTACTCG\n")
-		f.write("TACTGACAGCTACCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCTGTTCGATCAGTGCAGCCTT\n")
-		f.write("CTGGGACTGGTACATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTCGGTTAATGGAGTCCTGGTT\n")
-		f.write("TGCATCTCCAAGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGATCC\n")
-		f.write("TGAACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGAC\n")
-		f.write("CTTCTTTTGAGTTCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAAATCCACTTCCTCACTT\n")
-		f.write("CATCGTCATAAACTCGAGCCCTTAGGGCACCGAAGAATCAATGGATTGACGGGGGAATGTGTCAACAATC\n")
-		f.write("TTGACAACATCTTCCT\n")
-		f.write("\n")
-		f.write(">gi|226789927|gb|GO546141.1|GO546141 Mdas9010B19_e724.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM65322.1| unknown [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTCAGATACTAAAATTGCACGGATACAATATGTACATAGTTTCGTTTTCGACTTTATATACGTAT\n")
-		f.write("ACATTATTTGGGAATATCTGCAAAGAATCTGCTCTGTAATTTACAAATTTTATCCCCAGACTAGTAAAGC\n")
-		f.write("TCCACAACTTATTCTACTTCTTTCCTTCTACTTTAAGCTGCTGGATCCTCTGGCGTAGTCTTTTCCGATG\n")
-		f.write("ATCGTGTATCTTCCAAAGGCCATGACCCAATATCACAGCAGAGTATATGCCGTGCGTGATCATAGGCGTA\n")
-		f.write("AGCATATTGTTCGTCTGGATCCACTCAAAACCAAGATATAGGGCAAGAAGTCCTTCAAGCAGGGGAGAGT\n")
-		f.write("AAATCTTCTTCATTTGTCTCCTCTGATACCAAGCTGCAAAAAGCTTTTTCATGTCTTCACGACCAGAGCG\n")
-		f.write("AGATTGTAAAACTGGTGCAACTACATAAGCAGGATCTTTTGGAGAAGCTGCCACATAGTACAGAGAACCT\n")
-		f.write("GTGAGCGCAGCTGTAATCACCGCTGC\n")
-		f.write("\n")
-		f.write(">gi|226789926|gb|GO546140.1|GO546140 Mdas9010B11_e720.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC22214.1| putative plastid protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTAACCTTAATAAATAGTCTGAAATTGCACAAAACAACTAATACTGTTCAAGGT\n")
-		f.write("TTAGAATAGTTTATAGCCTTGAAGGTTCATCACGAACTCAAGGGTTTAACAACAGACAATGATAAAAAAA\n")
-		f.write("AACGTTCAGCTACTAAGCAAACTTTGGCATAATCGCCTTTTCACCAAGATATTTACATTGCTAGCCTTCC\n")
-		f.write("GTTTATTTCAACGGACATTTTCCCTTCGGCGCACATAACGGGTTCTGTCATTGTATCTTGGTCTGTCCTG\n")
-		f.write("AGCTCTCGAGGGCTGCGGCTCCACCCTCCTCTGCCTCTCAGGTGATCTTTGAACAATTTCTCCATTCACA\n")
-		f.write("TACAACTCAGCACCGTAGTCTTTGTACTCAGGATCAACATACGAATCCGGAAGAACAAAAAGAACACCGG\n")
-		f.write("GCAAGCCTTCAAGCTTATTCGAGGTCTCCTCATCAATCTCACAACCAAAACCAAAATACCTCTCACAAGA\n")
-		f.write("GACATTGTATATCTT\n")
-		f.write("\n")
-		f.write(">gi|226789925|gb|GO546139.1|GO546139 Mdas9002E23_e114.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTAAATAAGTTCCCTTTTTTGGATCAATACTTTCAGAATTCGAATATTAAATCACAAGATGAA\n")
-		f.write("CTAACTGATCTTTTTGTAGAGTCCAAGAACCTGGGGACTAACTACTCTCAGTCCTCATCGACTTTTGTTC\n")
-		f.write("ACCATAGGTCAAATAGTACACTCTCTTCTCGCTCCAAAAACATCGAACTAATGCACACGTTCACTGATAT\n")
-		f.write("CGCATTGATTGCATCTCAAAACAGGCGTTGTAATGTCCCAACTGCGATCCATGAAGATTGCCACTCAGAA\n")
-		f.write("AATTTTGCTCCTCAAGCTTAGGTACATGTGAAGACATCCCACAAAACGGTCCCAAGAAGTTGTTCCCATT\n")
-		f.write("TGCAGAACCGAAAACCATTTGCTGTCCCTCATCGGGCGATTTCCAGTCAATGCTCACGCTGGCCAACTTC\n")
-		f.write("TGGTGCTGGTGTGGCTGCTGCACCAGGGTTGAGGAGAGATCCGATGATGGT\n")
-		f.write("\n")
-		f.write(">gi|226789911|gb|GO546138.1|GO546138 Mdas9002N18_e155.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198818.1| thaumatin family [Arabidopsis thaliana] dbj|BAB10226.1| thaumatin-like protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTCCACAACATTATTTGTGGTGTTGATTATCAATTGTACATTAGCCTTTACACCCGAATTTCAAA\n")
-		f.write("GTAACACAACATGGGGCAAACTAGTCTTTAACCTACATGGAGATATACCCAGCACCAGCAGCACCCCACC\n")
-		f.write("CCGCAGGACAAAATGTGATCACATACTTACTCGCCTTGCAGGTCACCAATGGAGGTGGTGTATCATAAGC\n")
-		f.write("ATAGCTGTAATACGAAGGGCAAGCATCTTTGAATAACTTTGAGTACACACTCGGCTTGCATTTTTCTGGG\n")
-		f.write("GTTCCATACTCTTTCCGGCAACAATACGCGTCCGTATTAAACGCCAAGCAAGCGCTTTTGCACGCCACAA\n")
-		f.write("CTTCCCCTTTCTTGTTTAAAACCTTAAGCTCTTTGGGGCACCGAGTTTTCAAATCTTTCAAACACCCTCC\n")
-		f.write("GATAGTGCAATTGGATGCTACTGGATTTGATAAGACCACGACCGGAAGATTGTATCCATCAACCACGCTC\n")
-		f.write("ACATCGTAGAAATTCAGCTTGTCTTTGCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226789910|gb|GO546137.1|GO546137 Mdas9002P10_e161.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTGACAGACACAAAAATAAAGTTCATTAGCTAATTACATAACTTCGTAGATACATGAGAATGTACAACCG\n")
-		f.write("AATGTCGAATAATAGAGACAAAAGTGATTTGATGTGCAAATAATAATATAACATCGGATAGTGCCAATTC\n")
-		f.write("GAACATCAATTTGCAAACACTCCTCGTACAGCCAGCTGCCAATTATATATGCTTTATAATACACACATGA\n")
-		f.write("GCATACACAACTAAATCAGAGATTAAACGAGGAATTATATTGCGATTAGCTTAAAAAGAAGATTAGCAAG\n")
-		f.write("TGAAGAAAAAAGCAACGAGTAGCGTTGCAATTTGCTTTGATTGGAGTGGATTATCATGTTTAACCCAACA\n")
-		f.write("AAATGTATTTACAAGTTCTTCTTCGAACCTTGAAATTCAAGACCTTATTACATAATTAAGCCTAAAACCA\n")
-		f.write("GCTGCTAATCTAACTACCAAACGACGTCACAGCGTTTGGGTTTTGCCGAGCTGGACGTGGTTTCACCAAC\n")
-		f.write("TATTCTACTGCTCAATCATCCCATAATCTAACGACGTTACCGTT\n")
-		f.write("\n")
-		f.write(">gi|226789909|gb|GO546136.1|GO546136 Mdas9010B16_e723.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB10038.1| dihydropyrimidinase [Arabidopsis thaliana] gb|AAO33381.1|AF465755_1 dihydropyrimidine amidohydrolase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TGCAAACTGCAGTGAAAATCTTATTGATTGACCTTAAAGCGAATTCATATACATGACATACAATGAAAAT\n")
-		f.write("ACAAAAAACTTTGATCTTATTATTCAAACACGATGCGATATATACAGGAGCATCTTCTCCATTTCTAATC\n")
-		f.write("AAGTTTAAAAAAATAATACAAAAAAAGGAAAATAGTCAAAGTACCTGCAATTTTTAAACAGTTGCTCTAA\n")
-		f.write("AACGCTTTACAGGGGCTTTCATAAAAAATAGGTACTTAACATCTGCCTTGTCAATTCCATTAAAAAGATA\n")
-		f.write("TCCGAAAGGCGGCATTTCTATGTACTTTCCAAAACTAGGAACAACCTTCAATTCATCATTTTCCCAAACA\n")
-		f.write("ACCCTTCCACCAGAAATGGTCA\n")
-		f.write("\n")
-		f.write(">gi|226789908|gb|GO546135.1|GO546135 Mdas9002B23_e97.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD29671.1|AF126402_1 major allergen Mal d 1 [Malus x domestica] emb|CAD10375.1| allergen Mal d 1 [Malus x domestica], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTGATTAAAAAGTAATTTCATTATATTTATAGAAGATAATACACTCCGT\n")
-		f.write("TCAGTCTGCAACTTTTTTCCAAACAAAGACATCAATAGCAACAAGAAGATCATCACAACCATAACACTTA\n")
-		f.write("TTTTTCAAGCCCAAACTGCCCAAACCATGGTTATTACTTTTGGCTGACGTGAAAAAAACATACAAAGAAA\n")
-		f.write("AGCCACACAACCTTCGACTGACCATATAGTAACGGTAACACCCAAAACACCATAGATACTTATGATTAAT\n")
-		f.write("TTAGTTGTATGCGTCGGGGTGGTCCTTAAGGTAGCTCTCAATAAGTTTGAACAAACCATGGGCCTTCTCT\n")
-		f.write("TTTCCAGCCTTGACGTGCTCTTCCTTGATTTCAATGTTTCCCTTGGTGTGGTAATGACTGATGCTCTTGA\n")
-		f.write("TGGTGGAACCACTTCCACATGCCACCAA\n")
-		f.write("\n")
-		f.write(">gi|226789907|gb|GO546134.1|GO546134 Mdas9002L06_e143.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTCTCTGAAAACTGAATTCTTGAATTGAGATTTATATATCATAGAGTT\n")
-		f.write("CTAGGGCAATATATTACAAGCAGAATATTACGCAATTCTTCTTAAATAAACATAAATAGCAAAGCACAAG\n")
-		f.write("ACACAGAAATTGAAATAGCACAGATATAATTATATTTGAGGATGACGATAACAGCCTTTGTTGTACGTGC\n")
-		f.write("CGCAGTTTTCAAGTCTTACATCTGGTCTGGTTGTAGCGCAGGGGGGCAGCCTTGTCCGACCACATTGCGG\n")
-		f.write("CGTTAGCGT\n")
-		f.write("\n")
-		f.write(">gi|226789906|gb|GO546133.1|GO546133 Mdas9002G02_e119.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB77025.1| putative Rho GDP dissociation inhibitor [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TTTTTTGACAATTCAATTTTACATTTGTATCGATCACCCCTACAAGGAAAAGCTTATACAACAAAGATGT\n")
-		f.write("GTGGTTCATGGAGGAAGAAATAAATCTAAGGATCCCGGATCTTCCGAAAAAAATCAGCTATCTGCCCTTT\n")
-		f.write("TTGATCTCGAAGGAGTACTGAAGTTCCATATGGCATCTCCTGTCATCGTCTTCGAACTTAAGCTTTGCTG\n")
-		f.write("AATAAATGCCCCTTGCAAGCAACCCAGATGGAGTGGTCTCCTCTTCCAAAGTGTGCACGTATAGTTCTTT\n")
-		f.write("GTTAGGAGCAAACGTACCCAACATTCCTTTGCTCTGATCGACTTGGAGTCC\n")
-		f.write("\n")
-		f.write(">gi|226789905|gb|GO546132.1|GO546132 Mdas9002C11_e100.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_193037.1| oxidoreductase, zinc-binding dehydrogenase family [Arabidopsis thaliana] pir|T10203 hypothetical protein F25G13.100 - Arabidopsis thaliana emb|CAB45500.1| putative protein [Arabidopsis thaliana] emb|CAB78343.1| putative protein [, mRNA sequence\n")
-		f.write("CCGGGAGGGAGGAGCTTCAAGTTTCTGCGGCTCTTCGAAACGTTAGTTGGACTTACAACTGAGAGACTAT\n")
-		f.write("GGCCAATGAGACCATGCATGCGGTTCAGTACGACAACTATGGGGGCGGAACTTCTGGTTTAAAGCATGTT\n")
-		f.write("GAAGTTCCAATTCCAAATCCGAAAAATGATGAGGTGCTGCTGAAATTGGAGGCAACTAGTCTAAACGCAA\n")
-		f.write("TTGATTGGAAAGCTCAGAAAGGCATGCTCTGGCCTTTGTTGCCTCGCAGGTTTCCGCACATACCTGGTAT\n")
-		f.write("TGATGTGGCAGGAAAGGTTGTAAAGGTAGGACCTGGAGTAAAAAATTCAAACCTGGTGACAAAGTTGTTG\n")
-		f.write("GAAAGGTTAACACTCTTACTGGAGGTGGACTAGCTGAATTTGCCGTGACAATGGAGAGTTTAACTGTTGC\n")
-		f.write("AAGGCCATCGGAAGTTTCAGCAGCCAACGCTGTAGGATTACCCGTTGCTGGTCTCACAGCTCACCAGGCT\n")
-		f.write("CTTACACAAACTGCAGGGATCAAGCTTGATGGAAGTGGTCAGCAAGCAAACATCCTGATCACAGCTGCTT\n")
-		f.write("CAGGTGGTGTAGGTCTCTA\n")
-		f.write("\n")
-		f.write(">gi|226789641|gb|GO546131.1|GO546131 Mdas9002A16_e91.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n")
-		f.write("TTTTTTTTGAAAAACAGGAAGGCGCTCAATATATAAATGGTTTCACCTCGCACATTGTCTCTCGTGGCAA\n")
-		f.write("TATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATACAATTCATCAGAC\n")
-		f.write("ACAACTGAATTAGTTAACGGTAACTTTACCGACATGCCAGCTCCCTGGTGAGGAGAGCAGTAGAAAGAGT\n")
-		f.write("ATGAACCTTTTTCGGTCAAGGTGACGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGTCCTCCTCGCTCAT\n")
-		f.write("CGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTTGTGTGGGAATCCA\n")
-		f.write("GCATTGTTCTTGAACACAATCTTCTCGCCGGGGGCGACGGAGAAGCTGTTGGGGACGAAGGCCAAGCCCC\n")
-		f.write("CGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGCTGGCTGCGGTGGC\n")
-		f.write("GGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGAGGAGGCTGAGACC\n")
-		f.write("TTAACGGCAGCGCTAACCTTGGCTGCGCCAGAGGACTTGAGT\n")
-		f.write("\n")
-		f.write(">gi|226789640|gb|GO546130.1|GO546130 Mdas9002A15_e90.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P52706|MDL1_PRUSE (R)-mandelonitrile lyase isoform 1 precursor (Hydroxynitrile lyase 1) ((R)-oxynitrilase 1) pir|S32156 mandelonitrile lyase (EC 4.1.2.10) - black cherry emb|CAA51194.1| mandelonitrile lyase [Prunus serotina] gb|AAB38536.1| (R), mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAAATCTCAAGAGATCTAATTTTATTAGATAACCTCAACATTAAA\n")
-		f.write("AGAGAAATATGTTAAACATGAAATAAAGAGGTACAGATAGCCCGGTGCATAGAAAGAACACGTCCCTTTC\n")
-		f.write("GAGCAGCCAACCATAATCCCCAATAACTAATGGGTTTATTATTAAGGCATTGAAAAGTAAAGGATAGTGC\n")
-		f.write("ATAATTAAGGAAAATATCGGTTTGAATGTTGAATCACGCGGATGATATACCAATCCAAGGTGATCTCTCT\n")
-		f.write("TGCAGAATTTGAAGACCCATATACCTGCCTAACATCAGATAGAAGCCCATAGGGTGGCTCGCCGGTGTGA\n")
-		f.write("CAGGGAATGTGGAAGAATCAACAACGCGTAATGCATCGATCCCACTAACACGCAAACCACCGTCAACCAC\n")
-		f.write("CTTTCCAACAATGCATCCACCGTGGTAATGCCAATATGAGGCCAGTGAATCATGACAAAATGTTTCGAGT\n")
-		f.write("GCATCATCTGTTTGGTTATTTGGAAAAGGAACTCCTAAAAAGGTGAAGCCTTCTACACCTGGCAAATCTT\n")
-		f.write("CGGTTTTATATGGTTTAAATGCATCGGTCCTTAATAAATCACTGA\n")
-		f.write("\n")
-		f.write(">gi|226789639|gb|GO546129.1|GO546129 Mdas9002E22_e113.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATCCAAAAATTGCATATAAATCAAAAGGCCCTGAACATGGCCCTTACATGACACCATCCCAAAAACCCCA\n")
-		f.write("ACATATGAATGACATGTTTTCACAAAACTACAACATGTCCCTCCACAAACTCCAATACTATAAACCAACC\n")
-		f.write("AAAAAAAAAACCCCAAAATTATTTTTTCCCCCAAACACTTTTCATTAATTAAAGGGCCATAATCCCCTAA\n")
-		f.write("TTAAAAAGACACTTTTATTAATCCCATCCTAATTTGGTTCCCCGGGCTTACTGACCACAGGGGCAATTCA\n")
-		f.write("CACATGGGCAGGTTGTGCCACACTTGCACTTTCCCTCCTTCTCCGCTGCA\n")
-		f.write("\n")
-		f.write(">gi|226789638|gb|GO546128.1|GO546128 Mdas9002E11_e112.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_817268.1| ORF46c [Pinus koraiensis] gb|AAO74136.1| ORF46c [Pinus koraiensis], mRNA sequence\n")
-		f.write("TTAGGGGCCTTAGCTGGTGATCCGGGCTGTTTCCCTCTCGACGATGAAGCTTATCCCCCATCGTCTCACT\n")
-		f.write("GGCCGACCTTGACCCCTGTTATTTTGAGGTCATATCTAGTATTCAGAGTTTGCCTCGATTTGGTACCGCT\n")
-		f.write("CTCGCGGCCCGCACCGAAACAGTGCTTTACCCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTC\n")
-		f.write("GGGGAGAACCAGCTAGCTCTGGGTTCGAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTC\n")
-		f.write("AACATCAGTCGGTTCGGACCTCCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAG\n")
-		f.write("GTTCGGGTCCATAAGCAGTGACAATTGCCCTATGAAGACTCGCTTTCGCTACGGCTCCGGTGGGTTCCCT\n")
-		f.write("TAACCAAGCCACTGCCTATGAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCAGAGCCCTGGGCTCCT\n")
-		f.write("CCCTCGTGCCGAAA\n")
-		f.write("\n")
-		f.write(">gi|226789637|gb|GO546127.1|GO546127 Mdas9002L19_e144.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CCCTTGAAATCCTATTTGAAAGGTTTCATTAATAACATCTCATACAGTGCAGGATTAATATGAAGCCAGT\n")
-		f.write("AGTTTATAGCACAAACATATAACAGATACATGTTTCTCCACATCCATCCTTAAAATATACACTATCGTTT\n")
-		f.write("GCATTCTTCCGCATTGTACGCTCGCAAGACACTGCCTGGATTTTTCCTTCCGTATGAGTTACTCTGTTTG\n")
-		f.write("CACCAGGAAGGCCCTGAATGTAATCATTTGCATTGATGCTCACAGCCTTGAAACTGGTAAACCTAAGGCC\n")
-		f.write("TTTGAGTTGACAATGCTAGGACTGGCAGCAGGTGGCGGAGCATTCTCGTTGAGAAATGGTT\n")
-		f.write("\n")
-		f.write(">gi|226789636|gb|GO546126.1|GO546126 Mdas9002P14_e164.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTGTCTTTTTTCTATGCAAAATATAGGGAATTTTTTTACACAAAAAATACCTCTAAAGGTAGGCATG\n")
-		f.write("CTAAAATTACAACTAGGGAGTAAACCTCCTAATTTAAGTTAAAATAAAGGAGAGGGGAGGCAACCAAAAT\n")
-		f.write("GTCAGGACGAAATACCTAGAAGACAGGTTACCTCCACTTCTCTTTTAGTTCTTTCTTCTCCGACCAGACC\n")
-		f.write("CATGTTACATAGATTGCT\n")
-		f.write("\n")
-		f.write(">gi|226789635|gb|GO546125.1|GO546125 Mdas9002J20_e138.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179402.1| elongation factor beta-1 -related [Arabidopsis thaliana] sp|Q9SI20|EF1C_ARATH Probable elongation factor 1-beta (EF-1-beta) pir|D84560 probable elongation factor 1-beta [imported] - Arabidopsis thaliana gb|AAD31355.1| putative el, mRNA sequence\n")
-		f.write("GCAATCCATTCACTCTTATTAAAAGACTTTTCTAACAAGTTCTTTGAAAAAGATCAAAAGGATTGACAAG\n")
-		f.write("CACTGAATTCTTGTGAAAAATAAAAGGATCAACATCGAAGTCAAAAAACAAGCTACCAAAAACCACCATA\n")
-		f.write("ACAAAACTGAAATTATGTTTTCAACAGTAACTGAAACCATACCAAACAAGCAAACAGCCTCGGAAACTAT\n")
-		f.write("TCATCAAGGGAATACTAATACATCAAAACCAAATATAATGTCTCAAATCATACCGCCAGAAACAAAATAC\n")
-		f.write("ACATCCGCAAGCTCCAATCATATCTTGTTGAAGGCTACGATGTCGCAACTCTGGACATACTCGTTAATTG\n")
-		f.write("GTTCAACAGTAAGTTGCTCCTCAATGAAAGTATCAACAGAGACCAGGTCATCAACAATTGTCATCATTAT\n")
-		f.write("T\n")
-		f.write("\n")
-		f.write(">gi|226789634|gb|GO545875.1|GO545875 Mdas9005N07_e385.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CTGACATGTGTGCGAGTCAACGGGCGATCAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCC\n")
-		f.write("TGGGGGTTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGCGAGCATGCCTGTCGGGACC\n")
-		f.write("CGAAAGATGGTGAACTATGCCTGAGCGGGGCGAAGCCAGAGGAAACTCTGGTGGAGGCCCGCAGCGATAC\n")
-		f.write("TGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCGTCTAGTAGCTGGTT\n")
-		f.write("CCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGTGAACGAGTTCTATCGGGTAAAGCCAATGATTAGA\n")
-		f.write("GGCATCGGGGGCGCAACGCCCTCGACCTATTCTCAAACTTTAATAAGGTAGGGACGGCGCGGCTGCTTCG\n")
-		f.write("TTGAGCCGCGCCACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGAT\n")
-		f.write("GAACCGGAAGCCGGGTTACGGTGC\n")
-		f.write("\n")
-		f.write(">gi|226789633|gb|GO545874.1|GO545874 Mdas9004K09_e300.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n")
-		f.write("TTAAAAATAATATAAGGATATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAA\n")
-		f.write("CACCAAATTCGAAAACAAAAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGG\n")
-		f.write("TCTTGAAACCCTAATCAAGGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTAC\n")
-		f.write("GTACAACAACAATATTAATTACGACGAAGAAACATGATGAAACATGAATAACAACAACAACAACAACTTA\n")
-		f.write("GTAGCCTGCAGGCTTGTAGGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATA\n")
-		f.write("CGGATGAAGGCGTTGGGATAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGC\n")
-		f.write("ATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCGTAGTATCCTGGGGATTTGTGGTTCTC\n")
-		f.write("ACGGTACACAAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGGAAT\n")
-		f.write("\n")
-		f.write(">gi|226789632|gb|GO545873.1|GO545873 Mdas9005K05_e375.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_186921.1| protease-related [Arabidopsis thaliana] gb|AAF26988.1|AC018363_33 unknown protein [Arabidopsis thaliana] gb|AAN41347.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTACATGGAAATACGGCATACATAGATCAAAGAAAGAGTACGCCCTC\n")
-		f.write("GTAGATACAGACATCAACTTAGACATAACATACATGTCGCCTCTCGCTGGTCGAACATAGCATACATCTC\n")
-		f.write("TTATTATTTCAGAATAATAGTTAAACATAACTCACGCAAGCGGTTGACCTGGTAAATGGAGCTAGAATGA\n")
-		f.write("TACTTGAACATCAAGCAATGTCATCAACTGAGAAATGAACTCTGGGTGGCCTGGCCACGCTGCTCCAGTA\n")
-		f.write("ACCAAATTTCCATCCGTGAAGCAACGATCTATTGGATCAGGTTCCAGCCATGTGCCTCCCGAAAGAACCA\n")
-		f.write("CATTAAGCTTCACCGCAGGGTATGCAGTACATTTCTTTCCCTGCAGAACACCAGCAGCAGCTAAAATCTG\n")
-		f.write("CTGCCCATGGCAGATGGACGCAACTGGTTTCCTGGCTTCAACAATTTGCTTCACTAATGCAATAACTTTC\n")
-		f.write("TCATCCAATGCCAAATATTCAGGAGCTCGACCTCCAGGGATTACAAGCGCATCGTAACTTGAGACATCTA\n")
-		f.write("GAGCTTCAAAATCAGCTGTTAAA\n")
-		f.write("\n")
-		f.write(">gi|226789631|gb|GO545872.1|GO545872 Mdas9005N12_e386.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564944.1| bHLH protein family [Arabidopsis thaliana] pir|H96712 probable DNA-binding protein T6L1.1 [imported] - Arabidopsis thaliana gb|AAG51581.1|AC011665_2 putative DNA-binding protein [Arabidopsis thaliana] gb|AAG52041.1|AC011914_11 pu, mRNA sequence\n")
-		f.write("TTTTTTTTTAGTGAAATAGTACCATATATATGTAGTTCCAACAGTACCACAACTGTTCTGATCAATTCTC\n")
-		f.write("TTATTAGATAGAGAGTGATCAACAAAACTAGTAGCAAAAAAACAAAAACCCCAACACACAACACAGACAG\n")
-		f.write("ACTGCAACTTTGAGTTGAAAGCGGATCAAATCAAAGACCATGATGCAGTTTAGTTTCTATCTTTGGATTT\n")
-		f.write("TATATAAGGTTTCTCTCCTCACGAAAAAGATCCTTCACTGTTTTTTCCCTTCCTAGCAAACCAAAGCCCT\n")
-		f.write("TCTCTCTCTGCATATCTCTCCATCTCTCTCTCTCACCAATTTTTTGGAGTAATGCAGGTGGTACACAAAC\n")
-		f.write("CACACCATCATTACCCATTTGTGCACTCACGGAAATACACCACAACAAACACGCTAAACCAACCAAAAGA\n")
-		f.write("ACAAAAACCACCAAGAGAAATAAAAGAAGTTTAATTAAAACTAGTAAACCCTAGGCATGATATTAATTAG\n")
-		f.write("TCAGAGGGACCTGTGTTCAAGGATATTGATGTTATTAGTCCTTTGTCTCTTAGCACTCCCTGTGGAAGAT\n")
-		f.write("TGATCCTGATCGCCGCAGCCGGTTTTCTCCATGACAGCCTTCAGTGCTTCTTGAATCGAGCTTTTACATA\n")
-		f.write("CTGTTGATGCTGCATTTGTACTTGCTCT\n")
-		f.write("\n")
-		f.write(">gi|226789630|gb|GO545871.1|GO545871 Mdas9004L12_e304.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTCTCAACATATTTGAGAAGATGAGTACCACTGGAACTGGCTTTAGCAACCACGCTTTCACCATGCCCGG\n")
-		f.write("CGGTCTCCAAGTAAATGAGCAAACTAGCAAGAACAACACCCCATGCAACTTCCAGATGCCTCTGCACTAC\n")
-		f.write("CCAAGGTACCAAAAGAGTGACTATGAGAGCATGCCTGAATGGAAACTGGACTGCCTTATGAAGCAGTACG\n")
-		f.write("GCCTCCCACTCATTGGGGATGTCAACCAGAAAAAGAAGTTTGCCATGGGAGCCTTCCTTTGGCCTTCACA\n")
-		f.write("ATACGAATGATAAACCCTATCTAGTAGCTTAATTGCTACGATTTCTAATAATATTCTACATATATATGGT\n")
-		f.write("ATTACAAAAGACTACTGGCATGCATGTATATAGTGAAATAATATTAATTGCTTTTTAGTAGTATCCCTTA\n")
-		f.write("TTTAAGTACTGTCTATCTGTATTCAGCAGTGTATTACTGTG\n")
-		f.write("\n")
-		f.write(">gi|226789629|gb|GO545870.1|GO545870 Mdas9005F09_e355.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32980|ATPD_TOBAC ATP synthase delta chain, chloroplast precursor pir|S26198 H+-transporting two-sector ATPase (EC 3.6.3.14) delta chain precursor, chloroplast - common tobacco emb|CAA45153.1| chloroplast ATP synthase (delta subunit) [Nicotiana, mRNA sequence\n")
-		f.write("TTTTTTTTTTGTGAGCAAAAAGGCCTTCAAAATTGCCTCAAATTCACGTAAAAACTCCCCATACATACAT\n")
-		f.write("ATATATACTCAAACGTACGGTTTTACACATTACAGTGGTTAAACCATAATCAAAATCAAGAGCAAATTTG\n")
-		f.write("GAGTTATAAATTGAGCTTAATGTCACCCAAATCAAGCTCCGCCGCAATCTCCTCCAGCTGCTTCTTCACG\n")
-		f.write("CTCAAGTCAATAAGCTTCGACCCCGACTGCCCGTACCTCACCGTGAACCCCGCCACCAGGCTCGGATCAA\n")
-		f.write("TCTCCGTCTTGATCCTCACGTTCTGCGCCCCCGTCAGCTTCTGCACCTGCTTCGCTATCTGCGCCAAGTG\n")
-		f.write("CTGCGACTCCAGCTTCACCACCGAGCTCACGATCGCCAGCTCCGTGTCCGTTATCTTGTTGTACACCACC\n")
-		f.write("TCGAACTCCTTCACGATGTCCTTTATCAGGTCGATCCGCTTCGCGTCCACCAGGATGTTGAGGAAGTTGA\n")
-		f.write("TCGTGTGCGGCTGCAGCGCCGACGACTTGGCGATGTCGTCCAGCACCTGCCGCTTCTTCTCCAGGCCGAT\n")
-		f.write("TGTGGCCTCGTG\n")
-		f.write("\n")
-		f.write(">gi|226789628|gb|GO546124.1|GO546124 Mdas9002H19_e127.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565379.1| Calmodulin-binding protein [Arabidopsis thaliana] pir|A84533 hypothetical protein At2g15760 [imported] - Arabidopsis thaliana gb|AAD41988.1| expressed protein [Arabidopsis thaliana] gb|AAK31147.1|AF345343_1 unknown [Arabidopsis t, mRNA sequence\n")
-		f.write("TTTTTTTTTTGTGTAAAATTCAAACATCTATATTTCACAACGATGAAATTATAAAAAACAAAATGTATCT\n")
-		f.write("ACGACCACAGATTGAATTATTATCTGCATCCTCCACCACGTGTCAAAGACACGAATGCTCCTCTGGAAAC\n")
-		f.write("CTCGTGCAACCCAGTGTTGAATCCCAAGCAACCCAAGAGCCCATGCTTGTAAGGTAAGAAGGTCTTCCTC\n")
-		f.write("CTCATCTCCTCCGTAACCGCCCGGTTCGCCGTATAATGCAACTCGTGCGGCGAAACCGGTCCTTTCCTCC\n")
-		f.write("TCGAGCTCACCGACCCCACGCTGTCGGTGGACCGGAAACTCGAGTTCTTCACGTCCTGCGCTAAACTACT\n")
-		f.write("ACTCTTCATCTTGGGCGACAACATGGCATAGTTCCTCGAATGGTCTTTGCCCGTTGTGGCTCG\n")
-		f.write("\n")
-		f.write(">gi|226789627|gb|GO546123.1|GO546123 Mdas9002M24_e152.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTACATATTTATAAGTTCCGATTTTGTAGGTCACCAGCTGATTTCATACATATTGGAAT\n")
-		f.write("GAAGGTTCCAAATAGATTTTTGTACACAAGGCAAGCAGATAAAATTACAAGTTTTTTGTCCTACCAACGT\n")
-		f.write("TGCCCCTTCTCCTCCCGCACTTGAATCCCAATTAGAGTTCTCCTTCTTTCCTCACTTCGGGGAAAAAGAA\n")
-		f.write("GCAAAAATGGTGGCATGGCCGGGATCGGCGAGGTGAGCGAAGAGGTTGTCAATGGGGCCAGTCCCAGTGT\n")
-		f.write("AAATGTGTTGGAACCAAGCTCCCATCACAGCCAACATAGCCAGCCTTCCGTTCTTGATCTCCTTTGTCCT\n")
-		f.write("CAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGTCGAACCAGAGCCCTCCCGGGTAC\n")
-		f.write("CCAACATCTGTCCCGGTGAGCTTGTTGT\n")
-		f.write("\n")
-		f.write(">gi|226789626|gb|GO546122.1|GO546122 Mdas9002M07_e147.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF61440.1|AF138264_1 papain-like cysteine proteinase isoform I [Ipomoea batatas], mRNA sequence\n")
-		f.write("TTTTTTTTTAACAAGACATAAAAATGGACATTTAAGCTGTTCGGGCAAACACCGAGAATTATAAGATACA\n")
-		f.write("TGGGGTGTTATGTTTGTTTGGTCATTTGTTTAGCAAGCCCGACAGAAGACAGCAAACAACTGGAGTTTGC\n")
-		f.write("CCGATAAATATCACCACAACTGTATATACATTAAACAGAACTGCTATTGTAAGTTAGGGTTGAACCCTAC\n")
-		f.write("TACTCTGAGTTGGTCTTAACCGAAGCTGCAGCAACAGTCGAGACCATGGAGTCCACGCCACAGATGTTTC\n")
-		f.write("GGCCCCTGCAGATTTTGTAGAATCCACTCTCTCCCCAGTTCTCTCCCCATGAGTTCTTAATAATCCAGTA\n")
-		f.write("TGGCTTCTCCTTCAATCTGATGGGAGAATACCCAGCTGCACCATAACCTACGAGTAACACTCCGTGATCC\n")
-		f.write("AACCGCTTTGAGCATATGTAGGGGCATGACACTCCACCAACATA\n")
-		f.write("\n")
-		f.write(">gi|226789625|gb|GO546121.1|GO546121 Mdas9010A14_e717.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CATTATTTTATAGATTGGCATCTGCTTAAGTAGGACTACATAAATTACGTTACATTTCTCCATAAAATTA\n")
-		f.write("TGAAGTAGCTACAAACATTTAGAAATAAACTGTATATGCATAATTGCCAAAAAACTCATCATCACTCAGC\n")
-		f.write("TTCGATGAGTCCAATTCCGGCATGAAAATCAAAGCCTATGTGGTATAAAAGTACC\n")
-		f.write("\n")
-		f.write(">gi|226789624|gb|GO546120.1|GO546120 Mdas9002D05_e105.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTGCGTTTCAAGAACAGAGAGAGGCTTGAGTTTTAAGATGGTATAAAAGTTTAAATTTTGGATAAT\n")
-		f.write("TTTGTCTTTACATGTCCATATGGATTTGGTTTTCTTTTTACTAGTTGAACAGGATTTTTTTTATTTTTTT\n")
-		f.write("ATAGGAAAACAAACGAAAAATAAACTTGGAATTTGTATAAAAGTCAGAATTTATAAATTGACATATACCA\n")
-		f.write("ATTCCTTTGTTTGGATTCATAAACATACAAATTTAGAATTTTAGCGTGGAAAAAAACTTGGAATTTGGGA\n")
-		f.write("TCTCCAATTCTCAAGTTTAAATTCCATGTGAATAGGTGTCATTTCCCAATTTCTATGATTGAGAGTTTAA\n")
-		f.write("AAATAACAAATTCCATATTCATTTAGGTTAACCAAACAAAAAAATTCACAAATTCTAGAAAAATAAAATC\n")
-		f.write("CTATCAATTTCATCACCGTCATTTTTAAAATTTCTTAGTAATCTTAAATTTCTTCATCCAAACATAATGT\n")
-		f.write("AAAAGTGAACAGTACTAGGAGTGTTTCGTTAAAACTCCATTTTTT\n")
-		f.write("\n")
-		f.write(">gi|226789623|gb|GO546119.1|GO546119 Mdas9002P24_e169.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTAATTTTCCTTCCCGAAAAAAAACACCCATGCATGCAACAATGCTTTCACAAATAAAAACAAATGGTGT\n")
-		f.write("GTACAATATCCCATCCCAATTAACATCATCTCCATACCCTTAATAATCAAAAAAAAAAAATATTGGGGGG\n")
-		f.write("AAAATTAAACCAATGG\n")
-		f.write("\n")
-		f.write(">gi|226789622|gb|GO545869.1|GO545869 Mdas9004N13_e314.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTAGCCAGAAAAAACTAATGGTACTAATCAATAGGGCTAGTAACAATAATAATTATAAAATTCAGA\n")
-		f.write("AAAAAATTGCAACACTGAAAATTACAAATAAACATCTATTAGAATTCTTCAGGGATGCTCTTCAGGACTG\n")
-		f.write("GACCTACAGCACATAAAGTGCTAGCTGGAGATGACTCAATAGTAATACGACCTGTTGGAATTTGCGTAAG\n")
-		f.write("CTCACGAGCTACATCCTTGAAATCAAGAATGCCTCCATTTTTGCACTTTGAAAGCATTCGTGCCGCTTCT\n")
-		f.write("TGCTTTGTCATCTTGACTTTCACTCTAATCGCCCCTCTTTTCACATCTTCTATTTCCTCCTTGATCAGTG\n")
-		f.write("GTTCCGAATTTTCATGGTAAGTGCAACTGCTATTAACTTTTTGCTTCCTCGACAAGGGCTTGTTACTAAT\n")
-		f.write("TAACTCATCTATGTATACAACATTCTTTACGTAGGGTTTCCTAAGTTCTAGCATGTCATCTATTGGTTTG\n")
-		f.write("ATCCTACTGAAGAAAGAAAGCAAAGAATTCAACATTGTTGAGAGAGAGAGAGAGAGAGAGAGAGATTTAA\n")
-		f.write("ATCACAATAATTTCATACCAGAAAAGATCTTAACATTATTGAAACTACATTAGTTTTGATACAATCCACA\n")
-		f.write("AAAAATATCGGAAAGATGAGTCAACTGATGCCTCAAGGTCATGAAATGTCACTG\n")
-		f.write("\n")
-		f.write(">gi|226789621|gb|GO545868.1|GO545868 Mdas9005E13_e348.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P42896|ENO_RICCO Enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) pir|S39203 phosphopyruvate hydratase (EC 4.2.1.11) - castor bean emb|CAA82232.1| enolase [Ricinus communis], mRNA sequence\n")
-		f.write("AATTAGGCAGCTTCAAACACTTAAAAAAACAACTCAAAACAGAGTACATAGTCAAACATGCTTACTCGAA\n")
-		f.write("AATTTCCAGTGTACTGTTTTCAAGCTCTCAGAACAAAACTTATCTGAAAATTATTGGAAAAAGGGTTTCA\n")
-		f.write("AGTTCCACATAACTATTCCCTATGTTGTGAAACTCCGATTTCTCACATCCCGCAAAAGCTTTGGAAGCAC\n")
-		f.write("TTCATAATCTAATAGGGCTCCACGGGCACACGGAACTTGGCTCCAGCATACACTGCCTCTGAACCGAGCT\n")
-		f.write("CCTCCTCAATTCGCAAGAGCTGGTTGTACTTGGCAAGACGCTCTGACCTACAGGGAGCTCCTGTCTTGAT\n")
-		f.write("TTGTCCCGTGGCCAAACCCACGGAGAGATCAGCAATGAAGGTATCCTCGGTTTCTCCACTGCGGTGGCTG\n")
-		f.write("GCCATCACACCCCATCCAGCTTTCTTGGACATTCTTACAGCCTCAATGCTCTCAGTTACGGATCCAATTT\n")
-		f.write("GATTCACCTTGAGAAGAAGAGCATTGCAAGATTTCTCCTTGATTGCCTTCTCAACCCTCTTGGGGTTGGT\n")
-		f.write("GACCAACAGATCATCTCCCACAATTTGTACTTTTTCTCCAACTTCAGCTGTCATCT\n")
-		f.write("\n")
-		f.write(">gi|226789620|gb|GO545867.1|GO545867 Mdas9005D23_e344.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("CAATCAACCCCACTCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAAAGTGCCTCGAAAAAGGG\n")
-		f.write("ACAGAAAATTAAAGAAACAAATAGACCGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAAACCA\n")
-		f.write("CCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAAAACAA\n")
-		f.write("CTTAAACCCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGCCAAATCCAAT\n")
-		f.write("GATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCACCTCTTTCAACACCTGGGAAGAGTCG\n")
-		f.write("GTGCATCCGAAAATGGGCAGCTTCCACATTGTCCAGAACCTTCCATCAGAATATCCTGGGGATCTGT\n")
-		f.write("\n")
-		f.write(">gi|226789619|gb|GO545866.1|GO545866 Mdas9005K14_e377.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAAC\n")
-		f.write("ACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGG\n")
-		f.write("TCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTA\n")
-		f.write("CATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAA\n")
-		f.write("ACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTC\n")
-		f.write("TTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTG\n")
-		f.write("TCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTC\n")
-		f.write("AAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n")
-		f.write("AGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACACCTGCATGCATTGCA\n")
-		f.write("CTCTTCCTCCATTGCTTGCAATAGAGGTAATGTCA\n")
-		f.write("\n")
-		f.write(">gi|226789618|gb|GO545865.1|GO545865 Mdas9005L22_e380.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CACAATAACGGGGTATTATTTTTTAGGGTAAATTACATAGTTACCCCTCAAGTTTAAAGTCTATTACAAC\n")
-		f.write("TCTATACAACATCTTTAAAACATTTCACTTTCATACCCCACCTACTATTTTATTTCAAAATAGTACCTCC\n")
-		f.write("ATTACAACATTTACCCAGTAAAATACTTGACAATTTGAACATGGTACATAATTTACACTAATTCGGGAAA\n")
-		f.write("ATTCAATTGGATGAACGTAATTAAATCAAATATTCAAAGCTTATGACTAATTTGATCTGCTAATTAACCC\n")
-		f.write("AACAATCATTATGATCCCTTCTCTGAGGCTGCAGGCTCAGCAACCTTCTCCTTGGAAAATTCCTCCACAT\n")
-		f.write("CAGCCTTACCTTCATCCTTCACAGCCAGCAAGATCAAAACCAGCAGCACCGGATAACTCACGGGGTTGAG\n")
-		f.write("CGCGAAATTGGTAACCAATTGGGAAAGGAAGGATGCCTTGAGCGTATCCACTTGCCAA\n")
-		f.write("\n")
-		f.write(">gi|226789617|gb|GO545864.1|GO545864 Mdas9005I15_e369.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD41136.1| OSJNBa0084K20.16 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTGGAAACAAAGAAACTATATCTCTATATCTATCTGTCAATATATA\n")
-		f.write("GATACACACATGTTCATACATAATCAATTTCCCCAATTCCTAGATATCAGAAACCTATATCCAGTTGGAA\n")
-		f.write("AAATAAAATTTACATGGGCATTAATAATATCGAAGTTATGACTGGGACAGGCAAATAATGAACAATGACC\n")
-		f.write("ACAACATTGGTTTTAAGGGTAACATAATCATACAGCTGCAGCCCTGAAAAACAAAAAGTCTGAAATCTTG\n")
-		f.write("TTCGCGTACAAAATCTGGTTGTATGGAGTTGTCAGGACTCTGAAGCCCTGGTAAGGTGGTGACGCCCGAC\n")
-		f.write("AGAACAAGAATAGTTTTGCAACCACCATTTTGTCCAAACACAATATCCATATCTAATCTGTCCCCAACCA\n")
-		f.write("TGCAAATCTGCGACTTCAGAGATG\n")
-		f.write("\n")
-		f.write(">gi|226789616|gb|GO545863.1|GO545863 Mdas9005J04_e372.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849999.1| tyrosine decarboxylase -related [Arabidopsis thaliana] gb|AAL69507.1| putative tyrosine decarboxylase [Arabidopsis thaliana] gb|AAM20115.1| putative tyrosine decarboxylase [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CAGGACAAGGCGGTGGAGTGATACAAGGCACAGCGAGTGAAGCAGTTCTGGTTGTACTATTGGCTGCTCG\n")
-		f.write("TGATAGGATTTTGAGGGCGGAAGGAAAAAAAGCCCTCGAGAAGCTTGTTGTCTATGCATCTGATCAAACA\n")
-		f.write("CATTCAGCTTTACAAAAGGCTTGTCAGATAGGGGGAATCCATCCTGAGAATTGCAGGGTGCTGAGTACCG\n")
-		f.write("ATTCCTCTACTAACTATGCCCTTTCTCCCAATGTACTTAATGAGGCGATTTCAAATGACATCGCGAGTGG\n")
-		f.write("TTTAGTACCATTTTTCTTATGTGCAACGGTTGGTACTACTTCATCAACAGCGGTTGATCCTTTGCTGGAA\n")
-		f.write("CTGGGAAAGATTACTAAGAGCAATGGAATGTGGTTCCATGTGGATGCTGCATACGCTGGTAGCGCTTGTA\n")
-		f.write("TATGTCCAGAATACCGACACCACATTGATGGTGTTGAAGAAGCGGACTCATTTAACATGAATGCACATAA\n")
-		f.write("ATGGTTTCTTACGAACTTTGATTGTTCGTTGCTCTGGATCAAGGATAGAAACGCTTTGGTCCAGGCGCTG\n")
-		f.write("TCTACAAATCCTGAGTTCCTTAAAAACAAGGCCTCTCAAGCAAACCTGGTTGTGGATTACAAAGATTGGC\n")
-		f.write("AAATTCCACTTGGACGTCGGTTTAGATCATTAAA\n")
-		f.write("\n")
-		f.write(">gi|226789615|gb|GO546118.1|GO546118 Mdas9002G24_e124.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n")
-		f.write("TGATTTCTACATATTGGAATGAAGGTTCCAAATAGATTTTTGTACACAAGGCAAGCAGATAAAATTACAA\n")
-		f.write("GTTTTTTGTCCTACCAACGTTGCCCCTTCTCCTCCCGCACTTGAATCCCAATTAGAATTCTCCTTCTTTC\n")
-		f.write("CTCACTTCGGGGAAAAAGAAGCAAAAATGGTGGCATGGCCGGGATCGGCGAGGTGAGCGAAGAGGTTGTC\n")
-		f.write("AATGGGGCCAGTCCCAGTGTAAATGTGTTGGAACCAAGCTCCCATCACAGCCAACATAGCCAGCCTTCCG\n")
-		f.write("TTCTTGATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGTCGA\n")
-		f.write("ACCAGAGCCCTCCCGGGTACCCAACATCTGTCCCGGTGAGCTTGTTGTTGGGGAAGATTGGGTCTGTGTT\n")
-		f.write("AACAGACCCGGGCTTGAGGATGTCCGCCCATCTCCTTCCCTCGGCCCACCCGATCAAAACAAGCTCAACG\n")
-		f.write("ACGAAGAGAGTGGTGGTGTCTGTGAAGTACTCTTGCTCTCCGGC\n")
-		f.write("\n")
-		f.write(">gi|226789614|gb|GO546117.1|GO546117 Mdas9002D04_e104.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTCGTAAGTACCAAGTTTGCAATCTTTAAGTTGAGTACAAGGATACAAGTACCAACAG\n")
-		f.write("TGGACCGAGAACATATGCCATCCATGCAGATGTCCTCCGTTTCCGGTTGGAGCCACCAGTCCGACGTTGC\n")
-		f.write("CATTGCACTTGCAAAAGTCCATCTTGAAGTGAGAAATTATCTCCTCTTCACCCTTGTCTGCTTAATAGAC\n")
-		f.write("AAACAATAAAGATAAACCTAATAAGATACAGGACACATTTTTCTACATGGATAATGTTACATACAATATA\n")
-		f.write("TACACATCAACACTTCTACTGCAGTACATGCGTAAACACATTGATTACATGTTGCAGAAAGCAGTCGCGT\n")
-		f.write("TAAGAACTACTAGATTTTCCCCATGACCTAAAGAACCTAATCACGGGGTCATGGAGGTCTTCTTTGGCCC\n")
-		f.write("TCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226789613|gb|GO546116.1|GO546116 Mdas9002P23_e168.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTAGCATGAAGGCGCTCAATATATAAATGCTTTCACCTCGCACTTTGTCTCTCTCGC\n")
-		f.write("ACATTGTCTCTCATGGCAATCTGATCATTACAGAAGTCCTACTTTGCCTCCAAAAAAGGAAGCATAAATA\n")
-		f.write("TTATTAATCAGACAACTGAATTAGTTAACGGTAACTTTGCCGACCATGCCAGCTCCCTGGTGAGGAGAGC\n")
-		f.write("AGTAGAAAGAGTATGAACCTTTTTCGGTCAAGGTGATGGCGTAGGTTTCCCCGGGGGCATTCAGGAGGTC\n")
-		f.write("CTCCTCGCTCATCGAGATTTTTCCAGCATCCACACCGCTGGGAACCTCGTCCTCGTCAAACAAAACGTTG\n")
-		f.write("TGTGGGAATCCAGCATTGTTCTTGAACACAATCTTCTCACCGGGGGCGATGGAGAAGCTGTTGGGGACAA\n")
-		f.write("AGGCTAAGCCACCGTCATCGCTGCCTAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCACT\n")
-		f.write("GGCGGCAGTGGCGGCAACGGCCACACCAACATCCTTGAGGGATGACTTGACAATGCACA\n")
-		f.write("\n")
-		f.write(">gi|226789612|gb|GO546115.1|GO546115 Mdas9002K24_e142.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S31865 chlorophyll a/b-binding protein Lhcb5 - Scotch pine emb|CAA78900.1| Lhcb5 protein [Pinus sylvestris] prf|2104448A Lhcb5 gene, mRNA sequence\n")
-		f.write("GTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCAATTTGATATAC\n")
-		f.write("AATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGAGCTCTTTCGAT\n")
-		f.write("AGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATAGGTTTTCGACA\n")
-		f.write("GGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAGTCTTCCGTTCT\n")
-		f.write("TAATCTCCTTCACCTTTAGCAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGGTCAAAAGGACC\n")
-		f.write("ACCTGAGTGAAGCTTGTCC\n")
-		f.write("\n")
-		f.write(">gi|226789611|gb|GO546114.1|GO546114 Mdas9010C03_e727.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTGACTAAAGATTGTATTCCTTGAACAATGAATGAATTACAGAGAGGTGTTTGTTAT\n")
-		f.write("TTATACAAGTTTCTCCAGAGCTCTTCTCAGAAGACTTCTTCCACAACCACTTGCGCTCCATCTACGGTTC\n")
-		f.write("GATTCTCCAACTCCCCAACTAGCACATCACAATGTGTTCATCTACAACACACAACTACAATTTTACAGAG\n")
-		f.write("TCATCAAAAACCCACCTCAAATCCTCTTCAAAGTTGCACGAAACAGAAGATGAAAGCCTTAAATAGTTAG\n")
-		f.write("CCAACAACGAAATCCTTAGAGATTGTTGCTGCACAACTATAACTCCAACTAATACAGCAAAGCCTTTCAA\n")
-		f.write("ATTTAGGAAGCAAATTCTTTCCACCAAATCTAAAGCATTTAAGCAAAAAAGGAAAGACTTCGCTTATCGC\n")
-		f.write("ATTCTCTCACCTTTGCTTCAAATCCATTATCACACTATATAAGAATCAAAACAAAATGGATCTGCAG\n")
-		f.write("\n")
-		f.write(">gi|226789610|gb|GO546113.1|GO546113 Mdas9002C19_e102.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S16294 chlorophyll a/b-binding protein type I precursor - tomato, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAACGGACGTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAA\n")
-		f.write("AAGCCTTTAAAAGGACTCAATTTGATATACAATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAAC\n")
-		f.write("TTAAAATTACAGGGTTGGAGCTCTTTCGATAGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGA\n")
-		f.write("TCGCTCAGATGCTTTGATAGGTTTTCGACAGGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGA\n")
-		f.write("GCATGGAAAACATGGCAAGTCTTCCGTTCTTAATCTCCTTCACATTTAGCAATGCAGCCTGGTCTGGATC\n")
-		f.write("CTTAGCCAGCCCCAGTGGGTCAAAAGGACCACCTGGGTGAAGCTTGTCCTCCAATTCCAAACCGTTAGTG\n")
-		f.write("ATTCTGTAGTATTCAGCTCCACCAAGAAGAACAACCTCAGCAACAACAGCGAAAATAAGATTAATCGGTA\n")
-		f.write("TGTTCTTCCCAAAGTAATTCAGTGT\n")
-		f.write("\n")
-		f.write(">gi|226789609|gb|GO546112.1|GO546112 Mdas9002G13_e120.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176347.1| light-harvesting chlorophyll a/b binding protein [Arabidopsis thaliana] pir|E96640 PSI type III chlorophyll a/b-binding protein [imported] - Arabidopsis thaliana gb|AAD25555.1|AC005850_12 PSI type III chlorophyll a/b-binding prote, mRNA sequence\n")
-		f.write("TTTTAACATGTTTTTTCTCACAGAGTCACAGACAACCATAACAAACAACAAACAAAGGCCAAATTATATT\n")
-		f.write("AATTGTACAAACGTTACTTAATGGAACTTGAGGCTGGTCAAGATGTTGTTGTGAACTGGGTCAGCCAAAT\n")
-		f.write("GATCCAGAAGGTTCTGGTAAGGCCCCACACCAGTCACAAGACCCTGAATAAAATAACCCAATATTGCCAG\n")
-		f.write("CATGGCAAGCCTCCCATTCTTCACTTCCTTGAGCTTTAACTCGTTCAACGACTTTTCATCTTTCCCAAAC\n")
-		f.write("CCTAGCGGGTTGAACAAGGGCCCACCAGGGTAAGCCGGGTTCCCGGACCCACCCAAGTACTTCTCAAACC\n")
-		f.write("CCAAGAAGTATTGCTTGCCCATGGACCCGGGGTTGTACCAGTCCTGGAACCTCCGGTGCTCGGCGAAACC\n")
-		f.write("CCATTATGGCA\n")
-		f.write("\n")
-		f.write(">gi|226789608|gb|GO545862.1|GO545862 Mdas9004N10_e312.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n")
-		f.write("GTCAATCCATATTTTACTCATCATTACATTGCCCAATCAGGGCCCTTTTTTCATCAATATTGCAGTAAAC\n")
-		f.write("AACATGAAAGTAAGGGTCCTTCCTTGCACCAAGTTAACCCCATGACGCCCACACACAATATCCCAAAAGC\n")
-		f.write("CAAATTCTAACCAGAAAAGGCGGAAACAATACATAAACGAAGCAGATAGATAAATGAACACCGATTTTCA\n")
-		f.write("TGTCATCAAGCACCCACACTGTGAAGCACAACGGTCTCAACAGTGAGGCCAGGCCCAAATCCGAAGAGTA\n")
-		f.write("CGCCCCACTCCAGTCCTTCTCCAGTTGTTTTGAGTCCTTTCTCAGCAGACTTCCTCCTCACTTCGTCCAA\n")
-		f.write("AATAAACAAGACACACGCACTCGACATGTTGCCGTAATCAGACAGCACTTGTCTTGTAGCTTCTAGTTTC\n")
-		f.write("TCCGGCTTAAGGGCCAACTTGGACTCTACTTGGTCCAGAATAGCAGGGCCACCTGGGTGTGCAATCCAGA\n")
-		f.write("AGAGCGAGTTCCAGTCTGAAATGCCTATAGGCTTGAAGGCCTCGTTAAGGCTCTTTTCGATATTCTTGGA\n")
-		f.write("AATAAGCCCGGGAACGTCCTTGAGAAGGTGATATGTAAGCCCTACTTCACGGAGATGGCCGTCAATAGCC\n")
-		f.write("CCATCACTGTCGGGAAGAATGGTTTGTGCTGCTGACA\n")
-		f.write("\n")
-		f.write(">gi|226789607|gb|GO545861.1|GO545861 Mdas9005N01_e384.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("ATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCAA\n")
-		f.write("AAACAAACGAAAGTGCCTCGAAAAAGGGACAGAAAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCC\n")
-		f.write("CTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAAC\n")
-		f.write("AACATTATTTATGAAAATTGTAAAACAACTTAAACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACT\n")
-		f.write("GCACTTGACGGACATTGTCAAATCCAATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTC\n")
-		f.write("CAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTT\n")
-		f.write("CCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGC\n")
-		f.write("AGGGAACCCAGTTTTTGCG\n")
-		f.write("\n")
-		f.write(">gi|226789606|gb|GO545860.1|GO545860 Mdas9005B23_e333.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n")
-		f.write("TTCAAACAGAATAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGAC\n")
-		f.write("TGCTTTGAAGCAGTCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGG\n")
-		f.write("CGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCT\n")
-		f.write("CCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATC\n")
-		f.write("TGCAGACCCCGAGACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGT\n")
-		f.write("GCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGAGGCTGTCTGGTTCA\n")
-		f.write("AGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGCAACCCAAACCTTATCCATGCTCA\n")
-		f.write("GAGCATCTTGGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGGATACAGAGTTGGAGGA\n")
-		f.write("GGACCACTCGGTGAAGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCCCTTGGACTTGCTGATG\n")
-		f.write("ATCCCGAAG\n")
-		f.write("\n")
-		f.write(">gi|226789605|gb|GO545859.1|GO545859 Mdas9005L02_e379.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n")
-		f.write("TTTTGACTGTGCTGCTCATTACAAAAGTGAAGCAGACGTTGGAGAAGCACTTGCAGAAGCATTTAAGACT\n")
-		f.write("GGACTTGTTAAGAGGGAAGAACTTTTCATTACCACCAAGATTTGGAATTCAGACCATGGGCATGTGGTGG\n")
-		f.write("AGGCCTGTAAGAACAGCCTCGAGAAGCTTCAGATAGATTATCTGGATCTCTACCTGGTTCACTACCCAAT\n")
-		f.write("GCCCACAAAGCACAATGCAATTGGTAAAACTGCCAGTCTTTTGGGCGAGGATAAGGTGTTGGACATCGAT\n")
-		f.write("GTAACAATTTCCCTTCAACAAACCTGGGAGGGCATGGAAAAGACCGTCTCTTTGGGCTTAGTTCGCAGCA\n")
-		f.write("TTGGTCTCAGCAACTATGAGCTCTTTCTAACTAGAGATTGCTTGGCTTACTCCAAAATAAAGCCTGCTGT\n")
-		f.write("GAGCCAATTTGAAACCCACCCCTATTTCCAGCGCGACTCTCTCGTCAAATTCTGTATGAAACACGGCGTT\n")
-		f.write("CTTCCCACAGCTCACACCCCTCTCGGAGGTGCTGCTGCCCACAAGGATATGTTTGGTTCTGTT\n")
-		f.write("\n")
-		f.write(">gi|226789604|gb|GO545858.1|GO545858 Mdas9004M07_e309.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTAGAAATACACAGCCATAGGCATAGGGTAGGTAACCATTAAGTTGCATATAA\n")
-		f.write("TATGTAACACAGTCAACTCCAGCTCTGCTACCAACGGGTATTAGCACACAGAATAGTAGAATACTACTAC\n")
-		f.write("TTTTAGCACTACAGCACATAAATAGGCAGCCTCCGCTGCAGCACGCCTCTACATTATTTATCTATAATAT\n")
-		f.write("ATATAGTTCATATGTTGCCTCGGAGTTAGGGAAGGTGAGGCTTCTCCAAGTCCTCGATGCTGGTAGGGCG\n")
-		f.write("AAACCACGCCTCCTGCTCCATCACCGAGGATCCCTCCCCACCATCGCCCGTGGAGGAGCCGTCCTCCCTG\n")
-		f.write("CCTGCGGAAGATGTGTGTTCAGCTTCAGGCCCGAACACCCCCGGGTGGGGATGTGGAGCCCAGTACTTGT\n")
-		f.write("CCGGTTGGGGTGGGATCACATCATCTGGAACAAAGCTGGGTCGAGTTTGTTCCTCTGGGTTCTTGTCATA\n")
-		f.write("GGTCGAGGTGTGAGCAGCCCTCCTGAGAGTGAGAGCGGAGAGCTGAGCTGAATCGCGCGCTCGGATCTCG\n")
-		f.write("TTGATAAGTCGCTTCCCCAAGCTCGCGATACCTCGACTGCTCGAATTGGCGGCCATACAGTAAAA\n")
-		f.write("\n")
-		f.write(">gi|226789603|gb|GO545857.1|GO545857 Mdas9005D10_e341.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_181415.1| histone H2A, putative [Arabidopsis thaliana] ref|NP_850298.1| histone H2A, putative [Arabidopsis thaliana] ref|NP_850299.1| histone H2A, putative [Arabidopsis thaliana] pir|F84809 histone H2A [imported] - Arabidopsis thaliana gb, mRNA sequence\n")
-		f.write("TCGAGGATTGAGGCCAAGTACACAGCAGCAGTGGCGCCAACACGCCCATGAGCAGCAATTCGCTGTTTCA\n")
-		f.write("GCTGCCGATGAATTCGACCCACCGGAAACTGGATACCAGCGCGAGATGAACGAGAAACAGGCCTCTTCTT\n")
-		f.write("GTCCTTGTCCTTGTCCTTGTTAGCTGCTGTGGTTTTCGCTGCTATAAGCCCCTTCCCGCCCTTGCCCGCC\n")
-		f.write("ATTTCTACCTGAAGAGTTCTTGGGAAGCTTGAAGACCGAAGGGAACCGTAGAGAGAGAGAGGGGAAAGCT\n")
-		f.write("AAACCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226789602|gb|GO546111.1|GO546111 Mdas9002M09_e149.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93768|PSD3_TOBAC Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Nuclear antigen 21D7) pir|T02207 protein 21D7 - common tobacco dbj|BAA19252.1| 21D7 [Nicotiana tabacum], mRNA sequence\n")
-		f.write("ACCTGATAAACATGTTCAATGTCTGGTGAAAAATGTCAAATATTCAATGTTCGTATCATATATAACGGAA\n")
-		f.write("TGAAACAAGCAACCTCAAAATATGATTGAAACAGGTCGCTTAGGCTCAACACAACAAATCTTTAACATAA\n")
-		f.write("ACGGAAACAGGCACCATCCCGGGTCAATCAAACAAGGAACCAAAATGTTCTTGATAAACATTTTCAAAGA\n")
-		f.write("AACGCGGATAGCTTTTTGAAAGCATTGCACAGAGCGTAAATGTAACTGCTTCAAAACTCATCATCGTCCT\n")
-		f.write("CCTCAGCTATGTGCTTTGCAAGCTCTTGCTCCTGTTGTTGCCTCTCCCTCCTCTTCTCAGCACTTTCTTT\n")
-		f.write("CTCCTTGTGGGAATTTGGCGGGAATCGAAGCGCTCGCACTGCATCATTGTGCAAATTAAGGCAAAATGCA\n")
-		f.write("ATTCTCGTGTCAAATGCTGCTT\n")
-		f.write("\n")
-		f.write(">gi|226789601|gb|GO546110.1|GO546110 Mdas9002D02_e103.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTCATTATCTGTAGTTGGACTTCTATGAAACAGATAAATGCATCAGGAGGAAACGGAAGTGCGGAAATC\n")
-		f.write("ATTTTCCACGACAAACGCTCCAAAGATGCCAGAGGAAATAAAGGATCAACCCATTTAACTCTACTCATCA\n")
-		f.write("TCTAAAGACTCTCAGTGAGTGATTCACACA\n")
-		f.write("\n")
-		f.write(">gi|226789600|gb|GO546109.1|GO546109 Mdas9002D06_e106.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q41048|PSQ1_MAIZE Oxygen-evolving enhancer protein 3-1, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) pir|T01747 photosystem II oxygen-evolving complex protein 3 precursor - maize, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTATGATGCTTAAATATCACTAGATTTCCTCCAAATAGCATCCAAACA\n")
-		f.write("TTTTGATCTCATAAACAGGCAAACAAAGCTCTTAAAAAGCCTTATACATCAAATACATTAATCCCTTTTA\n")
-		f.write("GGGTTTTAGCCAAGCTTTGCAAGAACATCGTTGAGGGAAGATACGGTTGCGGTGTAGTACTTCTCTGCTT\n")
-		f.write("CCGGGGTGCTCTTGATCTTTGCTGCATAGTCCAAGCCGTCAATGTCTTTGAAGAGCTTTCCGGTGAGTTC\n")
-		f.write("CTTGAGGGGCTCCTTCTCGGCTTTAGATTTGGCAGAAATGACGGTCTTGAGGTCATAACGGAGATATGAG\n")
-		f.write("GCTCTGAGACGAAGATCGTTCTGGACGTAAGGCCATGCCTTTTTGTCAATGTACTCCTTGACAGCTAAAA\n")
-		f.write("TCTCCTTGGCTGACTCCTTCGCCCTCGCGGCTGCCTGAGCCGGAGTGAGTGGTTGGATGAAGAACCTCTC\n")
-		f.write("CTTCAATGGCAGGTCAAGGTCTCTTGCCTCATCCGAGTTTAGGGTTCCAGCCAATCC\n")
-		f.write("\n")
-		f.write(">gi|226789599|gb|GO546108.1|GO546108 Mdas9002P16_e165.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTAATAAAAACTCGTATTTGCTCTCTTCTCGTAATTCAGAACAGATTAAAGATTGTCCG\n")
-		f.write("AAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGCTCAAATCC\n")
-		f.write("ACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTCCGGGAACA\n")
-		f.write("AAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTTCTCCAATG\n")
-		f.write("GTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTT\n")
-		f.write("GAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAATGGGTCGAAGCTTCCG\n")
-		f.write("CCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAACTGCGCCC\n")
-		f.write("\n")
-		f.write(">gi|226789598|gb|GO546107.1|GO546107 Mdas9002A06_e89.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564664.1| expressed protein [Arabidopsis thaliana] gb|AAN13084.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TCGAGGATCCTCCTCCAATTAGATGCCTGCCATTCCAGTCAGACCGAAATCTATGAAAGGGATGAACAAC\n")
-		f.write("AGGTAGCAAATCCTTCCGCCTCATTTCAACCTCTTGACCAGGAACCTTCTCTATTTCCATCTCTCCGCGG\n")
-		f.write("GTAAGATCTTTACCAAAATTTAGCTCACCAGCAGCACATGGACTCATTGTATAGAAATATATCTTCGACT\n")
-		f.write("TTTGCCAGATTGGAATCCTTCCGGAATTGATCTGAACCTCAGCATTGGAGAGATACACATGAGATCGTTC\n")
-		f.write("AAGGGGTTTTGCCAACTCCTTATCCCCAACATCACTATCATCACAGTCAGAACTATCAATTGTGTCAATA\n")
-		f.write("TCTTCTTGTTTCCCAAGTATAACCCCAGAAAATGCATTCCTCTCTTTCAGGCCAATCATTTCTTCGGCAA\n")
-		f.write("ACATCCAAAAAATGAAGAGATTCAACTTTCACTCGCAAATCTTCATCCTGTATCTGTACTGAAGAACCTG\n")
-		f.write("GCCCTGCTCTCGAAGCAGCGTCGCCTGGCTCTCCTCCCAAT\n")
-		f.write("\n")
-		f.write(">gi|226789597|gb|GO546106.1|GO546106 Mdas9010B12_e721.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S20925 polyubiquitin - maize gb|AAB21993.1| polyubiquitin [Zea mays] gb|AAB21994.1| polyubiquitin [Zea mays], mRNA sequence\n")
-		f.write("CCGGAACCGAATTTATTTATAGAAACATAATATAAGATAACACAAACTTGCCCAGATGCCTCATCTTAGG\n")
-		f.write("AGGCAAAAACAGTACCATTAAACTTAAAAACATAAAATATAAACCATAAACTTCTTCCAACGGGAACAAA\n")
-		f.write("TAGCAGACGGTCACCGGCCACACCAGCACTTAGAAACCACCACGGAGACGGAGGACAAGGTGAAGGGTGG\n")
-		f.write("ACTCCTTCTGGATGTTGTAATCAGCCAGGGTCCTTCCATCCTACAACTGCTTACCAGCGAAGATCAACCT\n")
-		f.write("CTGCTGGTCCGGAGGAATACCCTCCTTGTCCTGGATCTTTGCCTTCACATTGTCGATGGTGTCCGAGCTC\n")
-		f.write("TCCACCTCCAAGGTGATGGTCTTCCCTGTCAAGGTCTTCACAAAGATCTGCATACCACCCCTCAGACGTA\n")
-		f.write("GCACCAAGTGAAGGGTCGACTCCTTCTGGATGTTGTAGTCCGCCAAAGTGCGGCCATCCTCGAGCTGCTT\n")
-		f.write("CCCGGCAAAGATCAGCCTCTGCTGGTCCGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTAACATTG\n")
-		f.write("TCGATGGTGTCGGAGCTCTCAACCTCCAAAGTGATGGTCTTGCCAGTCAGGGTCTTCACAAAAATCTGCA\n")
-		f.write("TGCCACCACGGAGACGAAGCACCAAATGGAGAG\n")
-		f.write("\n")
-		f.write(">gi|226789596|gb|GO545856.1|GO545856 Mdas9005C15_e336.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC69854.1| putative thioredoxin m2 [Pisum sativum], mRNA sequence\n")
-		f.write("TAAGTCACTAACATTCTCGTAAAGTAAAAAAAATAGTTACAACTTCATCCAGATAACTAACTATACAGGA\n")
-		f.write("GCAGACGTGAGTTTATTTTGGGAGAGAAGCCTCCGAAATCTGAGAGATCATAATCTAGAAAGAGAAGAAA\n")
-		f.write("CAGATACAAGGCACAGCTTAGGTCCAACAAGGGGAATAATACTTACCACACTCTACAAGAACTTCTCTAT\n")
-		f.write("GCTGGGGGTCAATGTAGATTTTGGAACAGCACCAATAACGGCATCTTTCTTCTCGCCACCTTTGAATATG\n")
-		f.write("ATGACAGTTGGGATGCTTCGAATCCCATATCGGGTTGCAATTGAAGCACTCTCATCAGTGTTAACTTTGT\n")
-		f.write("AGCATTTGAGCTTCCCAGCATATTGCTTTGCCAGTTCATCAATTATGGGGTGGATCATACGGCAAGGCCC\n")
-		f.write("ACACCACGGAGCCCAGAATTCAACCAAAACAGGGTATTCAGAATCTAGGACAAGTGACTGCCATGTTGCA\n")
-		f.write("TCACTAACAGCAGGCACTTCGACGGCAGTGTCCTGAGCCTCGCAGACGACGAGCCCGCCACGGCGGCTCG\n")
-		f.write("CTTGTCCGGAAGCGGGACCGTAACTCA\n")
-		f.write("\n")
-		f.write(">gi|226789595|gb|GO545855.1|GO545855 Mdas9005E17_e351.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CGAAGACTATCATATAGAATTTTATATGTCTGAACCAATCTCCAAAATAGAAGTGCAAAAACATGAAATA\n")
-		f.write("TAAATTATACTCGGCCACTCAAACACCATAGAAACAAACCCTAACAAAAAATAAGGACAAAAAAACACCA\n")
-		f.write("TTTCGAGTGAAGGGACTAGATTTAGATATTTTCACTTGAAGCACTTGGCATCCAAAAGAGCCTCTCCCT\n")
-		f.write("\n")
-		f.write(">gi|226789594|gb|GO545854.1|GO545854 Mdas9006P05_e481.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAATTCATATTCACACATGTAACCACTAATCCACCATTAACTTCCGACACTGATTTAATTGTTCATGAA\n")
-		f.write("ATATTACTGCAACGTAAAAGGATCCAGGTTACAATTCCTCGCACGAAAAAAGTAACTACATGAAAAAGTT\n")
-		f.write("TCACCTATAAAACCATATTGCGGTCTTCACCATCATCACTTGGATCAACATCGTAATCAAAGTCATGGCC\n")
-		f.write("GTCATTGTTTTCATCATACATATCATCTTCAAGAAAGTCATTTTCTTCTAAATCCTCGGGTTCTGATGAT\n")
-		f.write("TTGTCGCTGGAACTCTCCTTCTCTTCTGATTCATCATCGGAATCTTCGTTCTCTGATTCCTCTTCTTCCT\n")
-		f.write("CTTCAGAAATCTCATCCGGATAATCATTAAGCGGGTTGTTTTCAGCATTTGAATCATCAGATTCATATTC\n")
-		f.write("GGATTCATCAGGCCCATCATAAAAATCCTCGTCATCAACTTGGACCAAGGGGAATGGATTTGAAGATAAT\n")
-		f.write("TCGCGGACGCGTGGGT\n")
-		f.write("\n")
-		f.write(">gi|226789593|gb|GO545853.1|GO545853 Mdas9006N11_e469.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAATTCATATTCACACCTGTAACCACTAATCCACCATTAACTTCCGAAACTGATTTAATTGTTCATGAA\n")
-		f.write("AAATTACTGCCACGTAAAAGGATCCAGGTTACAATTCCTCCCACGAAGAAAGTATCTAAATGAAAAAGTT\n")
-		f.write("TCACCTAAAAAAACATATTGCGGGCCTCACCA\n")
-		f.write("\n")
-		f.write(">gi|226789592|gb|GO545852.1|GO545852 Mdas9005N24_e391.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("ATTTTAAAATATCTGTTTGACGAAACAACAGAAACGATACATTCAATGTACATCCTAGAGCTCAAATCCA\n")
-		f.write("ACACAGCAATTACCCCAAAAAAGCAACTCAAAAAAGAAGCAACTCTAAAAATTTATGCTTCTTGTACCCT\n")
-		f.write("TGCATAGGATGCTGATTGAAACATAACCAATGCAGGTGCTTTTCTCTAACTTGGTGGAC\n")
-		f.write("\n")
-		f.write(">gi|226789591|gb|GO545851.1|GO545851 Mdas9006M12_e463.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTTTTTACGGCATCTCTTGCTCTTAAATCTCTTTATTTTCTTTTGAAGCACTC\n")
-		f.write("ATTACATCACATTCCTATTAAAGTACATCAACATCCACTAGTGTTTTCAAATTCCTTGAAACATTAGGTA\n")
-		f.write("GTCTCCATTTTTCCTTAAATTAAATTTAGAAACATACTTGAATCCCTCTGGTGCGATTGGCCATAAGTTA\n")
-		f.write("GGCTTTCTGTACCGGACGCGTGGGT\n")
-		f.write("\n")
-		f.write(">gi|226789590|gb|GO545850.1|GO545850 Mdas9006J24_e457.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCCTAATCCTTGAATTAAGGTAAAAAGCCAAGGGAAAATGATATTAAATCCAAAAAGAAAAAAGGGTGTT\n")
-		f.write("ACTCATACATTCCTAGTTAGCCACTGTGGCCATCCTAAAAAATACATCTCGTCCTCTTATTAAGGACTTG\n")
-		f.write("AAAAAAAGACACAGGGAAGTCAAAACACGGAAAAACGGACGCGTGGGT\n")
-		f.write("\n")
-		f.write(">gi|226789589|gb|GO545849.1|GO545849 Mdas9006G18_e438.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_742507.1| glutamate-ammonia-ligase adenylyltransferase [Pseudomonas putida KT2440] gb|AAN65971.1|AE016225_4 glutamate-ammonia-ligase adenylyltransferase [Pseudomonas putida KT2440], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTCTTTTTTATTTTTTCTACTTCTCTATTGCCTCCCGATCCCTTCTTGATGTTCT\n")
-		f.write("CGGCCATTGCCCTGCTCCTCACTTCCTGCTGGATCATCTGCTTCATGGTGCGCATCGCTTCTATGGCGGA\n")
-		f.write("TAAGTCCAGGTAACGCCGGTAGACAAACGGTCGCAGCATGTCGAGCAGTTGTGCGCCAGCCACCTGGTCA\n")
-		f.write("CCCGCCACCACCCGCGCCTTGATCATGGCGTAACGTTCCCAGTCGCGGCCCTGATCCTGGTAGTACTGCT\n")
-		f.write("CCAGCGCGTTGAAGCTGAGCACTAGCGCCCCGGCTGAACCGTAGGGCCGCACGCGCATGT\n")
-		f.write("\n")
-		f.write(">gi|226789588|gb|GO546105.1|GO546105 Mdas9002H15_e126.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("CAACTGCATTTTTTCGTTATAACGCGAAAAAAAAAGGTGCATGATTCCGCGAATTTCTTCTGAAAAAAAA\n")
-		f.write("ATTGAAGAACCATAGCATTTCGCGATTCATTGGTAAATCTACTTTGATTCTCTATCAACCAATAATGTAA\n")
-		f.write("ACCATTAACAGGGTTAAAGCTAAACCGTTTGAAGTTCAGATGCAGCATGGTATTCTTTCTACTACTATGT\n")
-		f.write("TAGTTAATAAGTTAAGACAGAAATGGTTTCAAAACAAATAGTTGGAATTTTTTTTCGATATAAAACACTC\n")
-		f.write("ATGTCGATAAAATGATTTGAATCCGTTATTTGATTGGAAAAAATGGGTATTTCATCCCACGTTTTATCTT\n")
-		f.write("TTTTATCCAATGCTGAATCGATGACCTATGTATTATGTATTAAAGTAAGAAGAATTCTTTGAAAAAAACC\n")
-		f.write("TCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226789587|gb|GO546104.1|GO546104 Mdas9002J05_e136.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTAAGAAACATGACTGCACTTGCTATTTCCTTTCATAACTTAAAGTTTGACACTCATATCACACTATTGC\n")
-		f.write("TTGCTTGCTTGTAAGACTCTGGACAAAAGAAAACCCACAAAATCATTCATATCCCTGTAAACCCAAATGC\n")
-		f.write("ATGCAGAGAGATAAAAAAAAAAGACTCACACTGATGGGAGGAGGAAGATTGACACACAAATGGTAGTTAG\n")
-		f.write("AATACCAAGGGATCAAACAGACCGAGACCACAAGGACAACGAAGAAAAATAAATGAACAACGCTTCTGTA\n")
-		f.write("CCTGCTCCTAAAAATGGCATTGTATTTTCACTTGAAGCAGACCGAGGTTGACCAATAACAGAAGGACAAT\n")
-		f.write("CTGGGGAGGGAGGG\n")
-		f.write("\n")
-		f.write(">gi|226789586|gb|GO546103.1|GO546103 Mdas9002E03_e110.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P16059|PSBP_PEA Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|JS0771 photosystem II oxygen-evolving comp, mRNA sequence\n")
-		f.write("TTCATAACGATAGAAACAATAGAACGAACATAGGAACTCTGACGCTCGAGGGTAAACGCTCTTAACCACT\n")
-		f.write("CGAGTAAGAGGCCCGTAATTTCTTTGACTTACACAAGCAGAAGAGAACTGGTCCTTCTCTTAATACCATG\n")
-		f.write("AAACAACTATATATGCTCAACCATTTCCTCAGTTATAGCCAACTCTTAAACACTTGAGAGGAGAAAAGAA\n")
-		f.write("GAAGAAAAACTAGAGAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAA\n")
-		f.write("ATAAATTCTTATGCAACACTGAAAGAACTTGCAGTGCTCTCTACAAACTTCCTTGCTCCTTTGAACCACC\n")
-		f.write("TCTTGTCTCCGGCTTGTGCCTTTAGAATGTAGAGCTTGCCGTCTTTCACGGTGGCTGTGATAAGCTGGTG\n")
-		f.write("CTTGCCTCCTTCATCTCCGTCGGCTGTCCTTGTCAACACAGATACGTAGTAGTACTGCTTTCCGTCAATC\n")
-		f.write("ACTCGACTAGAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCACCCTCGG\n")
-		f.write("\n")
-		f.write(">gi|226789585|gb|GO546102.1|GO546102 Mdas9002M03_e145.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGTATCAATAGCTTGTTTAATAATTAAAACAAAATAATTGCAAGA\n")
-		f.write("ATTTCCATAGAAATACAAGCGCAAATTACAAAGAAAATATCAATAACCCAGCAAACAGAATATTTATTTT\n")
-		f.write("CTTCAGCTCCAATTACTCGTACTGACAGCTACCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCT\n")
-		f.write("GTTCGATCAGTGCAGCCTTCTGGGACTGGTACATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTC\n")
-		f.write("GGTTAATGGAGTCCTGGTTTGCATCTCCAAGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCT\n")
-		f.write("CTTCACATTGTCCTGCTCCTGAACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGT\n")
-		f.write("TGATCGAAAGTCGGGGGACCTTCTTTTGAGTTCACAAGCTTCTTCCCAATCCCG\n")
-		f.write("\n")
-		f.write(">gi|226789584|gb|GO546101.1|GO546101 Mdas9002M08_e148.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATC\n")
-		f.write("AACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAG\n")
-		f.write("AATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGA\n")
-		f.write("CCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGA\n")
-		f.write("CGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACG\n")
-		f.write("GATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCAT\n")
-		f.write("CCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCAC\n")
-		f.write("GGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAAC\n")
-		f.write("TTCCTTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACT\n")
-		f.write("\n")
-		f.write(">gi|226789583|gb|GO546100.1|GO546100 Mdas9002D09_e107.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAAGATGACAAACATCCCTCCATCCGCTTTATTAACAAAACTC\n")
-		f.write("ACATAAGTCCCAAACCGCATCAAATATCCACTATAACCATCACT\n")
-		f.write("\n")
-		f.write(">gi|226789582|gb|GO546099.1|GO546099 Mdas9002M17_e150.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P34105|MAOX_POPTR NADP-DEPENDENT MALIC ENZYME (NADP-ME) emb|CAA39690.1| malic enzyme [Populus balsamifera subsp. trichocarpa], mRNA sequence\n")
-		f.write("TTGATCTGCAGGAACAAATACAATTAGCATATTTATTCGAATTTTACAAACCCTTGTGATTTACACGCAT\n")
-		f.write("CATCTTTCACGAATTTTACAAGCACTGATACAGCACATCTTCAGAAACACACATTCTTGATAACTAGCCT\n")
-		f.write("CGAAGCGAAGCATAACACACAACAAACAACGGAGCCAGACACTGTTTAGCGGTAGTTTCTGTAGACGGGA\n")
-		f.write("CTGTACATGCAACTCTCGGCATGCTTCACAAGATTCTCAGGACGAGGGAGACGCGTAGCCACGCCTAGGT\n")
-		f.write("CATATGCCTTGGCAGCTACATTAGCAGCTACTTGGGCAGAAATCTTTCTGATGTTTGACAATGGTGGATA\n")
-		f.write("GATCAGCCCCTGTGCAAAATTCTCCTCGGAAACTTGCCCCGCCAAGGCTTCCGAGGCTGCCAGAAGCATG\n")
-		f.write("TCATCGTGAACACGGATTGCTCCAGAGATAACCAAACCCAGACCAAATCCAGGAAAAATGTATGCATTGT\n")
-		f.write("TGGACTGGCCAGGAACAAAAACTTTGCCCTTGTACTCAAAAGGATCAAATGGACTTCCGCTGGGCAAAAT\n")
-		f.write("TGCACGACCCTCACTGTAAGTATA\n")
-		f.write("\n")
-		f.write(">gi|226789581|gb|GO545848.1|GO545848 Mdas9006P17_e484.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTTCTGGCGTTTCGGTTGTGTGGATTATACAACGAAACACTTACAAGGGTTTAT\n")
-		f.write("ATTACAACAAATGGGAACAATTAATGAAGGAAACAAATAAAATTGCAATCCGAAAAACCAAGCTAAGCTC\n")
-		f.write("GACAGAGACACCTAATTTCAAAGGAGGCCAAAAAAGATTGACAGAAACGATACTTTCTCTACCTTAAGCT\n")
-		f.write("TTCAAAAAACACCCTCAGGAATCGATTATTTACTCTTAAACAATAAATTCATCGATAGCCCTATCGAGGA\n")
-		f.write("AGGCTTGAACGCCTGGATGAACTTCCAAGGTGGAGCCATCAAGGGGTCTTCTCTATTTGTTTTCTTC\n")
-		f.write("\n")
-		f.write(">gi|226789580|gb|GO545847.1|GO545847 Mdas9005P08_e396.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAATTCATATTCACACATGTAACCACTAATCCACCATTAACTTCCGAAACTGATTTAATTGTTCATGAA\n")
-		f.write("ATATTACTGCAACGTAAAAGGATCCAGGTTACAATTCCTCGCACGAAAAAAGTAACTACATGAAAAAGTT\n")
-		f.write("TCACCTATAAAACCATATTGCGGTCTTCACCATCATCACTTGGATCAACCTCGTAATCCAAGTCATGGCC\n")
-		f.write("GTCATTGTTTTCATCATACTTATCATCTTCAAGAAAGTCATTTTCTTCTAAATCCTCGG\n")
-		f.write("\n")
-		f.write(">gi|226789579|gb|GO545846.1|GO545846 Mdas9006A17_e402.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAAAAGAAACCGTCAGTACAGTACGTCTAGCTCAAATCAAATATATGGACCTAGCAACCAAGTTGGGAA\n")
-		f.write("CAAATTTATGCACTATCAAATGAGACTAGCTGCAAATGTCTCATGGCTATTGCAAGTCCGATCACCCCAC\n")
-		f.write("AAGCTCAAAGGGTCCCCGATACAATAAAAATC\n")
-		f.write("\n")
-		f.write(">gi|226789578|gb|GO545845.1|GO545845 Mdas9006P08_e482.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("AAAATTCATATTCACACATGTAACCCCTAATCCACCATTAACTTCCGACACTGATTTAATTGTTCATGAA\n")
-		f.write("ATATTACTGCAACGTAAAAAGATCCAAGTTAGAATTCCTCGCCCGAACAAAGTAGCTACATGAAAAAGGG\n")
-		f.write("TGACCTATAAAACCCTATTGCGGTCTTCACCATCATCACTTGGATCAACATCGTAACCCTTTTCATGGGC\n")
-		f.write("GTCATTGTTTTCATCATAC\n")
-		f.write("\n")
-		f.write(">gi|226789577|gb|GO545844.1|GO545844 Mdas9006N01_e465.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTCTGATGTGTATGTTACACAATGATATTTGGAGGGAACGTTGATGGATTTTACAATCTTGATGAAT\n")
-		f.write("CTGACAGCGTTTCTTACCAAAGGCAAAACTCCGGTGACCACTTAAACACTCAAAACCTCGTGAAGAATTT\n")
-		f.write("ACATTGAGGACCAACAAGCCAAGGAATCATAGAGTCGGAGGAAAACTTCCCATTGTCTTACATTTATGGT\n")
-		f.write("CACGTGCTATTCACATGGATCAAATGTTCGACACTCGTCCCATGGTGCATGAAAGTCAAGGGCTACAGGT\n")
-		f.write("AGAGATAGGACAAGAGGATAAATAAAGCTGCTGAGGCAGTGAGTGAGTGTAGAGTGGGGAGAGGTACTGC\n")
-		f.write("CCTAGGTGAGTCTCCCATGGCCAAACCGGCTAACCATGACCCATCTGCCAGCATTGCTTCACCAGCCCCC\n")
-		f.write("GTGCCGGAACCTGCCCCAGTACCCGTACCCGCACCCGTACCAGAACCAGACACTGCACCGCCTAAGCCGG\n")
-		f.write("CACCGGAATTCCAATAAGTAAACCCGGGATCCGACCCGGCGGTAG\n")
-		f.write("\n")
-		f.write(">gi|226789576|gb|GO545843.1|GO545843 Mdas9003I17_e213.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T45666 hypothetical protein F14P22.50 - Arabidopsis thaliana emb|CAB68184.1| putative protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTTTTGTAAACCATATCAGTGCTTTCATTTAAACAAGATGTTAGTGTGTGCAGTCAT\n")
-		f.write("ATCCCATATCCAGAATCTTTTGTCACCGAATCAAATATTCACCGCAAACAATATACAATATGCAGACATG\n")
-		f.write("AAACTTTACATAAACGCGATACCATATCTTTGGGAAGTCAGAGTTCGTTTGCTTGCTTGCATTTAGCCCT\n")
-		f.write("GTTGGCTCAGAATCTCCACTGCCACATTAAGATCCCCATCTGCAGCTGCTAGGGCAACTTCTACCTGTGT\n")
-		f.write("CCTCTCAAAACCCATTGATACAAGCTTTTGGATTTCTTCTTCAGATGCAACATAATCCTGATGGTGTACA\n")
-		f.write("GGAATTTCTGCCGCTGCATTATTTAGTGTTGCCTGCCTTCCATCAGATAAATTCTGTCCTGTACCAATAA\n")
-		f.write("CTGCCACATCTGATGGACGTTCTGAGTTGCTATTGTCCAAGAGTCTAGCCTGTAAGTTTGATTCTGAATC\n")
-		f.write("AGCATCAGAAATAGTACCTCGACCAGATCCAAGTGTTCTTCCTCTCCCAGGAAACATGTGACCATCTTGT\n")
-		f.write("GCTGACTGTACAG\n")
-		f.write("\n")
-		f.write(">gi|226789575|gb|GO545842.1|GO545842 Mdas9004H21_e286.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTAATATTAAACCATAATATACATAATATATTTCATTAATTACACAAAATGAAGAAATCAAATTA\n")
-		f.write("GTTAACCCAAAGTATTAACTAATCGTAAATTCCTCCGAAAAAACTAATTAAAATTACTAATACAAAAAAA\n")
-		f.write("TTCAAAACTTAAGAGAAATTAATTAATTTTCAATTACTTGATCGCTCAAAATGGATGCAAATTCCTGCTA\n")
-		f.write("ATCCCATTCACATTAGAGAAAAACCCCACAAAGTCCTGCCTGTACGGCAGGAACGACCGTCGTTTATCCC\n")
-		f.write("CTGCCTCCTCGGCCTTGCTCCTCACGACAAAACGCTCTCTATTCTCCGACACGCCGCCGCCGCCGCCGCC\n")
-		f.write("GTTGTCGACTCTTTTCCTCGTGACGTCATCTCCCTTGTTGTTGTTAGCTCTCTTGGTCGACGAGGGAGCT\n")
-		f.write("AAAAAGACGATGCCGTCGCTGCTGCTCCGGTGAAGAAGGTTCCAAAATTTCCACCGCTTCGACGACGAGC\n")
-		f.write("CTGCGGAGCTGCTCTTATTGCAGCGGCGCTGTCCAGGCGACGATTTCGGAGGGGCCCACTCGCAGTACGT\n")
-		f.write("GCCAGGTGGCAGGTTCTCGAGGTCGTCGGCCTCGGAGGACGA\n")
-		f.write("\n")
-		f.write(">gi|226789574|gb|GO545841.1|GO545841 Mdas9003G07_e202.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46486|PSAF_FLATR Photosystem I reaction centre subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa protein) (PSI-F) pir|S31165 photosystem I chain III precursor - Flaveria trinervia gb|AAA33344.1| photosystem I subunit III g, mRNA sequence\n")
-		f.write("TTTTTTTTCTTGTTTAACACATGCATTTGGTACCTTAATTCCTAGTAATTTTACAAATTATACGATGAAT\n")
-		f.write("TTAAAAACATATAATAAAAAGAAGCTCAAACGTCCTTGGCAACAAGTTCACCATTCACTATCTCTCTGTA\n")
-		f.write("AGCAGCCTTAGGCCAGCTGAAGCCTCTGAAAACCTAGCTAGTAGCCAAAGGCACATCAATGATGATCTCC\n")
-		f.write("TTCTGTGTCGGCTTCTTATCATCCCTAGTGGCAATCAAGTAGCTCCTCCCAACCCGCCCGATCCACCCAG\n")
-		f.write("CAATGTACAGGAACTAAATACCACGCGTGATAAACTCTCCCCATTGCCTCTGGTCACCGCTGACAATCCT\n")
-		f.write("ATGGGGGAGCCCATCCGACCCACAAAGTAAACCCTGCTTGCCATAGTTGGAAAACCTCCTCTGAGTCTTC\n")
-		f.write("TCTATGGTGGCCTTGATGGCTATCGCGGGTGCACTGTCGGGTGGATAGAGCTTCAGTGAGGACTCGAGTT\n")
-		f.write("TTTTTTTCTGCTGCTT\n")
-		f.write("\n")
-		f.write(">gi|226789573|gb|GO546098.1|GO546098 Mdas9002F02_e115.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB03604.1| putative glycoprotein [Oryza sativa (japonica cultivar-group)] dbj|BAB44013.1| putative glycoprotein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n")
-		f.write("AAAAAGGAGAAATTTCATAGTCAACTAGTGCAAATTACAACACAGTTCAAACAAGAAGAACAAGATGACC\n")
-		f.write("TATCTTATATAGATCGACAGCGAATCCTAAGTAGTTCAAATGAACAGAATCTAAACGGAATGCTACGATA\n")
-		f.write("ATTCATGAGATAAATATGAGATTTTAACTCCCTCAAGCCCGCATGGGTGGAATGGAATCCAGGAGCCAAT\n")
-		f.write("CGCTTCTACAGGAATGGAGGTAGGATCACCCATCGGCGCGGATACTTGGGTCTTCCGTCTTTCCCATCAA\n")
-		f.write("ATATCTTCTTAAGACGTCGGTGCTTTGTAAGCGCCCAATTGGTCATGATGGAAGCAGCAACTATGAGAAA\n")
-		f.write("GATAAAACCAGCGACTGTCTGCGTTGCTATATTGAAGCCCAACCATTGATAG\n")
-		f.write("\n")
-		f.write(">gi|226789572|gb|GO546097.1|GO546097 Mdas9002G16_e121.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29063|PR4B_TOBAC Pathogenesis-related protein PR-4B precursor emb|CAA42821.1| PR-4b protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAGCTAATGGTGCAGTTATACATTTATCATAAGATTGAAGTGCT\n")
-		f.write("TATACAATCTATATAATATAATACTTCTTGTTATAATTCAAGAAGCAATTCCACTTCAATTTATTCCATG\n")
-		f.write("GTGAAGCTTATTTATTAGTAATACATAGTTAAGTTCCCTACCAATACTGGAAGTAAAGAACTATATAGCT\n")
-		f.write("ATTGAAAAAATTAAGGTTTATAGGCTTTAGTCGCCGCAGTCGACAAAGTCGTAATTGACGATAAGGTGGC\n")
-		f.write("CTTGTTGGTAACCAATGCCGTCGGTGTCAATTTGGTTAAAAACATTCACGTCCAAGTCCAATCCTCCGTT\n")
-		f.write("GCTGCACTGATCAACAATTCTCACCGTTGCTTGAGCTCCAGTCCGAGTGTTTGTCACCAAGAGGCACCTT\n")
-		f.write("CCGCATGCGGCTTGCCCAGTAGGGCCAGCAGGTCCGCAAAAGGCAGTCCATCCATATTTGCTGCGCCATT\n")
-		f.write("CGAGGGATTTATCGGCATCCCATGTTGCGCAGTAGGCACTTACTGCCCGCAAGTCGTAATTGTTTTGCTG\n")
-		f.write("TGGATTGTAGA\n")
-		f.write("\n")
-		f.write(">gi|226789571|gb|GO546096.1|GO546096 Mdas9002M04_e146.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86214 protein T6D22.2 [imported] - Arabidopsis thaliana gb|AAF79822.1|AC026875_2 T6D22.2 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CTGAAGTCGGTCGCGAGATCTTCTTACGCTCCTCCATTTTCTTGAGATAATTTGCTGAAATTCCATCATG\n")
-		f.write("GGTAAGGAAAAATTTCACATCAACATTGTGGTCATTGGACATGTCGACTCTGGGAAGTCGACCACCACTG\n")
-		f.write("GTCACTTGATCTACAAGCTTGGAGGAATTGACAAGCGTGTCATCGAGAGGTTCGAGAAGGAAGCTGCCGA\n")
-		f.write("GATGAACAAGAGGTCATTCAAGTATGCCTGGGTGTTGGACAAGCTCAAGGCTGAGCGTGAGCGTGGTATT\n")
-		f.write("ACCATTGATATTGCCTTGTGTAAGTTTGAGACCACCAAGTACTACTGCACTGTTATTGATGCTCCCGGAC\n")
-		f.write("ATCGTGATTTCATTAAGAACATGATTACTGGTACCTCCCAGGCTGATTGTGCTGTCCTCATTATTGACTC\n")
-		f.write("CACCACTGGTGGTTTTGAAGCCGGTATTTCCAAGGATGGTCAGACTCGTGAGCATGCTTTGCTTGCTTTC\n")
-		f.write("ACTCTTGGTGTCAAGCAGATGATTTGCTGCTGCAACAAAATGGATGCCACCACTCCCAAGTACTCAAAAG\n")
-		f.write("CAAGGGAAGATGAA\n")
-		f.write("\n")
-		f.write(">gi|226789570|gb|GO546095.1|GO546095 Mdas9001P20_e87.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA86284.1| geranylgeranyl pyrophosphate synthase [Croton sublyratus], mRNA sequence\n")
-		f.write("ATTTGACCCATCTCTGTGTCGACTCTTATCCAGTTCTCCAACACAAACATGCGGATCAGACATTCTAAAT\n")
-		f.write("TCCCACGAACAAACATTAAATTCTACGGTACAACAAAAGGGTGTCTTTAGTTTTGCCTGTAAGCAATGTA\n")
-		f.write("GTTCGCCAGAGCAATCAAAGGGGCAGCCTTTTCGGGATCGAAACCGGCGAGCTGTTCCTTGGCGTCTTTG\n")
-		f.write("TTCAGTTTCTCTGCAAACTCTCTCGACTTCTCGATCCCCAACAGCTTCGGATAAGTCACCTTATCCGCCA\n")
-		f.write("CCAAGTCCTTCCCTGCCGTTTTCCCCAATTCCTGGGAAGATTTGGTCACGTCGAGGATGTCATCGACGAC\n")
-		f.write("CTGAAACAACAATCCAATGTACCGAGCGAAAGTCCTCAGCTTTTCGATTTCGGAATCCGACCCACCTCCC\n")
-		f.write("AGAACCGACCCCAGAACCACCGAGCACTCCAGCAGCGCC\n")
-		f.write("\n")
-		f.write(">gi|226789569|gb|GO546094.1|GO546094 Mdas9002I21_e133.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTATCATTCAACAATTTTATTAAAAAGAAAAATAAAAAGAAACAAAAACAATTTTTT\n")
-		f.write("AAGCTGACAATACTTAGCTGCCAATCAAACTATTGGCTTTTAACATACAAACTTATGGAGGCCAGCATGT\n")
-		f.write("TCTGTTTTACAAGTTACAACTGGCATCTAGCAACATCTCAACTTAACCATGTGACCGGCTTGAATTACGT\n")
-		f.write("CCATCAGTGACCGTTGGCAACCACACCGTTGGCATTGGT\n")
-		f.write("\n")
-		f.write(">gi|226789568|gb|GO546093.1|GO546093 Mdas9002K12_e141.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S00443 chlorophyll a/b-binding protein type I precursor (cab-6A) - tomato gb|AAA34140.1| chlorophyll a/b-binding protein prf|1402358A photosystem I protein CAB, mRNA sequence\n")
-		f.write("TTTTTTTTTGATAAGAAGTTCGGATTCATCGAAGATGGTTACATGGAATTCTAAACTTTACAGTGGGTGT\n")
-		f.write("GAAATCAATACTGCATGAATTAATCAAGGCAAAATCCCTTTGGGGATGATGACATCCCCAATGTTGTTGT\n")
-		f.write("GCCATGGATCAGCCAAGTGAGTAGCCAAGTTCTCCAACGGTCCGGTGCCAGGGTACGCCGATTGTTGAAC\n")
-		f.write("AACAAACCCGACGAAAGCCAACAACGCAAGCCGGCCATTTTTGACCTCTTTGACTTTGTATTCCTCGAAC\n")
-		f.write("TTCTTGGGGTCCTTGGAGTAGCCCAAGGGGTCAAAAGCGCCACCAGGGTACTTCTTCTTCTCAGGGTCCT\n")
-		f.write("TCTCCATGCTGCGTTGGTGTTCTACAAAGGCAATGGAAAGGAATTCGATGACCAAAATTGTAGGCAAAGT\n")
-		f.write("GCCCCATGGAACT\n")
-		f.write("\n")
-		f.write(">gi|226789567|gb|GO546092.1|GO546092 Mdas9002J23_e139.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD36199.1| NLS-TIR-NBS disease resistance protein [Populus tremula], mRNA sequence\n")
-		f.write("AAAAAGTGTACTTGAATATATTTCTATGTTTCCATCCAAAATGCACTAGTAATTAACTATACTGATGACA\n")
-		f.write("TTATTCCAGGAAACTAATTATATAAATACACCGTAAGGGGAAGAAATGTACGTACTCTCCTTCGTTGACA\n")
-		f.write("GGATGTCCTGACAAATTTGCTGCTTCTCTAAGAGCACTCCTCCATGCGAGGATCTTCTCCTTATTGTCCT\n")
-		f.write("CGAATTTGCACTCAAGTTTTTTGAACTCGTCACCGAAACTACTCGTTTGACTTCGTACATGGGACGGATC\n")
-		f.write("CACCTTGTAAAAAACTGGCAAAACTATTTGTTGCTTTGATTGTCTACATTGAAGAATCTTGACGAGCTCG\n")
-		f.write("TCCAAGCACCACCTTGAAGCTCCATAGGTTTTAGAGAATATGACGAGAGAAATTCTTGACTCTTCAATTG\n")
-		f.write("CTTGGAGGAGCGCTGGTGATATTTCTTCTCCTCTTACAAGTTGGCGATCAATGAAGGTGTGGATTCCCTT\n")
-		f.write("GTCGACCAAGGCCTTGTATAAATGATCTGTAAAAGTGGTGCGTGTATCC\n")
-		f.write("\n")
-		f.write(">gi|226789566|gb|GO545840.1|GO545840 Mdas9004B03_e255.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTATAGCAGCAAAAATGACATTACCTATTTAGTACATATGGAAAGATTACATTGTTCA\n")
-		f.write("CAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGC\n")
-		f.write("CAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGC\n")
-		f.write("CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACG\n")
-		f.write("AGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCC\n")
-		f.write("AAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGCGAGCGGGCCTTGGTTCCAAAAAGAGGGG\n")
-		f.write("CGATGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCAATTTCGCCGC\n")
-		f.write("GAGGCTCCCACTTATACTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGGT\n")
-		f.write("CTTCTTTCCCCGCTGATTCTGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACA\n")
-		f.write("GTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGG\n")
-		f.write("\n")
-		f.write(">gi|226789565|gb|GO545839.1|GO545839 Mdas9003K15_e218.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("CCATTGATGCAGTTTTTAAAGCTTGAGTTTACATACAAGCAGGTAGCTTAAAGATCATCTATTGTACACA\n")
-		f.write("CTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCCAGGCATTGTTGGTAACAGGAT\n")
-		f.write("CAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAGAAGCCGAA\n")
-		f.write("CATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCTCTGGGTCA\n")
-		f.write("TCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAAGGGGTCCTC\n")
-		f.write("CGGCAATGCGGTAACCCTCAACAGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAGAATGCTCTG\n")
-		f.write("TGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCTCCGGCTTTG\n")
-		f.write("AACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGCCCAAAGCAC\n")
-		f.write("CAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGCAAAGGTTTCGGGGTCTGCTGA\n")
-		f.write("TAGCCCAGCAGTGTCCCACCCGTAG\n")
-		f.write("\n")
-		f.write(">gi|226789564|gb|GO545838.1|GO545838 Mdas9003M10_e229.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n")
-		f.write("TGCAGCTATAGGTTTGCACTTTTACCCTATATGGGAAGCGGCTTCCGTTGATGAATGGTTATACAATGGT\n")
-		f.write("GGTCCTTATGAGCTAATTGTTCTACACTTCTTACTTGGTGTAGCTTGCTACATGGGTCGTGAGTGGGAAC\n")
-		f.write("TTAGTTTCCGTCTGGGTATGCGCCCTTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGC\n")
-		f.write("TGTTTTCTTGATATATCCAATTGGTCAAGGAAGCTTTTCTGACGGTATGCCTCTAGGAATCTCCGGTACT\n")
-		f.write("TTCAATTTCATGATTGTATTCCAAGCTGAGCACAACATCCTTATGCACCCATTTCACATGTTAGGCGTAG\n")
-		f.write("CTGGTGTATTCGGTGGCTCCCTATTCAGTGCTATGCATGGGTCTTTGGTAACCTCTAGTTTGATCAGGGA\n")
-		f.write("AACCACAGAAAATGAATCTGCTAATGAAGGTTACAGATTCGGTCAAGAGGAAGAAACCTACAATATCGTA\n")
-		f.write("GCCGCTCATGGTTATTTTGGCCGATTGATCTTCCAATATGCTAGTTTCAACAATTCTCGTTCTTTACACT\n")
-		f.write("TCTTCCTAGCTGCTTGGCCTGTAGAAGGTATCTGGTTCACCGCTTTACGTATCAGCACTATG\n")
-		f.write("\n")
-		f.write(">gi|226789563|gb|GO545837.1|GO545837 Mdas9004I08_e288.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_563649.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTTTCTTTTTGCAAAGTCATGCTAGATATTACATAAAAAAAAGGCAATGCTTTAGCGAAACTATGA\n")
-		f.write("GTTTTCGCCACATAAACTGCAATGGATGCCGTATTTTAATTAGTACATTACCTAATGAGTGCACAAGCTA\n")
-		f.write("CTCGACTCCTTTTTATTACCTAAATTTTCCATCTTGGCATTTTATCTCCTCATGACGCGGTGACGCTCTC\n")
-		f.write("GTTTGCGGAAGCGCTCGAGCATGAACTGATCTGTTGCAGCTTGCCTCTGCCCTGCTGCTTCTGTGCCAGT\n")
-		f.write("ATCATTTTGTCTGGAAACACCACCATCATCCTGTGAACTTTTGTCCTTGTACAGCTCGGGATGTTCTCGT\n")
-		f.write("CTAAGCTTCTCAACATAATCCCTGCCACGCTGGAAATAGTCAGCACTGTAACTTGAAGGGATGCTAAATT\n")
-		f.write("CTGATTTTGTCCGCCCAGTGAGCCGCTTCTCCTGCAAAAACTTCTTGGCAGCCTCAGTTTCCTCAATATT\n")
-		f.write("TCTCAGCTTATATTCAATGGGAAGCTGAACCTCGGCAATCCCAGTAGTCCATTGAGTGGAGCTTTCTTCT\n")
-		f.write("GAGTTCCGCCTTTTCACTTTAAGATGGTCAGGTATTTTGTACAACTCATCTTCAGCACGCTTTAAATCAT\n")
-		f.write("TTTCAACTTGATCTGAAGTATCAATTTTTTTGCCCCTCT\n")
-		f.write("\n")
-		f.write(">gi|226789562|gb|GO545836.1|GO545836 Mdas9004A20_e253.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n")
-		f.write("CACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACATACATACATACATACATAGATGGCAT\n")
-		f.write("GCTAAAAAAAAACCAAATAGCACCCATTAATTGAAAAGGACATTTAACCACTCAACTATTGTAGCGATAT\n")
-		f.write("TGTTGAAATTAAGCATCACACTCTCACTGATCACACCACATGATAACTAGTAAAAACACAACATTGCATA\n")
-		f.write("TGTAGTCAAAAAATGATGTTCCACAATCCACATAAATCTAAAAGTGGTGGTGCTTCTTCTTTCCATAAGC\n")
-		f.write("CTCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATGGAAGGCAAATCCACCCGAACCAACT\n")
-		f.write("GCAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCATGCTCTGGGTCTTTCTTTTCATTGT\n")
-		f.write("GCTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCT\n")
-		f.write("\n")
-		f.write(">gi|226789561|gb|GO545835.1|GO545835 Mdas9003P12_e244.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC38395.1| ferredoxin I [Solanum tuberosum], mRNA sequence\n")
-		f.write("GCCAAGGCTTTCACTCCCACTCTCTTTAGCCACAACACAAAAAAGCCTTGCAACCAAAGCAAACCAACAA\n")
-		f.write("ACATGGCAGCCACAGCTCTCTCAGGCACCATGGTCAGCACCTCCTTCATCCGCGGCCAGCCGATGACCAG\n")
-		f.write("CCTGCGGTTATCCCCCAACGTCGGTCAGGCCCTTTTCGGGCTCAAGGCCAACCGCGGAGGGCGTGTGGCG\n")
-		f.write("ATGGCTGCCTACAAGGTGAAGCTGCTCACACCACAAGGGCCACAAGAGTTTGAGTGCCCCGACGACGTGT\n")
-		f.write("ACATTCTCGACGCGGCGGAGGAGGCCGGGATTGACCTTCCCTACTCATGCAGGGCAGGGTCTTGCTCCTC\n")
-		f.write("GTGCGCCGGCAAAGTTGTGAGTGGGGGTGTGGATCAGTCGGACCAGAGCTTTTTGGATGATGAGCAGGAT\n")
-		f.write("GGACGGTGGATTTGTGCTCACTTGTGTGGCTTATCCGTCGTCTGACGTCACACTTGAGACCCACAAGGAA\n")
-		f.write("GAGGAGCTTACTGGTTAAGTGCTTTTGAGCTTTCTCATGATGACGTCATGTTTTGATGGCTGCTGGCTGG\n")
-		f.write("TTGGATCTGCCTTAAGTTTGTTTCAGGATAATGTTGTCTTGTTTCTAATTATATGAGTTGCTTAATGTTT\n")
-		f.write("GTGTACTCTCATTTGTGGTATGGAGATCATTGTATCTTGTAAACTCGCCCTTGTATGAATCT\n")
-		f.write("\n")
-		f.write(">gi|226789560|gb|GO545834.1|GO545834 Mdas9004I02_e287.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pdb|1CBG| Cyanogenic Beta-Glucosidase Mol_id: 1; Molecule: Cyanogenic Beta-Glucosidase; Chain: Null; Ec: 3.2.1.21, mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTATATAGTTGGCATATTTATTTCACGAAAAAGGAAGAACATTCATAAA\n")
-		f.write("GGAATACAATTATGAAAATAGGGAAATGATATGCTTGGCATATTTATTTCACGAACAACAACCGCAGCAG\n")
-		f.write("GATATCTTCACCATTATCCAAGGAAACATTTGAACCAGCTTGCTGAGAGTTTTGGGTGCCTCTTAAGTCC\n")
-		f.write("ATCATTGTAATCTATATAGACAAAACCAAATCGTAAGGTGTATCCAGAAGCCCATTCAAAATTGTCCAGC\n")
-		f.write("AATGACCATGCAAAGTATCCCTTCACATTTACACCATCATTGATTGCTTTTCGAAGATAGTCGAGGTGGT\n")
-		f.write("GGTAGTGGTAATCAATTCTGTGGGTATCATTGAGGGATTGCGGAAGTGACAATGTGGGATCATCGAACTC\n")
-		f.write("GTCAAGGCCGTTCTCAGCTAGGTCCAATGGCTTTTGCTGAGAAGATGGTACTGGCTTTGTTTTCGATGCT\n")
-		f.write("GATTGTTTTGTGGATGACAAGAAGCATAACGGAGGATATTCCGGGCTGGGGAGTCCTCTTCAACGGGCGT\n")
-		f.write("GCCGGAGATGGAACTGTCAGTGTTATGGTTGCAACATTTTTGTTCATATTTCCAAGCAAAAAGGAAAAGG\n")
-		f.write("GTGAGAAGTTGATGGACTGGGAAAAATGCAAGAAGCTACCCTGGA\n")
-		f.write("\n")
-		f.write(">gi|226789559|gb|GO546091.1|GO546091 Mdas9002H01_e125.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179106.1| expressed protein [Arabidopsis thaliana] pir|A84524 hypothetical protein At2g15020 [imported] - Arabidopsis thaliana gb|AAD03359.1| hypothetical protein [Arabidopsis thaliana] gb|AAL91197.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("CAAAAAGACTATCTGGGTTTCTGACATGTGTTCACTCTCCTCGGACAAACCCTACCTCGCTCTCTTACTC\n")
-		f.write("CAACTTCTCCAAGAAATTATAGCCCGTTCGCCCACCGCGCACGGTAGCGGCACCTGCCCGCGCTCCCAGC\n")
-		f.write("TTCAGGCCCTCAAACCCGACCCATTTTCTTGGATCATGGACTCCCACTCCCCCGAGTCCTTCTCCACGTT\n")
-		f.write("CTTCGACCTGGTTTTCATCACGCGCCTCTTCTGGCTCTGCGCGTGCGACTCTCCATCCGAAGTCGGCTCT\n")
-		f.write("CTGTACTTCAAGTCGCTGCTGGCTCCTAACCTCGAGGCGTTGTTGTGCAAGCACGCGCCGGCCCTGCGGA\n")
-		f.write("CGTTTCTGATCACCGCGGGTGTGGATGCGGAGCTGTGCTTCATGCGCACCCTCGGGTACATGTTAGCCAA\n")
-		f.write("ATGGTGCATTTTGAGAGATGTGGGCGTAGGTCTACAGACGCTGACGTCATCTCCCTCTCAGAACTTGGGT\n")
-		f.write("TTCTCTTACGC\n")
-		f.write("\n")
-		f.write(">gi|226789558|gb|GO546090.1|GO546090 Mdas9002E04_e111.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T06431 ribosomal protein L27-5 - garden pea gb|AAA86952.1| ribosomal protein L27 homolog, mRNA sequence\n")
-		f.write("TTTTTTTTTAAAATCGCAGGAAAATAAAGCAAAATCCAGAAATACCCAAAATAATACAAAATCTAATCAT\n")
-		f.write("TTTAGCTAAACATTAGTCCACTAAATCCATAAAACCGTCTCATTTCATTTCAAAATTCAATGAAACTCGA\n")
-		f.write("AAAAACATAAACCCAAAATCAGACAGACCCATTTACGATGCGACGCCGTATGGAAAGGTCCTCAGAACCT\n")
-		f.write("GAGCTTGGTGAAGAACCACCTGTTCTTCCCGGTTTTGAACCGCTCCTCGAACCGCTTCTTGACCTCCTTC\n")
-		f.write("AATGCAGTGACCTTCTTGTCCTTTGTCTGCAAGCACTCGACGTTGACGACGTCCTTGAGATCCACATCCA\n")
-		f.write("GGGTGTAGCGCGTGGGCATCAGGTGCTGGTAGTTCACGAGCTTGATGAAGGCCTTCACTCTGGATTTCTT\n")
-		f.write("CGCCGTCTTCTTGGCGGAGTCCTTGCGGATGACCTTGCCTGGGTACTTCTTAATCCCCGCAACCAAACAG\n")
-		f.write("TGGCCATAGG\n")
-		f.write("\n")
-		f.write(">gi|226789557|gb|GO546089.1|GO546089 Mdas9002F22_e117.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566435.1| membrane protein common family [Arabidopsis thaliana] dbj|BAB02418.1| gb|AAD25612.1 gene_id:MBK21.12 strong similarity to unknown protein [Arabidopsis thaliana] gb|AAK76578.1| unknown protein [Arabidopsis thaliana] gb|AAK95295.1|A, mRNA sequence\n")
-		f.write("TTTTGACATAACTTTAGATGTATTCAATACTACTTCTGGAATTATACATGGACACGTTCATTCAGTCATT\n")
-		f.write("CTCTCGAAAGAGATTGCGAAAAAAATTAAAGAAAACTCCAAATGACAAAATTATTTTCAAAGTTATATGT\n")
-		f.write("ACTGCTCACACTGAAAACACTAATATACATATAATTAAAATCGGTCGTTGGGAAACGCTTAAGCCAGTCC\n")
-		f.write("GTCGACATCAGCAGTTCTACTCGCCTTAGTGACCTCCCGGATTTCTGTTCCACGACAAATACGATGGGTC\n")
-		f.write("TCCAAGTTGCCTTGGCTTAACAAGATACACAACAGTGAAAGCCATGGCCAGAAAGAAGCACAACCCTCCA\n")
-		f.write("ACAGTGAGATAAGCAATGCCAAGGAAGTCATTCCTGCCACCAATCCAACTGGTGGTCGAGAGCACAAGCT\n")
-		f.write("TCTTTTTTCCATTAAAACTGTATGTGTTGTAATTGTTCTCCAGTGTCACTTCTATCGTATCATTTTCTTT\n")
-		f.write("CAGATCTACCTCTATCTTCCCGTACAGCTTTCTAAATGTCGGTAGTGCAGCAGTTCTCATCCAAACAATA\n")
-		f.write("AGGTCCTCTTGCTCACTTAATGGTTTAGAGGTATCCAGAGACTTGCCACCTTTAAGAGTTCCATTCTGAA\n")
-		f.write("AGTTCTTTGGAAAGACATTTTTGCCAAATTTGTGCTCCCTATCA\n")
-		f.write("\n")
-		f.write(">gi|226789556|gb|GO546088.1|GO546088 Mdas9010A19_e718.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S28827 chlorophyll a/b-binding protein type I - common tobacco emb|CAA45523.1| photosystem I light-harvesting chlorophyll a/b-binding protein [Nicotiana tabacum], mRNA sequence\n")
-		f.write("CAAACCCTTAATCTTGCAGGCACTAAATTTGCCAATGGCTTCCAACACTTTGATGAGCTGTGGCATCGCC\n")
-		f.write("ACTACTGCCTTCCCTTCAGTCCTCTCATCCTCCAAGTCTAAATTTGCGACCAGCGCAGTCCAGCTCCCAA\n")
-		f.write("GTATTGGTGCCAATGCCTCCTCCAGGTTCTCCATGTCCGCCGAGTGGATGCCCGGCGAGCCCCGCCCTCC\n")
-		f.write("TTACCTCGACGGCTCTGCCCCCGGTGACTTTGGATTTGACCCACTTCGGCTAGGAGAAGTGCCAGAGAAC\n")
-		f.write("TTAGAGAGGTTCAAGGAGTCCGAGCTCATTCACTGCAGATGGGCAATGCTTGCTGTTCCAGGGATTCTAG\n")
-		f.write("TACCAGAGGCTTTGGGATTGGGCAACTGGGTAAAAGCACAGGAGTGGGCTGCCGTTCCAGGAGGCCAAGC\n")
-		f.write("CACCTACTTAGGCAACCCAGTTCCATGGGGCACTTTGCCTACAATTTTGGTCATCGAATTCCTTTCCATT\n")
-		f.write("GCCTTTGTAGAACACCAACGCAGCATGGAGAA\n")
-		f.write("\n")
-		f.write(">gi|226789555|gb|GO546087.1|GO546087 Mdas9002P21_e167.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n")
-		f.write("TCAAATTGCATAAATGCAAATAATATTCAAAACTTGTAAACCACAAATCACAAAATTTGCACCAAATAAT\n")
-		f.write("AAAATGCAGGGCTTACTGCAACATCACACAAAGATAAACTTGAAACAAATCGAATAAAAACCTTAAAAAA\n")
-		f.write("ACAAAAAAAATGATGAAGGTTGAAAAGCCTTCTGCTCAGCGCAACTGAACACATCATGAGGGCCAGCGTC\n")
-		f.write("TTCACGGCCGACGCCGACTTTGTCAACGTAATACAGGTAATGGGAAATGATGTTGTTCATGGAGTCAACG\n")
-		f.write("TCACCTTGGCCACAGACTTGGTCCCCGTAAAGCACATTCATGGTGGTGCCAAAGCCAGGAACCCTTTTGG\n")
-		f.write("ACAAAGTGTCGTTCTTGGTTGGCTTCCA\n")
-		f.write("\n")
-		f.write(">gi|226789554|gb|GO545833.1|GO545833 Mdas9004H03_e280.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n")
-		f.write("TTTTTTAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATTTACATCACCGACAACAATACAAACGA\n")
-		f.write("AAGTACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTG\n")
-		f.write("GCGACTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAA\n")
-		f.write("AGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGC\n")
-		f.write("TTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCG\n")
-		f.write("AGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCA\n")
-		f.write("AGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGAGACCGCCCTCGCTGAAGGTCTGGGC\n")
-		f.write("TCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCGGGGAAAACGCAT\n")
-		f.write("CCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTGGCGAAGGTCTCTG\n")
-		f.write("GGTCGGCTGAGAGTCCAGCGG\n")
-		f.write("\n")
-		f.write(">gi|226789553|gb|GO545832.1|GO545832 Mdas9004B13_e258.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n")
-		f.write("TTTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAAC\n")
-		f.write("ACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGG\n")
-		f.write("TCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTA\n")
-		f.write("CATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAA\n")
-		f.write("ACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTC\n")
-		f.write("TTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTG\n")
-		f.write("TCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTC\n")
-		f.write("AAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n")
-		f.write("AGGGGAGGAAGGTAAGAGAGG\n")
-		f.write("\n")
-		f.write(">gi|226789552|gb|GO545831.1|GO545831 Mdas9004A03_e250.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC53656.1| 1-aminocyclopropene-1-carboxylate oxidase [Malus x domestica], mRNA sequence\n")
-		f.write("AATCTTGAAGTCATATTATATATAATAAAGTAGTGATCACATTGGTTACTTTCTACAACGATTTCCACAT\n")
-		f.write("TAATAGTAAATAAAACCTTGAAATCTAGTTCAAGGAAAAATTTCGTTCACACACCCATAATTACTTTTAA\n")
-		f.write("GCAAACAACCCTTTTTTCCAACAGCTTCTAGTAAAAGTATTTAATCACTCTCAAGCAGTACTTATAACTG\n")
-		f.write("GACCCAAACCAAAACTGGCCTTAATTTTCCACCGGCTTTCATGGCTTCAAATCTTGGTTCCTCGGCCTCG\n")
-		f.write("AACTTGACCCCAGCATAGAGCTTCATGTAGTCTTCGAACACGAATTTCGGGTACACTTGATTCTTCTCCT\n")
-		f.write("CTGCTTCTTTCTCCACTAGGGTTGGTGCTGGGTAGATCACCGCATCACTGCCTGGGTTGTAGAATGAAGC\n")
-		f.write("TATTGACATTCTGGTGCCATCTGTTTGGGCAATCACCCTGTGTTCCACACTCT\n")
-		f.write("\n")
-		f.write(">gi|226789551|gb|GO545830.1|GO545830 Mdas9003M05_e226.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTGAATACAAAAACTCTCATTTTATTTCAGATATAATTGAACCAAACTTGAGCATGT\n")
-		f.write("TCGCATGTCAAAATACACAAGACAGACCATAAAGTCTGAAGAATATATTAAATAGAAAGCCTAAAACGAC\n")
-		f.write("AGATTACAAAATAAATAACGGTCTTGAAACAACACAAATATATACTCCTGCAAGTGTAAGGGGTCTTTAG\n")
-		f.write("ATCCTAGATGGCCCCGACTGTTCCTGAAACTTTCGCTTCGGGAGAGAAGAAGCATAATCAAACCACAACC\n")
-		f.write("GGGTGACAAGCTAACAAATGAGAAGCGAAAATACAAAGCGCTACAAGATCTCCAAACGTCCTCATTGAAA\n")
-		f.write("GAATTCTGGACTAGTCGAGAACTTTTAGGGACTCGAACAGACCGCAACCTTTATTATGTATGCCGGTAAA\n")
-		f.write("GAAGAGATGCAACCTAGGCAGGCAGAGAATCAATAAACGAATTGCAGAGCTCATTGATGGCTAAATAGGC\n")
-		f.write("TGAAGAACTTCGACAAACAAGGATCTATGAACTCCTCAATTTAGCGGTGTCTCTGC\n")
-		f.write("\n")
-		f.write(">gi|226789550|gb|GO545829.1|GO545829 Mdas9003L20_e222.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TCGAGAAACAAATATTTTTCCAATTTGGAGATCATAAAGACGATGCCATTTTTGCCTATAAAGGTATCCA\n")
-		f.write("AGGAATATGCATTGGGAGGCACATGCATCAAATTTGGTGAGTCGTTTATCATCTGTGGAGCTTATGGTGG\n")
-		f.write("ATGGTGAACGGGTATGTTTAGCTAAAGGGCAAACTGAACAATAATTAATTTCAGAAAACTGAATGTCTTT\n")
-		f.write("TACATATGCTTGCATTAATCGGAAATGTTTATCGGAAAGGTGCCCAAGGCGTTCATGCCAAAGGCAGGAA\n")
-		f.write("ATAGCGGACTTGCTGACAAAATTGCAGATAGCCTCCATAGTAACAATGTTGAGATAGTAGAGTCATCCCC\n")
-		f.write("TTTCAGTTCTCGTCCCAATCATCATCCCCAAGCATTGGTCCTGTAACACAAATAGGTTTTTAGCAAAAAA\n")
-		f.write("GGCAATGTAGTCCGAGTGTTGGACAAGTTTAGCGACGGATATTAGATTCAATTGGAATGAAGGAACACAT\n")
-		f.write("AAGACATTACGAATGGTCAAATTGAGAGAGAATTTGACACTCCCTACGTGTGTAACAGTAGCACTCATGC\n")
-		f.write("CATTTGGTAATTGTATGGTTCGATTATGTATTAATGAGCACGTAATAAGTATGGCAGGAGAGTACACTAT\n")
-		f.write("ATGATCAGTTGCTCCTGTGTCAAGATCCCAGCTACGTCTTTCA\n")
-		f.write("\n")
-		f.write(">gi|226789549|gb|GO545828.1|GO545828 Mdas9003I08_e212.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK60319.1|AF385728_1 AT3g47831/T23J7 [Arabidopsis thaliana] gb|AAL77725.1| AT3g47831/T23J7 [Arabidopsis thaliana] dbj|BAC43208.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("GAAAAGTTTATTTAGTAAATATTGAAAAACAATTACATATTCGAGCTATCGAAATCACGTAGAAATAAAA\n")
-		f.write("TGCGTCATCCGAAACACAAATATGTCCATAGCATTTGGAAGTAAAGCCAACTGATGGCTCTACTGGTTCA\n")
-		f.write("AAATCTAATTCGATTACTTAAAACGCGAAGGACAAAGACCAACACTGTAATTTTCATAGAGGAATAAGGT\n")
-		f.write("TACCGACTCACCTGATTGCCGTGAAAACTCAAAATTAAGGGGCTTGCTCAGCAGAAGCACCCTCTTTCTC\n")
-		f.write("GATTTTCGATTGAGCTTTGTGCCAGGCGAGGCCTTTGTAGACATTGGCGGAGAAAGTGGCGGTGAGGTAT\n")
-		f.write("AAAGTGGTGACGCCGAGCCCCGCTGTGAACGCCTTGAATGCCCAATCCCCTGCCTTGCTCACTATCCCCA\n")
-		f.write("TCTCTATCTCAATCTCTCTCTCTCTCTCTGCGAGTTTTTTTGGTATCGTCCCTCGTGCCGAA\n")
-		f.write("\n")
-		f.write(">gi|226789548|gb|GO545827.1|GO545827 Mdas9003H03_e207.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24059|MT3_MALDO Metallothionein-like protein type 3 pir|T17015 metallothionein-like protein AMT2 - apple tree gb|AAC23698.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n")
-		f.write("AAGCGAAAACCCTAATTTAAACACATCTTCAGCTCCAAGTTCTTAAGTTTATCTTCAACATGTCGGGCAA\n")
-		f.write("GTGCGGCAACTGCGATTGTGCTGACAGCTCCCAGTGCGTGAAGAAGGGAAACGGCTACGACTTGGTGATC\n")
-		f.write("GTGGAGACTGAGAACCGCTCCATGGACACCGTCGTCGTGGACGCTCCTGCAGCCGAGAACGACGGAAAGT\n")
-		f.write("GCAAGTGTGGCACAACCTGCCCATGTGTGAACTGCACCTGTGGTCAGTAAGCCCAGATAACCAAATTAAA\n")
-		f.write("GATGTGATTAATAAAAGTGTCATATTAATTAAGGGATTATAGACCCTTAATTAATGAAAAGTGTTTGTGG\n")
-		f.write("GATAAAATAACGTTGTGGCTTTGTCTCTTGTTTGCTTATAGTATTTGAGTCTGTCGAGTGACATGTTGTA\n")
-		f.write("CGTCTGTGAAAACATGTCACTCATATGTTTGTGTTTCTGTGATTGTGTCATGTAATGGCCATGTTCATGG\n")
-		f.write("CCCTTTGATTTATATGCAAATATTAGAATAAAAAAAAAAAAAAAAAA\n")
-		f.write("\n")
-		f.write(">gi|226789547|gb|GO546086.1|GO546086 Mdas9002B15_e96.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40163|PSBR_LYCES Photosystem II 10 kDa polypeptide, chloroplast precursor emb|CAA65231.1| PSII polypeptide [Lycopersicon esculentum], mRNA sequence\n")
-		f.write("TTTTTTTTTGACAGTGGAAGGGCAACTTGCCCATTATTTAATTATTTGAGTGGACATTCACTGTTCTACA\n")
-		f.write("ACACATCACAATATATACAGGCATCAAACTGGATCCATGCCAAAACATTACAATTAAGGTTTGCACAGAG\n")
-		f.write("TATTTCTTTAATGTTCTTGTTTAGGGCAGCTAGTTGGGACAGGCTATAGTTATTAACAACACATAAATTA\n")
-		f.write("CAACCAAAGATGAATAATTAATAATTTTACTGTGACAAAGCACTTGTGTTGTAGACAAGAAGAGCACCCC\n")
-		f.write("CTGCAAGAATGCCAACTAGGGTAACTGCCCAGATGGACAAGCCAGTAACACCCCCAGCATAGACATCACC\n")
-		f.write("ACTTGGAGACCAGTCATCTTTGTTGTAGATGGGGCTGTATCCA\n")
-		f.write("\n")
-		f.write(">gi|226789546|gb|GO546085.1|GO546085 Mdas9011C13_e821.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n")
-		f.write("TTTTACGTAAGTGTACTTTTATCATTTATTTCTATAATAAAATATCGGAAGCATCGCGATATGAATTACA\n")
-		f.write("AGGAGCTAACAGGAAAACAAATGACAGTAGTACTAGTTACATGTATCTCGCAGACAAAGTACATACATAA\n")
-		f.write("CATTAAGTATAACTTTGGTCAGAATATGCTTCTGCAAACAACATGAAGAATGTTCACTTCTTTTGCGGAC\n")
-		f.write("AATGCTGCGAGATATTTACGTATGTAGATAGAAGCTTCAAAAACCGGCCACGATTTCATCTCATCTCAGC\n")
-		f.write("AGCAATACTTTTCGGTTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTGCCCTTAATCTTCTGTGTC\n")
-		f.write("AAGGCTTCTCTGTCTGGTTTGAAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAACCAATTCCTACAA\n")
-		f.write("GCTCAAGAACACCAGGGACTAAAGGAAGCCTATCAATTGCCGAGATCATTCCACTGAAGCCCCATACTGC\n")
-		f.write("AACAGCAACAGCTACTGCAAGTGAAGACACTGCATATTTATCTTCCACTTTCTCCCAAGCCCTCGTGCCG\n")
-		f.write("AA\n")
-		f.write("\n")
-		f.write(">gi|226789545|gb|GO546084.1|GO546084 Mdas9010K20_e773.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n")
-		f.write("TTTTTTTTTTTTTTTAAAAGCGTATCATCCTTCCATTATTATTCTGTTCCCATCATTTCTTACATACGCA\n")
-		f.write("CTTGTCTTATTTCTGCTTTAAAAAAATGAAAATCAGAACGTTATTTCTCTGCTCGTAAGGGAAGTTGCTG\n")
-		f.write("GGTACTCTGCGACTTATTTAGGAGTAATGTCGACACCCTTGATAACAAGCCCTTTCTTCCATTTCCCAAC\n")
-		f.write("AGTTTGACGGAGCATAAAATACATCCGGCCAGATTGCCCAGGCGATGTTGTAAATTCGGCAACTCGGACA\n")
-		f.write("TAACTCCACCATCTTCCTTTTGTCCTCAGATCAAGTGTAGAGTTTCTCGGGACAATCTGCAGGTTCTGAG\n")
-		f.write("GGGGAGTGACGCTGAATTCGACTTTATCTTCCCATCCATATTTTGGGTCCTTCATCATGATTATATATGA\n")
-		f.write("AACTTCATACACAGTTCCGGGTGTCAGGTATGCGGTCTCAAAATCCCCTTTCACTTCTAGCGA\n")
-		f.write("\n")
-		f.write(">gi|226789544|gb|GO546083.1|GO546083 Mdas9010J14_e763.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07080 shock protein SRC2 - soybean dbj|BAA19769.1| SRC2 [Glycine max], mRNA sequence\n")
-		f.write("CTAAGTCGAACTATCTTCTTCTTCCAAATTCCAATTTCAACAACTCTCAAGAATCATCGCCATGGATTGC\n")
-		f.write("AGGCCTCTGGAGGTAATCATCGACTCGGCCAACGACATCAAGGATGTCAACCTCTTCTCCAAGATGGACG\n")
-		f.write("TCTACGCCGCCGTTTCGGTCGCCGGCGACCCGCGCAACAAGAAGCAGAAGAACAAAACCCCCGTCGTCAA\n")
-		f.write("GGACGGAGGCACCAACCCCAAGTGGACCAGCTACCCCATCAGGTTCACCGTCGACGAAGCCGCCCTCCTC\n")
-		f.write("AACAACCGCCTCACCCTCAACATCAAGCTCGTCTCCGAACGCACTTTGGGAGACACCAAGATCGGCAAGG\n")
-		f.write("TCAAGATCCCGCTCAAGGACCTACTAGACACCATGAGCGGCGGCGATGATCACA\n")
-		f.write("\n")
-		f.write(">gi|226789543|gb|GO546082.1|GO546082 Mdas9010H14_e752.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86463 hypothetical protein F12G12.18 - Arabidopsis thaliana gb|AAG12539.1|AC015446_20 Unknown protein [Arabidopsis thaliana] gb|AAG12849.1|AC079286_6 photosystem II 22 kDa protein, putative; 13290-12539 [Arabidopsis thaliana] gb|AAK55677.1|A, mRNA sequence\n")
-		f.write("TTTTTTTATCAACGAGCTCTGGGGAACTTCTTCAATCGTTGAAATCCTGNTAAACATTGTAAGTAAAATA\n")
-		f.write("CAGCAGCGTATGATAGCCGAGTATTTCTTGCAAATGAAATTTAAACAAATTACTCAACAAAGTTACAAGT\n")
-		f.write("GAAACAGTGAATGTATCTGCAGTAGCTCCAGAGACAAGAAGGTATTAAGGCTTTCAACATCCCACCGGGC\n")
-		f.write("CGGTGTATCATTCCAGATCCAGTATTCCGAAATTTGAAAGAAGTATCTTTACTTGATCAACAAAGTCCGA\n")
-		f.write("GCCAGTTGCATACTCCGTTAGCATTCCAACAGCAAAACCGAACATTGCCCATCTGCCATTGCTAATCTCG\n")
-		f.write("TTCTTGCCAACAAAGCCAAAGAAAGGACCCTGGTTAGCAGCCTCAAGCTTCTTCTGCTTGAAGTACTCCT\n")
-		f.write("GAATCTCCTTAGCCTTCTGCCTCTGAAACTCCAAGGTCACCACATTCTTGTCCTCCACCATCGTCAGCCC\n")
-		f.write("GGAAACCTGGGCCGGATTCGAGGGCTGCTGAGGCGGTGGAGAAGGAGACGGAGGAGAAGGAGGCGTTGGT\n")
-		f.write("TTGAGAGGGGAAGACGGCTGGGAGGGTTCTCGGAGGGAAGGAGCAGCAGGTCTTCTGATAGGCCCTTCCG\n")
-		f.write("TCTTGGGAGCTCTTTATGCTAATTTTTA\n")
-		f.write("\n")
-		f.write(">gi|226789542|gb|GO545826.1|GO545826 Mdas9003M24_e233.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9M4S8|TPIC_FRAAN Triosephosphate isomerase, chloroplast precursor (TIM) gb|AAF66071.1|AF257322_1 triosephosphate isomerase [Fragaria x ananassa], mRNA sequence\n")
-		f.write("TCGAGTTTTTTTTTTTTTTTTTTAAGTGACCCATGGAAAATGGATAGAAGATATATTTTACTATCTTTAT\n")
-		f.write("GGAGGGGGAAACACTTCAAAAACGACCCAGGAAAAAAAATTCCTTATGATAAACTGGCTCATACATTTGT\n")
-		f.write("TACAATATGCTTCAATCTCAAGGTACCTTCGCATCGGCCCTTTATTTGATCTCGGAACCACCATAATCAA\n")
-		f.write("GCAGCAACTTTCTTGGCTGTCACAGCGTTGACGATAGTAGCAAATTCAGGGCCCTTTAGGGAAGCACCGC\n")
-		f.write("CAACAAGAAAACCATCAATATCTTCCTTCTTTGCGAGCTCAACAGAATTGCCTCCATTTACAGATCCTCC\n")
-		f.write("ATAAATAATTCTTGTTTTAGATGCAACTTCTGCTGACACATTCTGTTTCAGCCAATCACGAACAGCTACA\n")
-		f.write("TGTACTTCCTGAGCTTGTTCTGGACTGGCTACCTTACCAGTCCCAATGGCCCATACAGGCTCATAAGCAA\n")
-		f.write("CAACTATCTTATCCCAGCTGGGTACTGCGTCTGCAAAAGCCTTCAGCTGCTGAAAGCAGACGTCAAAAGT\n")
-		f.write("TTTCCCTGCTTCCCTTTCTTCTAGCTTCTCGCCCAATGCAAGCAATTACTCCGAGACCCTCATTCAACGC\n")
-		f.write("ATAGG\n")
-		f.write("\n")
-		f.write(">gi|226789541|gb|GO545825.1|GO545825 Mdas9003P18_e247.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_189513.1| expressed protein [Arabidopsis thaliana] sp|Q9LHA4|V0D2_ARATH Probable vacuolar ATP synthase subunit d 2 (V-ATPase d subunit 2) (Vacuolar proton pump d subunit 2) gb|AAL16278.1|AF428348_1 AT3g28715/MZN14_21 [Arabidopsis thaliana], mRNA sequence\n")
-		f.write("TTTTTTATAAACTCACTACGAGACTGCTACTATAGTAGCTCTCAAATTGCAATATATATATTCAATTTAT\n")
-		f.write("CCTCACAACTGTAACATGCTCGATTTCAGAACATGACATATTCCCTCTATGTAAAAACGACCGGAATAAT\n")
-		f.write("ATATGCAAAAGTGCTTATTAGGAAGGAACACCGGATAGTGCAAACAACGCAACCGCACCCATCTCTACAA\n")
-		f.write("TTCGTTCGGGGATATGATGGGGAGGAGATTTACAGAAGATTATGCGAAAGAACGAAGGATCATCTGTAAT\n")
-		f.write("GGTGTGTTCTGAGTCCCAATCCGACTAAAATATGAAGACCACGCTGTCGTGAACTCTGGACTTCTGGTTC\n")
-		f.write("TGAGCCACACACTCAGATATCCACATCAAATTTCTGATCTCCTGCTCCCTCAACCTCATGTATGCAAAGA\n")
-		f.write("AAACAGCGTAATGGAACTGTTGCTCAAATGCTAAGCAAAGCCTTTTCACCTCCTCTTCATAAAATGCCTT\n")
-		f.write("GTCAAGCATCTGGGTTTCGCCATAGGATAGTTTTGAAAAAATAGACTGATAAGGAGGATATTTTTCCATG\n")
-		f.write("CAACCACGTACCTGATCAATGTCCTCACATACAGCAAGTTCCTCATGGCCATAGGGAATAGAGTAAACCA\n")
-		f.write("AAGCTAGAGTACAACTTCCTGCGATCATCTCGAGTAAGCTCAGTTCAATACTATTTATGGGT\n")
-		f.write("\n")
-		f.close() 

--- a/commons/launcher/tests/MockOutputForBlat.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-class MockOutputForBlat(object):
-	
-	def write(self, inFileName):
-		f = open(inFileName, 'w')
-		f.write('gi|226792305|gb|GO545799.1|GO545799	290	551	Vein_ctg_10639	674	935	1.0e-130	463.0	93.51\n')
-		f.write('gi|226792305|gb|GO545799.1|GO545799	138	283	Vein_ctg_10639	519	664	1.0e-50	198.0	82.88\n')
-		f.write('gi|226792305|gb|GO545799.1|GO545799	577	686	Vein_ctg_10639	961	1070	1.4e-46	184.0	90.91\n')
-		f.write('gi|226792305|gb|GO545799.1|GO545799	566	572	Vein_ctg_10639	944	950	3.1e+05	13.0	100.00\n')
-		f.write('gi|226792293|gb|GO546055.1|GO546055	107	193	Vein_ctg_10638	87	1	2.2e-42	170.0	100.00\n')
-		f.write('gi|226792293|gb|GO546055.1|GO546055	34	91	Vein_ctg_10638	161	104	2.5e-22	103.0	94.83\n')
-		f.write('gi|226792293|gb|GO546055.1|GO546055	521	611	Vein_ctg_10639	1075	985	2.9e-38	156.0	92.31\n')
-		f.write('gi|226790810|gb|GO546215.1|GO546215	57	520	Vein_ctg_5197	1862	1399	8.7e-128	454.0	72.84\n')
-		f.write('gi|226790791|gb|GO546209.1|GO546209	135	199	Vein_ctg_5197	1994	1930	7.4e-25	112.0	93.85\n')
-		f.write('gi|226790791|gb|GO546209.1|GO546209	36	82	Vein_ctg_5197	2126	2080	1.9e-06	50.0	76.60\n')
-		f.write('gi|226790483|gb|GO545656.1|GO545656	280	541	Vein_ctg_10639	674	935	1.0e-130	463.0	93.51\n')
-		f.write('gi|226790483|gb|GO545656.1|GO545656	128	273	Vein_ctg_10639	519	664	1.0e-50	198.0	82.88\n')
-		f.write('gi|226790483|gb|GO545656.1|GO545656	567	640	Vein_ctg_10639	961	1034	1.1e-25	114.0	87.84\n')
-		f.write('gi|226790483|gb|GO545656.1|GO545656	556	562	Vein_ctg_10639	944	950	3.1e+05	13.0	100.00\n')
-		f.write('gi|226790458|gb|GO545644.1|GO545644	1	95	Vein_ctg_10638	1369	1275	3.5e-40	163.0	92.63\n')
-		f.write('gi|226790458|gb|GO545644.1|GO545644	146	185	Vein_ctg_10638	1225	1186	3.7e-07	53.0	82.50\n')
-		f.write('gi|226790049|gb|GO546186.1|GO546186	177	263	Vein_ctg_10638	87	1	5.6e-39	159.0	96.55\n')
-		f.write('gi|226790049|gb|GO546186.1|GO546186	106	161	Vein_ctg_10638	159	104	3.8e-21	99.0	94.64\n')
-		f.write('gi|226790011|gb|GO546174.1|GO546174	138	283	Vein_ctg_10639	519	664	1.0e-50	198.0	82.88\n')
-		f.write('gi|226789634|gb|GO545875.1|GO545875	135	306	Vein_ctg_10638	1446	1275	7.3e-80	294.0	91.86\n')
-		f.write('gi|226789634|gb|GO545875.1|GO545875	451	496	Vein_ctg_10638	1132	1087	1.8e-18	90.0	100.00\n')
-		f.write('gi|226789634|gb|GO545875.1|GO545875	357	393	Vein_ctg_10638	1225	1189	1.8e-05	47.0	81.08\n')
-		f.write('gi|226789597|gb|GO546106.1|GO546106	432	537	Vein_ctg_2286	1166	1061	5.0e-40	162.0	86.79\n')
-		f.write('gi|226789597|gb|GO546106.1|GO546106	538	632	Vein_ctg_2286	1008	914	6.0e-33	139.0	85.26\n')
-		f.write('gi|226789571|gb|GO546096.1|GO546096	353	474	Vein_ctg_5197	2426	2305	4.1e-46	182.0	84.43\n')
-		f.write('gi|226789566|gb|GO545840.1|GO545840	73	232	Vein_ctg_10639	776	935	2.5e-75	279.0	92.50\n')
-		f.write('gi|226789566|gb|GO545840.1|GO545840	258	372	Vein_ctg_10639	961	1075	4.2e-50	196.0	92.17\n')
-		f.write('gi|226789566|gb|GO545840.1|GO545840	247	253	Vein_ctg_10639	944	950	3.1e+05	13.0	100.00\n')
-		f.close() 

--- a/commons/launcher/tests/Test_BlatClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-import unittest
-from commons.launcher.BlatClusterLauncher import BlatClusterLauncher
-
-
-class Test_BlatClusterLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = BlatClusterLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (format='fasta')"
-        exp += "\n     -p: parameters for 'blat'"
-        exp += "\n     -Z: concatenate output files"
-        exp += "\n     -A: same sequences (all-by-all)"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_BlatClusterLauncher ) )
-if __name__ == "__main__":
-    unittest.TextTestRunner(verbosity=2).run( test_suite )

--- a/commons/launcher/tests/Test_BlatProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-import unittest
-from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
-
-
-class Test_BlatProgramLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = BlatProgramLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getHelpAsString( self ):
-        exp = ""
-        exp += "usage: BlatProgramLauncher.py [options]" 
-        exp += "\ngeneric options:"
-        exp += "\n     -h: this help"
-        exp += "\n     -i: name of the input file (format='fasta')"
-        exp += "\n     -c: clean"
-        exp += "\n     -v: verbosity level (default=0/1)"
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (database, format='fasta')"
-        exp += "\n     -p: parameters for 'blat'"
-        exp += "\n     -A: same sequences (all-by-all)"
-        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        obs = self._i.getHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setAttributesFromCmdLine( self ):
-        self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        self._i.setAttributesFromCmdLine( "-o", "dummyOutFile.align" )
-        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
-        
-        
-    def test_setWrapperCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "BlatProgramLauncher.py"
-        exp += " -i %s" % ( "dummyInFile.fa" )
-        exp += " -s %s" % ( "dummySubjectFile.fa" )
-        exp += " -o %s.align" % ( "dummyInFile.fa" )
-        exp += " -v 0"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        self._i.setProgramParameters( "-minIdentity=90" )
-        exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setListFilesToKeep( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        lExp = [ "dummyInFile.fa.align" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToRemove( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        lExp = [ "dummyInFile.fa.blast" ]
-        self._i.setListFilesToRemove()
-        lObs = self._i.getListFilesToRemove()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "input file: %s" % ( self._i.getInputFile() )
-        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
-        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-        
-        
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) )
-if __name__ == "__main__":
-    unittest.TextTestRunner(verbosity=2).run( test_suite )

--- a/commons/launcher/tests/Test_F_BlatProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-from devTools.tests.MockFastaSupctg30 import MockFastaSupctg30
-from devTools.tests.MockMiniProtBankSupctg30 import MockMiniProtBankSupctg30
-from commons.launcher.tests.MockDataBankForBlat import MockDataBankForBlat
-from commons.launcher.tests.MockESTBankForBlat import MockESTBankForBlat
-from commons.launcher.tests.MockOutputForBlat import MockOutputForBlat
-from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
-
-class Test_F_BlatProgramLauncher(unittest.TestCase):
-
-    def test_run_empty_result(self):
-        queryFileName = "smallProtBank_supctg30.fa"
-        mock = MockMiniProtBankSupctg30()
-        mock.write(queryFileName)
-        subjectFileName = "subjectBank.fa"
-        mock = MockFastaSupctg30()
-        mock.write(subjectFileName)
-        
-        expOutputFileName = "expBlatOutput.blast.align"
-        self.writeEmptyExpOutputFile(expOutputFileName)
-        
-        obsOutputFileName = "obsBlatOutput.blast.align"
-
-        bpl = BlatProgramLauncher()
-        bpl.setInputFile(queryFileName)
-        bpl.setSubjectFile(subjectFileName)
-        bpl.setOutputFile(obsOutputFileName)
-        bpl.setProgramParameters("")
-        bpl.run()
-        
-        blastFileName = queryFileName + ".blast"
-        
-        self.assertTrue(os.path.exists(obsOutputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
-        
-        os.remove(queryFileName)
-        os.remove(subjectFileName)
-        os.remove(blastFileName)
-        os.remove(expOutputFileName)
-        os.remove(obsOutputFileName)
-
-    def test_as_script_empty_result(self):
-        queryFileName = "smallProtBank_supctg30.fa"
-        mock = MockMiniProtBankSupctg30()
-        mock.write(queryFileName)
-        subjectFileName = "subjectBank.fa"
-        mock = MockFastaSupctg30()
-        mock.write(subjectFileName)
-        
-        expOutputFileName = "expBlatOutput.blast.align"
-        self.writeEmptyExpOutputFile(expOutputFileName)
-        
-        obsOutputFileName = "obsBlatOutput.blast.align"
-        
-        cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
-        
-        os.system(cmd2Launch)
-        
-        blastFileName = queryFileName + ".blast"
-                
-        self.assertTrue(os.path.exists(obsOutputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
-        
-        os.remove(queryFileName)
-        os.remove(subjectFileName)
-        os.remove(blastFileName)
-        os.remove(expOutputFileName)
-        os.remove(obsOutputFileName)
-
-    def test_run(self):
-        queryFileName = "smallESTBank.fa"
-        mock = MockESTBankForBlat()
-        mock.write(queryFileName)
-        subjectFileName = "subjectBank.fa"
-        mock = MockDataBankForBlat()
-        mock.write(subjectFileName)
-        
-        expOutputFileName = "expBlatOutput.blast.align"
-        mock = MockOutputForBlat()
-        mock.write(expOutputFileName)
-        
-        obsOutputFileName = "obsBlatOutput.blast.align"
-
-        bpl = BlatProgramLauncher()
-        bpl.setInputFile(queryFileName)
-        bpl.setSubjectFile(subjectFileName)
-        bpl.setOutputFile(obsOutputFileName)
-        bpl.setProgramParameters("")
-        bpl.run()
-        
-        blastFileName = queryFileName + ".blast"
-        
-        self.assertTrue(os.path.exists(obsOutputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
-        
-        os.remove(queryFileName)
-        os.remove(subjectFileName)
-        os.remove(blastFileName)
-        os.remove(expOutputFileName)
-        os.remove(obsOutputFileName)
-
-    def test_as_script(self):
-        queryFileName = "smallESTBank.fa"
-        mock = MockESTBankForBlat()
-        mock.write(queryFileName)
-        subjectFileName = "subjectBank.fa"
-        mock = MockDataBankForBlat()
-        mock.write(subjectFileName)
-        
-        expOutputFileName = "expBlatOutput.blast.align"
-        mock = MockOutputForBlat()
-        mock.write(expOutputFileName)
-        
-        obsOutputFileName = "obsBlatOutput.blast.align"
-        
-        cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
-        
-        os.system(cmd2Launch)
-        
-        blastFileName = queryFileName + ".blast"
-                
-        self.assertTrue(os.path.exists(obsOutputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
-        
-        os.remove(queryFileName)
-        os.remove(subjectFileName)
-        os.remove(blastFileName)
-        os.remove(expOutputFileName)
-        os.remove(obsOutputFileName)
-        
-    def writeEmptyExpOutputFile(self, outputFileName):
-        f = open(outputFileName, "w")
-        f.write("")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchBlastclust.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-import unittest
-import os
-from commons.launcher.LaunchBlastclust import LaunchBlastclust
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_LaunchBlastclust(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
-        os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
-        self._outputFileName = "%s_Blastclust.fa" % self._inputFileName
-        self._outBlastclustFileName = "%s_blastclust.txt" % self._inputFileName
-        
-    def tearDown(self):
-        if os.path.exists(self._outputFileName):
-            os.remove(self._outputFileName)
-        if os.path.exists(self._outBlastclustFileName):
-            os.remove(self._outBlastclustFileName)
-        os.remove(self._inputFileName)
-
-    def test_run(self):
-        iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
-        iLaunchBlastclust.run()
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        
-    def test_run_with_tweaked_params(self):
-        iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
-        iLaunchBlastclust.setBothSequences("F")
-        iLaunchBlastclust.setIdentityThreshold(0)
-        iLaunchBlastclust.setIsBlastToMap()
-        iLaunchBlastclust.run()
-        
-        faExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.fa" % os.environ["REPET_DATA"]
-        mapExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.map" % os.environ["REPET_DATA"]
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(faExpFileName, self._outputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(mapExpFileName, "%s.map" % os.path.splitext(self._outputFileName)[0]))
-        
-        os.remove("%s.map" % os.path.splitext(self._outputFileName)[0])
-      
-    def test_run_with_header_options(self):
-        inFileName = "dummyHeaderForTEdenovo.fa"
-        expFileName = "expDummyHeaderForTEdenovo.fa"
-        self._writeInputFile_header_options(inFileName)
-        self._writeExpFile_header_options(expFileName)
-        obsFileName = "%s_Blastclust.fa" % inFileName
-        
-        iLaunchBlastclust = LaunchBlastclust(inFileName, clean = True)
-        iLaunchBlastclust.setIsHeaderForTEdenovo(True)
-        iLaunchBlastclust.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(inFileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        os.remove("%s_blastclust.txt" % inFileName)
-          
-    def test_run_as_script(self):
-        cmd = "LaunchBlastclust.py -i %s" % self._inputFileName
-        os.system(cmd)
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        
-    def _writeInputFile_header_options(self, inFileName):
-        f = open(inFileName,"w")
-        f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
-        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-        f.write(">DTX-incomp_DmelChr4-B-R10-Map3_reversed\n")
-        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-        f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
-        f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
-        f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
-        f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
-        f.close()
-        
-    def _writeExpFile_header_options(self, expFileName):
-        f = open(expFileName,"w")
-        f.write(">DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\n")
-        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-        f.write(">DTX-incomp_Blc1_DmelChr4-B-R10-Map3_reversed\n")
-        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-        f.write(">PotentialHostGene-chim_Blc2_DmelChr4-B-R4-Map5_reversed\n")
-        f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
-        f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
-        f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchLastZ.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchLastZ import LaunchLastZ
-
-class Test_F_LaunchLastZ(unittest.TestCase):
-    
-    def setUp(self):
-        self._inFastaFileName = "%s/Tools/input_TestFLastZ.fa" % os.environ["REPET_DATA"]
-        self._expAxtFileName  = "%s/Tools/exp_TestFLastZ.axt" % os.environ["REPET_DATA"] 
-        self._obsAxtFileName = "obsLastZ.axt"
-        
-    def tearDown(self):
-        try:
-            os.remove(self._obsAxtFileName)
-        except:pass
-        
-    def test_run(self):
-        ilauncher = LaunchLastZ(self._inFastaFileName, self._inFastaFileName, self._obsAxtFileName,verbosity=1)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expAxtFileName, self._obsAxtFileName))
-        
-    def test_run_as_script(self):
-        #FIXME : change path 
-        cmd = 'python %s/commons/launcher/LaunchLastZ.py -q %s -r %s -o %s' % (os.environ["REPET_PATH"], self._inFastaFileName, self._inFastaFileName, self._obsAxtFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expAxtFileName, self._obsAxtFileName))
- 
-                       
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchMCL.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import unittest
-import os
-import shutil
-from commons.launcher.LaunchMCL import LaunchMCL
-
-class Test_F_LaunchMCL(unittest.TestCase):
-# TODO: test query coverage filter
-
-    def setUp(self):
-        self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
-        try:
-            shutil.rmtree("MCLtmpDirectory")
-            os.remove(self._inputFileName)
-        except:
-            pass
-        try:
-            os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
-        except:
-            pass
-        self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
-        
-    def tearDown(self):
-        try:
-            os.remove(self._inputFileName)
-            os.remove(self._outputFileName)
-            shutil.rmtree("MCLtmpDirectory")
-        except:
-            pass
-        try:
-            os.remove("DmelChr4_LTRharvest_expected_with_default_params_MCL.map")
-        except:
-            pass    
-        
-    def test_run(self):
-        iLaunchMCL = LaunchMCL(self._inputFileName, doClean = True, verbosity = 1)
-        iLaunchMCL.run()
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-
-    def test_run_with_map_file(self):
-        iLaunchMCL = LaunchMCL(self._inputFileName, isCluster2Map = True, doClean = False, verbosity = 1)
-#        iLaunchMCL.setCoverageThreshold(0.60)
-        iLaunchMCL.run()
-        expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
-        expMapFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.map" % os.environ["REPET_DATA"]
-        obsMapFileName = "%s.map" % os.path.splitext(self._outputFileName)[0]
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
-        
-        os.remove(obsMapFileName)
-
-    def test_run_clusterConsensus_headers(self):
-        os.remove(self._inputFileName)
-        self._inputFileName = "DmelChr4_LTRharvest_MCL_ClusterConsHeaders_input.fa"
-        os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
-        iLaunchMCL = LaunchMCL(self._inputFileName, isClusterConsensusHeaders = True, doClean = True, verbosity = 1)
-        iLaunchMCL.run()
-        expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_ClusterConsHeaders_expected.fa" % os.environ["REPET_DATA"]
-        self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
-      
-    def test_run_as_script(self):
-        cmd = "LaunchMCL.py -i %s -j -v 6" % self._inputFileName
-        os.system(cmd)
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
-
-    def test_run_as_script_allParams(self):
-        cmd = "LaunchMCL.py -i %s -j -I 1.5 -T 0.0 -m -v 6" % self._inputFileName
-        os.system(cmd)
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
-
-    def test_run_as_script_without_join(self):
-        cmd = "LaunchMCL.py -i %s -v 2" % self._inputFileName
-        os.system(cmd)
-        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchMap.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-import unittest
-import os
-import subprocess
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchMap import LaunchMap
-
-class Test_F_LaunchMap(unittest.TestCase):
-
-    def setUp(self):
-        self._fastaFileName = "LaunchMap_seqCluster1.fa"
-        fastaFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName)
-        os.symlink(fastaFilePath, self._fastaFileName)
-        self._obsFileName = "%s.fa_aln" % self._fastaFileName
-
-    def tearDown(self):
-        os.remove(self._fastaFileName)
-        try:
-            os.remove(self._obsFileName)
-        except: pass
-
-    def test_run_as_script(self):
-        expFileName = "%s/Tools/expLaunchMap_seqCluster1.fa.fa_aln" % os.environ["REPET_DATA"]
-        obsFileName = "obs.fa_aln"
-        cmd = "LaunchMap.py "
-        cmd += "-i %s " % self._fastaFileName
-        cmd += "-o %s " % obsFileName
-        cmd += "-c "
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        
-    def test_run(self):
-        expFileName = "%s/Tools/expLaunchMap_seqCluster1.fa.fa_aln" % os.environ["REPET_DATA"]
-        iLaunchMap = LaunchMap(self._fastaFileName)
-        iLaunchMap.setDoClean(True)
-        iLaunchMap.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._obsFileName))
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchMatcher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import unittest
-import os
-import subprocess
-from commons.launcher.LaunchMatcher import LaunchMatcher
-
-class Test_F_LaunchMatcher(unittest.TestCase):
-
-    def setUp(self):
-        self._inFileName = "DmelChr4.align"
-        self._fastaFileName = "DmelChr4.fa"
-        inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
-        inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName)
-        try:
-            os.remove(self._inFileName)
-        except:
-            pass
-        os.symlink(inFilePath, self._inFileName)
-        os.symlink(inFastaPath, self._fastaFileName)
-        self._iLaunchMatcher = LaunchMatcher(align=self._inFileName, queryFileName=self._fastaFileName, subjectFileName=self._fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True)
-        self._iLaunchMatcher.setVerbosity(2)
-
-    def tearDown(self):
-        try:
-            FileUtils.removeFilesByPattern("%s*" % self._inFileName)
-            os.remove(self._fastaFileName)
-        except:
-            pass
-
-    def test_run_as_class_1_file(self):
-        expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
-        expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
-        
-        obsPathFileName = "%s.match.path" % self._inFileName
-        obsTabFileName = "%s.match.tab" % self._inFileName
-        
-        self._iLaunchMatcher.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
-
-    def test_run_as_script(self):
-        expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
-        expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
-
-        cmd = "LaunchMatcher.py "
-        cmd += "-a %s " % self._inFileName
-        cmd += "-q %s " % self._fastaFileName
-        cmd += "-s %s " % self._fastaFileName
-        cmd += "-o DmelChr4.align "
-        cmd += "-j "
-        cmd += "-k "
-        cmd += "-e 1e-20 "
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        obsPathFileName = "%s.match.path" % self._inFileName
-        obsTabFileName = "%s.match.tab" % self._inFileName
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchMummerPlot.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchMummerPlot import LaunchMummerPlot
-
-class Test_F_LaunchMummerPlot(unittest.TestCase):
-    
-    def setUp(self):
-        self._queryFastaFileName = "query.fa"
-        self._refFastaFileName = "ref.fa"
-        self._writeInputFastaFiles()
-        
-        self._inputDeltaFileName = "inputNucmer.delta"
-        self._writeInputDeltaFileName()
-        
-        self._expGpFileName = "expMummerPlot.gp"
-        self._obsGpFileName = "obsMummerPlot.gp"
-        self._obsPngFileName = "obsMummerPlot.png"
-        
-    def tearDown(self):
-        try:
-            os.remove(self._queryFastaFileName)
-        except:pass
-        try:
-            os.remove(self._refFastaFileName)
-        except:pass
-        try:
-            os.remove(self._inputDeltaFileName)
-        except:pass
-        try:
-            os.remove(self._expGpFileName)
-        except:pass
-        try:
-            os.remove(self._obsGpFileName)
-        except:pass
-        try:
-            os.remove(self._obsPngFileName)
-        except:pass
-        
-    
-    def test_run(self):
-        self._writeExpGpFile()
-        ilaunchMummerPlot = LaunchMummerPlot(self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName,"obsMummerPlot",fat=True, filter=True, clean=True, verbosity=1)
-        ilaunchMummerPlot.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName))
-        
-    def test_run_as_script(self):
-        self._writeExpGpFile()
-        cmd = 'LaunchMummerPlot.py --input %s --Qfile %s --Rfile %s --prefix %s --fat --filter --clean' % (self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName, "obsMummerPlot")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName))
-        
-    def _writeInputFastaFiles(self):
-        InputFile = open(self._queryFastaFileName, 'w')
-        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
-        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
-        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
-        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
-        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
-        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
-        InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
-        InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
-        InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
-        InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
-        InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
-        InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
-        InputFile.write('CCAAAAAAAAA\n')
-        InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
-        InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
-        InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
-        InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
-        InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
-        InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
-        InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
-        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
-        InputFile.write('AAAAAAA\n')
-        InputFile.close()
-        
-        InputFile = open(self._refFastaFileName, 'w')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()
-        
-    def _writeExpGpFile(self):
-        f = open(self._expGpFileName, 'w')
-        f.write('set terminal png tiny size 800,800\n')
-        f.write('set output "obsMummerPlot.png"\n')
-        f.write('set xtics rotate ( \\\n')
-        f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n')
-        f.write(' "SINEC1B2_CF:classI:SINE:?" 389, \\\n')
-        f.write(' "SINE1A_SS:classI:SINE:SINE2/tRNA" 552, \\\n')
-        f.write(' "SUSINE2:classI:SINE:SINE2/tRNA" 682, \\\n')
-        f.write(' "Bovc-tA2:classI:SINE:SINE2/tRNA" 891, \\\n')
-        f.write(' "ALPINE1:classI:SINE:SINE2/tRNA" 1223, \\\n')
-        f.write(' "SINE2-1_Pca:classI:SINE:SINE2/tRNA" 1349, \\\n')
-        f.write(' "" 1694 \\\n')
-        f.write(')\n')
-        f.write('set ytics ( \\\n')
-        f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n')
-        f.write(' "SINEC1B2_CF:classI:SINE:?" 371, \\\n')
-        f.write(' "" 532 \\\n')
-        f.write(')\n')
-        f.write('set size 1,1\n')
-        f.write('set grid\n')
-        f.write('unset key\n')
-        f.write('set border 0\n')
-        f.write('set tics scale 0\n')
-        f.write('set xlabel "REF"\n')
-        f.write('set ylabel "QRY"\n')
-        f.write('set format "%.0f"\n')
-        f.write('set mouse format "%.0f"\n')
-        f.write('set mouse mouseformat "[%.0f, %.0f]"\n')
-        f.write('set mouse clipboardformat "[%.0f, %.0f]"\n')
-        f.write('set xrange [1:1694]\n')
-        f.write('set yrange [1:532]\n')
-        f.write('set style line 1  lt 1 lw 3 pt 6 ps 1\n')
-        f.write('set style line 2  lt 3 lw 3 pt 6 ps 1\n')
-        f.write('set style line 3  lt 2 lw 3 pt 6 ps 1\n')
-        f.write('plot \\\n')
-        f.write(' "obsMummerPlot.fplot" title "FWD" w lp ls 1, \\\n')
-        f.write(' "obsMummerPlot.rplot" title "REV" w lp ls 2\n')
-        f.write('')
-        f.close()
-        
-    def _writeInputDeltaFileName(self):
-        f = open(self._inputDeltaFileName, 'w')
-        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-        f.write('NUCMER\n')
-        f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
-        f.write('1 343 1 343 0 0 0\n')
-        f.write('0\n')
-        f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
-        f.write('1 161 1 161 0 0 0\n')
-        f.write('0\n')
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
-        
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchNucmer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchNucmer import LaunchNucmer
-
-class Test_F_LaunchNucmer(unittest.TestCase):
-    
-    def setUp(self):
-        self._queryFastaFileName = "query.fa"
-        self._refFastaFileName = "ref.fa"
-        self._writeInputFastaFiles()
-        self._expDeltaFileName = "expNucmer.delta"
-        self._writeExpDeltaFile()
-        self._obsDeltaFileName = "obsNucmer.delta"
-        self._obsCoordFileName= "obsNucmer.coords"
-        self._expCoordFileName= "expNucmer.coords"
-        
-    def tearDown(self):
-        try:
-            os.remove(self._queryFastaFileName)
-        except:pass
-        try:
-            os.remove(self._refFastaFileName)
-        except:pass
-        try:
-            os.remove(self._expDeltaFileName)
-        except:pass
-        try:
-            os.remove(self._obsDeltaFileName)
-        except:pass
-        
-    def test_run(self):
-        ilauncher = LaunchNucmer(self._refFastaFileName, self._queryFastaFileName,"obsNucmer",verbosity=1)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
-        
-    def test_run_as_script(self):
-        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
-        
-    def test_run_as_script_gencoords_output(self):
-        self._writeExpGenCoordsFile()
-        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
-        os.remove(self._obsCoordFileName)
-        os.remove(self._expCoordFileName)
-    
-    def test_run_as_script_with_mincluster(self):
-        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))      
-        
-    def test_run_as_script_showcoords_output(self):
-        self._writeExpShowCoordsFile()
-        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
-        os.remove(self._obsCoordFileName)
-        os.remove(self._expCoordFileName) 
-        
-    def _writeInputFastaFiles(self):
-        InputFile = open(self._queryFastaFileName, 'w')
-        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
-        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
-        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
-        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
-        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
-        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
-        InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
-        InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
-        InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
-        InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
-        InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
-        InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
-        InputFile.write('CCAAAAAAAAA\n')
-        InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
-        InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
-        InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
-        InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
-        InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
-        InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
-        InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
-        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
-        InputFile.write('AAAAAAA\n')
-        InputFile.close()
-        
-        InputFile = open(self._refFastaFileName, 'w')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()
-        
-    def _writeExpDeltaFile(self):
-        f = open(self._expDeltaFileName, 'w')
-        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-        f.write('NUCMER\n')
-        f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
-        f.write('1 343 1 343 0 0 0\n')
-        f.write('0\n')
-        f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
-        f.write('1 161 1 161 0 0 0\n')
-        f.write('0\n')
-        f.close()
-        
-    def _writeExpGenCoordsFile(self):
-        f = open(self._expCoordFileName, 'w')
-        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-        f.write('NUCMER\n\n')
-        f.write('    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  | [TAGS]\n')
-        f.write('=====================================================================================\n')
-        f.write('       1      161  |        1      161  |      161      161  |   100.00  | SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-        f.write('       1      343  |        1      343  |      343      343  |   100.00  | SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-        f.close()
-        
-    def _writeExpShowCoordsFile(self):
-        f = open(self._expCoordFileName, 'w')
-        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-        f.write('NUCMER\n\n')
-        f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
-        f.write('1\t161\t1\t161\t161\t161\t100.00\t164\t161\t98.17\t100.00\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-        f.write('1\t343\t1\t343\t343\t343\t100.00\t389\t371\t88.17\t92.45\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-        f.close()
-                       
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchPhyML.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from shutil import rmtree
-from commons.launcher.LaunchPhyML import LaunchPhyML
-
-
-class Test_F_LaunchPhyML(unittest.TestCase):
-    
-    def setUp(self):
-        self._curTestDir = os.getcwd()
-        self._testPrefix = 'test_LRA'
-        try:
-            os.makedirs(self._testPrefix)
-        except:pass
-        os.chdir(self._testPrefix)
-        
-
-        self._inputFastaFileName = "%s_input.fa" % self._testPrefix 
-        self._obsOutputFileName = self._inputFastaFileName +'_obs.phylip'
-        self._expOutputFileName = "%s_exp.phylip" % self._testPrefix 
-        self._writeInputFile()
-        
-#    def tearDown(self):
-#        os.chdir(self._curTestDir)
-#        try:
-#            rmtree(self._testPrefix)
-#        except:pass
-
-    def test_run(self):
-        #phylip use only same length sequences
-        self._writeExpFile()
-        ilauncher = LaunchPhyML(self._inputFastaFileName,verbosity=7)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
-        
-        
-#    def test_run_as_script(self):
-#        self._writeExpOutputFile_wo_refseq()
-#        cmd = 'LaunchPhyML.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
-#        os.system(cmd)
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))    
-
-               
-    def _writeInputFile(self):        
-        InputFile = open(self._inputFastaFileName, 'w')
-        InputFile.write(""">sequence1
-GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC
-GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT
-GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAG
->sequence2
-GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA
-GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG
-GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG
->sequence3
-ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTATAGCAATGTCC
-TTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGCGTCCAATAGCACAGACTTCA
-GCTTGAATGCTGGTGTATCTGCCCATTGATTCGTGGTATTTCAACCTGGG
-""")
-        InputFile.close()    
-        
-    def _writeExpFile(self):        
-        InputFile = open(self._expOutputFileName, 'w')
-        InputFile.write(""" 3  170
-sequence1      GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG
-sequence2      GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCG
-sequence3      ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTAT
-
-CCCCGGGTTCGATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGG
-TGATCCTGGAGACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAG
-AGCAATGTCCTTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGC
-
-AGTTTGCATGTTCTCCCTGTGCCTGCGTGGGTTCTCTCCGGGTACTCCGG
-CCTGCTTCTCCCTCTGCCTGGGGCGGCACGGTGGTGTGGTGGTTAGCACT
-GTCCAATAGCACAGACTTCAGCTTGAATGCTGGTGTATCTGCCCATTGAT
-
-CTTCCTCCCACAGTCCAAAG
-GTTGCCTCACAGCAAGAAGG
-TCGTGGTATTTCAACCTGGG""")
-        InputFile.close()    
-                                   
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchPromer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,231 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchPromer import LaunchPromer
-
-
-class Test_F_LaunchPromer(unittest.TestCase):
-    
-    def setUp(self):
-        self._queryFastaFileName = "query.fa"
-        self._refFastaFileName = "ref.fa"
-        self._writeInputFastaFiles()
-        self._expDeltaFileName = "expPromer.delta"
-        self._writeExpDeltaFile()
-        self._obsDeltaFileName = "obsPromer.delta"
-        self._obsCoordFileName= "obsPromer.coords"
-        self._expCoordFileName= "expPromer.coords"
-        
-    def tearDown(self):
-        try:
-            os.remove(self._queryFastaFileName)
-        except:pass
-        try:
-            os.remove(self._refFastaFileName)
-        except:pass
-        try:
-            os.remove(self._expDeltaFileName)
-        except:pass
-        try:
-            os.remove(self._obsDeltaFileName)
-        except:pass
-        
-    def test_run(self):
-        ilauncher = LaunchPromer(self._refFastaFileName, self._queryFastaFileName,"obsPromer",verbosity=1)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
-        
-    def test_run_as_script(self):
-        cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
-        
-    def test_run_as_script_gencoords_output(self):
-        self._writeExpGenCoordsFile()
-        cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
-        os.remove(self._obsCoordFileName)
-        os.remove(self._expCoordFileName)
-    
-    def test_run_as_script_with_mincluster(self):
-        cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))      
-        
-    def test_run_as_script_showcoords_output(self):
-        self._writeExpShowCoordsFile()
-        cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
-        os.remove(self._obsCoordFileName)
-        os.remove(self._expCoordFileName) 
-        
-    def _writeInputFastaFiles(self):
-        InputFile = open(self._queryFastaFileName, 'w')
-        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
-        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
-        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
-        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
-        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
-        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
-        InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
-        InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
-        InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
-        InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
-        InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
-        InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
-        InputFile.write('CCAAAAAAAAA\n')
-        InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
-        InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
-        InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
-        InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
-        InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
-        InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
-        InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
-        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
-        InputFile.write('AAAAAAA\n')
-        InputFile.close()
-        
-        InputFile = open(self._refFastaFileName, 'w')
-        InputFile.write('>SINE_FR2:classI:SINE:?\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()
-        
-    def _writeExpDeltaFile(self):
-        with open(self._expDeltaFileName, 'w') as f:
-            f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-            f.write('PROMER\n')
-            f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
-            f.write('1 387 1 369 6 6 10\n')
-            f.write('115\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('2 388 2 370 6 6 8\n')
-            f.write('115\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('3 389 3 371 6 6 16\n')
-            f.write('115\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('388 2 370 2 6 6 6\n')
-            f.write('10\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('387 1 369 1 6 6 5\n')
-            f.write('10\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('389 3 371 3 6 6 4\n')
-            f.write('11\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('1\n')
-            f.write('0\n')
-            f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
-            f.write('1 159 1 159 0 0 2\n')
-            f.write('0\n')
-            f.write('3 161 3 161 0 0 2\n')
-            f.write('0\n')
-            f.write('161 3 161 3 0 0 0\n')
-            f.write('0\n')
-            f.write('160 2 160 2 0 0 2\n')
-            f.write('0\n')
-            f.write('159 1 159 1 0 0 4\n')
-            f.write('0\n')
-            f.write('2 160 2 160 0 0 4\n')
-            f.write('0\n')
-       
-       
-
-        
-    def _writeExpGenCoordsFile(self):
-        with open(self._expCoordFileName, 'w') as f:
-            f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-            f.write('PROMER\n\n')
-            f.write('    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  [% SIM]  [% STP]  | [FRM]  [TAGS]\n')
-            f.write('==============================================================================================================\n')
-            f.write('       1      159  |        1      159  |      159      159  |   100.00   100.00     1.89  |  1  1  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('       2      160  |        2      160  |      159      159  |   100.00   100.00     3.77  |  2  2  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('       3      161  |        3      161  |      159      159  |   100.00   100.00     1.89  |  3  3  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('     159        1  |      159        1  |      159      159  |   100.00   100.00     3.77  | -3 -3  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('     160        2  |      160        2  |      159      159  |   100.00   100.00     1.89  | -2 -2  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('     161        3  |      161        3  |      159      159  |   100.00   100.00     0.00  | -1 -1  SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('       1      387  |        1      369  |      387      369  |    95.35    95.35     3.88  |  1  1  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('       2      388  |        2      370  |      387      369  |    95.35    95.35     3.10  |  2  2  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('       3      389  |        3      371  |      387      369  |    95.35    95.35     6.20  |  3  3  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('     387        1  |      369        1  |      387      369  |    95.35    95.35     1.94  | -3 -3  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('     388        2  |      370        2  |      387      369  |    95.35    95.35     2.33  | -2 -2  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('     389        3  |      371        3  |      387      369  |    95.35    95.35     1.55  | -1 -1  SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-    
-        
-    def _writeExpShowCoordsFile(self):
-        with open(self._expCoordFileName, 'w') as f:
-            f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
-            f.write('PROMER\n\n')
-            f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[% SIM]\t[% STP]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
-            f.write('1\t159\t1\t159\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('2\t160\t2\t160\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t2\t2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('3\t161\t3\t161\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t3\t3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('159\t1\t159\t1\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t-3\t-3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('160\t2\t160\t2\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t-2\t-2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('161\t3\t161\t3\t159\t159\t100.00\t100.00\t0.00\t164\t161\t96.95\t98.76\t-1\t-1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
-            f.write('1\t387\t1\t369\t387\t369\t95.35\t95.35\t3.88\t389\t371\t99.49\t99.46\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('2\t388\t2\t370\t387\t369\t95.35\t95.35\t3.10\t389\t371\t99.49\t99.46\t2\t2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('3\t389\t3\t371\t387\t369\t95.35\t95.35\t6.20\t389\t371\t99.49\t99.46\t3\t3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('387\t1\t369\t1\t387\t369\t95.35\t95.35\t1.94\t389\t371\t99.49\t99.46\t-3\t-3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('388\t2\t370\t2\t387\t369\t95.35\t95.35\t2.33\t389\t371\t99.49\t99.46\t-2\t-2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-            f.write('389\t3\t371\t3\t387\t369\t95.35\t95.35\t1.55\t389\t371\t99.49\t99.46\t-1\t-1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchRefAlign.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchRefAlign import LaunchRefAlign
-
-
-class Test_F_LaunchRefAlign(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFastaFileName = "input.fa"
-        self._obsOutputFileName = "obs"
-        self._expOutputFileName = "exp"
-        self._writeInputFile()
-        self._writeExpOutputFile()
-        
-#    def tearDown(self):
-#        try:
-#            os.remove(self._inputFastaFileName)
-#        except:pass
-#    
-#        try:
-#            os.remove(self._expOutputFileName)
-#        except:pass
-#        try:
-#            os.remove(self._obsOutputFileName)
-#        except:pass
-#        try:
-#            os.remove("input.fa.2.3.5.80.10.20.15.dat")
-#        except:pass
-    
-    def test_run(self):
-        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
-        
-#    def test_run_as_script(self):
-#        cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
-#        os.system(cmd)
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))    
-
-        
-    def _writeInputFile(self):        
-        InputFile = open(self._inputFastaFileName, 'w')
-        InputFile.write('>sequence\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>sequence2\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()    
-        
-    def _writeExpOutputFile(self):
-        with open(self._expOutputFileName,'w') as expOutputFile:
-            expOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
-2\t(GGT)5\tsequence\t10\t23
-3\t(GTGTGA)4\tsequence\t222\t242
-4\t(GTCCA)2\tsequence\t282\t292
-5\t(AGTG)4\tsequence\t355\t371
-6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
-7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
-8\t(TC)23\tsequence2\t107\t152
-""")
-
-                       
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchRefalign.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchRefAlign import LaunchRefAlign
-from shutil import rmtree
-
-
-class Test_F_LaunchRefAlign(unittest.TestCase):
-    
-    def setUp(self):
-        self._curTestDir = os.getcwd()
-        self._testPrefix = 'test_LRA'
-        try:
-            os.makedirs(self._testPrefix)
-        except:pass
-        os.chdir(self._testPrefix)
-        
-
-        self._inputFastaFileName = "%s_input.fa" % self._testPrefix 
-        self._obsOutputFileName = self._inputFastaFileName +'.fa_aln'
-        self._expOutputFileName = "%s_exp.fa_aln" % self._testPrefix 
-        self._writeInputFile()
-        
-    def tearDown(self):
-        os.chdir(self._curTestDir)
-        try:
-            rmtree(self._testPrefix)
-        except:pass
-
-    def test_run(self):
-        self._writeExpOutputFile_wo_refseq()
-        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
-        
-    def test_run_KeepRefSeq(self):
-        self._writeExpOutputFile_with_refseq()
-        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5, keepRefseq=True)
-        ilauncher.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
-        
-    def test_run_as_script(self):
-        self._writeExpOutputFile_wo_refseq()
-        cmd = 'LaunchRefAlign.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))    
-
-    def test_run_as_script_KeepRefSeq(self):
-        self._writeExpOutputFile_with_refseq()
-        cmd = 'LaunchRefAlign.py -i %s -r -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))   
-               
-    def _writeInputFile(self):        
-        InputFile = open(self._inputFastaFileName, 'w')
-        InputFile.write('>sequence\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>sequence2\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()    
-        
-    def _writeExpOutputFile_wo_refseq(self):
-        with open(self._expOutputFileName,'w') as expOutputFile:
-            expOutputFile.write(""">sequence2
-GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
-GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
-GCCTGTGTCTCTTCTCTC------------------------------------------
-------------------------------------------------------------
-----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
-------------------------------------------------------------
------------
-""")
-            
-    def _writeExpOutputFile_with_refseq(self):
-        with open(self._expOutputFileName,'w') as expOutputFile:
-            expOutputFile.write(""">sequence
-GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC
-GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT
-GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA
-TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA
-TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC
-CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCAAGCGGTAGAAAGTGAG
-TGAGTGAGTGA
->sequence2
-GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
-GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
-GCCTGTGTCTCTTCTCTC------------------------------------------
-------------------------------------------------------------
-----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
-------------------------------------------------------------
------------
-""")
-                               
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchRepeatMasker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchRepeatMasker import LaunchRepeatMasker
-
-
-class Test_F_RepeatMasker(unittest.TestCase):
-    
-    def setUp(self):
-        self._queryFastaFileName = "query.fa"
-        self._libFastaFileName = "lib.fa"
-        self._expMaskedQueryFileName = "expMaskedQuery.fa"
-        self._obsMaskedQueryFileName = "%s.masked" % self._queryFastaFileName
-        
-        self._expCatFileName = "expCat.fa"
-        self._obsCatFileName = "%s.cat" % self._queryFastaFileName
-        
-        self._writeInputFastaFiles()
-        self._writeExpMaskedQueryFile()
-        self._writeExpCatFile()
-   
-    def tearDown(self):
-        os.remove(self._queryFastaFileName)
-        os.remove(self._libFastaFileName)
-        os.remove(self._expMaskedQueryFileName)
-        os.remove(self._obsMaskedQueryFileName)
-        os.remove(self._expCatFileName)
-        os.remove(self._obsCatFileName)
-        os.remove("%s.tbl" % self._queryFastaFileName)
-        os.remove("%s.out" % self._queryFastaFileName)
-        os.remove("%s.ori.out" % self._queryFastaFileName)
-        
-    def test_run(self):
-        ilauncher = LaunchRepeatMasker(self._queryFastaFileName, self._libFastaFileName,verbosity=1 )
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
-        
-    def test_run_as_script(self):
-        #FIXME : change path to launcher
-        cmd = 'python %s/commons/launcher/LaunchRepeatMasker.py -q %s -l %s' % (os.environ["REPET_PATH"],self._queryFastaFileName, self._libFastaFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
-        
-    def _writeInputFastaFiles(self):
-        InputFile = open(self._queryFastaFileName, 'w')
-        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
-        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
-        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
-        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
-        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
-        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
-        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTACCTCCTTCCA\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
-        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
-        InputFile.write('AAAAAAA\n')
-        InputFile.close()
-        
-        InputFile = open(self._libFastaFileName, 'w')
-        InputFile.write('>RefLib\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.close()
-        
-    def _writeExpMaskedQueryFile(self):
-        f = open(self._expMaskedQueryFileName, 'w')  
-        f.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
-        f.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAG\n')
-        f.write('ACCCCGGTTCGATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGC\n')
-        f.write('TACCCACTCCAGTATTCTTGGGCTTCCCTGGTGGCTCAGACGGTAAAGAA\n')
-        f.write('TCCGCCTGCAATGCGGGAGACCTGGGTTCGATCCCTGGGTTGGGAAGATC\n')
-        f.write('CCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATC\n')
-        f.write('CCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
-        f.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTA\n')
-        f.write('CCTCCTTCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
-        f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
-        f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCTGCGTGGGTTCTCTCCG\n')
-        f.write('GGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGATTGGGGATTA\n')
-        f.write('GGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        f.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCC\n')
-        f.write('AGGGTGTACCCTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCC\n')
-        f.write('CGCGACCCTCAGTGGAGGAAGGGCAGCCTGGGTGGCTCAGCGGTTTAGCG\n')
-        f.write('CCTGCCTTTGGCCCAGGGCGTGATCCTGGAGACCCGGGATCGAGTCCCAC\n')
-        f.write('ATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTGGGGGAGGGTA\n')
-        f.write('TAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
-        f.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTC\n')
-        f.write('CCCCACCAAAAAAAAAA\n')
-        f.close()
-        
-    def _writeExpCatFile(self):
-        f = open(self._expCatFileName, 'w')  
-        f.write('958 0.00 0.00 0.00 Bovc-tA2:classI:SINE:SINE2/tRNA 361 480 (487) RefLib 1 120 (0) 5\n')
-        f.write('## Total Sequences: 1\n')
-        f.write('## Total Length: 967\n')
-        f.write('## Total NonMask ( excluding >20bp runs of N/X bases ): 967\n')
-        f.write('## Total NonSub ( excluding all non ACGT bases ):967\n')
-        f.write('RepeatMasker version open-3.2.6 , default mode\n')
-        f.write('run with blastp version 2.0MP-WashU\n')
-        f.write('RepBase Update 20080801, RM database version 20080801\n')
-        f.close()
-                       
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchTRF.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher.LaunchTRF import LaunchTRF
-
-
-class Test_F_LaunchTRF(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFastaFileName = "input.fa"
-        self._obsTRFOutputFileName = "obsTRF.TRF.set"
-        self._expTRFOutputFileName = "expTRF.TRF.set"
-        self._writeInputFile()
-        self._writeExpTRFOutputFile()
-        
-    def tearDown(self):
-        try:
-            os.remove(self._inputFastaFileName)
-        except:pass
-    
-        try:
-            os.remove(self._expTRFOutputFileName)
-        except:pass
-        try:
-            os.remove(self._obsTRFOutputFileName)
-        except:pass
-        try:
-            os.remove("input.fa.2.3.5.80.10.20.15.dat")
-        except:pass
-    
-    def test_run(self):
-        ilauncher = LaunchTRF(self._inputFastaFileName,self._obsTRFOutputFileName,verbosity=5)
-        ilauncher.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
-        
-    def test_run_as_script(self):
-        cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))    
-
-    def test_run_as_scriptNoOutputGiven(self):
-        cmd = 'LaunchTRF.py -i %s -v 3' % (self._inputFastaFileName)
-        os.system(cmd)
-        self._obsTRFOutputFileName = "input.fa.TRF.set"
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))  
-        
-    def test_run_as_scriptNoOutputGivenDoClean(self):
-        cmd = 'LaunchTRF.py -i %s -c -v 3' % (self._inputFastaFileName)
-        os.system(cmd)
-        self._obsTRFOutputFileName = "input.fa.TRF.set"
-        datFilePath = os.path.join(os.getcwd(),"%s.2.3.5.80.10.20.15.dat" % self._inputFastaFileName)
-        self.assertFalse(os.path.exists(datFilePath))
-        
-    def _writeInputFile(self):        
-        InputFile = open(self._inputFastaFileName, 'w')
-        InputFile.write('>sequence\n')
-        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
-        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
-        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
-        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
-        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
-        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
-        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
-        InputFile.write('>sequence2\n')
-        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
-        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
-        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
-        InputFile.close()    
-        
-    def _writeExpTRFOutputFile(self):
-        with open(self._expTRFOutputFileName,'w') as expTRFOutputFile:
-            expTRFOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
-2\t(GGT)5\tsequence\t10\t23
-3\t(GTGTGA)4\tsequence\t222\t242
-4\t(GTCCA)2\tsequence\t282\t292
-5\t(AGTG)4\tsequence\t355\t371
-6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
-7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
-8\t(TC)23\tsequence2\t107\t152
-""")
-
-                       
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_F_LaunchTallymer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,151 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-import shutil
-from commons.launcher.LaunchTallymer import LaunchTallymer
-
-class Test_F_LaunchTallymer(unittest.TestCase):
-
-    def setUp(self):
-        self._inFastaFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
-
-    def test_run_output_as_gff_cleaned(self):
-        iLaunchTallymer = LaunchTallymer(self._inFastaFileName,  clean = True, verbosity=2)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        
-    def test_run_with_remote_dir(self):
-        os.makedirs("sourceDir")
-        changedInFastaFileName = os.path.basename(self._inFastaFileName)
-        changedInFastaFilepath = os.path.join("sourceDir",changedInFastaFileName)
-        shutil.copy2(self._inFastaFileName, changedInFastaFilepath)
-        
-        iLaunchTallymer = LaunchTallymer(changedInFastaFilepath,  clean = True, verbosity=2)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        obsSourceDirFiles = os.listdir("sourceDir")
-        expSourceDirFiles = [changedInFastaFileName,]
-        self.assertEquals(expSourceDirFiles, obsSourceDirFiles)
-        
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        shutil.rmtree("sourceDir")
-
-
-    def test_run_output_as_gff_cleaned_changed_minOccs2(self):
-        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, minOccs=2, clean = True, verbosity=2)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20_minOcc2.gff" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        
-    def test_run_output_as_gff_cleaned_relative_input(self):
-        srcFastaFileName = self._inFastaFileName
-        dstFastaFileName = os.path.basename(self._inFastaFileName)
-        shutil.copy2(srcFastaFileName, dstFastaFileName)
-        iLaunchTallymer = LaunchTallymer(dstFastaFileName,  clean = True, verbosity=2)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        os.remove(dstFastaFileName)
-   
-    def test_run_as_script_output_as_gff_cleaned_relative_input_(self):
-        srcFastaFileName = self._inFastaFileName
-        dstFastaFileName = os.path.basename(self._inFastaFileName)
-        shutil.copy2(srcFastaFileName, dstFastaFileName)
-        
-        cmd = 'LaunchTallymer.py -i %s -s 20 -c -v 3' % (self._inFastaFileName)
-        os.system(cmd)
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        os.remove(dstFastaFileName)
-        
-    def test_run_output_as_wig_cleaned(self):
-        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, outputFormats="wig", clean=True)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.wig" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.wig"
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        os.remove("DmelChr4.tallymer.stat")
-
-    def test_run_output_as_gff_and_wig_k15_cleaned(self):
-        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, merSize=15, outputFormats="wig,gff3", clean=True)
-        iLaunchTallymer.run()
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.wig"
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff3"
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        
-        os.remove("DmelChr4.tallymer.stat")
-
-    def test_run_as_script_run_output_as_gff_and_wig_k15_cleaned(self):
-        logFileName = "test.log"
-        cmd = 'LaunchTallymer.py -i %s -s 15 -f gff,wig,vero -c -v 3 > %s' % (self._inFastaFileName, logFileName)
-        os.system(cmd)
-               
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.wig"
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        
-        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
-        obsFileName = "DmelChr4.tallymer.gff"
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(obsFileName)
-        
-        expLogFileName = "exp.log"
-        with open(expLogFileName, "w") as f:
-            f.write(" LaunchTallymer - WARNING - Warning: ignoring invalid formats: <vero>\n")
-            f.write(" LaunchTallymer - INFO - Starting to run tallymer search of sequence DmelChr4.fa \n")
-            f.write(" LaunchTallymer - INFO - Finished running tallymer scan of sequence DmelChr4.fa \n")
-            f.write(" LaunchTallymer - INFO - Starting to run tallymer search to map conversion\n")
-            f.write(" LaunchTallymer - INFO - Finished tallymer search to map conversion\n")
-            f.write(" LaunchTallymer - INFO - Generating wig file\n")
-            f.write(" LaunchTallymer - INFO - Generating gff file\n")
-        obsLogFileName = "obs.log"
-        os.system("cut -d'-' -f4,5,6 %s > %s" % (logFileName, obsLogFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expLogFileName, obsLogFileName))
-        
-        os.remove(logFileName)
-        os.remove(expLogFileName)
-        os.remove(obsLogFileName)
-        os.remove("DmelChr4.tallymer.stat")
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_LaunchBlastclust.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,237 +0,0 @@
-import unittest
-import time
-import os
-from commons.launcher.LaunchBlastclust import LaunchBlastclust
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_LaunchBlastclust( unittest.TestCase ):
-
-    def setUp(self):
-        self._iLaunchBlastclust = LaunchBlastclust()
-        self._iLaunchBlastclust.setClean()
-        self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S"), os.getpid())
-
-    def tearDown(self):
-        self._iLaunchBlastclust = None
-        self._uniqId = None
-
-    def test_getClustersFromTxtFile(self):
-        inFileName = "dummyInFile_%s"  % self._uniqId
-        inF = open(inFileName, "w")
-        inF.write("seq1 seq3 seq4 \n")
-        inF.write("seq2 seq5 \n")
-        inF.close()
-        dExp = {1:["seq1","seq3","seq4"], 2:["seq2","seq5"]}
-        self._iLaunchBlastclust.setTmpFileName(inFileName)
-        dObs = self._iLaunchBlastclust.getClustersFromTxtFile()
-        self.assertEqual(dObs, dExp)
-        os.remove(inFileName)
-        
-    def test_getClusteringResultsInFasta_without_filtering(self):
-        inFileName = "dummyInFile_%s"  % self._uniqId
-        inF = open(inFileName, "w")
-        inF.write(">seq1\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq2\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq3\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq4\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq5\n")
-        inF.write("gaattgtttactta\n")
-        inF.close()
-        
-        tmpFileName = "%s_blastclust.txt" % self._uniqId
-        inF = open(tmpFileName, "w")
-        inF.write("seq1 seq3 seq4 \n")
-        inF.write("seq2 seq5 \n")
-        inF.close()
-        self._iLaunchBlastclust.setTmpFileName(tmpFileName)
-        
-        fileExp = "getClusteringResultsInFastaExpected.fa"
-        outF = open(fileExp, "w")
-        outF.write(">BlastclustCluster1Mb1_seq1\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb2_seq3\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb3_seq4\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster2Mb1_seq2\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster2Mb2_seq5\n")
-        outF.write("gaattgtttactta\n")
-        outF.close()
-        
-        self._iLaunchBlastclust.getClusteringResultsInFasta(inFileName)
-        fileObs = "%s_Blastclust.fa" % os.path.splitext(inFileName)[0]
-        
-        if not FileUtils.are2FilesIdentical(fileObs, fileExp):
-            print "Files are different"
-            return
-        else:
-            print "Files are identical\n"
-
-        os.remove(inFileName)
-        os.remove(tmpFileName)
-        os.remove(fileExp)
-        os.remove(fileObs)
-
-    def test_getClusteringResultsInFasta_with_filtering(self):
-        inFileName = "dummyInFile_%s"  % self._uniqId
-        inF = open(inFileName, "w")
-        inF.write(">seq1\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq2\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq3\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq4\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">seq5\n")
-        inF.write("gaattgtttactta\n")
-        inF.close()
-        
-        tmpFileName = "%s_blastclust.txt" % self._uniqId
-        inF = open(tmpFileName, "w")
-        inF.write("seq1 seq3 seq4 \n")
-        inF.write("seq2\n")
-        inF.write("seq5\n")
-        inF.close()
-        self._iLaunchBlastclust.setTmpFileName(tmpFileName)
-        
-        fileExp = "getClusteringResultsInFastaExpected.fa"
-        outF = open(fileExp, "w")
-        outF.write(">BlastclustCluster1Mb1_seq1\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb2_seq3\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb3_seq4\n")
-        outF.write("gaattgtttactta\n")
-        outF.close()
-        
-        self._iLaunchBlastclust.setFilterUnclusteredSequences()
-        self._iLaunchBlastclust.getClusteringResultsInFasta(inFileName)
-        fileObs = "%s_Blastclust.fa" % os.path.splitext(inFileName)[0]
-        
-        if not FileUtils.are2FilesIdentical(fileObs, fileExp):
-            print "Files are different"
-            return
-        else:
-            print "Files are identical\n"
-
-        os.remove(inFileName)
-        os.remove(tmpFileName)
-        os.remove(fileExp)
-        os.remove(fileObs)
-
-    def test_getLinkInitNewHeaders(self):
-        inFileName = "dummyInput_%s.shortHlink" % self._uniqId
-        inF = open(inFileName, "w")
-        inF.write("seq1\tHeader1\t1\t5193\n")
-        inF.write("seq2\tHeader2\t1\t5193\n")
-        inF.write("seq3\tHeader3\t1\t5193\n")
-        inF.write("seq4\tHeader4\t1\t5193\n")
-        inF.close()
-        
-        self._iLaunchBlastclust.setInputFileName("dummyInput_%s" % self._uniqId)
-        dObs = self._iLaunchBlastclust.getLinkInitNewHeaders()
-        dExp = {"seq1":"Header1", "seq2":"Header2", "seq3":"Header3", "seq4":"Header4"}
-        
-        self.assertEqual(dObs, dExp)
-        os.remove(inFileName)
-        
-    def test_retrieveInitHeaders(self):
-        dIn = {"seq1":"Header1", "seq2":"Header2", "seq3":"Header3", "seq4":"Header4"}
-        
-        inFileName = "dummyInFile_%s"  % self._uniqId
-        outFilePrefix = self._uniqId
-        
-        tmpFileName = "%s_blastclust.txt" % outFilePrefix
-        inF = open(tmpFileName, "w")
-        inF.write("seq1 seq3 seq4\n")
-        inF.write("seq2\n")
-        inF.close()
-        
-        shortHFile = "%s.shortH_Blastclust.fa"  % inFileName
-        shF = open(shortHFile, "w")
-        shF.write(">BlastclustCluster1Mb1_seq1\n")
-        shF.write("gaattgtttactta\n")
-        shF.write(">BlastclustCluster1Mb2_seq3\n")
-        shF.write("gaattgtttactta\n")
-        shF.write(">BlastclustCluster1Mb3_seq4\n")
-        shF.write("gaattgtttactta\n")
-        shF.write(">BlastclustCluster2Mb1_seq2\n")
-        shF.write("gaattgtttactta\n")
-        shF.close()
-        
-        fileExp = "retrieveInitHeadersExpected.fa"
-        outF = open(fileExp, "w")
-        outF.write(">BlastclustCluster1Mb1_Header1\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb2_Header3\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster1Mb3_Header4\n")
-        outF.write("gaattgtttactta\n")
-        outF.write(">BlastclustCluster2Mb1_Header2\n")
-        outF.write("gaattgtttactta\n")
-        outF.close()
-
-        self._iLaunchBlastclust.setInputFileName(inFileName)
-        self._iLaunchBlastclust.setTmpFileName(tmpFileName)
-        self._iLaunchBlastclust.setOutputFilePrefix(outFilePrefix)
-        self._iLaunchBlastclust.retrieveInitHeaders(dIn)
-        fileObs = "%s_Blastclust.fa" % outFilePrefix
-        
-        if not FileUtils.are2FilesIdentical(fileObs, fileExp):
-            print "Files are different"
-            return
-        else:
-            print "Files are identical\n"
-        
-        os.remove(fileObs)
-        os.remove(fileExp)
-        os.remove(tmpFileName)
-
-    def test_filterUnclusteredSequences(self):
-        dClusterId2SeqHeaders = {1: ["seq1","seq2"], 2: ["seq3"]}
-        dExp = {1: ["seq1","seq2"]}
-        dObs = self._iLaunchBlastclust.filterUnclusteredSequences(dClusterId2SeqHeaders)
-        self.assertEqual(dObs, dExp)
-        
-    def test_blastclustToMap(self):
-        inFileName = "dummyBlastclustOut_%s.fa"  % self._uniqId
-        inF = open(inFileName, "w")
-        inF.write(">BlastclustCluster1Mb1_chunk1 (dbseq-nr 1) [1,14]\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">BlastclustCluster1Mb2_chunk1 (dbseq-nr 1) [30,44]\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">BlastclustCluster2Mb1_chunk2 (dbseq-nr 1) [100,114]\n")
-        inF.write("gaattgtttactta\n")
-        inF.write(">BlastclustCluster3Mb1_chunk5 (dbseq-nr 8) [1000,1014]\n")
-        inF.write("gaattgtttactta")
-        inF.close()
-        
-        fileExp = "blastclustToMapExpected.map"
-        outF = open(fileExp, "w")
-        outF.write("BlastclustCluster1Mb1\tchunk1\t1\t14\n")
-        outF.write("BlastclustCluster1Mb2\tchunk1\t30\t44\n")
-        outF.write("BlastclustCluster2Mb1\tchunk2\t100\t114\n")
-        outF.write("BlastclustCluster3Mb1\tchunk5\t1000\t1014\n")
-        outF.close()
-        
-        self._iLaunchBlastclust.blastclustToMap(inFileName)
-        fileObs = "%s.map" % os.path.splitext(inFileName)[0]
-        
-        if not FileUtils.are2FilesIdentical(fileObs, fileExp):
-            print "Files are different"
-            return
-        else:
-            print "Files are identical\n"
-        
-        os.remove(inFileName)
-        os.remove(fileObs)
-        os.remove(fileExp)
-
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_LaunchTallymer.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import os
-import unittest
-from commons.launcher.LaunchTallymer import ConvertUtils
-
-class Test_ConvertUtils(unittest.TestCase):
-
-    def test_convertTallymerFormatIntoMapFormatAndGenerateData(self):
-        inputFastaFileName = "input.fa"
-        inputTallymerSearchFileName = "input.tallymer"
-        expMapFileName = "exp.map"
-        obsMapFileName = "obs.map"
-        self._writeInputFasta(inputFastaFileName)
-        self._writeInputTallymerSearch(inputTallymerSearchFileName)
-        self._writeExpMap(expMapFileName)
-        
-        expOccNb = 4
-        expDKmer2Occ = {"caagatgcgtaacggccata":1,
-                        "aagatgcgtaacggccatac":1,
-                        "agatgcgtaacggccataca":1,
-                        "gatgcgtaacggccatacat":1}
-        expPlotData = {4379: 17,
-                       4380: 17,
-                       4381: 16,
-                       4382: 16}
-        
-        obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
-        
-        self.assertEquals(expOccNb, obsOccNb)
-        self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
-        self.assertEquals(expPlotData, obsPlotData)
-        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
-        
-        os.remove(inputFastaFileName)
-        os.remove(inputTallymerSearchFileName)
-        os.remove(expMapFileName)
-        os.remove(obsMapFileName)
-        
-    def test_convertTallymerFormatIntoMapFormatAndGenerateDataMultiFasta(self):
-        inputFastaFileName = "input.fa"
-        inputTallymerSearchFileName = "input.tallymer"
-        expMapFileName = "exp.map"
-        obsMapFileName = "obs.map"
-        self._writeInputMultiFasta(inputFastaFileName)
-        self._writeInputTallymerSearchMultiFasta(inputTallymerSearchFileName)
-        self._writeExpMapMultiFasta(expMapFileName)
-        
-        expOccNb = 6
-        expDKmer2Occ = {"caagatgcgtaacggccata":1,
-                        "aagatgcgtaacggccatac":1,
-                        "agatgcgtaacggccataca":1,
-                        "gatgcgtaacggccatacat":1,
-                        "agatgcgtaacggccataca":2,
-                        "gatgcgtaacggccatacat":2}
-        expPlotData = {4379: 17, 4380: 17, 4381: 16, 4382: 35}
-        
-        obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
-        
-        self.assertEquals(expOccNb, obsOccNb)
-        self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
-        self.assertEquals(expPlotData, obsPlotData)
-        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
-        
-        os.remove(inputFastaFileName)
-        os.remove(inputTallymerSearchFileName)
-        os.remove(expMapFileName)
-        os.remove(obsMapFileName)
-    
-    def _writeInputTallymerSearch(self, tallymerFormatFileName):
-        with open(tallymerFormatFileName, 'w') as f:
-            f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
-            f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
-            f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
-            f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
-             
-    def _writeInputFasta(self, fastaFileName):
-        with open(fastaFileName, 'w') as f:
-            f.write(">Seq1\n")
-            f.write("caagatgcgtaacggccata\n")
-            f.write("aagatgcgtaacggccatac\n")
-            f.write("agatgcgtaacggccataca\n")
-            f.write("gatgcgtaacggccatacat\n")
-            
-    def _writeExpMap(self, mapFileName):
-        with open(mapFileName, 'w') as f:
-            f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
-            f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
-            f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
-            f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
-            
-    def _writeInputTallymerSearchMultiFasta(self, tallymerFormatFileName):
-        with open(tallymerFormatFileName, 'w') as f:
-            f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
-            f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
-            f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
-            f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
-            f.write("1\t+4380\t16\tagatgcgtaacggccataca\n")
-            f.write("1\t+4381\t35\tgatgcgtaacggccatacat\n")
-            
-    def _writeInputMultiFasta(self, fastaFileName):
-        with open(fastaFileName, 'w') as f:
-            f.write(">Seq1\n")
-            f.write("caagatgcgtaacggccata\n")
-            f.write("aagatgcgtaacggccatac\n")
-            f.write("agatgcgtaacggccataca\n")
-            f.write("gatgcgtaacggccatacat\n")
-            f.write(">Seq2\n")
-            f.write("agatgcgtaacggccataca\n")
-            f.write("gatgcgtaacggccatacat\n")
-            
-    def _writeExpMapMultiFasta(self, mapFileName):
-        with open(mapFileName, 'w') as f:
-            f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
-            f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
-            f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
-            f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
-            f.write("agatgcgtaacggccataca_16\tSeq2\t4381\t4401\t16\n")
-            f.write("gatgcgtaacggccatacat_35\tSeq2\t4382\t4402\t35\n")
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_MafftClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-import unittest
-from commons.launcher.MafftClusterLauncher import MafftClusterLauncher
-
-
-class Test_MafftClusterLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = MafftClusterLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -p: parameters for 'mafft' (default='--auto')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-p", "dummyPrgParam" )
-        self.assertEqual( "dummyPrgParam", self._i.getProgramParameters() )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_MafftProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-import unittest
-from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
-
-class Test_MafftProgramLauncher( unittest.TestCase ):
-    
-    
-    def setUp( self ):
-        self._i = MafftProgramLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -p: parameters for '%s' (default='--auto')" % ( "mafft" )
-        exp += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-p", "'--auto --maxiterate 500'" )
-        self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
-        self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
-        
-        
-    def test_setWrapperCommandLine( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        exp = "MafftProgramLauncher.py"
-        exp += " -i %s" % ( inFile )
-        exp += " -p '%s'" % ( "--auto" )
-        exp += " -o %s.fa_aln" % ( inFile )
-        exp += " -v 0"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        exp = self._i.getProgramName()
-        exp += " %s" % ( "--auto" )
-        exp += " --quiet"
-        exp += " %s.shortH" % ( inFile )
-        exp += " > %s.shortH.fa_aln" % ( inFile )
-        exp += " 2> /dev/null"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setListFilesToKeep( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        self._i.setListFilesToKeep()
-        lExp = [ "dummyInFile.fa.fa_aln" ]
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        self._i._lFilesToKeep = []
-        
-        outFile = "dummyOutFile.fa_aln"
-        self._i.setOutputFile( outFile )
-        self._i.setListFilesToKeep()
-        lExp = [ outFile ]
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToRemove( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        self._i.setListFilesToRemove()
-        lExp = [ "dummyInFile.fa.shortH", \
-                 "dummyInFile.fa.shortH.fa_aln", \
-                 "dummyInFile.fa.shortHlink" ]
-        lObs = self._i.getListFilesToRemove()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        exp = "input file: %s" % ( "dummyInFile.fa" )
-        exp += "\nparameters: %s" % ( "--auto" )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-        
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_MapClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-import unittest
-from commons.launcher.MapClusterLauncher import MapClusterLauncher
-
-
-class Test_MapClusterLauncher( unittest.TestCase ):
-    
-    
-    def setUp( self ):
-        self._i = MapClusterLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() )
-        exp += "\n     -m: penalty for a mismatch (default='%i')" % ( self._i.getMismatchPenalty() )
-        exp += "\n     -O: penalty for a gap openning (default='%i')" % ( self._i.getGapOpenPenalty() )
-        exp += "\n     -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() )
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "42" )
-        self.assertEqual( 42, self._i.getGapSize() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-m", "-7" )
-        self.assertEqual( -7, self._i.getMismatchPenalty() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-O", "15" )
-        self.assertEqual( 15, self._i.getGapOpenPenalty() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-e", "5" )
-        self.assertEqual( 5, self._i.getGapExtendPenalty() )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_MapProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-import unittest
-from commons.launcher.MapProgramLauncher import MapProgramLauncher
-
-class Test_MapProgramLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = MapProgramLauncher()
-        
-    def tearDown( self ):
-        self._i = None
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() )
-        exp += "\n     -m: penalty for a mismatch (default='%i', match=10)" % ( self._i.getMismatchPenalty() )
-        exp += "\n     -O: penalty for a gap opening (default='%i')" % (  self._i.getGapOpenPenalty())
-        exp += "\n     -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() )
-        exp += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "40" )
-        self.assertEqual( 40, self._i.getGapSize() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-m", "-7" )
-        self.assertEqual( -7, self._i.getMismatchPenalty() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-O", "15" )
-        self.assertEqual( 15, self._i.getGapOpenPenalty() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-e", "5" )
-        self.assertEqual( 5, self._i.getGapExtendPenalty() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
-        self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
-        
-    def test_setWrapperCommandLine( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        exp = "MapProgramLauncher.py"
-        exp += " -i %s" % ( inFile )
-        exp += " -s 50"
-        exp += " -m -8"
-        exp += " -O 16"
-        exp += " -e 4"
-        exp += " -o %s.fa_aln" % ( inFile )
-        exp += " -v 0"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-    def test_setProgramCommandLine( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        exp = self._i.getProgramName()
-        exp += " %s.shortH" % ( inFile )
-        exp += " 50"
-        exp += " -8"
-        exp += " 16"
-        exp += " 4"
-        exp += " > %s.shortH.fa_aln" % ( inFile )
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-    def test_setListFilesToKeep( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        self._i.setListFilesToKeep()
-        lExp = [ "dummyInFile.fa.fa_aln" ]
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        self._i._lFilesToKeep = []
-        
-        outFile = "dummyOutFile.fa_aln"
-        self._i.setOutputFile( outFile )
-        self._i.setListFilesToKeep()
-        lExp = [ outFile ]
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-    def test_getListFilesToRemove( self ):
-        inFile = "dummyInFile.fa"
-        self._i.setInputFile( inFile )
-        self._i.setListFilesToRemove()
-        lExp = [ "dummyInFile.fa.shortH", \
-                 "dummyInFile.fa.shortH.fa_aln", \
-                 "dummyInFile.fa.shortHlink" ]
-        lObs = self._i.getListFilesToRemove()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setGapSize( 104 )
-        exp = "input file: %s" % ( "dummyInFile.fa" )
-        exp += "\ngap size: %i" % ( self._i.getGapSize() )
-        exp += "\nmismatch penalty: %i" % ( self._i.getMismatchPenalty() )
-        exp += "\ngap openning penalty: %i" % ( self._i.getGapOpenPenalty() )
-        exp += "\ngap extension penalty: %i" % ( self._i.getGapExtendPenalty() )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_NWalignProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-import unittest
-from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher
-
-
-class Test_NWalignProgramLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = NWalignProgramLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (format='fasta')"
-        exp += "\n     -p: parameters for 'NWalign'"
-        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
-        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
-        
-        
-    def test_setWrapperCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "NWalignProgramLauncher.py"
-        exp += " -i %s" % ( "dummyInFile.fa" )
-        exp += " -s %s" % ( "dummySubjectFile.fa" )
-        exp += " -o %s.align" % ( "dummyInFile.fa" )
-        exp += " -v 0"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        self._i.setProgramParameters( "-m 2" )
-        exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setListFilesToKeep( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        lExp = [ "dummyInFile.fa.afa" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "input file: %s" % ( self._i.getInputFile() )
-        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
-        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_RepeatMaskerClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-import unittest
-from commons.launcher.RepeatMaskerClusterLauncher import RepeatMaskerClusterLauncher
-
-
-class Test_RepeatmaskerClusterLauncher( unittest.TestCase ):
-    
-    
-    def setUp( self ):
-        self._i = RepeatMaskerClusterLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (repeats, format='fasta')"
-        exp += "\n     -n: nb of processors to use in parallel (default=1)"
-        exp += "\n     -g: calculate the GC content"
-        exp += "\n     -b: skip bacterial insertion element check"
-        exp += "\n     -l: mask low-complexity DNA or simple repeats"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
-        self.assertEqual( 2, self._i.getNbProcessors() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-g" )
-        self.assertTrue( self._i.getCalculateGCcontent() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-b" )
-        self.assertTrue( self._i.getSkipBacterialIsCheck() )
-
-        self._i.setASpecificAttributeFromCmdLine( "-l" )
-        self.assertFalse( self._i.getMaskSsr() )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_RepeatMaskerProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,171 +0,0 @@
-import unittest
-from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
-
-
-class Test_RepeatMaskerProgramLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = RepeatMaskerProgramLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (repeats, format='fasta')"
-        exp += "\n     -n: nb of processors to use in parallel (default='%i')" % ( self._i.getNbProcessors() )
-        exp += "\n     -g: calculate the GC content"
-        exp += "\n     -b: skip bacterial insertion element check"
-        exp += "\n     -l: does not mask low-complexity DNA or simple repeats"
-        exp += "\n     -m: only masks low complex/simple repeats (no interspersed repeats)"
-        exp += "\n     -o: name of the output file"
-        exp += "\n         with -s: format='align', default=inFile+'.cat.align')"
-        exp += "\n         with -m: format='path', default=inFile+'.cat.path')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
-        self.assertEqual( 2, self._i.getNbProcessors() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-g" )
-        self.assertEqual( True, self._i.getCalculateGCcontent() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-b" )
-        self.assertEqual( True, self._i.getSkipBacterialIsCheck() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-l" )
-        self.assertEqual( False, self._i.getMaskSsr() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
-        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
-        
-        
-    def test_setWrapperCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "RepeatMaskerProgramLauncher.py"
-        exp += " -i %s" % ( "dummyInFile.fa" )
-        exp += " -s %s" % ( "dummySubjectFile.fa" )
-        exp += " -n 1"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        self._i.setCalculateGCcontent()
-        self._i.setSkipBacterialIsCheck()
-        exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow -lib dummySubjectFile.fa dummyInFile.fa"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine_withoutSubjects_withMaskSsr( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setCalculateGCcontent()
-        self._i.setSkipBacterialIsCheck()
-        exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow dummyInFile.fa"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setListFilesToKeep_onlyInFile( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setOnlySsr()
-        lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.path" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToKeep_withSubjectFile( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySbjFile.fa" )
-        lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.align" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToKeep_inFileAndOutFile( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setOutputFile( "dummyOutFile.align" )
-        lExp = [ "dummyInFile.fa.cat", "dummyOutFile.align" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToKeep_inFileAndOutFileAndSsr( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.unsetMaskSsr()
-        self._i.setOutputFile( "dummyOutFile.path" )
-        lExp = [ "dummyInFile.fa.cat", "dummyOutFile.path" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setListFilesToRemove( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        lExp = [ "dummyInFile.fa.out", \
-                 "dummyInFile.fa.log", \
-                 "dummyInFile.fa.stderr", \
-                 "dummyInFile.fa.ori.out", \
-                 "dummyInFile.fa.masked", \
-                 "dummyInFile.fa.tbl", \
-                 "dummyInFile.fa.ref" ]
-        self._i.setListFilesToRemove()
-        lObs = self._i.getListFilesToRemove()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "input file: %s" % ( self._i.getInputFile() )
-        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
-        exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
-        exp += "\nmask low-complexity DNA or simple repeats"
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.path" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setSummary_noMaskSsr( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        self._i.unsetMaskSsr()
-        exp = "input file: %s" % ( self._i.getInputFile() )
-        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
-        exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.align" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_YassClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-import unittest
-from commons.launcher.YassClusterLauncher import YassClusterLauncher
-
-class Test_YassClusterLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = YassClusterLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (format='fasta')"
-        exp += "\n     -p: parameters for 'yass'"
-        exp += "\n     -Z: concatenate output files"
-        exp += "\n     -A: same sequences (all-by-all)"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_YassProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-import unittest
-from commons.launcher.YassProgramLauncher import YassProgramLauncher
-
-
-
-class Test_YassProgramLauncher( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = YassProgramLauncher()
-        
-        
-    def tearDown( self ):
-        self._i = None
-        
-        
-    def test_getSpecificHelpAsString( self ):
-        exp = ""
-        exp += "\nspecific options:"
-        exp += "\n     -s: name of the subject file (format='fasta')"
-        exp += "\n     -p: parameters for 'yass'"
-        exp += "\n     -A: same sequences (all-by-all)"
-        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
-        obs = self._i.getSpecificHelpAsString()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setASpecificAttributeFromCmdLine( self ):
-        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
-        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
-        
-        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
-        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
-        
-        
-    def test_setWrapperCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "YassProgramLauncher.py"
-        exp += " -i %s" % ( "dummyInFile.fa" )
-        exp += " -s %s" % ( "dummySubjectFile.fa" )
-        exp += " -o %s.align" % ( "dummyInFile.fa" )
-        exp += " -v 0"
-        self._i.setWrapperCommandLine()
-        obs = self._i.getWrapperCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setProgramCommandLine( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "yass -d 2 -o dummyInFile.fa.blast dummyInFile.fa dummySubjectFile.fa"
-        self._i.setProgramCommandLine()
-        obs = self._i.getProgramCommandLine()
-        self.assertEqual( exp, obs )
-        
-        
-    def test_setListFilesToKeep( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        lExp = [ "dummyInFile.fa.align" ]
-        self._i.setListFilesToKeep()
-        lObs = self._i.getListFilesToKeep()
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_setSummary( self ):
-        self._i.setInputFile( "dummyInFile.fa" )
-        self._i.setSubjectFile( "dummySubjectFile.fa" )
-        exp = "input file: %s" % ( self._i.getInputFile() )
-        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
-        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
-        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
-        self._i.setSummary()
-        obs = self._i.getSummary()
-        self.assertEqual( exp, obs )
-         
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/launcher/tests/Test_launchTEclass.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.launcher import launchTEclass
-
-
-class Test_launchTEclass( unittest.TestCase ):
-    
-    def test_parseFastaFileFromTEclass( self ):
-        inFile = "dummyLibFile.fa"
-        inHandler = open( inFile, "w" )
-        inHandler.write( ">1360|TEclass result: DNA|ORFs: 1360..2226:+1\n" )
-        inHandler.write( "AGCATGACGCA\n" )
-        inHandler.write( ">FB|TEclass result: unclear\n" )
-        inHandler.write( "GCATGCAGCGACGCGAC\n" )
-        inHandler.close()
-        
-        expFile = "dummyExpFile.map"
-        expHandler = open( expFile, "w" )
-        expHandler.write( "DNA\t1360\t1\t11\n" )
-        expHandler.write( "unclear\tFB\t1\t17\n" )
-        expHandler.close()
-        
-        obsFile = "dummyObsFile.map"
-        
-        launchTEclass.parseFastaFileFromTEclass( inFile, obsFile )
-        
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, expFile, obsFile ]:
-            os.remove( f )
-
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/AlignList.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-## class of list of align object
-#
-class AlignList:
-
-    list;
-    
-    def __init__( self ):
-        self.list = []
-
-    ## append align instance in the align instance list
-    #
-    # @param AlignInstance instance of align object
-    #
-    def append(self, AlignInstance):
-        self.list.append(AlignInstance)
-       
-    ## get length of list of align instance
-    #
-    #@return length integer length of list
-    #
-    def len(self):
-        return len(self.list)   
-    
-    ## get list of align instance
-    #
-    #@return list of align instance
-    #
-    def getList(self):
-        return self.list
-    
-    ## get item in list of align instance according to index
-    #
-    #@param index integer index of list
-    #@return align instance item of list of align instance
-    #
-    def get(self, index):
-        return self.list[index]
-    
-    ## extend align instance in the align instance list
-    #
-    # @param AlignInstance instance of align object
-    #
-    def extend(self, AlignInstance):
-        self.list.extend(AlignInstance)
-        
-    ## take off an align instance from the align instance list
-    #
-    # @param AlignInstance instance of align object
-    #
-    def remove(self, AlignInstance):
-       self.list.remove(AlignInstance)
\ No newline at end of file

--- a/commons/pyRepetUnit/align/AlignListUtils.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-import os
-import commons.core.coord.Align
-import commons.pyRepetUnit.align.AlignList
-from commons.core.utils.FileUtils import FileUtils
-
-class AlignListUtils:  
-  
-    ##read a file in align format and return a AlignList
-    #
-    # @param inFileName string name of file
-    # @return listAlignInstance list list of align instance
-    #
-    def read( inFileName ):
-        alignInstance = commons.core.coord.Align.Align() 
-        listAlignInstance = commons.pyRepetUnit.align.AlignList.AlignList()
-        f = open( inFileName , "r")
-        while alignInstance.read( f ):
-            listAlignInstance.append(alignInstance)
-            alignInstance = commons.core.coord.Align.Align()
-        f.close
-        return (listAlignInstance)
-    
-    read = staticmethod( read )
-    
-    ## write a file in align format from an AlignList
-    #
-    # @param alignListInstance list list of align instance object
-    # @param  inFileName string name of file
-    def write( alignListInstance, inFileName ):
-        f = open( inFileName , "w")
-        for alignInstance in alignListInstance.getList():
-            alignInstance.write( f )
-        f.close
-        
-    write = staticmethod( write )
-    
-    ## Filter an AlignList by removing all is <= minScore
-    #
-    # @param listAlignInstance list list of align instance object
-    # @param minScore integer minimum score to keep in result
-    # 
-    def filterOnAMinimalScore( listAlignInstance, minScore ):
-        listAlignInstanceOld = commons.pyRepetUnit.align.AlignList.AlignList() 
-        for alignInstance in listAlignInstance.getList():  
-            listAlignInstanceOld.append(alignInstance)
-        for alignInstance in listAlignInstanceOld.getList():
-            if alignInstance.score <= minScore:
-                listAlignInstance.remove(alignInstance)
-        
-    filterOnAMinimalScore = staticmethod( filterOnAMinimalScore )    
-    
-if __name__ == "__main__":                 
-    main() 

--- a/commons/pyRepetUnit/align/hmmOutputParsing/HmmpfamOutput2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
-
-##data processor : read an output from hmmpfam and transform it into .align file
-#    
-class HmmpfamOutput2align( object ):
-
-    ## constructor
-    #
-    def __init__(self):
-        self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
-        self._inputFile = "" 
-        self._outputFile =  ""    
-    
-    ## set input file
-    #
-    # @param input file input file
-    #    
-    def setInputFile(self, input):
-        self._inputFile = input
-    
-    ## set output file
-    #
-    # @param output file output file
-    #         
-    def setOutputFile(self, output):
-        self._outputFile = output   
-    
-    
-    ##read a hmmpfam output file, parse it and, write the corresponding .align file
-    #
-    def run( self ):
-        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )

--- a/commons/pyRepetUnit/align/hmmOutputParsing/HmmscanOutput2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
-##data processor : read an output from hmmscan and transform it into .align file
-#
-class HmmscanOutput2align( object ):
-    
-    ## constructor
-    #
-    def __init__(self):
-        self.hmmscanOutputProcess = HmmscanOutputProcessing()
-        self._inputFile = "" 
-        self._outputFile =  ""    
-     
-    ## set input file
-    #
-    # @param input file input file
-    #    
-    def setInputFile(self, input):
-        self._inputFile = input
-    ## set output file
-    # @param output file output file
-    #     
-    def setOutputFile(self, output):
-        self._outputFile = output   
-    
-    ##read a hmmscan output file, parse it and, write the corresponding .align file
-    #    
-    def run( self ):
-        self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/HmmpfamOutput2AlignTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-import unittest
-import sys
-from Test_F_HmmpfamOutput2align import Test_F_HmmpfamOutput2align
-from Test_F_HmmscanOutput2align import Test_F_HmmscanOutput2align
-from Test_F_Hmmerpfam2align import Test_F_Hmmerpfam2align
-from commons.tools.tests.Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script import Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script
-
-def main():
-
-        hmmerTestSuite = unittest.TestSuite() 
-        hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmpfamOutput2align,'test'))
-        hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmscanOutput2align,'test'))
-        hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script,'test'))
-        hmmerTestSuite.addTest(unittest.makeSuite(Test_F_Hmmerpfam2align,'test'))
-        
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(hmmerTestSuite)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_Hmmerpfam2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-import os
-import unittest
-import commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_Hmmerpfam2align(unittest.TestCase):
-    
-    def setUp(self):
-        self.hmmpfamOutputProcess = commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing.HmmpfamOutputProcessing()
-        self._inputFile = "./datas/test_hmmpfam_output" 
-        self._outputFile =  "./datas/PostProcessResult.align" 
-        
-    def testAcceptanceHmmpfam2align(self):
-        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile))
-        os.remove(self._outputFile)
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmpfamOutput2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align import HmmpfamOutput2align
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_HmmpfamOutput2align(unittest.TestCase):
-    
-    def setUp(self):
-        self.hmmpfamOutput2align = HmmpfamOutput2align()
-        self._inputFile = "./datas/test_hmmpfam_output"
-        self._outputFile = "./datas/hmmpfam_output.align"
-        
-    def testParseHmmpfamOutput2align(self):
-        self.hmmpfamOutput2align.setInputFile(self._inputFile)
-        self.hmmpfamOutput2align.setOutputFile(self._outputFile)
-        self.hmmpfamOutput2align.run()
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile))
-        os.remove( self._outputFile )
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmscanOutput2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.align.hmmOutputParsing.HmmscanOutput2align import HmmscanOutput2align
-from commons.core.utils.FileUtils import FileUtils 
-
-CURRENT_DIR = os.getcwd()
-
-class Test_F_HmmscanOutput2align(unittest.TestCase):
-
-    def setUp(self):
-        self.hmmscanOutput2align = HmmscanOutput2align()
-        self._inputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput"
-        self._outputFile = "./datas/test_hmmscanOutput.align"
-        os.chdir(CURRENT_DIR)
-
-    def testParseHmmscanOutput2align(self):
-        self.hmmscanOutput2align.setInputFile(self._inputFile)
-        self.hmmscanOutput2align.setOutputFile(self._outputFile)
-        self.hmmscanOutput2align.run()
-        expectedFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align"
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(expectedFile, self._outputFile))
-        os.remove( self._outputFile )
-        
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/ConsensusTestFile_nt.fsa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
->blumeria_Grouper_590_20:NoCat
-TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA
-AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT
-ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA
-ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA
-CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC
-TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC
-TCCATAATTTCAACACTNAAGAATATTTGTA
->blumeria_Grouper_4152_12:NoCat
-GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA
-AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC
-GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC
-GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC
-TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT
-TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT
-GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG
-CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC
-ATATCTACCTCGGGGACATTG

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,406 +0,0 @@
-hmmpfam - search one or more sequences against HMM database
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-HMM file:                 /home/choede/hmmer3/Pfam_fs
-Sequence file:            ConsensusTestFile_aaWithoutStop.fsa
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Query sequence: blumeria_Grouper_590_20:NoCat_1
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model           Description                             Score    E-value  N 
---------        -----------                             -----    ------- ---
-DUF234          Archaea bacterial proteins of unknown     3.2        1.5   1
-DUF1414         Protein of unknown function (DUF1414)     2.9        6.3   1
-
-Parsed for domains:
-Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------        ------- ----- -----    ----- -----      -----  -------
-DUF234            1/1      91   108 ..     5    22 ..     3.2      1.5
-DUF1414           1/1     111   119 ..     1     9 [.     2.9      6.3
-
-Alignments of top-scoring domains:
-DUF234: domain 1 of 1, from 91 to 108: score 3.2, E = 1.5
-                   *->VyPNrseIEsGnikevle<-*
-                      VyPN++ IEs ++k++++   
-  blumeria_G    91    VYPNIEIIESSTPKPLIN    108  
-
-DUF1414: domain 1 of 1, from 111 to 119: score 2.9, E = 6.3
-                   *->HkAPvDLSL<-*
-                      H  ++DLSL   
-  blumeria_G   111    HXSSPDLSL    119  
-
-//
-
-Query sequence: blumeria_Grouper_590_20:NoCat_2
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-	[no hits above thresholds]
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-	[no hits above thresholds]
-
-Alignments of top-scoring domains:
-	[no hits above thresholds]
-//
-
-Query sequence: blumeria_Grouper_590_20:NoCat_3
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-CPW_WPC  Plasmodium falciparum domain of unknown func     1.5        7.7   1
-HECT     HECT-domain (ubiquitin-transferase)              0.0        9.2   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-CPW_WPC    1/1      30    37 ..     1     9 [.     1.5      7.7
-HECT       1/1      55    69 ..   341   355 .]     0.0      9.2
-
-Alignments of top-scoring domains:
-CPW_WPC: domain 1 of 1, from 30 to 37: score 1.5, E = 7.7
-                   *->CerdYsisk<-*
-                      C++dYs sk   
-  blumeria_G    30    CQFDYS-SK    37   
-
-HECT: domain 1 of 1, from 55 to 69: score 0.0, E = 9.2
-                   *->LllAIneeteGFgle<-*
-                      Ll+A+n+ + G+ ++   
-  blumeria_G    55    LLTAVNNANTGYTQS    69   
-
-//
-
-Query sequence: blumeria_Grouper_590_20:NoCat_4
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-DUF46    Putative integral membrane protein DUF46         6.4       0.11   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-DUF46      1/1      82    91 ..   173   182 .]     6.4     0.11
-
-Alignments of top-scoring domains:
-DUF46: domain 1 of 1, from 82 to 91: score 6.4, E = 0.11
-                   *->YkLGlKdVpW<-*
-                      Y+LGlK V++   
-  blumeria_G    82    YLLGLKGVWY    91   
-
-//
-
-Query sequence: blumeria_Grouper_590_20:NoCat_5
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-POC4     POC4 chaperone                                  -1.7        6.3   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-POC4       1/1     121   125 ..   276   280 .]    -1.7      6.3
-
-Alignments of top-scoring domains:
-POC4: domain 1 of 1, from 121 to 125: score -1.7, E = 6.3
-                   *->SGLYI<-*
-                      SGLYI   
-  blumeria_G   121    SGLYI    125  
-
-//
-
-Query sequence: blumeria_Grouper_590_20:NoCat_6
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-	[no hits above thresholds]
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-	[no hits above thresholds]
-
-Alignments of top-scoring domains:
-	[no hits above thresholds]
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_1
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model         Description                               Score    E-value  N 
---------      -----------                               -----    ------- ---
-Peptidase_S29 Hepatitis C virus NS3 protease              4.7        1.1   1
-DGOK          2-keto-3-deoxy-galactonokinase              0.5        1.3   1
-TNV_CP        Satellite tobacco necrosis virus coat p     0.1        7.9   1
-TrbL          TrbL/VirB6 plasmid conjugal transfer pr     0.8          8   1
-Amino_oxidase Flavin containing amine oxidoreductase     -0.6        9.1   1
-DUF1301       Protein of unknown function (DUF1301)       0.4        9.9   1
-
-Parsed for domains:
-Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------      ------- ----- -----    ----- -----      -----  -------
-Amino_oxidase   1/1      27    38 ..   471   482 .]    -0.6      9.1
-TrbL            1/1      33    67 ..   231   285 .]     0.8        8
-TNV_CP          1/1      58    80 ..   167   189 ..     0.1      7.9
-DGOK            1/1      94   109 ..   283   298 .]     0.5      1.3
-Peptidase_S29   1/1     113   127 ..     1    15 [.     4.7      1.1
-DUF1301         1/1     148   157 ..     1    10 [.     0.4      9.9
-
-Alignments of top-scoring domains:
-Amino_oxidase: domain 1 of 1, from 27 to 38: score -0.6, E = 9.1
-                CS    HHHHHHHHHHHH   
-                   *->veSGlrAAaril<-*
-                      veSG rAA  +l   
-  blumeria_G    27    VESGXRAASTLL    38   
-
-TrbL: domain 1 of 1, from 33 to 67: score 0.8, E = 8
-                   *->ksstiesfnlfvllaivllslvlilllkqipgiAqglvgavvtlgga
-                      ++st+ +     +++ ++ +++++l+l++ ++iA             
-  blumeria_G    33    AASTLLI-----AVEHIVNCAAFCLALRSSASIA------------- 61   
-
-                   vaaalaGG<-*
-                     a+ +GG   
-  blumeria_G    62 --ASNSGG    67   
-
-TNV_CP: domain 1 of 1, from 58 to 80: score 0.1, E = 7.9
-                CS    SSSGGGB-TTEEEEEEEES-SS-   
-                   *->AdvAaSNgpgAvFvLeigdkvag<-*
-                      A++AaSN  g vF+L   +++ g   
-  blumeria_G    58    ASIAASNSGGCVFFLPAASSAGG    80   
-
-DGOK: domain 1 of 1, from 94 to 109: score 0.5, E = 1.3
-                   *->VdGDeAvrAGLseiAr<-*
-                      VdG  A  AGL ++ r   
-  blumeria_G    94    VDGVSALFAGLTSAGR    109  
-
-Peptidase_S29: domain 1 of 1, from 113 to 127: score 4.7, E = 1.1
-                   *->GevqvLgTaTqsflG<-*
-                      G+v++ + aT+ flG   
-  blumeria_G   113    GTVMRFSGATTVFLG    127  
-
-DUF1301: domain 1 of 1, from 148 to 157: score 0.4, E = 9.9
-                   *->gVKvFSlSTS<-*
-                       ++vFS+STS   
-  blumeria_G   148    SARVFSFSTS    157  
-
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_2
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model          Description                              Score    E-value  N 
---------       -----------                              -----    ------- ---
-DUF1602        Protein of unknown function (DUF1602)      5.0       0.39   1
-Toxin_18       Conotoxin O-superfamily                    4.2        4.4   1
-ABC_transp_aux ABC-type uncharacterized transport sys     1.1        5.2   1
-
-Parsed for domains:
-Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------       ------- ----- -----    ----- -----      -----  -------
-Toxin_18         1/1      21    26 ..    50    55 .]     4.2      4.4
-ABC_transp_aux   1/1     126   137 ..   276   287 .]     1.1      5.2
-DUF1602          1/1     143   159 ..    23    39 .]     5.0     0.39
-
-Alignments of top-scoring domains:
-Toxin_18: domain 1 of 1, from 21 to 26: score 4.2, E = 4.4
-                   *->gfCLpr<-*
-                      +fCL+r   
-  blumeria_G    21    NFCLHR    26   
-
-ABC_transp_aux: domain 1 of 1, from 126 to 137: score 1.1, E = 5.2
-                   *->wGvrldpdlVlD<-*
-                      wG+r+dp+l+l    
-  blumeria_G   126    WGIRWDPRLALR    137  
-
-DUF1602: domain 1 of 1, from 143 to 159: score 5.0, E = 0.39
-                   *->kPPlSSsGalfanplrP<-*
-                      +P l + G+l + +lrP   
-  blumeria_G   143    MPKLNRRGFLASRLLRP    159  
-
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_3
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model      Description                                  Score    E-value  N 
---------   -----------                                  -----    ------- ---
-zf-P11     P-11 zinc finger                               3.6        1.8   1
-V-ATPase_G Vacuolar (H+)-ATPase G subunit                 2.4        5.3   1
-
-Parsed for domains:
-Model      Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------   ------- ----- -----    ----- -----      -----  -------
-zf-P11       1/1     102   122 ..     1    20 [.     3.6      1.8
-V-ATPase_G   1/1     126   135 ..     1    10 [.     2.4      5.3
-
-Alignments of top-scoring domains:
-zf-P11: domain 1 of 1, from 102 to 122: score 3.6, E = 1.8
-                   *->GplnCKs..CWfkdknLveCsd<-*
-                      Gp +C+s+ CW + + L  C d   
-  blumeria_G   102    GPHFCRSrxCW-NRDALLGCDD    122  
-
-V-ATPase_G: domain 1 of 1, from 126 to 135: score 2.4, E = 5.3
-                   *->sqsqGIQqLL<-*
-                      ++s+GIQ LL   
-  blumeria_G   126    GGSGGIQDLL    135  
-
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_4
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model        Description                                Score    E-value  N 
---------     -----------                                -----    ------- ---
-XhoI         Restriction endonuclease XhoI                9.9      0.014   1
-Endomucin    Endomucin                                    0.1          6   1
-
-Parsed for domains:
-Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------     ------- ----- -----    ----- -----      -----  -------
-XhoI           1/1      92   122 ..   172   202 .]     9.9    0.014
-Endomucin      1/1     113   119 ..   261   267 .]     0.1        6
-
-Alignments of top-scoring domains:
-XhoI: domain 1 of 1, from 92 to 122: score 9.9, E = 0.014
-                   *->klvlerfytrpasllrdaqavlqGiikeprk<-*
-                      ++++ ++yt ++   +d++++ qG  k+ ++   
-  blumeria_G    92    RSSRQKKYTPSRIACSDRSGGAQGKTKSRAI    122  
-
-Endomucin: domain 1 of 1, from 113 to 119: score 0.1, E = 6
-                   *->AQGKtKN<-*
-                      AQGKtK    
-  blumeria_G   113    AQGKTKS    119  
-
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_5
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model          Description                              Score    E-value  N 
---------       -----------                              -----    ------- ---
-SLT            Transglycosylase SLT domain                4.5        1.2   1
-DUF881         Bacterial protein of unknown function      4.0        1.6   1
-DUF2346        Uncharacterized conserved protein (DUF     3.2        2.8   1
-DUF1798        Bacterial domain of unknown function (     3.0        3.3   1
-LBP_BPI_CETP   LBP / BPI / CETP family, N-terminal do     1.8        3.8   1
-Jun            Jun-like transcription factor             -0.7        6.5   1
-
-Parsed for domains:
-Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------       ------- ----- -----    ----- -----      -----  -------
-DUF1798          1/1       2    19 ..    35    52 ..     3.0      3.3
-DUF881           1/1      46    69 ..   214   237 .]     4.0      1.6
-Jun              1/1      77    93 ..   264   284 ..    -0.7      6.5
-SLT              1/1      89   108 ..     1    20 [.     4.5      1.2
-DUF2346          1/1      93   115 ..    63    85 .]     3.2      2.8
-LBP_BPI_CETP     1/1     124   139 ..   191   209 .]     1.8      3.8
-
-Alignments of top-scoring domains:
-DUF1798: domain 1 of 1, from 2 to 19: score 3.0, E = 3.3
-                   *->KPfvdevdqllaeWkelA<-*
-                      +P+vd+vd++++++k+lA   
-  blumeria_G     2    VPEVDMVDAEVEKLKTLA    19   
-
-DUF881: domain 1 of 1, from 46 to 69: score 4.0, E = 1.6
-                   *->VeksdditiPAydgplklrYAkPv<-*
-                      V  + +it+PA++ p  +r Ak++   
-  blumeria_G    46    VAPEKRITVPALPRPAEVRPAKRA    69   
-
-Jun: domain 1 of 1, from 77 to 93: score -0.7, E = 6.5
-                   *->qHheNPpgfqhsavgpPRlaa<-*
-                      +++eNPp+    a++pP+l a   
-  blumeria_G    77    AGAENPPL----APQPPALEA    93   
-
-SLT: domain 1 of 1, from 89 to 108: score 4.5, E = 1.2
-                CS    HHHHHHHHHHTS-HHHHHHH   
-                   *->dliikaaekygidpsllaAi<-*
-                      ++ ++a+ k+ ++p llaAi   
-  blumeria_G    89    PALEAAGRKNTHPPELLAAI    108  
-
-DUF2346: domain 1 of 1, from 93 to 115: score 3.2, E = 2.8
-                   *->AtKRrEkhdneLlealeeeEaKk<-*
-                      A  R+  h  eLl+a+e eE+     
-  blumeria_G    93    AAGRKNTHPPELLAAIEAEERRA    115  
-
-LBP_BPI_CETP: domain 1 of 1, from 124 to 139: score 1.8, E = 3.8
-                CS    HHHHHHHCHHHH...HTTS   
-                   *->lCPviessVnslNvhLstl<-*
-                      +C +++ssV++    L++l   
-  blumeria_G   124    ICSTAISSVEAA---LQPL    139  
-
-//
-
-Query sequence: blumeria_Grouper_4152_12:NoCat_6
-Accession:      [none]
-Description:    [none]
-
-Scores for sequence family classification (score includes all domains):
-Model      Description                                  Score    E-value  N 
---------   -----------                                  -----    ------- ---
-DUF258     Protein of unknown function, DUF258            1.5        3.8   1
-TRAP_alpha Translocon-associated protein (TRAP), alph     0.1        4.1   1
-DUF1289    Protein of unknown function (DUF1289)          2.8        5.3   1
-SOCS_box   SOCS box                                       2.4        9.7   1
-
-Parsed for domains:
-Model      Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
---------   ------- ----- -----    ----- -----      -----  -------
-DUF258       1/1      50    62 ..   293   305 .]     1.5      3.8
-SOCS_box     1/1      85    90 ..     1     6 [.     2.4      9.7
-DUF1289      1/1      95   115 ..    36    56 .]     2.8      5.3
-TRAP_alpha   1/1     106   116 ..   317   327 .]     0.1      4.1
-
-Alignments of top-scoring domains:
-DUF258: domain 1 of 1, from 50 to 62: score 1.5, E = 3.8
-                CS    -HHHHHHHHHHHH   
-                   *->seeRYesYlklle<-*
-                      s++R+++Y+ l++   
-  blumeria_G    50    SASRFQHYRDLQK    62   
-
-SOCS_box: domain 1 of 1, from 85 to 90: score 2.4, E = 9.7
-                   *->prSLqh<-*
-                      prSLqh   
-  blumeria_G    85    PRSLQH    90   
-
-DUF1289: domain 1 of 1, from 95 to 115: score 2.8, E = 5.3
-                   *->dERravlqllpqRlaalglkp<-*
-                      +E+ + lq+++qR +++++ +   
-  blumeria_G    95    AEKIHTLQNCLQRSKRRSAGQ    115  
-
-TRAP_alpha: domain 1 of 1, from 106 to 116: score 0.1, E = 4.1
-                   *->kRkvKRsvGdD<-*
-                      +R  +Rs+G+D   
-  blumeria_G   106    QRSKRRSAGQD    116  
-
-//

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/PostPostProcessTestFiltered.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-blumeria_Grouper_590_20:NoCat	271	324	DUF234	5	22	1.5	3	0.000000
-blumeria_Grouper_590_20:NoCat	331	357	DUF1414	1	9	6.3	2	0.000000
-blumeria_Grouper_590_20:NoCat	90	113	CPW_WPC	1	9	7.7	1	0.000000
-blumeria_Grouper_590_20:NoCat	119	148	DUF46	182	173	0.11	6	0.000000
-blumeria_Grouper_4152_12:NoCat	97	201	TrbL	231	285	8	0	0.000000
-blumeria_Grouper_4152_12:NoCat	172	240	TNV_CP	167	189	7.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	280	327	DGOK	283	298	1.3	0	0.000000
-blumeria_Grouper_4152_12:NoCat	337	381	Peptidase_S29	1	15	1.1	4	0.000000
-blumeria_Grouper_4152_12:NoCat	442	471	DUF1301	1	10	9.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	62	79	Toxin_18	50	55	4.4	4	0.000000
-blumeria_Grouper_4152_12:NoCat	377	412	ABC_transp_aux	276	287	5.2	1	0.000000
-blumeria_Grouper_4152_12:NoCat	428	478	DUF1602	23	39	0.39	5	0.000000
-blumeria_Grouper_4152_12:NoCat	306	368	zf-P11	1	20	1.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	378	407	V-ATPase_G	1	10	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	136	228	XhoI	202	172	0.014	9	0.000000
-blumeria_Grouper_4152_12:NoCat	145	165	Endomucin	267	261	6	0	0.000000
-blumeria_Grouper_4152_12:NoCat	444	497	DUF1798	52	35	3.3	3	0.000000
-blumeria_Grouper_4152_12:NoCat	294	365	DUF881	237	214	1.6	4	0.000000
-blumeria_Grouper_4152_12:NoCat	177	236	SLT	20	1	1.2	4	0.000000
-blumeria_Grouper_4152_12:NoCat	156	224	DUF2346	85	63	2.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	84	131	LBP_BPI_CETP	209	191	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	314	352	DUF258	305	293	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	230	247	SOCS_box	6	1	9.7	2	0.000000
-blumeria_Grouper_4152_12:NoCat	155	217	DUF1289	56	36	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	152	184	TRAP_alpha	327	317	4.1	0	0.000000

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscanTransformedExpected.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-Polinton-1_DY:classII:Polinton	2974	3642	DNA_pol_B_2	13	252	3.7e-06	24	0.000000
-Polinton-1_DY:classII:Polinton	7897	7944	ASFV_p27	59	74	6	4	0.000000
-Polinton-1_DY:classII:Polinton	9022	9123	Ribosomal_S4	39	72	18	4	0.000000
-Polinton-1_DY:classII:Polinton	11896	11955	Homo_sperm_syn	49	68	8.8	2	0.000000
-Polinton-1_DY:classII:Polinton	5480	5932	rve	168	4	6.7e-30	103	0.000000
-Polinton-1_DY:classII:Polinton	5099	5191	Chromo	51	4	8.5e-06	24	0.000000
-Polinton-1_DY:classII:Polinton	8408	8434	GARS_A	204	196	11	2	0.000000

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/repetHmmscan.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,314 +0,0 @@
->SAR:satellite:satellite
-acagtatataatatatattttgggtactttgatattttatgtacagtatataatatatat
-tttgggtactttgatattttatgt
->BARI_DM:classII:TIR
-acagtcatggtcaaaattattttcacaaagtgcatttttgtgcatgggtcacaaacagtt
-gcttgtgcagcaagtggggggaggtgaaatgcaaaaaaacttttgcttttgcaaattcaa
-acctatgcagagtcagatgaaagaagaattgaaaaaataactgttcctatgcgcaaggaa
-gaggcaaatgaagagatctttatcagttgtcagaagtatttgcacacggtttcgtcgcat
-cacaattattttcacaacgcaatttcttcttcagtgattggtttagagtgacaagtgccg
-gtttgtttgcttaaatacatttaaattattgaataaaaattagatttaatcattttccta
-ttacagttattaaataaaatgcccaaaacaaaagagttaacagttgaggcccgggctggt
-attgttgctaggtttaaagccggtacacctgcggccaaaatagctgaaatatatcaaatt
-tcgcgtagaactgtctactacttaataaaaaagtttgatacagttggcacattaaaaaat
-aaaaaaagatcaggccgaaaacctgtgctggaccaaaggcaatgcaggcaaatacttgga
-gttgtggcgaagaatcctagtgccagtccggtaaaaattgccttagaatcaaaaaataca
-attggcaaacaagttagtagttctacaattcgtcgcaggctaaaagaagctgattttaag
-acatacgttgttcgcaaaacgattgagatcacaccaaccaacaaaacaaaacgtcttcga
-tttgcgttggaatatgttaagaagcctcttgacttttggtttaatattttatggactgat
-gagtctgcatttcagtaccaggggtcatacagcaagcattttatgcatttgaaaaataat
-caaaagcatttggcagcccagccaaccaatagatttggtgggggcacagtcatgttttgg
-ggatgtctttcctattatggattcggagacttggtaccgatagaaggaactttaaatcag
-aacggataccttcttatcttaaacaaccatgcttttacgtctggaaatagactttttcca
-actactgaatggattcttcagcaggacaatgctccatgccataagggtaggataccaaca
-aaatttttaaacgaccttaatctggcggttcttccgtggcccccccaaagcccagacctt
-aatatcattgaaaacgtttgggcttttattaaaaaccaacgaactattgataaaaataga
-aaacgagagggagccatcattgaaatagcggagatttggtccaaattgacattagaattt
-gcacaaactttggtaaggtcaataccaaaaagacttcaagcagttattgatgccaaaggt
-ggtgttacaaaatattagtattgtatttatataaaataaagaaattcttatgttgaaatt
-agatgttaagctgaaatttactaaattaagttgagtgaaaatacttttgaagcgcaataa
-acatgtgaaaatactattgacaacttgcatgcatattttcttttgctttaagctttgtac
-tatgaaccgttatctttcgtatttcttttcgactaccttctgcatagatcaagctaagcg
-ataagaactatttcaggcaaatcggacaacaacaagaagaaatataacaaaaagaagttg
-aagtttgcaaatattgtgcgttgtgaaaatacttttgaccacctctgt
->MOLLY_SN:classII:TIR
-acgtacctcacgggttggccggacacacggtttggccggacacttttgccaagcccccac
-caaattctacctctcaacgtgatgcctcaacaacaacaccagatagacccttctagcgaa
-cgtcatatacagactgcccttcaagctcttaaacaagacgcgacactgtccttgcgacgc
-gctgcagctatctataacgtctctcgagcaacactaagcgatcgacgcgctggacggcct
-tcacaagcagattgctggcctaaaacaaagaatctaactaagactgaggaggacgtagtt
-gttaagcatatacttgagctggttacgcgtggatttcctcctaggctcgcagctgtggct
-gatatggctaattccctgcgcgctgagcgcggtctgggccaagttggctcaaactggccc
-agtacgttcgtcaaacgccgccctgagctccaaacgaagtttaatcgcaaatacgactac
-aagagagccctctgcgaggatcctgaggttatacgagactggttccggcttgtagagaac
-atgaaggcgaagcacggtatccttgatggcgacatgtacaactttgacgagtctggcttt
-atgatgggccagatctcaactggagcagtcgttacagcttcagagcgacgaggacggccg
-aagacagtgcaacagggcaatcgagagtggacgacggtcatccagggcgtcaacgcaaca
-gggtgggccattccacccttcatcatcttcaagggccgccaccacctctcagcttggtat
-aaggaggaggatctacctcataattgggttattgcagtctctaagaacggctggacaaca
-aatgagctcggtctgcagtggttaaagcactttgatgagcatacaaagaggagggttaca
-ggcgcttatcggctgcttattatcgacggccatgagagccacgactcgcttgaattccag
-caatactgcaaggataacaagattatcactctctgcatgcctcctcactcgtcgcacctc
-ctgcagcctcttgatgtgggttgttttgcctctttaaagaaggcgtacagacgccaagcc
-gaagagctcatgcgcaaccggatcacgcacatcacgaaacttgagttcctaccgtgcttt
-aagcgcgcctttgacgcagcaattactcctagtaatatccaaggagggtttcgaggcgct
-ggattggtcccatttgacccagagcgggtcatattagcccttgacgtccgcatccgtacc
-ccaccgttgcccaccgtcgaagactgtccctggcagtcgcaaactccaagtaataccctt
-gaattaggatcgcaatcgacgcttgtaaaggcaaggattcagaggcatatagatagctca
-ccaacgtctatggtggaggcctttgagaaggtctcaaaaggggcagcgattattgcgcac
-aagctagtgttggcgcagaaggagattgctgagcttcgagcagctaataaggccgccacg
-cgacgtaaatcgcacaaaagaaagcgtgtacaggaagaagggaccttgacggtcgaggac
-ggtcttcgacggacgactctaaaggagtttggtgcgcgtagtgatgggaagaaggcgaag
-aagcaggttcgcgctggtgcaggcgagccctcccaaaggcggtgtggacggtgcaatgag
-actgggcataatgcgcgtacgtgtaagaaaacagtagaagtagactctgaatgatattgc
-atcttgctttgtactatacagggccaaagtgggttgttttgcgccagaatagggtggttt
-tggtgggggcttggcaaaagtgtccggccaaaccgtgtgtccggccaacccgtgaggtac
-gt
->Polinton-1_DY:classII:Polinton
-aaaaaaaaaacaagttgggtgtcattggaaaggatttttcaagccctttccaatggtatg
-cttttcacgattctgaaattaaaaatacgacttttcataaaaactctcaaaattacaatt
-gcacttcttcgcgcacaagcaatcttggaagggggtgtacctgcgcgcacaagcagtcat
-aaggatgatcgcaagggtgggggtgagatttctgttcaaggctatgcaccttactgtgtc
-ctcaattttctgggaaggtaactggtggttggattattagttgagaaatatttagaaata
-tcaaacaaactggttatagggtcgtgtatacgtatatataaaaaatcatataatcataaa
-accgttaaaaaaccgtcgttcccgtatattccagctactttcagctaaaagctatggagc
-cgttgagaagaaaatctaaacaatctgaagtcatagcgactttcagcttaaggctaccca
-cgttttaaatgtatgccttgcaaaatgttacttataaagtaacaatgactagtagtcacc
-aataatttcatgatccctgactgcggtcatccgaaataattccctacagagatatgtatt
-tcagattatctgtgatctgtctccattttcattatgctaggagaccccataaaatcaaat
-atttatgactctttgaacctattatcgagaaagtcaagcggctatttacctgcatccaaa
-cccatagctcgccctccttttctgacttccccattgcagtctgtgcagtctgcagtctgt
-gaaggctccttaaatcgagaaccaatcaggtggattctaagagtagacaccccctgtaga
-tgtcaaactctctaatcctcgtgtataaaaatggatccccttaaattgctcaggatcagt
-tcttataatacctcagcactgcattcttataatataatttcggtcgaacttgctcgggat
-atcacgtctaaccgttttaattgtttgtgtggactcaaaccatttactgtgaaaaatttt
-aaaaacgaattaaaatatataaataaaatatatttataaaaaattcaaaatggaatcatc
-agtggcttgtgatttgtgcaaccaatgcatcgaaattagtgagtttgtctctcattacgc
-gaagtgctcagaacccagtaaagcctgcgaggctttaatgttaaactctaacattagatg
-tgacttatgctctaatctagtaaaaaattgtgaatttgatgatcactaccaacgctgtga
-aggaccccgaaatgcatttagcattttaatgggtagaggaaaactggatgaagaagaccg
-ccctatgacatcagctaagtctataaaacgattgaggatggaagaggataaggaaatatc
-taaccccccaaaaagaaaacaaattgacttaagaagggaactcttatgtcctactcagag
-aacgtcaacatattttgaccgatatacataaaaatgcgtcggccagagaagttaagaaca
-atgcgaatatcatattgcttacatcagagacgacatttccagtaaaatcatatcgaattg
-atagtccattatttaaaagagtatataagtgtatatggtacatatataaagcaaacagat
-gaaggagttacagtggaaacaatgaagcactttaaaactgcctacaaatctgtatacata
-aatgaagacattattgatgagctaaattcggccatagattgcttacttacattaagcagc
-gaatttcaagaaaaagactcaggctgggctattaaaaattttaactattttgaaactact
-ataataaaactggaaaacattcctgccagcggatacattaaagctcctcaaaaaataaga
-gcccgtaatgcgctaataaacgtgcagaatgccgacgtattttgtttcaagtggtgtata
-ctagcatttatagctaatcaaaaccatgaaaataggacttttacaaccccccagcaaagg
-aaatattcgagagaaaggatgacaaagcctcaaagctataacattaatattaatgatgaa
-actattgtgtatggcggaatgactttagatttttcgggaattaaatttccaatcgaaaaa
-ataggagttcgacattttgagaaaaacaatgtcaactttagcataaatatttatgaaatt
-gatgaagcaggtgaaaaaattgttggtcccacgattaaaacaaaagaaagaaaacggaac
-cacattaatatattgggaatcgataatattacccaaaacattatgcattatgcgtatata
-acaaatctttatacattatgctcttcacaattttctaaaggaaaatcgggaggatatttt
-tgtgagaactgtcttcagtgttatcacgtgaaaagcactactcacaacaaactggaatgc
-ggaaaagtgtcctcattttatccggaccctaatacgacaacatcgtttaaaggatatcac
-aaaaaattatctcctccagtggtaatttatgcagacattgaggctgttcttgaaaattac
-aaaacatgcttgaattcttctgcttcctcgtcaaccacgcaagtacaaaagcatacggca
-tgtgcagtatctttttatgttgcccataaagattatcctaatcttaacgagctgtggacc
-tacgaaggtaaacagaacaacatttttataaaattatatttaacttacatatttaaattt
-tataattttataggcgttgattgcatacaaacattttgtaaaactcttaaagaaaaaact
-ttaagcctgtattacaaatattgggttaactccaagaaaccgagggatgacactttcgat
-gaacagcttcaaaagggaaattgttgcgcctgcgagaaagaaataaatgcgagcgacctg
-gacaaattctttgatcaattttctggagaatacgtaggtcctatccatagaaattgtaag
-cctaagtttagattaagtgaccctttctttcctgtagtgttccataatttatctaaatat
-gatattcatttatttattactgaattagagggggacttaagtcccataccttgcaataaa
-gagctctatatagcacttacgcaaactataaaaatcaatgctacaagcagatacaaaata
-agatacatagattcagtccgatttttaaattcaagtttagataaactatcaagctatatg
-gaagataaagattttaaaattctaagtacgaaatttcagggagaaaaatttaagcaaatg
-aggaggaagggggtgtttccctatgactacttagatagttttgaaaagtttaatgatacc
-caacttccaagcattgatagtttttataattctcttagtgaagaaaattgtagtatagat
-aactttaatttcgcacagaaagtctgggagacatttaactgtcgaactattaaagactat
-ttaaaactatatttagaaagcgatgttttaattttagcagatgtgtttgaaaattttagg
-aaaatttgcaaaaaaatttataagttagatcccattaattatgttactgcgccatcaata
-tcatgggatgctatgcttaagttcactaatgtaaatttagaactaataagtgatggtgat
-atgtataattttttaaaaagagcaattcggggagggttgactcaatgcactcagcgcatt
-tctatagcaaataataaatacttaaaaaacttcgatccaaaaaaaccgaacaatttttta
-agttatattgatgccaataatttatatgggtgggctatgagtcaacccttaccactatca
-gggtttcagtttttggataaagaagaagttgattcattcgactataaaaatatagcatgt
-gatggtagtatagggtatatgctagaagttgatctggagtatcctgccgataagcatgat
-ttacataattatttaccattctgtcctgaaaataaaattccacccgggggcaagcaaaga
-aagcttatagctgatttaactaataaaagtgaatacataattcacttaaaacagcttcaa
-ctttgtttagagcatggtcttattgtaagaaaggtacaccgagttttgtcctttacgcaa
-tcatgctggctgaagccttatatcgacctaaacacacagcagagaaaattggctgaaaat
-gattttgaaaaaaatttttttaagctaatgaataatgctgtttacggaaaaacaatggag
-aatgtagcaaagcgtcgtcaagtagctttagttaaacattatcaatcgaaacaaaattct
-ccaggttttagacagcgcatagctagaaatgattttcatagcgtagaaatatttggttca
-gacttagcagcaattgagtcaacaccgtccaaaattatgtatgataaacccatatatata
-ggagtaacggttttagaactctcaaaatggctaatgtatgaattttattatgacttcctt
-ttaattaaaagtccatctacgaaaataatatatatggatacagattcatttatactatct
-tcagaagaagatttttatcaaactataaaagacaacccacaacgctttgatacttctaac
-tataagcaagaaaaccaatttaatataatacaggctaataataaagaaccaggaaaaatg
-aaagatgaacatgccggtaaggttatgacctcttttgcgggacttaaggctaaggcatac
-tcttgtttagttgatggagaaggaaatgaccccgaatgcataaaaaaaattaaaggtgta
-aaaaaatctgttattaagaggctgaatcatgtagattatattgaatgtattaagtataaa
-aagacattttatggctcacagagagtaattcgtagtaggtctcacattctttataccgaa
-attgtaaataaaattagtcttaactataaggatgataagagatatatttcaccagataat
-tgtaacactttagcccacggtcattataatatagataatataattagcagtaactttact
-aatactcaataacaaaaaattattgtatacccttgtaaattacaaaacaatacagaaatg
-taaataaacaaaaaccaaattgaatttgaaattattttattgtgtttgattacttaagca
-tatcatttacagatatccatgagttgtggctggagtcgaaaccgctccactttacaagca
-cctggttcttttttcttttaattattttctctattagaaacgcatttttatcttttactt
-tctgaagttcctcttcataaaacgaaccttgaatagggttactcatataatcttctattt
-catacgttacaggccttgttgacttaacttttaaaactttaaaaacttctgtagtccaat
-taggttcatatcccttcataaatactcccttgtatttacttattctaacgaaatccccta
-ctgaaaatttatgttttgggaatatttttggtatattatatactgattttaaaatgaact
-cttcatttttgacacccacatccacaggcttcattttaatagttcgatgataagaattat
-tgtattgatctacaagaaatttgattttatgaatccatttatagtcacctttcatactga
-acattttccacatacgattttttagagttcgattgaagcgttcacatatagaagccttta
-ggtgtgtataagtatggtaatgatttatatgaaattttgtcattaattccctaaaagcgg
-aattaaaaaactcttttccttgatctgactgaatgttcttaggtctacatttactagttc
-taaaaacagtttccattgcctgtactacatctggggcagactttgtcttaaccgcttcgg
-cgaacgcatactttgaaaacgtgtcaataacggttagtaaatatttatatcccttatttt
-ctttactaaatggaatcatttcaaccaaatcaatttgccatgtatcatttattccttttt
-gaacgaattttcggcgtttaaaatttttccgagcaggcttatgaatttcattaacaactt
-gttgtttgctcatgatcaggatttgatttctttgagttactttttattataagacgttgc
-ttgattagataatagtgattgcttatatactagtacatcccgttttatttcaacacgcat
-ctttttagaaatttcaaaacataatcgagttaaatctatttgtacatctttatcatagga
-accctccaaatcagacagttgaatatctaacttttgtaaggatgcacacttaggaattat
-atgtttgtgataaagataaataacttgttgtcgtaatatggaattccagcacaaaaatgt
-ggtaaaaaagatacccaatcttaataaagatctccaggactcacaatcgaactcaatttt
-gttaccatattgattaattactcaataatagtatctggcatcaggaagtcatactggtca
-agcttcagctgtatacgagtatattccttatatgtgagcacttgcatccattcgtcttta
-tcaaatccaatgtaattgtttttactttgctgcatccaaatcatgaccgaaaaattacga
-gaagttgacagaccacatttcaactttaggttatgaccaacataatattcgaaaccaaaa
-atgacttcatgattctgggtctttcgagaagatttcattctttttacttatgcacgtatc
-cattggcttagagtgctttattcaaactaaaagtatattctgatcttggcggtatataaa
-ggaggaaaactcaccctcagttgattaaaaagtcaaccaatcatcatgaacactgtagat
-cgaaattcaagcattatagtactttcaatatttactgggaaacaacaaacaagtttttgt
-aaaagagttagcgtttatgccggccggaactgtcatacctaatttctttcattttaaacc
-accatttaacattaaggaattggataatgaaactcttaagcaactacattttaatcatca
-gaaaattaacggattggactggtcagctggagatattccgtatacatgtcttgaagaaat
-actttcaccgctaaacaaataccgtacagttatcgttcgtggtgaaattaagaaaatctt
-tttaagcaagtatttaacagcaaacataattgatatagatattggaaaaagtttaactca
-gctacccaatttttttaccaattgtagaatacataagaaaaaacttccacttcgctgttc
-attaaataatttgtttaagttatttgtattcctagaaaactcgaattatgaaatatacag
-taatggtgacacatatgtctaaacttaaataaaaaataatttgtaaaccatttagatcgt
-ctactatggattccgttaaaaagttgtttggtaataatcctgagaaaaaaggatactctc
-gacttatatattgtaattattgcggatctgatacgcatttcgagaagaactgcgccaaga
-aacgcgaccaggaaaatcataaaaaagcatagtatatttcataacaaatatacaataaat
-aacggaaaaatatacattttatagtttatcttgtataaaataaatcagtgaatatacatt
-taaaatgtttcgacaatttatacatccttacacaatgttaatttgcggaccttcaggatc
-gggaaaaacaacatttctagaaaatctgataaacaagaagaatgatctttttaatgtttc
-aattgatcgaattatttggtgttatggggaggagagtgctaagccaaattttaataacat
-tgaatactttaaaggagttcctgaaaccatcgaaaatgaaactaatgagcctattctctt
-gatattggacgatttgatgatgggagcctttaacaaaaatgtatgtgaactctttactaa
-aggttcccaccaccgaaatttatctgttattgttgttactcaaaatatatttcacaaatc
-atcgcataccagagatatttcacttaacactaaatatataattgcatttaaaaatcctcg
-tgacaaactgcaatttcaatgcctggcaagacaaatttatccggaaaaccccatggagtt
-atttagaatatataaagaagtaacagaacaaccacacgggtatttacttattgatcttac
-tcagggaataaacgatctcttgagatttagatcagacatttttaattcggaatatacagt
-gtgctattctgacgaatatggtttacaaaaagagcctaaatcgcttgaaagcgaacaaac
-atatattgtatgttctcaaaagggccaacaacaaactacggaaggcaattataagcaatg
-gtgataatgagctggtaaaaacaatagtagaaatagttttaaatacattacgaggaaatc
-agacagtcaataaagcgcatctaagtgctttaaaaaagtataaaaatgcattgcgatata
-tttcatgtccaaagcgtacattaaactctaagagaaaagtcctaattcaaaaaggtggtt
-ttttaccaattctaattagttcgttgctttcaggaatttttggaaaaattttaaaaaatg
-atcaaaaataagcataatttaaataaagtaattttaatgaacccgaataccttacaaaaa
-ttacttaataatgatcgagggaatgaattaataattacaaaatttttaccaattttaaat
-aataacaaaataagtgattttgataaatggattaagattcgtcaagaactaagtttctat
-caaaataaaaaacgtagtaaatcatggaatacttcaaatgaacaaaaatcatacttaaat
-tcaacgagaacagctgaatctcaaacaatagaatcgattgatataagtcctaacacttca
-aaattaaattcaaagttttcaccgaacatgtcggagctctcggatttacctcaaaaaact
-gatgaagaagattttaaatcaaaagaaactgctaagttattgaatgttaaaaaaaaggta
-aaatccggtattttactttcaagaaacgaagagattcctgacttacctccagaaagtgat
-gatgaaattccaaataaaattatcaataaacgaaagataagcaacacttcgttttcagat
-gataaagaagatataaaaaaacaagcagtagtaagagtaaagcttactgaaaaacaacgc
-aggttaagagaaaagttaaataaaattaaagcaacggaaacattaccatatcaaaattta
-aattatataacaggtcgtgaaaaattgcgaagatcaactagaaaaaatttagtgcaaata
-gggaaaaacaaacttaattggatatcttaccaatagcagaaatttaaatataaaaatgaa
-ttatgtaaatgatttctttattacattgctcagtaatgactcattgaatgtatttcctga
-taatgtaaagtgtgcatttacaaacattgtaaatatccccgaagacatgaatgatgactg
-ggaagtaggcattacagatatgtatctgaataattatattagcaaaacaactgcaaaaga
-aacaaatttatctgaagaagcagagtttgtgagtttagtaaatgctgaaacatttagata
-taaaaacgtcgctgtcgaatcgaaaatatctgaatgtggattgatttttatttacactga
-cataattaaacccaggtctgttggtagtatgagaccccgatgtcttcgtgtaatgcatta
-taacggaaaagaaaaaaatattcattttaaaaatattgaatattatcctttggatatatg
-gtctccaaatgaaatctcaatattaattactgattcaagtggatataaagtacctttcga
-gacttccgcagtgccgatttttgttactcttcactttagaaaaaggagaaggtcaaatct
-ataaataatacatacccaaataatgcttacttagaacactaatagtcatcatggtgaaat
-cttatcaggattattatgtaaatcagtgtggagcaggtttgtccaatataggaaccctat
-atgtaaccccgcgaattattcaacaaggtcgaggaatcggaaacttttttagtggacttt
-ttaattacataaaaccacttttcatttcgggtttaaatgctataaaaaatcaagctgcag
-agactggaaaagctgtaattaatgaatttggtagaaagccattaagaaatattattcaag
-aacagagtaaaattgctttacaaaacctatcaaataaagcaataaataaaatgacacggt
-ttcaaaatggcagtggaaaaagaaataaaaagcgaggtggtagaaaaaaacgaaatcatt
-taacatctaaacgacaacgtaaacatacccaaccgtctcataaaaraaaaaaatcatcaa
-ggaaattaaatattacggatattttttctaacacaaaatgagtaaccatatagaatgtat
-gaaaggcgaattggatttgtttgcaccacaccctacgcaaagttcaattctacgaaccga
-agaggtttcttataatccaattgcatccttggatggtgcctcctcaatcgaatttgtttg
-tttaggaaatggtgaaacatatcgagatctatcaagtgtttatttacgacttgtggtgca
-attgaaaaaaaatgataacagcgtcattgaaggaaatgctgtcggtgtagtaaacaatat
-cttacattcaatatttagaagttcatcagtatatttaaataacatattagtttcgcagag
-tgataataattatcattatagagcatatctgcaaacagttttaaactatgggagtgacgc
-ctcggaaagccacttggcctcgcaaggttattttccaaatttcggacgattaacatcagg
-aaaatacgtttatccgagctctaatgaaactctgaaaaatatatttcaaaatagtaataa
-ggtagaactatttggaaaaattcatggtgatatatttaatcaaacgaaacttcttgtcaa
-taatgttgacttaagaattaattttaatattgaaaaaactgcattttatttaatggaaaa
-ggatagcgaatcaaatttaaagatattagaagcacaacttttcatgaatcatgtaactgt
-gaacccaagcattttattggctcatcatcatgttttacaaacaaaaaatgctctttaccc
-attcagtaaagtagaagtaaaatcgtttacaatttacccaggaaacaatacgctatcaat
-agacaatgctgtaattggacaattaccaaattttctagctttttgtatgattaaaaaccg
-ttcatactcaggcaacagaggactagatccatttaattttgaacattttaaaatgcaacg
-ctttaatctaatggtgaatggagttcaagttccttcgcaagctctggaatttgactactc
-gaactctgaaaacgttcaaagctcaagaggctataatatgctattcagatcaagcggaat
-aaaacattatgatcggggtcttcaaattaccaaggaaatgtttgatacgaacagttttat
-attagcctttgatttaactgctgatcagtcaaataccaccatatgttcaaatttgatgtc
-gcaaggcacaataagaatcgaaggaagattttcagaacctcttagtgaagccgttacttg
-tctggtatattgtgaatacgattccatgattgatattgataagcatagaaatattcgaac
-ccttttttaaaatgaatactttacaaattcacaatttgcttacaaaacatatatacacaa
-aatcaatttttaaaggagttttcccttcagaccagcttccaaaaactatttcaaagtatc
-cggctttaattattgcaaacaccgacacttcagatcaaccaggaactcattggattgcat
-tctatttcgaaagtcgcaaatcagcagaattttttgattcctatggacaatttccccaaa
-acaaggaattcgtgacatttttaaaatctaacgcaaataaatattgctataacaagcaac
-aactacaaggatatttttctaatacgtgtggtcattattgcataatgtatggtcttttta
-aatgtaaaaagaaaacgctaaaatatttattaacaaattttaagagaaatgacttttcat
-ataacgataaattaatacttaaaatgtttaagtctaattttaaaaaataaaatgcaagat
-atttaagaaaatcaatgtagtttatttattaagtcgtttgtttagcttataatattttaa
-cataatattgaaggcctcgtctcttaaaattggaagcctatgacactggcacgtatcggg
-tccttccgaagcgtcatcatcactccagggacaaagcttgtagtggaatccatatttaga
-atggatcagttctttatcctctaagtcctccagagtgctcttcaaatatataagctgcgt
-tacgtgctcctcaaatatcatgtcttcgaactgcatcaagaagagctcaatttgtttgga
-gtccattttcgttatggttcttttaaggttttttaaagactgatgttggatttagaaaac
-tcaaacctttatattggaaaatttcatttacttatttatttactgataaaaattcaattc
-gtgcagaactatatctatttacatccttccccttatataccatatgggtaataccattct
-catttaatttcctaaaaggtgtcttagtacagaatttgtttacataactcttaggtagaa
-aaatccaaacatctttttcgtccttgtctgctaaataaagagctaccttagttccataag
-gtgtctttttcagcttacaaccagtgatcttatactcaaatccaatacatagatcttcag
-tttttgtataaccaatcacaggcttcgattcattcagagtctctaggaaatcctagaaat
-tcaataaaatttgaacaggatttatttattaatgtcctatatgcataccatttctgacca
-acgtgagatttgattcgttatgctcttgtaactattcgtattatactaatgcatttactt
-acaattacgagacttttatactgttcagcactacatatatatatatatatatatatatta
-caagaacaaaatactacgtgaaagagataccaatatatctgttatgctctttatatacat
-aaactcagttaagcctatgtagaatatttttatatacttgagtatatctatctcattttg
-tataaatatataacttcatatgaaataaaaggttactacaaacctaatataagacagcac
-ttttctcgaaaactcagattcaatttttactctcagaatgacaaagttgtattgtgagtt
-gtgttcggaaacaaaatcgtttgcttcacgcagcggtttaaaaaaacataccttaaaagt
-gcataacttcagctatcaaaaatcaaaatcttcttattattgttgctttttctgtcccaa
-tgaacgaaaattctggttgcgatataattacaatgttcatctcttgctgatgcacgatgc
-agaattaaagagtatgcgtaaatcaatggaaagttatcaaataaagataaaacaagtttg
-agaatttaattttgtaaaatagttttatttaataaatttctgtataatatagacaaatta
-aaaacctagatcaaataaaacgtctagtaatgaatggtcatcttcatccttcattattcg
-taaataaatgttgggttgacttggctcgatgaactgatcaaaaatatgatcatcatcagg
-aaactcatagattataggatctgtgtgcagtatatccatatcgaaatgctgtgcacattg
-catttcttgatcgtctccattgcctcgtataagatcatttaaaacgtcctgcgttgccgc
-tccaaaaggaaaatcgctccactcaagagacgcaaattcacttccaatttttgtagtggg
-ggtagatgacatagaagggtcaaatactcctcttaagaagcgatctatcgaatcctctgt
-gtcgatagcctccacataaccttccttcgagccttcaattatttcgacatcagagtcttg
-agttaatggaacatttattccatttactgagtcaacaaactctacagtaagatccattgg
-tatgcagtgctgaggtattataagaactgatcctgagcaatttaaggggatccattttta
-tacacgaggattagagagtttgacatctacagggggtgtctactcttagaatccacctga
-ttggttctcgatttaaggagccttcacagactgcagactgcacagactgcaatggggaag
-tcagaaaaggagggcgagctatgggtttggatgcaggtaaatagccgcttgactttctcg
-ataataggttcaaagagtcataaatatttgattttatggggtctcctagcataatgaaaa
-tggagacagatcacagataatctgaaatacatatctctgtagggaattatttcggatgac
-cgcagtcagggatcatgaaattattggtgactactagtcattgttactttataagtaaca
-ttttgcaaggcatacatttaaaacgtgggtagccttaagctgaaagtcgctatgacttca
-gattgtttagattttcttctcaacggctccatagcttttagctgaaagtagctggaatat
-acgggaacgacggttttttaacggttttatgattatatgattttttatatatacgtatac
-acgaccctataaccagtttgtttgatatttctaaatatttctcaactaataatccaacca
-ccagttaccttcccagaaaattgaggacacagtaaggtgcatagccttgaacagaaatct
-cacccccacccttgcgatcatc

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,321 +0,0 @@
-hmmpfam - search one or more sequences against HMM database
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-HMM file:                 myhmms
-Sequence file:            test.fa
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Query sequence: pkinase_full
-Accession:      [none]
-Description:    Dario rerio
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          266.6    3.3e-80   1
-pkinase  Protein kinase domain                          265.4    7.6e-80   1
-rrm                                                     -42.5        2.5   1
-rrm                                                      -8.7        3.7   1
-fn3      Fibronectin type III domain                    -45.8        3.7   1
-fn3      Fibronectin type III domain                     -9.0        3.8   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
-fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
-rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
-pkinase    1/1     258   540 ..     1   294 []   266.6  3.3e-80
-pkinase    1/1     258   537 ..     1   289 [.   265.4  7.6e-80
-fn3        1/1     434   506 ..     1    84 []   -45.8      3.7
-
-Alignments of top-scoring domains:
-rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
-                   *->nGkelggrklrv<-*
-                      n++    ++l v   
-  pkinase_fu   169    NKQDPHQHRLSV    180  
-
-fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
-                CS    CCCC   
-                   *->GpeS<-*
-                      G eS   
-  pkinase_fu   197    GGES    200  
-
-rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
-                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
-                         +N++  +d+ e    + F+ +        +++           +
-  pkinase_fu   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  
-
-                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
-                     +  V++ +ee+ ++  ++++ +  l++   +    
-  pkinase_fu   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  
-
-pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYLHs
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
-  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  
-
-                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
-                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
-  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  
-
-                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
-                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
-  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  
-
-                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
-                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
-  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  
-
-                   LlkkcLnkDPskRpGsatakeilnhpwf<-*
-                   L++ c+   P++Rp   ++  i  h  +   
-  pkinase_fu   518 LMRLCWSGHPTDRP---SFASI--HRIL    540  
-
-pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYLHs
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
-  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  
-
-                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
-                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
-  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  
-
-                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
-                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
-  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  
-
-                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
-                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
-  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  
-
-                   LlkkcLnkDPskRpGsatakeil<-*
-                   L++ c+   P++Rp   ++  i+   
-  pkinase_fu   518 LMRLCWSGHPTDRP---SFASIH    537  
-
-fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7
-                CS    CCCCCEEEEEECCTTCCEEEEECCC        CCCCCCCEEEEE.E
-                   *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq
-                        a    ++++   + + ++W pp++   ++ +  +++  Y v + +
-  pkinase_fu   434    IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477  
-
-                CS CCCCCC  CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
-                   pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
-                   +  + + ++   +                    ++V+  +g+    S   
-  pkinase_fu   478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS    506  
-
-//
-
-Query sequence: pkinase_part
-Accession:      [none]
-Description:    Dario rerio
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          101.5    1.7e-30   1
-pkinase  Protein kinase domain                          -94.7    1.5e-05   1
-rrm                                                     -42.5        2.5   1
-rrm                                                      -8.7        3.7   1
-fn3      Fibronectin type III domain                     -9.0        3.8   1
-fn3      Fibronectin type III domain                    -52.2        5.9   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
-fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
-fn3        1/1     233   299 ..     1    84 []   -52.2      5.9
-rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
-pkinase    1/1     258   400 .]     1   116 [.   101.5  1.7e-30
-pkinase    1/1     258   400 .]     1   294 []   -94.7  1.5e-05
-
-Alignments of top-scoring domains:
-rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
-                   *->nGkelggrklrv<-*
-                      n++    ++l v   
-  pkinase_pa   169    NKQDPHQHRLSV    180  
-
-fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
-                CS    CCCC   
-                   *->GpeS<-*
-                      G eS   
-  pkinase_pa   197    GGES    200  
-
-fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9
-                CS    CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
-                   *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
-                      P +  ++l   ++  +s  ls + p  +  i++    +R + ++g  
-  pkinase_pa   233    PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267  
-
-                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
-                   neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
-                         g   ++   gL P  + ++  +    +  ++S   
-  pkinase_pa   268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS    299  
-
-rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
-                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
-                         +N++  +d+ e    + F+ +        +++           +
-  pkinase_pa   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  
-
-                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
-                     +  V++ +ee+ ++  ++++ +  l++   +    
-  pkinase_pa   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  
-
-pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYL<-
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL  
-  pkinase_pa   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL   400  
-
-                   *
-                    
-  pkinase_pa     -   -    
-
-pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi
-                   +                                                 
-  pkinase_pa   353 RC------------------------------------------------ 354  
-
-                   aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL
-                        A++   s + +t++ ++     PE                     
-  pkinase_pa   355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377  
-
-                   yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee
-                                                    +P s             
-  pkinase_pa   378 --------------------------------YPPLS------------- 382  
-
-                   lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp
-                         +       + ++S+ +   +                        
-  pkinase_pa   383 -----CQ------EQLSISKQVAAGM-----------A------------ 398  
-
-                   wf<-*
-                   ++   
-  pkinase_pa   399 YL    400  
-
-//
-
-Query sequence: S13421
-Accession:      [none]
-Description:    S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum.
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                         -171.6       0.19   1
-rrm                                                     -32.5       0.26   1
-rrm                                                      -6.1       0.92   1
-fn3      Fibronectin type III domain                    -39.7        1.2   1
-pkinase  Protein kinase domain                           -9.2        1.8   1
-fn3      Fibronectin type III domain                     -7.5        1.9   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-fn3        1/1     143   224 ..     1    84 []   -39.7      1.2
-pkinase    1/1     233   241 ..     1     9 [.    -9.2      1.8
-rrm        1/1     440   456 ..     1    17 [.    -6.1     0.92
-rrm        1/1     669   731 ..     1    77 []   -32.5     0.26
-pkinase    1/1     906  1127 ..     1   294 []  -171.6     0.19
-fn3        1/1     923   934 ..     1    12 [.    -7.5      1.9
-
-Alignments of top-scoring domains:
-fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2
-                CS    C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
-                   *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
-                       + ++t+l++ dv    ++ sWs+ +g+ + tg  v  R + ng  +
-      S13421   143    IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185  
-
-                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                     +++ ++ + + l  L +    +  V  v ++ +G      
-      S13421   186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH    224  
-
-pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8
-                   *->yelleklGe<-*
-                        +l+klGe   
-      S13421   233    VSTLKKLGE    241  
-
-rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92
-                   *->lfVgNLppdvteedLkd<-*
-                      + ++ L++   + d+ d   
-      S13421   440    VIISFLNEGLRQADIVD    456  
-
-rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26
-                   *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG
-                        V  L+++d+    +   +  f  i   k++ D            +
-      S13421   669    --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699  
-
-                   faFVeFeseedAekAlealnGkelggr.klrv<-*
-                   + FV   ++ + e+ ++ l  k+++   +l++   
-      S13421   700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI    731  
-
-pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19
-                   *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes
-                      ++l         G++ ++ +  ++ ++ ++ + ++VAv +     ++
-      S13421   906    FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942  
-
-                   ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy
-                   + +            L+      ++  fe   + +  v++       +d 
-      S13421   943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980  
-
-                   lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde
-                   l +    +++ +s    ++   Q+                       lde
-      S13421   981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 
-
-                   ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l
-                   +  ++ +    LAr+l +++   + + +++++f+  +++      ++++l
-      S13421  1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 
-
-                   egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif
-                    +r  s ++  W++++ vi+ ++  g                        
-      S13421  1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 
-
-                   vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL
-                    l++ +++       dp   + +  k   l  + ++++ ++l+ L +k++
-      S13421  1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 
-
-                   nkDPskRpGsatakeilnhpwf<-*
-                   +k  +k p      +i     f   
-      S13421  1114 TKVFTKHP----DYQI----LF    1127 
-
-fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9
-                CS    CCCCCEEEEEEC   
-                   *->PsaPtnltvtdv<-*
-                        + t+l++++v   
-      S13421   923    INPITGLSAREV    934  
-
-//
-

--- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-pkinase_full	169	180	rrm	66	77	3.7	-8.7	0
-pkinase_full	197	200	fn3	81	84	3.8	-9.0	0
-pkinase_full	256	319	rrm	1	77	2.5	-42.5	0
-pkinase_full	258	540	pkinase	1	294	3.3e-80	266.6	0
-pkinase_full	258	537	pkinase	1	289	7.6e-80	265.4	0
-pkinase_full	434	506	fn3	1	84	3.7	-45.8	0
-pkinase_part	169	180	rrm	66	77	3.7	-8.7	0
-pkinase_part	197	200	fn3	81	84	3.8	-9.0	0
-pkinase_part	233	299	fn3	1	84	5.9	-52.2	0
-pkinase_part	256	319	rrm	1	77	2.5	-42.5	0
-pkinase_part	258	400	pkinase	1	116	1.7e-30	101.5	0
-pkinase_part	258	400	pkinase	1	294	1.5e-05	-94.7	0
-S13421	143	224	fn3	1	84	1.2	-39.7	0
-S13421	233	241	pkinase	1	9	1.8	-9.2	0
-S13421	440	456	rrm	1	17	0.92	-6.1	0
-S13421	669	731	rrm	1	77	0.26	-32.5	0
-S13421	906	1127	pkinase	1	294	0.19	-171.6	0
-S13421	923	934	fn3	1	12	1.9	-7.5	0

--- a/commons/pyRepetUnit/align/tests/Test_AlignListUtils.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.align.AlignList import AlignList
-from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.coord.Range import Range
-from commons.core.coord.Align import Align
-
-class Test_AlignListUtils (unittest.TestCase):
-    
-    def setUp(self):
-        self.inputFileName = "dummyAlignFile.align"
-        self.outputFileName = "dummyAlignFile.out"
-        
-    def testRead(self):
-        f = open(self.inputFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t2.6e-60\t0\t3.2\n")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t0\t2.9\n")
-        f.close() 
-        alignRead = AlignListUtils()      
-        tableauAlignInstance = alignRead.read(self.inputFileName)            
-        self.assertEquals(tableauAlignInstance.get(0).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
-        self.assertEquals(tableauAlignInstance.get(0).range_query.start, 91)
-        self.assertEquals(tableauAlignInstance.get(0).range_query.end, 108)  
-        self.assertEquals(tableauAlignInstance.get(0).range_subject.seqname, "DUF234")
-        self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5)
-        self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22)
-        self.assertEquals(tableauAlignInstance.get(0).e_value, 2.6e-60) 
-        self.assertEquals(tableauAlignInstance.get(0).score, 0)
-        self.assertEquals(tableauAlignInstance.get(0).identity, 3.2)
-        self.assertEquals(tableauAlignInstance.get(1).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
-        self.assertEquals(tableauAlignInstance.get(1).range_query.start, 111)
-        self.assertEquals(tableauAlignInstance.get(1).range_query.end, 119)  
-        self.assertEquals(tableauAlignInstance.get(1).range_subject.seqname, "DUF1414")
-        self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1)
-        self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9)
-        self.assertEquals(tableauAlignInstance.get(1).e_value, 6.3)
-        self.assertEquals(tableauAlignInstance.get(1).score, 0)
-        self.assertEquals(tableauAlignInstance.get(1).identity, 2.9)
-        os.system("rm " + self.inputFileName)
-        
-    def testWrite(self):
-        f = open("expectedAlignFile.align", "w")
-        f.write("biduleChouetteQuery\t20\t55\tbiduleChouetteSubject\t2\t15\t0.005\t20\t0.000000\n")
-        f.write("trucBiduleQuery\t110\t155\ttrucBiduleSubject\t1\t35\t2\t1\t0.000000\n")
-        f.write("dummyQuery\t1\t65\tdummySubject\t1\t25\t2.6e-60\t50\t0.000000\n")
-        f.close()        
-        listAlignInstance = AlignList()
-        align1 = Align()
-        align1.range_query = Range("biduleChouetteQuery", 20, 55)
-        align1.range_subject = Range("biduleChouetteSubject", 2, 15)
-        align1.e_value = 0.005
-        align1.score = 20
-        listAlignInstance.append(align1)
-        align2 = Align()
-        align2.range_query = Range("trucBiduleQuery", 110, 155)
-        align2.range_subject = Range("trucBiduleSubject", 1, 35)
-        align2.e_value = 2
-        align2.score = 1.5
-        listAlignInstance.append(align2)
-        align3 = Align()
-        align3.range_query = Range("dummyQuery", 1, 65)
-        align3.range_subject = Range("dummySubject", 1, 25)
-        align3.e_value = 2.6e-60
-        align3.score = 50
-        listAlignInstance.append(align3)
-        f = open(self.outputFileName, "w")
-        alignUtils = AlignListUtils()
-        alignUtils.write(listAlignInstance, self.outputFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(self.outputFileName, "expectedAlignFile.align"))
-        os.system("rm " + self.outputFileName)        
-        os.system("rm expectedAlignFile.align")
-        
-    def testFilterOnAMinimalScore(self):
-        listAlignInstance = AlignList()
-        align1 = Align()
-        align1.range_query = Range("biduleChouetteQuery", 20, 55)
-        align1.range_subject = Range("biduleChouetteSubject", 2, 15)
-        align1.e_value = 5
-        align1.score = -0.5
-        listAlignInstance.append(align1)
-        align2 = Align()
-        align2.range_query = Range("trucBiduleQuery", 110, 155)
-        align2.range_subject = Range("trucBiduleSubject", 1, 35)
-        align2.e_value = 2
-        align2.score = -2.0
-        listAlignInstance.append(align2)
-        align3 = Align()
-        align3.range_query = Range("dummyQuery", 1, 65)
-        align3.range_subject = Range("dummySubject", 1, 25)
-        align3.e_value = 2.6e-60
-        align3.score = 50
-        listAlignInstance.append(align3)
-        expectedAlignInstance = align3
-        alignUtils = AlignListUtils()
-        alignUtils.filterOnAMinimalScore(listAlignInstance, 0)
-        self.assertEquals(listAlignInstance.get(0), expectedAlignInstance)
-        
-if __name__ == "__main__" :
-    unittest.main() 
\ No newline at end of file

--- a/commons/pyRepetUnit/align/tests/hmmpfamOutputParsingTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-'''
-Created on 29 mai 2009
-
-@author: oinizan
-'''
-import unittest
-import sys
-from commons.pyRepetUnit.align.tests.Test_AlignListUtils import Test_AlignListUtils
-
-
-def main():
-
-        hmmpfamOutputParsingTestSuite = unittest.TestSuite() 
-        hmmpfamOutputParsingTestSuite.addTest(unittest.makeSuite(Test_AlignListUtils,'test'))
-        
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(hmmpfamOutputParsingTestSuite)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/TransformAACoordIntoNtCoordInAlignFormat.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-import os
-import sys
-from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils
-from commons.core.seq.BioseqUtils import BioseqUtils
-from commons.core.checker.RepetException import RepetException
-
-### Transform amino acid query coord in an align format to nucleotide coord 
-### according to the frame specified at the end of seqName
-#
-class TransformAACoordIntoNtCoordInAlignFormat( object ):
-    
-    def __init__(self):
-        self._inFileName = None
-        self._clean = False
-        self._outFileName = None
-        self._consensusFileName = None
-        self._IsFiltered = True
-
-    ## read input file, transform it and write the output file
-    # 
-    def run(self):   
-        alignUtils = AlignListUtils()         
-        listAlignInstance = alignUtils.read(self._inFileName)
-        self.transformQueryCoord(listAlignInstance)
-        #self.getOriginalQueryNameForAlignList(listAlignInstance)
-        if self._IsFiltered:
-            alignUtils.filterOnAMinimalScore(listAlignInstance, 0)
-        alignUtils.write(listAlignInstance, self._outFileName)
-        if self._clean:
-            self.clean()
-    
-    ## Transform the amino acid query coord into nucleotides and switch subject coord if the strand is reversed
-    # @param listAlignInstance list of align object instance
-    #
-    def transformQueryCoord(self, listAlignInstance):
-        bioseqList = BioseqUtils.extractBioseqListFromFastaFile( self._consensusFileName )
-        for alignInstance in listAlignInstance.getList():
-            try:
-                frame = self.extractFrameFromSeqName(alignInstance)
-            except RepetException, e:
-                raise e
-            previousEnd = alignInstance.range_query.end                            
-            previousStart = alignInstance.range_query.start
-            alignInstance.range_query.seqname = self._getOriginalQueryNameForAlignInstance(alignInstance)
-            if frame < 4:
-                self._changeStartInAAIntoNtInPositiveFrame(alignInstance, frame, previousStart) 
-                self._changeEndInAAIntoNtInPositiveFrame(alignInstance, frame, previousEnd)                
-            else:
-                self._checkIfSeqNameIsInDNASeqFile(bioseqList, alignInstance.range_query.seqname)
-                consensusLength = BioseqUtils.getSeqLengthWithSeqName(bioseqList, alignInstance.range_query.seqname)              
-                self._changeStartInAAIntoNtInNegativeFrame(alignInstance, frame, consensusLength, previousEnd)
-                self._changeEndInAAIntoNtInNegativeFrame(alignInstance, frame, consensusLength, previousStart)
-                self._invertedSubjectCoord(alignInstance)
-    
-    ## remove the input file
-    #
-    def clean(self):
-        os.remove(self._inFileName)
-        
-    ## set input file name
-    #
-    # @param fileName string name of file
-    #
-    def setInFileName(self, fileName):  
-        self._inFileName = fileName  
-    
-    ## set output file name
-    #
-    # @param fileName string name of file
-    #
-    def setOutFileName(self, fileName):  
-        self._outFileName = fileName    
-        
-    ## set consensus file name
-    #
-    # @param fileName string name of file
-    #
-    def setConsensusFileName(self, fileName):  
-        self._consensusFileName = fileName     
-    
-    ## set is clean will be done
-    #
-    # @param clean boolean clean
-    #
-    def setIsClean(self, clean):
-        self._clean = clean
-        
-    ## get input file name
-    #
-    def getInFileName(self):
-        return self._inFileName
-    
-    ## set is negativ score filter will be done
-    #
-    # @param isFiltered boolean isFiltered
-    #
-    def setIsFiltered(self, isFiltered):
-        self._IsFiltered = isFiltered
-
-    def _getOriginalQueryNameForAlignInstance(self, alignInstance):
-        return alignInstance.range_query.seqname[0:len(alignInstance.range_query.seqname) - 2]
-
-    def _invertedSubjectCoord(self, alignInstance):
-        return alignInstance.range_subject.reverse()
-
-    def _changeEndInAAIntoNtInPositiveFrame(self, alignInstance, frame, previousEnd):
-        alignInstance.range_query.end = 3 * previousEnd + frame - 1
-
-    def _changeStartInAAIntoNtInPositiveFrame(self, alignInstance, frame, previousStart):
-        alignInstance.range_query.start = 3 * (previousStart - 1) + frame
-    
-    def _changeEndInAAIntoNtInNegativeFrame(self, alignInstance, frame, consensusLength, previousStart):
-        alignInstance.range_query.end = consensusLength - 3 * (previousStart - 1) - frame + 4
-
-    def _changeStartInAAIntoNtInNegativeFrame(self, alignInstance, frame, consensusLength, previousEnd):
-        alignInstance.range_query.start = consensusLength - 3 * (previousEnd - 1) - frame + 2
-
-    def extractFrameFromSeqName(self, alignInstance):
-        try:
-            frame = int(alignInstance.range_query.seqname[len(alignInstance.range_query.seqname) - 1])
-        except ValueError:
-            raise RepetException("Unable to extract frame from sequence name")
-        return frame
-
-    def _checkIfSeqNameIsInDNASeqFile(self, bioseqList, seqName):
-        isSeqNameInBioseqList = False
-        for bioseq in bioseqList:
-            if seqName == bioseq.header:
-                isSeqNameInBioseqList = True
-        if not isSeqNameInBioseqList:
-            sys.stderr.write("seqName : " + seqName + " is not in the consensus file " + self._consensusFileName + "\n")
-            sys.exit(1)
-    
\ No newline at end of file

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_F_TransformAACoordIntoNtCoordAndScoreFiltering.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_TransformAACoordIntoNtCoordAndScoreFiltering (unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFile = "./datas/OutputHmmpfamTest.align"
-        self._consensusFile = "./datas/ConsensusTestFile_nt.fsa"
-        self._outputFile = "./datas/alignTransformedToTest.align"
-        self._expectedFile = "./datas/PostPostProcessTest.align"
-        self._expectedFileFiltered = "./datas/PostPostProcessTestFiltered.align"
-        self._alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-    
-    def testRun_with_no_filter(self):
-        self._alignTransformation.setInFileName(self._inputFile)
-        self._alignTransformation.setOutFileName(self._outputFile)
-        self._alignTransformation.setConsensusFileName(self._consensusFile)       
-        self._alignTransformation.setIsFiltered(False)
-        self._alignTransformation.run()
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile))
-        os.remove(self._outputFile) 
-        
-    def testRun_with_filter(self):
-        self._alignTransformation.setInFileName(self._inputFile)
-        self._alignTransformation.setOutFileName(self._outputFile)
-        self._alignTransformation.setConsensusFileName(self._consensusFile)       
-        self._alignTransformation.setIsFiltered(True)
-        self._alignTransformation.run()
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFileFiltered, self._outputFile))
-        os.remove(self._outputFile)
-        
-            
-if __name__ == "__main__" :
-    unittest.main() 
\ No newline at end of file

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_TransformAACoordIntoNtCoordInAlignFormat.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,237 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils
-from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.coord.Align import Align
-from commons.core.coord.Range import Range
-from commons.core.checker.RepetException import RepetException
-
-class Test_TransformAACoordIntoNtCoordInAlignFormat(unittest.TestCase):
-    
-    def setUp(self):
-        self.inputFileName = "alignFile.align"
-        self.consensusFile = "consensus.fa"
-        self.outputFileName = "outputFile.align"
-        self._expFileName = "expFile.align"
-        
-    def tearDown(self):
-        if FileUtils.isRessourceExists(self.inputFileName):
-            os.remove(self.inputFileName)
-        if FileUtils.isRessourceExists(self.consensusFile):
-            os.remove(self.consensusFile)
-        if FileUtils.isRessourceExists(self.outputFileName):
-            os.remove(self.outputFileName)
-        if FileUtils.isRessourceExists(self._expFileName):
-            os.remove(self._expFileName)
-    
-    def test_transformQueryCoord(self):
-        f = open(self.inputFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">blumeria_Grouper_590_20:NoCat\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignRead = AlignListUtils()      
-        tableauAlignInstance = alignRead.read(self.inputFileName)
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setConsensusFileName(self.consensusFile)
-        alignTransformation.transformQueryCoord(tableauAlignInstance)
-        #check query coord
-        self.assertEquals(tableauAlignInstance.get(0).range_query.start, 271)
-        self.assertEquals(tableauAlignInstance.get(0).range_query.end, 324) 
-        self.assertEquals(tableauAlignInstance.get(1).range_query.start, 331)
-        self.assertEquals(tableauAlignInstance.get(1).range_query.end, 357) 
-        self.assertEquals(tableauAlignInstance.get(2).range_query.start, 90)
-        self.assertEquals(tableauAlignInstance.get(2).range_query.end, 113) 
-        self.assertEquals(tableauAlignInstance.get(3).range_query.start, 165)
-        self.assertEquals(tableauAlignInstance.get(3).range_query.end, 209) 
-        self.assertEquals(tableauAlignInstance.get(4).range_query.start, 119)
-        self.assertEquals(tableauAlignInstance.get(4).range_query.end, 148) 
-        self.assertEquals(tableauAlignInstance.get(5).range_query.start, 16)
-        self.assertEquals(tableauAlignInstance.get(5).range_query.end, 30) 
-        #check subject (profiles) coord
-        #positive frame : they don't change
-        self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5)
-        self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22) 
-        self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1)
-        self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9) 
-        self.assertEquals(tableauAlignInstance.get(2).range_subject.start, 1)
-        self.assertEquals(tableauAlignInstance.get(2).range_subject.end, 9) 
-        self.assertEquals(tableauAlignInstance.get(3).range_subject.start, 341)
-        self.assertEquals(tableauAlignInstance.get(3).range_subject.end, 355) 
-        #negative frame : they must be inverted
-        self.assertEquals(tableauAlignInstance.get(4).range_subject.start, 182)
-        self.assertEquals(tableauAlignInstance.get(4).range_subject.end, 173) 
-        self.assertEquals(tableauAlignInstance.get(5).range_subject.start, 280)
-        self.assertEquals(tableauAlignInstance.get(5).range_subject.end, 276) 
-    
-    def test_transformQueryCoord_with_seqName_not_in_consensus_file(self):
-        f = open(self.inputFileName, "w")
-        f.write("dummy_Grouper_590_20:NoCat_4\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("dummy_Grouper_590_20:NoCat_4\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">blumeria_Grouper_590_20:NoCat\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignRead = AlignListUtils()      
-        tableauAlignInstance = alignRead.read(self.inputFileName)
-        
-        isSystemExitRaised = False
-        try:
-            alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-            alignTransformation.setConsensusFileName(self.consensusFile)
-            alignTransformation.transformQueryCoord(tableauAlignInstance)
-        except SystemExit:
-            isSystemExitRaised = True
-        self.assertTrue(isSystemExitRaised)
-    
-    def test_run(self):
-        f = open(self.inputFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">blumeria_Grouper_590_20:NoCat\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setInFileName(self.inputFileName)
-        alignTransformation.setOutFileName(self.outputFileName)
-        alignTransformation.setConsensusFileName(self.consensusFile)
-        alignTransformation.run()
-        f = open(self._expFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat\t271\t324\tDUF234\t5\t22\t1.5\t3\t0.000000\n")
-        f.write("blumeria_Grouper_590_20:NoCat\t331\t357\tDUF1414\t1\t9\t6.3\t2\t0.000000\n")
-        f.write("blumeria_Grouper_590_20:NoCat\t90\t113\tCPW_WPC\t1\t9\t7.7\t1\t0.000000\n")
-        f.write("blumeria_Grouper_590_20:NoCat\t119\t148\tDUF46\t182\t173\t0.11\t6\t0.000000\n")
-        f.close()
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, self.outputFileName))
-  
-    #TODO: is it normal ?
-    def test_run_header_without_frame(self):
-        f = open(self.inputFileName, "w")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t186\t218\tPF02022.11_Integrase_Zn_INT_13.5\t1\t40\t8.9\t-20.4\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t209\t266\tPF04236.7_Transp_Tc5_C_Tase_25.0\t1\t61\t8.5\t-38.8\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t256\t266\tPF04236.7_Transp_Tc5_C_Tase_30.0\t51\t61\t2.3\t-0.2\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t388\t395\tPF10576.1_EndIII_4Fe-2S_EN_17.5\t10\t17\t3.9\t-0.0\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t425\t433\tPF05410.5_Peptidase_C31_CYP_25.0\t98\t106\t1.9\t-2.0\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t487\t497\tPF09225.2_Endonuc-PvuII_EN_25.0\t127\t137\t4.9\t-3.5\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t574\t581\tPF02093.8_Gag_p30_GAG_10.5\t1\t8\t7.3\t-4.5\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t693\t706\tPF00910.14_RNA_helicase_HEL_20.0\t1\t14\t3.8\t-1.0\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t735\t743\tPF09569.2_RE_ScaI_EN_25.0\t1\t9\t7.1\t-3.3\t0\n")
-        f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t737\t743\tPF03577.7_Peptidase_C69_CYP_25.0\t459\t465\t6.2\t-4.8\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setInFileName(self.inputFileName)
-        alignTransformation.setOutFileName(self.outputFileName)
-        alignTransformation.setConsensusFileName(self.consensusFile)
-        self.assertRaises(RepetException, alignTransformation.run)
-        
-    def test_extractFrameFromSeqName(self):
-        alignInstance = Align()
-        rangeQuery = Range()
-        rangeQuery.seqname = "BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp"
-        alignInstance.range_query = rangeQuery
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        self.assertRaises(RepetException, alignTransformation.extractFrameFromSeqName, alignInstance)
-        
-    def test_run_no_filter(self):
-        f = open(self.inputFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">blumeria_Grouper_590_20:NoCat\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setInFileName(self.inputFileName)
-        alignTransformation.setOutFileName(self.outputFileName)
-        alignTransformation.setConsensusFileName(self.consensusFile)
-        alignTransformation.setIsFiltered(False)
-        alignTransformation.run()
-        self.assertTrue(FileUtils.getNbLinesInSingleFile(self.outputFileName), 6) 
-        self.assertTrue(FileUtils.isRessourceExists(self.inputFileName)) 
-    
-    def test_run_no_filter_clean_option(self):
-        f = open(self.inputFileName, "w")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        f = open(self.consensusFile, "w")
-        f.write(">blumeria_Grouper_590_20:NoCat\n")
-        f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n")
-        f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n")
-        f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n")
-        f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n")
-        f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n")
-        f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n")
-        f.write("TCCATAATTTCAACACTNAAGAATATTTGTA")
-        f.close() 
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setInFileName(self.inputFileName)
-        alignTransformation.setOutFileName(self.outputFileName)
-        alignTransformation.setConsensusFileName(self.consensusFile)
-        alignTransformation.setIsFiltered(True)
-        alignTransformation.setIsClean(True)
-        alignTransformation.run()
-        self.assertTrue(FileUtils.getNbLinesInSingleFile(self.outputFileName), 6) 
-        self.assertFalse(FileUtils.isRessourceExists(self.inputFileName))        
-            
-if __name__ == "__main__" :
-    unittest.main() 
\ No newline at end of file

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/TransformAACoordIntoNtCoordTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-import unittest
-import sys
-import TestTransformAACoordIntoNtCoordInAlignFormat
-import TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering
-
-def main():
-
-        TransformAlignTestSuite = unittest.TestSuite() 
-        TransformAlignTestSuite.addTest(unittest.makeSuite(TestTransformAACoordIntoNtCoordInAlignFormat.TestTransformAACoordIntoNtCoordInAlignFormat,'test'))
-        TransformAlignTestSuite.addTest(unittest.makeSuite(TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering.TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering,'test'))
-        
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(TransformAlignTestSuite)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/ConsensusTestFile_nt.fsa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
->blumeria_Grouper_590_20:NoCat
-TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA
-AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT
-ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA
-ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA
-CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC
-TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC
-TCCATAATTTCAACACTNAAGAATATTTGTA
->blumeria_Grouper_4152_12:NoCat
-GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA
-AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC
-GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC
-GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC
-TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT
-TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT
-GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG
-CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC
-ATATCTACCTCGGGGACATTG

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/OutputHmmpfamTest.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-blumeria_Grouper_590_20:NoCat_1	91	108	DUF234	5	22	1.5	3.2	0
-blumeria_Grouper_590_20:NoCat_1	111	119	DUF1414	1	9	6.3	2.9	0
-blumeria_Grouper_590_20:NoCat_3	30	37	CPW_WPC	1	9	7.7	1.5	0
-blumeria_Grouper_590_20:NoCat_3	55	69	HECT	341	355	9.2	0.0	0
-blumeria_Grouper_590_20:NoCat_4	82	91	DUF46	173	182	0.11	6.4	0
-blumeria_Grouper_590_20:NoCat_5	121	125	POC4	276	280	6.3	-1.7	0
-blumeria_Grouper_4152_12:NoCat_1	27	38	Amino_oxidase	471	482	9.1	-0.6	0
-blumeria_Grouper_4152_12:NoCat_1	33	67	TrbL	231	285	8	0.8	0
-blumeria_Grouper_4152_12:NoCat_1	58	80	TNV_CP	167	189	7.9	0.1	0
-blumeria_Grouper_4152_12:NoCat_1	94	109	DGOK	283	298	1.3	0.5	0
-blumeria_Grouper_4152_12:NoCat_1	113	127	Peptidase_S29	1	15	1.1	4.7	0
-blumeria_Grouper_4152_12:NoCat_1	148	157	DUF1301	1	10	9.9	0.4	0
-blumeria_Grouper_4152_12:NoCat_2	21	26	Toxin_18	50	55	4.4	4.2	0
-blumeria_Grouper_4152_12:NoCat_2	126	137	ABC_transp_aux	276	287	5.2	1.1	0
-blumeria_Grouper_4152_12:NoCat_2	143	159	DUF1602	23	39	0.39	5.0	0
-blumeria_Grouper_4152_12:NoCat_3	102	122	zf-P11	1	20	1.8	3.6	0
-blumeria_Grouper_4152_12:NoCat_3	126	135	V-ATPase_G	1	10	5.3	2.4	0
-blumeria_Grouper_4152_12:NoCat_4	92	122	XhoI	172	202	0.014	9.9	0
-blumeria_Grouper_4152_12:NoCat_4	113	119	Endomucin	261	267	6	0.1	0
-blumeria_Grouper_4152_12:NoCat_5	2	19	DUF1798	35	52	3.3	3.0	0
-blumeria_Grouper_4152_12:NoCat_5	46	69	DUF881	214	237	1.6	4.0	0
-blumeria_Grouper_4152_12:NoCat_5	77	93	Jun	264	284	6.5	-0.7	0
-blumeria_Grouper_4152_12:NoCat_5	89	108	SLT	1	20	1.2	4.5	0
-blumeria_Grouper_4152_12:NoCat_5	93	115	DUF2346	63	85	2.8	3.2	0
-blumeria_Grouper_4152_12:NoCat_5	124	139	LBP_BPI_CETP	191	209	3.8	1.8	0
-blumeria_Grouper_4152_12:NoCat_6	50	62	DUF258	293	305	3.8	1.5	0
-blumeria_Grouper_4152_12:NoCat_6	85	90	SOCS_box	1	6	9.7	2.4	0
-blumeria_Grouper_4152_12:NoCat_6	95	115	DUF1289	36	56	5.3	2.8	0
-blumeria_Grouper_4152_12:NoCat_6	106	116	TRAP_alpha	317	327	4.1	0.1	0

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTest.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-blumeria_Grouper_590_20:NoCat	271	324	DUF234	5	22	1.5	3	0.000000
-blumeria_Grouper_590_20:NoCat	331	357	DUF1414	1	9	6.3	2	0.000000
-blumeria_Grouper_590_20:NoCat	90	113	CPW_WPC	1	9	7.7	1	0.000000
-blumeria_Grouper_590_20:NoCat	165	209	HECT	341	355	9.2	0	0.000000
-blumeria_Grouper_590_20:NoCat	119	148	DUF46	182	173	0.11	6	0.000000
-blumeria_Grouper_590_20:NoCat	16	30	POC4	280	276	6.3	-1	0.000000
-blumeria_Grouper_4152_12:NoCat	79	114	Amino_oxidase	471	482	9.1	0	0.000000
-blumeria_Grouper_4152_12:NoCat	97	201	TrbL	231	285	8	0	0.000000
-blumeria_Grouper_4152_12:NoCat	172	240	TNV_CP	167	189	7.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	280	327	DGOK	283	298	1.3	0	0.000000
-blumeria_Grouper_4152_12:NoCat	337	381	Peptidase_S29	1	15	1.1	4	0.000000
-blumeria_Grouper_4152_12:NoCat	442	471	DUF1301	1	10	9.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	62	79	Toxin_18	50	55	4.4	4	0.000000
-blumeria_Grouper_4152_12:NoCat	377	412	ABC_transp_aux	276	287	5.2	1	0.000000
-blumeria_Grouper_4152_12:NoCat	428	478	DUF1602	23	39	0.39	5	0.000000
-blumeria_Grouper_4152_12:NoCat	306	368	zf-P11	1	20	1.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	378	407	V-ATPase_G	1	10	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	136	228	XhoI	202	172	0.014	9	0.000000
-blumeria_Grouper_4152_12:NoCat	145	165	Endomucin	267	261	6	0	0.000000
-blumeria_Grouper_4152_12:NoCat	444	497	DUF1798	52	35	3.3	3	0.000000
-blumeria_Grouper_4152_12:NoCat	294	365	DUF881	237	214	1.6	4	0.000000
-blumeria_Grouper_4152_12:NoCat	222	272	Jun	284	264	6.5	0	0.000000
-blumeria_Grouper_4152_12:NoCat	177	236	SLT	20	1	1.2	4	0.000000
-blumeria_Grouper_4152_12:NoCat	156	224	DUF2346	85	63	2.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	84	131	LBP_BPI_CETP	209	191	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	314	352	DUF258	305	293	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	230	247	SOCS_box	6	1	9.7	2	0.000000
-blumeria_Grouper_4152_12:NoCat	155	217	DUF1289	56	36	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	152	184	TRAP_alpha	327	317	4.1	0	0.000000

--- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTestFiltered.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-blumeria_Grouper_590_20:NoCat	271	324	DUF234	5	22	1.5	3	0.000000
-blumeria_Grouper_590_20:NoCat	331	357	DUF1414	1	9	6.3	2	0.000000
-blumeria_Grouper_590_20:NoCat	90	113	CPW_WPC	1	9	7.7	1	0.000000
-blumeria_Grouper_590_20:NoCat	119	148	DUF46	182	173	0.11	6	0.000000
-blumeria_Grouper_4152_12:NoCat	97	201	TrbL	231	285	8	0	0.000000
-blumeria_Grouper_4152_12:NoCat	172	240	TNV_CP	167	189	7.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	280	327	DGOK	283	298	1.3	0	0.000000
-blumeria_Grouper_4152_12:NoCat	337	381	Peptidase_S29	1	15	1.1	4	0.000000
-blumeria_Grouper_4152_12:NoCat	442	471	DUF1301	1	10	9.9	0	0.000000
-blumeria_Grouper_4152_12:NoCat	62	79	Toxin_18	50	55	4.4	4	0.000000
-blumeria_Grouper_4152_12:NoCat	377	412	ABC_transp_aux	276	287	5.2	1	0.000000
-blumeria_Grouper_4152_12:NoCat	428	478	DUF1602	23	39	0.39	5	0.000000
-blumeria_Grouper_4152_12:NoCat	306	368	zf-P11	1	20	1.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	378	407	V-ATPase_G	1	10	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	136	228	XhoI	202	172	0.014	9	0.000000
-blumeria_Grouper_4152_12:NoCat	145	165	Endomucin	267	261	6	0	0.000000
-blumeria_Grouper_4152_12:NoCat	444	497	DUF1798	52	35	3.3	3	0.000000
-blumeria_Grouper_4152_12:NoCat	294	365	DUF881	237	214	1.6	4	0.000000
-blumeria_Grouper_4152_12:NoCat	177	236	SLT	20	1	1.2	4	0.000000
-blumeria_Grouper_4152_12:NoCat	156	224	DUF2346	85	63	2.8	3	0.000000
-blumeria_Grouper_4152_12:NoCat	84	131	LBP_BPI_CETP	209	191	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	314	352	DUF258	305	293	3.8	1	0.000000
-blumeria_Grouper_4152_12:NoCat	230	247	SOCS_box	6	1	9.7	2	0.000000
-blumeria_Grouper_4152_12:NoCat	155	217	DUF1289	56	36	5.3	2	0.000000
-blumeria_Grouper_4152_12:NoCat	152	184	TRAP_alpha	327	317	4.1	0	0.000000

--- a/commons/pyRepetUnit/blastnForClassifierStep1/RepbaseBLRnForClassifierStep1.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-"""
-Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table.
-"""
-
-import os
-import ConfigParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.LoggerFactory import LoggerFactory
-
-LOG_DEPTH = "repet.tools"
-
-class RepbaseBLRnForClassifierStep1( object ):
-    
-    """
-    Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table.
-    
-    @param inFileName: name of the input fasta file
-    @type inFileName: string
-    
-    @param launch_1: generic command at the beginning of a specific command
-    @type launch_1: string
-    
-    @param launch_2: generic command at the end of a specific command
-    @type launch_2: string
-
-    @return: all the commands to run the job
-    @rtype: string
-    
-    @param cDir: current directory (where to retrieve the result files)
-    @ype cDir: string
-
-    @param tmpDir: temporary directory (where the job will run)
-    @type tmpDir: string
-    
-    @param configFileName: configuration file name
-    @type configFileName: string
-    
-    @param logger: a logger Instance
-    @type logger: logger
-    
-    @param verbose: verbose(0/1/2)
-    @type verbose: int
-    
-    @param pL: program launcher
-    @type pL: programLauncher Instance
-    
-    @param project: project name
-    @type project: string
-    
-    """
-
-    def __init__(self, inFileName, launch_1, launch_2, cDir, tmpDir, configFileName, verbose, pL, project):
-        """
-        Constructor
-        """
-        self._inFileName = inFileName
-        self._launch_1 = launch_1
-        self._launch_2 = launch_2
-        self._cDir = cDir
-        self._tmpDir = tmpDir
-        self._verbose = verbose
-        self._pL = pL
-        self._project = project
-        self._fileUtils = FileUtils()
-        self._config = ConfigParser.ConfigParser()
-        self._configFileName = configFileName
-        self._config.readfp( open(self._configFileName) )
-        self._bank = self._config.get("detect_features","TE_nucl_bank")
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose)
-
-    def formatRepbase_ntIfNecessary( self ):
-        """
-        Format Repbase (make 'cut' files).
-        """
-        if not os.path.exists( "%s_cut" % ( self._bank ) ):
-            self._log.debug("prepare bank '%s'..." % ( self._bank ))
-            prg = os.environ["REPET_PATH"] + "/bin/blaster"
-            cmd = prg
-            cmd += " -s %s" % ( self._bank )
-            cmd += " -n blastn"
-            if self._config.get("detect_features","wublast") == "yes":
-                cmd += " -W"
-            cmd += " -r"
-            cmd += " -P"
-            self._pL.launch( prg, cmd )
-            os.system( "rm -f %s-blastn-*.param" % ( self._bank ) )
-        
-    def createCmdToLaunch( self ):
-        cmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster"
-        cmd += " -q %s" % ( self._inFileName )
-        cmd += " -s %s/%s" % ( self._cDir, self._bank )
-        cmd += " -B %s_BLRn_%s" % ( self._inFileName, self._bank )
-        cmd += " -n blastn"
-        if self._config.get("detect_features","wublast") == "yes":
-            cmd += " -W"
-        cmd += " -r"
-        cmd += " -v 1"
-        cmd += self._launch_2
-    
-        cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, self._bank )
-        cmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
-        cmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName )
-        cmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName )
-        cmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName )
-        cmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, self._bank )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, self._bank )
-    
-        cmd += self._launch_1
-        cmd += os.environ["REPET_PATH"] + "/bin/matcher"
-        cmd += " -m %s_BLRn_%s.align" % ( self._inFileName, self._bank )
-        cmd += " -q %s" % ( self._inFileName )
-        cmd += " -s %s/%s" % ( self._cDir, self._bank )
-        cmd += " -j"
-        cmd += " -v 1"
-        cmd += self._launch_2
-    
-        cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, self._bank )
-        cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
-        cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, self._bank )
-        cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, self._bank )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, self._bank )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, self._bank )
-        cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, self._bank )
-        cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, self._bank )
-    
-        if self._tmpDir != self._cDir:
-            cmd += "if os.path.exists( \"%s\" ):\n" % ( self._bank )
-            cmd += "\tos.remove( \"%s\" )\n" % ( self._bank )
-            
-        return cmd
-    
-    def collectRepbaseBLRn( self ):
-        """
-        Concatenate the outputs of blastn, adapt the ID and load the results into a table.
-        """
-        bankFull = self._bank
-        bankPath, bank = os.path.split( bankFull )
-        self._concatPathFile(bank)
-        self._adaptIDInPathFile(bank)
-        self._loadPathFileInTable(bank)    
-        self._findAndRemoveUselessFiles(bank)
-        
-    def _concatPathFile(self, bank):
-        FileUtils.catFilesByPattern("../batch_*.fa_BLRn_%s.align.clean_match.path" % bank,
-                                        "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank))
-
-    def _adaptIDInPathFile(self, bank):
-        if os.path.exists(os.environ["REPET_PATH"] + "/bin/pathnum2id"):
-            prg = os.environ["REPET_PATH"] + "/bin/pathnum2id"
-            cmd = prg
-            cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
-            cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
-            cmd += " -v %i" % (self._verbose - 1)
-            self._pL.launch(prg, cmd)
-        else:
-            prg = os.environ["REPET_PATH"] + "/bin/pathnum2id.py"
-            cmd = prg
-            cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
-            cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
-            self._pL.launch(prg, cmd)
-
-    def _loadPathFileInTable(self, bank):
-        prg = os.environ["REPET_PATH"] + "/bin/srptCreateTable.py"
-        cmd = prg
-        cmd += " -f %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
-        cmd += " -n %s_TE_BLRn_path" % (self._project)
-        cmd += " -t path"
-        cmd += " -c ../%s" % (self._configFileName)
-        self._pL.launch(prg, cmd)
-
-    def _findAndRemoveUselessFiles(self, bank):
-        prg = "find"
-        cmd = prg
-        cmd += " .. -name \"batch_*.fa_BLRn_%s.*\" -exec rm {} \;" % (bank)
-        self._pL.launch(prg, cmd)
-        prg = "rm"
-        cmd = prg
-        cmd += " %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
-        self._pL.launch(prg, cmd)

--- a/commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,343 +0,0 @@
-import unittest
-import os
-import shutil
-import ConfigParser
-import sys
-from commons.pyRepetUnit.blastnForClassifierStep1.RepbaseBLRnForClassifierStep1 import RepbaseBLRnForClassifierStep1
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.coord.Path import Path
-import pyRepet.launcher.programLauncher
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-NB_EXPECTED_LINES_IN_PATH_FILE = 10
-CURRENT_DIR = os.getcwd()
-
-
-class Test_RepbaseBLRnForClassifierStep1( unittest.TestCase ):
-    
-    
-    def setUp( self ):
-        os.chdir(CURRENT_DIR)
-        self._inFileName = "dummyFileName"
-        self._launch_1 = "log = os.system( \""
-        self._launch_2 = "\" )\n"
-        self._launch_2 += "if log != 0:\n"
-        self._launch_2 += "\tsys.exit(1)\n"
-        self._cDir = "/home/user/dummy_cdir"
-        self._tmpDir = "/home/user/dummy_tmpDir"
-        self._configFileName = "configFile"
-        self._repbaseName = "dummyRepbase_nt.fa"
-        f = open(self._configFileName, "w")
-        f.write("[repet_env]\n")
-        f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
-        f.write("repet_user: %s\n" % os.environ["REPET_USER"])
-        f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
-        f.write("repet_db: %s\n" % os.environ["REPET_DB"])
-        f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
-        f.write("[detect_features]\n")
-        f.write("TE_BLRn: yes\n")
-        f.write("TE_nucl_bank: %s\n" % self._repbaseName)
-        f.write("wublast: yes\n")
-        f.close()
-        self._verbose = 0
-        self._config = ConfigParser.ConfigParser()
-        self._config.readfp( open(self._configFileName) )
-        self._pL = pyRepet.launcher.programLauncher.programLauncher()
-        self._project = "dummyProject"
-        self._repbaseBLRn = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project)
-        self._expFileName = "expFile"
-        self._bank = self._config.get("detect_features","TE_nucl_bank")
-        self._db = DbFactory.createInstance()
-        
-        
-    def tearDown( self ):
-        self._db.dropTable("%s_TE_BLRn_path" % (self._project))
-        os.chdir(CURRENT_DIR)
-        self._repbaseBLRn = None
-        os.remove(self._configFileName)
-        if os.path.isfile("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)):
-            os.remove("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank))
-        if os.path.isfile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)):
-            os.remove("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))
-        if os.path.isfile("batch_1.fa_BLRn_%s.*" % (self._bank)):
-            os.remove("batch_1.fa_BLRn_%s.*" % (self._bank))
-        if os.path.isfile("batch_2.fa_BLRn_%s.*" % (self._bank)):
-            os.remove("batch_2.fa_BLRn_%s.*" % (self._bank))
-        if os.path.isfile("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)):
-            os.remove("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank))
-        if os.path.isfile("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)):
-            os.remove("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank))
-        if os.path.isfile(self._repbaseName):
-            os.remove(self._repbaseName)
-            os.remove(self._repbaseName + "_cut")
-            os.remove(self._repbaseName + "_cut.xnd")
-            os.remove(self._repbaseName + "_cut.xns")
-            os.remove(self._repbaseName + "_cut.xnt")
-            os.remove(self._repbaseName + ".Nstretch.map")
-            os.remove("last_time_stamp.log")
-        if os.path.isdir( "TE_BLRn" ):
-            os.chdir( "TE_BLRn" )
-            os.chdir(CURRENT_DIR)
-            shutil.rmtree("TE_BLRn")
-        if os.path.isfile(self._expFileName):
-            os.remove(self._expFileName)
-            
-            
-    def test_formatRepbase_ntIfNecessaryWithoutLog( self ):
-        f = open(self._repbaseName, "w")
-        f.write(">seq1\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.write(">seq2\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.close()
-        f = open(self._expFileName, "w")
-        f.write(">1  seq1 {Cut} 1..180\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.write(">2  seq2 {Cut} 1..180\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.close()
-        self._repbaseBLRn.formatRepbase_ntIfNecessary()
-        obsFileName = self._repbaseName + "_cut"
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
-        
-        
-    def test_formatRepbase_ntIfNecessary_withLogFile( self ):
-        f = open(self._repbaseName, "w")
-        f.write(">seq1\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.write(">seq2\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.close()
-        f = open(self._expFileName, "w")
-        f.write(">1  seq1 {Cut} 1..180\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.write(">2  seq2 {Cut} 1..180\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
-        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
-        f.close()
-        repbaseBLRnWithLog = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project)
-        repbaseBLRnWithLog.formatRepbase_ntIfNecessary()
-        obsFileName = self._repbaseName + "_cut"
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
-        
-        
-    def test_createCmdToLaunch( self ):
-        bank = self._config.get("detect_features","TE_nucl_bank")
-        obsCmd = self._repbaseBLRn.createCmdToLaunch()
-        expCmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster"
-        expCmd += " -q %s" % ( self._inFileName )
-        expCmd += " -s %s/%s" % ( self._cDir, bank )
-        expCmd += " -B %s_BLRn_%s" % ( self._inFileName, bank )
-        expCmd += " -n blastn"
-        if self._config.get("detect_features","wublast") == "yes":
-            expCmd += " -W"
-        expCmd += " -r"
-        expCmd += " -v 1"
-        expCmd += self._launch_2
-        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, bank )
-        expCmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, bank, self._cDir )
-        expCmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName )
-        expCmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName )
-        expCmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName )
-        expCmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, bank )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, bank )
-        expCmd += self._launch_1
-        expCmd += os.environ["REPET_PATH"] + "/bin/matcher"
-        expCmd += " -m %s_BLRn_%s.align" % ( self._inFileName, bank )
-        expCmd += " -q %s" % ( self._inFileName )
-        expCmd += " -s %s/%s" % ( self._cDir, bank )
-        expCmd += " -j"
-        expCmd += " -v 1"
-        expCmd += self._launch_2
-        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, bank )
-        expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, bank, self._cDir )
-        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, bank )
-        expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, bank, self._cDir )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, bank )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, bank )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, bank )
-        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, bank )
-        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, bank )
-        if self._tmpDir != self._cDir:
-            expCmd += "if os.path.exists( \"%s\" ):\n" % ( bank )
-            expCmd += "\tos.remove( \"%s\" )\n" % ( bank )
-        self.assertEquals( expCmd, obsCmd )
-        
-        
-    def test_concatPathFile( self ):
-        os.chdir(CURRENT_DIR)
-        if not FileUtils.isRessourceExists("TE_BLRn"):
-            os.mkdir( "TE_BLRn" )
-        self._createPathFiles(self._bank)
-        os.chdir( "TE_BLRn" )
-        f = open(self._expFileName, "w")
-        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        FileUtils.sortFileContent(self._expFileName)
-        obsFileName = "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)
-        self._repbaseBLRn._concatPathFile(self._bank)
-        FileUtils.sortFileContent(obsFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
-        
-        
-    def test_adaptIDInPathFile( self ):
-        f = open("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank), "w")
-        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        self._repbaseBLRn._adaptIDInPathFile(self._bank)
-        f = open(self._expFileName, "w")
-        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        obsFileName = "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
-        
-        
-    def test_loadPathFileInTable( self ):
-        os.chdir(CURRENT_DIR)
-        if not FileUtils.isRessourceExists("TE_BLRn"):
-            os.mkdir( "TE_BLRn" )
-        self._createPathFiles(self._bank)
-        os.chdir( "TE_BLRn" )
-        f = open("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank), "w")
-        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        self._repbaseBLRn._loadPathFileInTable(self._bank)
-        resultFromFilePathList = self._readPathResultsFromFileAndFillList()
-        resultFromTablePathList = self._readPathResultsFromTableAndFillList() 
-        self.assertEquals(resultFromFilePathList, resultFromTablePathList)
-        
-        
-    def test_findAndRemoveUselessFiles( self ):
-        self._createFile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))
-        self._createFile("batch_1.fa_BLRn_%s.*" % (self._bank))
-        self._createFile("batch_2.fa_BLRn_%s.*" % (self._bank))
-        self._repbaseBLRn._findAndRemoveUselessFiles(self._bank)
-        self.assertFalse(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)))
-        self.assertFalse(FileUtils.isRessourceExists("batch_1.fa_BLRn_%s.*" % (self._bank)))
-        self.assertFalse(FileUtils.isRessourceExists("batch_2.fa_BLRn_%s.*" % (self._bank)))
-        
-        
-    def test_collectRepbaseBLRn( self ):
-        os.chdir(CURRENT_DIR)
-        if not FileUtils.isRessourceExists("TE_BLRn"):
-            os.mkdir( "TE_BLRn" )
-        self._createPathFiles(self._bank)
-        os.chdir( "TE_BLRn" )
-        self._repbaseBLRn.collectRepbaseBLRn()  
-        self.assertTrue(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank )))
-        self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, FileUtils.getNbLinesInSingleFile("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank )))
-        self.assertTrue(self._db.doesTableExist("%s_TE_BLRn_path" % (self._project)))
-        self._db.execute('select * from %s_TE_BLRn_path' % (self._project))
-        self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, len(self._db.fetchall()))
-        self._db.dropTable("%s_TE_BLRn_path" % (self._project))
-        
-        
-    def _createPathFiles( self, bankFull ):
-        bank = os.path.split(bankFull)[1]
-        fileName = "batch_1.fa_BLRn_" + bank + ".align.clean_match.path"
-        f = open(fileName, "w")
-        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        fileName = "batch_2.fa_BLRn_" + bank + ".align.clean_match.path"
-        f = open(fileName, "w")
-        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
-        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
-        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
-        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
-        f.close()
-        
-        
-    def _readPathResultsFromTableAndFillList( self ):
-        tablePathAdaptatorInstance = TablePathAdaptator (self._db, "%s_TE_BLRn_path" % (self._project))
-        pathList = tablePathAdaptatorInstance.getListOfAllPaths()
-        return pathList
-    
-    
-    def _readPathResultsFromFileAndFillList( self ):
-        pathInstance = Path()
-        pathList = []
-        f = open( "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) , "r")
-        while pathInstance.read( f ):
-            pathList.append(pathInstance)
-            pathInstance = Path()
-        f.close()
-        return pathList
-   
-   
-    def _createFile( self, nameFile ):
-        f = open(nameFile, "w")
-        f.close()
-        
-        
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_RepbaseBLRnForClassifierStep1 ) )
-if __name__ == "__main__":
-    unittest.TextTestRunner(verbosity=2).run( test_suite )

--- a/commons/pyRepetUnit/components/AbstractClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,606 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import getopt
-import time
-import glob
-import sys
-import os
-
-from commons.core.checker.CheckerException import CheckerException
-from commons.core.sql.RepetJob import RepetJob
-from commons.core.sql.Job import Job
-from commons.core.stat.Stat import Stat
-from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
-
-GENERIC_IN_FILE = "zDUMMYz"
-
-
-## Abstract class to launch a program in parallel on a cluster.
-#
-class AbstractClusterLauncher( object ):  #( IClusterLauncher )
-     
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        self._inputDir = ""            # path to the directory with input files
-        self._queueName = ""           # name of the queue on the cluster
-        self._groupId = ""             # identifier of the group of jobs (groupid)
-        self._inputFileSuffix = "fa"   # suffix of the input files (default='fa')
-        self._prgAcronym = ""          # acronym of the program to launch
-        self._configFile = ""          # name of the configuration file (connect to MySQL)
-        self._currentDir = os.getcwd() # path to the current directory
-        self._tmpDir = ""              # path to the temporary directory
-        self._jobTable = "jobs"        # name of the table recording the jobs
-        self._catOutFiles = False      # concatenate output files of all jobs
-        self._clean = False            # clean job file, job stdout, job table...
-        self._verbose = 1              # verbosity level
-        self.jobdb = None              # RepetJob instance
-        self.job = Job()               # Job instance
-        
-        self._nbJobs = 0
-        self._cmdLineGenericOptions = "hi:Q:g:S:a:C:d:j:Zcv:"
-        self._cmdLineSpecificOptions = ""
-        
-        self._exeWrapper = "AbstractProgramLauncher.py"
-        self._prgLauncher = None
-        # list of instances derived from AbstractProgramLauncher()
-        # If several program are launched successively in the same job,
-        # 'lPrgLaunchers' has to be filled before run().
-        self.lPrgLaunchers = []
-    
-    def setProgramLauncherAttributeFromCmdLine(self, o, a=""):
-        self.getProgramLauncherInstance().setASpecificAttributeFromCmdLine(o, a)
-      
-    def setClusterLauncherAttributeFromCmdLine(self, o, a=""):
-        if o == "-h":
-            print self.getHelpAsString()
-            sys.exit(0)
-        elif o == "-i":
-            self.setInputDirectory(a)
-        elif o == "-Q":
-            self.setQueueName(a)
-        elif o == "-g":
-            self.setGroupIdentifier(a)
-        elif o == "-S":
-            self.setInputFileSuffix(a)
-        elif o == "-a":
-            self.setAcronym(a)
-        elif o == "-C":
-            self.setConfigFile(a)
-        elif o == "-d":
-            self.setTemporaryDirectory(a)
-        elif o == "-j":
-            self.setJobTableName(a)
-        elif o == "-Z":
-            self.setCatOutputFiles()
-        elif o == "-c":
-            self.setClean()
-        elif o == "-v":
-            self.setVerbosityLevel(a)
-
-    def setAttributesFromCmdLine(self):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:], self.getCmdLineOptions())
-        except getopt.GetoptError, err:
-            print str(err);
-            print self.getHelpAsString()
-            sys.exit(1)
-        for o, a in opts:
-            self.setClusterLauncherAttributeFromCmdLine(o, a)
-            self.setProgramLauncherAttributeFromCmdLine(o, a)
-    
-    def setAGenericAttributeFromCmdLine( self, o, a="" ):
-        self.setClusterLauncherAttributeFromCmdLine(o, a)
-        
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        self.setProgramLauncherAttributeFromCmdLine(o, a)
-        
-    def setInputDirectory( self, arg ):
-        self._inputDir = arg
-        
-    def setQueueName( self, arg ):
-        self._queueName = arg
-        
-    def setGroupIdentifier( self, arg ):
-        self._groupId = arg
-        
-    def setInputFileSuffix( self, arg ):
-        self._inputFileSuffix = arg
-        
-    def setAcronym( self, arg ):
-        self._prgAcronym = arg
-        
-    def setConfigFile( self, arg ):
-        if os.path.dirname( arg ) == "":
-            self._configFile = "%s/%s" % ( os.getcwd(), arg )
-        else:
-            self._configFile = arg
-            
-    def setCurrentDirectory( self, arg =os.getcwd()):
-        self._currentDir = arg
-        
-    def setTemporaryDirectory( self, arg ):
-        self._tmpDir = arg
-        
-    def setJobTableName( self, arg ):
-        self._jobTable = arg
-
-    def setCatOutputFiles( self ):
-        self._catOutFiles = True
-   
-    def setClean( self):
-        self._clean = True
-        
-    def setVerbosityLevel( self, arg ):
-        self._verbose = int(arg)
-        
-    def setExecutableWrapper( self, arg = "AbstractProgramLauncher.py" ):
-        self._exeWrapper = arg
-
-    def setSingleProgramLauncher( self ):
-        """
-        Set the wrapper and program command-lines of the program launcher.
-        Append the program launcher to 'self.lPrgLaunchers'.
-        """
-        self.getProgramLauncherInstance().setWrapperCommandLine()
-        self.getProgramLauncherInstance().setProgramCommandLine()
-        self.lPrgLaunchers.append( self.getProgramLauncherInstance() )      
-        
-    def getGenericHelpAsString( self ):
-        string = ""
-        string += "usage: %s.py [options]" % (type(self).__name__ )
-        string += "\ngeneric options:"
-        string += "\n     -h: this help"
-        string += "\n     -i: directory with input files (absolute path)"
-        string += "\n     -Q: name of the queue on the cluster"
-        string += "\n     -g: identifier of the group of jobs (groupid)"
-        string += "\n     -S: suffix of the input files (default='fa')"
-        string += "\n     -a: acronym of the program to be launched (default='%s')" % ( self.getAcronym() )
-        string += "\n     -C: configuration file to connect to MySQL (absolute path or in current dir)"
-        string += "\n     -d: temporary directory (absolute path, default=None)"
-        string += "\n     -j: table recording the jobs (default='jobs')"
-        string += "\n     -c: clean the temporary data"
-        string += "\n     -v: verbosity level (default=0/1/2)"
-        return string
-        
-    def getSpecificHelpAsString( self ):
-        pass
-    
-    def getHelpAsString(self):
-        return self.getGenericHelpAsString() + self.getSpecificHelpAsString()
-    
-    def getInputDirectory( self ):
-        return self._inputDir
-        
-    def getQueueName( self ):
-        return self._queueName
-        
-    def getGroupIdentifier( self ):
-        return self._groupId
-        
-    def getInputFileSuffix( self ):
-        return self._inputFileSuffix
-    
-    def getAcronym( self ):
-        return self._prgAcronym
-        
-    def getConfigFile( self ):
-        return self._configFile
-        
-    def getCurrentDirectory( self ):
-        return self._currentDir
-        
-    def getTemporaryDirectory( self ):
-        return self._tmpDir
-        
-    def getJobTableName( self ):
-        return self._jobTable
-    
-    def getCatOutputFiles( self ):
-        return self._catOutFiles
-    
-    def getClean( self ):
-        return self._clean
-        
-    def getVerbosityLevel( self ):
-        return self._verbose
-    
-    def getWrapperName( self ):
-        return self.getProgramLauncherInstance().getWrapperName()
-    
-    def getProgramName( self ):
-        return self.getProgramLauncherInstance().getProgramName()
-    
-    def getPatternToConcatenate( self ):
-        return self.getProgramLauncherInstance().getOutputFile().replace( GENERIC_IN_FILE, "*" )
-    
-    def getProgramLauncherInstance( self ):
-        if self._prgLauncher == None:
-            self._prgLauncher = AbstractProgramLauncher()
-        return self._prgLauncher
-    
-    def getInputFilesList(self):
-        lInFiles = glob.glob("%s/*.%s" % (self._inputDir, self._inputFileSuffix))
-        return lInFiles
-    
-    def getCmdLineOptions(self):
-        return "hi:Q:g:S:a:C:d:j:Zcv:"
-
-                        
-    def getProgramCommandLineAsString( self ):
-        """
-        Return the command-line to launch in each job.
-        Specified in each wrapper.
-        """
-        pass
-    
-    
-    def getListFilesToKeep( self ):
-        """
-        Return the list of files to keep at the end of each job.
-        Specified in each wrapper.
-        """
-        pass
-    
-    
-    def getListFilesToRemove( self ):
-        """
-        Return the list of files to remove at the end of each job.
-        Specified in each wrapper.
-        """
-        pass
-    
-    
-    def getJobFileNameAsString( self, count ):
-        """
-        Return the name of the job file as a string.
-        @param count: job number (e.g. '1') or '*'
-        @type count: integer or string
-        """
-        jobFile = "ClusterLauncher"
-        jobFile += "_groupid%s" % ( self.getGroupIdentifier() )
-        if count != "*":
-            jobFile += "_job%i" % ( count )
-            jobFile += "_time%s" % ( time.strftime("%Y-%m-%d-%H-%M-%S") )
-        else:
-            jobFile += "_job*"
-            jobFile += "_time%s-*" % ( time.strftime("%Y-%m") )
-        jobFile += ".py"
-        return jobFile
-    
-    
-    def getCmdUpdateJobStatusAsString( self, newStatus ):
-        """
-        Return the command to update the job status in the table.
-        """
-        prg = os.environ["REPET_PATH"] + "/bin/srptChangeJobStatus.py"
-        cmd = prg
-        cmd += " -t %s" % ( self.job.tablename )
-        if str(self.job.jobid).isdigit():
-            cmd += " -j %s" % ( self.job.jobname )
-        else:
-            cmd += " -j %s" % ( self.job.jobid )
-        cmd += " -g %s" % ( self.job.groupid )
-        if self.job.queue != "":
-            cmd += " -q %s" % ( self.job.queue )
-        cmd += " -s %s" % ( newStatus )
-        cmd += " -c %s" % ( self.getConfigFile() )
-        cmd += " -v %i" % ( self._verbose )
-        return "os.system( \"%s\" )\n" % ( cmd )
-    
-    
-    def getCmdToLaunchWrapper( self, fileName, genericCmd, exeWrapper ):
-        """
-        Return the launching command as a string.
-        Launch the wrapper, retrieve its exit status, update status if error.
-        """
-        specificCmd = genericCmd.replace( GENERIC_IN_FILE, fileName )
-        cmd = ""
-        cmd += "print \"LAUNCH: %s\"\n" % ( specificCmd )
-        cmd += "sys.stdout.flush()\n"
-        cmd += "exitStatus = os.system ( \"%s\" )\n" % ( specificCmd )
-        cmd += "if exitStatus != 0:\n"
-        cmd += "\tprint \"ERROR: wrapper '%s'" % ( exeWrapper )
-        cmd += " returned exit status '%i'\" % ( exitStatus )\n"
-        cmd += "\tos.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() )
-        cmd += "\tshutil.move( newDir, '%s' )\n" % ( self.getCurrentDirectory() )
-        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
-        cmd += "\tsys.exit(1)\n"
-        return cmd
-    
-    
-    def getCmdToKeepFiles( self, fileName, lFilesToKeep ):
-        """
-        Return the commands to keep the output files.
-        """
-        cmd = ""
-        for f in lFilesToKeep:
-            f = f.replace( GENERIC_IN_FILE, fileName )
-            cmd += "if not os.path.exists( \"%s\" ):\n" % ( f )
-            cmd += "\tprint \"ERROR: output file '%s' doesn't exist\"\n" % ( f )
-            cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
-            cmd += "\tsys.exit(1)\n"
-            cmd += "if not os.path.exists( \"%s/%s\" ):\n" \
-                   % ( self._currentDir, f )
-            cmd += "\tshutil.copy( \"%s\", \"%s/%s\" )\n" % ( f, self.getCurrentDirectory(), f )
-        return cmd
-    
-    
-    def getCmdToRemoveFiles( self, fileName, lFilesToRemove ):
-        """
-        Return the commands to remove the temporary files.
-        """
-        cmd = ""
-        if lFilesToRemove != []:
-            for f in lFilesToRemove:
-                f = f.replace( GENERIC_IN_FILE, fileName )
-                cmd += "if os.path.exists( \"%s\" ):\n" % ( f )
-                cmd += "\tos.remove( \"%s\" )\n" % ( f )
-        return cmd
-    
-    
-    def getJobCommandsAsString( self, fileName, jobName, minFreeGigaInTmpDir=1 ):
-        """
-        Return all the job commands as a string.
-        """
-        cmd = "#!/usr/bin/env python\n"
-        cmd += "\n"
-        cmd += "import os\n"
-        cmd += "import sys\n"
-        cmd += "import shutil\n"
-        cmd += "import time\n"
-        cmd += "\n"
-        cmd += "print \"system:\", os.uname()\n"
-        cmd += "beginTime = time.time()\n"
-        cmd += "print 'beginTime=%f' % ( beginTime )\n"
-        cmd += "\n"
-        cmd += self.getCmdUpdateJobStatusAsString( "running" )
-        cmd += "\n"
-        cmd += "if not os.path.exists( \"%s\" ):\n" % ( self.getTemporaryDirectory() )
-        cmd += "\tprint \"ERROR: working dir '%s' doesn't exist\"\n" % ( \
-            self.getTemporaryDirectory() )
-        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
-        cmd += "\tsys.exit(1)\n"
-        cmd += "freeSpace = os.statvfs( \"%s\" )\n" % ( self.getTemporaryDirectory() )
-        cmd += "if ( freeSpace.f_bavail * freeSpace.f_frsize ) / 1073741824.0 < %i:\n" % ( minFreeGigaInTmpDir ) # nb blocs * bloc size in bytes > 1 GigaByte ?
-        cmd += "\tprint \"ERROR: less than %iGb in '%s'\"\n" % ( minFreeGigaInTmpDir, self.getTemporaryDirectory() )
-        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
-        cmd += "\tsys.exit(1)\n"
-        cmd += "print \"working dir: %s\"\n" % ( self.getTemporaryDirectory() )
-        cmd += "sys.stdout.flush()\n"
-        cmd += "os.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() )
-        cmd += "\n"
-        cmd += "newDir = \"%s_%s_%s\"\n" % ( self.getGroupIdentifier(), jobName, time.strftime("%Y%m%d-%H%M%S") )
-        cmd += "if os.path.exists( newDir ):\n"
-        cmd += "\tshutil.rmtree( newDir )\n"
-        cmd += "os.mkdir( newDir )\n"
-        cmd += "os.chdir( newDir )\n"
-        cmd += "\n"
-        cmd += "if not os.path.exists( \"%s\" ):\n" % ( fileName )
-        cmd += "\tos.symlink( \"%s/%s\", \"%s\" )\n" % \
-               ( self._inputDir, fileName, fileName )
-        cmd += "\n"
-        
-        for pL in self.lPrgLaunchers:
-            cmd += self.getCmdToLaunchWrapper( \
-                fileName, \
-                pL.getWrapperCommandLine(), \
-                "%s.py" % ( type(pL).__name__ ) )
-            cmd += "\n"
-            cmd += self.getCmdToKeepFiles( fileName, pL.getListFilesToKeep() )
-            cmd += "\n"
-            cmd += self.getCmdToRemoveFiles( fileName, \
-                                             pL.getListFilesToRemove() )
-            
-        cmd += "if os.path.exists( \"%s\" ):\n" % ( fileName )
-        cmd += "\tos.remove( \"%s\" )\n" % ( fileName )
-        cmd += "os.chdir( \"..\" )\n"
-        cmd += "shutil.rmtree( newDir )\n"
-        cmd += self.getCmdUpdateJobStatusAsString( "finished" )
-        cmd += "\n"
-        cmd += "endTime = time.time()\n"
-        cmd += "print 'endTime=%f' % ( endTime)\n"
-        cmd += "print 'executionTime=%f' % ( endTime - beginTime )\n"
-        cmd += "print \"system:\", os.uname()\n"
-        cmd += "sys.exit(0)\n"
-        return cmd
-    
-    def getStatsOfExecutionTime( self ):
-        """
-        Return a Stat object about the execution time of each job as a
-        float expressed in seconds since the epoch, in UTC.
-        """
-        stat = Stat()
-        pattern = "%s/%s*.o*" % ( self.getCurrentDirectory(), \
-                                  self.getAcronym() )
-        lJobFiles = glob.glob( pattern )
-        for f in lJobFiles:
-            fH = open( f, "r" )
-            while True:
-                line = fH.readline()
-                if line == "":
-                    break
-                if "executionTime" in line:
-                    stat.add( float(line[:-1].split("=")[1] ) )
-                    break
-            fH.close()
-        return stat
-    
-    
-    def formatGroupidAndTime(self):
-        return self.job.groupid + " " + time.strftime("%Y-%m-%d %H:%M:%S") + ""
-
-    def submitJob(self, lInFiles):
-        count = 0
-        for inFile in lInFiles:
-            count += 1
-            fileName = os.path.basename(inFile)
-            if self._verbose > 1:
-                print "processing '%s' # %i..." % (fileName, count)
-                sys.stdout.flush()
-            
-            self.initializeJob(fileName, count)
-            time.sleep(0.5)
-            exitStatus = self.jobdb.submitJob(self.job)
-            if exitStatus != 0:
-                print "ERROR while submitting job '%i' to the cluster" % (count)
-                sys.exit(1)
-
-    def checkClusterLauncherAttributes( self ):
-        if self.getInputDirectory() == "":
-            message = "ERROR: missing input directory"
-            raise CheckerException(message)
-        if not os.path.exists( self.getInputDirectory() ):
-            message = "ERROR: input directory '%s' doesn't exist" % ( self.getInputDirectory() )
-            raise CheckerException(message)
-        if self.getGroupIdentifier() == "":
-            message = "ERROR: missing group identifier"
-            raise CheckerException(message)
-        if self.getAcronym() == "":
-            message = "ERROR: missing program acronym"
-            raise CheckerException(message)
-        if self.getConfigFile() == "":
-            message = "ERROR: missing config file to access MySQL"
-            raise CheckerException(message)
-        if not os.path.exists( self.getConfigFile() ):
-            message = "ERROR: config file '%s' doesn't exist" % ( self.getConfigFile() )
-            raise CheckerException(message)   
-        if self.getTemporaryDirectory() == "":
-            self.setTemporaryDirectory(self._currentDir)
-    
-    def checkGenericAttributes( self ):
-        self.checkClusterLauncherAttributes()
-        
-    def checkProgramLauncherAttributes( self ):
-        self.getProgramLauncherInstance().checkSpecificAttributes()
-    
-    def checkSpecificAttributes( self ):
-        self.checkProgramLauncherAttributes()
-        
-    def start( self ):
-            
-        if self.lPrgLaunchers == []:
-            self.setSingleProgramLauncher()
-        for pL in self.lPrgLaunchers:
-            if pL.getWrapperCommandLine() == "":
-                string = "ERROR: wrapper command is empty !"
-                print string
-                sys.exit(1)
-            if pL.getProgramCommandLine() == "":
-                string = "ERROR: program command is empty !"
-                print string
-                sys.exit(1)
-        self.checkProgramAvailability()
-        
-        try:
-            self.checkProgramLauncherAttributes()
-        except CheckerException, msg:
-            print msg
-            print self.getHelpAsString()
-            sys.exit(1)
-        
-        if self.getVerbosityLevel() > 0:
-            string = "START %s" % ( type(self).__name__ )
-            print string
-        self.job.tablename = self.getJobTableName()
-        self.job.groupid = self.getGroupIdentifier()
-        tokens = self.getQueueName().replace("'","").split(" ")
-        self.job.setQueue( tokens[0] )
-        if len(tokens) > 1:
-            lResources = tokens[1:]
-            self.job.lResources = lResources
-        if self.getVerbosityLevel() > 0:
-            print "groupid: %s" % ( self.getGroupIdentifier() )
-        self.jobdb = RepetJob( cfgFileName=self.getConfigFile() )
-        if self.jobdb.hasUnfinishedJob( self.job.tablename, \
-                                          self.job.groupid ):
-            self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid )
-            return
-        self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid )
-        sys.stdout.flush()
-   
-    def end( self ):
-        if self.getClean():
-            self.removeAllJobFiles()
-            self.removeAllJobStdouts()
-            self.removeAllJobStderrs()
-            
-        if self.getCatOutputFiles():
-            self.catOutputFiles()
-        
-        self.jobdb.close()
-        
-        if self.getVerbosityLevel() > 0:
-            string = "END %s" % ( type(self).__name__ )
-            print string
-        sys.stdout.flush()
-        
-    def run( self ):
-        try:
-            self.checkClusterLauncherAttributes()
-        except CheckerException, msg:
-            print msg
-            print self.getHelpAsString()
-            sys.exit(1)
-            
-        self.start()
-        
-        lInFiles = self.getInputFilesList()
-        self._nbJobs = len(lInFiles)
-        
-        if self._verbose > 0:
-            string = "submitting " + str(self._nbJobs) +  " jobs... " + self.formatGroupidAndTime() 
-            print string; sys.stdout.flush()
-        
-        self.submitJob(lInFiles)
-        
-        if self._verbose > 0:        
-            string = "waiting for jobs... " + self.formatGroupidAndTime() 
-            print string; sys.stdout.flush()
-        
-        self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid )
-        
-        if self._verbose > 0:
-            string = "all jobs completed ! " + self.formatGroupidAndTime() 
-            print string; sys.stdout.flush()
-            statsExecutionTime = self.getStatsOfExecutionTime()
-            print "execution time of all jobs (seconds): %f" % statsExecutionTime.getSum()
-            print "execution time per job: %s" % statsExecutionTime.string()
-            sys.stdout.flush()
-            
-        self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid )
-        
-        self.end()
-            
-    

--- a/commons/pyRepetUnit/components/AbstractProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-#!/usr/bin/env python
-##@file
-# Abstract class to launch a program.
-
-import getopt
-import sys
-import os
-import pyRepet.launcher.AbstractProgramLauncher
-
-class AbstractProgramLauncher( pyRepet.launcher.AbstractProgramLauncher.AbstractProgramLauncher ):  #( IProgramLauncher )
-    
-    def getHelpAsString( self ):
-        """
-        Return the generic help as a string.
-        """
-        string = ""
-        string += "usage: %s.py [options]" % ( type(self).__name__ )
-        string += "\ngeneric options:"
-        string += "\n     -h: this help"
-        string += "\n     -i: name of the input file (format='%s')" % ( self.getFormatInputFile() )
-        string += "\n     -c: clean"
-        string += "\n     -v: verbosity level (default=0/1)"
-        return string
-    
-    def setAttributesFromCmdLine( self, o, a="" ):
-        """
-        Set a generic attribute from the command-line arguments.
-        """
-        if o == "-h":
-            print self.getHelpAsString()
-            sys.exit(0)
-        elif o == "-i":
-            self.setInputFile( a )
-        elif o == "-c":
-            self.setClean()
-        elif o == "-v":
-            self.setVerbosityLevel( a )
-    
-    def checkAttributesFromCmdLine( self ):
-        """
-        Set the attributes from the command-line arguments.
-        """
-        try:
-            opts, args = getopt.getopt( sys.argv[1:], "%s" % (self.getCmdLineOptions()) )
-        except getopt.GetoptError, err:
-            print str(err);
-            print self.getHelpAsString()
-            sys.exit(1)
-        for o, a in opts:
-            self.setAttributesFromCmdLine( o, a )
-    
-    def getCmdLineOptions(self):
-        return self._cmdLineGenericOptions
-            
-    def check( self ):
-        """
-        Check the generic attributes before running the program.
-        """
-        self._checkProgramName()
-        self.checkInput()
-
-    def checkInput(self):
-        if self.getInputFile() == "":
-            string = "ERROR: missing input file"
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)
-        
-        if not os.path.exists(self.getInputFile()):
-            string = "ERROR: input file '%s' doesn't exist" % (self.getInputFile())
-            print string
-            print self.getHelpAsString()
-            sys.exit(1)

--- a/commons/pyRepetUnit/components/IClusterLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,290 +0,0 @@
-
-## Interface for AbstractClusterLauncher 
-#
-class IClusterLauncher(object):
-    
-    ## Constructor.
-    #
-    def __init__( self ):
-        pass
-    
-    ## Useful commands before running the program (check, open database connector...).
-    #
-    def start(self):
-        pass
-    
-    ## Useful commands after the program was run (clean, close database connector...).
-    #
-    def end(self):
-        pass
-    
-    ## Launch jobs in parallel on each file in the query directory.
-    #
-    def run(self):
-        pass
-    
-    ## Initialize the job (jobname, command, launcher).
-    #
-    def initializeJob(self, fileName, count):
-        pass
-    
-    ## Return all the job commands as a string.
-    #
-    def getJobCommandsAsString(self, fileName, jobName, minFreeGigaInTmpDir=1):
-        pass
-    
-    ## Return the generic help as a string.
-    #
-    def getGenericHelpAsString(self):
-        pass
-    
-    ## Check the generic attributes before running the program.
-    #
-    def checkGenericAttributes(self):
-        pass
-    
-    ## Check the specific attributes of each program launcher.
-    #
-    def checkSpecificAttributes(self):
-        pass
-    
-    ## Check that all required programs are in the user's PATH.
-    #
-    def checkProgramAvailability(self):
-        pass
-    
-    ## Return the command-line to launch in each job. Specified in each wrapper.
-    #
-    def getProgramCommandLineAsString(self):
-        pass
-    
-    ## Return the list of files to keep at the end of each job. Specified in each wrapper.
-    #
-    def getListFilesToKeep(self):
-        pass
-    
-    ## Return the list of files to remove at the end of each job. Specified in each wrapper.
-    #
-    def getListFilesToRemove(self):
-        pass
-    
-    ## Return the name of the job file as a string.
-    #
-    def getJobFileNameAsString(self, count):
-        pass
-    
-    ## Return the command to update the job status in the table.
-    #
-    def getCmdUpdateJobStatusAsString(self, newStatus):
-        pass
-    
-    ## Return the launching command as a string. Launch the wrapper, retrieve its exit status, update status if error.
-    #
-    def getCmdToLaunchWrapper(self, fileName, genericCmd, exeWrapper):
-        pass
-    
-    ## Return the commands to keep the output files.
-    #
-    def getCmdToKeepFiles( self, fileName, lFilesToKeep ):
-        pass
-    
-    ## Return the commands to remove the temporary files.
-    #
-    def getCmdToRemoveFiles( self, fileName, lFilesToRemove ):
-        pass
-    
-    ## Remove all job files.
-    #   
-    def removeAllJobFiles( self ):
-        pass
-            
-    ## Remove all job stdout.
-    # 
-    def removeAllJobStdouts( self ):
-        pass
-            
-    ## Remove all job stderr.
-    #
-    def removeAllJobStderrs( self ):
-        pass
-            
-    ## Process the output file if necessary.
-    #        
-    def processOutputFile( self, tmpFile, outFile ):
-        pass
-        
-    ## Concatenate output files from all jobs.
-    #    
-    def catOutputFiles( self ):
-        pass
-    
-    ## Return the specific help as a string.
-    #
-    def getSpecificHelpAsString( self ):
-        pass
-    
-    ## Return the help as a string.
-    #
-    def getHelpAsString( self ):
-        pass
-    
-    ##Set a generic attribute from the command-line arguments.
-    #
-    def setAGenericAttributeFromCmdLine( self, o, a="" ):
-        pass
-            
-    ## Set the specific attributes from the command-line arguments.
-    #       
-    def setASpecificAttributeFromCmdLine( self, o, a="" ):
-        pass
-        
-    ## Set the attributes from the command-line arguments.
-    #
-    def setAttributesFromCmdLine( self ):
-        pass
-            
-    ## 
-    #        
-    def setInputDirectory( self, arg ):
-        pass
-
-    ## 
-    #
-    def setQueueName( self, arg ):
-        pass
-    
-    ##
-    #    
-    def setGroupIdentifier( self, arg ):
-        pass
-    
-    ##
-    #
-    def setInputFileSuffix( self, arg ):
-        pass
-    
-    ##
-    #   
-    def setAcronym( self, arg ):
-        pass
-    
-    ##
-    #    
-    def setConfigFile( self, arg ):
-        pass
-    
-    ##
-    #        
-    def setCurrentDirectory( self ):
-        pass
-    
-    ##
-    #    
-    def setTemporaryDirectory( self, arg ):
-        pass
-    
-    ##
-    #
-    def setJobTableName( self, arg ):
-        pass
-    
-    ##
-    #
-    def setCatOutputFiles( self ):
-        pass
-    
-    ##
-    #
-    def setClean( self ):
-        pass
-    
-    ##
-    #
-    def setVerbosityLevel( self, arg ):
-        pass
-    
-    ##
-    #
-    def setExecutableWrapper( self, arg ):
-        pass
-    
-    ## Set the wrapper and program command-lines of the program launcher. Append the program launcher to 'self.lPrgLaunchers'.
-    #
-    def setSingleProgramLauncher( self ):
-        pass
-        
-    ##
-    #
-    def getInputDirectory( self ):
-        pass
-    
-    ##
-    #    
-    def getQueueName( self ):
-        pass
-    
-    ##
-    #    
-    def getGroupIdentifier( self ):
-        pass
-    
-    ##
-    #
-    def getInputFileSuffix( self ):
-        pass
-    
-    ##
-    #
-    def getAcronym( self ):
-        pass
-    
-    ##
-    #    
-    def getConfigFile( self ):
-        pass
-    
-    ##
-    #
-    def getCurrentDirectory( self ):
-        pass
-    
-    ##
-    #   
-    def getTemporaryDirectory( self ):
-        pass
-    
-    ##
-    # 
-    def getJobTableName( self ):
-        pass
-    
-    ##
-    #
-    def getCatOutputFiles( self ):
-        pass
-    
-    ##
-    #
-    def getClean( self ):
-        pass
-    
-    ##
-    #
-    def getVerbosityLevel( self ):
-        pass
-    
-    ##
-    #
-    def getWrapperName( self ):
-        pass
-    
-    ##
-    #
-    def getProgramName( self ):
-        pass
-    
-    ##
-    #
-    def getPatternToConcatenate( self ):
-        pass
-    
\ No newline at end of file

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/blastx2GFFTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-import unittest
-import sys
-import Test_BlasterClusterLauncher
-import Test_BlasterProgramLauncher
-import Test_F_BlasterClusterLauncher
-import Test_F_BlasterComponent
-import Test_F_BlasterMatcher2GFF3
-import Test_F_BlasterMatcherComponent
-import Test_F_BlasterProgramLauncher
-
-def main():
-    
-        commonsTestSuite = unittest.TestSuite() 
-        commonsTestSuite.addTest( unittest.makeSuite( Test_BlasterClusterLauncher.Test_BlasterClusterLauncher, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_BlasterProgramLauncher.Test_BlasterProgramLauncher, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterClusterLauncher.Test_F_BlasterClusterLauncher, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterComponent.Test_F_BlasterComponent, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterMatcher2GFF3.Test_F_BlasterMatcher2GFF3, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterMatcherComponent.Test_F_BlasterMatcherComponent, "test" ) )
-        commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterProgramLauncher.Test_F_BlasterProgramLauncher, "test" ) )
-        runner = unittest.TextTestRunner( sys.stderr, 2, 2 )
-        runner.run( commonsTestSuite )
-
-      
-if __name__ == "__main__":
-    main()

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.path	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-1	lm_SuperContig_30_v2	35498	35914	mito_010 NADH dehydrogenase (ubiquinone) chain 5	307	445	1e-62	244	82.73
-1	lm_SuperContig_30_v2	37314	37823	mito_010 NADH dehydrogenase (ubiquinone) chain 5	494	663	8e-67	258	67.65
-161	lm_SuperContig_29_v2	193781	194212	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	228	85	1e-40	84	30.56
-161	lm_SuperContig_29_v2	192832	193704	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	522	229	1e-40	106	23.99
-174	lm_SuperContig_29_v2	78031	78588	xnc164_090 related to multidrug resistance protein	19	209	3e-21	101	30.89

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.tab	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-lm_SuperContig_30_v2	35498	37823	927	0.00598594	1.29469	mito_010	307	663	309	0.431564	8e-67	424	74.4336	1
-lm_SuperContig_29_v2	192832	194212	1305	0.00649448	2.13934	1nc550_030	522	85	438	0.718033	1e-40	99	26.1649	161
-lm_SuperContig_29_v2	78031	78588	558	0.00277695	0.980668	xnc164_090	19	209	191	0.335677	3e-21	101	30.89	174

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/exp_dummy.gff	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-##gff-version 3
-lm_SuperContig_30_v2	blastx_ProtBank	match	35498	37823	8e-67	+	.	ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001;Target=mito_010+307+663;Name=lm_SuperContig_30_v2_mito_010;target_pcover=43.15;target_pident=74.43;evalue=8e-67;target_description=NADH dehydrogenase (ubiquinone) chain 5;target_length=716;lib=BlastBank;program=blastx
-lm_SuperContig_30_v2	blastx_ProtBank	match_part	35498	35914	1e-62	+	0	ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001mp0001;Target=mito_010+307+445;Parent=BlastBank_lm_SuperContig_30_v2_mito_010_m0001
-lm_SuperContig_30_v2	blastx_ProtBank	match_part	37314	37823	8e-67	+	2	ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001mp0002;Target=mito_010+494+663;Parent=BlastBank_lm_SuperContig_30_v2_mito_010_m0001
-lm_SuperContig_29_v2	blastx_ProtBank	match	192832	194212	1e-40	-	.	ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002;Target=1nc550_030+85+522;Name=lm_SuperContig_30_v2_1nc550_030;target_pcover=71.80;target_pident=26.16;evalue=1e-40;target_description=related to putative multidrug transporter Mfs1.1 (major facilitator family protein);target_length=610;lib=BlastBank;program=blastx
-lm_SuperContig_29_v2	blastx_ProtBank	match_part	193781	194212	1e-40	-	0	ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002mp0002;Target=1nc550_030+85+228;Parent=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002
-lm_SuperContig_29_v2	blastx_ProtBank	match_part	192832	193704	1e-40	-	2	ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002mp0001;Target=1nc550_030+229+522;Parent=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002
-lm_SuperContig_29_v2	blastx_ProtBank	match	78031	78588	3e-21	+	.	ID=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003;Target=xnc164_090+19+209;Name=lm_SuperContig_30_v2_xnc164;target_pcover=33.56;target_pident=30.89;evalue=3e-21;target_description=related to multidrug resistance protein;target_length=569;lib=BlastBank;program=blastx
-lm_SuperContig_29_v2	blastx_ProtBank	match_part	78031	78588	3e-21	+	1	ID=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003mp0001;Target=xnc164_090+19+209;Parent=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003
\ No newline at end of file

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,456 +0,0 @@
-lm_SuperContig_30_v2	23817	24089	mito_010 NADH dehydrogenase (ubiquinone) chain 5	1	91	7e-25	119	63.74
-lm_SuperContig_30_v2	27615	28001	mito_010 NADH dehydrogenase (ubiquinone) chain 5	109	237	1e-53	214	77.52
-lm_SuperContig_30_v2	29503	29673	mito_010 NADH dehydrogenase (ubiquinone) chain 5	254	310	3e-21	107	92.98
-lm_SuperContig_30_v2	35498	35914	mito_010 NADH dehydrogenase (ubiquinone) chain 5	307	445	1e-62	244	82.73
-lm_SuperContig_30_v2	37314	37823	mito_010 NADH dehydrogenase (ubiquinone) chain 5	494	663	8e-67	258	67.65
-lm_SuperContig_30_v2	23817	24089	mito_020 predicted ND5 intron 2 protein	1	91	7e-25	119	63.74
-lm_SuperContig_30_v2	27615	28001	mito_020 predicted ND5 intron 2 protein	109	237	1e-53	214	77.52
-lm_SuperContig_30_v2	28681	29418	mito_020 predicted ND5 intron 2 protein	303	540	4e-37	159	41.2
-lm_SuperContig_30_v2	94306	95085	mito_020 predicted ND5 intron 2 protein	544	279	2e-22	110	28.46
-lm_SuperContig_30_v2	18181	19317	mito_030 predicted ND5 intron 1 protein	167	528	3e-57	226	37.76
-lm_SuperContig_30_v2	22437	23375	mito_030 predicted ND5 intron 1 protein	219	528	1e-43	181	32.59
-lm_SuperContig_30_v2	23817	24089	mito_030 predicted ND5 intron 1 protein	1	91	7e-25	119	63.74
-lm_SuperContig_30_v2	26190	27509	mito_030 predicted ND5 intron 1 protein	84	525	0	666	76.52
-lm_SuperContig_30_v2	32527	33390	mito_030 predicted ND5 intron 1 protein	236	518	6e-40	169	36.15
-lm_SuperContig_30_v2	35963	37213	mito_030 predicted ND5 intron 1 protein	114	525	4e-62	242	38.08
-lm_SuperContig_30_v2	55780	56187	mito_030 predicted ND5 intron 1 protein	492	357	1e-34	96	36.96
-lm_SuperContig_30_v2	56292	56582	mito_030 predicted ND5 intron 1 protein	351	255	1e-34	74	38.78
-lm_SuperContig_30_v2	61805	62656	mito_030 predicted ND5 intron 1 protein	528	241	3e-55	219	38.89
-lm_SuperContig_30_v2	63837	64676	mito_030 predicted ND5 intron 1 protein	511	232	1e-35	155	35.21
-lm_SuperContig_30_v2	80861	81706	mito_030 predicted ND5 intron 1 protein	525	242	5e-44	182	35.66
-lm_SuperContig_30_v2	82749	83615	mito_030 predicted ND5 intron 1 protein	525	236	3e-47	193	35.27
-lm_SuperContig_30_v2	86928	87770	mito_030 predicted ND5 intron 1 protein	525	242	3e-47	193	36.14
-lm_SuperContig_30_v2	90399	91238	mito_030 predicted ND5 intron 1 protein	528	249	1e-37	161	32.52
-lm_SuperContig_30_v2	109092	109925	mito_030 predicted ND5 intron 1 protein	525	243	2e-49	200	38.16
-lm_SuperContig_30_v2	115228	116103	mito_030 predicted ND5 intron 1 protein	236	528	6e-48	195	35.93
-lm_SuperContig_30_v2	116645	117925	mito_030 predicted ND5 intron 1 protein	121	526	6e-60	235	37.12
-lm_SuperContig_30_v2	117965	119308	mito_030 predicted ND5 intron 1 protein	87	525	1e-63	248	35.79
-lm_SuperContig_30_v2	141039	141308	mito_030 predicted ND5 intron 1 protein	250	342	8e-47	58	34.41
-lm_SuperContig_30_v2	141292	141858	mito_030 predicted ND5 intron 1 protein	337	525	8e-47	155	42.11
-lm_SuperContig_30_v2	146223	147503	mito_030 predicted ND5 intron 1 protein	114	528	2e-64	250	37.61
-lm_SuperContig_30_v2	149559	149744	mito_030 predicted ND5 intron 1 protein	233	296	6e-40	41	35.94
-lm_SuperContig_30_v2	149749	150444	mito_030 predicted ND5 intron 1 protein	299	530	6e-40	149	37.02
-lm_SuperContig_30_v2	150994	152199	mito_030 predicted ND5 intron 1 protein	121	525	4e-58	229	36.3
-lm_SuperContig_30_v2	21984	22220	mito_040 NADH dehydrogenase (ubiquinone) chain 4L	1	79	3e-30	136	84.81
-lm_SuperContig_30_v2	18466	19329	mito_050 predicted ND4L intron protein	145	438	6e-54	215	40.53
-lm_SuperContig_30_v2	21984	22229	mito_050 predicted ND4L intron protein	1	82	8e-31	138	82.93
-lm_SuperContig_30_v2	22509	23387	mito_050 predicted ND4L intron protein	145	438	7e-81	305	49
-lm_SuperContig_30_v2	26661	27530	mito_050 predicted ND4L intron protein	145	438	1e-43	181	35.67
-lm_SuperContig_30_v2	32542	33390	mito_050 predicted ND4L intron protein	145	424	6e-43	179	38.91
-lm_SuperContig_30_v2	36323	37234	mito_050 predicted ND4L intron protein	145	438	4e-49	199	40.39
-lm_SuperContig_30_v2	61793	62650	mito_050 predicted ND4L intron protein	438	145	3e-49	200	40.33
-lm_SuperContig_30_v2	63768	64748	mito_050 predicted ND4L intron protein	438	111	4e-45	186	37.09
-lm_SuperContig_30_v2	80849	81703	mito_050 predicted ND4L intron protein	435	145	1e-45	188	39.6
-lm_SuperContig_30_v2	82737	83594	mito_050 predicted ND4L intron protein	435	145	1e-45	188	37.46
-lm_SuperContig_30_v2	86916	87767	mito_050 predicted ND4L intron protein	435	145	4e-45	186	36.49
-lm_SuperContig_30_v2	90387	91259	mito_050 predicted ND4L intron protein	438	144	2e-39	167	33.33
-lm_SuperContig_30_v2	109071	109925	mito_050 predicted ND4L intron protein	438	145	7e-42	175	35.67
-lm_SuperContig_30_v2	115249	116115	mito_050 predicted ND4L intron protein	145	438	1e-43	181	38.41
-lm_SuperContig_30_v2	117050	117943	mito_050 predicted ND4L intron protein	145	438	1e-42	178	37.62
-lm_SuperContig_30_v2	118442	119320	mito_050 predicted ND4L intron protein	145	435	3e-44	183	38.64
-lm_SuperContig_30_v2	141021	141260	mito_050 predicted ND4L intron protein	146	228	6e-38	52	40.96
-lm_SuperContig_30_v2	141295	141879	mito_050 predicted ND4L intron protein	241	438	6e-38	131	39.51
-lm_SuperContig_30_v2	146610	147515	mito_050 predicted ND4L intron protein	149	438	4e-37	159	34.18
-lm_SuperContig_30_v2	149583	149747	mito_050 predicted ND4L intron protein	145	199	3e-39	58	47.27
-lm_SuperContig_30_v2	149743	150450	mito_050 predicted ND4L intron protein	199	438	3e-39	130	35.34
-lm_SuperContig_30_v2	151234	152220	mito_050 predicted ND4L intron protein	118	438	2e-35	154	34.72
-lm_SuperContig_30_v2	53343	53696	mito_060 probable NADH dehydrogenase (ubiquinone) chain 3	117	1	2e-26	121	50
-lm_SuperContig_30_v2	5079	5582	mito_080 NADH dehydrogenase (ubiquinone) chain 2	403	582	7e-41	172	49.73
-lm_SuperContig_30_v2	53703	54143	mito_080 NADH dehydrogenase (ubiquinone) chain 2	582	425	3e-30	134	46.91
-lm_SuperContig_30_v2	55010	55561	mito_080 NADH dehydrogenase (ubiquinone) chain 2	423	242	1e-47	191	57.22
-lm_SuperContig_30_v2	59011	59799	mito_080 NADH dehydrogenase (ubiquinone) chain 2	271	1	1e-68	264	52.71
-lm_SuperContig_30_v2	64707	65165	mito_110 cytochrome-c oxidase chain III	227	74	2e-55	220	68.18
-lm_SuperContig_30_v2	103508	103711	mito_150 H+-transporting ATP synthase protein 6	261	194	7e-26	122	85.29
-lm_SuperContig_30_v2	108494	108691	mito_150 H+-transporting ATP synthase protein 6	179	114	3e-23	113	77.27
-lm_SuperContig_30_v2	110007	110387	mito_150 H+-transporting ATP synthase protein 6	134	6	2e-31	140	54.96
-lm_SuperContig_30_v2	17614	18054	mito_170 probable NADH dehydrogenase (ubiquinone) chain 4	83	229	3e-56	223	70.75
-lm_SuperContig_30_v2	19465	20481	mito_170 probable NADH dehydrogenase (ubiquinone) chain 4	195	536	3e-130	469	67.54
-lm_SuperContig_30_v2	17614	19341	mito_180 predicted ND4 intron protein	83	666	0	664	57.81
-lm_SuperContig_30_v2	22509	23405	mito_180 predicted ND4 intron protein	372	668	3e-57	226	39
-lm_SuperContig_30_v2	26640	27542	mito_180 predicted ND4 intron protein	365	666	9e-53	211	40.46
-lm_SuperContig_30_v2	32542	33390	mito_180 predicted ND4 intron protein	372	648	6e-64	248	44.14
-lm_SuperContig_30_v2	36329	37252	mito_180 predicted ND4 intron protein	374	668	2e-62	243	43.91
-lm_SuperContig_30_v2	42209	42388	mito_180 predicted ND4 intron protein	319	380	2e-21	26	30.16
-lm_SuperContig_30_v2	42457	42879	mito_180 predicted ND4 intron protein	384	528	2e-21	101	37.24
-lm_SuperContig_30_v2	55774	56199	mito_180 predicted ND4 intron protein	624	480	9e-27	79	32.41
-lm_SuperContig_30_v2	56307	56585	mito_180 predicted ND4 intron protein	473	383	9e-27	64	43.01
-lm_SuperContig_30_v2	61781	62653	mito_180 predicted ND4 intron protein	666	371	3e-63	246	42.62
-lm_SuperContig_30_v2	63756	64718	mito_180 predicted ND4 intron protein	666	347	2e-57	227	42.25
-lm_SuperContig_30_v2	80825	81706	mito_180 predicted ND4 intron protein	667	371	1e-57	228	41.28
-lm_SuperContig_30_v2	82716	83615	mito_180 predicted ND4 intron protein	666	365	1e-60	237	41.45
-lm_SuperContig_30_v2	86895	87770	mito_180 predicted ND4 intron protein	666	371	4e-57	226	41.47
-lm_SuperContig_30_v2	90384	91256	mito_180 predicted ND4 intron protein	663	372	4e-43	179	32.55
-lm_SuperContig_30_v2	109059	109979	mito_180 predicted ND4 intron protein	666	354	3e-58	229	37.7
-lm_SuperContig_30_v2	115189	116127	mito_180 predicted ND4 intron protein	352	666	8e-59	231	37.85
-lm_SuperContig_30_v2	117050	117955	mito_180 predicted ND4 intron protein	372	666	9e-54	215	41.5
-lm_SuperContig_30_v2	118439	119344	mito_180 predicted ND4 intron protein	371	667	3e-54	216	41.56
-lm_SuperContig_30_v2	125743	126138	mito_180 predicted ND4 intron protein	384	515	4e-23	113	41.67
-lm_SuperContig_30_v2	141030	141308	mito_180 predicted ND4 intron protein	376	469	3e-54	65	38.3
-lm_SuperContig_30_v2	141292	141897	mito_180 predicted ND4 intron protein	464	668	3e-54	173	43.9
-lm_SuperContig_30_v2	146610	147527	mito_180 predicted ND4 intron protein	376	666	6e-48	195	39.23
-lm_SuperContig_30_v2	149580	149747	mito_180 predicted ND4 intron protein	371	426	7e-54	59	44.64
-lm_SuperContig_30_v2	149743	150465	mito_180 predicted ND4 intron protein	425	667	7e-54	178	39.18
-lm_SuperContig_30_v2	151309	152232	mito_180 predicted ND4 intron protein	369	666	3e-50	203	40.76
-lm_SuperContig_30_v2	44197	44541	mito_190 NADH dehydrogenase (ubiquinone) chain 1	98	212	3e-43	180	76.52
-lm_SuperContig_30_v2	46832	47305	mito_190 NADH dehydrogenase (ubiquinone) chain 1	213	370	5e-44	182	59.01
-lm_SuperContig_30_v2	89139	89414	mito_210 cytochrome-c oxidase chain I	533	442	1e-22	111	58.7
-lm_SuperContig_30_v2	89713	89913	mito_210 cytochrome-c oxidase chain I	441	375	6e-24	116	79.1
-lm_SuperContig_30_v2	93858	94202	mito_210 cytochrome-c oxidase chain I	364	250	6e-51	205	87.83
-lm_SuperContig_30_v2	102101	102604	mito_210 cytochrome-c oxidase chain I	169	2	4e-74	282	80.36
-lm_SuperContig_30_v2	6405	6605	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	1	67	2e-23	114	76.12
-lm_SuperContig_30_v2	9733	9936	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	68	136	2e-27	127	89.86
-lm_SuperContig_30_v2	14626	15192	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	194	384	8e-78	295	73.82
-lm_SuperContig_30_v2	15860	16315	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	228	384	3e-37	160	56.25
-lm_SuperContig_30_v2	6405	6605	mito_230 related to cob intron2 maturase/endonuclease	1	67	2e-23	114	76.12
-lm_SuperContig_30_v2	9733	9936	mito_230 related to cob intron2 maturase/endonuclease	68	136	2e-27	127	89.86
-lm_SuperContig_30_v2	6405	6605	mito_240 related to cob intron1 maturase	1	67	2e-23	114	76.12
-lm_SuperContig_30_v2	9733	9927	mito_240 related to cob intron1 maturase	68	132	6e-27	126	90.77
-lm_SuperContig_30_v2	18442	19341	mito_155 predicted ATP6 intron maturase	56	357	3e-68	263	45.07
-lm_SuperContig_30_v2	22509	23387	mito_155 predicted ATP6 intron maturase	64	353	2e-37	161	31.19
-lm_SuperContig_30_v2	26607	27542	mito_155 predicted ATP6 intron maturase	46	357	7e-50	202	37.34
-lm_SuperContig_30_v2	32494	33504	mito_155 predicted ATP6 intron maturase	46	360	4e-52	209	37.64
-lm_SuperContig_30_v2	36323	37249	mito_155 predicted ATP6 intron maturase	64	358	2e-63	247	45.02
-lm_SuperContig_30_v2	61781	62650	mito_155 predicted ATP6 intron maturase	357	64	2e-58	230	41.75
-lm_SuperContig_30_v2	63756	64655	mito_155 predicted ATP6 intron maturase	357	60	1e-47	194	38.64
-lm_SuperContig_30_v2	80828	81703	mito_155 predicted ATP6 intron maturase	357	64	3e-51	206	39.6
-lm_SuperContig_30_v2	82716	83594	mito_155 predicted ATP6 intron maturase	357	64	1e-50	204	38.8
-lm_SuperContig_30_v2	86895	87767	mito_155 predicted ATP6 intron maturase	357	64	7e-50	202	37.92
-lm_SuperContig_30_v2	90381	91256	mito_155 predicted ATP6 intron maturase	355	64	8e-32	142	31
-lm_SuperContig_30_v2	109056	110081	mito_155 predicted ATP6 intron maturase	358	11	4e-91	338	51.85
-lm_SuperContig_30_v2	115198	116127	mito_155 predicted ATP6 intron maturase	47	357	1e-50	204	37.78
-lm_SuperContig_30_v2	116981	117955	mito_155 predicted ATP6 intron maturase	36	357	4e-53	213	37.01
-lm_SuperContig_30_v2	118442	119341	mito_155 predicted ATP6 intron maturase	64	357	7e-42	175	35.5
-lm_SuperContig_30_v2	125740	126240	mito_155 predicted ATP6 intron maturase	75	237	3e-30	136	46.11
-lm_SuperContig_30_v2	141021	141311	mito_155 predicted ATP6 intron maturase	65	161	2e-51	79	42.86
-lm_SuperContig_30_v2	141292	141891	mito_155 predicted ATP6 intron maturase	155	357	2e-51	150	40
-lm_SuperContig_30_v2	146610	147533	mito_155 predicted ATP6 intron maturase	68	359	2e-52	210	42.22
-lm_SuperContig_30_v2	149583	149747	mito_155 predicted ATP6 intron maturase	64	117	6e-49	55	45.45
-lm_SuperContig_30_v2	149746	150462	mito_155 predicted ATP6 intron maturase	117	357	6e-49	165	38.93
-lm_SuperContig_30_v2	151258	152232	mito_155 predicted ATP6 intron maturase	42	357	2e-52	210	39.34
-lm_SuperContig_30_v2	44996	45490	mito_195 predicted ND1 intron protein	39	206	3e-48	196	57.74
-lm_SuperContig_30_v2	45636	45911	mito_195 predicted ND1 intron protein	209	300	2e-21	107	58.7
-lm_SuperContig_30_v2	46058	46228	mito_195 predicted ND1 intron protein	44	100	1e-70	58	51.72
-lm_SuperContig_30_v2	46230	46769	mito_195 predicted ND1 intron protein	101	304	1e-70	235	58.54
-lm_SuperContig_30_v2	14662	15189	SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual	206	381	1e-42	178	48.86
-lm_SuperContig_30_v2	15941	16303	SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual	260	378	1e-22	111	48.76
-lm_SuperContig_30_v2	64752	65204	SPMIT.04 |cox3||cytochrome c oxidase 3|Schizosaccharomyces pombe|chr mitochondrial|||Manual	215	65	2e-34	150	50.98
-lm_SuperContig_30_v2	94345	95262	SPMIT.03 |||hypothetical protein|Schizosaccharomyces pombe|chr mitochondrial||Partial|Manual	312	3	1e-94	350	57.68
-lm_SuperContig_30_v2	93876	94202	SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual	360	251	3e-30	136	58.56
-lm_SuperContig_30_v2	102098	102580	SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual	171	10	3e-48	196	54.94
-lm_SuperContig_29_v2	77989	78369	Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	3	126	2e-22	105	40.94
-lm_SuperContig_29_v2	193985	194365	Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	126	3	1e-21	105	40.94
-lm_SuperContig_29_v2	78109	78582	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	20	177	7e-59	207	58.86
-lm_SuperContig_29_v2	78662	78817	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	180	231	7e-59	42	30.77
-lm_SuperContig_29_v2	192760	193692	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	485	180	2e-128	275	41.8
-lm_SuperContig_29_v2	193772	194245	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	177	20	2e-128	207	58.86
-lm_SuperContig_29_v2	78010	78567	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	21	208	5e-23	100	29.79
-lm_SuperContig_29_v2	78662	78808	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	216	261	5e-23	28	26.53
-lm_SuperContig_29_v2	192766	193692	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	535	216	3e-40	88	22.53
-lm_SuperContig_29_v2	193787	194344	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	208	21	3e-40	100	29.79
-lm_SuperContig_29_v2	78109	78588	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	45	204	1e-39	144	43.75
-lm_SuperContig_29_v2	78662	78817	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	205	258	1e-39	40	45.61
-lm_SuperContig_29_v2	192754	193692	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	521	205	2e-83	188	33.33
-lm_SuperContig_29_v2	193766	194245	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	204	45	2e-83	144	43.75
-lm_SuperContig_29_v2	78061	78573	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	15	189	3e-22	87	29.71
-lm_SuperContig_29_v2	78662	78814	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	195	242	3e-22	39	39.22
-lm_SuperContig_29_v2	192760	193692	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	506	195	1e-49	133	27.85
-lm_SuperContig_29_v2	193781	194293	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	189	15	1e-49	87	29.71
-lm_SuperContig_29_v2	78007	78576	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	48	237	2e-59	198	47.37
-lm_SuperContig_29_v2	78662	78817	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	242	293	2e-59	52	46.15
-lm_SuperContig_29_v2	193288	193692	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	375	242	1e-79	122	43.7
-lm_SuperContig_29_v2	193778	194347	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	237	48	1e-79	198	47.37
-lm_SuperContig_29_v2	78133	78576	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	77	224	2e-44	159	51.35
-lm_SuperContig_29_v2	78662	78817	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	229	282	2e-44	41	41.07
-lm_SuperContig_29_v2	192760	193692	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	541	229	3e-91	200	35.65
-lm_SuperContig_29_v2	193778	194221	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	224	77	3e-91	159	51.35
-lm_SuperContig_29_v2	10942	11625	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	1	2e-29	132	35.06
-lm_SuperContig_29_v2	16462	17082	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	208	2	4e-30	135	37.2
-lm_SuperContig_29_v2	31597	31836	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	147	6e-25	46	33.73
-lm_SuperContig_29_v2	31868	32272	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	136	4	6e-25	95	38.52
-lm_SuperContig_29_v2	41484	42080	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	8e-32	142	38.69
-lm_SuperContig_29_v2	91888	92562	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	4	3e-27	126	35.53
-lm_SuperContig_29_v2	101404	102000	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	3e-31	140	38.69
-lm_SuperContig_29_v2	133669	134343	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	226	2	3e-37	159	37.78
-lm_SuperContig_29_v2	167776	168372	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	9e-34	145	38.69
-lm_SuperContig_29_v2	178590	179264	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	4	1e-29	133	35.96
-lm_SuperContig_29_v2	78184	78585	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	53	186	2e-25	96	35.07
-lm_SuperContig_29_v2	78644	78814	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	186	239	2e-25	41	40.35
-lm_SuperContig_29_v2	192964	193710	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	430	186	3e-59	156	35.74
-lm_SuperContig_29_v2	193769	194170	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	186	53	3e-59	96	35.07
-lm_SuperContig_29_v2	78049	78567	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	19	191	3e-23	101	27.75
-lm_SuperContig_29_v2	78659	78775	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	198	236	3e-23	28	28.21
-lm_SuperContig_29_v2	192904	193695	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	459	198	9e-43	96	26.12
-lm_SuperContig_29_v2	193787	194305	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	191	19	9e-43	101	27.75
-lm_SuperContig_29_v2	78151	78576	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	93	235	3e-31	124	41.96
-lm_SuperContig_29_v2	78662	78814	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	242	293	3e-31	32	30.77
-lm_SuperContig_29_v2	192760	193692	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	552	242	6e-83	207	32.69
-lm_SuperContig_29_v2	193778	194203	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	235	93	6e-83	124	41.96
-lm_SuperContig_29_v2	78109	78576	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	34	189	3e-49	169	50
-lm_SuperContig_29_v2	78650	78814	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	190	245	3e-49	48	35.71
-lm_SuperContig_29_v2	192772	193704	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	501	190	2e-97	210	32.27
-lm_SuperContig_29_v2	193778	194245	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	189	34	2e-97	169	50
-lm_SuperContig_29_v2	78115	78576	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	51	204	6e-62	204	58.44
-lm_SuperContig_29_v2	78662	78817	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	209	260	6e-62	55	40.38
-lm_SuperContig_29_v2	192754	193692	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	520	209	1e-132	293	43.77
-lm_SuperContig_29_v2	193778	194239	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	204	51	1e-132	204	58.44
-lm_SuperContig_29_v2	192868	193695	Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92	482	201	1e-31	70	21.48
-lm_SuperContig_29_v2	193784	194323	Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92	195	16	1e-31	89	25
-lm_SuperContig_29_v2	193303	193707	fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5	308	174	6e-29	54	28.06
-lm_SuperContig_29_v2	193793	194221	fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5	169	27	6e-29	97	32.87
-lm_SuperContig_29_v2	192877	193695	fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168	483	215	7e-40	109	24.18
-lm_SuperContig_29_v2	193784	194221	fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168	205	60	7e-40	78	27.4
-lm_SuperContig_29_v2	77956	78576	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	2	220	7e-35	126	34.25
-lm_SuperContig_29_v2	78650	78814	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	221	272	7e-35	42	34.55
-lm_SuperContig_29_v2	192883	193704	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	490	221	7e-62	135	29.2
-lm_SuperContig_29_v2	193778	194398	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	220	2	7e-62	126	34.25
-lm_SuperContig_29_v2	78124	78576	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	62	212	4e-45	166	52.32
-lm_SuperContig_29_v2	78662	78718	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	217	236	4e-45	36	65
-lm_SuperContig_29_v2	192769	193692	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	537	217	1e-92	197	32.61
-lm_SuperContig_29_v2	193778	194230	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	212	62	1e-92	166	52.32
-lm_SuperContig_29_v2	193222	193707	fg12717 related to putative multidrug transporter, Contig fg_contig_1.37	402	218	2e-26	66	25
-lm_SuperContig_29_v2	193778	194383	fg12717 related to putative multidrug transporter, Contig fg_contig_1.37	219	15	2e-26	76	25.85
-lm_SuperContig_29_v2	193036	193695	b13o8_150 conserved hypothetical protein	460	238	3e-31	73	23.35
-lm_SuperContig_29_v2	193784	194248	b13o8_150 conserved hypothetical protein	232	73	3e-31	85	28.12
-lm_SuperContig_29_v2	78010	78585	b18d24_100 related to tetracycline efflux protein (otrb)	9	199	2e-27	99	28.12
-lm_SuperContig_29_v2	78644	78814	b18d24_100 related to tetracycline efflux protein (otrb)	197	250	2e-27	43	42.11
-lm_SuperContig_29_v2	192916	193710	b18d24_100 related to tetracycline efflux protein (otrb)	457	197	4e-60	155	33.96
-lm_SuperContig_29_v2	193769	194344	b18d24_100 related to tetracycline efflux protein (otrb)	199	9	4e-60	99	28.12
-lm_SuperContig_29_v2	78184	78576	b5k2_230 related to major facilitator (MFS1) transporter	211	341	4e-42	141	50.38
-lm_SuperContig_29_v2	78662	78814	b5k2_230 related to major facilitator (MFS1) transporter	346	396	4e-42	51	49.06
-lm_SuperContig_29_v2	192760	193692	b5k2_230 related to major facilitator (MFS1) transporter	657	346	7e-99	243	38.1
-lm_SuperContig_29_v2	193778	194170	b5k2_230 related to major facilitator (MFS1) transporter	341	211	7e-99	141	50.38
-lm_SuperContig_29_v2	192832	193704	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	522	229	1e-40	106	23.99
-lm_SuperContig_29_v2	193781	194212	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	228	85	1e-40	84	30.56
-lm_SuperContig_29_v2	77941	78576	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	28	241	1e-30	111	28.97
-lm_SuperContig_29_v2	78662	78736	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	246	270	1e-30	42	56
-lm_SuperContig_29_v2	192760	193692	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	559	246	5e-62	149	28.3
-lm_SuperContig_29_v2	193778	194413	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	241	28	5e-62	111	28.97
-lm_SuperContig_29_v2	192817	193695	6nc360_090 related to DHA14-like major facilitator	491	194	8e-44	132	28.9
-lm_SuperContig_29_v2	193778	194086	6nc360_090 related to DHA14-like major facilitator	188	86	8e-44	69	38.83
-lm_SuperContig_29_v2	78112	78576	29e8_240 probable aflatoxin efflux pump AFLT	62	216	1e-56	190	55.48
-lm_SuperContig_29_v2	78662	78817	29e8_240 probable aflatoxin efflux pump AFLT	221	272	1e-56	50	40.38
-lm_SuperContig_29_v2	192769	193692	29e8_240 probable aflatoxin efflux pump AFLT	535	221	2e-117	256	41.14
-lm_SuperContig_29_v2	193778	194242	29e8_240 probable aflatoxin efflux pump AFLT	216	62	2e-117	190	55.48
-lm_SuperContig_29_v2	192940	193695	7nc450_010 related to multidrug resistance protein	484	228	3e-24	79	25
-lm_SuperContig_29_v2	193787	194218	7nc450_010 related to multidrug resistance protein	221	78	3e-24	57	20.83
-lm_SuperContig_29_v2	192865	193692	4nc446_010 related to putative multidrug transporter	530	259	3e-48	134	28.26
-lm_SuperContig_29_v2	193781	194218	4nc446_010 related to putative multidrug transporter	253	106	3e-48	82	29.73
-lm_SuperContig_29_v2	192904	193704	b11e5_230 related to multidrug resistance protein fnx1	518	253	1e-40	93	25.27
-lm_SuperContig_29_v2	193766	194239	b11e5_230 related to multidrug resistance protein fnx1	254	97	1e-40	97	29.75
-lm_SuperContig_29_v2	77935	78576	xnc126_050 probable DHA14-like major facilitator; ABC transporter	38	241	7e-60	190	46.26
-lm_SuperContig_29_v2	78662	78817	xnc126_050 probable DHA14-like major facilitator; ABC transporter	246	298	7e-60	62	43.4
-lm_SuperContig_29_v2	192757	193692	xnc126_050 probable DHA14-like major facilitator; ABC transporter	559	246	2e-130	299	45.08
-lm_SuperContig_29_v2	193778	194419	xnc126_050 probable DHA14-like major facilitator; ABC transporter	241	38	2e-130	190	46.26
-lm_SuperContig_29_v2	78109	78576	4nc135_070 related to aflatoxin efflux pump AFLT	17	172	2e-53	184	53.85
-lm_SuperContig_29_v2	78662	78817	4nc135_070 related to aflatoxin efflux pump AFLT	177	238	2e-53	46	38.71
-lm_SuperContig_29_v2	192751	193692	4nc135_070 related to aflatoxin efflux pump AFLT	494	177	4e-99	201	34.46
-lm_SuperContig_29_v2	193778	194245	4nc135_070 related to aflatoxin efflux pump AFLT	172	17	4e-99	184	53.85
-lm_SuperContig_29_v2	78031	78588	xnc164_090 related to multidrug resistance protein	19	209	3e-21	101	30.89
-lm_SuperContig_29_v2	192802	193692	xnc164_090 related to multidrug resistance protein	509	210	1e-42	95	26.77
-lm_SuperContig_29_v2	193766	194323	xnc164_090 related to multidrug resistance protein	209	19	1e-42	101	30.89
-lm_SuperContig_29_v2	192916	193704	YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane	384	116	3e-23	74	23.53
-lm_SuperContig_29_v2	193766	194107	YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane	117	6	3e-23	57	27.19
-lm_SuperContig_29_v2	192985	193692	YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane	335	66	7e-28	95	28.04
-lm_SuperContig_29_v2	193778	193954	YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane	61	3	7e-28	52	38.98
-lm_SuperContig_29_v2	197021	197416	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	282	151	3e-22	107	39.39
-lm_SuperContig_29_v2	197024	197422	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	298	166	5e-24	113	45.52
-lm_SuperContig_29_v2	197027	197413	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	292	164	2e-23	111	46.56
-lm_SuperContig_29_v2	197039	197437	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	310	170	2e-22	108	46.1
-lm_SuperContig_29_v2	16081	17274	YGR109w-b TY3B TY3B protein	1008	616	4e-35	152	30.33
-lm_SuperContig_29_v2	40143	42272	YGR109w-b TY3B TY3B protein	1301	616	6e-39	165	26.47
-lm_SuperContig_29_v2	91762	92754	YGR109w-b TY3B TY3B protein	944	618	4e-23	113	30.24
-lm_SuperContig_29_v2	100993	102192	YGR109w-b TY3B TY3B protein	1008	616	8e-35	151	30.92
-lm_SuperContig_29_v2	133543	134535	YGR109w-b TY3B TY3B protein	943	616	4e-34	149	32.23
-lm_SuperContig_29_v2	167371	168564	YGR109w-b TY3B TY3B protein	1008	616	2e-35	151	30.83
-lm_SuperContig_29_v2	178464	179477	YGR109w-b TY3B TY3B protein	944	611	1e-21	107	29.03
-lm_SuperContig_29_v2	78139	78582	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	70	217	1e-27	105	39.19
-lm_SuperContig_29_v2	78662	78724	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	220	240	1e-27	39	57.14
-lm_SuperContig_29_v2	193630	193692	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	240	220	6e-27	39	57.14
-lm_SuperContig_29_v2	193772	194215	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	217	70	6e-27	105	39.19
-lm_SuperContig_29_v2	197024	197410	YHL028w WSC4 Cell wall integrity and stress response component 4	314	179	6e-22	106	47.79
-lm_SuperContig_29_v2	197024	197413	YHL028w WSC4 Cell wall integrity and stress response component 4	323	190	3e-23	111	47.01
-lm_SuperContig_29_v2	197024	197425	YHL028w WSC4 Cell wall integrity and stress response component 4	290	148	2e-23	111	49.65
-lm_SuperContig_29_v2	197024	197434	YHL028w WSC4 Cell wall integrity and stress response component 4	257	117	8e-21	103	42.55
-lm_SuperContig_29_v2	197024	197434	YHL028w WSC4 Cell wall integrity and stress response component 4	332	197	2e-22	108	42.03
-lm_SuperContig_29_v2	197024	197437	YHL028w WSC4 Cell wall integrity and stress response component 4	276	136	3e-25	117	47.52
-lm_SuperContig_29_v2	197024	197482	YHL028w WSC4 Cell wall integrity and stress response component 4	300	147	5e-22	107	41.29
-lm_SuperContig_29_v2	197027	197482	YHL028w WSC4 Cell wall integrity and stress response component 4	336	184	5e-22	107	39.22
-lm_SuperContig_29_v2	16081	17274	YIL082w-a TY3B TY3B protein	1034	642	1e-34	150	30.33
-lm_SuperContig_29_v2	40143	42272	YIL082w-a TY3B TY3B protein	1327	642	8e-39	165	26.47
-lm_SuperContig_29_v2	91762	92754	YIL082w-a TY3B TY3B protein	970	644	5e-23	112	30.24
-lm_SuperContig_29_v2	100993	102192	YIL082w-a TY3B TY3B protein	1034	642	3e-34	150	30.92
-lm_SuperContig_29_v2	133543	134535	YIL082w-a TY3B TY3B protein	969	642	1e-33	147	32.23
-lm_SuperContig_29_v2	167371	168564	YIL082w-a TY3B TY3B protein	1034	642	6e-35	149	30.83
-lm_SuperContig_29_v2	178464	179477	YIL082w-a TY3B TY3B protein	970	637	1e-21	106	29.03
-lm_SuperContig_29_v2	197021	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	300	165	6e-33	143	57.35
-lm_SuperContig_29_v2	197021	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	360	219	3e-25	118	52.08
-lm_SuperContig_29_v2	197024	197392	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	222	102	1e-26	122	56.91
-lm_SuperContig_29_v2	197024	197395	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	240	118	1e-31	139	59.68
-lm_SuperContig_29_v2	197024	197398	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	246	123	1e-31	139	60
-lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	267	132	1e-33	145	58.09
-lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	290	156	2e-33	144	57.78
-lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	303	174	3e-32	140	57.46
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	261	126	3e-33	144	58.39
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	276	141	6e-33	143	57.66
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	281	144	1e-32	142	55.8
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	285	147	6e-33	143	57.55
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	314	174	3e-31	137	55.32
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	350	201	1e-28	128	52
-lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	372	228	2e-24	115	48.28
-lm_SuperContig_29_v2	197027	197437	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	244	108	2e-31	138	57.97
-lm_SuperContig_29_v2	197030	197404	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	248	124	3e-32	140	59.2
-lm_SuperContig_29_v2	197036	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	378	246	7e-23	109	42.86
-lm_SuperContig_29_v2	197039	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	318	183	1e-31	139	57.35
-lm_SuperContig_29_v2	78112	78576	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	31	185	7e-29	105	33.55
-lm_SuperContig_29_v2	78662	78778	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	190	227	7e-29	43	48.72
-lm_SuperContig_29_v2	192985	193692	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	459	190	4e-43	94	27.68
-lm_SuperContig_29_v2	193778	194242	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	185	31	4e-43	105	33.55
-lm_SuperContig_29_v2	197024	197434	YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3	272	139	4e-22	107	45.65
-lm_SuperContig_29_v2	197042	197422	YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3	275	147	8e-21	103	45.8
-lm_SuperContig_29_v2	10747	11856	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	192757	193695	SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual	499	183	1e-35	89	22.84
-lm_SuperContig_29_v2	193787	194218	SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual	176	33	1e-35	85	31.25
-lm_SuperContig_29_v2	10747	11856	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	10747	11856	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	1e-36	157	31.18
-lm_SuperContig_29_v2	16081	17289	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	2e-39	166	28.15
-lm_SuperContig_29_v2	41079	42287	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	3e-42	176	28.89
-lm_SuperContig_29_v2	91693	92700	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	452	1e-37	161	32.94
-lm_SuperContig_29_v2	100993	102531	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	312	3e-44	183	27.86
-lm_SuperContig_29_v2	133341	133436	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	800	2e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	358	2e-46	184	28.54
-lm_SuperContig_29_v2	167371	168579	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	8e-43	175	29.38
-lm_SuperContig_29_v2	178395	179504	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	1e-37	160	30.91
-lm_SuperContig_29_v2	77950	78588	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	34	242	5e-29	109	30.99
-lm_SuperContig_29_v2	78662	78799	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	243	286	5e-29	39	41.3
-lm_SuperContig_29_v2	192844	193692	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	525	243	2e-50	113	28.03
-lm_SuperContig_29_v2	193766	194404	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	242	34	2e-50	109	30.99
-lm_SuperContig_29_v2	10747	11856	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	192760	193692	SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	551	242	7e-34	72	21.77
-lm_SuperContig_29_v2	193781	194482	SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	236	4	7e-34	95	23.93
-lm_SuperContig_29_v2	10747	11856	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	78133	78570	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	97	242	3e-30	115	39.04
-lm_SuperContig_29_v2	78662	78799	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	249	292	3e-30	37	42.55
-lm_SuperContig_29_v2	192874	193692	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	518	249	2e-55	124	27.37
-lm_SuperContig_29_v2	193784	194221	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	242	97	2e-55	115	39.04
-lm_SuperContig_29_v2	77950	78588	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	34	242	8e-30	114	30.99
-lm_SuperContig_29_v2	78662	78736	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	243	267	8e-30	37	52
-lm_SuperContig_29_v2	192844	193692	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	525	243	3e-53	118	30.8
-lm_SuperContig_29_v2	193766	194404	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	242	34	3e-53	114	30.99
-lm_SuperContig_29_v2	10747	11856	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	10747	11856	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-36	157	31.18
-lm_SuperContig_29_v2	16081	17289	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-39	166	28.15
-lm_SuperContig_29_v2	41079	42287	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	3e-42	176	28.89
-lm_SuperContig_29_v2	91693	92700	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	1e-37	161	32.94
-lm_SuperContig_29_v2	100993	102531	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	3e-44	183	27.86
-lm_SuperContig_29_v2	133341	133436	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	2e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	2e-46	184	28.54
-lm_SuperContig_29_v2	167371	168579	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	8e-43	175	29.38
-lm_SuperContig_29_v2	178395	179504	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-37	160	30.91
-lm_SuperContig_29_v2	10747	11856	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	10747	11856	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-36	157	31.18
-lm_SuperContig_29_v2	16081	17289	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-39	166	28.15
-lm_SuperContig_29_v2	41079	42287	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	3e-42	176	28.89
-lm_SuperContig_29_v2	91693	92700	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	1e-37	161	32.94
-lm_SuperContig_29_v2	100993	102531	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	3e-44	183	27.86
-lm_SuperContig_29_v2	133341	133436	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	2e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	2e-46	184	28.54
-lm_SuperContig_29_v2	167371	168579	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	8e-43	175	29.38
-lm_SuperContig_29_v2	178395	179504	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-37	160	30.91
-lm_SuperContig_29_v2	10747	11856	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	10747	11856	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-lm_SuperContig_29_v2	16081	17289	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-lm_SuperContig_29_v2	41079	42287	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-lm_SuperContig_29_v2	91693	92700	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-lm_SuperContig_29_v2	100993	102531	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-lm_SuperContig_29_v2	133341	133436	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-lm_SuperContig_29_v2	133471	134754	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-lm_SuperContig_29_v2	167371	168579	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-lm_SuperContig_29_v2	178395	179504	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-lm_SuperContig_29_v2	77980	78567	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	18	211	5e-25	114	31
-lm_SuperContig_29_v2	192772	193695	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	529	218	2e-42	82	20.7
-lm_SuperContig_29_v2	193787	194374	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	211	18	2e-42	114	31
-lm_SuperContig_29_v2	78115	78588	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	53	210	2e-53	183	55.06
-lm_SuperContig_29_v2	78662	78814	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	211	264	2e-53	47	44.44
-lm_SuperContig_29_v2	192760	193692	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	534	211	2e-104	220	36.92
-lm_SuperContig_29_v2	193766	194239	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	210	53	2e-104	183	55.06
-lm_SuperContig_29_v2	78112	78570	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	94	246	7e-23	104	35.95
-lm_SuperContig_29_v2	78659	78802	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	253	297	7e-23	24	25
-lm_SuperContig_29_v2	192760	193695	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	560	253	5e-40	84	19.43
-lm_SuperContig_29_v2	193784	194242	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	246	94	5e-40	104	35.95
-lm_SuperContig_29_v2	78019	78567	um01964 related to multidrug resistance protein, Contig um_contig_1.72	40	220	1e-24	113	33.7
-lm_SuperContig_29_v2	192901	193695	um01964 related to multidrug resistance protein, Contig um_contig_1.72	490	227	7e-43	85	24.16
-lm_SuperContig_29_v2	193787	194335	um01964 related to multidrug resistance protein, Contig um_contig_1.72	220	40	7e-43	113	33.7
-lm_SuperContig_29_v2	77890	78591	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	38	263	1e-32	115	32.07
-lm_SuperContig_29_v2	78659	78814	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	264	313	1e-32	46	36.54
-lm_SuperContig_29_v2	192760	193695	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	575	264	1e-65	158	30.6
-lm_SuperContig_29_v2	193763	194464	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	263	38	1e-65	115	32.07
-lm_SuperContig_29_v2	78136	78576	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	133	280	1e-21	91	30.41
-lm_SuperContig_29_v2	78650	78814	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	280	331	1e-21	33	29.09
-lm_SuperContig_29_v2	192754	193704	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	598	280	3e-45	114	25.93
-lm_SuperContig_29_v2	193778	194218	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	280	133	3e-45	91	30.41
-lm_SuperContig_29_v2	77938	78585	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	27	239	2e-24	93	30.73
-lm_SuperContig_29_v2	78650	78808	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	236	285	2e-24	40	33.96
-lm_SuperContig_29_v2	192757	193704	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	554	236	1e-48	124	25.7
-lm_SuperContig_29_v2	193769	194416	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	239	27	1e-48	93	30.73
-lm_SuperContig_29_v2	77938	78576	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	13	215	4e-45	167	39.91
-lm_SuperContig_29_v2	78650	78736	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	216	244	4e-45	36	55.17
-lm_SuperContig_29_v2	192826	193704	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	511	216	2e-98	216	37.04
-lm_SuperContig_29_v2	193778	194416	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	215	13	2e-98	167	39.91
-lm_SuperContig_29_v2	193006	193692	um05421 related to Multidrug resistance protein , Contig um_contig_1.192	496	272	6e-41	107	27.07
-lm_SuperContig_29_v2	193778	194107	um05421 related to Multidrug resistance protein , Contig um_contig_1.192	267	158	6e-41	83	35.45

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.map	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,341 +0,0 @@
-Afu3g02110.115	lm_SuperContig_29_v2	77989	78369
-Afu3g02110.116	lm_SuperContig_29_v2	194365	193985
-Afu3g01520.117	lm_SuperContig_29_v2	78109	78817
-Afu3g01520.118	lm_SuperContig_29_v2	194245	192760
-Afu3g02520.119	lm_SuperContig_29_v2	78010	78808
-Afu3g02520.120	lm_SuperContig_29_v2	194344	192766
-Afu3g02720.121	lm_SuperContig_29_v2	78109	78817
-Afu3g02720.122	lm_SuperContig_29_v2	194245	192754
-Afu6g03320.123	lm_SuperContig_29_v2	78061	78814
-Afu6g03320.124	lm_SuperContig_29_v2	194293	192760
-Afu6g02220.125	lm_SuperContig_29_v2	78007	78817
-Afu6g02220.126	lm_SuperContig_29_v2	194347	193288
-Afu8g00940.127	lm_SuperContig_29_v2	78133	78817
-Afu8g00940.128	lm_SuperContig_29_v2	194221	192760
-Afu4g02630.129	lm_SuperContig_29_v2	134343	133669
-Afu4g02630.130	lm_SuperContig_29_v2	168372	167776
-Afu4g02630.131	lm_SuperContig_29_v2	42080	41484
-Afu4g02630.132	lm_SuperContig_29_v2	102000	101404
-Afu4g02630.133	lm_SuperContig_29_v2	32272	31597
-Afu4g02630.134	lm_SuperContig_29_v2	17082	16462
-Afu4g02630.135	lm_SuperContig_29_v2	179264	178590
-Afu4g02630.136	lm_SuperContig_29_v2	11625	10942
-Afu4g02630.137	lm_SuperContig_29_v2	92562	91888
-Afu4g03920.138	lm_SuperContig_29_v2	78184	78814
-Afu4g03920.139	lm_SuperContig_29_v2	194170	192964
-Afu6g09110.140	lm_SuperContig_29_v2	78049	78775
-Afu6g09110.141	lm_SuperContig_29_v2	194305	192904
-Afu6g14640.142	lm_SuperContig_29_v2	78151	78814
-Afu6g14640.143	lm_SuperContig_29_v2	194203	192760
-Afu6g09710.144	lm_SuperContig_29_v2	78109	78814
-Afu6g09710.145	lm_SuperContig_29_v2	194245	192772
-Afu5g01540.146	lm_SuperContig_29_v2	78115	78817
-Afu5g01540.147	lm_SuperContig_29_v2	194239	192754
-Afu2g15140.148	lm_SuperContig_29_v2	194323	192868
-fg00095.149	lm_SuperContig_29_v2	194221	193303
-fg12051.150	lm_SuperContig_29_v2	194221	192877
-fg12074.151	lm_SuperContig_29_v2	77956	78814
-fg12074.152	lm_SuperContig_29_v2	194398	192883
-fg12335.153	lm_SuperContig_29_v2	78124	78718
-fg12335.154	lm_SuperContig_29_v2	194230	192769
-fg12717.155	lm_SuperContig_29_v2	194383	193222
-b13o8_150.156	lm_SuperContig_29_v2	194248	193036
-b18d24_100.157	lm_SuperContig_29_v2	78010	78814
-b18d24_100.158	lm_SuperContig_29_v2	194344	192916
-b5k2_230.159	lm_SuperContig_29_v2	78184	78814
-b5k2_230.160	lm_SuperContig_29_v2	194170	192760
-1nc550_030.161	lm_SuperContig_29_v2	194212	192832
-1nc570_120.162	lm_SuperContig_29_v2	77941	78736
-1nc570_120.163	lm_SuperContig_29_v2	194413	192760
-6nc360_090.164	lm_SuperContig_29_v2	194086	192817
-29e8_240.165	lm_SuperContig_29_v2	78112	78817
-29e8_240.166	lm_SuperContig_29_v2	194242	192769
-7nc450_010.167	lm_SuperContig_29_v2	194218	192940
-4nc446_010.168	lm_SuperContig_29_v2	194218	192865
-b11e5_230.169	lm_SuperContig_29_v2	194239	192904
-xnc126_050.170	lm_SuperContig_29_v2	77935	78817
-xnc126_050.171	lm_SuperContig_29_v2	194419	192757
-4nc135_070.172	lm_SuperContig_29_v2	78109	78817
-4nc135_070.173	lm_SuperContig_29_v2	194245	192751
-xnc164_090.174	lm_SuperContig_29_v2	78031	78588
-xnc164_090.175	lm_SuperContig_29_v2	194323	192802
-YBR293w.176	lm_SuperContig_29_v2	194107	192916
-YCL069w.177	lm_SuperContig_29_v2	193954	192985
-YDL037c.178	lm_SuperContig_29_v2	197422	197024
-YDL037c.179	lm_SuperContig_29_v2	197413	197027
-YDL037c.180	lm_SuperContig_29_v2	197437	197039
-YDL037c.181	lm_SuperContig_29_v2	197416	197021
-YGR109w-b.182	lm_SuperContig_29_v2	42272	40143
-YGR109w-b.183	lm_SuperContig_29_v2	17274	16081
-YGR109w-b.184	lm_SuperContig_29_v2	102192	100993
-YGR109w-b.185	lm_SuperContig_29_v2	168564	167371
-YGR109w-b.186	lm_SuperContig_29_v2	134535	133543
-YGR109w-b.187	lm_SuperContig_29_v2	92754	91762
-YGR109w-b.188	lm_SuperContig_29_v2	179477	178464
-YGR224w.189	lm_SuperContig_29_v2	78139	78724
-YGR224w.190	lm_SuperContig_29_v2	194215	193630
-YHL028w.191	lm_SuperContig_29_v2	197437	197024
-YHL028w.192	lm_SuperContig_29_v2	197413	197024
-YHL028w.193	lm_SuperContig_29_v2	197425	197024
-YHL028w.194	lm_SuperContig_29_v2	197434	197024
-YHL028w.195	lm_SuperContig_29_v2	197482	197024
-YHL028w.196	lm_SuperContig_29_v2	197482	197027
-YHL028w.197	lm_SuperContig_29_v2	197410	197024
-YHL028w.198	lm_SuperContig_29_v2	197434	197024
-YIL082w-a.199	lm_SuperContig_29_v2	42272	40143
-YIL082w-a.200	lm_SuperContig_29_v2	17274	16081
-YIL082w-a.201	lm_SuperContig_29_v2	102192	100993
-YIL082w-a.202	lm_SuperContig_29_v2	168564	167371
-YIL082w-a.203	lm_SuperContig_29_v2	134535	133543
-YIL082w-a.204	lm_SuperContig_29_v2	92754	91762
-YIL082w-a.205	lm_SuperContig_29_v2	179477	178464
-YJR151c.206	lm_SuperContig_29_v2	197425	197024
-YJR151c.207	lm_SuperContig_29_v2	197425	197024
-YJR151c.208	lm_SuperContig_29_v2	197434	197024
-YJR151c.209	lm_SuperContig_29_v2	197425	197021
-YJR151c.210	lm_SuperContig_29_v2	197434	197024
-YJR151c.211	lm_SuperContig_29_v2	197434	197024
-YJR151c.212	lm_SuperContig_29_v2	197434	197024
-YJR151c.213	lm_SuperContig_29_v2	197425	197024
-YJR151c.214	lm_SuperContig_29_v2	197404	197030
-YJR151c.215	lm_SuperContig_29_v2	197398	197024
-YJR151c.216	lm_SuperContig_29_v2	197395	197024
-YJR151c.217	lm_SuperContig_29_v2	197434	197039
-YJR151c.218	lm_SuperContig_29_v2	197437	197027
-YJR151c.219	lm_SuperContig_29_v2	197434	197024
-YJR151c.220	lm_SuperContig_29_v2	197434	197024
-YJR151c.221	lm_SuperContig_29_v2	197392	197024
-YJR151c.222	lm_SuperContig_29_v2	197425	197021
-YJR151c.223	lm_SuperContig_29_v2	197434	197024
-YJR151c.224	lm_SuperContig_29_v2	197434	197036
-YKR105c.225	lm_SuperContig_29_v2	78112	78778
-YKR105c.226	lm_SuperContig_29_v2	194242	192985
-YNL283c.227	lm_SuperContig_29_v2	197434	197024
-YNL283c.228	lm_SuperContig_29_v2	197422	197042
-SPAC167.08.229	lm_SuperContig_29_v2	134754	133341
-SPAC167.08.230	lm_SuperContig_29_v2	102531	100993
-SPAC167.08.231	lm_SuperContig_29_v2	42287	41079
-SPAC167.08.232	lm_SuperContig_29_v2	168579	167371
-SPAC167.08.233	lm_SuperContig_29_v2	17289	16081
-SPAC167.08.234	lm_SuperContig_29_v2	92700	91693
-SPAC167.08.235	lm_SuperContig_29_v2	179504	178395
-SPAC167.08.236	lm_SuperContig_29_v2	11856	10747
-SPBC12C2.13c.237	lm_SuperContig_29_v2	194218	192757
-SPAPB15E9.03c.238	lm_SuperContig_29_v2	134754	133341
-SPAPB15E9.03c.239	lm_SuperContig_29_v2	102531	100993
-SPAPB15E9.03c.240	lm_SuperContig_29_v2	42287	41079
-SPAPB15E9.03c.241	lm_SuperContig_29_v2	168579	167371
-SPAPB15E9.03c.242	lm_SuperContig_29_v2	17289	16081
-SPAPB15E9.03c.243	lm_SuperContig_29_v2	92700	91693
-SPAPB15E9.03c.244	lm_SuperContig_29_v2	179504	178395
-SPAPB15E9.03c.245	lm_SuperContig_29_v2	11856	10747
-SPBC1289.17.246	lm_SuperContig_29_v2	134754	133341
-SPBC1289.17.247	lm_SuperContig_29_v2	102531	100993
-SPBC1289.17.248	lm_SuperContig_29_v2	42287	41079
-SPBC1289.17.249	lm_SuperContig_29_v2	168579	167371
-SPBC1289.17.250	lm_SuperContig_29_v2	17289	16081
-SPBC1289.17.251	lm_SuperContig_29_v2	92700	91693
-SPBC1289.17.252	lm_SuperContig_29_v2	179504	178395
-SPBC1289.17.253	lm_SuperContig_29_v2	11856	10747
-SPAC3H1.06c.254	lm_SuperContig_29_v2	77950	78799
-SPAC3H1.06c.255	lm_SuperContig_29_v2	194404	192844
-SPCC1020.14.256	lm_SuperContig_29_v2	134754	133341
-SPCC1020.14.257	lm_SuperContig_29_v2	102531	100993
-SPCC1020.14.258	lm_SuperContig_29_v2	42287	41079
-SPCC1020.14.259	lm_SuperContig_29_v2	168579	167371
-SPCC1020.14.260	lm_SuperContig_29_v2	17289	16081
-SPCC1020.14.261	lm_SuperContig_29_v2	92700	91693
-SPCC1020.14.262	lm_SuperContig_29_v2	179504	178395
-SPCC1020.14.263	lm_SuperContig_29_v2	11856	10747
-SPBC3E7.06c.264	lm_SuperContig_29_v2	194482	192760
-SPAC26A3.13c.265	lm_SuperContig_29_v2	134754	133341
-SPAC26A3.13c.266	lm_SuperContig_29_v2	102531	100993
-SPAC26A3.13c.267	lm_SuperContig_29_v2	42287	41079
-SPAC26A3.13c.268	lm_SuperContig_29_v2	168579	167371
-SPAC26A3.13c.269	lm_SuperContig_29_v2	17289	16081
-SPAC26A3.13c.270	lm_SuperContig_29_v2	92700	91693
-SPAC26A3.13c.271	lm_SuperContig_29_v2	179504	178395
-SPAC26A3.13c.272	lm_SuperContig_29_v2	11856	10747
-SPBC16A3.17c.273	lm_SuperContig_29_v2	78133	78799
-SPBC16A3.17c.274	lm_SuperContig_29_v2	194221	192874
-SPAC1399.02.275	lm_SuperContig_29_v2	77950	78736
-SPAC1399.02.276	lm_SuperContig_29_v2	194404	192844
-SPAC2E1P3.03c.277	lm_SuperContig_29_v2	134754	133341
-SPAC2E1P3.03c.278	lm_SuperContig_29_v2	102531	100993
-SPAC2E1P3.03c.279	lm_SuperContig_29_v2	42287	41079
-SPAC2E1P3.03c.280	lm_SuperContig_29_v2	168579	167371
-SPAC2E1P3.03c.281	lm_SuperContig_29_v2	17289	16081
-SPAC2E1P3.03c.282	lm_SuperContig_29_v2	92700	91693
-SPAC2E1P3.03c.283	lm_SuperContig_29_v2	179504	178395
-SPAC2E1P3.03c.284	lm_SuperContig_29_v2	11856	10747
-SPAC19D5.09c.285	lm_SuperContig_29_v2	134754	133341
-SPAC19D5.09c.286	lm_SuperContig_29_v2	102531	100993
-SPAC19D5.09c.287	lm_SuperContig_29_v2	42287	41079
-SPAC19D5.09c.288	lm_SuperContig_29_v2	168579	167371
-SPAC19D5.09c.289	lm_SuperContig_29_v2	17289	16081
-SPAC19D5.09c.290	lm_SuperContig_29_v2	92700	91693
-SPAC19D5.09c.291	lm_SuperContig_29_v2	179504	178395
-SPAC19D5.09c.292	lm_SuperContig_29_v2	11856	10747
-SPAC27E2.08.293	lm_SuperContig_29_v2	134754	133341
-SPAC27E2.08.294	lm_SuperContig_29_v2	102531	100993
-SPAC27E2.08.295	lm_SuperContig_29_v2	42287	41079
-SPAC27E2.08.296	lm_SuperContig_29_v2	168579	167371
-SPAC27E2.08.297	lm_SuperContig_29_v2	17289	16081
-SPAC27E2.08.298	lm_SuperContig_29_v2	92700	91693
-SPAC27E2.08.299	lm_SuperContig_29_v2	179504	178395
-SPAC27E2.08.300	lm_SuperContig_29_v2	11856	10747
-SPAC13D1.01c.301	lm_SuperContig_29_v2	134754	133341
-SPAC13D1.01c.302	lm_SuperContig_29_v2	102531	100993
-SPAC13D1.01c.303	lm_SuperContig_29_v2	42287	41079
-SPAC13D1.01c.304	lm_SuperContig_29_v2	168579	167371
-SPAC13D1.01c.305	lm_SuperContig_29_v2	17289	16081
-SPAC13D1.01c.306	lm_SuperContig_29_v2	92700	91693
-SPAC13D1.01c.307	lm_SuperContig_29_v2	179504	178395
-SPAC13D1.01c.308	lm_SuperContig_29_v2	11856	10747
-SPBC9B6.02c.309	lm_SuperContig_29_v2	134754	133341
-SPBC9B6.02c.310	lm_SuperContig_29_v2	102531	100993
-SPBC9B6.02c.311	lm_SuperContig_29_v2	42287	41079
-SPBC9B6.02c.312	lm_SuperContig_29_v2	168579	167371
-SPBC9B6.02c.313	lm_SuperContig_29_v2	17289	16081
-SPBC9B6.02c.314	lm_SuperContig_29_v2	92700	91693
-SPBC9B6.02c.315	lm_SuperContig_29_v2	179504	178395
-SPBC9B6.02c.316	lm_SuperContig_29_v2	11856	10747
-SPAC9.04.317	lm_SuperContig_29_v2	134754	133341
-SPAC9.04.318	lm_SuperContig_29_v2	102531	100993
-SPAC9.04.319	lm_SuperContig_29_v2	42287	41079
-SPAC9.04.320	lm_SuperContig_29_v2	168579	167371
-SPAC9.04.321	lm_SuperContig_29_v2	17289	16081
-SPAC9.04.322	lm_SuperContig_29_v2	92700	91693
-SPAC9.04.323	lm_SuperContig_29_v2	179504	178395
-SPAC9.04.324	lm_SuperContig_29_v2	11856	10747
-um00679.325	lm_SuperContig_29_v2	77980	78567
-um00679.326	lm_SuperContig_29_v2	194374	192772
-um00842.327	lm_SuperContig_29_v2	78115	78814
-um00842.328	lm_SuperContig_29_v2	194239	192760
-um01882.329	lm_SuperContig_29_v2	78112	78802
-um01882.330	lm_SuperContig_29_v2	194242	192760
-um01964.331	lm_SuperContig_29_v2	78019	78567
-um01964.332	lm_SuperContig_29_v2	194335	192901
-um02062.333	lm_SuperContig_29_v2	77890	78814
-um02062.334	lm_SuperContig_29_v2	194464	192760
-um02598.335	lm_SuperContig_29_v2	78136	78814
-um02598.336	lm_SuperContig_29_v2	194218	192754
-um03115.337	lm_SuperContig_29_v2	77938	78808
-um03115.338	lm_SuperContig_29_v2	194416	192757
-um05414.339	lm_SuperContig_29_v2	77938	78736
-um05414.340	lm_SuperContig_29_v2	194416	192826
-um05421.341	lm_SuperContig_29_v2	194107	193006
-mito_010.1	lm_SuperContig_30_v2	35498	37823
-mito_010.2	lm_SuperContig_30_v2	27615	29673
-mito_010.3	lm_SuperContig_30_v2	23817	24089
-mito_020.4	lm_SuperContig_30_v2	27615	29418
-mito_020.5	lm_SuperContig_30_v2	95085	94306
-mito_020.6	lm_SuperContig_30_v2	23817	24089
-mito_030.7	lm_SuperContig_30_v2	23817	27509
-mito_030.8	lm_SuperContig_30_v2	62656	61805
-mito_030.9	lm_SuperContig_30_v2	146223	147503
-mito_030.10	lm_SuperContig_30_v2	109925	109092
-mito_030.11	lm_SuperContig_30_v2	117965	119308
-mito_030.12	lm_SuperContig_30_v2	83615	82749
-mito_030.13	lm_SuperContig_30_v2	35963	37213
-mito_030.14	lm_SuperContig_30_v2	87770	86928
-mito_030.15	lm_SuperContig_30_v2	116645	117925
-mito_030.16	lm_SuperContig_30_v2	81706	80861
-mito_030.17	lm_SuperContig_30_v2	150994	152199
-mito_030.18	lm_SuperContig_30_v2	56582	55780
-mito_030.19	lm_SuperContig_30_v2	18181	19317
-mito_030.20	lm_SuperContig_30_v2	91238	90399
-mito_030.21	lm_SuperContig_30_v2	141039	141858
-mito_030.22	lm_SuperContig_30_v2	64676	63837
-mito_030.23	lm_SuperContig_30_v2	115228	116103
-mito_030.24	lm_SuperContig_30_v2	149559	150444
-mito_030.25	lm_SuperContig_30_v2	22437	23375
-mito_030.26	lm_SuperContig_30_v2	32527	33390
-mito_040.27	lm_SuperContig_30_v2	21984	22220
-mito_050.28	lm_SuperContig_30_v2	21984	23387
-mito_050.29	lm_SuperContig_30_v2	62650	61793
-mito_050.30	lm_SuperContig_30_v2	18466	19329
-mito_050.31	lm_SuperContig_30_v2	81703	80849
-mito_050.32	lm_SuperContig_30_v2	36323	37234
-mito_050.33	lm_SuperContig_30_v2	83594	82737
-mito_050.34	lm_SuperContig_30_v2	149583	150450
-mito_050.35	lm_SuperContig_30_v2	64748	63768
-mito_050.36	lm_SuperContig_30_v2	118442	119320
-mito_050.37	lm_SuperContig_30_v2	87767	86916
-mito_050.38	lm_SuperContig_30_v2	26661	27530
-mito_050.39	lm_SuperContig_30_v2	109925	109071
-mito_050.40	lm_SuperContig_30_v2	115249	116115
-mito_050.41	lm_SuperContig_30_v2	91259	90387
-mito_050.42	lm_SuperContig_30_v2	32542	33390
-mito_050.43	lm_SuperContig_30_v2	141021	141879
-mito_050.44	lm_SuperContig_30_v2	117050	117943
-mito_050.45	lm_SuperContig_30_v2	146610	147515
-mito_050.46	lm_SuperContig_30_v2	151234	152220
-mito_060.47	lm_SuperContig_30_v2	53696	53343
-mito_080.48	lm_SuperContig_30_v2	5079	5582
-mito_080.49	lm_SuperContig_30_v2	59799	53703
-mito_110.50	lm_SuperContig_30_v2	65165	64707
-mito_150.51	lm_SuperContig_30_v2	110387	108494
-mito_150.52	lm_SuperContig_30_v2	103711	103508
-mito_170.53	lm_SuperContig_30_v2	17614	20481
-mito_180.54	lm_SuperContig_30_v2	17614	19341
-mito_180.55	lm_SuperContig_30_v2	62653	61781
-mito_180.56	lm_SuperContig_30_v2	32542	33390
-mito_180.57	lm_SuperContig_30_v2	83615	82716
-mito_180.58	lm_SuperContig_30_v2	36329	37252
-mito_180.59	lm_SuperContig_30_v2	109979	109059
-mito_180.60	lm_SuperContig_30_v2	141030	141897
-mito_180.61	lm_SuperContig_30_v2	81706	80825
-mito_180.62	lm_SuperContig_30_v2	149580	150465
-mito_180.63	lm_SuperContig_30_v2	64718	63756
-mito_180.64	lm_SuperContig_30_v2	115189	116127
-mito_180.65	lm_SuperContig_30_v2	87770	86895
-mito_180.66	lm_SuperContig_30_v2	22509	23405
-mito_180.67	lm_SuperContig_30_v2	91256	90384
-mito_180.68	lm_SuperContig_30_v2	118439	119344
-mito_180.69	lm_SuperContig_30_v2	56585	55774
-mito_180.70	lm_SuperContig_30_v2	117050	117955
-mito_180.71	lm_SuperContig_30_v2	26640	27542
-mito_180.72	lm_SuperContig_30_v2	151309	152232
-mito_180.73	lm_SuperContig_30_v2	146610	147527
-mito_180.74	lm_SuperContig_30_v2	42209	42879
-mito_180.75	lm_SuperContig_30_v2	125743	126138
-mito_190.76	lm_SuperContig_30_v2	44197	47305
-mito_210.77	lm_SuperContig_30_v2	102604	102101
-mito_210.78	lm_SuperContig_30_v2	94202	89139
-mito_220.79	lm_SuperContig_30_v2	14626	15192
-mito_220.80	lm_SuperContig_30_v2	15860	16315
-mito_220.81	lm_SuperContig_30_v2	9733	9936
-mito_220.82	lm_SuperContig_30_v2	6405	6605
-mito_230.83	lm_SuperContig_30_v2	9733	9936
-mito_230.84	lm_SuperContig_30_v2	6405	6605
-mito_240.85	lm_SuperContig_30_v2	9733	9927
-mito_240.86	lm_SuperContig_30_v2	6405	6605
-mito_155.87	lm_SuperContig_30_v2	18442	19341
-mito_155.88	lm_SuperContig_30_v2	110081	109056
-mito_155.89	lm_SuperContig_30_v2	36323	37249
-mito_155.90	lm_SuperContig_30_v2	62650	61781
-mito_155.91	lm_SuperContig_30_v2	141021	141891
-mito_155.92	lm_SuperContig_30_v2	81703	80828
-mito_155.93	lm_SuperContig_30_v2	149583	150462
-mito_155.94	lm_SuperContig_30_v2	83594	82716
-mito_155.95	lm_SuperContig_30_v2	116981	117955
-mito_155.96	lm_SuperContig_30_v2	87767	86895
-mito_155.97	lm_SuperContig_30_v2	146610	147533
-mito_155.98	lm_SuperContig_30_v2	64655	63756
-mito_155.99	lm_SuperContig_30_v2	151258	152232
-mito_155.100	lm_SuperContig_30_v2	91256	90381
-mito_155.101	lm_SuperContig_30_v2	32494	33504
-mito_155.102	lm_SuperContig_30_v2	115198	116127
-mito_155.103	lm_SuperContig_30_v2	26607	27542
-mito_155.104	lm_SuperContig_30_v2	118442	119341
-mito_155.105	lm_SuperContig_30_v2	22509	23387
-mito_155.106	lm_SuperContig_30_v2	125740	126240
-mito_195.107	lm_SuperContig_30_v2	44996	45911
-mito_195.108	lm_SuperContig_30_v2	46058	46769
-SPMIT.05.109	lm_SuperContig_30_v2	14662	15189
-SPMIT.05.110	lm_SuperContig_30_v2	15941	16303
-SPMIT.04.111	lm_SuperContig_30_v2	65204	64752
-SPMIT.03.112	lm_SuperContig_30_v2	95262	94345
-SPMIT.01.113	lm_SuperContig_30_v2	102580	102098
-SPMIT.01.114	lm_SuperContig_30_v2	94202	93876

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.path	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,456 +0,0 @@
-1	lm_SuperContig_30_v2	35498	35914	mito_010 NADH dehydrogenase (ubiquinone) chain 5	307	445	1e-62	244	82.73
-1	lm_SuperContig_30_v2	37314	37823	mito_010 NADH dehydrogenase (ubiquinone) chain 5	494	663	8e-67	258	67.65
-2	lm_SuperContig_30_v2	27615	28001	mito_010 NADH dehydrogenase (ubiquinone) chain 5	109	237	1e-53	214	77.52
-2	lm_SuperContig_30_v2	29503	29673	mito_010 NADH dehydrogenase (ubiquinone) chain 5	254	310	3e-21	107	92.98
-3	lm_SuperContig_30_v2	23817	24089	mito_010 NADH dehydrogenase (ubiquinone) chain 5	1	91	7e-25	119	63.74
-4	lm_SuperContig_30_v2	27615	28001	mito_020 predicted ND5 intron 2 protein	109	237	1e-53	214	77.52
-4	lm_SuperContig_30_v2	28681	29418	mito_020 predicted ND5 intron 2 protein	303	540	4e-37	159	41.2
-5	lm_SuperContig_30_v2	94306	95085	mito_020 predicted ND5 intron 2 protein	544	279	2e-22	110	28.46
-6	lm_SuperContig_30_v2	23817	24089	mito_020 predicted ND5 intron 2 protein	1	91	7e-25	119	63.74
-7	lm_SuperContig_30_v2	23817	24089	mito_030 predicted ND5 intron 1 protein	1	91	7e-25	119	63.74
-7	lm_SuperContig_30_v2	26190	27509	mito_030 predicted ND5 intron 1 protein	84	525	0	666	76.52
-8	lm_SuperContig_30_v2	61805	62656	mito_030 predicted ND5 intron 1 protein	528	241	3e-55	219	38.89
-9	lm_SuperContig_30_v2	146223	147503	mito_030 predicted ND5 intron 1 protein	114	528	2e-64	250	37.61
-10	lm_SuperContig_30_v2	109092	109925	mito_030 predicted ND5 intron 1 protein	525	243	2e-49	200	38.16
-11	lm_SuperContig_30_v2	117965	119308	mito_030 predicted ND5 intron 1 protein	87	525	1e-63	248	35.79
-12	lm_SuperContig_30_v2	82749	83615	mito_030 predicted ND5 intron 1 protein	525	236	3e-47	193	35.27
-13	lm_SuperContig_30_v2	35963	37213	mito_030 predicted ND5 intron 1 protein	114	525	4e-62	242	38.08
-14	lm_SuperContig_30_v2	86928	87770	mito_030 predicted ND5 intron 1 protein	525	242	3e-47	193	36.14
-15	lm_SuperContig_30_v2	116645	117925	mito_030 predicted ND5 intron 1 protein	121	526	6e-60	235	37.12
-16	lm_SuperContig_30_v2	80861	81706	mito_030 predicted ND5 intron 1 protein	525	242	5e-44	182	35.66
-17	lm_SuperContig_30_v2	150994	152199	mito_030 predicted ND5 intron 1 protein	121	525	4e-58	229	36.3
-18	lm_SuperContig_30_v2	56292	56582	mito_030 predicted ND5 intron 1 protein	351	255	1e-34	74	38.78
-18	lm_SuperContig_30_v2	55780	56187	mito_030 predicted ND5 intron 1 protein	492	357	1e-34	96	36.96
-19	lm_SuperContig_30_v2	18181	19317	mito_030 predicted ND5 intron 1 protein	167	528	3e-57	226	37.76
-20	lm_SuperContig_30_v2	90399	91238	mito_030 predicted ND5 intron 1 protein	528	249	1e-37	161	32.52
-21	lm_SuperContig_30_v2	141039	141308	mito_030 predicted ND5 intron 1 protein	250	342	8e-47	58	34.41
-21	lm_SuperContig_30_v2	141292	141858	mito_030 predicted ND5 intron 1 protein	337	525	8e-47	155	42.11
-22	lm_SuperContig_30_v2	63837	64676	mito_030 predicted ND5 intron 1 protein	511	232	1e-35	155	35.21
-23	lm_SuperContig_30_v2	115228	116103	mito_030 predicted ND5 intron 1 protein	236	528	6e-48	195	35.93
-24	lm_SuperContig_30_v2	149559	149744	mito_030 predicted ND5 intron 1 protein	233	296	6e-40	41	35.94
-24	lm_SuperContig_30_v2	149749	150444	mito_030 predicted ND5 intron 1 protein	299	530	6e-40	149	37.02
-25	lm_SuperContig_30_v2	22437	23375	mito_030 predicted ND5 intron 1 protein	219	528	1e-43	181	32.59
-26	lm_SuperContig_30_v2	32527	33390	mito_030 predicted ND5 intron 1 protein	236	518	6e-40	169	36.15
-27	lm_SuperContig_30_v2	21984	22220	mito_040 NADH dehydrogenase (ubiquinone) chain 4L	1	79	3e-30	136	84.81
-28	lm_SuperContig_30_v2	21984	22229	mito_050 predicted ND4L intron protein	1	82	8e-31	138	82.93
-28	lm_SuperContig_30_v2	22509	23387	mito_050 predicted ND4L intron protein	145	438	7e-81	305	49
-29	lm_SuperContig_30_v2	61793	62650	mito_050 predicted ND4L intron protein	438	145	3e-49	200	40.33
-30	lm_SuperContig_30_v2	18466	19329	mito_050 predicted ND4L intron protein	145	438	6e-54	215	40.53
-31	lm_SuperContig_30_v2	80849	81703	mito_050 predicted ND4L intron protein	435	145	1e-45	188	39.6
-32	lm_SuperContig_30_v2	36323	37234	mito_050 predicted ND4L intron protein	145	438	4e-49	199	40.39
-33	lm_SuperContig_30_v2	82737	83594	mito_050 predicted ND4L intron protein	435	145	1e-45	188	37.46
-34	lm_SuperContig_30_v2	149583	149747	mito_050 predicted ND4L intron protein	145	199	3e-39	58	47.27
-34	lm_SuperContig_30_v2	149743	150450	mito_050 predicted ND4L intron protein	199	438	3e-39	130	35.34
-35	lm_SuperContig_30_v2	63768	64748	mito_050 predicted ND4L intron protein	438	111	4e-45	186	37.09
-36	lm_SuperContig_30_v2	118442	119320	mito_050 predicted ND4L intron protein	145	435	3e-44	183	38.64
-37	lm_SuperContig_30_v2	86916	87767	mito_050 predicted ND4L intron protein	435	145	4e-45	186	36.49
-38	lm_SuperContig_30_v2	26661	27530	mito_050 predicted ND4L intron protein	145	438	1e-43	181	35.67
-39	lm_SuperContig_30_v2	109071	109925	mito_050 predicted ND4L intron protein	438	145	7e-42	175	35.67
-40	lm_SuperContig_30_v2	115249	116115	mito_050 predicted ND4L intron protein	145	438	1e-43	181	38.41
-41	lm_SuperContig_30_v2	90387	91259	mito_050 predicted ND4L intron protein	438	144	2e-39	167	33.33
-42	lm_SuperContig_30_v2	32542	33390	mito_050 predicted ND4L intron protein	145	424	6e-43	179	38.91
-43	lm_SuperContig_30_v2	141021	141260	mito_050 predicted ND4L intron protein	146	228	6e-38	52	40.96
-43	lm_SuperContig_30_v2	141295	141879	mito_050 predicted ND4L intron protein	241	438	6e-38	131	39.51
-44	lm_SuperContig_30_v2	117050	117943	mito_050 predicted ND4L intron protein	145	438	1e-42	178	37.62
-45	lm_SuperContig_30_v2	146610	147515	mito_050 predicted ND4L intron protein	149	438	4e-37	159	34.18
-46	lm_SuperContig_30_v2	151234	152220	mito_050 predicted ND4L intron protein	118	438	2e-35	154	34.72
-47	lm_SuperContig_30_v2	53343	53696	mito_060 probable NADH dehydrogenase (ubiquinone) chain 3	117	1	2e-26	121	50
-48	lm_SuperContig_30_v2	5079	5582	mito_080 NADH dehydrogenase (ubiquinone) chain 2	403	582	7e-41	172	49.73
-49	lm_SuperContig_30_v2	59011	59799	mito_080 NADH dehydrogenase (ubiquinone) chain 2	271	1	1e-68	264	52.71
-49	lm_SuperContig_30_v2	55010	55561	mito_080 NADH dehydrogenase (ubiquinone) chain 2	423	242	1e-47	191	57.22
-49	lm_SuperContig_30_v2	53703	54143	mito_080 NADH dehydrogenase (ubiquinone) chain 2	582	425	3e-30	134	46.91
-50	lm_SuperContig_30_v2	64707	65165	mito_110 cytochrome-c oxidase chain III	227	74	2e-55	220	68.18
-51	lm_SuperContig_30_v2	110007	110387	mito_150 H+-transporting ATP synthase protein 6	134	6	2e-31	140	54.96
-51	lm_SuperContig_30_v2	108494	108691	mito_150 H+-transporting ATP synthase protein 6	179	114	3e-23	113	77.27
-52	lm_SuperContig_30_v2	103508	103711	mito_150 H+-transporting ATP synthase protein 6	261	194	7e-26	122	85.29
-53	lm_SuperContig_30_v2	17614	18054	mito_170 probable NADH dehydrogenase (ubiquinone) chain 4	83	229	3e-56	223	70.75
-53	lm_SuperContig_30_v2	19465	20481	mito_170 probable NADH dehydrogenase (ubiquinone) chain 4	195	536	3e-130	469	67.54
-54	lm_SuperContig_30_v2	17614	19341	mito_180 predicted ND4 intron protein	83	666	0	664	57.81
-55	lm_SuperContig_30_v2	61781	62653	mito_180 predicted ND4 intron protein	666	371	3e-63	246	42.62
-56	lm_SuperContig_30_v2	32542	33390	mito_180 predicted ND4 intron protein	372	648	6e-64	248	44.14
-57	lm_SuperContig_30_v2	82716	83615	mito_180 predicted ND4 intron protein	666	365	1e-60	237	41.45
-58	lm_SuperContig_30_v2	36329	37252	mito_180 predicted ND4 intron protein	374	668	2e-62	243	43.91
-59	lm_SuperContig_30_v2	109059	109979	mito_180 predicted ND4 intron protein	666	354	3e-58	229	37.7
-60	lm_SuperContig_30_v2	141030	141308	mito_180 predicted ND4 intron protein	376	469	3e-54	65	38.3
-60	lm_SuperContig_30_v2	141292	141897	mito_180 predicted ND4 intron protein	464	668	3e-54	173	43.9
-61	lm_SuperContig_30_v2	80825	81706	mito_180 predicted ND4 intron protein	667	371	1e-57	228	41.28
-62	lm_SuperContig_30_v2	149580	149747	mito_180 predicted ND4 intron protein	371	426	7e-54	59	44.64
-62	lm_SuperContig_30_v2	149743	150465	mito_180 predicted ND4 intron protein	425	667	7e-54	178	39.18
-63	lm_SuperContig_30_v2	63756	64718	mito_180 predicted ND4 intron protein	666	347	2e-57	227	42.25
-64	lm_SuperContig_30_v2	115189	116127	mito_180 predicted ND4 intron protein	352	666	8e-59	231	37.85
-65	lm_SuperContig_30_v2	86895	87770	mito_180 predicted ND4 intron protein	666	371	4e-57	226	41.47
-66	lm_SuperContig_30_v2	22509	23405	mito_180 predicted ND4 intron protein	372	668	3e-57	226	39
-67	lm_SuperContig_30_v2	90384	91256	mito_180 predicted ND4 intron protein	663	372	4e-43	179	32.55
-68	lm_SuperContig_30_v2	118439	119344	mito_180 predicted ND4 intron protein	371	667	3e-54	216	41.56
-69	lm_SuperContig_30_v2	56307	56585	mito_180 predicted ND4 intron protein	473	383	9e-27	64	43.01
-69	lm_SuperContig_30_v2	55774	56199	mito_180 predicted ND4 intron protein	624	480	9e-27	79	32.41
-70	lm_SuperContig_30_v2	117050	117955	mito_180 predicted ND4 intron protein	372	666	9e-54	215	41.5
-71	lm_SuperContig_30_v2	26640	27542	mito_180 predicted ND4 intron protein	365	666	9e-53	211	40.46
-72	lm_SuperContig_30_v2	151309	152232	mito_180 predicted ND4 intron protein	369	666	3e-50	203	40.76
-73	lm_SuperContig_30_v2	146610	147527	mito_180 predicted ND4 intron protein	376	666	6e-48	195	39.23
-74	lm_SuperContig_30_v2	42209	42388	mito_180 predicted ND4 intron protein	319	380	2e-21	26	30.16
-74	lm_SuperContig_30_v2	42457	42879	mito_180 predicted ND4 intron protein	384	528	2e-21	101	37.24
-75	lm_SuperContig_30_v2	125743	126138	mito_180 predicted ND4 intron protein	384	515	4e-23	113	41.67
-76	lm_SuperContig_30_v2	44197	44541	mito_190 NADH dehydrogenase (ubiquinone) chain 1	98	212	3e-43	180	76.52
-76	lm_SuperContig_30_v2	46832	47305	mito_190 NADH dehydrogenase (ubiquinone) chain 1	213	370	5e-44	182	59.01
-77	lm_SuperContig_30_v2	102101	102604	mito_210 cytochrome-c oxidase chain I	169	2	4e-74	282	80.36
-78	lm_SuperContig_30_v2	93858	94202	mito_210 cytochrome-c oxidase chain I	364	250	6e-51	205	87.83
-78	lm_SuperContig_30_v2	89713	89913	mito_210 cytochrome-c oxidase chain I	441	375	6e-24	116	79.1
-78	lm_SuperContig_30_v2	89139	89414	mito_210 cytochrome-c oxidase chain I	533	442	1e-22	111	58.7
-79	lm_SuperContig_30_v2	14626	15192	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	194	384	8e-78	295	73.82
-80	lm_SuperContig_30_v2	15860	16315	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	228	384	3e-37	160	56.25
-81	lm_SuperContig_30_v2	9733	9936	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	68	136	2e-27	127	89.86
-82	lm_SuperContig_30_v2	6405	6605	mito_220 ubiquinol--cytochrome-c reductase cytochrome b	1	67	2e-23	114	76.12
-83	lm_SuperContig_30_v2	9733	9936	mito_230 related to cob intron2 maturase/endonuclease	68	136	2e-27	127	89.86
-84	lm_SuperContig_30_v2	6405	6605	mito_230 related to cob intron2 maturase/endonuclease	1	67	2e-23	114	76.12
-85	lm_SuperContig_30_v2	9733	9927	mito_240 related to cob intron1 maturase	68	132	6e-27	126	90.77
-86	lm_SuperContig_30_v2	6405	6605	mito_240 related to cob intron1 maturase	1	67	2e-23	114	76.12
-87	lm_SuperContig_30_v2	18442	19341	mito_155 predicted ATP6 intron maturase	56	357	3e-68	263	45.07
-88	lm_SuperContig_30_v2	109056	110081	mito_155 predicted ATP6 intron maturase	358	11	4e-91	338	51.85
-89	lm_SuperContig_30_v2	36323	37249	mito_155 predicted ATP6 intron maturase	64	358	2e-63	247	45.02
-90	lm_SuperContig_30_v2	61781	62650	mito_155 predicted ATP6 intron maturase	357	64	2e-58	230	41.75
-91	lm_SuperContig_30_v2	141021	141311	mito_155 predicted ATP6 intron maturase	65	161	2e-51	79	42.86
-91	lm_SuperContig_30_v2	141292	141891	mito_155 predicted ATP6 intron maturase	155	357	2e-51	150	40
-92	lm_SuperContig_30_v2	80828	81703	mito_155 predicted ATP6 intron maturase	357	64	3e-51	206	39.6
-93	lm_SuperContig_30_v2	149583	149747	mito_155 predicted ATP6 intron maturase	64	117	6e-49	55	45.45
-93	lm_SuperContig_30_v2	149746	150462	mito_155 predicted ATP6 intron maturase	117	357	6e-49	165	38.93
-94	lm_SuperContig_30_v2	82716	83594	mito_155 predicted ATP6 intron maturase	357	64	1e-50	204	38.8
-95	lm_SuperContig_30_v2	116981	117955	mito_155 predicted ATP6 intron maturase	36	357	4e-53	213	37.01
-96	lm_SuperContig_30_v2	86895	87767	mito_155 predicted ATP6 intron maturase	357	64	7e-50	202	37.92
-97	lm_SuperContig_30_v2	146610	147533	mito_155 predicted ATP6 intron maturase	68	359	2e-52	210	42.22
-98	lm_SuperContig_30_v2	63756	64655	mito_155 predicted ATP6 intron maturase	357	60	1e-47	194	38.64
-99	lm_SuperContig_30_v2	151258	152232	mito_155 predicted ATP6 intron maturase	42	357	2e-52	210	39.34
-100	lm_SuperContig_30_v2	90381	91256	mito_155 predicted ATP6 intron maturase	355	64	8e-32	142	31
-101	lm_SuperContig_30_v2	32494	33504	mito_155 predicted ATP6 intron maturase	46	360	4e-52	209	37.64
-102	lm_SuperContig_30_v2	115198	116127	mito_155 predicted ATP6 intron maturase	47	357	1e-50	204	37.78
-103	lm_SuperContig_30_v2	26607	27542	mito_155 predicted ATP6 intron maturase	46	357	7e-50	202	37.34
-104	lm_SuperContig_30_v2	118442	119341	mito_155 predicted ATP6 intron maturase	64	357	7e-42	175	35.5
-105	lm_SuperContig_30_v2	22509	23387	mito_155 predicted ATP6 intron maturase	64	353	2e-37	161	31.19
-106	lm_SuperContig_30_v2	125740	126240	mito_155 predicted ATP6 intron maturase	75	237	3e-30	136	46.11
-107	lm_SuperContig_30_v2	44996	45490	mito_195 predicted ND1 intron protein	39	206	3e-48	196	57.74
-107	lm_SuperContig_30_v2	45636	45911	mito_195 predicted ND1 intron protein	209	300	2e-21	107	58.7
-108	lm_SuperContig_30_v2	46058	46228	mito_195 predicted ND1 intron protein	44	100	1e-70	58	51.72
-108	lm_SuperContig_30_v2	46230	46769	mito_195 predicted ND1 intron protein	101	304	1e-70	235	58.54
-109	lm_SuperContig_30_v2	14662	15189	SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual	206	381	1e-42	178	48.86
-110	lm_SuperContig_30_v2	15941	16303	SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual	260	378	1e-22	111	48.76
-111	lm_SuperContig_30_v2	64752	65204	SPMIT.04 |cox3||cytochrome c oxidase 3|Schizosaccharomyces pombe|chr mitochondrial|||Manual	215	65	2e-34	150	50.98
-112	lm_SuperContig_30_v2	94345	95262	SPMIT.03 |||hypothetical protein|Schizosaccharomyces pombe|chr mitochondrial||Partial|Manual	312	3	1e-94	350	57.68
-113	lm_SuperContig_30_v2	102098	102580	SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual	171	10	3e-48	196	54.94
-114	lm_SuperContig_30_v2	93876	94202	SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual	360	251	3e-30	136	58.56
-115	lm_SuperContig_29_v2	77989	78369	Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	3	126	2e-22	105	40.94
-116	lm_SuperContig_29_v2	193985	194365	Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	126	3	1e-21	105	40.94
-117	lm_SuperContig_29_v2	78109	78582	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	20	177	7e-59	207	58.86
-117	lm_SuperContig_29_v2	78662	78817	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	180	231	7e-59	42	30.77
-118	lm_SuperContig_29_v2	193772	194245	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	177	20	2e-128	207	58.86
-118	lm_SuperContig_29_v2	192760	193692	Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	485	180	2e-128	275	41.8
-119	lm_SuperContig_29_v2	78010	78567	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	21	208	5e-23	100	29.79
-119	lm_SuperContig_29_v2	78662	78808	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	216	261	5e-23	28	26.53
-120	lm_SuperContig_29_v2	193787	194344	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	208	21	3e-40	100	29.79
-120	lm_SuperContig_29_v2	192766	193692	Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	535	216	3e-40	88	22.53
-121	lm_SuperContig_29_v2	78109	78588	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	45	204	1e-39	144	43.75
-121	lm_SuperContig_29_v2	78662	78817	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	205	258	1e-39	40	45.61
-122	lm_SuperContig_29_v2	193766	194245	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	204	45	2e-83	144	43.75
-122	lm_SuperContig_29_v2	192754	193692	Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100	521	205	2e-83	188	33.33
-123	lm_SuperContig_29_v2	78061	78573	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	15	189	3e-22	87	29.71
-123	lm_SuperContig_29_v2	78662	78814	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	195	242	3e-22	39	39.22
-124	lm_SuperContig_29_v2	193781	194293	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	189	15	1e-49	87	29.71
-124	lm_SuperContig_29_v2	192760	193692	Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	506	195	1e-49	133	27.85
-125	lm_SuperContig_29_v2	78007	78576	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	48	237	2e-59	198	47.37
-125	lm_SuperContig_29_v2	78662	78817	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	242	293	2e-59	52	46.15
-126	lm_SuperContig_29_v2	193778	194347	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	237	48	1e-79	198	47.37
-126	lm_SuperContig_29_v2	193288	193692	Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101	375	242	1e-79	122	43.7
-127	lm_SuperContig_29_v2	78133	78576	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	77	224	2e-44	159	51.35
-127	lm_SuperContig_29_v2	78662	78817	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	229	282	2e-44	41	41.07
-128	lm_SuperContig_29_v2	193778	194221	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	224	77	3e-91	159	51.35
-128	lm_SuperContig_29_v2	192760	193692	Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102	541	229	3e-91	200	35.65
-129	lm_SuperContig_29_v2	133669	134343	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	226	2	3e-37	159	37.78
-130	lm_SuperContig_29_v2	167776	168372	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	9e-34	145	38.69
-131	lm_SuperContig_29_v2	41484	42080	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	8e-32	142	38.69
-132	lm_SuperContig_29_v2	101404	102000	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	200	2	3e-31	140	38.69
-133	lm_SuperContig_29_v2	31868	32272	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	136	4	6e-25	95	38.52
-133	lm_SuperContig_29_v2	31597	31836	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	147	6e-25	46	33.73
-134	lm_SuperContig_29_v2	16462	17082	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	208	2	4e-30	135	37.2
-135	lm_SuperContig_29_v2	178590	179264	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	4	1e-29	133	35.96
-136	lm_SuperContig_29_v2	10942	11625	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	1	2e-29	132	35.06
-137	lm_SuperContig_29_v2	91888	92562	Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	229	4	3e-27	126	35.53
-138	lm_SuperContig_29_v2	78184	78585	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	53	186	2e-25	96	35.07
-138	lm_SuperContig_29_v2	78644	78814	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	186	239	2e-25	41	40.35
-139	lm_SuperContig_29_v2	193769	194170	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	186	53	3e-59	96	35.07
-139	lm_SuperContig_29_v2	192964	193710	Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104	430	186	3e-59	156	35.74
-140	lm_SuperContig_29_v2	78049	78567	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	19	191	3e-23	101	27.75
-140	lm_SuperContig_29_v2	78659	78775	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	198	236	3e-23	28	28.21
-141	lm_SuperContig_29_v2	193787	194305	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	191	19	9e-43	101	27.75
-141	lm_SuperContig_29_v2	192904	193695	Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	459	198	9e-43	96	26.12
-142	lm_SuperContig_29_v2	78151	78576	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	93	235	3e-31	124	41.96
-142	lm_SuperContig_29_v2	78662	78814	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	242	293	3e-31	32	30.77
-143	lm_SuperContig_29_v2	193778	194203	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	235	93	6e-83	124	41.96
-143	lm_SuperContig_29_v2	192760	193692	Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	552	242	6e-83	207	32.69
-144	lm_SuperContig_29_v2	78109	78576	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	34	189	3e-49	169	50
-144	lm_SuperContig_29_v2	78650	78814	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	190	245	3e-49	48	35.71
-145	lm_SuperContig_29_v2	193778	194245	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	189	34	2e-97	169	50
-145	lm_SuperContig_29_v2	192772	193704	Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108	501	190	2e-97	210	32.27
-146	lm_SuperContig_29_v2	78115	78576	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	51	204	6e-62	204	58.44
-146	lm_SuperContig_29_v2	78662	78817	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	209	260	6e-62	55	40.38
-147	lm_SuperContig_29_v2	193778	194239	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	204	51	1e-132	204	58.44
-147	lm_SuperContig_29_v2	192754	193692	Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53	520	209	1e-132	293	43.77
-148	lm_SuperContig_29_v2	193784	194323	Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92	195	16	1e-31	89	25
-148	lm_SuperContig_29_v2	192868	193695	Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92	482	201	1e-31	70	21.48
-149	lm_SuperContig_29_v2	193793	194221	fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5	169	27	6e-29	97	32.87
-149	lm_SuperContig_29_v2	193303	193707	fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5	308	174	6e-29	54	28.06
-150	lm_SuperContig_29_v2	193784	194221	fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168	205	60	7e-40	78	27.4
-150	lm_SuperContig_29_v2	192877	193695	fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168	483	215	7e-40	109	24.18
-151	lm_SuperContig_29_v2	77956	78576	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	2	220	7e-35	126	34.25
-151	lm_SuperContig_29_v2	78650	78814	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	221	272	7e-35	42	34.55
-152	lm_SuperContig_29_v2	193778	194398	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	220	2	7e-62	126	34.25
-152	lm_SuperContig_29_v2	192883	193704	fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35	490	221	7e-62	135	29.2
-153	lm_SuperContig_29_v2	78124	78576	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	62	212	4e-45	166	52.32
-153	lm_SuperContig_29_v2	78662	78718	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	217	236	4e-45	36	65
-154	lm_SuperContig_29_v2	193778	194230	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	212	62	1e-92	166	52.32
-154	lm_SuperContig_29_v2	192769	193692	fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231	537	217	1e-92	197	32.61
-155	lm_SuperContig_29_v2	193778	194383	fg12717 related to putative multidrug transporter, Contig fg_contig_1.37	219	15	2e-26	76	25.85
-155	lm_SuperContig_29_v2	193222	193707	fg12717 related to putative multidrug transporter, Contig fg_contig_1.37	402	218	2e-26	66	25
-156	lm_SuperContig_29_v2	193784	194248	b13o8_150 conserved hypothetical protein	232	73	3e-31	85	28.12
-156	lm_SuperContig_29_v2	193036	193695	b13o8_150 conserved hypothetical protein	460	238	3e-31	73	23.35
-157	lm_SuperContig_29_v2	78010	78585	b18d24_100 related to tetracycline efflux protein (otrb)	9	199	2e-27	99	28.12
-157	lm_SuperContig_29_v2	78644	78814	b18d24_100 related to tetracycline efflux protein (otrb)	197	250	2e-27	43	42.11
-158	lm_SuperContig_29_v2	193769	194344	b18d24_100 related to tetracycline efflux protein (otrb)	199	9	4e-60	99	28.12
-158	lm_SuperContig_29_v2	192916	193710	b18d24_100 related to tetracycline efflux protein (otrb)	457	197	4e-60	155	33.96
-159	lm_SuperContig_29_v2	78184	78576	b5k2_230 related to major facilitator (MFS1) transporter	211	341	4e-42	141	50.38
-159	lm_SuperContig_29_v2	78662	78814	b5k2_230 related to major facilitator (MFS1) transporter	346	396	4e-42	51	49.06
-160	lm_SuperContig_29_v2	193778	194170	b5k2_230 related to major facilitator (MFS1) transporter	341	211	7e-99	141	50.38
-160	lm_SuperContig_29_v2	192760	193692	b5k2_230 related to major facilitator (MFS1) transporter	657	346	7e-99	243	38.1
-161	lm_SuperContig_29_v2	193781	194212	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	228	85	1e-40	84	30.56
-161	lm_SuperContig_29_v2	192832	193704	1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)	522	229	1e-40	106	23.99
-162	lm_SuperContig_29_v2	77941	78576	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	28	241	1e-30	111	28.97
-162	lm_SuperContig_29_v2	78662	78736	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	246	270	1e-30	42	56
-163	lm_SuperContig_29_v2	193778	194413	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	241	28	5e-62	111	28.97
-163	lm_SuperContig_29_v2	192760	193692	1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter)	559	246	5e-62	149	28.3
-164	lm_SuperContig_29_v2	193778	194086	6nc360_090 related to DHA14-like major facilitator	188	86	8e-44	69	38.83
-164	lm_SuperContig_29_v2	192817	193695	6nc360_090 related to DHA14-like major facilitator	491	194	8e-44	132	28.9
-165	lm_SuperContig_29_v2	78112	78576	29e8_240 probable aflatoxin efflux pump AFLT	62	216	1e-56	190	55.48
-165	lm_SuperContig_29_v2	78662	78817	29e8_240 probable aflatoxin efflux pump AFLT	221	272	1e-56	50	40.38
-166	lm_SuperContig_29_v2	193778	194242	29e8_240 probable aflatoxin efflux pump AFLT	216	62	2e-117	190	55.48
-166	lm_SuperContig_29_v2	192769	193692	29e8_240 probable aflatoxin efflux pump AFLT	535	221	2e-117	256	41.14
-167	lm_SuperContig_29_v2	193787	194218	7nc450_010 related to multidrug resistance protein	221	78	3e-24	57	20.83
-167	lm_SuperContig_29_v2	192940	193695	7nc450_010 related to multidrug resistance protein	484	228	3e-24	79	25
-168	lm_SuperContig_29_v2	193781	194218	4nc446_010 related to putative multidrug transporter	253	106	3e-48	82	29.73
-168	lm_SuperContig_29_v2	192865	193692	4nc446_010 related to putative multidrug transporter	530	259	3e-48	134	28.26
-169	lm_SuperContig_29_v2	193766	194239	b11e5_230 related to multidrug resistance protein fnx1	254	97	1e-40	97	29.75
-169	lm_SuperContig_29_v2	192904	193704	b11e5_230 related to multidrug resistance protein fnx1	518	253	1e-40	93	25.27
-170	lm_SuperContig_29_v2	77935	78576	xnc126_050 probable DHA14-like major facilitator; ABC transporter	38	241	7e-60	190	46.26
-170	lm_SuperContig_29_v2	78662	78817	xnc126_050 probable DHA14-like major facilitator; ABC transporter	246	298	7e-60	62	43.4
-171	lm_SuperContig_29_v2	193778	194419	xnc126_050 probable DHA14-like major facilitator; ABC transporter	241	38	2e-130	190	46.26
-171	lm_SuperContig_29_v2	192757	193692	xnc126_050 probable DHA14-like major facilitator; ABC transporter	559	246	2e-130	299	45.08
-172	lm_SuperContig_29_v2	78109	78576	4nc135_070 related to aflatoxin efflux pump AFLT	17	172	2e-53	184	53.85
-172	lm_SuperContig_29_v2	78662	78817	4nc135_070 related to aflatoxin efflux pump AFLT	177	238	2e-53	46	38.71
-173	lm_SuperContig_29_v2	193778	194245	4nc135_070 related to aflatoxin efflux pump AFLT	172	17	4e-99	184	53.85
-173	lm_SuperContig_29_v2	192751	193692	4nc135_070 related to aflatoxin efflux pump AFLT	494	177	4e-99	201	34.46
-174	lm_SuperContig_29_v2	78031	78588	xnc164_090 related to multidrug resistance protein	19	209	3e-21	101	30.89
-175	lm_SuperContig_29_v2	193766	194323	xnc164_090 related to multidrug resistance protein	209	19	1e-42	101	30.89
-175	lm_SuperContig_29_v2	192802	193692	xnc164_090 related to multidrug resistance protein	509	210	1e-42	95	26.77
-176	lm_SuperContig_29_v2	193766	194107	YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane	117	6	3e-23	57	27.19
-176	lm_SuperContig_29_v2	192916	193704	YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane	384	116	3e-23	74	23.53
-177	lm_SuperContig_29_v2	193778	193954	YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane	61	3	7e-28	52	38.98
-177	lm_SuperContig_29_v2	192985	193692	YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane	335	66	7e-28	95	28.04
-178	lm_SuperContig_29_v2	197024	197422	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	298	166	5e-24	113	45.52
-179	lm_SuperContig_29_v2	197027	197413	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	292	164	2e-23	111	46.56
-180	lm_SuperContig_29_v2	197039	197437	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	310	170	2e-22	108	46.1
-181	lm_SuperContig_29_v2	197021	197416	YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3	282	151	3e-22	107	39.39
-182	lm_SuperContig_29_v2	40143	42272	YGR109w-b TY3B TY3B protein	1301	616	6e-39	165	26.47
-183	lm_SuperContig_29_v2	16081	17274	YGR109w-b TY3B TY3B protein	1008	616	4e-35	152	30.33
-184	lm_SuperContig_29_v2	100993	102192	YGR109w-b TY3B TY3B protein	1008	616	8e-35	151	30.92
-185	lm_SuperContig_29_v2	167371	168564	YGR109w-b TY3B TY3B protein	1008	616	2e-35	151	30.83
-186	lm_SuperContig_29_v2	133543	134535	YGR109w-b TY3B TY3B protein	943	616	4e-34	149	32.23
-187	lm_SuperContig_29_v2	91762	92754	YGR109w-b TY3B TY3B protein	944	618	4e-23	113	30.24
-188	lm_SuperContig_29_v2	178464	179477	YGR109w-b TY3B TY3B protein	944	611	1e-21	107	29.03
-189	lm_SuperContig_29_v2	78139	78582	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	70	217	1e-27	105	39.19
-189	lm_SuperContig_29_v2	78662	78724	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	220	240	1e-27	39	57.14
-190	lm_SuperContig_29_v2	193772	194215	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	217	70	6e-27	105	39.19
-190	lm_SuperContig_29_v2	193630	193692	YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs	240	220	6e-27	39	57.14
-191	lm_SuperContig_29_v2	197024	197437	YHL028w WSC4 Cell wall integrity and stress response component 4	276	136	3e-25	117	47.52
-192	lm_SuperContig_29_v2	197024	197413	YHL028w WSC4 Cell wall integrity and stress response component 4	323	190	3e-23	111	47.01
-193	lm_SuperContig_29_v2	197024	197425	YHL028w WSC4 Cell wall integrity and stress response component 4	290	148	2e-23	111	49.65
-194	lm_SuperContig_29_v2	197024	197434	YHL028w WSC4 Cell wall integrity and stress response component 4	332	197	2e-22	108	42.03
-195	lm_SuperContig_29_v2	197024	197482	YHL028w WSC4 Cell wall integrity and stress response component 4	300	147	5e-22	107	41.29
-196	lm_SuperContig_29_v2	197027	197482	YHL028w WSC4 Cell wall integrity and stress response component 4	336	184	5e-22	107	39.22
-197	lm_SuperContig_29_v2	197024	197410	YHL028w WSC4 Cell wall integrity and stress response component 4	314	179	6e-22	106	47.79
-198	lm_SuperContig_29_v2	197024	197434	YHL028w WSC4 Cell wall integrity and stress response component 4	257	117	8e-21	103	42.55
-199	lm_SuperContig_29_v2	40143	42272	YIL082w-a TY3B TY3B protein	1327	642	8e-39	165	26.47
-200	lm_SuperContig_29_v2	16081	17274	YIL082w-a TY3B TY3B protein	1034	642	1e-34	150	30.33
-201	lm_SuperContig_29_v2	100993	102192	YIL082w-a TY3B TY3B protein	1034	642	3e-34	150	30.92
-202	lm_SuperContig_29_v2	167371	168564	YIL082w-a TY3B TY3B protein	1034	642	6e-35	149	30.83
-203	lm_SuperContig_29_v2	133543	134535	YIL082w-a TY3B TY3B protein	969	642	1e-33	147	32.23
-204	lm_SuperContig_29_v2	91762	92754	YIL082w-a TY3B TY3B protein	970	644	5e-23	112	30.24
-205	lm_SuperContig_29_v2	178464	179477	YIL082w-a TY3B TY3B protein	970	637	1e-21	106	29.03
-206	lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	267	132	1e-33	145	58.09
-207	lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	290	156	2e-33	144	57.78
-208	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	261	126	3e-33	144	58.39
-209	lm_SuperContig_29_v2	197021	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	300	165	6e-33	143	57.35
-210	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	285	147	6e-33	143	57.55
-211	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	276	141	6e-33	143	57.66
-212	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	281	144	1e-32	142	55.8
-213	lm_SuperContig_29_v2	197024	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	303	174	3e-32	140	57.46
-214	lm_SuperContig_29_v2	197030	197404	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	248	124	3e-32	140	59.2
-215	lm_SuperContig_29_v2	197024	197398	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	246	123	1e-31	139	60
-216	lm_SuperContig_29_v2	197024	197395	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	240	118	1e-31	139	59.68
-217	lm_SuperContig_29_v2	197039	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	318	183	1e-31	139	57.35
-218	lm_SuperContig_29_v2	197027	197437	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	244	108	2e-31	138	57.97
-219	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	314	174	3e-31	137	55.32
-220	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	350	201	1e-28	128	52
-221	lm_SuperContig_29_v2	197024	197392	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	222	102	1e-26	122	56.91
-222	lm_SuperContig_29_v2	197021	197425	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	360	219	3e-25	118	52.08
-223	lm_SuperContig_29_v2	197024	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	372	228	2e-24	115	48.28
-224	lm_SuperContig_29_v2	197036	197434	YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth	378	246	7e-23	109	42.86
-225	lm_SuperContig_29_v2	78112	78576	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	31	185	7e-29	105	33.55
-225	lm_SuperContig_29_v2	78662	78778	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	190	227	7e-29	43	48.72
-226	lm_SuperContig_29_v2	193778	194242	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	185	31	4e-43	105	33.55
-226	lm_SuperContig_29_v2	192985	193692	YKR105c  Putative member of family of basic amino acid transporters localised to vacuolar membrane	459	190	4e-43	94	27.68
-227	lm_SuperContig_29_v2	197024	197434	YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3	272	139	4e-22	107	45.65
-228	lm_SuperContig_29_v2	197042	197422	YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3	275	147	8e-21	103	45.8
-229	lm_SuperContig_29_v2	133471	134754	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-229	lm_SuperContig_29_v2	133341	133436	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-230	lm_SuperContig_29_v2	100993	102531	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-231	lm_SuperContig_29_v2	41079	42287	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-232	lm_SuperContig_29_v2	167371	168579	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-233	lm_SuperContig_29_v2	16081	17289	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-234	lm_SuperContig_29_v2	91693	92700	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-235	lm_SuperContig_29_v2	178395	179504	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-236	lm_SuperContig_29_v2	10747	11856	SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-237	lm_SuperContig_29_v2	193787	194218	SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual	176	33	1e-35	85	31.25
-237	lm_SuperContig_29_v2	192757	193695	SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual	499	183	1e-35	89	22.84
-238	lm_SuperContig_29_v2	133471	134754	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-238	lm_SuperContig_29_v2	133341	133436	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-239	lm_SuperContig_29_v2	100993	102531	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-240	lm_SuperContig_29_v2	41079	42287	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-241	lm_SuperContig_29_v2	167371	168579	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-242	lm_SuperContig_29_v2	16081	17289	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-243	lm_SuperContig_29_v2	91693	92700	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-244	lm_SuperContig_29_v2	178395	179504	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-245	lm_SuperContig_29_v2	10747	11856	SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-246	lm_SuperContig_29_v2	133471	134754	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	358	2e-46	184	28.54
-246	lm_SuperContig_29_v2	133341	133436	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	800	2e-46	27	46.88
-247	lm_SuperContig_29_v2	100993	102531	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	312	3e-44	183	27.86
-248	lm_SuperContig_29_v2	41079	42287	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	3e-42	176	28.89
-249	lm_SuperContig_29_v2	167371	168579	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	8e-43	175	29.38
-250	lm_SuperContig_29_v2	16081	17289	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	2e-39	166	28.15
-251	lm_SuperContig_29_v2	91693	92700	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	452	1e-37	161	32.94
-252	lm_SuperContig_29_v2	178395	179504	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	1e-37	160	30.91
-253	lm_SuperContig_29_v2	10747	11856	SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	1e-36	157	31.18
-254	lm_SuperContig_29_v2	77950	78588	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	34	242	5e-29	109	30.99
-254	lm_SuperContig_29_v2	78662	78799	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	243	286	5e-29	39	41.3
-255	lm_SuperContig_29_v2	193766	194404	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	242	34	2e-50	109	30.99
-255	lm_SuperContig_29_v2	192844	193692	SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual	525	243	2e-50	113	28.03
-256	lm_SuperContig_29_v2	133471	134754	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	358	4e-46	183	28.31
-256	lm_SuperContig_29_v2	133341	133436	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	800	4e-46	27	46.88
-257	lm_SuperContig_29_v2	100993	102531	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	312	7e-44	182	27.67
-258	lm_SuperContig_29_v2	41079	42287	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	7e-42	175	28.64
-259	lm_SuperContig_29_v2	167371	168579	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	2e-42	174	29.14
-260	lm_SuperContig_29_v2	16081	17289	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	831	427	4e-39	165	27.9
-261	lm_SuperContig_29_v2	91693	92700	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	452	3e-37	159	32.64
-262	lm_SuperContig_29_v2	178395	179504	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	418	3e-37	158	30.65
-263	lm_SuperContig_29_v2	10747	11856	SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual	786	418	3e-36	155	30.91
-264	lm_SuperContig_29_v2	193781	194482	SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	236	4	7e-34	95	23.93
-264	lm_SuperContig_29_v2	192760	193692	SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	551	242	7e-34	72	21.77
-265	lm_SuperContig_29_v2	133471	134754	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-265	lm_SuperContig_29_v2	133341	133436	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-266	lm_SuperContig_29_v2	100993	102531	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-267	lm_SuperContig_29_v2	41079	42287	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-268	lm_SuperContig_29_v2	167371	168579	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-269	lm_SuperContig_29_v2	16081	17289	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-270	lm_SuperContig_29_v2	91693	92700	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-271	lm_SuperContig_29_v2	178395	179504	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-272	lm_SuperContig_29_v2	10747	11856	SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-273	lm_SuperContig_29_v2	78133	78570	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	97	242	3e-30	115	39.04
-273	lm_SuperContig_29_v2	78662	78799	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	249	292	3e-30	37	42.55
-274	lm_SuperContig_29_v2	193784	194221	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	242	97	2e-55	115	39.04
-274	lm_SuperContig_29_v2	192874	193692	SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual	518	249	2e-55	124	27.37
-275	lm_SuperContig_29_v2	77950	78588	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	34	242	8e-30	114	30.99
-275	lm_SuperContig_29_v2	78662	78736	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	243	267	8e-30	37	52
-276	lm_SuperContig_29_v2	193766	194404	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	242	34	3e-53	114	30.99
-276	lm_SuperContig_29_v2	192844	193692	SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual	525	243	3e-53	118	30.8
-277	lm_SuperContig_29_v2	133471	134754	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-277	lm_SuperContig_29_v2	133341	133436	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-278	lm_SuperContig_29_v2	100993	102531	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-279	lm_SuperContig_29_v2	41079	42287	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-280	lm_SuperContig_29_v2	167371	168579	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-281	lm_SuperContig_29_v2	16081	17289	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-282	lm_SuperContig_29_v2	91693	92700	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-283	lm_SuperContig_29_v2	178395	179504	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-284	lm_SuperContig_29_v2	10747	11856	SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-285	lm_SuperContig_29_v2	133471	134754	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	2e-46	184	28.54
-285	lm_SuperContig_29_v2	133341	133436	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	2e-46	27	46.88
-286	lm_SuperContig_29_v2	100993	102531	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	3e-44	183	27.86
-287	lm_SuperContig_29_v2	41079	42287	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	3e-42	176	28.89
-288	lm_SuperContig_29_v2	167371	168579	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	8e-43	175	29.38
-289	lm_SuperContig_29_v2	16081	17289	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-39	166	28.15
-290	lm_SuperContig_29_v2	91693	92700	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	1e-37	161	32.94
-291	lm_SuperContig_29_v2	178395	179504	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-37	160	30.91
-292	lm_SuperContig_29_v2	10747	11856	SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-36	157	31.18
-293	lm_SuperContig_29_v2	133471	134754	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-293	lm_SuperContig_29_v2	133341	133436	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-294	lm_SuperContig_29_v2	100993	102531	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-295	lm_SuperContig_29_v2	41079	42287	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-296	lm_SuperContig_29_v2	167371	168579	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-297	lm_SuperContig_29_v2	16081	17289	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-298	lm_SuperContig_29_v2	91693	92700	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-299	lm_SuperContig_29_v2	178395	179504	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-300	lm_SuperContig_29_v2	10747	11856	SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-301	lm_SuperContig_29_v2	133471	134754	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	2e-46	184	28.54
-301	lm_SuperContig_29_v2	133341	133436	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	2e-46	27	46.88
-302	lm_SuperContig_29_v2	100993	102531	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	3e-44	183	27.86
-303	lm_SuperContig_29_v2	41079	42287	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	3e-42	176	28.89
-304	lm_SuperContig_29_v2	167371	168579	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	8e-43	175	29.38
-305	lm_SuperContig_29_v2	16081	17289	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-39	166	28.15
-306	lm_SuperContig_29_v2	91693	92700	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	1e-37	161	32.94
-307	lm_SuperContig_29_v2	178395	179504	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-37	160	30.91
-308	lm_SuperContig_29_v2	10747	11856	SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	1e-36	157	31.18
-309	lm_SuperContig_29_v2	133471	134754	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	358	4e-46	183	28.31
-309	lm_SuperContig_29_v2	133341	133436	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	800	4e-46	27	46.88
-310	lm_SuperContig_29_v2	100993	102531	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	312	7e-44	182	27.67
-311	lm_SuperContig_29_v2	41079	42287	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	7e-42	175	28.64
-312	lm_SuperContig_29_v2	167371	168579	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	2e-42	174	29.14
-313	lm_SuperContig_29_v2	16081	17289	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	831	427	4e-39	165	27.9
-314	lm_SuperContig_29_v2	91693	92700	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	452	3e-37	159	32.64
-315	lm_SuperContig_29_v2	178395	179504	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	3e-37	158	30.65
-316	lm_SuperContig_29_v2	10747	11856	SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual	786	418	3e-36	155	30.91
-317	lm_SuperContig_29_v2	133471	134754	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	358	4e-46	183	28.31
-317	lm_SuperContig_29_v2	133341	133436	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	800	4e-46	27	46.88
-318	lm_SuperContig_29_v2	100993	102531	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	312	7e-44	182	27.67
-319	lm_SuperContig_29_v2	41079	42287	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	7e-42	175	28.64
-320	lm_SuperContig_29_v2	167371	168579	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	2e-42	174	29.14
-321	lm_SuperContig_29_v2	16081	17289	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	831	427	4e-39	165	27.9
-322	lm_SuperContig_29_v2	91693	92700	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	452	3e-37	159	32.64
-323	lm_SuperContig_29_v2	178395	179504	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-37	158	30.65
-324	lm_SuperContig_29_v2	10747	11856	SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual	786	418	3e-36	155	30.91
-325	lm_SuperContig_29_v2	77980	78567	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	18	211	5e-25	114	31
-326	lm_SuperContig_29_v2	193787	194374	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	211	18	2e-42	114	31
-326	lm_SuperContig_29_v2	192772	193695	um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17	529	218	2e-42	82	20.7
-327	lm_SuperContig_29_v2	78115	78588	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	53	210	2e-53	183	55.06
-327	lm_SuperContig_29_v2	78662	78814	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	211	264	2e-53	47	44.44
-328	lm_SuperContig_29_v2	193766	194239	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	210	53	2e-104	183	55.06
-328	lm_SuperContig_29_v2	192760	193692	um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27	534	211	2e-104	220	36.92
-329	lm_SuperContig_29_v2	78112	78570	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	94	246	7e-23	104	35.95
-329	lm_SuperContig_29_v2	78659	78802	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	253	297	7e-23	24	25
-330	lm_SuperContig_29_v2	193784	194242	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	246	94	5e-40	104	35.95
-330	lm_SuperContig_29_v2	192760	193695	um01882 related to multidrug resistance proteins, Contig um_contig_1.70	560	253	5e-40	84	19.43
-331	lm_SuperContig_29_v2	78019	78567	um01964 related to multidrug resistance protein, Contig um_contig_1.72	40	220	1e-24	113	33.7
-332	lm_SuperContig_29_v2	193787	194335	um01964 related to multidrug resistance protein, Contig um_contig_1.72	220	40	7e-43	113	33.7
-332	lm_SuperContig_29_v2	192901	193695	um01964 related to multidrug resistance protein, Contig um_contig_1.72	490	227	7e-43	85	24.16
-333	lm_SuperContig_29_v2	77890	78591	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	38	263	1e-32	115	32.07
-333	lm_SuperContig_29_v2	78659	78814	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	264	313	1e-32	46	36.54
-334	lm_SuperContig_29_v2	193763	194464	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	263	38	1e-65	115	32.07
-334	lm_SuperContig_29_v2	192760	193695	um02062 related to multidrug resistance proteins, Contig um_contig_1.75	575	264	1e-65	158	30.6
-335	lm_SuperContig_29_v2	78136	78576	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	133	280	1e-21	91	30.41
-335	lm_SuperContig_29_v2	78650	78814	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	280	331	1e-21	33	29.09
-336	lm_SuperContig_29_v2	193778	194218	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	280	133	3e-45	91	30.41
-336	lm_SuperContig_29_v2	192754	193704	um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86	598	280	3e-45	114	25.93
-337	lm_SuperContig_29_v2	77938	78585	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	27	239	2e-24	93	30.73
-337	lm_SuperContig_29_v2	78650	78808	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	236	285	2e-24	40	33.96
-338	lm_SuperContig_29_v2	193769	194416	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	239	27	1e-48	93	30.73
-338	lm_SuperContig_29_v2	192757	193704	um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105	554	236	1e-48	124	25.7
-339	lm_SuperContig_29_v2	77938	78576	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	13	215	4e-45	167	39.91
-339	lm_SuperContig_29_v2	78650	78736	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	216	244	4e-45	36	55.17
-340	lm_SuperContig_29_v2	193778	194416	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	215	13	2e-98	167	39.91
-340	lm_SuperContig_29_v2	192826	193704	um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192	511	216	2e-98	216	37.04
-341	lm_SuperContig_29_v2	193778	194107	um05421 related to Multidrug resistance protein , Contig um_contig_1.192	267	158	6e-41	83	35.45
-341	lm_SuperContig_29_v2	193006	193692	um05421 related to Multidrug resistance protein , Contig um_contig_1.192	496	272	6e-41	107	27.07

--- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.tab	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,342 +0,0 @@
-query.name	query.start	query.end	query.length	query.length.%	match.length.%	subject.name	subject.start	subject.end	subject.length	subject.length.%	E.value	Score	Identity	path
-lm_SuperContig_30_v2	35498	37823	927	0.00598594	1.29469	mito_010	307	663	309	0.431564	8e-67	424	74.4336	1
-lm_SuperContig_30_v2	27615	29673	558	0.00360318	0.77933	mito_010	109	310	186	0.259777	1e-53	244	82.2577	2
-lm_SuperContig_30_v2	23817	24089	273	0.00176285	0.381285	mito_010	1	91	91	0.127095	7e-25	119	63.74	3
-lm_SuperContig_30_v2	27615	29418	1125	0.00726449	2.06044	mito_020	109	540	367	0.672161	1e-53	329	53.6941	4
-lm_SuperContig_30_v2	94306	95085	780	0.00503671	1.42857	mito_020	544	279	266	0.487179	2e-22	110	28.46	5
-lm_SuperContig_30_v2	23817	24089	273	0.00176285	0.5	mito_020	1	91	91	0.166667	7e-25	119	63.74	6
-lm_SuperContig_30_v2	23817	27509	1593	0.0102865	2.98315	mito_030	1	525	525	0.983146	0	680	74.3298	7
-lm_SuperContig_30_v2	61805	62656	852	0.00550164	1.59551	mito_030	528	241	288	0.539326	3e-55	219	38.89	8
-lm_SuperContig_30_v2	146223	147503	1281	0.00827183	2.39888	mito_030	114	528	415	0.777154	2e-64	250	37.61	9
-lm_SuperContig_30_v2	109092	109925	834	0.00538541	1.5618	mito_030	525	243	283	0.529963	2e-49	200	38.16	10
-lm_SuperContig_30_v2	117965	119308	1344	0.00867864	2.51685	mito_030	87	525	439	0.822097	1e-63	248	35.79	11
-lm_SuperContig_30_v2	82749	83615	867	0.0055985	1.6236	mito_030	525	236	290	0.543071	3e-47	193	35.27	12
-lm_SuperContig_30_v2	35963	37213	1251	0.00807811	2.3427	mito_030	114	525	412	0.771536	4e-62	242	38.08	13
-lm_SuperContig_30_v2	86928	87770	843	0.00544352	1.57865	mito_030	525	242	284	0.531835	3e-47	193	36.14	14
-lm_SuperContig_30_v2	116645	117925	1281	0.00827183	2.39888	mito_030	121	526	406	0.7603	6e-60	235	37.12	15
-lm_SuperContig_30_v2	80861	81706	846	0.00546289	1.58427	mito_030	525	242	284	0.531835	5e-44	182	35.66	16
-lm_SuperContig_30_v2	150994	152199	1206	0.00778753	2.25843	mito_030	121	525	405	0.758427	4e-58	229	36.3	17
-lm_SuperContig_30_v2	55780	56582	699	0.00451367	1.30899	mito_030	492	255	233	0.43633	1e-34	118	37.7177	18
-lm_SuperContig_30_v2	18181	19317	1137	0.00734197	2.12921	mito_030	167	528	362	0.677903	3e-57	226	37.76	19
-lm_SuperContig_30_v2	90399	91238	840	0.00542415	1.57303	mito_030	528	249	280	0.524345	1e-37	161	32.52	20
-lm_SuperContig_30_v2	141039	141858	820	0.005295	1.53558	mito_030	250	525	276	0.516854	8e-47	212	39.6261	21
-lm_SuperContig_30_v2	63837	64676	840	0.00542415	1.57303	mito_030	511	232	280	0.524345	1e-35	155	35.21	22
-lm_SuperContig_30_v2	115228	116103	876	0.00565661	1.64045	mito_030	236	528	293	0.548689	6e-48	195	35.93	23
-lm_SuperContig_30_v2	149559	150444	882	0.00569536	1.65169	mito_030	233	530	296	0.554307	6e-40	189	36.7922	24
-lm_SuperContig_30_v2	22437	23375	939	0.00606342	1.75843	mito_030	219	528	310	0.580524	1e-43	181	32.59	25
-lm_SuperContig_30_v2	32527	33390	864	0.00557912	1.61798	mito_030	236	518	283	0.529963	6e-40	169	36.15	26
-lm_SuperContig_30_v2	21984	22220	237	0.00153038	2.63333	mito_040	1	79	79	0.877778	3e-30	136	84.81	27
-lm_SuperContig_30_v2	21984	23387	1125	0.00726449	2.48344	mito_050	1	438	376	0.830022	7e-81	419	56.4194	28
-lm_SuperContig_30_v2	61793	62650	858	0.00554038	1.89404	mito_050	438	145	294	0.649007	3e-49	200	40.33	29
-lm_SuperContig_30_v2	18466	19329	864	0.00557912	1.90728	mito_050	145	438	294	0.649007	6e-54	215	40.53	30
-lm_SuperContig_30_v2	80849	81703	855	0.00552101	1.88742	mito_050	435	145	291	0.642384	1e-45	188	39.6	31
-lm_SuperContig_30_v2	36323	37234	912	0.00588908	2.01325	mito_050	145	438	294	0.649007	4e-49	199	40.39	32
-lm_SuperContig_30_v2	82737	83594	858	0.00554038	1.89404	mito_050	435	145	291	0.642384	1e-45	188	37.46	33
-lm_SuperContig_30_v2	149583	150450	868	0.00560495	1.91611	mito_050	145	438	294	0.649007	3e-39	188	37.5948	34
-lm_SuperContig_30_v2	63768	64748	981	0.00633463	2.16556	mito_050	438	111	328	0.724062	4e-45	186	37.09	35
-lm_SuperContig_30_v2	118442	119320	879	0.00567598	1.9404	mito_050	145	435	291	0.642384	3e-44	183	38.64	36
-lm_SuperContig_30_v2	86916	87767	852	0.00550164	1.88079	mito_050	435	145	291	0.642384	4e-45	186	36.49	37
-lm_SuperContig_30_v2	26661	27530	870	0.00561787	1.92053	mito_050	145	438	294	0.649007	1e-43	181	35.67	38
-lm_SuperContig_30_v2	109071	109925	855	0.00552101	1.88742	mito_050	438	145	294	0.649007	7e-42	175	35.67	39
-lm_SuperContig_30_v2	115249	116115	867	0.0055985	1.91391	mito_050	145	438	294	0.649007	1e-43	181	38.41	40
-lm_SuperContig_30_v2	90387	91259	873	0.00563724	1.92715	mito_050	438	144	295	0.651214	2e-39	167	33.33	41
-lm_SuperContig_30_v2	32542	33390	849	0.00548226	1.87417	mito_050	145	424	280	0.618102	6e-43	179	38.91	42
-lm_SuperContig_30_v2	141021	141879	825	0.00532729	1.82119	mito_050	146	438	281	0.620309	6e-38	179	39.9318	43
-lm_SuperContig_30_v2	117050	117943	894	0.00577284	1.97351	mito_050	145	438	294	0.649007	1e-42	178	37.62	44
-lm_SuperContig_30_v2	146610	147515	906	0.00585033	2	mito_050	149	438	290	0.640177	4e-37	159	34.18	45
-lm_SuperContig_30_v2	151234	152220	987	0.00637338	2.17881	mito_050	118	438	321	0.708609	2e-35	154	34.72	46
-lm_SuperContig_30_v2	53343	53696	354	0.00228589	2.39189	mito_060	117	1	117	0.790541	2e-26	121	50	47
-lm_SuperContig_30_v2	5079	5582	504	0.00325449	0.863014	mito_080	403	582	180	0.308219	7e-41	172	49.73	48
-lm_SuperContig_30_v2	53703	59799	1782	0.0115069	3.05137	mito_080	582	1	581	0.994863	1e-68	218	52.6717	49
-lm_SuperContig_30_v2	64707	65165	459	0.00296391	1.7	mito_110	227	74	154	0.57037	2e-55	220	68.18	50
-lm_SuperContig_30_v2	108494	110387	579	0.00373879	2.20992	mito_150	179	6	174	0.664122	2e-31	150	62.5893	51
-lm_SuperContig_30_v2	103508	103711	204	0.00131729	0.778626	mito_150	261	194	68	0.259542	7e-26	122	85.29	52
-lm_SuperContig_30_v2	17614	20481	1458	0.00941477	2.68015	mito_170	83	536	454	0.834559	3e-130	620	68.5109	53
-lm_SuperContig_30_v2	17614	19341	1728	0.0111582	2.58296	mito_180	83	666	584	0.872945	0	664	57.81	54
-lm_SuperContig_30_v2	61781	62653	873	0.00563724	1.30493	mito_180	666	371	296	0.442451	3e-63	246	42.62	55
-lm_SuperContig_30_v2	32542	33390	849	0.00548226	1.26906	mito_180	372	648	277	0.414051	6e-64	248	44.14	56
-lm_SuperContig_30_v2	82716	83615	900	0.00581159	1.34529	mito_180	666	365	302	0.45142	1e-60	237	41.45	57
-lm_SuperContig_30_v2	36329	37252	924	0.00596656	1.38117	mito_180	374	668	295	0.440957	2e-62	243	43.91	58
-lm_SuperContig_30_v2	109059	109979	921	0.00594719	1.37668	mito_180	666	354	313	0.467862	3e-58	229	37.7	59
-lm_SuperContig_30_v2	141030	141897	868	0.00560495	1.29746	mito_180	376	668	293	0.437967	3e-54	237	42.1346	60
-lm_SuperContig_30_v2	80825	81706	882	0.00569536	1.31839	mito_180	667	371	297	0.443946	1e-57	228	41.28	61
-lm_SuperContig_30_v2	149580	150465	886	0.00572119	1.32436	mito_180	371	667	297	0.443946	7e-54	237	40.2095	62
-lm_SuperContig_30_v2	63756	64718	963	0.0062184	1.43946	mito_180	666	347	320	0.478326	2e-57	227	42.25	63
-lm_SuperContig_30_v2	115189	116127	939	0.00606342	1.40359	mito_180	352	666	315	0.470852	8e-59	231	37.85	64
-lm_SuperContig_30_v2	86895	87770	876	0.00565661	1.30942	mito_180	666	371	296	0.442451	4e-57	226	41.47	65
-lm_SuperContig_30_v2	22509	23405	897	0.00579222	1.34081	mito_180	372	668	297	0.443946	3e-57	226	39	66
-lm_SuperContig_30_v2	90384	91256	873	0.00563724	1.30493	mito_180	663	372	292	0.436472	4e-43	179	32.55	67
-lm_SuperContig_30_v2	118439	119344	906	0.00585033	1.35426	mito_180	371	667	297	0.443946	3e-54	216	41.56	68
-lm_SuperContig_30_v2	55774	56585	705	0.00455241	1.05381	mito_180	624	383	236	0.352765	9e-27	90	36.6049	69
-lm_SuperContig_30_v2	117050	117955	906	0.00585033	1.35426	mito_180	372	666	295	0.440957	9e-54	215	41.5	70
-lm_SuperContig_30_v2	26640	27542	903	0.00583096	1.34978	mito_180	365	666	302	0.45142	9e-53	211	40.46	71
-lm_SuperContig_30_v2	151309	152232	924	0.00596656	1.38117	mito_180	369	666	298	0.445441	3e-50	203	40.76	72
-lm_SuperContig_30_v2	146610	147527	918	0.00592782	1.3722	mito_180	376	666	291	0.434978	6e-48	195	39.23	73
-lm_SuperContig_30_v2	42209	42879	603	0.00389376	0.901345	mito_180	319	528	207	0.309417	2e-21	123	35.1266	74
-lm_SuperContig_30_v2	125743	126138	396	0.0025571	0.591928	mito_180	384	515	132	0.197309	4e-23	113	41.67	75
-lm_SuperContig_30_v2	44197	47305	819	0.00528855	2.20161	mito_190	98	370	273	0.733871	5e-44	248	66.386	76
-lm_SuperContig_30_v2	102101	102604	504	0.00325449	0.903226	mito_210	169	2	168	0.301075	4e-74	282	80.36	77
-lm_SuperContig_30_v2	89139	94202	822	0.00530792	1.47312	mito_210	533	250	274	0.491039	6e-51	151	75.9144	78
-lm_SuperContig_30_v2	14626	15192	567	0.0036613	1.46512	mito_220	194	384	191	0.49354	8e-78	295	73.82	79
-lm_SuperContig_30_v2	15860	16315	456	0.00294454	1.17829	mito_220	228	384	157	0.405685	3e-37	160	56.25	80
-lm_SuperContig_30_v2	9733	9936	204	0.00131729	0.527132	mito_220	68	136	69	0.178295	2e-27	127	89.86	81
-lm_SuperContig_30_v2	6405	6605	201	0.00129792	0.51938	mito_220	1	67	67	0.173127	2e-23	114	76.12	82
-lm_SuperContig_30_v2	9733	9936	204	0.00131729	0.425887	mito_230	68	136	69	0.14405	2e-27	127	89.86	83
-lm_SuperContig_30_v2	6405	6605	201	0.00129792	0.419624	mito_230	1	67	67	0.139875	2e-23	114	76.12	84
-lm_SuperContig_30_v2	9733	9927	195	0.00125918	0.434298	mito_240	68	132	65	0.144766	6e-27	126	90.77	85
-lm_SuperContig_30_v2	6405	6605	201	0.00129792	0.447661	mito_240	1	67	67	0.14922	2e-23	114	76.12	86
-lm_SuperContig_30_v2	18442	19341	900	0.00581159	2.47934	mito_155	56	357	302	0.831956	3e-68	263	45.07	87
-lm_SuperContig_30_v2	109056	110081	1026	0.00662521	2.82645	mito_155	358	11	348	0.958678	4e-91	338	51.85	88
-lm_SuperContig_30_v2	36323	37249	927	0.00598594	2.55372	mito_155	64	358	295	0.812672	2e-63	247	45.02	89
-lm_SuperContig_30_v2	61781	62650	870	0.00561787	2.39669	mito_155	357	64	294	0.809917	2e-58	230	41.75	90
-lm_SuperContig_30_v2	141021	141891	871	0.00562433	2.39945	mito_155	65	357	293	0.807163	2e-51	228	40.9341	91
-lm_SuperContig_30_v2	80828	81703	876	0.00565661	2.41322	mito_155	357	64	294	0.809917	3e-51	206	39.6	92
-lm_SuperContig_30_v2	149583	150462	880	0.00568244	2.42424	mito_155	64	357	294	0.809917	6e-49	220	40.1497	93
-lm_SuperContig_30_v2	82716	83594	879	0.00567598	2.42149	mito_155	357	64	294	0.809917	1e-50	204	38.8	94
-lm_SuperContig_30_v2	116981	117955	975	0.00629589	2.68595	mito_155	36	357	322	0.887052	4e-53	213	37.01	95
-lm_SuperContig_30_v2	86895	87767	873	0.00563724	2.40496	mito_155	357	64	294	0.809917	7e-50	202	37.92	96
-lm_SuperContig_30_v2	146610	147533	924	0.00596656	2.54545	mito_155	68	359	292	0.804408	2e-52	210	42.22	97
-lm_SuperContig_30_v2	63756	64655	900	0.00581159	2.47934	mito_155	357	60	298	0.820937	1e-47	194	38.64	98
-lm_SuperContig_30_v2	151258	152232	975	0.00629589	2.68595	mito_155	42	357	316	0.870523	2e-52	210	39.34	99
-lm_SuperContig_30_v2	90381	91256	876	0.00565661	2.41322	mito_155	355	64	292	0.804408	8e-32	142	31	100
-lm_SuperContig_30_v2	32494	33504	1011	0.00652835	2.78512	mito_155	46	360	315	0.867769	4e-52	209	37.64	101
-lm_SuperContig_30_v2	115198	116127	930	0.00600531	2.56198	mito_155	47	357	311	0.856749	1e-50	204	37.78	102
-lm_SuperContig_30_v2	26607	27542	936	0.00604405	2.57851	mito_155	46	357	312	0.859504	7e-50	202	37.34	103
-lm_SuperContig_30_v2	118442	119341	900	0.00581159	2.47934	mito_155	64	357	294	0.809917	7e-42	175	35.5	104
-lm_SuperContig_30_v2	22509	23387	879	0.00567598	2.42149	mito_155	64	353	290	0.798898	2e-37	161	31.19	105
-lm_SuperContig_30_v2	125740	126240	501	0.00323512	1.38017	mito_155	75	237	163	0.449036	3e-30	136	46.11	106
-lm_SuperContig_30_v2	44996	45911	771	0.00497859	2.52787	mito_195	39	300	260	0.852459	3e-48	295	58.0837	107
-lm_SuperContig_30_v2	46058	46769	711	0.00459115	2.33115	mito_195	44	304	261	0.855738	1e-70	293	56.8997	108
-lm_SuperContig_30_v2	14662	15189	528	0.00340947	1.36434	SPMIT.05	206	381	176	0.45478	1e-42	178	48.86	109
-lm_SuperContig_30_v2	15941	16303	363	0.00234401	0.937984	SPMIT.05	260	378	119	0.307494	1e-22	111	48.76	110
-lm_SuperContig_30_v2	64752	65204	453	0.00292517	1.65934	SPMIT.04	215	65	151	0.553114	2e-34	150	50.98	111
-lm_SuperContig_30_v2	94345	95262	918	0.00592782	2.84211	SPMIT.03	312	3	310	0.959752	1e-94	350	57.68	112
-lm_SuperContig_30_v2	102098	102580	483	0.00311889	0.899441	SPMIT.01	171	10	162	0.301676	3e-48	196	54.94	113
-lm_SuperContig_30_v2	93876	94202	327	0.00211154	0.608939	SPMIT.01	360	251	110	0.204842	3e-30	136	58.56	114
-lm_SuperContig_29_v2	77989	78369	381	0.00189609	1.99476	Afu3g02110	3	126	124	0.649215	2e-22	105	40.94	115
-lm_SuperContig_29_v2	193985	194365	381	0.00189609	1.99476	Afu3g02110	126	3	124	0.649215	1e-21	105	40.94	116
-lm_SuperContig_29_v2	78109	78817	630	0.00313526	1.14964	Afu3g01520	20	231	210	0.383212	7e-59	244	51.9044	117
-lm_SuperContig_29_v2	192760	194245	1407	0.00700209	2.56752	Afu3g01520	485	20	464	0.846715	2e-128	384	47.5473	118
-lm_SuperContig_29_v2	78010	78808	705	0.00350851	1.20926	Afu3g02520	21	261	234	0.401372	5e-23	122	29.1103	119
-lm_SuperContig_29_v2	192766	194344	1485	0.00739027	2.54717	Afu3g02520	535	21	508	0.871355	3e-40	83	25.258	120
-lm_SuperContig_29_v2	78109	78817	636	0.00316512	1.10035	Afu3g02720	45	258	214	0.370242	1e-39	180	44.2062	121
-lm_SuperContig_29_v2	192754	194245	1419	0.00706181	2.45502	Afu3g02720	521	45	477	0.82526	2e-83	234	36.8547	122
-lm_SuperContig_29_v2	78061	78814	666	0.00331442	1.19784	Afu6g03320	15	242	223	0.401079	3e-22	121	31.8947	123
-lm_SuperContig_29_v2	192760	194293	1446	0.00719618	2.60072	Afu6g03320	506	15	487	0.875899	1e-49	119	28.5099	124
-lm_SuperContig_29_v2	78007	78817	726	0.00361302	1.13972	Afu6g02220	48	293	242	0.379906	2e-59	245	47.1079	125
-lm_SuperContig_29_v2	193288	194347	975	0.00485219	1.53061	Afu6g02220	375	48	324	0.508634	1e-79	251	45.8455	126
-lm_SuperContig_29_v2	78133	78817	600	0.00298597	1.02389	Afu8g00940	77	282	202	0.34471	2e-44	195	48.6772	127
-lm_SuperContig_29_v2	192760	194221	1377	0.00685279	2.34983	Afu8g00940	541	77	461	0.786689	3e-91	263	40.7123	128
-lm_SuperContig_29_v2	133669	134343	675	0.00335921	1.80481	Afu4g02630	226	2	225	0.601604	3e-37	159	37.78	129
-lm_SuperContig_29_v2	167776	168372	597	0.00297104	1.59626	Afu4g02630	200	2	199	0.532086	9e-34	145	38.69	130
-lm_SuperContig_29_v2	41484	42080	597	0.00297104	1.59626	Afu4g02630	200	2	199	0.532086	8e-32	142	38.69	131
-lm_SuperContig_29_v2	101404	102000	597	0.00297104	1.59626	Afu4g02630	200	2	199	0.532086	3e-31	140	38.69	132
-lm_SuperContig_29_v2	31597	32272	645	0.00320991	1.7246	Afu4g02630	229	4	216	0.57754	6e-25	96	36.7377	133
-lm_SuperContig_29_v2	16462	17082	621	0.00309047	1.66043	Afu4g02630	208	2	207	0.553476	4e-30	135	37.2	134
-lm_SuperContig_29_v2	178590	179264	675	0.00335921	1.80481	Afu4g02630	229	4	226	0.604278	1e-29	133	35.96	135
-lm_SuperContig_29_v2	10942	11625	684	0.003404	1.82888	Afu4g02630	229	1	229	0.612299	2e-29	132	35.06	136
-lm_SuperContig_29_v2	91888	92562	675	0.00335921	1.80481	Afu4g02630	229	4	226	0.604278	3e-27	126	35.53	137
-lm_SuperContig_29_v2	78184	78814	573	0.0028516	1.06903	Afu4g03920	53	239	187	0.348881	2e-25	134	36.6457	138
-lm_SuperContig_29_v2	192964	194170	1149	0.00571812	2.14366	Afu4g03920	430	53	378	0.705224	3e-59	173	35.5056	139
-lm_SuperContig_29_v2	78049	78775	636	0.00316512	1.16912	Afu6g09110	19	236	212	0.389706	3e-23	124	27.8346	140
-lm_SuperContig_29_v2	192904	194305	1311	0.00652434	2.40993	Afu6g09110	459	19	435	0.799632	9e-43	105	26.7653	141
-lm_SuperContig_29_v2	78151	78814	579	0.00288146	0.969849	Afu6g14640	93	293	195	0.326633	3e-31	151	39.0031	142
-lm_SuperContig_29_v2	192760	194203	1359	0.00676321	2.27638	Afu6g14640	552	93	454	0.760469	6e-83	236	35.5958	143
-lm_SuperContig_29_v2	78109	78814	633	0.00315019	1.16575	Afu6g09710	34	245	212	0.390424	3e-49	213	46.2751	144
-lm_SuperContig_29_v2	192772	194245	1401	0.00697223	2.58011	Afu6g09710	501	34	468	0.861878	2e-97	282	38.1927	145
-lm_SuperContig_29_v2	78115	78817	618	0.00307554	1.09381	Afu5g01540	51	260	206	0.364602	6e-62	254	53.8812	146
-lm_SuperContig_29_v2	192754	194239	1401	0.00697223	2.47965	Afu5g01540	520	51	466	0.824779	1e-132	399	48.6076	147
-lm_SuperContig_29_v2	192868	194323	1368	0.006808	2.44286	Afu2g15140	482	16	462	0.825	1e-31	63	22.8695	148
-lm_SuperContig_29_v2	193303	194221	834	0.00415049	1.86161	fg00095	308	27	278	0.620536	6e-29	91	30.5342	149
-lm_SuperContig_29_v2	192877	194221	1257	0.0062556	2.19755	fg12051	483	60	415	0.725524	7e-40	99	25.302	150
-lm_SuperContig_29_v2	77956	78814	786	0.00391162	1.29917	fg12074	2	272	271	0.447934	7e-35	164	34.313	151
-lm_SuperContig_29_v2	192883	194398	1443	0.00718125	2.38512	fg12074	490	2	489	0.808264	7e-62	161	31.3733	152
-lm_SuperContig_29_v2	78124	78718	510	0.00253807	0.882353	fg12335	62	236	171	0.295848	4e-45	197	53.7372	153
-lm_SuperContig_29_v2	192769	194230	1377	0.00685279	2.38235	fg12335	537	62	472	0.816609	1e-92	266	39.0941	154
-lm_SuperContig_29_v2	193222	194383	1092	0.00543446	1.81697	fg12717	402	15	388	0.645591	2e-26	65	25.4717	155
-lm_SuperContig_29_v2	193036	194248	1125	0.00559869	1.9198	b13o8_150	460	73	383	0.653584	3e-31	78	25.3216	156
-lm_SuperContig_29_v2	78010	78814	747	0.00371753	1.28571	b18d24_100	9	250	242	0.416523	2e-27	139	31.3225	157
-lm_SuperContig_29_v2	192916	194344	1371	0.00682293	2.35972	b18d24_100	457	9	449	0.772806	4e-60	160	31.5064	158
-lm_SuperContig_29_v2	78184	78814	546	0.00271723	0.767932	b5k2_230	211	396	182	0.255977	4e-42	187	50.0101	159
-lm_SuperContig_29_v2	192760	194170	1326	0.00659898	1.86498	b5k2_230	657	211	443	0.623066	7e-99	291	41.7395	160
-lm_SuperContig_29_v2	192832	194212	1305	0.00649448	2.13934	1nc550_030	522	85	438	0.718033	1e-40	99	26.1649	161
-lm_SuperContig_29_v2	77941	78736	711	0.00353837	1.13942	1nc570_120	28	270	239	0.383013	1e-30	148	31.8213	162
-lm_SuperContig_29_v2	192760	194413	1569	0.0078083	2.51442	1nc570_120	559	28	528	0.846154	5e-62	151	28.5716	163
-lm_SuperContig_29_v2	192817	194086	1188	0.00591221	1.8193	6nc360_090	491	86	401	0.614089	8e-44	117	31.4828	164
-lm_SuperContig_29_v2	78112	78817	621	0.00309047	0.885877	29e8_240	62	272	207	0.295292	1e-56	235	51.6868	165
-lm_SuperContig_29_v2	192769	194242	1389	0.00691251	1.98146	29e8_240	535	62	470	0.670471	2e-117	349	45.9406	166
-lm_SuperContig_29_v2	192940	194218	1188	0.00591221	2.05536	7nc450_010	484	78	401	0.693772	3e-24	52	23.4836	167
-lm_SuperContig_29_v2	192865	194218	1266	0.00630039	1.15196	4nc446_010	530	106	420	0.382166	3e-48	127	28.7686	168
-lm_SuperContig_29_v2	192904	194239	1275	0.00634518	2.12146	b11e5_230	518	97	422	0.702163	1e-40	102	26.9355	169
-lm_SuperContig_29_v2	77935	78817	798	0.00397133	1.34343	xnc126_050	38	298	257	0.43266	7e-60	247	45.7009	170
-lm_SuperContig_29_v2	192757	194419	1578	0.00785309	2.65657	xnc126_050	559	38	518	0.872054	2e-130	380	45.5601	171
-lm_SuperContig_29_v2	78109	78817	624	0.0031054	1.16636	4nc135_070	17	238	218	0.407477	2e-53	225	50.065	172
-lm_SuperContig_29_v2	192751	194245	1410	0.00701702	2.63551	4nc135_070	494	17	474	0.885981	4e-99	286	40.8958	173
-lm_SuperContig_29_v2	78031	78588	558	0.00277695	0.980668	xnc164_090	19	209	191	0.335677	3e-21	101	30.89	174
-lm_SuperContig_29_v2	192802	194323	1449	0.00721111	2.54657	xnc164_090	509	19	491	0.862917	1e-42	95	28.3566	175
-lm_SuperContig_29_v2	192916	194107	1131	0.00562855	2.38608	YBR293w	384	6	379	0.799578	3e-23	53	24.6367	176
-lm_SuperContig_29_v2	192985	193954	885	0.0044043	1.93231	YCL069w	335	3	329	0.718341	7e-28	82	30.228	177
-lm_SuperContig_29_v2	197024	197422	399	0.00198567	1.21646	YDL037c	298	166	133	0.405488	5e-24	113	45.52	178
-lm_SuperContig_29_v2	197027	197413	387	0.00192595	1.17988	YDL037c	292	164	129	0.393293	2e-23	111	46.56	179
-lm_SuperContig_29_v2	197039	197437	399	0.00198567	1.21646	YDL037c	310	170	141	0.429878	2e-22	108	46.1	180
-lm_SuperContig_29_v2	197021	197416	396	0.00197074	1.20732	YDL037c	282	151	132	0.402439	3e-22	107	39.39	181
-lm_SuperContig_29_v2	40143	42272	2130	0.0106002	1.37686	YGR109w-b	1301	616	686	0.443439	6e-39	165	26.47	182
-lm_SuperContig_29_v2	16081	17274	1194	0.00594207	0.771816	YGR109w-b	1008	616	393	0.25404	4e-35	152	30.33	183
-lm_SuperContig_29_v2	100993	102192	1200	0.00597193	0.775695	YGR109w-b	1008	616	393	0.25404	8e-35	151	30.92	184
-lm_SuperContig_29_v2	167371	168564	1194	0.00594207	0.771816	YGR109w-b	1008	616	393	0.25404	2e-35	151	30.83	185
-lm_SuperContig_29_v2	133543	134535	993	0.00494177	0.641888	YGR109w-b	943	616	328	0.212023	4e-34	149	32.23	186
-lm_SuperContig_29_v2	91762	92754	993	0.00494177	0.641888	YGR109w-b	944	618	327	0.211377	4e-23	113	30.24	187
-lm_SuperContig_29_v2	178464	179477	1014	0.00504628	0.655462	YGR109w-b	944	611	334	0.215902	1e-21	107	29.03	188
-lm_SuperContig_29_v2	78139	78724	507	0.00252314	0.82708	YGR224w	70	240	169	0.275693	1e-27	139	41.4205	189
-lm_SuperContig_29_v2	193630	194215	507	0.00252314	0.82708	YGR224w	240	70	169	0.275693	6e-27	106	41.4205	190
-lm_SuperContig_29_v2	197024	197437	414	0.00206032	0.684298	YHL028w	276	136	141	0.233058	3e-25	117	47.52	191
-lm_SuperContig_29_v2	197024	197413	390	0.00194088	0.644628	YHL028w	323	190	134	0.221488	3e-23	111	47.01	192
-lm_SuperContig_29_v2	197024	197425	402	0.0020006	0.664463	YHL028w	290	148	143	0.236364	2e-23	111	49.65	193
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.679339	YHL028w	332	197	136	0.224793	2e-22	108	42.03	194
-lm_SuperContig_29_v2	197024	197482	459	0.00228426	0.758678	YHL028w	300	147	154	0.254545	5e-22	107	41.29	195
-lm_SuperContig_29_v2	197027	197482	456	0.00226933	0.753719	YHL028w	336	184	153	0.252893	5e-22	107	39.22	196
-lm_SuperContig_29_v2	197024	197410	387	0.00192595	0.639669	YHL028w	314	179	136	0.224793	6e-22	106	47.79	197
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.679339	YHL028w	257	117	141	0.233058	8e-21	103	42.55	198
-lm_SuperContig_29_v2	40143	42272	2130	0.0106002	1.4219	YIL082w-a	1327	642	686	0.457944	8e-39	165	26.47	199
-lm_SuperContig_29_v2	16081	17274	1194	0.00594207	0.797063	YIL082w-a	1034	642	393	0.26235	1e-34	150	30.33	200
-lm_SuperContig_29_v2	100993	102192	1200	0.00597193	0.801068	YIL082w-a	1034	642	393	0.26235	3e-34	150	30.92	201
-lm_SuperContig_29_v2	167371	168564	1194	0.00594207	0.797063	YIL082w-a	1034	642	393	0.26235	6e-35	149	30.83	202
-lm_SuperContig_29_v2	133543	134535	993	0.00494177	0.662884	YIL082w-a	969	642	328	0.218959	1e-33	147	32.23	203
-lm_SuperContig_29_v2	91762	92754	993	0.00494177	0.662884	YIL082w-a	970	644	327	0.218291	5e-23	112	30.24	204
-lm_SuperContig_29_v2	178464	179477	1014	0.00504628	0.676903	YIL082w-a	970	637	334	0.222964	1e-21	106	29.03	205
-lm_SuperContig_29_v2	197024	197425	402	0.0020006	0.346253	YJR151c	267	132	136	0.11714	1e-33	145	58.09	206
-lm_SuperContig_29_v2	197024	197425	402	0.0020006	0.346253	YJR151c	290	156	135	0.116279	2e-33	144	57.78	207
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	261	126	136	0.11714	3e-33	144	58.39	208
-lm_SuperContig_29_v2	197021	197425	405	0.00201553	0.348837	YJR151c	300	165	136	0.11714	6e-33	143	57.35	209
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	285	147	139	0.119724	6e-33	143	57.55	210
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	276	141	136	0.11714	6e-33	143	57.66	211
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	281	144	138	0.118863	1e-32	142	55.8	212
-lm_SuperContig_29_v2	197024	197425	402	0.0020006	0.346253	YJR151c	303	174	130	0.111972	3e-32	140	57.46	213
-lm_SuperContig_29_v2	197030	197404	375	0.00186623	0.322997	YJR151c	248	124	125	0.107666	3e-32	140	59.2	214
-lm_SuperContig_29_v2	197024	197398	375	0.00186623	0.322997	YJR151c	246	123	124	0.106804	1e-31	139	60	215
-lm_SuperContig_29_v2	197024	197395	372	0.0018513	0.320413	YJR151c	240	118	123	0.105943	1e-31	139	59.68	216
-lm_SuperContig_29_v2	197039	197434	396	0.00197074	0.341085	YJR151c	318	183	136	0.11714	1e-31	139	57.35	217
-lm_SuperContig_29_v2	197027	197437	411	0.00204539	0.354005	YJR151c	244	108	137	0.118002	2e-31	138	57.97	218
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	314	174	141	0.121447	3e-31	137	55.32	219
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	350	201	150	0.129199	1e-28	128	52	220
-lm_SuperContig_29_v2	197024	197392	369	0.00183637	0.317829	YJR151c	222	102	121	0.10422	1e-26	122	56.91	221
-lm_SuperContig_29_v2	197021	197425	405	0.00201553	0.348837	YJR151c	360	219	142	0.122308	3e-25	118	52.08	222
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.354005	YJR151c	372	228	145	0.124892	2e-24	115	48.28	223
-lm_SuperContig_29_v2	197036	197434	399	0.00198567	0.343669	YJR151c	378	246	133	0.114556	7e-23	109	42.86	224
-lm_SuperContig_29_v2	78112	78778	582	0.00289639	1	YKR105c	31	227	193	0.331615	7e-29	143	36.5996	225
-lm_SuperContig_29_v2	192985	194242	1173	0.00583756	2.01546	YKR105c	459	31	425	0.730241	4e-43	115	30.007	226
-lm_SuperContig_29_v2	197024	197434	411	0.00204539	0.817097	YNL283c	272	139	134	0.266402	4e-22	107	45.65	227
-lm_SuperContig_29_v2	197042	197422	381	0.00189609	0.757455	YNL283c	275	147	129	0.256461	8e-21	103	45.8	228
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC167.08	831	358	461	0.345836	4e-46	116	29.6018	229
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC167.08	831	312	520	0.390098	7e-44	182	27.67	230
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC167.08	831	427	405	0.303826	7e-42	175	28.64	231
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC167.08	831	427	405	0.303826	2e-42	174	29.14	232
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC167.08	831	427	405	0.303826	4e-39	165	27.9	233
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC167.08	786	452	335	0.251313	3e-37	159	32.64	234
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC167.08	786	418	369	0.276819	3e-37	158	30.65	235
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC167.08	786	418	369	0.276819	3e-36	155	30.91	236
-lm_SuperContig_29_v2	192757	194218	1371	0.00682293	2.58192	SPBC12C2.13c	499	33	461	0.868173	1e-35	78	25.49	237
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAPB15E9.03c	831	358	461	0.345836	4e-46	116	29.6018	238
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAPB15E9.03c	831	312	520	0.390098	7e-44	182	27.67	239
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAPB15E9.03c	831	427	405	0.303826	7e-42	175	28.64	240
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAPB15E9.03c	831	427	405	0.303826	2e-42	174	29.14	241
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAPB15E9.03c	831	427	405	0.303826	4e-39	165	27.9	242
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAPB15E9.03c	786	452	335	0.251313	3e-37	159	32.64	243
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAPB15E9.03c	786	418	369	0.276819	3e-37	158	30.65	244
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAPB15E9.03c	786	418	369	0.276819	3e-36	155	30.91	245
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPBC1289.17	831	358	461	0.345836	2e-46	117	29.8158	246
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPBC1289.17	831	312	520	0.390098	3e-44	183	27.86	247
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPBC1289.17	831	427	405	0.303826	3e-42	176	28.89	248
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPBC1289.17	831	427	405	0.303826	8e-43	175	29.38	249
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPBC1289.17	831	427	405	0.303826	2e-39	166	28.15	250
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPBC1289.17	786	452	335	0.251313	1e-37	161	32.94	251
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPBC1289.17	786	418	369	0.276819	1e-37	160	30.91	252
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPBC1289.17	786	418	369	0.276819	1e-36	157	31.18	253
-lm_SuperContig_29_v2	77950	78799	777	0.00386683	1.31919	SPAC3H1.06c	34	286	253	0.429542	5e-29	144	32.8211	254
-lm_SuperContig_29_v2	192844	194404	1488	0.0074052	2.52632	SPAC3H1.06c	525	34	492	0.835314	2e-50	119	29.3011	255
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPCC1020.14	831	358	461	0.345836	4e-46	116	29.6018	256
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPCC1020.14	831	312	520	0.390098	7e-44	182	27.67	257
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPCC1020.14	831	427	405	0.303826	7e-42	175	28.64	258
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPCC1020.14	831	427	405	0.303826	2e-42	174	29.14	259
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPCC1020.14	831	427	405	0.303826	4e-39	165	27.9	260
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPCC1020.14	786	452	335	0.251313	3e-37	159	32.64	261
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPCC1020.14	786	418	369	0.276819	3e-37	158	30.65	262
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPCC1020.14	786	418	369	0.276819	3e-36	155	30.91	263
-lm_SuperContig_29_v2	192760	194482	1635	0.00813676	2.83362	SPBC3E7.06c	551	4	543	0.941075	7e-34	54	22.6974	264
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC26A3.13c	831	358	461	0.345836	4e-46	116	29.6018	265
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC26A3.13c	831	312	520	0.390098	7e-44	182	27.67	266
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC26A3.13c	831	427	405	0.303826	7e-42	175	28.64	267
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC26A3.13c	831	427	405	0.303826	2e-42	174	29.14	268
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC26A3.13c	831	427	405	0.303826	4e-39	165	27.9	269
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC26A3.13c	786	452	335	0.251313	3e-37	159	32.64	270
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC26A3.13c	786	418	369	0.276819	3e-37	158	30.65	271
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC26A3.13c	786	418	369	0.276819	3e-36	155	30.91	272
-lm_SuperContig_29_v2	78133	78799	576	0.00286653	0.961603	SPBC16A3.17c	97	292	190	0.317195	3e-30	147	39.8809	273
-lm_SuperContig_29_v2	192874	194221	1257	0.0062556	2.0985	SPBC16A3.17c	518	97	416	0.694491	2e-55	151	31.4364	274
-lm_SuperContig_29_v2	77950	78736	714	0.0035533	1.21222	SPAC1399.02	34	267	234	0.397284	8e-30	147	33.1969	275
-lm_SuperContig_29_v2	192844	194404	1488	0.0074052	2.52632	SPAC1399.02	525	34	492	0.835314	3e-53	129	30.8816	276
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC2E1P3.03c	831	358	461	0.345836	4e-46	116	29.6018	277
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC2E1P3.03c	831	312	520	0.390098	7e-44	182	27.67	278
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC2E1P3.03c	831	427	405	0.303826	7e-42	175	28.64	279
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC2E1P3.03c	831	427	405	0.303826	2e-42	174	29.14	280
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC2E1P3.03c	831	427	405	0.303826	4e-39	165	27.9	281
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC2E1P3.03c	786	452	335	0.251313	3e-37	159	32.64	282
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC2E1P3.03c	786	418	369	0.276819	3e-37	158	30.65	283
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC2E1P3.03c	786	418	369	0.276819	3e-36	155	30.91	284
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC19D5.09c	831	358	461	0.345836	2e-46	117	29.8158	285
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC19D5.09c	831	312	520	0.390098	3e-44	183	27.86	286
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC19D5.09c	831	427	405	0.303826	3e-42	176	28.89	287
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC19D5.09c	831	427	405	0.303826	8e-43	175	29.38	288
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC19D5.09c	831	427	405	0.303826	2e-39	166	28.15	289
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC19D5.09c	786	452	335	0.251313	1e-37	161	32.94	290
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC19D5.09c	786	418	369	0.276819	1e-37	160	30.91	291
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC19D5.09c	786	418	369	0.276819	1e-36	157	31.18	292
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC27E2.08	831	358	461	0.345836	4e-46	116	29.6018	293
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC27E2.08	831	312	520	0.390098	7e-44	182	27.67	294
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC27E2.08	831	427	405	0.303826	7e-42	175	28.64	295
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC27E2.08	831	427	405	0.303826	2e-42	174	29.14	296
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC27E2.08	831	427	405	0.303826	4e-39	165	27.9	297
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC27E2.08	786	452	335	0.251313	3e-37	159	32.64	298
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC27E2.08	786	418	369	0.276819	3e-37	158	30.65	299
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC27E2.08	786	418	369	0.276819	3e-36	155	30.91	300
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC13D1.01c	831	358	461	0.345836	2e-46	117	29.8158	301
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC13D1.01c	831	312	520	0.390098	3e-44	183	27.86	302
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC13D1.01c	831	427	405	0.303826	3e-42	176	28.89	303
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC13D1.01c	831	427	405	0.303826	8e-43	175	29.38	304
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC13D1.01c	831	427	405	0.303826	2e-39	166	28.15	305
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC13D1.01c	786	452	335	0.251313	1e-37	161	32.94	306
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC13D1.01c	786	418	369	0.276819	1e-37	160	30.91	307
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC13D1.01c	786	418	369	0.276819	1e-36	157	31.18	308
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPBC9B6.02c	831	358	461	0.345836	4e-46	116	29.6018	309
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPBC9B6.02c	831	312	520	0.390098	7e-44	182	27.67	310
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPBC9B6.02c	831	427	405	0.303826	7e-42	175	28.64	311
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPBC9B6.02c	831	427	405	0.303826	2e-42	174	29.14	312
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPBC9B6.02c	831	427	405	0.303826	4e-39	165	27.9	313
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPBC9B6.02c	786	452	335	0.251313	3e-37	159	32.64	314
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPBC9B6.02c	786	418	369	0.276819	3e-37	158	30.65	315
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPBC9B6.02c	786	418	369	0.276819	3e-36	155	30.91	316
-lm_SuperContig_29_v2	133341	134754	1380	0.00686772	1.03526	SPAC9.04	831	358	461	0.345836	4e-46	116	29.6018	317
-lm_SuperContig_29_v2	100993	102531	1539	0.007659	1.15454	SPAC9.04	831	312	520	0.390098	7e-44	182	27.67	318
-lm_SuperContig_29_v2	41079	42287	1209	0.00601672	0.906977	SPAC9.04	831	427	405	0.303826	7e-42	175	28.64	319
-lm_SuperContig_29_v2	167371	168579	1209	0.00601672	0.906977	SPAC9.04	831	427	405	0.303826	2e-42	174	29.14	320
-lm_SuperContig_29_v2	16081	17289	1209	0.00601672	0.906977	SPAC9.04	831	427	405	0.303826	4e-39	165	27.9	321
-lm_SuperContig_29_v2	91693	92700	1008	0.00501642	0.756189	SPAC9.04	786	452	335	0.251313	3e-37	159	32.64	322
-lm_SuperContig_29_v2	178395	179504	1110	0.00552404	0.832708	SPAC9.04	786	418	369	0.276819	3e-37	158	30.65	323
-lm_SuperContig_29_v2	10747	11856	1110	0.00552404	0.832708	SPAC9.04	786	418	369	0.276819	3e-36	155	30.91	324
-lm_SuperContig_29_v2	77980	78567	588	0.00292625	1.01379	um00679	18	211	194	0.334483	5e-25	114	31	325
-lm_SuperContig_29_v2	192772	194374	1512	0.00752463	2.6069	um00679	529	18	506	0.872414	2e-42	90	24.7056	326
-lm_SuperContig_29_v2	78115	78814	627	0.00312033	1.07179	um00842	53	264	212	0.362393	2e-53	226	52.4685	327
-lm_SuperContig_29_v2	192760	194239	1407	0.00700209	2.40513	um00842	534	53	482	0.823932	2e-104	305	43.0311	328
-lm_SuperContig_29_v2	78112	78802	603	0.0030009	1.005	um01882	94	297	198	0.33	7e-23	123	33.3351	329
-lm_SuperContig_29_v2	192760	194242	1395	0.00694237	2.325	um01882	560	94	461	0.768333	5e-40	91	24.8656	330
-lm_SuperContig_29_v2	78019	78567	549	0.00273216	0.90894	um01964	40	220	181	0.299669	1e-24	113	33.7	331
-lm_SuperContig_29_v2	192901	194335	1344	0.00668856	2.22517	um01964	490	40	445	0.736755	7e-43	104	28.0569	332
-lm_SuperContig_29_v2	77890	78814	858	0.00426993	1.33645	um02062	38	313	276	0.429907	1e-32	158	32.8827	333
-lm_SuperContig_29_v2	192760	194464	1638	0.00815169	2.5514	um02062	575	38	538	0.838006	1e-65	161	31.23	334
-lm_SuperContig_29_v2	78136	78814	606	0.00301583	0.795276	um02598	133	331	199	0.261155	1e-21	120	30.0506	335
-lm_SuperContig_29_v2	192754	194218	1392	0.00692744	1.82677	um02598	598	133	466	0.611549	3e-45	109	27.3493	336
-lm_SuperContig_29_v2	77938	78808	807	0.00401612	1.30161	um03115	27	285	259	0.417742	2e-24	130	31.3664	337
-lm_SuperContig_29_v2	192757	194416	1596	0.00794267	2.57419	um03115	554	27	528	0.851613	1e-48	108	27.7423	338
-lm_SuperContig_29_v2	77938	78736	726	0.00361302	1.24528	um05414	13	244	232	0.397942	4e-45	199	41.7387	339
-lm_SuperContig_29_v2	192826	194416	1518	0.00755449	2.60377	um05414	511	13	499	0.855918	2e-98	279	38.2481	340
-lm_SuperContig_29_v2	193006	194107	1017	0.00506121	1.44255	um05421	496	158	335	0.475177	6e-41	118	29.7892	341

--- a/commons/pyRepetUnit/convCoord/ConvMapChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-from copy import deepcopy
-from commons.core.sql.TableMapAdaptator import TableMapAdaptator
-from commons.core.coord.Map import Map
-import os
-
-class ConvMapChr2Chunk(object):
-
-    def __init__(self, db, table, chunk_table, outtable):
-        self._tablename = table
-        self._chunk_table = chunk_table
-        self._db = db
-        self._outtable = outtable
-        
-    def convert(self):
-        """
-        Convert a 'set' table format.
-        """
-        temp_file=str(os.getpid()) + ".on_chunk"
-        fout=open(temp_file,'w')
-
-        str_mask = "SELECT * FROM "+\
-            self._chunk_table + " WHERE chr='%s' AND ("+\
-            "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
-                            
-        iTMA = TableMapAdaptator(self._db, self._tablename)
-        chr_list = iTMA.getSeqNameList()
-
-        for chr in chr_list:        
-            mlist = iTMA.getMapListFromChr(chr)  
-            for m in mlist:
-                sql_cmd = str_mask%(m.seqname,m.getMin(),m.getMax(),m.getMin(),m.getMax())
-                self._db.execute(sql_cmd)
-                res = self._db.fetchall()
-                for i in res:
-                    chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
-                
-                    new_m = deepcopy(m)
-                    new_m.seqname = chunk.name
- 
-                    if (m.start > chunk.start and m.start < chunk.end):
-                        new_m.start = m.start - chunk.start + 1 
-                    if (m.end > chunk.start and m.end < chunk.end):
-                        new_m.end = m.end - chunk.start + 1
-                                                   
-                    if m.isOnDirectStrand():
-                        if m.start <= chunk.start:
-                            new_m.start = 1
-                        if m.end >= chunk.end:
-                            new_m.end = chunk.end - chunk.start + 1
-                    else:
-                        if m.end <= chunk.start:
-                            new_m.end = 1
-                        if m.start >= chunk.end:
-                            new_m.start = chunk.end - chunk.start + 1
-                            
-                    new_m.write(fout)
- 
-        fout.close()
-    
-        self._db.createTable(self._outtable, "map", temp_file)
-    
-        os.remove(temp_file)           
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/ConvPathChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-from copy import deepcopy
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.coord.PathUtils import PathUtils
-from commons.core.coord.Map import Map
-from commons.core.coord.Path import Path
-import os
-
-class ConvPathChr2Chunk(object):
-
-    def __init__(self, db, table, chunk_table, outtable):
-        self._tablename = table
-        self._chunk_table = chunk_table
-        self._db = db
-        self._outtable = outtable
-        
-    def convert(self):
-        """
-        Convert a 'path' table format.
-        """
-        temp_file = str(os.getpid()) + ".on_chunk"
-        fout = open(temp_file,'w')
-
-        str_mask = "SELECT * FROM "+\
-            self._chunk_table + " WHERE chr='%s' AND ("+\
-            "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
-                            
-        iTPA = TablePathAdaptator(self._db, self._tablename)
-        path_num_list = iTPA.getIdList()
-
-        for path_num in path_num_list:        
-            slist = iTPA.getPathListFromId(path_num)  
-            for r in slist:
-                r_min, r_max = PathUtils.getQueryMinMaxFromPathList([r])   
-                sql_cmd = str_mask%(r.range_query.seqname,r_min,r_max,r_min,r_max)
-                self._db.execute(sql_cmd)
-                res = self._db.fetchall()
-                for i in res:
-                    chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
-                
-                    new_r = Path()
-                    new_r = deepcopy(r)
-                    new_r.range_query.seqname = chunk.name
- 
-                    if (r.range_query.start > chunk.start and r.range_query.start < chunk.end):
-                        new_r.range_query.start = r.range_query.start - chunk.start + 1 
-                    if (r.range_query.end > chunk.start and r.range_query.end < chunk.end):
-                        new_r.range_query.end = r.range_query.end - chunk.start + 1
-                                                   
-                    if r.range_query.isOnDirectStrand():
-                        if r.range_query.start <= chunk.start:
-                            new_r.range_query.start = 1
-                        if r.range_query.end >= chunk.end:
-                            new_r.range_query.end = chunk.end - chunk.start + 1
-                    else:
-                        if r.range_query.end <= chunk.start:
-                            new_r.range_query.end = 1
-                        if r.range_query.start >= chunk.end:
-                            new_r.range_query.start = chunk.end - chunk.start + 1
-                            
-                    new_r.write(fout)
- 
-        fout.close()
-    
-        self._db.createTable(self._outtable, "path", temp_file)
-    
-        os.remove(temp_file)           
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-from copy import deepcopy
-from commons.core.sql.TableSetAdaptator import TableSetAdaptator
-from commons.core.coord.Map import Map
-from commons.core.coord.Set import Set
-import os
-
-class ConvSetChr2Chunk(object):
-
-    def __init__(self, db, table, chunk_table, outtable):
-        self._tablename = table
-        self._chunk_table = chunk_table
-        self._db = db
-        self._outtable = outtable
-        
-    def convert(self):
-        """
-        Convert a 'set' table format.
-        """
-        temp_file = str(os.getpid()) + ".on_chunk"
-        fout = open(temp_file,'w')
-
-        str_mask = "SELECT * FROM "+\
-            self._chunk_table + " WHERE chr='%s' AND ("+\
-            "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
-            " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
-                            
-        iTSA = TableSetAdaptator(self._db, self._tablename)
-        path_num_list = iTSA.getIdList()
-
-        for path_num in path_num_list:        
-            slist = iTSA.getSetListFromId(path_num)  
-            for r in slist:
-                sql_cmd = str_mask%(r.seqname,r.getMin(),r.getMax(),r.getMin(),r.getMax())
-                self._db.execute(sql_cmd)
-                res = self._db.fetchall()
-                for i in res:
-                    chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
-                
-                    new_r = Set()
-                    new_r = deepcopy(r)
-                    new_r.seqname = chunk.name
- 
-                    if (r.start > chunk.start and r.start < chunk.end):
-                        new_r.start = r.start - chunk.start + 1 
-                    if (r.end > chunk.start and r.end < chunk.end):
-                        new_r.end = r.end - chunk.start + 1
-                                                   
-                    if r.isOnDirectStrand():
-                        if r.start <= chunk.start:
-                            new_r.start = 1
-                        if r.end >= chunk.end:
-                            new_r.end = chunk.end - chunk.start + 1
-                    else:
-                        if r.end <= chunk.start:
-                            new_r.end = 1
-                        if r.start >= chunk.end:
-                            new_r.start = chunk.end - chunk.start + 1
-                            
-                    new_r.write(fout)
- 
-        fout.close()
-    
-        self._db.createTable(self._outtable, "set", temp_file)
-    
-        os.remove(temp_file)           
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/PathChunkConnector.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-from pyRepet.coord.Map import Map
-import commons.core.sql.TablePathAdaptator
-
-
-## Connect overlapping chunks in a single fragment  
-#
-class PathChunkConnector( object):
-    
-    def __init__(self, mapFileName, db, table, verbose):
-       
-        self._verbose = verbose
-        self._chunk = self._getChunkDictFromMapFileForConnectPathChunks( mapFileName )
-        self._tablePathAdaptator = commons.core.sql.TablePathAdaptator.TablePathAdaptator( db, table )
-    
-    def run (self):
-        for num_chunk in xrange(1,len(self._chunk.keys())):
-            chunkName = "chunk"+str(num_chunk)
-            if self._verbose > 1:
-                print chunkName
-            next_chunkName="chunk"+str(num_chunk+1)
-    
-            if next_chunkName not in self._chunk.keys():
-                break
-            
-            start=self._chunk[chunkName][2]
-            end=self._chunk[next_chunkName][1]
-            
-            if self._chunk[chunkName][0] == self._chunk[next_chunkName][0]:
-                lpath=self._tablePathAdaptator.getPathListIncludedInQueryCoord(self._chunk[chunkName][0],start,end)
-            
-                if self._verbose > 1:
-                    print "----------"
-                
-                lpath.sort()
-                chg_path_id={}
-                pathnum_to_ins=[]
-                pathnum_to_del=[]
-                
-                self._createDirectAndReversePaths(lpath)
-                        
-                self._mergeDirectPaths(chg_path_id, pathnum_to_ins, pathnum_to_del)
-                
-                if self._verbose > 1:
-                    print "..........."
-     
-                self._mergeReversePaths(chg_path_id, pathnum_to_ins, pathnum_to_del)
-                
-                if self._verbose > 1:
-                    print "..........."
-                    print pathnum_to_del
-                    
-                self._tablePathAdaptator.deleteFromIdList(pathnum_to_del)
-                
-                if self._verbose > 1:
-                    print pathnum_to_ins
-                
-                self._tablePathAdaptator.deleteFromIdList(pathnum_to_ins)
-                
-                self._insertDirectPaths(chg_path_id, pathnum_to_ins)
-               
-                self._insertReversePaths(chg_path_id, pathnum_to_ins)
-    
-
-    def _createDirectAndReversePaths(self, lpath):
-        self._dpath = []
-        self._rpath = []
-        for i in lpath:
-            if i.range_query.isOnDirectStrand() and i.range_subject.isOnDirectStrand():
-                self._dpath.append(i)
-            else:
-                self._rpath.append(i)
-                
-    def _insertDirectPaths (self, chg_path_id, pathnum_to_ins):
-        self._insertPaths(chg_path_id, pathnum_to_ins, self._dpath)
-
-    def _insertReversePaths (self, chg_path_id, pathnum_to_ins):
-        self._insertPaths(chg_path_id, pathnum_to_ins, self._rpath)
-
-    def _insertPaths(self, chg_path_id, pathnum_to_ins, paths2Insert):
-        for i in paths2Insert:
-            if chg_path_id.has_key(i.id):
-                i.id = chg_path_id[i.id]
-            
-            if self._verbose > 1:
-                i.show()
-            
-            if i.id in pathnum_to_ins:
-                self._tablePathAdaptator.insert(i)
-                if self._verbose > 1:
-                    print "--> inserted!"
-            
-            if self._verbose > 1:
-                print "=========="
-    
-    def _mergeDirectPaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del):
-        self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._dpath)
-    
-    def _mergeReversePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del):
-        self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._rpath)
-            
-    def _mergePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del, dpath):
-        x = 0
-        while x < len(dpath) - 1:
-            x = x + 1
-            if self._verbose > 1:
-                print "++++"
-                dpath[x - 1].show()
-                dpath[x].show()
-            
-            if dpath[x - 1].canMerge(dpath[x]):
-                chg_path_id[dpath[x].id] = dpath[x - 1].id
-                if dpath[x - 1].id not in pathnum_to_ins:
-                    pathnum_to_ins.append(dpath[x - 1].id)
-                
-                if dpath[x].id not in pathnum_to_del:
-                    pathnum_to_del.append(dpath[x].id)
-                
-                dpath[x - 1].merge(dpath[x])
-                del dpath[x]
-                x = x - 1
-                if self._verbose > 1:
-                    print "--> merged"
-                
-    def _getChunkDictFromMapFileForConnectPathChunks(self, mapFileName):
-        mapDict = {}
-        mapFile = open(mapFileName)
-        mapInstance = Map()
-        while True:
-            if not mapInstance.read(mapFile):
-                break
-            mapDict[mapInstance.name] = (mapInstance.seqname, mapInstance.start, mapInstance.end)
-            
-        mapFile.close()
-        return mapDict

--- a/commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,169 +0,0 @@
-import unittest
-import os
-import time
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbMySql import DbMySql
-
-
-class Test_ConvCoordWithOverlaps( unittest.TestCase ):
-    pass
-
-#    def setUp(self):
-#        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-#        self._mapFile = "map_file.map"
-#        _MockMapFile( self._mapFile )
-#        self._resultFile = "dummyObsFile_%s" % ( self._uniqId )
-#        self._refFileToCompare = "dummyExpFile_%s" % ( self._uniqId )
-#        self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
-#        configF = open(self._configFileName, "w" )
-#        configF.write( "[repet_env]\n" )
-#        configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
-#        configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
-#        configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
-#        configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
-#        configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
-#        configF.close()
-#        self._db = DbMySql( cfgFileName = self._configFileName )
-#        
-#    def tearDown(self):
-#        os.remove( self._mapFile )
-#        os.remove( self._resultFile )
-#        os.remove( self._refFileToCompare )
-#        self._db.close()
-#        self._uniqId = None
-#        
-#        
-#    def test_run_TwoHitsOverlapOnFirstAndSecondChunks( self ):
-#        file2Process = "two_hits_overlap_on_first_and_second_chunk.align"
-#        linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" +  "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" +  "125467" + "\t" +  "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", 
-#                           "chunk2" + "\t" +  "5544" + "\t" +    "5575" + "\t" +   "sbj2" + "\t" +   "125457"  + "\t" + "133465" + "\t" +  "2e-38" + "\t" +   "83" + "\t" +  "65" + "\n" ]
-#        _MockAlignFile( file2Process, linesToProcess )
-#        
-#        convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#        
-#        refLine = ["dmel_chr4" + "\t" + "95535" + "\t" +  "95575" + "\t" +   "sbj2" + "\t" +   "125423" + "\t" +  "133465" + "\t" + "2e-38" + "\t" +  "83" + "\t" +  "97.78" + "\n"]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
-#        os.remove( file2Process )
-#
-#        
-#    def test_run_ThreeHitsOverlapOnFirstAndSecondChunks( self ):
-#        file2Process = "three_hits_overlap_on_first_and_second_chunk.align"
-#        linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" +  "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" +  "125467" + "\t" +  "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", 
-#                           "chunk2" + "\t" +  "5544" + "\t" +    "5575" + "\t" +   "sbj2" + "\t" +   "125457"  + "\t" + "133465" + "\t" +  "2e-38" + "\t" +   "83" + "\t" +  "65" + "\n"
-#                           "chunk2" + "\t" +  "5540" + "\t" +  "5573" + "\t" +  "sbj2" + "\t" +  "125454" + "\t"  +"125750" + "\t" + "8e-58" + "\t" +  "224" + "\t" +  "86.43" + "\n" ]
-#        _MockAlignFile( file2Process, linesToProcess )
-#        
-#        convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#
-#        refLine = ["dmel_chr4" + "\t" + "95535" + "\t" +  "95575" + "\t" +   "sbj2" + "\t" +   "125423" + "\t" +  "133465" + "\t" + "8e-58" + "\t" +  "224" + "\t" +  "97.78" + "\n"]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
-#        os.remove( file2Process )
-#
-#     
-#    def test_run_HitsOnDifferentStrandsAndDifferentSubjects( self ):
-#        file2Process = "hits_on_different_strands_and_different_subjects.align"
-#        linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" +  "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" +  "125467" + "\t" +  "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", 
-#                           "chunk2" + "\t" +  "5575" + "\t" +    "5544" + "\t" +   "sbj2" + "\t" +   "125457"  + "\t" + "133465" + "\t" +  "2e-38" + "\t" +   "83" + "\t" +  "65" + "\n",
-#                           "chunk2" + "\t" +  "5540" + "\t" +  "5573" + "\t" +  "sbj3" + "\t" +  "125454" + "\t"  +"125750" + "\t" + "8e-58" + "\t" +  "224" + "\t" +  "86.43" + "\n" ]
-#        _MockAlignFile( file2Process, linesToProcess )
-#
-#        convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#
-#        refLine = ["dmel_chr4" + "\t" + "95535" + "\t" +  "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" +  "125467" + "\t" +  "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
-#                   "dmel_chr4" + "\t" + "95544" + "\t" +  "95575" + "\t" +   "sbj2" + "\t" +   "133465"  + "\t" + "125457" + "\t" +  "2e-38" + "\t" +   "83" + "\t" +  "65" + "\n",
-#                   "dmel_chr4" + "\t" + "95540" + "\t" +  "95573" + "\t" +  "sbj3" + "\t" +  "125454" + "\t"  +"125750" + "\t" + "8e-58" + "\t" +  "224" + "\t" +  "86.43" + "\n" ]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
-#        os.remove( file2Process )
-#    
-#    
-#    def test_run_TwoHitsOnChunksOnlyAndOnOverlap( self ):
-#        file2Process = "two_hits_on_chunks_only_and_on_overlap.align"
-#        linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" +  "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
-#                           "chunk3" + "\t" + "1000"  + "\t" +" 5000" + "\t" + "sbj2" + "\t" + "125454" + "\t" + "125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
-#        _MockAlignFile( file2Process, linesToProcess )
-#        
-#        convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#        
-#        refLine = ["dmel_chr4"  + "\t" + "175000"+ "\t" +  "185000"+ "\t" +  "sbj2"+ "\t" + "125454"+ "\t" + "133465"+ "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
-#        os.remove( file2Process )
-#
-#        
-#    def test_run_TwoHitsOnChunks_And_OnOverlap_OnReverseStrand_ForSubject( self ):
-#        file2Process = "two_hits_on_chunks_and_on_overlap_on_reverse_strand_for_subject.align"                                   
-#        linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "133465"  + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
-#                           "chunk3" + "\t" + "1000"  + "\t" + "5000" + "\t" + "sbj2" + "\t" +  "125750" + "\t" + "125454" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]                                                                                     
-#        _MockAlignFile( file2Process, linesToProcess )
-#        
-#        convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#        
-#        refLine = ["dmel_chr4"  + "\t" + "175000"+ "\t" +  "185000" + "\t" +  "sbj2"+ "\t" + "133465" + "\t" + "125454" + "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )        
-#        os.remove( file2Process )
-#        
-#        
-#    def test_run_ThreeHitsAllByAllWithTwoHitsWithinAChunkOverlap( self ):
-#        file2Process = "dummyAlignFile_%s" % ( self._uniqId )
-#        linesToProcess = [ "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
-#                           "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
-#                           "chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
-#        _MockAlignFile( file2Process, linesToProcess )
-#        
-#        mapFileName = "dummyMapFile_%s" % ( self._uniqId )
-#        mapF = open( mapFileName, "w" )
-#        mapF.write( "chunk1\tdmel_chr4\t1\t200\n" )
-#        mapF.write( "chunk2\tdmel_chr4\t191\t390\n" )
-#        mapF.close()
-#        
-#        convCoord = ConvCoord( file2Process, "qs", mapFileName, self._resultFile, "", 0, self._db )
-#        convCoord.run()
-#        
-#        refLine = [ "dmel_chr4"+"\t"+"192"+"\t"+"197"+"\t"+"dmel_chr4"+"\t"+"241"+"\t"+"246"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
-#        _MockAlignFile( self._refFileToCompare, refLine )
-#        
-#        self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
-#        os.remove( file2Process )
-#        os.remove( mapFileName )
-#        
-#        
-#class _MockAlignFile:
-#    
-#    def __init__(self, fileName, lines):
-#        alignF = open(fileName, "w");
-#        for line in lines:
-#            alignF.write(line)
-#        alignF.close    
-#
-#
-#class _MockMapFile:
-#    
-#    def __init__ (self, fileName):
-#        mapF = open(fileName, "w")
-#        line1 = "chunk1" + '\t'   + "dmel_chr4" + '\t' +   "1" + '\t'+   "100000" + "\n"
-#        line2 = "chunk2" + '\t'   + "dmel_chr4" + '\t' +   "90001" + '\t'+   "190000" + "\n"
-#        line3 = "chunk3" + '\t'   + "dmel_chr4" + '\t' +   "180001" + '\t' + "280000" + "\n"  
-#        mapF.write(line1)
-#        mapF.write(line2)
-#        mapF.write(line3)
-#        mapF.close
-
-
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_ConvCoordWithOverlaps ) )
-if __name__ == "__main__":
-    unittest.TextTestRunner(verbosity=2).run( test_suite )

--- a/commons/pyRepetUnit/convCoord/test/Test_ConvMapChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.utils.FileUtils import FileUtils
-from commons.pyRepetUnit.convCoord.ConvMapChr2Chunk import ConvMapChr2Chunk
-import unittest
-import os
-
-class Test_ConvMapChr2Chunk(unittest.TestCase):
-
-    def setUp(self):
-        self._mapfilename="dummy.map"
-        self._maptablename="dummy_map"
-        
-        self._chunkmapfilename="chunk.map"
-        self._chunkmaptable="test_chunk_map"
-        
-        self._resfilename="dummy_res.map"
-        
-        map4convData="chunk1\tchr1\t1\t100\n"
-        map4convData+="chunk2\tchr1\t90\t200\n"
-        map4convData+="chunk3\tchr1\t190\t300\n"
-
-        map4conv=open(self._chunkmapfilename,"w")
-        map4conv.write(map4convData)
-        map4conv.close()
-        
-        self._db = DbFactory.createInstance()
-        self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True)
-        
-        map2convData="reg1\tchr1\t10\t80\n"
-        map2convData+="reg1\tchr1\t90\t110\n"
-        map2convData+="reg2\tchr1\t150\t160\n"
-        
-        map2convData+="reg3\tchr1\t70\t210\n"
-        map2convData+="reg4\tchr1\t85\t100\n"
-        map2convData+="reg5\tchr1\t85\t110\n"
-        
-        map2convData+="reg6\tchr1\t80\t10\n"
-        map2convData+="reg6\tchr1\t110\t90\n"
-        map2convData+="reg7\tchr1\t160\t150\n"
-        map2convData+="reg8\tchr1\t190\t300\n"
-        
-        map2convData+="reg9\tchr1\t210\t70\n"
-        map2convData+="reg10\tchr1\t100\t85\n"
-        map2convData+="reg11\tchr1\t110\t85\n"
-        map2convData+="reg12\tchr1\t300\t190\n"
-                        
-        map2conv=open(self._mapfilename,"w")
-        map2conv.write(map2convData)
-        map2conv.close()
-        
-        self._db.createTable(self._maptablename, "map", self._mapfilename, True)
-
-        mapResData="reg1\tchunk1\t10\t80\n"
-        mapResData+="reg1\tchunk1\t90\t100\n"
-        mapResData+="reg1\tchunk2\t1\t21\n"
-        mapResData+="reg2\tchunk2\t61\t71\n"
-
-        mapResData+="reg3\tchunk1\t70\t100\n"
-        mapResData+="reg3\tchunk2\t1\t111\n"
-        mapResData+="reg3\tchunk3\t1\t21\n"
-        
-        mapResData+="reg4\tchunk1\t85\t100\n"
-        mapResData+="reg4\tchunk2\t1\t11\n"
-        mapResData+="reg5\tchunk1\t85\t100\n"
-        mapResData+="reg5\tchunk2\t1\t21\n"
-        
-        mapResData+="reg6\tchunk1\t80\t10\n"
-        mapResData+="reg6\tchunk1\t100\t90\n"
-        mapResData+="reg6\tchunk2\t21\t1\n"
-        mapResData+="reg7\tchunk2\t71\t61\n"
-        mapResData+="reg8\tchunk2\t101\t111\n"
-        mapResData+="reg8\tchunk3\t1\t111\n"
-        
-        mapResData+="reg9\tchunk1\t100\t70\n"
-        mapResData+="reg9\tchunk2\t111\t1\n"
-        mapResData+="reg9\tchunk3\t21\t1\n"
-        
-        mapResData+="reg10\tchunk1\t100\t85\n"
-        mapResData+="reg10\tchunk2\t11\t1\n"
-        mapResData+="reg11\tchunk1\t100\t85\n"
-        mapResData+="reg11\tchunk2\t21\t1\n"
-        mapResData+="reg12\tchunk2\t111\t101\n"       
-        mapResData+="reg12\tchunk3\t111\t1\n"       
-                
-        mapRes=open(self._resfilename,"w")
-        mapRes.write(mapResData)
-        mapRes.close()
-        
-    def tearDown(self):
-        self._db.dropTable(self._chunkmaptable)
-        self._db.dropTable(self._maptablename)
-        self._db.close()
-        os.remove(self._resfilename)
-        os.remove(self._mapfilename)
-        os.remove(self._chunkmapfilename)
-
-    def test_convert(self):
-        conv = ConvMapChr2Chunk(self._db,self._maptablename, self._chunkmaptable, self._maptablename+"_onchk")
-        conv.convert()
-        obsFileName = "dummy_map.onchk"
-        self._db.exportDataToFile("dummy_map_onchk", obsFileName)
-        self._db.dropTable("dummy_map_onchk")
-        self.assertTrue(FileUtils.are2FilesIdentical(self._resfilename, obsFileName))
-        os.remove(obsFileName)
-        
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_ConvMapChr2Chunk ) )
-if __name__ == '__main__':
-    unittest.TextTestRunner(verbosity=2).run( test_suite )
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/test/Test_ConvPathChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.pyRepetUnit.convCoord.ConvPathChr2Chunk import ConvPathChr2Chunk
-import unittest
-import os
-
-class Test_ConvPathChr2Chunk(unittest.TestCase):
-
-    def setUp(self):
-        self._pathfilename="dummy.path"
-        self._pathtablename="dummy_path"
-        
-        self._chunkmapfilename="chunk.map"
-        self._chunkmaptable="test_chunk_map"
-        
-        self._resfilename="dummy_res.path"
-        
-        map4convData="chunk1\tchr1\t1\t100\n"
-        map4convData+="chunk2\tchr1\t90\t200\n"
-        map4convData+="chunk3\tchr1\t190\t300\n"
-
-        map4conv=open(self._chunkmapfilename,"w")
-        map4conv.write(map4convData)
-        map4conv.close()
-        
-        self._db = DbFactory.createInstance()
-        self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True)
-        
-        path2convData="1\tchr1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="1\tchr1\t90\t110\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="2\tchr1\t150\t160\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        path2convData+="3\tchr1\t70\t210\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="4\tchr1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="5\tchr1\t85\t110\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        path2convData+="6\tchr1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="6\tchr1\t90\t110\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="7\tchr1\t150\t160\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="8\tchr1\t190\t300\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        path2convData+="9\tchr1\t70\t210\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="10\tchr1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="11\tchr1\t85\t110\tsub1\t10\t50\t0.01\t1000\t99\n"
-        path2convData+="12\tchr1\t190\t300\tsub1\t10\t50\t0.01\t1000\t99\n"
-                        
-        path2conv=open(self._pathfilename,"w")
-        path2conv.write(path2convData)
-        path2conv.close()
-        
-        self._db.createTable(self._pathtablename, "path", self._pathfilename)
-
-        pathResData="1\tchunk1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="1\tchunk1\t90\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="1\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="2\tchunk2\t61\t71\tsub1\t10\t50\t0.01\t1000\t99\n"
-
-        pathResData+="3\tchunk1\t70\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="3\tchunk2\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="3\tchunk3\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        pathResData+="4\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="4\tchunk2\t1\t11\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="5\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="5\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        pathResData+="6\tchunk1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="6\tchunk1\t90\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="6\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="7\tchunk2\t61\t71\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="8\tchunk2\t101\t111\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="8\tchunk3\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        pathResData+="9\tchunk1\t70\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="9\tchunk2\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="9\tchunk3\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        
-        pathResData+="10\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="10\tchunk2\t1\t11\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="11\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="11\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n"
-        pathResData+="12\tchunk2\t101\t111\tsub1\t10\t50\t0.01\t1000\t99\n"       
-        pathResData+="12\tchunk3\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n"       
-                
-        pathRes=open(self._resfilename,"w")
-        pathRes.write(pathResData)
-        pathRes.close()
-        
-    def tearDown(self):
-        self._db.dropTable(self._chunkmaptable)
-        self._db.dropTable(self._pathtablename)
-        self._db.close()
-        os.remove(self._resfilename)
-        os.remove(self._pathfilename)
-        os.remove(self._chunkmapfilename)
-
-    def test_convert(self):
-        conv=ConvPathChr2Chunk(self._db,self._pathtablename, self._chunkmaptable, self._pathtablename+"_onchk")
-        conv.convert()
-        expPath = self._resfilename
-        obsPath = "dummy_path.onchk"
-        self._db.exportDataToFile("dummy_path_onchk", obsPath)
-        self._db.dropTable("dummy_path_onchk")
-        self.assertTrue(FileUtils.are2FilesIdentical(expPath, obsPath))
-        os.remove(obsPath)
-
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_ConvPathChr2Chunk ) )
-if __name__ == '__main__':
-    unittest.TextTestRunner(verbosity=2).run( test_suite )
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/test/Test_ConvSetChr2Chunk.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.utils.FileUtils import FileUtils
-from commons.pyRepetUnit.convCoord.ConvSetChr2Chunk import ConvSetChr2Chunk
-import unittest
-import os
-
-class Test_ConvSetChr2Chunk(unittest.TestCase):
-
-    def setUp(self):
-        self._setfilename="dummy.set"
-        self._settablename="dummy_set"
-        
-        self._chunkmapfilename="chunk.map"
-        self._chunkmaptable="test_chunk_map"
-        
-        self._resfilename="dummy_res.set"
-        
-        map4convData="chunk1\tchr1\t1\t100\n"
-        map4convData+="chunk2\tchr1\t90\t200\n"
-        map4convData+="chunk3\tchr1\t190\t300\n"
-
-        map4conv=open(self._chunkmapfilename,"w")
-        map4conv.write(map4convData)
-        map4conv.close()
-        
-        self._db = DbFactory.createInstance()
-        self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True)
-        
-        set2convData="1\treg1\tchr1\t10\t80\n"
-        set2convData+="1\treg1\tchr1\t90\t110\n"
-        set2convData+="2\treg2\tchr1\t150\t160\n"
-        
-        set2convData+="3\treg3\tchr1\t70\t210\n"
-        set2convData+="4\treg4\tchr1\t85\t100\n"
-        set2convData+="5\treg5\tchr1\t85\t110\n"
-        
-        set2convData+="6\treg6\tchr1\t80\t10\n"
-        set2convData+="6\treg6\tchr1\t110\t90\n"
-        set2convData+="7\treg7\tchr1\t160\t150\n"
-        set2convData+="8\treg8\tchr1\t190\t300\n"
-        
-        set2convData+="9\treg9\tchr1\t210\t70\n"
-        set2convData+="10\treg10\tchr1\t100\t85\n"
-        set2convData+="11\treg11\tchr1\t110\t85\n"
-        set2convData+="12\treg12\tchr1\t300\t190\n"
-                        
-        set2conv=open(self._setfilename,"w")
-        set2conv.write(set2convData)
-        set2conv.close()
-        
-        self._db.createTable(self._settablename, "set", self._setfilename, True)
-
-        setResData="1\treg1\tchunk1\t10\t80\n"
-        setResData+="1\treg1\tchunk1\t90\t100\n"
-        setResData+="1\treg1\tchunk2\t1\t21\n"
-        setResData+="2\treg2\tchunk2\t61\t71\n"
-
-        setResData+="3\treg3\tchunk1\t70\t100\n"
-        setResData+="3\treg3\tchunk2\t1\t111\n"
-        setResData+="3\treg3\tchunk3\t1\t21\n"
-        
-        setResData+="4\treg4\tchunk1\t85\t100\n"
-        setResData+="4\treg4\tchunk2\t1\t11\n"
-        setResData+="5\treg5\tchunk1\t85\t100\n"
-        setResData+="5\treg5\tchunk2\t1\t21\n"
-        
-        setResData+="6\treg6\tchunk1\t80\t10\n"
-        setResData+="6\treg6\tchunk1\t100\t90\n"
-        setResData+="6\treg6\tchunk2\t21\t1\n"
-        setResData+="7\treg7\tchunk2\t71\t61\n"
-        setResData+="8\treg8\tchunk2\t101\t111\n"
-        setResData+="8\treg8\tchunk3\t1\t111\n"
-        
-        setResData+="9\treg9\tchunk1\t100\t70\n"
-        setResData+="9\treg9\tchunk2\t111\t1\n"
-        setResData+="9\treg9\tchunk3\t21\t1\n"
-        
-        setResData+="10\treg10\tchunk1\t100\t85\n"
-        setResData+="10\treg10\tchunk2\t11\t1\n"
-        setResData+="11\treg11\tchunk1\t100\t85\n"
-        setResData+="11\treg11\tchunk2\t21\t1\n"
-        setResData+="12\treg12\tchunk2\t111\t101\n"       
-        setResData+="12\treg12\tchunk3\t111\t1\n"       
-                
-        setRes=open(self._resfilename,"w")
-        setRes.write(setResData)
-        setRes.close()
-        
-    def tearDown(self):
-        self._db.dropTable(self._chunkmaptable)
-        self._db.dropTable(self._settablename)
-        self._db.close()
-        os.remove(self._resfilename)
-        os.remove(self._setfilename)
-        os.remove(self._chunkmapfilename)
-
-    def test_convert(self):
-        conv = ConvSetChr2Chunk(self._db,self._settablename, self._chunkmaptable, self._settablename+"_onchk")
-        conv.convert()
-        obsFileName = "dummy_set.onchk"
-        self._db.exportDataToFile("dummy_set_onchk", obsFileName)
-        self._db.dropTable("dummy_set_onchk")
-        self.assertTrue(FileUtils.are2FilesIdentical(self._resfilename, obsFileName))
-        os.remove(obsFileName)
-
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_ConvSetChr2Chunk ) )
-if __name__ == '__main__':
-    unittest.TextTestRunner(verbosity=2).run( test_suite )
\ No newline at end of file

--- a/commons/pyRepetUnit/convCoord/test/Test_PathChunkConnector.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-import unittest
-import time
-import os
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.pyRepetUnit.convCoord.PathChunkConnector import PathChunkConnector
-from commons.core.sql.DbMySql import DbMySql
-
-
-class Test_PathChunkConnector( unittest.TestCase ):
-    
-    def setUp(self):
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-        self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
-        configF = open(self._configFileName, "w" )
-        configF.write( "[repet_env]\n" )
-        configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
-        configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
-        configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
-        configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
-        configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
-        configF.close()
-        self._db = DbMySql( cfgFileName=self._configFileName )
-        self._table = "dummyPathTable_%s" % ( self._uniqId )
-        self._tpA = TablePathAdaptator( self._db, self._table )
-        self._mapDict = {'chunk1': ('dmel_chr4', 1, 100000),'chunk2': ('dmel_chr4', 90001, 190000),'chunk3': ('dmel_chr4', 180001, 280000), }
-        self._mapFileName = "map_file.map"
-        
-    def tearDown(self):
-        self._db.close()
-        
-    def testTwoQueryOverlapsOnPlusStrand (self):
-        lines = [
-                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n",
-                 "2\tdmel_chr4\t95545\t95576\tsbj2\t125457\t133465\t2e-38\t83\t65\n"
-                ]
-        
-        expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 125423, 133465, 2e-38, 83,97.78)]
-        self._templateTest(lines, expectedList)
-        
-    def testTwoQueryOverlapsOnReverseStrand (self):
-        lines = [
-                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125467\t125423\t7e-15\t82\t97.78\n",
-                 "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n"
-                ]
-
-        expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 133465, 125423, 2e-38, 83,97.78)]
-        self._templateTest(lines, expectedList)
-        
-    def testTwoQueryOverlapsOnDifferentStrands (self):
-        lines = [                   
-                 "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n",
-                 "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n"
-                ]
-        expectedList =[
-                       ("dmel_chr4", 95535, 95570, "sbj2", 125423, 125467, 7e-15, 82,97.78),
-                       ("dmel_chr4", 95545, 95576, "sbj2", 133465, 125457, 2e-38, 83,65)
-                       ]
-        self._templateTest(lines, expectedList)
-        
-    def _templateTest(self, datas2TestList, expectedList ):
-        pathFileName = "dummyPathFile_%s" % ( self._uniqId )
-        _MockPathFile(pathFileName, datas2TestList)
-        
-
-        self._db.createTable( self._table, "path", pathFileName )
-
-        _MockMapFile(self._mapFileName)
-        chunkConnector = PathChunkConnector(self._mapFileName, self._db, self._table, 0)
-        chunkConnector.run()
-       
-        sql_cmd = 'select * from %s' % (self._table)
-        self._db.execute(sql_cmd)
-        res = self._db.fetchall()
-        
-        for i in xrange(len(expectedList)):
-            resultTuple = res[i]
-            expectedTuple = expectedList[i]
-            self._assertExpectedTupleEqualsObsTuple(expectedTuple, resultTuple)
-        
-        self._db.dropTable( self._table )
-        os.remove(pathFileName)
-        os.remove(self._mapFileName)
-        
-    def _assertExpectedTupleEqualsObsTuple(self, expectedTuple, resultTuple):
-        self.assertEquals(expectedTuple[0], resultTuple[1])
-        self.assertEquals(expectedTuple[1], resultTuple[2])
-        self.assertEquals(expectedTuple[2], resultTuple[3])
-        self.assertEquals(expectedTuple[3], resultTuple[4])
-        self.assertEquals(expectedTuple[4], resultTuple[5])
-        self.assertEquals(expectedTuple[5], resultTuple[6])
-        self.assertEquals(expectedTuple[6], resultTuple[7])
-        self.assertEquals(expectedTuple[7], resultTuple[8])
-        self.assertEquals(expectedTuple[8], resultTuple[9])
-        
-
-class _MockPathFile:
-    
-    def __init__(self, fileName, lines):
-        path = open(fileName, "w");
-        for line in lines:
-            path.write(line)
-        path.close
-        
-        
-class _MockMapFile:
-    
-    def __init__ (self, fileName):
-        map = open(fileName, "w")
-        line1 = "chunk1" + '\t'   + "dmel_chr4" + '\t' +   "1" + '\t'+   "100000" + "\n"
-        line2 = "chunk2" + '\t'   + "dmel_chr4" + '\t' +   "90001" + '\t'+   "190000" + "\n"
-        line3 = "chunk3" + '\t'   + "dmel_chr4" + '\t' +   "180001" + '\t' + "280000" + "\n"  
-        map.write(line1)
-        map.write(line2)
-        map.write(line3)
-        map.close
-        
-        
-test_suite = unittest.TestSuite()
-test_suite.addTest( unittest.makeSuite( Test_PathChunkConnector ) )
-if __name__ == "__main__":
-    unittest.TextTestRunner(verbosity=2).run( test_suite )

--- a/commons/pyRepetUnit/convCoord/test/convCoordTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-import unittest
-import sys
-import TestConvCoordWithOverlapps
-import TestConvMapChr2Chunk
-import TestConvSetChr2Chunk
-import TestConvPathChr2Chunk
-
-def main():
-    commonsTestSuite = unittest.TestSuite() 
-    commonsTestSuite.addTest(unittest.makeSuite(TestConvCoordWithOverlapps.Test_ConvCoordWithOverlaps,'test'))
-    commonsTestSuite.addTest(unittest.makeSuite(TestConvMapChr2Chunk.Test_ConvMapChr2Chunk,'test'))
-    commonsTestSuite.addTest(unittest.makeSuite(TestConvSetChr2Chunk.Test_ConvSetChr2Chunk,'test'))
-    commonsTestSuite.addTest(unittest.makeSuite(TestConvPathChr2Chunk.Test_ConvPathChr2Chunk,'test'))
-    runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-    runner.run(commonsTestSuite)
-    
-if __name__ == "__main__":
-    main()

--- a/commons/pyRepetUnit/doc/api-objects.txt	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-commons.Checker	commons.Checker-module.html
-commons.Checker.DEFAULT_LOGGER_NAME	commons.Checker-module.html#DEFAULT_LOGGER_NAME
-commons.Checker.LOG_FILE	commons.Checker-module.html#LOG_FILE
-commons.IComponentWrapper	commons.IComponentWrapper-module.html
-commons.IDataProcessor	commons.IDataProcessor-module.html
-commons.Checker.Checker	commons.Checker.Checker-class.html
-commons.Checker.Checker.getLogger	commons.Checker.Checker-class.html#getLogger
-commons.Checker.Checker.__init__	commons.Checker.Checker-class.html#__init__
-commons.Checker.Checker.setLogger	commons.Checker.Checker-class.html#setLogger
-commons.Checker.Checker._handle	commons.Checker.Checker-class.html#_handle
-commons.Checker.IChecker.check	commons.Checker.IChecker-class.html#check
-commons.Checker.CheckerException	commons.Checker.CheckerException-class.html
-commons.Checker.CheckerException.msg	commons.Checker.CheckerException-class.html#msg
-commons.Checker.CheckerException.__init__	commons.Checker.CheckerException-class.html#__init__
-commons.Checker.ConfigChecker	commons.Checker.ConfigChecker-class.html
-commons.Checker.ConfigChecker.optionsDict	commons.Checker.ConfigChecker-class.html#optionsDict
-commons.Checker.ConfigChecker.check	commons.Checker.ConfigChecker-class.html#check
-commons.Checker.ConfigChecker.__init__	commons.Checker.ConfigChecker-class.html#__init__
-commons.Checker.ConfigChecker.sectionName	commons.Checker.ConfigChecker-class.html#sectionName
-commons.Checker.ConfigException	commons.Checker.ConfigException-class.html
-commons.Checker.ConfigException.messages	commons.Checker.ConfigException-class.html#messages
-commons.Checker.ConfigException.msg	commons.Checker.ConfigException-class.html#msg
-commons.Checker.ConfigException.__init__	commons.Checker.ConfigException-class.html#__init__
-commons.Checker.IChecker	commons.Checker.IChecker-class.html
-commons.Checker.IChecker.check	commons.Checker.IChecker-class.html#check
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-  <script type="text/javascript" src="epydoc.js"></script>
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-    <li> <strong class="uidlink"><a href="commons.Checker.ConfigException-class.html">commons.Checker.ConfigException</a></strong>:
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--- a/commons/pyRepetUnit/doc/commons.Checker-module.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-  <script type="text/javascript" src="epydoc.js"></script>
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-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
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-<table width="100%" cellpadding="0" cellspacing="0">
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-        Package&nbsp;commons ::
-        Module&nbsp;Checker
-      </span>
-    </td>
-    <td>
-      <table cellpadding="0" cellspacing="0">
-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
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-<p>Created on 9 avr. 2009</p>
-
-<hr />
-<div class="fields">      <p><strong>Author:</strong>
-        oinizan
-      </p>
-</div><!-- ==================== CLASSES ==================== -->
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-<table class="summary" border="1" cellpadding="3"
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-</tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
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-      A concrete checker implementation with a logging.
-    </td>
-  </tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-        <a href="commons.Checker.CheckerException-class.html" class="summary-name">CheckerException</a><br />
-      Exception raised during check.
-    </td>
-  </tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-        <a href="commons.Checker.ConfigChecker-class.html" class="summary-name">ConfigChecker</a><br />
-      A checker for config file.
-    </td>
-  </tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-        <a href="commons.Checker.ConfigException-class.html" class="summary-name">ConfigException</a><br />
-      A exception raised by check method class ConfigChecker
-    </td>
-  </tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-        <a href="commons.Checker.IChecker-class.html" class="summary-name">IChecker</a><br />
-      Interface emulation for a checker
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-    <table border="0" cellpadding="0" cellspacing="0" width="100%">
-      <tr valign="top">
-        <td align="left"><span class="table-header">Variables</span></td>
-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-Variables"
-         class="privatelink" onclick="toggle_private();"
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-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-        <a name="DEFAULT_LOGGER_NAME"></a><span class="summary-name">DEFAULT_LOGGER_NAME</span> = <code title="'log02'"><code class="variable-quote">'</code><code class="variable-string">log02</code><code class="variable-quote">'</code></code>
-    </td>
-  </tr>
-<tr>
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-        <a href="commons.Checker-module.html#LOG_FILE" class="summary-name">LOG_FILE</a> = <code title="'/home/oinizan/workspace/repet_pipe/pyRepetUnit/blaster/check/longconf\
-.ini'"><code class="variable-quote">'</code><code class="variable-string">/home/oinizan/workspace/repet_pipe/pyRepetUnit/bla</code><code class="variable-ellipsis">...</code></code>
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-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-VariablesDetails"
-         class="privatelink" onclick="toggle_private();"
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-  <h3 class="epydoc">LOG_FILE</h3>
-  
-  <dl class="fields">
-  </dl>
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-    <dt>Value:</dt>
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-<code class="variable-quote">'</code><code class="variable-string">/home/oinizan/workspace/repet_pipe/pyRepetUnit/blaster/check/longconf</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
-<code class="variable-string">.ini</code><code class="variable-quote">'</code>
-</pre></td></tr></table>
-</dd>
-  </dl>
-</td></tr></table>
-</div>
-<br />
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
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-
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
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-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
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-    Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009
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-  // visible); but by default, we want to hide them.  So hide
-  // them unless we have a cookie that says to show them.
-  checkCookie();
-  // -->
-</script>
-</body>
-</html>

--- a/commons/pyRepetUnit/doc/commons.Checker-pysrc.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,259 +0,0 @@
-<?xml version="1.0" encoding="ascii"?>
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-          "DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>commons.Checker</title>
-  <link rel="stylesheet" href="epydoc.css" type="text/css" />
-  <script type="text/javascript" src="epydoc.js"></script>
-</head>
-
-<body bgcolor="white" text="black" link="blue" vlink="#204080"
-      alink="#204080">
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Index link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
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-</table>
-<table width="100%" cellpadding="0" cellspacing="0">
-  <tr valign="top">
-    <td width="100%">
-      <span class="breadcrumbs">
-        Package&nbsp;commons ::
-        Module&nbsp;Checker
-      </span>
-    </td>
-    <td>
-      <table cellpadding="0" cellspacing="0">
-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
-        <tr><td align="right"><span class="options"
-            >[<a href="frames.html" target="_top">frames</a
-            >]&nbsp;|&nbsp;<a href="commons.Checker-pysrc.html"
-            target="_top">no&nbsp;frames</a>]</span></td></tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<h1 class="epydoc">Source Code for <a href="commons.Checker-module.html">Module commons.Checker</a></h1>
-<pre class="py-src">
-<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
-<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Created on 9 avr. 2009</tt> </tt>
-<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
-<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">@author: oinizan</tt> </tt>
-<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
-<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">config</tt> </tt>
-<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">ConfigParser</tt> </tt>
-<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">ConfigParser</tt> <tt class="py-keyword">import</tt> <tt class="py-name">NoSectionError</tt> </tt>
-<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">ConfigParser</tt> <tt class="py-keyword">import</tt> <tt class="py-name">NoOptionError</tt> </tt>
-<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"> </tt>
-<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable commons.Checker.LOG_FILE=commons.Checker-module.html#LOG_FILE"><a title="commons.Checker.LOG_FILE" class="py-name" href="#" onclick="return doclink('link-0', 'LOG_FILE', 'link-0');">LOG_FILE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"/home/oinizan/workspace/repet_pipe/pyRepetUnit/blaster/check/longconf.ini"</tt> </tt>
-<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable commons.Checker.DEFAULT_LOGGER_NAME=commons.Checker-module.html#DEFAULT_LOGGER_NAME"><a title="commons.Checker.DEFAULT_LOGGER_NAME" class="py-name" href="#" onclick="return doclink('link-1', 'DEFAULT_LOGGER_NAME', 'link-1');">DEFAULT_LOGGER_NAME</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"log02"</tt> </tt>
-<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"> </tt>
-<a name="IChecker"></a><div id="IChecker-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="IChecker-toggle" onclick="return toggle('IChecker');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker.IChecker-class.html">IChecker</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IChecker-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IChecker-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">    Interface emulation for a checker </tt> </tt>
-<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="IChecker.check"></a><div id="IChecker.check-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="IChecker.check-toggle" onclick="return toggle('IChecker.check');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.IChecker-class.html#check">check</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">arg</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IChecker.check-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IChecker.check-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">        perform check, raise a CheckerException if error occured</tt> </tt>
-<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
-<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">        @param arg:  a collecting parameter: put here all you need to perform check  </tt> </tt>
-<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">        @type arg: choose the appropriate type</tt> </tt>
-<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
-</div></div><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"> </tt>
-<a name="Checker"></a><div id="Checker-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="Checker-toggle" onclick="return toggle('Checker');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker.Checker-class.html">Checker</a> <tt class="py-op">(</tt><tt class="py-base-class">IChecker</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="Checker-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Checker-expanded"><a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    A concrete checker implementation with a logging.</tt> </tt>
-<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">    Logger instance is a singleton of logging module </tt> </tt>
-<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="Checker._handle"></a><div id="Checker._handle-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Checker._handle-toggle" onclick="return toggle('Checker._handle');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.Checker-class.html#_handle">_handle</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="Checker._handle-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Checker._handle-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
-<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">            <tt class="py-name">single</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name" targets="Class commons.Checker._Logger=commons.Checker._Logger-class.html"><a title="commons.Checker._Logger" class="py-name" href="#" onclick="return doclink('link-2', '_Logger', 'link-2');">_Logger</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
-<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt id="link-3" class="py-name"><a title="commons.Checker._Logger" class="py-name" href="#" onclick="return doclink('link-3', '_Logger', 'link-2');">_Logger</a></tt><tt class="py-op">,</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> </tt>
-<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">            <tt class="py-name">single</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt> </tt>
-<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">single</tt>     </tt>
-</div><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">     </tt>
-<a name="Checker.__init__"></a><div id="Checker.__init__-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="Checker.__init__-toggle" onclick="return toggle('Checker.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.Checker-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="Checker.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Checker.__init__-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">        <tt class="py-name">logger</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method commons.Checker.Checker._handle()=commons.Checker.Checker-class.html#_handle"><a title="commons.Checker.Checker._handle" class="py-name" href="#" onclick="return doclink('link-4', '_handle', 'link-4');">_handle</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
-<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log</tt> <tt class="py-op">=</tt> <tt class="py-name">logger</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method commons.Checker.Checker.getLogger()=commons.Checker.Checker-class.html#getLogger,Method commons.Checker._Logger.getLogger()=commons.Checker._Logger-class.html#getLogger"><a title="commons.Checker.Checker.getLogger
-commons.Checker._Logger.getLogger" class="py-name" href="#" onclick="return doclink('link-5', 'getLogger', 'link-5');">getLogger</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
-</div><a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    </tt>
-<a name="Checker.setLogger"></a><div id="Checker.setLogger-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="Checker.setLogger-toggle" onclick="return toggle('Checker.setLogger');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.Checker-class.html#setLogger">setLogger</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">logger</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="Checker.setLogger-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Checker.setLogger-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">        set (change) default logger</tt> </tt>
-<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
-<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">        @param logger: a new logger</tt> </tt>
-<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">        @type logger: class Logger </tt> </tt>
-<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log</tt> <tt class="py-op">=</tt> <tt class="py-name">logger</tt> </tt>
-</div><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"> </tt>
-<a name="Checker.getLogger"></a><div id="Checker.getLogger-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="Checker.getLogger-toggle" onclick="return toggle('Checker.getLogger');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.Checker-class.html#getLogger">getLogger</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="Checker.getLogger-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Checker.getLogger-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">        returns the logger instance</tt> </tt>
-<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log</tt> </tt>
-</div></div><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"> </tt>
-<a name="CheckerException"></a><div id="CheckerException-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="CheckerException-toggle" onclick="return toggle('CheckerException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker.CheckerException-class.html">CheckerException</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="CheckerException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CheckerException-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-docstring">    Exception raised during check. </tt> </tt>
-<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
-<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring">    @ivar msg : message embeded in Execption class   </tt> </tt>
-<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">    @type msg: str</tt> </tt>
-<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
-<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="CheckerException.__init__"></a><div id="CheckerException.__init__-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="CheckerException.__init__-toggle" onclick="return toggle('CheckerException.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.CheckerException-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">msg</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="CheckerException.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CheckerException.__init__-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">msg</tt> <tt class="py-op">=</tt> <tt class="py-name">msg</tt> </tt>
-<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-name">Exception</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method commons.Checker.Checker.__init__()=commons.Checker.Checker-class.html#__init__,Method commons.Checker.CheckerException.__init__()=commons.Checker.CheckerException-class.html#__init__,Method commons.Checker.ConfigChecker.__init__()=commons.Checker.ConfigChecker-class.html#__init__,Method commons.Checker.ConfigException.__init__()=commons.Checker.ConfigException-class.html#__init__,Method commons.Checker._Logger.__init__()=commons.Checker._Logger-class.html#__init__"><a title="commons.Checker.Checker.__init__
-commons.Checker.CheckerException.__init__
-commons.Checker.ConfigChecker.__init__
-commons.Checker.ConfigException.__init__
-commons.Checker._Logger.__init__" class="py-name" href="#" onclick="return doclink('link-6', '__init__', 'link-6');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
-</div></div><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"> </tt>
-<a name="ConfigChecker"></a><div id="ConfigChecker-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="ConfigChecker-toggle" onclick="return toggle('ConfigChecker');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker.ConfigChecker-class.html">ConfigChecker</a> <tt class="py-op">(</tt><tt class="py-base-class">IChecker</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="ConfigChecker-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ConfigChecker-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    A checker for config file. </tt> </tt>
-<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    @ivar sectionName: section to check in config file</tt> </tt>
-<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">    @type sectionName: str</tt> </tt>
-<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
-<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    @ivar optionsDict: dict with option to check as keys and empty strings "" as values</tt> </tt>
-<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">    @type optionsDict: class Dict</tt> </tt>
-<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"> </tt>
-<a name="ConfigChecker.__init__"></a><div id="ConfigChecker.__init__-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="ConfigChecker.__init__-toggle" onclick="return toggle('ConfigChecker.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.ConfigChecker-class.html#__init__">__init__</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sectionName</tt><tt class="py-op">,</tt> <tt class="py-param">optionsDict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="ConfigChecker.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ConfigChecker.__init__-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sectionName</tt> <tt class="py-op">=</tt> <tt class="py-name">sectionName</tt> </tt>
-<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_optionsDict</tt> <tt class="py-op">=</tt> <tt class="py-name">optionsDict</tt> </tt>
-</div><a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-string">"""</tt> </tt>
-<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-string">    Check options stored in optionsDict. 3 checks are performed:</tt> </tt>
-<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-string">    (i) config file existence, (ii) section existence, (iii) options existences</tt> </tt>
-<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-string">    If a check fail, raise a ConfigException with a list of messages</tt> </tt>
-<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-string">    """</tt> </tt>
-<a name="ConfigChecker.check"></a><div id="ConfigChecker.check-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="ConfigChecker.check-toggle" onclick="return toggle('ConfigChecker.check');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.ConfigChecker-class.html#check">check</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">configFile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="ConfigChecker.check-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ConfigChecker.check-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">config</tt> <tt class="py-op">=</tt> <tt class="py-name">ConfigParser</tt><tt class="py-op">.</tt><tt class="py-name">ConfigParser</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
-<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-name">msg</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
-<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
-<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">            <tt class="py-name">config</tt><tt class="py-op">.</tt><tt class="py-name">readfp</tt><tt class="py-op">(</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">configFile</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
-<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-name">e</tt><tt class="py-op">:</tt> </tt>
-<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">            <tt class="py-name">msg</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"CONFIG FILE not found - "</tt> <tt class="py-op">+</tt> <tt class="py-name">e</tt><tt class="py-op">.</tt><tt class="py-name">message</tt><tt class="py-op">)</tt> </tt>
-<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt id="link-7" class="py-name" targets="Class commons.Checker.ConfigException=commons.Checker.ConfigException-class.html"><a title="commons.Checker.ConfigException" class="py-name" href="#" onclick="return doclink('link-7', 'ConfigException', 'link-7');">ConfigException</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt>  </tt>
-<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"> </tt>
-<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">config</tt><tt class="py-op">.</tt><tt class="py-name">has_section</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sectionName</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">            <tt class="py-name">msg</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"["</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sectionName</tt> <tt class="py-op">+</tt> <tt class="py-string">"]"</tt> <tt class="py-op">+</tt> <tt class="py-string">" section not found - "</tt><tt class="py-op">)</tt> </tt>
-<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt id="link-8" class="py-name"><a title="commons.Checker.ConfigException" class="py-name" href="#" onclick="return doclink('link-8', 'ConfigException', 'link-7');">ConfigException</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
-<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">          </tt>
-<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-name">isExceptionOccured</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt>         </tt>
-<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_optionsDict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
-<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_optionsDict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">config</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sectionName</tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt>  </tt>
-<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">NoOptionError</tt><tt class="py-op">,</tt> <tt class="py-name">e</tt><tt class="py-op">:</tt> </tt>
-<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">                <tt class="py-name">msg</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"["</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sectionName</tt> <tt class="py-op">+</tt> <tt class="py-string">"]"</tt> <tt class="py-op">+</tt> <tt class="py-string">" - "</tt> <tt class="py-op">+</tt> <tt class="py-name">e</tt><tt class="py-op">.</tt><tt class="py-name">message</tt><tt class="py-op">)</tt> </tt>
-<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                <tt class="py-name">isExceptionOccured</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
-<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">         </tt>
-<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">isExceptionOccured</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt id="link-9" class="py-name"><a title="commons.Checker.ConfigException" class="py-name" href="#" onclick="return doclink('link-9', 'ConfigException', 'link-7');">ConfigException</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt>  </tt>
-</div></div><a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"> </tt>
-<a name="ConfigException"></a><div id="ConfigException-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="ConfigException-toggle" onclick="return toggle('ConfigException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker.ConfigException-class.html">ConfigException</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="ConfigException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ConfigException-expanded"><a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">     </tt>
-<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"><tt class="py-docstring">    A exception raised by check method class ConfigChecker</tt> </tt>
-<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
-<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-docstring">    @ivar msg : message embeded in Execption class   </tt> </tt>
-<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"><tt class="py-docstring">    @type msg: str</tt> </tt>
-<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
-<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-docstring">    @ivar messages: list of messages</tt> </tt>
-<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">    @type messages: Class list</tt> </tt>
-<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring">     </tt> </tt>
-<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="ConfigException.__init__"></a><div id="ConfigException.__init__-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="ConfigException.__init__-toggle" onclick="return toggle('ConfigException.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker.ConfigException-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">msg</tt><tt class="py-op">,</tt> <tt class="py-param">messages</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="ConfigException.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ConfigException.__init__-expanded"><a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">messages</tt> <tt class="py-op">=</tt> <tt class="py-name">messages</tt> </tt>
-<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt class="py-name">Exception</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="commons.Checker.Checker.__init__
-commons.Checker.CheckerException.__init__
-commons.Checker.ConfigChecker.__init__
-commons.Checker.ConfigException.__init__
-commons.Checker._Logger.__init__" class="py-name" href="#" onclick="return doclink('link-10', '__init__', 'link-6');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
-</div></div><a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"> </tt>
-<a name="_Logger"></a><div id="_Logger-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="_Logger-toggle" onclick="return toggle('_Logger');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.Checker._Logger-class.html">_Logger</a><tt class="py-op">:</tt> </tt>
-</div><div id="_Logger-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Logger-expanded"><a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">     </tt>
-<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-name">__single</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
-<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">     </tt>
-<a name="_Logger.__init__"></a><div id="_Logger.__init__-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="_Logger.__init__-toggle" onclick="return toggle('_Logger.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker._Logger-class.html#__init__">__init__</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">loggerName</tt> <tt class="py-op">=</tt><tt class="py-string">""</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="_Logger.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Logger.__init__-expanded"><a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-11" class="py-name"><a title="commons.Checker._Logger" class="py-name" href="#" onclick="return doclink('link-11', '_Logger', 'link-2');">_Logger</a></tt><tt class="py-op">.</tt><tt class="py-name">__single</tt><tt class="py-op">:</tt> </tt>
-<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt id="link-12" class="py-name"><a title="commons.Checker._Logger" class="py-name" href="#" onclick="return doclink('link-12', '_Logger', 'link-2');">_Logger</a></tt><tt class="py-op">.</tt><tt class="py-name">__single</tt> </tt>
-<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">config</tt><tt class="py-op">.</tt><tt class="py-name">fileConfig</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="commons.Checker.LOG_FILE" class="py-name" href="#" onclick="return doclink('link-13', 'LOG_FILE', 'link-0');">LOG_FILE</a></tt><tt class="py-op">)</tt> </tt>
-<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">loggerName</tt> <tt class="py-op">!=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__log</tt> <tt class="py-op">=</tt> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="commons.Checker.Checker.getLogger
-commons.Checker._Logger.getLogger" class="py-name" href="#" onclick="return doclink('link-14', 'getLogger', 'link-5');">getLogger</a></tt><tt class="py-op">(</tt><tt class="py-name">loggerName</tt><tt class="py-op">)</tt> </tt>
-<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
-<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__log</tt> <tt class="py-op">=</tt> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="commons.Checker.Checker.getLogger
-commons.Checker._Logger.getLogger" class="py-name" href="#" onclick="return doclink('link-15', 'getLogger', 'link-5');">getLogger</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="commons.Checker.DEFAULT_LOGGER_NAME" class="py-name" href="#" onclick="return doclink('link-16', 'DEFAULT_LOGGER_NAME', 'link-1');">DEFAULT_LOGGER_NAME</a></tt><tt class="py-op">)</tt> </tt>
-<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt id="link-17" class="py-name"><a title="commons.Checker._Logger" class="py-name" href="#" onclick="return doclink('link-17', '_Logger', 'link-2');">_Logger</a></tt><tt class="py-op">.</tt><tt class="py-name">__single</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
-</div><a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"> </tt>
-<a name="_Logger.getLogger"></a><div id="_Logger.getLogger-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="_Logger.getLogger-toggle" onclick="return toggle('_Logger.getLogger');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.Checker._Logger-class.html#getLogger">getLogger</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="_Logger.getLogger-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Logger.getLogger-expanded"><a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__log</tt> </tt>
-</div></div><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"> </tt><script type="text/javascript">
-<!--
-expandto(location.href);
-// -->
-</script>
-</pre>
-<br />
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Help link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
-  </tr>
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-    <td align="left" class="footer">
-    Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009
-    </td>
-    <td align="right" class="footer">
-      <a target="mainFrame" href="http://epydoc.sourceforge.net"
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-  <!--
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--- a/commons/pyRepetUnit/doc/commons.Checker.Checker-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,244 +0,0 @@
-<?xml version="1.0" encoding="ascii"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-          "DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>commons.Checker.Checker</title>
-  <link rel="stylesheet" href="epydoc.css" type="text/css" />
-  <script type="text/javascript" src="epydoc.js"></script>
-</head>
-
-<body bgcolor="white" text="black" link="blue" vlink="#204080"
-      alink="#204080">
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
-  <!-- Tree link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Index link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Help link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
-  </tr>
-</table>
-<table width="100%" cellpadding="0" cellspacing="0">
-  <tr valign="top">
-    <td width="100%">
-      <span class="breadcrumbs">
-        Package&nbsp;commons ::
-        <a href="commons.Checker-module.html">Module&nbsp;Checker</a> ::
-        Class&nbsp;Checker
-      </span>
-    </td>
-    <td>
-      <table cellpadding="0" cellspacing="0">
-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
-        <tr><td align="right"><span class="options"
-            >[<a href="frames.html" target="_top">frames</a
-            >]&nbsp;|&nbsp;<a href="commons.Checker.Checker-class.html"
-            target="_top">no&nbsp;frames</a>]</span></td></tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<!-- ==================== CLASS DESCRIPTION ==================== -->
-<h1 class="epydoc">Class Checker</h1><p class="nomargin-top"><span class="codelink"><a href="commons.Checker-pysrc.html#Checker">source&nbsp;code</a></span></p>
-<pre class="base-tree">
-<a href="commons.Checker.IChecker-class.html">IChecker</a> --+
-           |
-          <strong class="uidshort">Checker</strong>
-</pre>
-
-<hr />
-<p>A concrete checker implementation with a logging. Logger instance is a
-  singleton of logging module</p>
-
-<!-- ==================== INSTANCE METHODS ==================== -->
-<a name="section-InstanceMethods"></a>
-<table class="summary" border="1" cellpadding="3"
-       cellspacing="0" width="100%" bgcolor="white">
-<tr bgcolor="#70b0f0" class="table-header">
-  <td colspan="2" class="table-header">
-    <table border="0" cellpadding="0" cellspacing="0" width="100%">
-      <tr valign="top">
-        <td align="left"><span class="table-header">Instance Methods</span></td>
-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-InstanceMethods"
-         class="privatelink" onclick="toggle_private();"
-         >hide private</a>]</span></td>
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-  </td>
-</tr>
-<tr>
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
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-      <table width="100%" cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td>
-          <td align="right" valign="top">
-            <span class="codelink"><a href="commons.Checker-pysrc.html#Checker.__init__">source&nbsp;code</a></span>
-            
-          </td>
-        </tr>
-      </table>
-      
-    </td>
-  </tr>
-<tr class="private">
-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
-    </td><td class="summary">
-      <table width="100%" cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td><span class="summary-sig"><a name="_handle"></a><span class="summary-sig-name">_handle</span>(<span class="summary-sig-arg">self</span>)</span></td>
-          <td align="right" valign="top">
-            <span class="codelink"><a href="commons.Checker-pysrc.html#Checker._handle">source&nbsp;code</a></span>
-            
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-    </td>
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-    <td width="15%" align="right" valign="top" class="summary">
-      <span class="summary-type">&nbsp;</span>
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-      <table width="100%" cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td><span class="summary-sig"><a name="getLogger"></a><span class="summary-sig-name">getLogger</span>(<span class="summary-sig-arg">self</span>)</span><br />
-      returns the logger instance</td>
-          <td align="right" valign="top">
-            <span class="codelink"><a href="commons.Checker-pysrc.html#Checker.getLogger">source&nbsp;code</a></span>
-            
-          </td>
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-      
-    </td>
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--- a/commons/pyRepetUnit/doc/commons.Checker.CheckerException-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/commons/pyRepetUnit/doc/commons.Checker.ConfigChecker-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,244 +0,0 @@
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-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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-  <script type="text/javascript" src="epydoc.js"></script>
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-<body bgcolor="white" text="black" link="blue" vlink="#204080"
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-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
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-      <span class="breadcrumbs">
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-        Class&nbsp;ConfigChecker
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-    <td>
-      <table cellpadding="0" cellspacing="0">
-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
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-<hr />
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-<a name="section-InstanceMethods"></a>
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-<tr bgcolor="#70b0f0" class="table-header">
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-<div>
-<table class="details" border="1" cellpadding="3"
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-  <table width="100%" cellpadding="0" cellspacing="0" border="0">
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-  </td><td align="right" valign="top"
-    ><span class="codelink"><a href="commons.Checker-pysrc.html#ConfigChecker.check">source&nbsp;code</a></span>&nbsp;
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-  </tr></table>
-  
-  <p>perform check, raise a CheckerException if error occured</p>
-  <dl class="fields">
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-    <dt>Overrides:
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-        <dd><em class="note">(inherited documentation)</em></dd>
-    </dt>
-  </dl>
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-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
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-
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-    <td align="left" class="footer">
-    Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009
-    </td>
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-
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-  // -->
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--- a/commons/pyRepetUnit/doc/commons.Checker.ConfigException-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,280 +0,0 @@
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-          "DTD/xhtml1-transitional.dtd">
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-  <title>commons.Checker.ConfigException</title>
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-  <script type="text/javascript" src="epydoc.js"></script>
-</head>
-
-<body bgcolor="white" text="black" link="blue" vlink="#204080"
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-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
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-</table>
-<table width="100%" cellpadding="0" cellspacing="0">
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-    <td width="100%">
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-        Package&nbsp;commons ::
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-        Class&nbsp;ConfigException
-      </span>
-    </td>
-    <td>
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-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
-        <tr><td align="right"><span class="options"
-            >[<a href="frames.html" target="_top">frames</a
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-<h1 class="epydoc">Class ConfigException</h1><p class="nomargin-top"><span class="codelink"><a href="commons.Checker-pysrc.html#ConfigException">source&nbsp;code</a></span></p>
-<pre class="base-tree">
-              object --+        
-                       |        
-exceptions.BaseException --+    
-                           |    
-        exceptions.Exception --+
-                               |
-                              <strong class="uidshort">ConfigException</strong>
-</pre>
-
-<hr />
-<p>A exception raised by check method class ConfigChecker</p>
-
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-    </td>
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-         class="privatelink" onclick="toggle_private();"
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-        <td align="right" valign="top"
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-  </td>
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-  <tr>
-    <td colspan="2" class="summary">
-    <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.BaseException</code></b>:
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-      <code>message</code>
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-    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
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-  <td colspan="2" class="table-header">
-    <table border="0" cellpadding="0" cellspacing="0" width="100%">
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-        <td align="left"><span class="table-header">Method Details</span></td>
-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-MethodDetails"
-         class="privatelink" onclick="toggle_private();"
-         >hide private</a>]</span></td>
-      </tr>
-    </table>
-  </td>
-</tr>
-</table>
-<a name="__init__"></a>
-<div>
-<table class="details" border="1" cellpadding="3"
-       cellspacing="0" width="100%" bgcolor="white">
-<tr><td>
-  <table width="100%" cellpadding="0" cellspacing="0" border="0">
-  <tr valign="top"><td>
-  <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
-        <span class="sig-arg">msg</span>,
-        <span class="sig-arg">messages</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span>
-    <br /><em class="fname">(Constructor)</em>
-  </h3>
-  </td><td align="right" valign="top"
-    ><span class="codelink"><a href="commons.Checker-pysrc.html#ConfigException.__init__">source&nbsp;code</a></span>&nbsp;
-    </td>
-  </tr></table>
-  
-  <p>x.__init__(...) initializes x; see x.__class__.__doc__ for 
-  signature</p>
-  <dl class="fields">
-    <dt>Overrides:
-        object.__init__
-        <dd><em class="note">(inherited documentation)</em></dd>
-    </dt>
-  </dl>
-</td></tr></table>
-</div>
-<br />
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Index link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
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-    <td align="left" class="footer">
-    Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009
-    </td>
-    <td align="right" class="footer">
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-        >http://epydoc.sourceforge.net</a>
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-  <!--
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-  // them unless we have a cookie that says to show them.
-  checkCookie();
-  // -->
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--- a/commons/pyRepetUnit/doc/commons.Checker.IChecker-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
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-          "DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>commons.Checker.IChecker</title>
-  <link rel="stylesheet" href="epydoc.css" type="text/css" />
-  <script type="text/javascript" src="epydoc.js"></script>
-</head>
-
-<body bgcolor="white" text="black" link="blue" vlink="#204080"
-      alink="#204080">
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
-  <!-- Tree link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
-  </tr>
-</table>
-<table width="100%" cellpadding="0" cellspacing="0">
-  <tr valign="top">
-    <td width="100%">
-      <span class="breadcrumbs">
-        Package&nbsp;commons ::
-        <a href="commons.Checker-module.html">Module&nbsp;Checker</a> ::
-        Class&nbsp;IChecker
-      </span>
-    </td>
-    <td>
-      <table cellpadding="0" cellspacing="0">
-        <!-- hide/show private -->
-        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
-        <tr><td align="right"><span class="options"
-            >[<a href="frames.html" target="_top">frames</a
-            >]&nbsp;|&nbsp;<a href="commons.Checker.IChecker-class.html"
-            target="_top">no&nbsp;frames</a>]</span></td></tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<!-- ==================== CLASS DESCRIPTION ==================== -->
-<h1 class="epydoc">Class IChecker</h1><p class="nomargin-top"><span class="codelink"><a href="commons.Checker-pysrc.html#IChecker">source&nbsp;code</a></span></p>
-<dl><dt>Known Subclasses:</dt>
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-
-<hr />
-<p>Interface emulation for a checker</p>
-
-<!-- ==================== INSTANCE METHODS ==================== -->
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-<table class="summary" border="1" cellpadding="3"
-       cellspacing="0" width="100%" bgcolor="white">
-<tr bgcolor="#70b0f0" class="table-header">
-  <td colspan="2" class="table-header">
-    <table border="0" cellpadding="0" cellspacing="0" width="100%">
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-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-InstanceMethods"
-         class="privatelink" onclick="toggle_private();"
-         >hide private</a>]</span></td>
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-        <tr>
-          <td><span class="summary-sig"><a href="commons.Checker.IChecker-class.html#check" class="summary-sig-name">check</a>(<span class="summary-sig-arg">self</span>,
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-      perform check, raise a CheckerException if error occured</td>
-          <td align="right" valign="top">
-            <span class="codelink"><a href="commons.Checker-pysrc.html#IChecker.check">source&nbsp;code</a></span>
-            
-          </td>
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-      
-    </td>
-  </tr>
-</table>
-<!-- ==================== METHOD DETAILS ==================== -->
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-       cellspacing="0" width="100%" bgcolor="white">
-<tr bgcolor="#70b0f0" class="table-header">
-  <td colspan="2" class="table-header">
-    <table border="0" cellpadding="0" cellspacing="0" width="100%">
-      <tr valign="top">
-        <td align="left"><span class="table-header">Method Details</span></td>
-        <td align="right" valign="top"
-         ><span class="options">[<a href="#section-MethodDetails"
-         class="privatelink" onclick="toggle_private();"
-         >hide private</a>]</span></td>
-      </tr>
-    </table>
-  </td>
-</tr>
-</table>
-<a name="check"></a>
-<div>
-<table class="details" border="1" cellpadding="3"
-       cellspacing="0" width="100%" bgcolor="white">
-<tr><td>
-  <table width="100%" cellpadding="0" cellspacing="0" border="0">
-  <tr valign="top"><td>
-  <h3 class="epydoc"><span class="sig"><span class="sig-name">check</span>(<span class="sig-arg">self</span>,
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-    <dd><ul class="nomargin-top">
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-  </dl>
-</td></tr></table>
-</div>
-<br />
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
-  <!-- Tree link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Index link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Help link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
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-    <td align="right" class="footer">
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-        >http://epydoc.sourceforge.net</a>
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-
-<script type="text/javascript">
-  <!--
-  // Private objects are initially displayed (because if
-  // javascript is turned off then we want them to be
-  // visible); but by default, we want to hide them.  So hide
-  // them unless we have a cookie that says to show them.
-  checkCookie();
-  // -->
-</script>
-</body>
-</html>

--- a/commons/pyRepetUnit/doc/commons.Checker._Logger-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
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-<head>
-  <title>commons.Checker._Logger</title>
-  <link rel="stylesheet" href="epydoc.css" type="text/css" />
-  <script type="text/javascript" src="epydoc.js"></script>
-</head>
-
-<body bgcolor="white" text="black" link="blue" vlink="#204080"
-      alink="#204080">
-<!-- ==================== NAVIGATION BAR ==================== -->
-<table class="navbar" border="0" width="100%" cellpadding="0"
-       bgcolor="#a0c0ff" cellspacing="0">
-  <tr valign="middle">
-
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-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
-
-  <!-- Index link -->
-      <th>&nbsp;&nbsp;&nbsp;<a
-        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
-
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-        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
-
-      <th class="navbar" width="100%"></th>
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-</table>
-<table width="100%" cellpadding="0" cellspacing="0">
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--- a/commons/pyRepetUnit/doc/commons.IComponentWrapper-module.html	Mon Apr 29 03:23:29 2013 -0400
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--- a/commons/pyRepetUnit/doc/commons.IComponentWrapper-pysrc.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
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-<h1 class="epydoc">Source Code for <a href="commons.IComponentWrapper-module.html">Module commons.IComponentWrapper</a></h1>
-<pre class="py-src">
-<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"> </tt>
-<a name="IComponentWrapper"></a><div id="IComponentWrapper-def"><a name="L2"></a><tt class="py-lineno"> 2</tt> <a class="py-toggle" href="#" id="IComponentWrapper-toggle" onclick="return toggle('IComponentWrapper');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.IComponentWrapper.IComponentWrapper-class.html">IComponentWrapper</a><tt class="py-op">:</tt> </tt>
-</div><div id="IComponentWrapper-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="IComponentWrapper-expanded"><a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-docstring">     A interface wrapper for all pipelines component</tt> </tt>
-<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
-<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line">     </tt>
-<a name="IComponentWrapper.run"></a><div id="IComponentWrapper.run-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="IComponentWrapper.run-toggle" onclick="return toggle('IComponentWrapper.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.IComponentWrapper.IComponentWrapper-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IComponentWrapper.run-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="IComponentWrapper.run-expanded"><a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-docstring">        run the component</tt> </tt>
-<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
-</div><a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line">     </tt>
-<a name="IComponentWrapper.loadConfig"></a><div id="IComponentWrapper.loadConfig-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="IComponentWrapper.loadConfig-toggle" onclick="return toggle('IComponentWrapper.loadConfig');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.IComponentWrapper.IComponentWrapper-class.html#loadConfig">loadConfig</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">configParserInstance</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IComponentWrapper.loadConfig-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="IComponentWrapper.loadConfig-expanded"><a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-docstring">        load component config</tt> </tt>
-<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
-<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-docstring">        @param configParserInstance: config parser where config file is loaded</tt> </tt>
-<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-docstring">        @type  configParserInstance: class ConfigParser</tt> </tt>
-<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
-</div><a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"> </tt>
-<a name="IComponentWrapper.clean"></a><div id="IComponentWrapper.clean-def"><a name="L22"></a><tt class="py-lineno">22</tt> <a class="py-toggle" href="#" id="IComponentWrapper.clean-toggle" onclick="return toggle('IComponentWrapper.clean');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.IComponentWrapper.IComponentWrapper-class.html#clean">clean</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IComponentWrapper.clean-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="IComponentWrapper.clean-expanded"><a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-docstring">        clean files generated by run method</tt> </tt>
-<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
-</div><a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line">     </tt>
-<a name="IComponentWrapper.getComponent"></a><div id="IComponentWrapper.getComponent-def"><a name="L28"></a><tt class="py-lineno">28</tt> <a class="py-toggle" href="#" id="IComponentWrapper.getComponent-toggle" onclick="return toggle('IComponentWrapper.getComponent');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.IComponentWrapper.IComponentWrapper-class.html#getComponent">getComponent</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IComponentWrapper.getComponent-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="IComponentWrapper.getComponent-expanded"><a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line"><tt class="py-docstring">        return component wrapped</tt> </tt>
-<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-</div></div><a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"> </tt><script type="text/javascript">
-<!--
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--- a/commons/pyRepetUnit/doc/commons.IComponentWrapper.IComponentWrapper-class.html	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,231 +0,0 @@
-<?xml version="1.0" encoding="ascii"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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--- a/commons/pyRepetUnit/doc/commons.IDataProcessor-module.html	Mon Apr 29 03:23:29 2013 -0400
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--- a/commons/pyRepetUnit/doc/commons.IDataProcessor-pysrc.html	Mon Apr 29 03:23:29 2013 -0400
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-<pre class="py-src">
-<a name="IDataProcessor"></a><div id="IDataProcessor-def"><a name="L1"></a><tt class="py-lineno"> 1</tt> <a class="py-toggle" href="#" id="IDataProcessor-toggle" onclick="return toggle('IDataProcessor');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="commons.IDataProcessor.IDataProcessor-class.html">IDataProcessor</a><tt class="py-op">:</tt> </tt>
-</div><div id="IDataProcessor-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="IDataProcessor-expanded"><a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
-<a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"><tt class="py-docstring">    A interface for all pipelines data processor</tt> </tt>
-<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt>     </tt>
-<a name="IDataProcessor.run"></a><div id="IDataProcessor.run-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="IDataProcessor.run-toggle" onclick="return toggle('IDataProcessor.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="commons.IDataProcessor.IDataProcessor-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
-</div><div id="IDataProcessor.run-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="IDataProcessor.run-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
-<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-docstring">        run: process the data</tt> </tt>
-<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
-<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
-</div></div><a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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--- a/commons/pyRepetUnit/doc/commons.IDataProcessor.IDataProcessor-class.html	Mon Apr 29 03:23:29 2013 -0400
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-<h1 class="toc">Table&nbsp;of&nbsp;Contents</h1>
-<hr />
-  <a target="moduleFrame" href="toc-everything.html">Everything</a>
-  <br />
-  <h2 class="toc">Modules</h2>
-    <a target="moduleFrame" href="toc-commons.Checker-module.html"
-     onclick="setFrame('toc-commons.Checker-module.html','commons.Checker-module.html');"     >commons.Checker</a><br />    <a target="moduleFrame" href="toc-commons.IComponentWrapper-module.html"
-     onclick="setFrame('toc-commons.IComponentWrapper-module.html','commons.IComponentWrapper-module.html');"     >commons.IComponentWrapper</a><br />    <a target="moduleFrame" href="toc-commons.IDataProcessor-module.html"
-     onclick="setFrame('toc-commons.IDataProcessor-module.html','commons.IDataProcessor-module.html');"     >commons.IDataProcessor</a><br /><hr />
-  <span class="options">[<a href="javascript:void(0);" class="privatelink"
-    onclick="toggle_private();">hide&nbsp;private</a>]</span>
-
-<script type="text/javascript">
-  <!--
-  // Private objects are initially displayed (because if
-  // javascript is turned off then we want them to be
-  // visible); but by default, we want to hide them.  So hide
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--- a/commons/pyRepetUnit/fastaTranslation/allFrames/TranslateInAllFramesAndReplaceStopByX.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.seq.BioseqUtils import BioseqUtils
-
-class TranslateInAllFramesAndReplaceStopByX(object):
-
-    def __init__(self):
-        self._inputFile = "" 
-        self._outputFile =  ""
-    
-    def setInputFile(self, input):
-        self._inputFile = input
-
-    def setOutputFile(self, output):
-        self._outputFile = output    
-        
-    def run(self):
-        """
-        read a fasta file with nucleotide sequences and translate all sequences in all frames, write the result in a file
-        """
-        if not FileUtils.isRessourceExists(self._inputFile):
-            raise Exception("Warning your input file %s does not exist!\n" % self._inputFile)
-        bioseqList = BioseqUtils.extractBioseqListFromFastaFile(self._inputFile)
-        bioseqListInAllFrames = BioseqUtils.translateBioseqListInAllFrames(bioseqList)
-        bioseqListTranslatedAndStopsReplace = BioseqUtils.replaceStopCodonsByXInBioseqList(bioseqListInAllFrames)
-        BioseqUtils.writeBioseqListIntoFastaFile(bioseqListTranslatedAndStopsReplace, self._outputFile)   
-                
\ No newline at end of file

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_TranslateAfastaFileInAllFrameAndReplaceStopsByX(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFile = "./datas/ConsensusTestFile_nt.fsa"
-        self._outputFile = "./datas/PreprocessOuputFile"
-        self._prg = "translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
-        
-        
-    def testAcceptanceTranslateAfastaFileInAllFrameAndReplaceStopsByX_script(self):
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile )
-        cmd += " -o %s" % ( self._outputFile )
-        os.system( cmd )        
-        self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "./datas/ConsensusTestFile_aaWithoutStop.fsa"))
-        os.system( "rm " + self._outputFile )
-               
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateInAllFramesAndReplaceStopByX.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
-from commons.core.seq.Bioseq import Bioseq
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase):
-    
-    def setUp(self):
-        self.bioseq = Bioseq()
-        self.preProcess = TranslateInAllFramesAndReplaceStopByX()
-        self._inputFile = "./datas/test_input_nt.fa" 
-        self._outputFile =  "./datas/PreProcessResult.fa" 
-        
-        
-    def testAcceptanceTranslateAfastaFileInAllFrame(self):
-        self.preProcess.setInputFile(self._inputFile)
-        self.preProcess.setOutputFile(self._outputFile)
-        self.preProcess.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._outputFile, "./datas/test_input_aa.fa"))
-        os.system("rm " + self._outputFile)
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFile = "dummyInputFile"
-        self._outputFile = "dummyOuputFile"
-        self._prg = "translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
-        
-        
-    def testTranslateAfastaFileInAllFrameAndReplaceStopsByX_script(self):
-        f = open(self._inputFile, "w")
-        f.write(">header1 description\n")
-        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n")
-        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
-        f.write(">header2\n")
-        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n")
-        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA")
-        f.close()
-        # expected fasta translated file
-        f = open("expectedTranslated.fa", "w")
-        f.write(">header1_1 description\n")
-        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
-        f.write(">header1_2 description\n")
-        f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n")
-        f.write(">header1_3 description\n")
-        f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n")
-        f.write(">header1_4 description\n")
-        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
-        f.write(">header1_5 description\n")
-        f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n")
-        f.write(">header1_6 description\n")
-        f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n")
-        f.write(">header2_1\n")
-        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
-        f.write(">header2_2\n")
-        f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n")
-        f.write(">header2_3\n")
-        f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n")
-        f.write(">header2_4\n")
-        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
-        f.write(">header2_5\n")
-        f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n")
-        f.write(">header2_6\n")
-        f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n")
-        f.close()
-         
-        #normal launch
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile )
-        cmd += " -o %s" % ( self._outputFile )
-        os.system( cmd )        
-        self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa"))
-        os.system( "rm " + self._outputFile )
-        
-        #verbose option
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile )
-        cmd += " -o %s" % ( self._outputFile )
-        cmd += " -v 1"
-        os.system( cmd )        
-        self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa"))
-        os.system( "rm " + self._outputFile )
-        
-        #clean option
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile )
-        cmd += " -o %s" % ( self._outputFile )
-        cmd += " -c"
-        os.system( cmd )        
-        self.assertTrue( FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa" ) )
-        self.assertFalse( FileUtils.isRessourceExists( self._inputFile ) )
-        os.system( "rm " + self._outputFile)
-        os.system("rm expectedTranslated.fa")
-        
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
-from commons.core.seq.Bioseq import Bioseq
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase):
-    
-    def setUp(self):
-        self.bioseq = Bioseq()
-        self.preProcess = TranslateInAllFramesAndReplaceStopByX()
-        self._inputFile = "./datas/dummy.fa" 
-        self._outputFile =  "./datas/dummyoutput.fa" 
-        
-        
-    def testRun(self):
-        self.preProcess.setInputFile(self._inputFile)
-        self.preProcess.setOutputFile(self._outputFile)
-        # real fasta file
-        f = open(self._inputFile, "w")
-        f.write(">header1 description\n")
-        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n")
-        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
-        f.write(">header2\n")
-        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n")
-        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA")
-        f.close()
-        # expected fasta translated file
-        f = open("./datas/expectedTranslated.fa", "w")
-        f.write(">header1_1 description\n")
-        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
-        f.write(">header1_2 description\n")
-        f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n")
-        f.write(">header1_3 description\n")
-        f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n")
-        f.write(">header1_4 description\n")
-        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
-        f.write(">header1_5 description\n")
-        f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n")
-        f.write(">header1_6 description\n")
-        f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n")
-        f.write(">header2_1\n")
-        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
-        f.write(">header2_2\n")
-        f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n")
-        f.write(">header2_3\n")
-        f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n")
-        f.write(">header2_4\n")
-        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
-        f.write(">header2_5\n")
-        f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n")
-        f.write(">header2_6\n")
-        f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n")
-        f.close()
-        self.preProcess.run()
-        self.assertTrue(FileUtils.are2FilesIdentical("./datas/expectedTranslated.fa", self._outputFile))
-        os.system("rm " + self._inputFile)
-        os.system("rm " + self._outputFile)
-        os.system("rm ./datas/expectedTranslated.fa")
-        # empty fasta file
-        #self.preProcess.translateAfastaFileInAllFrame()
-        #self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
-
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_aaWithoutStop.fsa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
->blumeria_Grouper_590_20:NoCat_1
-FRSYXNVXPTTXFVDLLVEGSLCNNEGXKDVNSTTLLNTDTRLLLIPIDSPCGISYXQQX
-TTLTQGIRNLRSPNTSLSGLLIIEPSRIDNVYPNIEIIESSTPKPLINNCHXSSPDLSLY
-SIISTLKNIC
->blumeria_Grouper_590_20:NoCat_2
-FDXIEMYNPLLSSWTCWXREAYAIMKDKRMSIRLLFXTQIPDSFXSQXIARAGSPINSSK
-QRXHRVYAISVRQTPVCRDYXLSSLVGSTMCIPTXKXXKAQHPNPSSITAINHHLTYLCT
-PXFQHXRIFV
->blumeria_Grouper_590_20:NoCat_3
-SIXLKCITHYLVRGLVGRGKLMQXXRIKGCQFDYSSKHRYQTPFNPNRXPVRDLLLTAVN
-NANTGYTQSPFAKHQSVGTTNYRAXXDRQCVSQHRNNRKLNTQTPHQXLPLIITXLISVL
-HNFNTXEYL
->blumeria_Grouper_590_20:NoCat_4
-YKYSXVLKLWSTEISQVMINGSYXXGVWVLSFLLFLCWDTHCRSYXARXLVVPTDWCLAN
-GDCVYPVLALFTAVNRRSRTGYLLGLKGVWYLCLEEXSNXHPFILHYCISFPLPTSPRTK
-XWVIHFNXIE
->blumeria_Grouper_590_20:NoCat_5
-TNILXCXNYGVQRXVRXXLMAVIDEGFGCXAFYYFYVGIHIVDPTRLDNXXSRQTGVWRT
-EIAYTLCXRCLLLLIGDPARAIYWDXKESGICVXKSSRIDILLSFIIAXASLYQQVHELS
-SGLYISIXSK
->blumeria_Grouper_590_20:NoCat_6
-QIFXSVEIMEYRDKSGDDXWQLLMRGLGVELSIISMLGYTLSILLGSIISSPDRLVFGER
-RLRIPCVSVVYCCXXEIPHGLSIGIKRSLVSVFRRVVELTSFYPSLLHKLPSTNKSTNXV
-VGYTFQXDR
->blumeria_Grouper_4152_12:NoCat_1
-GPAATNCAIAARKXTLMESTKFLSSPVESGXRAASTLLIAVEHIVNCAAFCLALRSSASI
-AASNSGGCVFFLPAASSAGGCGASGGFSAPAALVDGVSALFAGLTSAGRGSAGTVMRFSG
-ATTVFLGDPVGSKTCSASSGLEDAQTESARVFSFSTSASTISTSGTL
->blumeria_Grouper_4152_12:NoCat_2
-DRPPRIARLLLASRLXWSLQNFCLHRWRAVEELPRHCXXPSSILXIARLFVLPCAPPLRS
-LQAILEGVYFFCLLLLVLEAAGPVEGFRLLLPXWMVFQPFSRASLLQVAVVLEPXCASRV
-RRRFFWGIRWDPRLALRLLGWRMPKLNRRGFLASRLLRPPYLPRGH
->blumeria_Grouper_4152_12:NoCat_3
-TGRHELRDCCSQVDFDGVYKIFVFTGGERLKSCLDTANSRRAYCELRGFLSCPALLRFDR
-CKQFWRVCIFSACCFXCWRLRGQWRVFGSCCLSGWCFSPFRGPHFCRSRXCWNRDALLGC
-DDGFSGGSGGIQDLLCVFWAGGCPNXIGEGFXLLDFCVHHIYLGDI
->blumeria_Grouper_4152_12:NoCat_4
-QCPRGRYGGRRSREAKNPRRFSLGILQPRRRRASLGSHRIPQKNRRRTREAHHGSSTTAT
-CRSEAREKGXNTIHXGSRSRKPSTGPAASSTRSSRQKKYTPSRIACSDRSGGAQGKTKSR
-AIHNMLDGYXQCRGSSSTALHRXRQKFCRLHQSLLASSNRAIRGGRS
->blumeria_Grouper_4152_12:NoCat_5
-NVPEVDMVDAEVEKLKTLADSVWASSSPEDAEQVLDPTGSPRKTVVAPEKRITVPALPRP
-AEVRPAKRAETPSTKAAGAENPPLAPQPPALEAAGRKNTHPPELLAAIEAEERRARQKAA
-QFTICSTAISSVEAALQPLSTGEDKNFVDSIKVYLRAAIAQFVAAG
->blumeria_Grouper_4152_12:NoCat_6
-MSPRXIWWTQKSRSXKPSPIQFGHPPAQKTQSKSWIPPDPPEKPSSHPRSASRFQHYRDL
-QKXGPRKGLKHHPLRQQEPKTLHWPRSLQHXKQQAEKIHTLQNCLQRSKRRSAGQDKKPR
-NSQYARRLLAVSRQLFNRSPPVKTKILXTPSKSTCEQQSRNSWRPV

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_nt.fsa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
->blumeria_Grouper_590_20:NoCat
-TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA
-AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT
-ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA
-ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA
-CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC
-TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC
-TCCATAATTTCAACACTNAAGAATATTTGTA
->blumeria_Grouper_4152_12:NoCat
-GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA
-AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC
-GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC
-GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC
-TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT
-TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT
-GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG
-CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC
-ATATCTACCTCGGGGACATTG

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_aa.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,258 +0,0 @@
->blumeria_Grouper_28830_3_1
-CGFXLISLXSQXFHVGVSWLRLINNIMRVELETNKTXIXFYNTGSPTYLNIPPHHVSQST
-AHNLHGRVSINWDPQTIPLLKTSCPQLIXITSXLEILLWYHSNXILAEFLSVFLSCSSIR
-RLPYHRLRTGCPSRTYAGNRFVPLYLLPNLYPPGDIKEXVLLLXQAATAHGPSXXGSILC
-LRWRTRSTQSPGAXVRISAFSSWRXARILSLVAFILLTXERAIGAGCFLPSSSAQRRSSD
-SVASRVYTGXEFSSSGGXVPKSKKXGLYPLGETLRLKFITASERAPASVILGESRRTLTS
-MAFRTPFACSTLPFPLGLAGVVWTTCSCWLAXNRCASMPPKQPALSLIICFGFPKFWIIY
-VSRGTVLAKSALGTKRDSSQPVAYSIALSKTWGPTXVXSIPHRVRGGAGTIGVKLPSNGS
-GGFMSXQDLHFRTASXAARISSGCQNLRPNSRIVLPIDAWPWPSXTFTAVDTRSSYSKIS
-SRVAAPDGPGASPTCCDGFFLMRCNLELYIAKLSRTQVAAIFRGSASPKVRNSVMHCRSM
-RLSSCGCFISSISSSLSAPLWILEFSLSSVATFPSPSSLERNRTSQGRERKSARTFAFPR
-RXIILILKCSIASKKRTILTGCSALVXIVRRDSWSVITVTSPPSTQXRQCCSDSKIPSNS
-LSCAEXRCWVSFSFLEKXAMGCSTERSELLEHRMYGWSMTAPTNFWEASVSNMTGSLQSN
-FFTTGDVVSASLILFHDXIDWSVRMTGQFLGPEDWSVSGPASWEKFLMRQRRXPAAFTNP
-LISEVVVGIGLSLIAETFSGSAAMPCLEIWKPRKIPSETNSLHFEALRRRPXEANLEKIS
-INRECNSAIESAQTATSSRSPATNGRNGSRTSSIKHWKVAGALHRPKGITSHSXTPKGVT
-NAVFSEESLCIRICQNPFSRSRNAXKLCPAARXISSXAFGRGWACFFVILLSSLXSTQIR
-QTVWLVWVSVFFWCXXQRCSPWSLTFAYELSRSCVAQESPRMACCCAGAISPRRGVLNWV
-DNYPVSMRVFLSWESFIPFGGRDLSKSXRGIXLXYCREKLXCGMKGGLGAIXPLEYLKXX
-RLFGLGEYXLXDXELVGQLSXEVAVCHLINIVAPVHGIKFVQVSHLLGMCHLGQLLETLX
-IPESRMIQGDSSKETVQLKLHPXKLLGQGHQCLTFXKXXMYYKKSNIXRKTVKHNMLKSR
-SQKKLKIGHRENELFVQKTFCVACHILPVEVVLLGVAQICPFLRPQSRYSGCPIHKFLHF
-AFDIEWLQFRHRAAHLLFGLQGLFALDPNLLAQQGKXKXQALMNDRVVLQVLHIFYFSLI
-GKFSXIYRXNATRCIXRLVHIPFVLLIPPALFSSTGSLSPSGLSFRNXSIRNACRELGMI
-YLFLQCLVTQRRLAHTTLDQLWMRQMLEAFRLLTLRSELVHWTRNVXIHHPQVSTLXYRV
-XLEPLDPQAPRWXVWGDYWKXWSRYVEVRVEYAASVYLXSEALPXHPKVGXRKLSGVVAQ
-IVIESRRFLQLFVQMLSKATRVHHCRTVFXGYSLQLLPNRGVDXXLFFAPRXNLHPFPLQ
-FXXPKQNMEAYVESSMIACGIIYSLCSHQQSAISIVVGIPRVFFYLPLLKGRADFQLRNA
-KRNLGSTALFFALVQXHSMVRXLTGGINXXSHLCFAHHCLGWALFHRIAPRXRVFSXAET
-RLAWLRVARRCLLKSQIAPPGMVFYFQMALLPKVERGLNFSKKFLFPRLHFYLLVWKLSR
-SLQTFVXLEEKFVIGSLQTFDRFSWRDLLSLPLQLHXLRKNFRWLWFARQCDPSSSFPTE
-HYSGRPXXLNRWXNAXKIWRRLKLGXPRIVRFSQQKYIILWLLVDQFMITMISRRCLVAP
-TNQQYNASRAXDXXNVNFILXYRTANLFKYSPAPREPINSTQFARSGFHQLGST
->blumeria_Grouper_28830_3_2
-VASSXSVYDHNDFTXVSRGSDXSTIXCEXSLRLIKREFXSIIQDRQLIXIFPRTTXANQQ
-RTICTVGFPSIGIHKLSPFSKLAVHSLFKLQVNXKFYYGITQTKSLLNFXVSFYPAPAYG
-GYHTIDYELGVLHVHMPGIGLCRCTCCLICIHPVILRSRYYYYDKLLRPMARHSRAPSCV
-FAGVLAVPSLRGRKYVXVPFLPGGKPVFYPXLLSYYXRRSVLLVRGVSFRVLRPRGAPLI
-LWLHGYILDKNFPPPGAECRRVRSKGYTRWVRLFDXNSLPRVRERQLVXFXENPGELXPV
-WLSERHLPVRLCHFLLAXLVWYGQPAVVGXLEIVVLLCLRSSQHCHXXSALAFQSSGXYT
-XAEAQCXRSLHWELSGIPASLLRTQLHXARLGVLLEYDLYPTVSEEVLVLXELSFPVTGL
-EVSXADRTCIFGQLREPRGSVRGAKTYALIPAXYCRLTHGLGPHEHLRPSILDPHIPRFL
-VGLRRQMDQVHRLLVATGSFXXDAIWNCTSQNYLGPKWQLYLGEVPLLRLEIRXCTAGRC
-GXVRVGALFPPSQVLFLHHFGFXSFRCRQXLHSLPLLPXREIEHHRDGRENQREHLLFRD
-GRXSXYXNALXHLKNGPFXRAARLWSEXFVEIHGQLSPLRRRLLPSDANVVVTVKSQVIP
-SLVLNNAAGYRLVFLRSKLWDAALNDRNCWSIACTVGVXLHPRTFGKRQFPIXREVSNQI
-FLQLVMLXALVXYFSMIESIGPSEXQGNFXVQRIGPXVALLVGRNFXXDNVGNQLHLQIL
-LFPRXLLAXACLXSLKLFRGLLQCHVXKYGNQGRFPLKQIACTLKHXGGDHRKRIXKKXV
-STVSAILPLSLPRQLHRPGALRQMDGMALELLPXNTGKXLVRCIGRKAXLAIHRHRKESQ
-MLFSLKSLCAYVSAKIRFPGRGMHRSYVLLRAEFHLEHLVGDGRVSSXSCXALYSQHKYA
-KRFGXSGLASFFGVNNRGAAHGPLHLRMNXAGHVLHKKVPGWLVVAPGLYRLGGEFXIGL
-TITPFLCGCFCLGRVLSHLAGEIYRKVEGEFNFDIVGKNCNAEXRVGWVPFDHWNIXSSE
-DFSVWESINYRIKNWLVNXVEKLQFAIXXTSXPQFMEXSLSKCHICWECAIWDNSXRHCE
-FLSPEXFKVIRAKKLCSXNCILRNCWARATNAXHFRNNRCIIRSQIFRERLXNITCXRAV
-VKKNXKLDIGKMSYSCKKHSVWLAISFPXRLSFWGWLKFALSYGHKVGIRAVLFINFFIS
-HSIXNGFNFVIELLIFYLAFRAYLLLIQIFWLNKESRSDRLXXTIVWCYRFYIFFIFHXL
-VSFPEFIAETRRGVFSVWCIFPLFFXFHRRCFHQPAVFRPVACLSAIEAFVTLVVNWVXF
-ICFCNVLXRKDVLPIRPWISYGCVKCWKLFAFXRXDRNWCIGLGMFEYIILKCPPCNTAC
-DLNHSIRKLRAGEFGEIIGNDGPGTWKXESNMLPQYISSLRPYHDIRRXAKESFPESSRK
-LXLSLVVSCSYSCKCCQRRPEYIIVEQYFKDTVYSSCPIEVLTDDCSSRRDEIFIHFHCN
-SDSPSRIWKHMLNHQXLHVVXYIHYVLISKVQFPLWWEYRACFSICLFXRAVRIFSFGTR
-KEIWEVPLYFSLLFSNIQWFVNXLAVXINSPIFVLLIIAXVGRCFIELRRGKGSFLRLKH
-DWPGCGSRGAACXKVKXLLPVWFFIFRWPCFRKLKGDXIFRRSFCFHVFISTYXFGNXVV
-HCRHLFDXKRNLXLGLFKPLIDSLGEIFCHCLCSFISFGKIFVGFGLPGNVILHQAFQLS
-IIQADHDDXIGGEMRKKFGDVLNWDDLELXGSLNKNIXFCGFXLISLXSQXFHVGVSWLR
-QINNIMRVELETNKTXISFYNTGPPTYLNIPPHHVSQSTAHNLHGRVSINWDP
->blumeria_Grouper_28830_3_3
-WLLVDQFMITMISRRCLVAPTNQQYNASRAXDXXNVNXILXYRIANLFKYSPAPREPINS
-AQFARSGFHQLGSTNYPPSQNXLSTAYLNYKLIRNFIMVSLKLNPCXIFECLSILLQHTA
-ATIPXTTNWVSFTYICREXVCAVVLVAXFVSTRXYXGVGIIIMTSCYGPWPVIVGLHLVS
-SLAYSQYPVSGGVSTYKCLFFLEVSPYFIPSCFHTTNVGACYWCGVFPSEFFGPEALLXF
-CGFTGIYWIRIFLLRGLSAEEXEVRAIPAGXDSSIEIHYREXESASXCNFRRIQENSDQY
-GFQNAICLFDFAISSWPSWCGMDNLQLLASLKSLCFYASEAASIVTDNLLWLSKVLDNIR
-EQRHSVSEVCIGNXAGFQPACCVLNCIEQDLGSYLSMIYTPPCQRRCWYYRSXASQXRVW
-RFHELTGLAFSDSFVSREDQFGVPKPTPXFPHSIADXRMALALMNIYGRRYXILIFQDFX
-XGCGARWTRCIAYLLRRVLFDEMQFGIVHRKIISDPSGSYIXGKCLSXGXKFGDALQVDA
-VEFVWVLYFLHLKFSFCTTLDSRVFVVVSSYIPFPFFPREKXNITGTGEKISENICFSAT
-VDNPDIKMLYSIXKTDHSDGLLGFGLNSSXRFMVSYHRYVAAFYPVTPMLXXQXNPKXFP
-LLCXITLLGIVXFSXEVSYGMQHXTIGIVGASHVRLEYDCTHELLGSVSFQYDGKSPIKF
-FYNWXCCKRXFDTFPXLNRLVRQNDRAIFRSRGLVREWPCXLGEIFNETTXVTSCIYKSS
-YFRGSCWHRPVSDRXNFFGVCCNAMFRNMETKEDSLXNKXPALXSIEEETIGSESRKNKY
-QPXVQFCHXVCPDSYIVQEPCDKWTEWLXNFFHKTLESSWCVAXAERHNXPFIDTERSHK
-CCFLXRVFVHTYLPKSVFQVEECIEVMSCCALNFILSIWXGMGVFLRNLVKLSIVNTNTP
-NGLVSLGXRLFLVLITEVQPMVPYICVXIEPVMCCTRKSPDGLLLRRGYIASEGSFKLGX
-QLPRFYAGVSVLGEFYPIWRERFIEKLKGNLTLILXGKTVMRNEGWAGCHLTIGIFEVVK
-TFRFGRVLIIGLRIGWSIKLRSCSLPFDKHRSPSSWNKVCPSVTSAGNVPSGTTPRDTVN
-SXVQNDSRXFEQRNCAVKIASLEIVGPGPPMPDILEIIDVLXEVKYLEKDCETXHAEEPX
-SKKTENWTXGKXVIRAKNILCGLPYPSRRGCPFGGGSNLPFPTATKXVFGLSYSXISSFR
-IRYRMASISSSSCSSSIWPSGLICSXSKSSGSTRKVEVTGFDERSCGVTGFTYFLFFIDW
-XVFLNLSLKRDEVYLAFGAYSLCSFDSTGAVFINRQSFAQWPVFPQLKHSXRLSXIGYDL
-SVSAMSCDAKTSCPYDLGSAMDASNAGSFSPFDAEIGIGALDSECLNTSSSSVHLVIPRV
-TXTTRSASSALVSLGRLLEMMVQVRGSESRICCLSISLVXGPTMTSEGRLKKAFRSRRAN
-CNXVSSFLAVIRANVVKGDPSTSLSNSILRIQSTAPAQSRCXLMIVLRAEMKSSSISIAI
-LIAQAEYGSICXIINDCMWYNIFIMFSSAKCNFHCGGNTARVFLFASFKGPCGFSASERE
-KKSGKYRFIFRSCSVTFNGSLTDWRYKLIVPSLFCSSLLRLGVVSXNCAEVKGLFLGXNT
-IGLVAGREALPAEKSNSSSRYGFLFSDGPASESXKGTEFFEEVFVSTSSFLLTSLEIKSF
-IADICLTRREICDWVSSNLXSILLERSFVTAFAASLASEKFSLALVCPAMXSFIKLSNXA
-LFRPTMMIEXVVKCVKNLETSXIGMTXNCEVLSTKIYNFVASSXSVYDHNDFTXVSRGSD
-KSTIXCEXSLRLIKREFHSIIQDRQLIXIFPRTTXANQQHTICTVGFPSIGIH
->blumeria_Grouper_28830_3_4
-CGSQLMETRPCKLCAVDWLTWCGGIFKXVGGPVLXNEIHVLLVSSSTRIILLICRSHETP
-TXNHCDHKLINXKPQNYIFLLREPHNSRSSQFKTSPNFLRISPPIQSSWSAXIMLSWKAX
-XRITLPGKPKPTKIFPKLMKLQRQXQKISPRESIKGLKRPNHKFLFXSNKCLQXTTXFPN
-XXVEMKTWKQKLLRKIQSPFNFRKQGHLKIKNHTGRSYLTFQQAAPRDPQPGQSCFSLRK
-DPLPRRNSMKQRPTXAMMSKTKMGLLIYTASQLTNHXMLLNKSEKXSGTSQISFRVPKLK
-IRTALXKRQIEKHARYSHHNGNCTLLMRTXXIYYTTCNHXXFNICFHILLGLSELQWKWM
-KISSRREEQSSVNTSIGQELXTVSLKYCSTMMYSGRLXQHLHEXLQETTRLNYNLRDDSG
-KLSLAYLRMSWXGLRLEIYXGSIFDSHFHVPGPSFPIISPNSPARSLRIEWFKSHAVLQG
-GHLRMMYSNIPSPMHQFRSQRQKAKSFQHLTHPXLIQGRMGKTSLRHKTLQKQINHTQFT
-TSVTNASIAERQATGRKTAGXXKQRRWNQKNKGNMHQTLNTPRRVSAINSGKLTNQXKIK
-NMXNLXHHTIVHQSLSLLLSLLSQKIWIKSKXALKAKXKMSSSMTKLKPFYIECEMKKFM
-NRTARIPTLWPXERANLSHPQKDNLYGKDMASHTECFLHEXLIFPMSNFQFFLTTALQHV
-MFHSLSLNIXLLIIHLLFLKCQALVALAQQFLRMQFXLHSFFARITLNHSGLRNSQCLXE
-LSQMAHSQQMXHLDKLYSMNWGYDVYQMANCNFSTXLTNQFLILXLILSQTEKSSLLQIF
-QWSNGTQPTLHSALQFFPTISKLNSPSTFRXISPAKWDKTLPRQKHPHRNGVIVNPIXNS
-PPRRYSPGATTSHPGTFLCNTXPAQFIRKCKGPWAAPLLLTPKKDANPDXPNRLAYLCXL
-XRAXQDYEETRPSPTKCSRXNSARSRTXLLCIPRPGKRILADTYAQRLFRENSICDSFRC
-LXMASYAFRPMQRTSYFPVFYGRSSRAIPSICRRAPGRCSCLGRLNGRIALTVDTYFFXI
-RFLWSPPQCFKVQAICFRGNLPWFPYFXTWHCSRPRKSFSDQRQAYANNYLGNKRICKCS
-WLPTLSHXKFLPTSRATHGPILWTXKLPCHSDGPIDSIMEKYQTSAYNITSCKKIXLETS
-RHIGNXRFPKVRGCSHTPTVHAMLQQFRSFSAASHSLLLKKTKRYPAALFSTREGITWDF
-TVTTTLASLGRRRRRNGDNXPXISTNYSDQSRAARQNGPFFRCYRAFXYQDYLPSRKSKC
-SRXFSLPSLXCSISLXGRRGRECSYXRQRKLXNPKWCRKRTXDGGNKAPTRTQPHRPAVH
-HRISNLRRGTSPKYSCHLGPRXFCDVQFQIASHQKEPVATSRRCTWSIWRRNPTRNLGIX
-GSSIDGRKCSXGPRPCVNRQYYAGIRAXVLAPRTDPRGSRSCPKMQVLSAHETSRPVTGK
-LNSYSTSTSSDTVGYRSYSSRTPSLAQCNXVRNRLAGIPLSSQCRLRXHCASAHVYYPEL
-WKAKADYQXQCWLLRRHRSTTISSXPTTAGCPYHTSXAKRKWQSRTGKWRSESHTGQSSP
-GFSXNYTSWRSLTRGNEFQSKSLTQRVXPLLLTLRHSAPGGGKFLSSIYPXSHRIRGAPL
-GRRTRKETPRTNSTLLRXXYESNXGXNTGLPPGRKGTYTYLRPRRLGTASTPAKTQDGAL
-LXRAMGRSSLSXXXYLLLNITGWIQIRQQVQRHKPIPGICTXRTPSSXSMVWXPPYAGAG
-XKDTQKFSKDLVXVIPXXNFXLTCNLNKLWTASFEKGDSLWIPIDGNPTVQIVRCXLAHV
-VRGNIXISWRSCIIEXNSRFISLKLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT
->blumeria_Grouper_28830_3_5
-VDPNXWKPDRANCVLLIGSRGAGEYLNKLAVLYYRMKFTFYXSQALLALYCXFVGATRHL
-REIIVIINXSTRSHKIIYFCXENLTILGHPNLRRLQIFYAFHHLFNHHGRPEXCSVGKLD
-EGSHCRANQSQRKFFRSXXSCKGSDKRSLQENRSKVXRDPITNFSSSQTNVCNERLNFQT
-SKXKXRRGNKNFFEKFSPLSTFGSRAIXKXKTIPGGAIXLFSRQRLATRNQANRVSAXEK
-TLYLGAILXNNAQPKQXXAKQRWDYXFIPPVSXRTIECYXTRAKNKAVLPRFLFAFRSXK
-SARPFKRGKXKNTRGIPTTMEIALCXXEHNEYIIPHAIIDDSTYASIFCLGYQNCNGNGX
-RFHLGAKNNHQSTPRLGRSCRLYPXNTVRQXCTRVAFDNICTNNCKKRRDSITICATTPE
-SFLXPTFGCHGRASDXRYTEAAYSTLTSTYLDHHFQXSPQTHQRGACGSSGSSHTRYYKV
-DTXGXCIQTFRVQCTNSDLSVKRRKASSIXRIHSXSKVVWARRLCVTRHCRNRXIIPNSR
-QALRMLQLRKDRPLGERLPVDENSAGGIKRTKGICTKRXIHLVAFQRXIQENLPINEKXK
-ICKTCNTTRSFIKACHFYFPCXARRFGSRANKPXRPNRRXAARXRNXSHSISNAKXRNLX
-IGQPEYLLCGRRKGQIXATPKRTTSTGRIWQATQNVFCTNNSFSLCPIFSFFXLRLFSML
-CFTVFLXIFDFLXYIYYFXNVRHWWPWPNNFXGCNFNCTVSLLESPXIILDSGIHSVSRS
-CPRWHIPSRCDTWTNFIPXTGATMFIKWQTATSQLNXPTNSXSYNXYSPKPKSLHYFKYS
-NGQMAPSPPFIPHYSFSLQYQSXIPLQLFDKSLPPNGIKLSQDRNTRIETGXLSTQFKTP
-LRGDIAPAQQQAIRGLSCATHDRLNSYANVRDHGLHLCYXHQKKTLTQTNQTVWRICVDY
-RELNKITKKHAHPLPNAQDEIQRAAGHNFYAFLDLENGFWQIRMHKDSSEKTAFVTPFGV
-YEWLVMPFGLCNAPATFQCFMEEVLEPFRPFVAGLLDDVAVWADSMAELHSRLILIFSRF
-ASYGLLLNASKCRLFVSEGIFLGFHISKHGIAADPEKVSAIRDRPMPTTTSEIRGFVNAA
-GYLRCLIKNFSQLAGPLTDQSSGPKNCPVILTDQSIQSWKSIKLALTTSPVVKKFDWRLP
-VILETDASQKFVGAVILQPYMRCSNNSDRSVLHPIAYFSRKLNDTQQRYSAQERELLGIL
-LSLQHWRHWVEGGDVTVITDHESLRTIQTKAEQPVRMVRFLDAIEHFNIRIIYRRGKANV
-LADFLSRPCDVLFLSREEGEGNVATDDNENSRIQSGAERELEMEEIKHPHELNRIDLQCI
-TEFLTLGEALPLNIAATWVRDNFAMYNSKLHLIKKNPSQQVGDAPGPSGAATLLEILEYE
-DLVSTAVNVHEGQGHASIGNTMRELGRRFWHPELILAAHEAVRKCKSCQLMKPPDPLLGS
-LTPIVPAPPLTRWGIDHTQVGPQVLLNAIEYATGWLESRLVPNADFANTVPLLTYIIQNF
-GKPKQIISDNAGCFGGIEAQRFQASQQLQVVHTTPARPRGNGKVEQANGVLKAILVRVLL
-DSPKITLAGALSLAVMNFNRRVSPSGYSPYFLLFGTQPPEEENSYPVYTREATESEERLW
-AEELGRKHPAPIARSYVSSMKATRDKIRAYLQEEKALIRTYAPGDWVLRVRQRRHKMEPY
-YDGPWAVAACHNNNTYSLISPGGYKLGNKYNGTNLFPAYVREGHPVRSLWYGSRRMLEQD
-RKTLKNSARIXFEXYHNKISNXLVIXISCGQLVLRRGIVCGSQLMETRPCKLCAVDWLTW
-CGGIFKXVGDPVLXNXIHVLLVSSSTRIILLISRSHETPTXNHCDHKLINXKP
->blumeria_Grouper_28830_3_6
-WIPIDGNPTVQIVCCXLAHVVRGNIXISWRSCIIEXNSRFISLKLYSHYIVDLSEPRDTY
-VKSLXSXTDQLEATKLYIFVERTSQFXVIPIXDVSKFFTHFTTYSIIMVGLNNAQLESLM
-KDHIAGQTKANENFSEANEAAKAVTKDLSKRIDQRFEETQSQISLLVKQMSAMNDLISKL
-VSRNEDVETKTSSKNSVPFQLSEAGPSENKKPYREELFDFSAGSASRPATRPIVFQPKKR
-PFTSAQFYETTPNLSNDEQNKDGTINLYRQSVNEPLNVTEQERKIKRYFPDFFSRSEAEN
-PHGPLKEANRKTRAVFPPQWKLHFADENIMNILYHMQSLMIQHMLPYSAWAIRIAMEMDE
-DFISARRTIISQHLDWAGAVDCILKILFDNDVLGSPLTTFARITARNDETQLQFARRLRK
-AFFSLPSDVMVGPQTRDILRQHIRLSLPRTWTIISNNLPKLTSAELADRVVQVTRGITRW
-TLEDDVFKHSESNAPIPISASKGEKLPAFDASIADPRSYGQDVFASQDIAETDKSYPIHD
-KRYECFNCGKTGHWAKDCRLMKTAPVESKEQREYAPNAKYTSSRFSDKFRKTYQSMKNKK
-YVKPVTPHDRSSKPVTSTFLVEPEDLDQEQISPEGQIEDEQLDDEIEAILYRMRNEEIYE
-XDSPNTYFVAVGKGKFEPPPKGQPLREGYGKPHRMFFARITHFPYVQFSVFFDYGSSACY
-VSQSFSKYLTSYNTSIISKMSGIGGPGPTISKDAILTAQFLCSNHLESFWTQEFTVSLGV
-VPDGTFPADVTLGQTLFHELGLRCLSNGKLQLLNLIDQPILNPIINTLPNRKVFTTSNIP
-MVKWHPAHPSFRITVFPYNIKVKFPFNFSINLSRQMGXNSPKTETPAXKRGNCQPNLKLP
-SEAIXPRRNNKPSGDFLVQHMTGSIHTQMXGTMGCTSVINTKKRRXPRLTKPFGVFVLTI
-ESLTRLRRNTPIPYQMLKMKFSAQQDITSMHSSTWKTDFGRYVCTKTLQRKQHLXLLSVS
-MNGXLCLSAYATHQLLSSVLWKKFXSHSVHLSQGSWTMXLSGQTQWQNCTHGXYLFFLDS
-LPMVSSSMLQSAGYLFQRESSLVSIFLNMALQQTPKKFQRSETGLCQQLPRKXEDLXMQL
-VTYVVSLKISPNXQGHSRTNPLDLKIALSFXRTNRFNHGKVSNXRLQHHQLXKNLIGDFP
-SYWKLTLPKSSWVQSYSNRTCDAPTIPIVQCCIPXLTSQENXTIPSSVIQHKRGNYLGFY
-CHYNIGVTGXKAATXRXXLTMNLYELFRPKPSSPSEWSVFXMLXSILISGLSTVAEKQMF
-SLIFSPVPVMFYFSLGKKGKGMXLLTTTKTLESKVVQKENLRWRKXSTHTNSTASTCSAS
-PNFXPXERHFPXIXLPLGSEIILRCTIPNCISSKRTRRNKXAMHLVHLAPQPYXKSWNMR
-IXYRRPXMFMRAKAMRQSAILCGNXGVGFGTPNXSSRLTKLSENASPVSSXNLQTRYWEA
-XLLXYQHLLXHGGVXIILKXDPKSCSMQLSTQQAGWNPAXFPMQTSLTLCLCSRILSRTL
-ESQSRLSVTMLAASEAXKHNDFKLANNCRLSIPHQLGQEEMAKSNRQMAFXKPYWSEFSW
-ILLKLHXLALSHSRXXISIEESHPAGIALTSYSSALSPRRRKILIQYIPVKPQNQRSASG
-PKNSEGNTPHQXHAPTLVVXKQLGIKYGLTSRKKRHLYVLTPPETGYCEYASEDTRWSPT
-MTGHGPXQLVIIIIPTPXYHRVDTNXATSTTAQTYSRHMYVKDTQFVVYGMVAAVCWSRI
-ERHSKIQQGFSLSDTIIKFLINLXFKXAVDSXFXEGGXFVDPNXWKPDRANCALLIGSRG
-AGEYLNKLAILYYRXKFTFYXSQALLALYCXLVGATRHLREIIVIINXSTRSH
->blumeria_Grouper_14770_3_1
-GXTDTVSLVXSCGRKNXLETSVLRCMVLSKTELIRVRLRVRISYQLRFLTSIYQSPWIIS
-YDPCRCKSIYVQIYEPEIXSXIHVCRXXIRETFNLHLIHNHLMECXCEINANVRXTFREE
-CADDNDIGRXIXXPNXPDLQMSYPWHSRIYNISTPLLTLHRGXIHKXKTVSIFIVISHLM
-LVWXTRQWLYXYQKLKCINRCALVSVSLLYIYLRDFXLKEHVIVXASRLQFFPLXNDKRC
-RYVXKHHLVLDCEQVQWQPYCQSRLLLGCCLQGIGEVRAKSRYIVWMRALLPCTQLRRLN
->blumeria_Grouper_14770_3_2
-VRPIQXVSYEVVEGRIDWKQVYXDVWFXVKLSXXEXDCVCAYLINXGFXPVFINLHGSXV
-MIPVDVNLYTYRYMSQKYKAKYMCVGNRSEKPLTCIXYIIIXWNASVKXMPMYVKLSVRN
-VLMTMIXEGEFDNLISRTYKXVILGIPGYTIFQHPSSLCIEDRYISEKLLVYLLSFLIXC
-WYGRHASGCTSTKNXSAXIGVPWSRXAFCTYICEIFSXRNMXXCKRAVFNSFPCKMISDV
-DMFRSIIXFWIVSKFNGSRIVSRDCCWDAVSKESVKSAQNPDILFGCERYCHVLSFAGXM
->blumeria_Grouper_14770_3_3
-LDRYSKSRMKLWKEELTGNKCIEMYGSEXNXADKSEIACAHILSTEVFDQYLSISMDHKL
-XSLXMXIYIRTDIXARNIKLNTCVSVIDPRNLXPAFDTXSSDGMLVXNKCQCTLNFPXGM
-CXXQXYRKVNLITXLAGLTNELSLAFQDIQYFNTPPHFASRIDTXVKNCXYIYCHFSSNA
-GMVDTPVVVLVPKTEVHKSVCLGLGKPFVHISARFLAEGTCNSVSEPSSILSLVKXXAMS
-ICLEASFSFGLXASSMAAVLSVEIAAGMLSPRNRXSPRKIQIYCLDASAIAMYSASQVE
->blumeria_Grouper_14770_3_4
-HSTCEAEYMAIALASKQYIWILRGLHRFLGDSIPAAISTDNTAAIELAHNPKLNDASKHI
-DIAYHFTRERIEDGSLTLLHVPSAKNLADICTKGLPRPRHTDLCTSVFGTSTTTGVSTIP
-ALDEKXQXIYXQFFTYVSILDAKXGGVLKYCISWNAKDNSFVSPANXVIKFTFLYHCHQH
-IPHGKFNVHWHLFHTSIPSDDYVSNAGXRFLGSITDTHVFSFIFLAHISVRIXIYIYRDH
-NLXSMEIDKYWSKTSVDKICAHAISLLSAQFYSEPYISIHLFPVNSSFHNFIRDLLYRSN
->blumeria_Grouper_14770_3_5
-IQPAKLSTWQXRSHPNNISGFCADFTDSLETASQQQSRLTIRLPLNLLTIQNXMMLLNIS
-TSLIILQGKELKTARLHYYMFLQLKISQIYVQKAYRDQGTPIYALQFLVLVQPLACLPYQ
-HXMRNDNKYTNSFSLMYLSSMQSEEGCXNIVYPGMPRITHLXVRLIRLSNSPSYIIVIST
-FLTESLTYIGIYFTLAFHQMIMYQMQVKGFSDLLPTHMYLALYFWLIYLYVYRFTSTGII
-TYDPWRLINTGQKPQLIRYAHTQSHSYQLSFTQNHTSQYTCFQSILPSTTSYETYCIGLT
->blumeria_Grouper_14770_3_6
-FNLRSXVHGNSARIQTIYLDFARTSPIPWRQHPSSNLDXQYGCHXTCSQSKTKXCFXTYR
-HRLSFYKGKNXRRLAYTITCSFSXKSRRYMYKRLTETKAHRFMHFSFWYXYNHWRVYHTS
-IRXEMTINILTVFHLCIYPRCKVRRGVEILYILECQGXLICKSGXLGYQIHLPISLSSAH
-SSRKVXRTLAFISHXHSIRXLCIKCRLKVSRIYYRHTCIXLYISGSYICTYIDLHLQGSX
-LMIHGDXXILVKNLSXXDMRTRNLTLISSVLLRTIHLNTLVSSQFFLPQLHTRLTVSVX
->blumeria_Grouper_1717_12_1
-ISSILPXRASKSXSNSFRSLSSVTGSNSLQNPMMKRSACAERVWNILPCSARNLVATIXG
-DGVCWCGELRXLASXIGSTNCCVGCCDGGCGPLRTISTSXRVEHXVGRGGQEPASAEDWG
-GMSEXGLWQCEIVDGIRRAXR
->blumeria_Grouper_1717_12_2
-FPVSCPEGPVSPDRIVFEVSRQXLVPTACRTQXXSALLVRSASGISCPVRRGIWSRRFEA
-TEFVGAVSFDDSPRRLALQIVVWVVVMAVVARXGPFRRLDASNIELGGGAKSQPLRRTGA
-AXVSEVCGSVRSXMVYGALEG
->blumeria_Grouper_1717_12_3
-FQYLALKGQXVLIEXFSKSLVSDWFQQLAEPNDEALCLCGARLEYPALFGEEFGRDDLRR
-RSLLVRXASMTRLVDWLYKLLCGLLXWRLWPVKDHFDVLTRRTLSWEGGPRASLCGGLGR
-HEXVRFVAVXDRRWYTARLK
->blumeria_Grouper_1717_12_4
-PFKRAVYHLRSHTATNLTHSCRPSPPQRLALGPPSQLNVRRVKTSKWSLTGHNRHHNNPH
-NNLXSQSTRRVIEAHRTNKLRRLKSSRPNSSPNRAGYSRRAPHKQSASSLGSASCWNQSL
-TRDFENYSIRTYWPFRARYWK
->blumeria_Grouper_1717_12_5
-PSSAPYTIYDLTLPQTSLTHAAPVLRRGWLLAPPPNSMFDASRRRNGPXRATTAITTTHT
-TICRANLRGESSKLTAPTNSVASNRRDQIPRRTGQDIPDALRTSRALHHWVLQAVGTSHX
-RETSKTIRSGLTGPSGQDTGN
->blumeria_Grouper_1717_12_6
-LQARRIPSTISHCHKPHSLMPPQSSAEAGSWPPLPTQCSTRQDVEMVLNGPQPPSQQPTQ
-QFVEPIYEASHRSSPHQQTPSPQIVATKFLAEQGRIFQTRSAQAERFIIGFCKLLEPVTD
-ERLRKLFDQDLLALQGKILE

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_nt.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
->blumeria_Grouper_28830_3
-TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC
-CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC
-TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA
-GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC
-AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT
-CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG
-CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG
-TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA
-TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT
-CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT
-TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG
-CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT
-TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG
-AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC
-GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT
-ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT
-GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG
-AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC
-GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG
-CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA
-CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT
-GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC
-AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG
-CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT
-AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT
-TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT
-ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG
-CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT
-TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG
-AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA
-CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG
-GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG
-TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC
-CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG
-GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT
-GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT
-TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT
-TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT
-GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT
-CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG
-TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT
-AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT
-ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC
-CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT
-GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA
-AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG
-TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT
-AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC
-CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC
-CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC
-CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT
-GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC
-GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG
-TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA
-AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT
-TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT
-GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA
-ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG
-CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG
-TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT
-AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC
-TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC
-CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC
-GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT
-CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG
-GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT
-GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT
-ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC
-AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT
-TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG
-CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG
-CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG
-TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA
-TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT
-GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA
-ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC
-CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA
-GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA
-TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT
-ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG
-CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG
-AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT
-CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA
-GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA
-CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC
-GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT
-TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT
-TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT
-GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA
-AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG
-CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA
-CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG
-TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG
-ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA
-TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC
-ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA
->blumeria_Grouper_14770_3
-GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA
-AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG
-CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT
-TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC
-TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT
-CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA
-TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA
-ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT
-CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG
-CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG
-TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA
-CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT
-CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT
-TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA
-TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT
-G
->blumeria_Grouper_1717_12
-ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC
-TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG
-GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC
-GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT
-TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA
-CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC
-GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA
-AGGG
-

--- a/commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-#!/usr/bin/env python
-
-from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
-from commons.core.utils.FileUtils import FileUtils
-import os
-import sys
-import getopt
-
-#------------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the command-line parameters.
-    """
-
-    print ""
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the nucleotidic input file (format='fasta')"
-    print "     -o: name of the output file (default=inFileName+'_aa')"
-    print "     -v: verbose (default=0/1/2)"
-    print "     -c: clean"
-    print ""
-
-#------------------------------------------------------------------------------
-
-def main():
-
-    inFileName = ""
-    outFileName = ""
-    verbose = 0
-    clean = False
-
-    try:
-        opts = getopt.getopt(sys.argv[1:],"hi:o:v:c")[0]
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-        elif o == "-c":
-            clean = True
-            
-    if inFileName == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "beginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    if outFileName == "":
-        outFileName = "%s_aa" % ( inFileName )
-    
-    iTIAFARSBX = TranslateInAllFramesAndReplaceStopByX()
-    iTIAFARSBX.setInputFile( inFileName )
-    iTIAFARSBX.setOutputFile( outFileName )
-    iTIAFARSBX.run( )
-    
-    if clean == True:
-        os.remove( inFileName )
-
-    if verbose > 0:
-        if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )):
-            print "%s finished successfully" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-        else:
-            print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-
-    return 0
-
-#------------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-import os
-from pyRepet.launcher.Launcher import HmmpfamLauncher
-
-
-class HmmpfamClusterComponent( object ):
-    
-    def __init__(self):
-        self._component = None 
-        self._profilDatabank = ""
-        self._resultDir = ""
-        self._queryDir = ""
-        self._tmpDir = ""
-        self._jobDb = None
-        self._SGEQueue = ""
-        self._SGEGroupId = "" 
-        
-    def loadConfig( self, config ):
-        self._profilDatabank = config.get( "profil_search","ProfilDatabank" )
-        self._queryDir = config.get( "hmmer_config","query_dir" )
-        self._tmpDir = config.get( "hmmer_config", "tmp_dir" )
-        self._resultDir = config.get( "hmmer_config", "result_dir" )    
-        self._SGEQueue = config.get( "sge_config", "queue" )
-        self._SGEGroupId = config.get( "sge_config", "groupid" )
-        
-    def run(self):
-        params = {"param":"--informat FASTA -E 10", 
-                  "profilDB": self._profilDatabank, 
-                  "outputDir": self._resultDir,
-                  "query": self._queryDir,
-                  "job_table":"jobs", 
-                  "queue" : self._SGEQueue, 
-                  "groupid" : self._SGEGroupId,
-                  "tmpDir": self._tmpDir,
-                  "cDir" : "."}
-        self._component = HmmpfamLauncher(self._jobDb, params)
-        self._component.run()
-        
-    def clean (self): 
-        dirToClean = self._tmpDir
-        os.system("rm  " + dirToClean + "/*")
-        dirToClean = self._resultDir
-        os.system("rm  " + dirToClean + "/*")
-        
-    def setProfilDatabank (self, profilDatabank):
-        self._profilDatabank = profilDatabank    
-
-    def getProfilDatabank(self):
-        return self._profilDatabank    
-
-    def setQueryDir(self, input):
-        self._queryDir = input
-         
-    def getQueryDir( self ):
-        return self._queryDir
-
-    def setSubjectDir(self, input):
-        self._subjectDir = input
-         
-    def getSubjectDir( self ):
-        return self._subjectDir
-    
-    def setSGEQueue(self, queue):
-        self._SGEQueue = queue
-        
-    def getSGEQueue( self ):
-        return self._SGEQueue
-        
-    def setSGEGrouId(self, id):
-        self._SGEGroupId = id    
-    
-    def getSGEGroupId( self ):
-        return self._SGEGroupId;    
-    
-    def setTmpDir(self, tmpDir):
-        self._tmpDir = tmpDir
-
-    def getTmpDir( self ):
-        return self._tmpDir
-    
-    def setResultDir(self, wkDir):
-        self._resultDir = wkDir
-        
-    def getResultDir(self):
-        return self._resultDir
-    
-    def setJobDb (self, jobDb):
-        self._jobDb = jobDb
-        
-    def getJobDb (self):
-        return self._jobDb
-     
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/LaunchPreProcessHmmpfamPostProcessNotInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-import os
-import unittest
-from pyRepet.launcher.programLauncher import *
-from pyRepet.util.file.FileUtils import *
-import commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX
-import commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing
-import ConfigParser 
-
-class LaunchPreProcessHmmpfamPostProcessNotInParallel:
-
-    def __init__( self ): 
-          
-        #for global analysis
-        self._configFile = ""
-        self._inputFile = ""
-        self._outputFile = ""
-        self.fileUtils = FileUtils()
-        self._programLauncherInstance = programLauncher()
-        #specific to PreProcess
-        self.bioseq = Bioseq()
-        self.preProcess = commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX.TranslateInAllFramesAndReplaceStopByX()        
-        self._outputFilePreprocess =  "" 
-        #specific to PostProcess
-        self.hmmpfamOutputProcess = commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing.HmmpfamOutputProcessing()       
-
-    def _cleanTemporaryFiles(self, outputFilePreProcess, outputFileHmmpfam):        
-        os.remove( outputFilePreProcess )       
-        os.remove( outputFileHmmpfam )       
-        
-    def _launchPostProcess(self, outputFileHmmpfam):
-        return self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(outputFileHmmpfam, self._outputFile)
-
-
-    def _launchHmmpfam(self, outputFilePreprocess):
-        config = ConfigParser.ConfigParser()
-        config.readfp(open(self._configFile))
-        self._programLauncherInstance.reset(outputFilePreprocess)
-        outputFileHmmpfam = outputFilePreprocess + ".hmmpfamOut"
-        self._programLauncherInstance.setOutputFileName(outputFileHmmpfam)
-        self._programLauncherInstance.launchHmmpfam(evalFilter=config.get("profil_search", "Evalue"), inputFormat=config.get("profil_search", "InputFormat"), profilDatabank=config.get("profil_search", "ProfilDatabank"))
-        return outputFileHmmpfam
-
-
-    def _launchHmmpfamPreProcess(self):
-        self.preProcess.setInputFile(self._inputFile)
-        outputFilePreprocess = self._inputFile + ".translated"
-        self.preProcess.setOutputFile(outputFilePreprocess)
-        self.preProcess.run()
-        return outputFilePreprocess
-          
-    def setInputFile( self, input ):
-         self._inputFile = input;
-
-    def setOutputFile( self, output ):
-         self._outputFile = output;
-            
-    def setConfigFile ( self, configFile ):
-        self._configFile = configFile
-    
-    def checkInputFile(self):
-        return self._checkFileExitsAndNotEmpty( self._inputFile )
-    
-    def checkConfigFile(self):
-        return self._checkFileExitsAndNotEmpty( self._configFile )
-    
-    def _checkFileExitsAndNotEmpty(self, fileName):
-        fileUtils = FileUtils() 
-        if fileUtils.isRessourceExists(fileName) and not fileUtils.isFileEmpty(fileName):
-            return 1
-        return 0
-    
-    def run(self):
-        
-        if not self.checkInputFile():
-            print "Warning : there is no input file : " + self._inputFile + "\n"
-            return 0        
-        if not self.checkConfigFile():
-            print "Warning : there is no config file : " + self._configFile + "\n"
-            return 0 
-        outputFilePreProcess = self._launchHmmpfamPreProcess()    
-        outputFileHmmpfam = self._launchHmmpfam(outputFilePreProcess)
-        self._launchPostProcess(outputFileHmmpfam)
-        self._cleanTemporaryFiles(outputFilePreProcess, outputFileHmmpfam)
-        
-        
-if __name__ == "__main__":                 
-    main() 
-          
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-if __name__ == "__main__":                 
-    main() 
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/check/OldDetectFeatureConfigChecker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-'''
-Created on 14 avr. 2009
-
-@author: oinizan
-'''
-import re
-from commons.core.checker.IChecker import IChecker
-from commons.core.checker.OldConfigChecker import ConfigChecker
-from commons.core.checker.ConfigException import ConfigException
-from commons.core.checker.CheckerException import CheckerException
-
-class DetectFeatureConfigChecker (IChecker):
-    '''
-    classdocs
-    '''
-    def __init__(self):
-        '''
-        Constructor
-        '''
-        self._dict = {"te_hmmer" : "", 
-                      "te_blrn" : ""                                  
-        }
-        self._specifiqueDict = {"te_hmmer_evalue" : "",
-                                "te_hmm_profiles" : ""                
-        }
-
-    def _appendMessageToConfigExceptionMessage(self, messages):
-        appendedMessages = []
-        for msg in messages:
-            if (re.match("\[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features'", msg)):
-                appendedMessages.append(msg + " whereas te_hmmer is set")
-            
-            if (re.match("\[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features'", msg)):
-                appendedMessages.append(msg + " whereas te_hmmer is set - Default value will be set")
-
-        return appendedMessages
-
-        
-    def check(self, configFile):
-        chk = ConfigChecker("detect_features", self._dict)
-        try :
-            chk.check(configFile)
-        except ConfigException, e :
-            raise e
-
-        if self._dict["te_hmmer"] == "yes":                  
-            isErrorOccured = False
-            try:
-                chk = ConfigChecker("detect_features", self._specifiqueDict)
-                chk.check(configFile)                
-            except ConfigException, e:
-                appendedMessages = self._appendMessageToConfigExceptionMessage(e.messages) 
-                raise ConfigException("", appendedMessages)    
-                        
-        
-if __name__ == "__main__":                 
-    pass

--- a/commons/pyRepetUnit/hmmer/check/test/Test_OldDetectFeaturesConfigChecker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-import unittest
-import re
-import os
-from commons.pyRepetUnit.hmmer.check.OldDetectFeatureConfigChecker import DetectFeatureConfigChecker
-from commons.core.checker.ConfigException import ConfigException
-
-class Test_DetectFeaturesConfigChecker(unittest.TestCase):
-
-    def setUp(self):
-        self._detectFeatureConfigChecker = DetectFeatureConfigChecker()
-
-    def testWithDefaultLogger (self):
-        lineFound = False
-        try:
-            self._detectFeatureConfigChecker.check("dummyConfig")
-        except ConfigException, e:
-            for msg in e.messages:
-                if (re.match("CONFIG FILE not found.*", msg)):
-                    lineFound = True
-        self.assertTrue(lineFound)
-        
-    def testWithNoConfigFile(self):
-        lineFound = False
-        try:
-            self._detectFeatureConfigChecker.check("dummyConfig")
-        except ConfigException, e:
-            for msg in e.messages:
-                if (re.match("CONFIG FILE not found.*", msg)):
-                    lineFound = True
-        self.assertTrue(lineFound)
-
-    def testWithNoSectionInConfigFile(self):
-        config = open("config.cfg", "w");
-        config.close()
-        lineFound = False
-        try:
-            self._detectFeatureConfigChecker.check("config.cfg")
-        except ConfigException, e:
-            for msg in e.messages:
-                if (re.match("\[detect_features\] section not found.*", msg)):
-                    lineFound = True
-        self.assertTrue(lineFound)
-        os.remove("config.cfg")
-        
-    def testMissingOptionsInConfig (self):
-        dict = {}
-        MockConfigFile("config.cfg", dict)
-        hmmProfilsFound = False
-        TE_BLRnFound = False
-        try :
-            self._detectFeatureConfigChecker.check("config.cfg")
-        except ConfigException, e:
-            for msg in e.messages:
-                if (re.match("\[detect_features\] - No option 'te_hmmer' in section: 'detect_features'", msg)):
-                    hmmProfilsFound = True
-                if (re.match("\[detect_features\] - No option 'te_blrn' in section: 'detect_features'", msg)):
-                    TE_BLRnFound = True
-        self.assertTrue(hmmProfilsFound)
-        self.assertTrue(TE_BLRnFound)
-        os.remove("config.cfg")
-   
-    def testOptionsIfHmmProfilsSetAtYESInConfig (self):
-        
-        dict = {
-                "TE_HMMER" : "yes", 
-                "TE_BLRn" : "no"                
-        }
-        
-        profilDatabankFound = False
-        evalueFound = False
-        MockConfigFile("config.cfg", dict)
-        try :
-            self._detectFeatureConfigChecker.check("config.cfg")
-        except ConfigException, e:
-            for msg in e.messages:
-                print msg
-                if (re.match("\[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features' whereas te_hmmer is set", msg)):
-                    profilDatabankFound = True   
-                if (re.match("\[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features' whereas te_hmmer is set - Default value will be set", msg)):
-                    evalueFound = True
-        self.assertTrue(profilDatabankFound)
-        self.assertTrue(evalueFound)
-        os.remove("config.cfg")
-        
-            
-    def testOptionsIfHmmProfilsSetAtNOInConfig (self):
-        profilDatabankFound = False
-        inputFormatFound = False
-        evalueFound = False
-        dict = {
-                "TE_HMMER" : "no"                
-        }
-        MockConfigFile("config.cfg", dict)
-        try :
-            self._detectFeatureConfigChecker.check("config.cfg")
-        except ConfigException, e:
-            for msg in e.messages:
-                if (re.match(".+INFO \[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features' whereas te_hmmer is set", msg)):
-                    profilDatabankFound = True   
-                if (re.match(".+INFO \[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features' whereas te_hmmer is set - Default value will be set", msg)):
-                    evalueFound = True
-        self.assertFalse(profilDatabankFound)
-        self.assertFalse(inputFormatFound)
-        self.assertFalse(evalueFound)
-        os.remove("config.cfg")
-        
-    def testTE_BLRnAndTE_hmmerAtNoInConfig (self):
-        
-        dict = {
-                "TE_HMMER" : "no", 
-                "TE_BLRn" : "no"                
-        }
-        
-        exceptionNotRaised = True
-        MockConfigFile("config.cfg", dict)
-        try :
-            self._detectFeatureConfigChecker.check("config.cfg")
-        except ConfigException:
-            exceptionNotRaised = False
-        
-        self.assertTrue(exceptionNotRaised)
-        
-        os.remove("config.cfg")
-        
-class MockConfigFile:
-    
-    def __init__ (self, fileName, optionsDict):
-        
-        self._fileName = fileName
-        config = open(fileName, "w");
-        config.write("[detect_features]\n")
-        for key in optionsDict.keys():
-            config.write(key + ":" + optionsDict[key] + "\n")
-        config.close()
-
-
-if __name__ == "__main__":
-    unittest.main()

--- a/commons/pyRepetUnit/hmmer/check/test/detectFeatureConfigCheckerTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-'''
-Created on 29 mai 2009
-
-@author: oinizan
-'''
-import unittest
-import sys
-import TestDetectFeaturesConfigChecker
-
-
-
-
-def main():
-
-        commonsTestSuite = unittest.TestSuite() 
-        commonsTestSuite.addTest(unittest.makeSuite(TestDetectFeaturesConfigChecker.TestDetectFeaturesConfigChecker,'test'))
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(commonsTestSuite)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmOutput.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-## List of Hmmpfam or Hmmscan Output (that are too lists).
-#
-class HmmOutput( object ):
-   
-    list;
-    
-    def __init__( self ):
-        self._hmmpfamOutput = []
-    
-    ## append an output in the list of output
-    #    
-    # @param list name of the list  
-    #
-    def append( self, list ):
-        self._hmmpfamOutput.append(list)
-    
-    ## return the length of the list of output
-    def len (self):
-        return len(self._hmmpfamOutput)
-    
-    ## return the output corresponding at the element number index in the list of output
-    # 
-    # @param index number of index
-    # 
-    def get(self, index):
-        return self._hmmpfamOutput[index]
-    
-    ## return the list of output
-    def getList(self):
-        return self._hmmpfamOutput

--- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-import os
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
-
-##Concrete implementation for hmmscan and  hmmpfam output methods
-#
-class HmmOutputProcessing (object):
-   
-    ## write a align file from a HmmOutput object
-    #
-    # @param fout handle of align file
-    # @param HmmOutput HmmOutput object in fact a list of hmmOutput containing datas required
-    #        
-    def writeHmmOutputToAlignFile( self, pfamOutput, fout ):    
-        for item in pfamOutput.getList():
-            for i in item:
-                fout.write(i + "\t")
-            fout.write("0\n")
-    
-    ## read an output file from hmm profiles search program and write the corresponding .align file
-    #
-    # @param inputFile file
-    # @param outputFile file
-    #
-    def readHmmOutputsAndWriteAlignFile( self, inputFile, outputFile ):
-        if not os.path.exists(inputFile):
-            print "Warning your input file " + inputFile + " does not exist!\n"
-            return
-        file2parse = open( inputFile )
-        pfamOutput = HmmOutput()
-        if outputFile == "":
-            print "Warning have to specify an output name file!\n"
-            return
-        fout = open(outputFile, "w")        
-        while pfamOutput != None:      
-            pfamOutput = self.readHmmOutput(file2parse)             
-            if pfamOutput != None:  
-                self.writeHmmOutputToAlignFile(pfamOutput, fout)
-        fout.close()
-        file2parse.close() 

--- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmpfamOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
-import re
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
-
-##Concrete implementation for specific methods
-#
-class HmmpfamOutputProcessing (HmmOutputProcessing):
-    
-    ##read an output from hmmpfam and return a array with results useful to build a .align file
-    #    
-    # @param file handle of file generated by software searching hmm profiles
-    #
-    def readHmmOutput( self, hmmerOutputFile ):
-        #Tested with HMMER 2.3.2 on Linux (Debian) and on Unix (Solaris)
-        line = hmmerOutputFile.readline()
-        tabResult = None
-        aRecup = 0        
-        if (line == ""):            
-            tabResult = None            
-            return tabResult
-        tabResult = HmmOutput()
-        while not re.match("Alignments of top-scoring domains:.*", line):
-            line = hmmerOutputFile.readline()                   
-            m = re.match("Query sequence:\s*(.*)", line)
-            if m:                    
-                seqName = m.group(1)
-            #warning : do no use a return character because they change between several OS                                              
-            if re.match("--------\s+-------\s+-----\s+-----\s+-----\s+-----\s+-----\s+-------.*", line):
-                aRecup = 1                
-            m = re.match("(\S+)\s+\d+\/\d+\s+(\d+)\s+(\d+)\s+.+\s+(\d+)\s+(\d+)\s+.+\s+(.+\.\d)\s+(.+)", line)
-            if m and aRecup == 1:                
-                tabResult.append([seqName, m.group(2), m.group(3), m.group(1), m.group(4), m.group(5), m.group(7), m.group(6)]) 
-            if line == "":            
-                tabResult = None            
-                return tabResult
-        return tabResult

--- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmscanOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-import re
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
-    
-##Concrete implementation for hmmscan output specific methods
-#
-class HmmscanOutputProcessing (HmmOutputProcessing):
-    
-    ## read an hmmscan output from a file, return a array with results useful to build a .align file
-    #    
-    # @param file handle of file generated by software searching hmm profiles
-    #
-    def readHmmOutput( self, hmmerOutputFile ):
-        #Tested with HMMER 3 on Linux
-        line = hmmerOutputFile.readline()
-        tabResult = None
-        if (line == ""):            
-            tabResult = None
-            return tabResult
-        tabResult = HmmOutput()
-        
-        while line != "":
-            line = hmmerOutputFile.readline()
-            if not(re.match("^#.*$", line)) and line != "":            
-                lLines = re.split("\s+", line)
-                seqName = lLines[3]
-                profilName = lLines[0]
-                iValue = lLines[12]
-                score =  lLines[13]
-                queryCoordStart =lLines[17]
-                queryCoordEnd = lLines[18]
-                subjectCoordStart = lLines[15]
-                subjectCoordEnd = lLines[16]
-                tabResult.append([seqName, queryCoordStart, queryCoordEnd, profilName, subjectCoordStart, subjectCoordEnd, iValue, score]) 
-        return tabResult
-

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
-from commons.core.utils.FileUtils import FileUtils
-
-class TestHmmOutputProcessing(unittest.TestCase):
-    
-    def setUp(self):
-        self.hmmOutput = HmmOutputProcessing()
-        self._inputFile = "./datas/test_hmmpfam_output" 
-        self._outputFile =  "./datas/dummyoutput.align" 
-        self._inputFileScan2 = "./datas/hmmscanOutput"
-        self._outputFileScan2 = "./datas/hmmscanOutput.align"       
-        
-    def test_writeHmmOutputToAlignFile(self):
-        output = open("./datas/output.align", "w")
-        output.write("SAR:satellite:satellite_5\t3\t9\tDUF751\t5\t11\t5.4\t5.4\t0\n")
-        output.write("SAR:satellite:satellite_5\t17\t23\tDUF751\t5\t11\t5.1\t5.5\t0\n")
-        output.write("SAR:satellite:satellite_5\t3\t21\tClenterotox\t173\t191\t0.66\t7.4\t0\n")
-        output.close()
-        pfamOutput = HmmOutput()
-        pfamOutput.append(["SAR:satellite:satellite_5", "3", "9", "DUF751", "5", "11", "5.4", "5.4"])
-        pfamOutput.append(["SAR:satellite:satellite_5", "17", "23", "DUF751", "5", "11", "5.1", "5.5"])
-        pfamOutput.append(["SAR:satellite:satellite_5", "3", "21", "Clenterotox", "173", "191", "0.66", "7.4"])
-        fout = open("./datas/outputGen.align", "w")
-        self.hmmOutput.writeHmmOutputToAlignFile(pfamOutput, fout)
-        fout.close()
-        self.assertTrue(FileUtils.are2FilesIdentical("./datas/output.align", "./datas/outputGen.align"))
-        os.remove("./datas/output.align")
-        os.remove("./datas/outputGen.align")
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
-from commons.core.utils.FileUtils import FileUtils
-
-class TestHmmpfamOutputProcessing(unittest.TestCase):
-    
-    def setUp(self):
-        self.fileUtils = FileUtils()
-        self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
-        self._inputFile = "./datas/Outputhmmpfam" 
-        self._inputFile2 = "./datas/test_hmmpfam_output"
-        self._outputFile = "./datas/dummyAlignFile.align"
-        
-    def testReadHmmOutput(self):
-        file = open( self._inputFile )
-        pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
-        self.assertEqual(["7LES_DROME", "437", "522", "fn3", "1", "84", "8.8e-15", "48.3"], pfamOutput.get(0))
-        self.assertEqual(["7LES_DROME", "825", "914", "fn3", "1", "84", "2.2e-06", "13.4"], pfamOutput.get(1))
-        self.assertEqual(["7LES_DROME", "1292", "1389", "fn3", "1", "84", "1.2e-06", "15.9"], pfamOutput.get(2))
-        self.assertEqual(["7LES_DROME", "1799", "1891", "fn3", "1", "84", "2.3e-19", "63.5"], pfamOutput.get(3))
-        self.assertEqual(["7LES_DROME", "1899", "1978", "fn3", "1", "84", "1.5e-06", "15.2"], pfamOutput.get(4))
-        self.assertEqual(["7LES_DROME", "1993", "2107", "fn3", "1", "84", "4.3e-07", "20.3"], pfamOutput.get(5))
-        self.assertEqual(["7LES_DROME", "2209", "2483", "pkinase", "1", "294", "6e-95", "314.6"], pfamOutput.get(6))
-        self.assertEqual(["7LES_DROME", "2223", "2284", "rrm", "1", "77", "0.72", "-40.4"], pfamOutput.get(7))
-        file.close()
-        
-    def test_readHmmOutput_empty_file(self):
-        file = open( "./datas/OutputhmmpfamEmpty", "w" )
-        file.close()
-        file = open( "./datas/OutputhmmpfamEmpty")
-        pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
-        file.close()
-        self.assertEqual(None, pfamOutput)
-        os.system("rm ./datas/OutputhmmpfamEmpty")
-        
-    def testParseHmmpfamOutput2Align(self):
-        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile2, self._outputFile)
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertEqual(18, FileUtils.getNbLinesInSingleFile(self._outputFile))
-        os.system("rm " + self._outputFile)
-        
-    def test_parseHmmpfamOutput2Align_empty_file(self):
-        file = open("./datas/dummy_hmmpfam_output", "w")
-        file.close()
-        self._inputFile = "./datas/dummy_hmmpfam_output"
-        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
-        self.assertTrue(FileUtils.isEmpty(self._outputFile))
-        os.system("rm " + self._inputFile)
-        os.system("rm " + self._outputFile)
-        
-    def test_parseHmmpfamOutput2Align_file_not_exists(self):
-        self._inputFile = "./datas/dummy_hmmpfam_output"
-        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile )
-        self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmscanOutputProcessing.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
-from commons.core.utils.FileUtils import FileUtils
-
-class TestHmmscanOutputProcessing(unittest.TestCase):
-    
-    def setUp(self):
-        self.hmmscanOutputProcess = HmmscanOutputProcessing()
-        self._inputFile = "./datas/hmmscanOutputTab.txt"
-        self._inputFileScan2 = "./datas/hmmscanOutput" 
-        self._outputFileScan2 = "./datas/hmmscanOutput.align"
-        self._outputFile = "./datas/dummyFile.align"
-        
-    def tearDown(self):
-        if os.path.exists(self._outputFile):
-            os.remove(self._outputFile)
-        
-    def testReadHmmerscanOutput(self):
-        file = open( self._inputFile )
-        pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file)
-        self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2742", "2766", "rve", "50", "78", "2.4e+03", "-3.3"], pfamOutput.get(0))
-        self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2951", "3101", "rve", "4", "168", "6.7e-30", "103.4"], pfamOutput.get(1))
-        self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "3198", "3228", "Chromo", "4", "51", "8.5e-06", "24.7"], pfamOutput.get(2))
-        self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2117", "2125", "GARS_A", "196", "204", "11", "2.5"], pfamOutput.get(3))
-        file.close()
-        
-    def test_readHmmerscanOutput_empty_file(self):
-        file = open( "./datas/OutputhmmscanEmpty", "w" )
-        file.close()
-        file = open( "./datas/OutputhmmscanEmpty")
-        pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file)
-        file.close()
-        self.assertEqual(None, pfamOutput)
-        os.system("rm ./datas/OutputhmmscanEmpty")
-        
-    def testParseHmmscanOutput2Align(self):
-        self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFileScan2, self._outputFile)
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileScan2, self._outputFile))
-        os.system("rm " + self._outputFile)
-        
-    def test_parseHmmscanOutput2Align_empty_file(self):
-        file = open("./datas/dummy_hmmpfam_output", "w")
-        file.close()
-        self._inputFile = "./datas/dummy_hmmpfam_output"
-        self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
-        self.assertTrue(FileUtils.isEmpty(self._outputFile))
-        os.system("rm " + self._inputFile)
-        os.system("rm " + self._outputFile)
-        
-    def test_parseHmmscanOutput2Align_file_not_exists(self):
-        self._inputFile = "./datas/dummy_hmmpfam_output"
-        self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile )
-        self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
-        
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/Test_HmmOutput.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
-
-class Test_HmmOutput(unittest.TestCase):
-    
-    def testAppend(self):
-        hmmpfamOutput = HmmOutput()
-        self.assertEquals(0, hmmpfamOutput.len())
-        list = ["a","b"]
-        hmmpfamOutput.append(list)
-        self.assertEquals(1, hmmpfamOutput.len())
-        list2 = ["c","d"]
-        hmmpfamOutput.append(list2)
-        self.assertEquals(2, hmmpfamOutput.len())
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/Outputhmmpfam	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,148 +0,0 @@
-hmmpfam - search one or more sequences against HMM database
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-HMM file:                 myhmms
-Sequence file:            7LES_DROME
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Query sequence: 7LES_DROME
-Accession:      P13368
-Description:    SEVENLESS PROTEIN (EC 2.7.1.112).
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          314.6      6e-95   1
-fn3      Fibronectin type III domain                    176.6      2e-53   6
-rrm                                                     -40.4       0.72   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-fn3        1/6     437   522 ..     1    84 []    48.3  8.8e-15
-fn3        2/6     825   914 ..     1    84 []    13.4  2.2e-06
-fn3        3/6    1292  1389 ..     1    84 []    15.9  1.2e-06
-fn3        4/6    1799  1891 ..     1    84 []    63.5  2.3e-19
-fn3        5/6    1899  1978 ..     1    84 []    15.2  1.5e-06
-fn3        6/6    1993  2107 ..     1    84 []    20.3  4.3e-07
-pkinase    1/1    2209  2483 ..     1   294 []   314.6    6e-95
-rrm        1/1    2223  2284 ..     1    77 []   -40.4     0.72
-
-Alignments of top-scoring domains:
-fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 8.8e-15
-                CS    C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
-                   *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
-                      P saP   + +++ ++ l ++W p +  ngpi+gY++++ +++ g+ 
-  7LES_DROME   437    PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482  
-
-                CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                   + e+ vp    sy+++ L++gt+Y++ +  +n +G+Gp     
-  7LES_DROME   483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA    522  
-
-fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 2.2e-06
-                CS    CCCCCEEEEEECCTTCCEEEEECCC       CCCCCCCEEEEE.EC
-                   *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
-                       ++P  l++   ++  + +sW+ p++++ ++ + +   +Ye+++  +
-  7LES_DROME   825    GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869  
-
-                CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC  CCCC   
-                   knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*
-                   + +++ ++++++ g+   + l+ L+P+  Y++rV+A+n +G++G+++   
-  7LES_DROME   870 VASQSAFSIRnIRGPI--FGLQRLQPDNLYQLRVRAINVDGepGEWT    914  
-
-fn3: domain 3 of 6, from 1292 to 1389: score 15.9, E = 1.2e-06
-                CS    CCCCCEEEE      EEC  CTTCCEEEEECCC    CCCCCCCEEE
-                   *->PsaPtnltv......tdv..tstsltlsWsppt....gngpitgYev
-                      Ps+P++l+v  ++  t++++   s++l+W++p+++++       Y +
-  7LES_DROME  1292    PSQPRRLRVfverlaTALqeANVSAVLRWDAPEqgqeAPMQALEYHI 1338 
-
-                CS EE.ECCCCCCCCCCEEECCCC CECECCEEEEECCCCEEEEEECCC    
-                   tyRqpknggewneltvpgttt.sytltgLkPgteYevrVqAvnggG....
-                   ++ +   g e +e    +++  ++ ++ L+P+ +Y+++V A+ ++++   
-  7LES_DROME  1339 SC-W--VGSELHEELRLNQSAlEARVEHLQPDQTYHFQVEARVAATgaaa 1385 
-
-                CS CCCC   
-                   GpeS<-*
-                   G++S   
-  7LES_DROME  1386 GAAS    1389 
-
-fn3: domain 4 of 6, from 1799 to 1891: score 63.5, E = 2.3e-19
-                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC 
-                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
-                      Ps+P+n++v+ +++ +l +sW pp++ +++  +Y++++ q++ +ge+
-  7LES_DROME  1799    PSPPRNFSVRVLSPRELEVSWLPPEqLRSESVYYTLHW-QQELDGEn 1844 
-
-                CS        CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   .......wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                    +++++ + + +   t+ ++ ltg kPg+ Y+++VqA+ + +++  S   
-  7LES_DROME  1845 vqdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTkSNSS    1891 
-
-fn3: domain 5 of 6, from 1899 to 1978: score 15.2, E = 1.5e-06
-                CS    CCCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCCC
-                   *->PsaPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggewn
-                        +   l+  +++++sl+l+W       p+ + ++++R   ++ e  
-  7LES_DROME  1899    FAELPELQLLELGPYSLSLTWAGT--PDPLGSLQLECR---SSAEQL 1940 
-
-                CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                   +++v g+ t ++++ L+P t+Y+ r+    ++++G++    
-  7LES_DROME  1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL    1978 
-
-fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 4.3e-07
-                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC 
-                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
-                      Ps+P+ ++ + + +  ++++W++++++++pi  Y+++   ++++  +
-  7LES_DROME  1993    PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038 
-
-                CS                            CCCCEEECCCC CECECCEEEEE
-                   ...........................wneltvpgttt.sytltgLkPgt
-                   +++++++++++++ ++ +  +++   ++++l+  +tt  s++++ L   +
-  7LES_DROME  2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088 
-
-                CS CCCCEEEEEE CCC CCCC   
-                   eYevrVqAvn.ggG.GpeS<-*
-                      +rV+A++ ++G Gp+S   
-  7LES_DROME  2089 LLLFRVRARSlEHGwGPYS    2107 
-
-pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 6e-95
-                   *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
-                      ++ll+ lG+G+fG+Vy++++k+++++  ++VA+K l+k+++++ e  
-  7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253 
-
-                   flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
-                   +l E+q++ +++H+NIvrl g++  + +++ l+mE+me GdL++ylr+ +
-  7LES_DROME  2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302 
-
-                   ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
-                    +++++++++  ls  e++ ++ ++++G +YL+++++vHRDL+ +N+L++
-  7LES_DROME  2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352 
-
-                   en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
-                   e +++++++ tvKi+DFGLAr++++++++++ + +  p+++m+PE  l +
-  7LES_DROME  2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401 
-
-                   rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
-                     +++++DvW++Gv+++E+lt g                         ++
-  7LES_DROME  2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426 
-
-                   PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
-                   P+         ++ +e+++++k+ g+rl +p+ c e l++Ll  c++ DP
-  7LES_DROME  2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468 
-
-                   skRpGsatakeilnhpwf<-*
-                   ++Rp   +++ + n +     
-  7LES_DROME  2469 WERP---SFRRCYNTLHA    2483 
-
-rrm: domain 1 of 1, from 2223 to 2284: score -40.4, E = 0.72
-                   *->lfVgNL.......ppdvteedLkdlFskfGpi.vsikivkDhkektk
-                      ++ g L+++++++p+ v  + L++  s+f +   +++++ +      
-  7LES_DROME  2223    VYEGQLktedseePQRVAIKSLRKGASEFAELlQEAQLMSN------ 2263 
-
-                   etgkskGfaFVeFeseedAekAlealnGkelggrklrv<-*
-                               F+     e+ ++ l G+ ++   +     
-  7LES_DROME  2264 ------------FKH----ENIVR-LVGICFDTESISL    2284 
-
-//

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#                                                                                        --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
-# target name        accession   tlen query name                       accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
-#------------------- ---------- -----             -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
-DNA_pol_B_2          PF03175.5    531 Polinton-1_DY:classII:Polinton_1 -           4927   3.7e-06   24.2  16.0   1   3   1.4e-09   3.7e-06   24.2  11.1    13   252   992  1214   987  1218 0.76 DNA polymerase type B, organellar and viral
-DNA_pol_B_2          PF03175.5    531 Polinton-1_DY:classII:Polinton_1 -           4927   3.7e-06   24.2  16.0   2   3      0.11   2.9e+02   -2.0   0.2   393   433  1367  1397  1364  1398 0.85 DNA polymerase type B, organellar and viral
-DNA_pol_B_2          PF03175.5    531 Polinton-1_DY:classII:Polinton_1 -           4927   3.7e-06   24.2  16.0   3   3      0.33   8.5e+02   -3.5   0.2   175   193  2832  2850  2827  2852 0.85 DNA polymerase type B, organellar and viral
-ASFV_p27             PF06556.3    131 Polinton-1_DY:classII:Polinton_1 -           4927       2.4    5.8   1.6   1   1    0.0023         6    4.5   1.1    59    74  2633  2648  2626  2652 0.90 IAP-like protein p27 C-terminus
-Ribosomal_S4         PF00163.11   110 Polinton-1_DY:classII:Polinton_1 -           4927       5.5    5.7   1.1   1   1    0.0068        18    4.1   0.7    39    72  3008  3041  3002  3043 0.92 Ribosomal protein S4/S9 N-terminal domain
-Homo_sperm_syn       PF06408.3    487 Polinton-1_DY:classII:Polinton_1 -           4927       6.3    2.4   0.3   1   1    0.0034       8.8    2.0   0.2    49    68  3966  3985  3960  3987 0.88 Homospermidine synthase
-rve                  PF00665.18   169 Polinton-1_DY:classII:Polinton_4 -           4927   5.4e-30  103.7   1.8   1   2       0.7   2.4e+03   -3.3   0.0    50    78  2742  2766  2739  2766 0.80 Integrase core domain
-rve                  PF00665.18   169 Polinton-1_DY:classII:Polinton_4 -           4927   5.4e-30  103.7   1.8   2   2   1.9e-33   6.7e-30  103.4   0.7     4   168  2951  3101  2947  3102 0.92 Integrase core domain
-Chromo               PF00385.16    69 Polinton-1_DY:classII:Polinton_4 -           4927   3.3e-06   26.0   0.0   1   1   2.5e-09   8.5e-06   24.7   0.0     4    51  3198  3228  3195  3239 0.75 'chromo' (CHRromatin Organisation MOdifier) domain
-GARS_A               PF01071.11   208 Polinton-1_DY:classII:Polinton_4 -           4927       7.6    3.0   0.7   1   1    0.0031        11    2.5   0.5   196   204  2117  2125  2117  2125 0.95 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-Polinton-1_DY:classII:Polinton_1	992	1214	DNA_pol_B_2	13	252	3.7e-06	24.2	0
-Polinton-1_DY:classII:Polinton_1	1367	1397	DNA_pol_B_2	393	433	2.9e+02	-2.0	0
-Polinton-1_DY:classII:Polinton_1	2832	2850	DNA_pol_B_2	175	193	8.5e+02	-3.5	0
-Polinton-1_DY:classII:Polinton_1	2633	2648	ASFV_p27	59	74	6	4.5	0
-Polinton-1_DY:classII:Polinton_1	3008	3041	Ribosomal_S4	39	72	18	4.1	0
-Polinton-1_DY:classII:Polinton_1	3966	3985	Homo_sperm_syn	49	68	8.8	2.0	0
-Polinton-1_DY:classII:Polinton_4	2742	2766	rve	50	78	2.4e+03	-3.3	0
-Polinton-1_DY:classII:Polinton_4	2951	3101	rve	4	168	6.7e-30	103.4	0
-Polinton-1_DY:classII:Polinton_4	3198	3228	Chromo	4	51	8.5e-06	24.7	0
-Polinton-1_DY:classII:Polinton_4	2117	2125	GARS_A	196	204	11	2.5	0

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutputTab.txt	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#                                                                                        --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
-# target name        accession   tlen query name                       accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
-#------------------- ---------- -----             -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
-rve                  PF00665.18   169 Polinton-1_DY:classII:Polinton_4 -           4927   5.4e-30  103.7   1.8   1   2       0.7   2.4e+03   -3.3   0.0    50    78  2742  2766  2739  2766 0.80 Integrase core domain
-rve                  PF00665.18   169 Polinton-1_DY:classII:Polinton_4 -           4927   5.4e-30  103.7   1.8   2   2   1.9e-33   6.7e-30  103.4   0.7     4   168  2951  3101  2947  3102 0.92 Integrase core domain
-Chromo               PF00385.16    69 Polinton-1_DY:classII:Polinton_4 -           4927   3.3e-06   26.0   0.0   1   1   2.5e-09   8.5e-06   24.7   0.0     4    51  3198  3228  3195  3239 0.75 'chromo' (CHRromatin Organisation MOdifier) domain
-GARS_A               PF01071.11   208 Polinton-1_DY:classII:Polinton_4 -           4927       7.6    3.0   0.7   1   1    0.0031        11    2.5   0.5   196   204  2117  2125  2117  2125 0.95 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,321 +0,0 @@
-hmmpfam - search one or more sequences against HMM database
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-HMM file:                 myhmms
-Sequence file:            test.fa
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Query sequence: pkinase_full
-Accession:      [none]
-Description:    Dario rerio
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          266.6    3.3e-80   1
-pkinase  Protein kinase domain                          265.4    7.6e-80   1
-rrm                                                     -42.5        2.5   1
-rrm                                                      -8.7        3.7   1
-fn3      Fibronectin type III domain                    -45.8        3.7   1
-fn3      Fibronectin type III domain                     -9.0        3.8   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
-fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
-rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
-pkinase    1/1     258   540 ..     1   294 []   266.6  3.3e-80
-pkinase    1/1     258   537 ..     1   289 [.   265.4  7.6e-80
-fn3        1/1     434   506 ..     1    84 []   -45.8      3.7
-
-Alignments of top-scoring domains:
-rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
-                   *->nGkelggrklrv<-*
-                      n++    ++l v   
-  pkinase_fu   169    NKQDPHQHRLSV    180  
-
-fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
-                CS    CCCC   
-                   *->GpeS<-*
-                      G eS   
-  pkinase_fu   197    GGES    200  
-
-rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
-                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
-                         +N++  +d+ e    + F+ +        +++           +
-  pkinase_fu   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  
-
-                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
-                     +  V++ +ee+ ++  ++++ +  l++   +    
-  pkinase_fu   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  
-
-pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYLHs
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
-  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  
-
-                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
-                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
-  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  
-
-                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
-                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
-  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  
-
-                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
-                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
-  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  
-
-                   LlkkcLnkDPskRpGsatakeilnhpwf<-*
-                   L++ c+   P++Rp   ++  i  h  +   
-  pkinase_fu   518 LMRLCWSGHPTDRP---SFASI--HRIL    540  
-
-pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYLHs
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
-  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  
-
-                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
-                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
-  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  
-
-                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
-                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
-  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  
-
-                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
-                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
-  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  
-
-                   LlkkcLnkDPskRpGsatakeil<-*
-                   L++ c+   P++Rp   ++  i+   
-  pkinase_fu   518 LMRLCWSGHPTDRP---SFASIH    537  
-
-fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7
-                CS    CCCCCEEEEEECCTTCCEEEEECCC        CCCCCCCEEEEE.E
-                   *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq
-                        a    ++++   + + ++W pp++   ++ +  +++  Y v + +
-  pkinase_fu   434    IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477  
-
-                CS CCCCCC  CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
-                   pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
-                   +  + + ++   +                    ++V+  +g+    S   
-  pkinase_fu   478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS    506  
-
-//
-
-Query sequence: pkinase_part
-Accession:      [none]
-Description:    Dario rerio
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          101.5    1.7e-30   1
-pkinase  Protein kinase domain                          -94.7    1.5e-05   1
-rrm                                                     -42.5        2.5   1
-rrm                                                      -8.7        3.7   1
-fn3      Fibronectin type III domain                     -9.0        3.8   1
-fn3      Fibronectin type III domain                    -52.2        5.9   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
-fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
-fn3        1/1     233   299 ..     1    84 []   -52.2      5.9
-rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
-pkinase    1/1     258   400 .]     1   116 [.   101.5  1.7e-30
-pkinase    1/1     258   400 .]     1   294 []   -94.7  1.5e-05
-
-Alignments of top-scoring domains:
-rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
-                   *->nGkelggrklrv<-*
-                      n++    ++l v   
-  pkinase_pa   169    NKQDPHQHRLSV    180  
-
-fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
-                CS    CCCC   
-                   *->GpeS<-*
-                      G eS   
-  pkinase_pa   197    GGES    200  
-
-fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9
-                CS    CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
-                   *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
-                      P +  ++l   ++  +s  ls + p  +  i++    +R + ++g  
-  pkinase_pa   233    PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267  
-
-                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
-                   neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
-                         g   ++   gL P  + ++  +    +  ++S   
-  pkinase_pa   268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS    299  
-
-rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
-                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
-                         +N++  +d+ e    + F+ +        +++           +
-  pkinase_pa   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  
-
-                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
-                     +  V++ +ee+ ++  ++++ +  l++   +    
-  pkinase_pa   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  
-
-pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   ng........................gplsekeakkialQilrGleYL<-
-                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL  
-  pkinase_pa   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL   400  
-
-                   *
-                    
-  pkinase_pa     -   -    
-
-pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05
-                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
-                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
-  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  
-
-                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
-                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
-  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  
-
-                   nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi
-                   +                                                 
-  pkinase_pa   353 RC------------------------------------------------ 354  
-
-                   aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL
-                        A++   s + +t++ ++     PE                     
-  pkinase_pa   355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377  
-
-                   yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee
-                                                    +P s             
-  pkinase_pa   378 --------------------------------YPPLS------------- 382  
-
-                   lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp
-                         +       + ++S+ +   +                        
-  pkinase_pa   383 -----CQ------EQLSISKQVAAGM-----------A------------ 398  
-
-                   wf<-*
-                   ++   
-  pkinase_pa   399 YL    400  
-
-//
-
-Query sequence: S13421
-Accession:      [none]
-Description:    S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum.
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                         -171.6       0.19   1
-rrm                                                     -32.5       0.26   1
-rrm                                                      -6.1       0.92   1
-fn3      Fibronectin type III domain                    -39.7        1.2   1
-pkinase  Protein kinase domain                           -9.2        1.8   1
-fn3      Fibronectin type III domain                     -7.5        1.9   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-fn3        1/1     143   224 ..     1    84 []   -39.7      1.2
-pkinase    1/1     233   241 ..     1     9 [.    -9.2      1.8
-rrm        1/1     440   456 ..     1    17 [.    -6.1     0.92
-rrm        1/1     669   731 ..     1    77 []   -32.5     0.26
-pkinase    1/1     906  1127 ..     1   294 []  -171.6     0.19
-fn3        1/1     923   934 ..     1    12 [.    -7.5      1.9
-
-Alignments of top-scoring domains:
-fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2
-                CS    C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
-                   *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
-                       + ++t+l++ dv    ++ sWs+ +g+ + tg  v  R + ng  +
-      S13421   143    IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185  
-
-                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                     +++ ++ + + l  L +    +  V  v ++ +G      
-      S13421   186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH    224  
-
-pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8
-                   *->yelleklGe<-*
-                        +l+klGe   
-      S13421   233    VSTLKKLGE    241  
-
-rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92
-                   *->lfVgNLppdvteedLkd<-*
-                      + ++ L++   + d+ d   
-      S13421   440    VIISFLNEGLRQADIVD    456  
-
-rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26
-                   *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG
-                        V  L+++d+    +   +  f  i   k++ D            +
-      S13421   669    --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699  
-
-                   faFVeFeseedAekAlealnGkelggr.klrv<-*
-                   + FV   ++ + e+ ++ l  k+++   +l++   
-      S13421   700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI    731  
-
-pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19
-                   *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes
-                      ++l         G++ ++ +  ++ ++ ++ + ++VAv +     ++
-      S13421   906    FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942  
-
-                   ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy
-                   + +            L+      ++  fe   + +  v++       +d 
-      S13421   943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980  
-
-                   lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde
-                   l +    +++ +s    ++   Q+                       lde
-      S13421   981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 
-
-                   ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l
-                   +  ++ +    LAr+l +++   + + +++++f+  +++      ++++l
-      S13421  1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 
-
-                   egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif
-                    +r  s ++  W++++ vi+ ++  g                        
-      S13421  1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 
-
-                   vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL
-                    l++ +++       dp   + +  k   l  + ++++ ++l+ L +k++
-      S13421  1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 
-
-                   nkDPskRpGsatakeilnhpwf<-*
-                   +k  +k p      +i     f   
-      S13421  1114 TKVFTKHP----DYQI----LF    1127 
-
-fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9
-                CS    CCCCCEEEEEEC   
-                   *->PsaPtnltvtdv<-*
-                        + t+l++++v   
-      S13421   923    INPITGLSAREV    934  
-
-//
-

--- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/hmmOutputTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-import unittest
-import sys
-import TestHmmOutputProcessing
-import Test_HmmOutput
-import TestHmmpfamOutputProcessing
-import TestHmmscanOutputProcessing
-
-
-def main():
-
-        hmmOutputTestSuite = unittest.TestSuite() 
-        hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmOutputProcessing.TestHmmOutputProcessing,'test'))
-        hmmOutputTestSuite.addTest(unittest.makeSuite(Test_HmmOutput.Test_HmmOutput,'test'))
-        hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmpfamOutputProcessing.TestHmmpfamOutputProcessing,'test'))
-        hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmscanOutputProcessing.TestHmmscanOutputProcessing,'test'))
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(hmmOutputTestSuite)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/ProfilesSearch.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-import subprocess
-import os
-import sys
-
-## Prepare profiles databank and create command to search profiles from a profiles databank in a nucleotides databank
-#
-class ProfilesSearch(object):
-
-    ## launch command to prepare profiles bank
-    #
-    # @param launch_1 string corresponding to pre command
-    # @param launch_2 string corresponding to post command
-    # @param config configParser object instance
-    # @param cDir string current directory
-    # @param verbose int (default = 0)
-    #
-    def prepareProfilesBank(self, launch_1, launch_2, config, cDir, verbose = 0):
-        bank = self._getBankBaseName(config)
-        prg = "hmmpress"
-        if verbose > 0:
-            print "prepare bank '%s'..." % ( bank ); sys.stdout.flush()
-        cmd = ""
-        cmd += prg + " -f "
-        cmd += "%s/%s " % ( cDir, bank )
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        if process.returncode != 0:
-            raise Exception("ERROR when launching '%s'" % cmd)
-    
-    ## create command to detect Hmm profiles in a nt sequence file
-    #
-    # @param inFileName string name of input file
-    # @param launch_1 string corresponding to pre command
-    # @param launch_2 string corresponding to post command
-    # @param cDir string current directory
-    # @param tmpDir string temporary directory
-    # @param config configParser object instance
-    # @return cmd string command to launch
-    #        
-    def detectHmmProfiles(self, inFileName, launch_1, launch_2, cDir, tmpDir, config):
-        bank = self._getBankBaseName(config)
-        evalueMax = config.get("detect_features","TE_HMMER_evalue")
-        
-        cmd = ""
-        
-        cmd += launch_1
-        cmd += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
-        cmd += " -i %s" % ( inFileName )
-        cmd += " -o %s_translated" % ( inFileName )
-        cmd += launch_2
-        
-        cmd += launch_1
-        cmd += "hmmscan "
-        cmd += " -o %s_tr.hmmScanOut" % ( inFileName )
-        cmd += " --domtblout %s_tr.hmmScanOutTab" % ( inFileName )
-        cmd += " --noali -E " + evalueMax
-        cmd += " --cpu 1 "        
-        cmd += "%s/%s" % ( cDir, bank ) + " " + "%s_translated" % ( inFileName )
-        cmd += launch_2
-        
-        cmd += "if os.path.exists( \"%s_translated\" ):\n" % ( inFileName )
-        cmd += "\tos.remove( \"%s_translated\" )\n" % ( inFileName )
-        
-        cmd += launch_1
-        cmd += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
-        cmd += " -i %s_tr.hmmScanOutTab" % ( inFileName )
-        cmd += " -o %s_profiles_%s.align" % ( inFileName, bank )
-        cmd += " -T %s" % ( inFileName )
-        cmd += " -p hmmscan"
-        cmd += " -c"
-        cmd += launch_2
-        
-        cmd += launch_1
-        cmd += os.environ["REPET_PATH"] + "/bin/matcher"
-        cmd += " -m %s_profiles_%s.align" % ( inFileName, bank )
-        cmd += " -j"
-        cmd += " -E 10"
-        cmd += " -L 0"
-        cmd += " -v 1"
-        cmd += launch_2
-        
-        cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( cDir, inFileName, bank )
-        cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inFileName, bank, cDir )
-        cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( cDir, inFileName, bank )
-        cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inFileName, bank, cDir )
-        cmd += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inFileName, bank )
-        cmd += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inFileName, bank )
-        cmd += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inFileName, bank )
-        cmd += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inFileName, bank )
-        cmd += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inFileName )
-        cmd += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inFileName )
-        
-        if tmpDir != cDir:
-            cmd += "if os.path.exists( \"%s\" ):\n" % ( bank )
-            cmd += "\tos.remove( \"%s\" )\n" % ( bank )
-            
-        return cmd
-    
-    def _getBankBaseName(self, config):
-        profilsHmmBank = config.get("detect_features", "TE_HMM_profiles")
-        bank = os.path.basename(profilsHmmBank)
-        return bank
-

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/Test_ProfilesSearch.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-import unittest
-import os
-import ConfigParser
-import shutil
-from commons.pyRepetUnit.hmmer.profilsSearchInTEClassifier.ProfilesSearch import ProfilesSearch
-
-class Test_ProfilesSearch(unittest.TestCase):
-
-
-    def setUp(self):
-        self._section = 'detect_features'
-        self._option1 = 'TE_HMM_profiles'
-        self._option2 = 'TE_HMMER_evalue'
-        self._config = ConfigParser.ConfigParser()
-        self._config.add_section(self._section)
-        self._config.set(self._section, self._option1, './datas/hmmbank_test')        
-        self._config.set(self._section, self._option2, '10')
-        self._iProfilesSearch = ProfilesSearch()
-        self._launch1 = 'First Command\n'
-        self._launch2 = '\nSecond Command\n'
-        self._cDir = '.'
-        self._profileBank = self._config.get(self._section, self._option1)
-        self._bank = os.path.basename(self._profileBank)
-        shutil.copy(self._profileBank, self._cDir + "/" + self._bank)
-
-    def tearDown(self):
-        os.remove(self._cDir + "/" + self._bank)
-
-    def test_prepareProfilesBank(self):
-        hmmpressLaunched = False
-        self._iProfilesSearch.prepareProfilesBank( self._launch1, self._launch2, self._config, self._cDir )
-        if ( os.path.exists(self._cDir + "/" + self._bank + ".h3m") \
-            and os.path.exists(self._cDir + "/" + self._bank + ".h3i") \
-            and os.path.exists(self._cDir + "/" + self._bank + ".h3f") \
-            and os.path.exists(self._cDir + "/" + self._bank + ".h3p")) :
-            hmmpressLaunched = True
-            os.remove(self._cDir + "/" + self._bank + ".h3m")
-            os.remove(self._cDir + "/" + self._bank + ".h3i")
-            os.remove(self._cDir + "/" + self._bank + ".h3f")
-            os.remove(self._cDir + "/" + self._bank + ".h3p")
-        self.assertTrue(hmmpressLaunched)
-
-    def test_detectHmmProfiles(self):
-        inputFileName = ' FileName'
-        dirTemp = 'Tempory directory'
-        eValueMax = self._config.get(self._section, self._option2)
-        
-        expCommand = self._launch1 
-        expCommand += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
-        expCommand += " -i %s" % ( inputFileName ) + " -o %s_translated" % ( inputFileName )
-        expCommand += self._launch2
-        
-        expCommand += self._launch1
-        expCommand += "hmmscan "
-        expCommand += " -o %s_tr.hmmScanOut" % ( inputFileName )
-        expCommand += " --domtblout %s_tr.hmmScanOutTab" % ( inputFileName )
-        expCommand += " --noali "
-        expCommand += "-E " + eValueMax
-        expCommand += " --cpu 1" 
-        expCommand += " " + self._cDir + "/" + self._bank + " " + "%s_translated" % ( inputFileName )
-        
-        expCommand += self._launch2
-        
-        expCommand += "if os.path.exists( \"%s_translated\" ):\n" % ( inputFileName )
-        expCommand += "\tos.remove( \"%s_translated\" )\n" % ( inputFileName )
-
-        expCommand += self._launch1
-        expCommand += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
-        expCommand += " -i %s_tr.hmmScanOutTab" % ( inputFileName )
-        expCommand += " -o %s_profiles_%s.align" % ( inputFileName, self._bank )
-        expCommand += " -T %s" % ( inputFileName )
-        expCommand += " -p hmmscan"
-        expCommand += " -c"
-        expCommand += self._launch2
-
-        expCommand += self._launch1
-        expCommand += os.environ["REPET_PATH"] + "/bin/matcher"
-        expCommand += " -m %s_profiles_%s.align" % ( inputFileName, self._bank )
-        expCommand += " -j"
-        expCommand += " -E 10"
-        expCommand += " -L 0"
-        expCommand += " -v 1"
-        expCommand += self._launch2
-
-        expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( self._cDir, inputFileName, self._bank )
-        expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inputFileName, self._bank, self._cDir )
-        expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( self._cDir, inputFileName, self._bank )
-        expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inputFileName, self._bank, self._cDir )
-        expCommand += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inputFileName, self._bank )
-        expCommand += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inputFileName, self._bank )
-        expCommand += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inputFileName, self._bank )
-        expCommand += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inputFileName, self._bank )
-        expCommand += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inputFileName )
-        expCommand += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inputFileName )
-
-        if dirTemp != dir:
-            expCommand += "if os.path.exists( \"%s\" ):\n" % ( self._bank )
-            expCommand += "\tos.remove( \"%s\" )\n" % ( self._bank )
-        
-        obsCommand = self._iProfilesSearch.detectHmmProfiles( inputFileName, self._launch1, self._launch2, self._cDir, dirTemp, self._config )
-        self.assertEquals(expCommand, obsCommand)
-        
-
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/ConsensusFile_test.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,141 +0,0 @@
->blumeria_Grouper_590_20:NoCat
-TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA
-AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT
-ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA
-ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA
-CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC
-TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC
-TCCATAATTTCAACACTNAAGAATATTTGTA
->blumeria_Grouper_4152_12:NoCat
-GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA
-AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC
-GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC
-GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC
-TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT
-TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT
-GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG
-CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC
-ATATCTACCTCGGGGACATTG
->blumeria_Grouper_28830_3
-TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC
-CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC
-TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA
-GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC
-AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT
-CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG
-CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG
-TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA
-TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT
-CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT
-TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG
-CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT
-TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG
-AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC
-GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT
-ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT
-GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG
-AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC
-GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG
-CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA
-CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT
-GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC
-AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG
-CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT
-AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT
-TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT
-ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG
-CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT
-TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG
-AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA
-CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG
-GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG
-TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC
-CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG
-GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT
-GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT
-TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT
-TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT
-GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT
-CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG
-TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT
-AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT
-ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC
-CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT
-GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA
-AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG
-TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT
-AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC
-CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC
-CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC
-CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT
-GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC
-GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG
-TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA
-AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT
-TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT
-GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA
-ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG
-CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG
-TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT
-AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC
-TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC
-CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC
-GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT
-CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG
-GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT
-GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT
-ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC
-AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT
-TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG
-CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG
-CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG
-TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA
-TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT
-GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA
-ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC
-CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA
-GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA
-TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT
-ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG
-CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG
-AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT
-CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA
-GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA
-CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC
-GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT
-TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT
-TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT
-GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA
-AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG
-CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA
-CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG
-TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG
-ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA
-TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC
-ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA
->blumeria_Grouper_14770_3
-GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA
-AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG
-CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT
-TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC
-TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT
-CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA
-TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA
-ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT
-CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG
-CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG
-TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA
-CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT
-CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT
-TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA
-TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT
-G
->blumeria_Grouper_1717_12
-ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC
-TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG
-GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC
-GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT
-TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA
-CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC
-GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA
-AGGG

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_aa.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
->GYPSY11_AG1p:classI:LTR_retrotransposon
-AATTTNVFKKVPYTCNFYGRSCINMQKLLEKIEILDRTYDQVRQLNKCYRLCALTTLRNN
-TKELYDEIQELLRKHESSIKDEILTTLVKKSRHLYYEINKCIKIHFERHPDSLNTTLSEN
-QFDITIETKSDKMADIIELIKITTSLISKYDGNEKDLKGVVSNLNVLKKIVKPENRETII
-ELVLGRLTGKARIVVGEAPKSIEDIVNKLQDRCSIKVTPEIVVSKMDNTKQTGTIEDFGS
-IIEKLTQQLEEAYIAEEITPEVARKKATKSGISALSYGLKDGETKIIMRSSKFETLHEAI
-EQAVKLELEDRTKKGKNEQTKILYSNATRNNRGYGNNYQGRNNYNRFTNNNNNRYQTQNP
-PRFPPARYGHNNNRNNNNYRNNNFNNTRNQHANRQNNSNRNQYVQSNQRNNSNLQNNRAP
-IHNTVTAEEQNNFLGQPQASENTQY
->GYPSY10_AG2p:classI:LTR_retrotransposon
-AIRQPKFFRATRATKSSALHSGGDPEPTGGPALHKPIRATYTINVQKSNFIKTRLGLADS
-ICNLFVDSGSDISIIKGNKVRPTQTYKPKDIVDIISVGEGTITTHGSTITDVIVEGKKIQ
-QLFHIVPDNFKIPADGILGRDFFMDHRCIINYDTWIFSVKHDGEFLETPIEDTINDKTLI
-PPRCEVIRKLDKLKELDTDAVVCAEQLQEDVLVGNCIVNKNYPFIKIINTSNKAKLVNIS
-HIKTIPLNEFEIVKTNNHKNENRLAIIKELIRKENISEDTDTSFEQLLLSYNDIFHLPND
-HLTTNNFYKQDIKLEDKRPVYIPNYKQNHSQGPEIKKQIEKMLQDDVIEHSVSHYNSPIL
-LVPKKSSDEKKWRLVVDFRQLNKKLLPDKFPLPRIDSILDQLGRAKFFSTLDLMSGFHQI
-PLEESSKKYTAFSSTDGHYQFKRLPFGLNISPNSFQRMMTIAMTGLTPECAFVYVDDIVV
-VGASENHHLKNLEKVFDRLRHYNLKLNPEKSCFFKKEVTYLGHKITDKGILPDDSKYDSI
-KNYPIPQNADDVRRYVAFCNYYRKFIPNFALKAKPLNSLLKKNTKFEWTQECQEAFEYLK
-NTLISPQVLQYPDFSKPFILTTDASTMACGAVLAQEHGGKDMPICFASRTFTKGEANKAI
-IEKELAAIHWAIMHFKHYLYGKKFTVKTDHRPIVYLFGMKNPSSKLTRMRLDLEEFDFTV
-EFVKGKQNVVADALSRIKITSDEIKSINVITKSMSKPVTSDNVLGNTSESDQLKMFHALA
-YDEVKDLPKLESSVKKNEDTIELIGKILNKRKSKELLSVRDIHLKTDIGLQEPLLVKDFQ
-RRKEKSAIVQFIKNIEKKLVMKSITQLAISETDEIFKEVHPNELKQIANNHLKNIQILIY
-TKPQKITNEKTINDILDKVHNTPTGGHIGQYKMYKKIRREYSWNKMKKTIKEFLDKCLTC
-KLNKHQTKTAEPFVKTDTPNTPFEAVSIDTVGPFQKTNNNNRYAVTIQCNLTKHVTVIAI
-PNKEANTVARAVIEKIMLIYGTNIKKFRTDMGTEYKNEIFKNISEILKIEHKFSTPYHPQ
-TIGALERNHRCLNEYLRIFTNEHKDDWDDWINYYSFAYNTTPNLDHGYTPFELVFGRNER
-ITPNVKDTYSPLYNYDDYSKEFKYRLKIAHNRTRKHIEQVKFKLLKEQQNINQVNFEIGD
-QIALTNENRTKLDPVYKGPYKVKEINGPNMIIENTEGVVQKIHKNRAIKL
->ORF1p_TCN4#2:classI:LTR_retrotransposon
-ALLSHQKIFFDTITPIEDQSKPRLRQDTPFPEMTTPPTDKESLQRKIKQIEDERKREREE
-HKREMAELQAQMRGLLKREAEKRDLPPHNPATSSLPAKSESPHPPIMYDSLPQPKYSFPV
-LSEHADAAAIHQHISKLRSIFTLMAAGYRYEPTAFEARKLAHAAQSLTGIRHLQFLEGDG
-LQCRTFDDWAKAFKSAMLPLGWVSETEKKIYSLQPQLLRLDKIPLAIMDFKQWFALLKDS
-DSPMSEDVATHWLRNHMTPGLLAELERDFGGENQLRQASLAELLKHMEICATRLLRYQSA
-FAPIAPTRTPIAAVSPEASSPIDIAQWLNPRLPLPKGGAGRRARAHLASEQRCFLCRQPG
-HKSPDCPKRKEPTAIAAVSTFDHEEAEFEQEEGEMFAEVLATHLAPELSVPPILLECRIG
-TNGSPFLALFDTGATVTLVDPSLITTHQLQTYPSEQRRVVSLAGGARGPALQRRVGVEVC
-IQNQVFALHGYVMPLHARYKVILGLDFIRSHGLLSGASRLGNLAPDLLGPVVASVTTADG
-YXDLRLAILHEYHDIFPDNIGEVANYPPICDANSKVRHHINLTPGAIPFKSASYRSPHMW
-RQQLIEEIQKHREAGRLRPSSSPWAAPAFLVKKENGKFRFICDYRGLNKVTTPDSTPVPN
-VDDILHRAACGKIFAKIDLSDAFFQTLMHEPDIEKTAITTELGLFEWVVMPQGACNSPAT
-QQRRLNEALRGLLGDSCEAYVDDIIVWAADAEDLDKRLRAVLAALRKSGLVCSPTKSEFF
-RHKVKFLGHVISANHIGPDPAKLRTIASWPLPQSVKELRSFLGLLQYLRKFIPSLATHTR
-TLTALLPPTPAAEKAWEKQQRALRKGQSPKDVLSWVWAWSSEATAAFEILKAKVAEISGL
-RPLDYAAALSGECPIYLFTDASNHGTGAWLGQGPDPDHAFPVAYDSRSLSAAERNYPTHE
-KELLAIVRALKLWRPLLLDVPIQVQTDHFTLKWFLQQRDLSERQKRWLGXLSRFDLRIDH
-ISGVNNFIADALSRLGGVDDEQDGMETAEVSVAVLGLLGQDTSTITKVAQGYAQDQVMGA
-WLQEEDRAPGVTLENVENGQGRSTSGVAMGRQAMCARYQX
->Neptune2_Ap_1p:classI:LINE
-ANTRPVVDSENIDKYRNTAKKIGKYRNTASKVDEIPKLQKRGIRRNLLKDFDLFARRMRL
-KDIFSRERNKQHPFHVKSTWEPPVQQSVALETFLEEVEFELANSPSKRPKDNLSPGERRA
-LHNLLGDKTIIVKKADKGTTTVIMSREQKIKEGQILLNDLDNYRPLEKQMADETVEKIKQ
-LTTSMLTESHIDEMTVKWLSQTPNPPRIPEFYTLTKIHRPTLVGRPIISGCDGPTERISC
-FVDRLIQPIAQQQESYLKDSKDFINFIENTKLPKNTILASKDVTSLYTNIPQEEGITTVC
-KAYEDFYKNRLPIPTNFLRRMLCLILKENSFQFNKRHYLQTHGTAMGTKMAVAFANIFMA
-KIEKGIISKSIIKPLVWKRYIDDVFCLWDTNEDNIKEFVTRANHYHDNIKFTAEISDSEI
-AFLGHKSVQRREIQQRLPPSMCKRIINKQRPFNTRNFYSCHPPGVKKGFIKGEALHLLRT
-NSSHSTFNKNMQSFKTRLKNRGYPNEFLEKKGPX
->ERV45_MD_I_2p:classI:LTR_retrotransposon
-ASSKHATGKLQTGPGPGPSKQWGNNCGAQSEKPIPSPTIRSLHRATPGSAGLDLCAASGL
-ILTPDSPPALIPTGVKGPLPEGTMGLIIGRSSVSLRGIVVTPGVIDSDFTGELQIIVQPP
-XKTVTIMKGQRIAQLLILPYVQTXNPILKTSRGQGGFGSSNWAFWVQEIKNSRPMKILNI
-SGKNIEGLLDTGADTSCIAGKHWPPTWPTKISPSNLIGIGKITNAAQSSQILTWSDGNLS
-GQFCPHVVPSLPVTIWGRDILSQMKVSLVTPEEDAQTPPNDEPLDFPEGPSPR

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_nt.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,501 +0,0 @@
->Polinton-1_DY:classII:Polinton
-aaaaaaaaaacaagttgggtgtcattggaaaggatttttcaagccctttccaatggtatg
-cttttcacgattctgaaattaaaaatacgacttttcataaaaactctcaaaattacaatt
-gcacttcttcgcgcacaagcaatcttggaagggggtgtacctgcgcgcacaagcagtcat
-aaggatgatcgcaagggtgggggtgagatttctgttcaaggctatgcaccttactgtgtc
-ctcaattttctgggaaggtaactggtggttggattattagttgagaaatatttagaaata
-tcaaacaaactggttatagggtcgtgtatacgtatatataaaaaatcatataatcataaa
-accgttaaaaaaccgtcgttcccgtatattccagctactttcagctaaaagctatggagc
-cgttgagaagaaaatctaaacaatctgaagtcatagcgactttcagcttaaggctaccca
-cgttttaaatgtatgccttgcaaaatgttacttataaagtaacaatgactagtagtcacc
-aataatttcatgatccctgactgcggtcatccgaaataattccctacagagatatgtatt
-tcagattatctgtgatctgtctccattttcattatgctaggagaccccataaaatcaaat
-atttatgactctttgaacctattatcgagaaagtcaagcggctatttacctgcatccaaa
-cccatagctcgccctccttttctgacttccccattgcagtctgtgcagtctgcagtctgt
-gaaggctccttaaatcgagaaccaatcaggtggattctaagagtagacaccccctgtaga
-tgtcaaactctctaatcctcgtgtataaaaatggatccccttaaattgctcaggatcagt
-tcttataatacctcagcactgcattcttataatataatttcggtcgaacttgctcgggat
-atcacgtctaaccgttttaattgtttgtgtggactcaaaccatttactgtgaaaaatttt
-aaaaacgaattaaaatatataaataaaatatatttataaaaaattcaaaatggaatcatc
-agtggcttgtgatttgtgcaaccaatgcatcgaaattagtgagtttgtctctcattacgc
-gaagtgctcagaacccagtaaagcctgcgaggctttaatgttaaactctaacattagatg
-tgacttatgctctaatctagtaaaaaattgtgaatttgatgatcactaccaacgctgtga
-aggaccccgaaatgcatttagcattttaatgggtagaggaaaactggatgaagaagaccg
-ccctatgacatcagctaagtctataaaacgattgaggatggaagaggataaggaaatatc
-taaccccccaaaaagaaaacaaattgacttaagaagggaactcttatgtcctactcagag
-aacgtcaacatattttgaccgatatacataaaaatgcgtcggccagagaagttaagaaca
-atgcgaatatcatattgcttacatcagagacgacatttccagtaaaatcatatcgaattg
-atagtccattatttaaaagagtatataagtgtatatggtacatatataaagcaaacagat
-gaaggagttacagtggaaacaatgaagcactttaaaactgcctacaaatctgtatacata
-aatgaagacattattgatgagctaaattcggccatagattgcttacttacattaagcagc
-gaatttcaagaaaaagactcaggctgggctattaaaaattttaactattttgaaactact
-ataataaaactggaaaacattcctgccagcggatacattaaagctcctcaaaaaataaga
-gcccgtaatgcgctaataaacgtgcagaatgccgacgtattttgtttcaagtggtgtata
-ctagcatttatagctaatcaaaaccatgaaaataggacttttacaaccccccagcaaagg
-aaatattcgagagaaaggatgacaaagcctcaaagctataacattaatattaatgatgaa
-actattgtgtatggcggaatgactttagatttttcgggaattaaatttccaatcgaaaaa
-ataggagttcgacattttgagaaaaacaatgtcaactttagcataaatatttatgaaatt
-gatgaagcaggtgaaaaaattgttggtcccacgattaaaacaaaagaaagaaaacggaac
-cacattaatatattgggaatcgataatattacccaaaacattatgcattatgcgtatata
-acaaatctttatacattatgctcttcacaattttctaaaggaaaatcgggaggatatttt
-tgtgagaactgtcttcagtgttatcacgtgaaaagcactactcacaacaaactggaatgc
-ggaaaagtgtcctcattttatccggaccctaatacgacaacatcgtttaaaggatatcac
-aaaaaattatctcctccagtggtaatttatgcagacattgaggctgttcttgaaaattac
-aaaacatgcttgaattcttctgcttcctcgtcaaccacgcaagtacaaaagcatacggca
-tgtgcagtatctttttatgttgcccataaagattatcctaatcttaacgagctgtggacc
-tacgaaggtaaacagaacaacatttttataaaattatatttaacttacatatttaaattt
-tataattttataggcgttgattgcatacaaacattttgtaaaactcttaaagaaaaaact
-ttaagcctgtattacaaatattgggttaactccaagaaaccgagggatgacactttcgat
-gaacagcttcaaaagggaaattgttgcgcctgcgagaaagaaataaatgcgagcgacctg
-gacaaattctttgatcaattttctggagaatacgtaggtcctatccatagaaattgtaag
-cctaagtttagattaagtgaccctttctttcctgtagtgttccataatttatctaaatat
-gatattcatttatttattactgaattagagggggacttaagtcccataccttgcaataaa
-gagctctatatagcacttacgcaaactataaaaatcaatgctacaagcagatacaaaata
-agatacatagattcagtccgatttttaaattcaagtttagataaactatcaagctatatg
-gaagataaagattttaaaattctaagtacgaaatttcagggagaaaaatttaagcaaatg
-aggaggaagggggtgtttccctatgactacttagatagttttgaaaagtttaatgatacc
-caacttccaagcattgatagtttttataattctcttagtgaagaaaattgtagtatagat
-aactttaatttcgcacagaaagtctgggagacatttaactgtcgaactattaaagactat
-ttaaaactatatttagaaagcgatgttttaattttagcagatgtgtttgaaaattttagg
-aaaatttgcaaaaaaatttataagttagatcccattaattatgttactgcgccatcaata
-tcatgggatgctatgcttaagttcactaatgtaaatttagaactaataagtgatggtgat
-atgtataattttttaaaaagagcaattcggggagggttgactcaatgcactcagcgcatt
-tctatagcaaataataaatacttaaaaaacttcgatccaaaaaaaccgaacaatttttta
-agttatattgatgccaataatttatatgggtgggctatgagtcaacccttaccactatca
-gggtttcagtttttggataaagaagaagttgattcattcgactataaaaatatagcatgt
-gatggtagtatagggtatatgctagaagttgatctggagtatcctgccgataagcatgat
-ttacataattatttaccattctgtcctgaaaataaaattccacccgggggcaagcaaaga
-aagcttatagctgatttaactaataaaagtgaatacataattcacttaaaacagcttcaa
-ctttgtttagagcatggtcttattgtaagaaaggtacaccgagttttgtcctttacgcaa
-tcatgctggctgaagccttatatcgacctaaacacacagcagagaaaattggctgaaaat
-gattttgaaaaaaatttttttaagctaatgaataatgctgtttacggaaaaacaatggag
-aatgtagcaaagcgtcgtcaagtagctttagttaaacattatcaatcgaaacaaaattct
-ccaggttttagacagcgcatagctagaaatgattttcatagcgtagaaatatttggttca
-gacttagcagcaattgagtcaacaccgtccaaaattatgtatgataaacccatatatata
-ggagtaacggttttagaactctcaaaatggctaatgtatgaattttattatgacttcctt
-ttaattaaaagtccatctacgaaaataatatatatggatacagattcatttatactatct
-tcagaagaagatttttatcaaactataaaagacaacccacaacgctttgatacttctaac
-tataagcaagaaaaccaatttaatataatacaggctaataataaagaaccaggaaaaatg
-aaagatgaacatgccggtaaggttatgacctcttttgcgggacttaaggctaaggcatac
-tcttgtttagttgatggagaaggaaatgaccccgaatgcataaaaaaaattaaaggtgta
-aaaaaatctgttattaagaggctgaatcatgtagattatattgaatgtattaagtataaa
-aagacattttatggctcacagagagtaattcgtagtaggtctcacattctttataccgaa
-attgtaaataaaattagtcttaactataaggatgataagagatatatttcaccagataat
-tgtaacactttagcccacggtcattataatatagataatataattagcagtaactttact
-aatactcaataacaaaaaattattgtatacccttgtaaattacaaaacaatacagaaatg
-taaataaacaaaaaccaaattgaatttgaaattattttattgtgtttgattacttaagca
-tatcatttacagatatccatgagttgtggctggagtcgaaaccgctccactttacaagca
-cctggttcttttttcttttaattattttctctattagaaacgcatttttatcttttactt
-tctgaagttcctcttcataaaacgaaccttgaatagggttactcatataatcttctattt
-catacgttacaggccttgttgacttaacttttaaaactttaaaaacttctgtagtccaat
-taggttcatatcccttcataaatactcccttgtatttacttattctaacgaaatccccta
-ctgaaaatttatgttttgggaatatttttggtatattatatactgattttaaaatgaact
-cttcatttttgacacccacatccacaggcttcattttaatagttcgatgataagaattat
-tgtattgatctacaagaaatttgattttatgaatccatttatagtcacctttcatactga
-acattttccacatacgattttttagagttcgattgaagcgttcacatatagaagccttta
-ggtgtgtataagtatggtaatgatttatatgaaattttgtcattaattccctaaaagcgg
-aattaaaaaactcttttccttgatctgactgaatgttcttaggtctacatttactagttc
-taaaaacagtttccattgcctgtactacatctggggcagactttgtcttaaccgcttcgg
-cgaacgcatactttgaaaacgtgtcaataacggttagtaaatatttatatcccttatttt
-ctttactaaatggaatcatttcaaccaaatcaatttgccatgtatcatttattccttttt
-gaacgaattttcggcgtttaaaatttttccgagcaggcttatgaatttcattaacaactt
-gttgtttgctcatgatcaggatttgatttctttgagttactttttattataagacgttgc
-ttgattagataatagtgattgcttatatactagtacatcccgttttatttcaacacgcat
-ctttttagaaatttcaaaacataatcgagttaaatctatttgtacatctttatcatagga
-accctccaaatcagacagttgaatatctaacttttgtaaggatgcacacttaggaattat
-atgtttgtgataaagataaataacttgttgtcgtaatatggaattccagcacaaaaatgt
-ggtaaaaaagatacccaatcttaataaagatctccaggactcacaatcgaactcaatttt
-gttaccatattgattaattactcaataatagtatctggcatcaggaagtcatactggtca
-agcttcagctgtatacgagtatattccttatatgtgagcacttgcatccattcgtcttta
-tcaaatccaatgtaattgtttttactttgctgcatccaaatcatgaccgaaaaattacga
-gaagttgacagaccacatttcaactttaggttatgaccaacataatattcgaaaccaaaa
-atgacttcatgattctgggtctttcgagaagatttcattctttttacttatgcacgtatc
-cattggcttagagtgctttattcaaactaaaagtatattctgatcttggcggtatataaa
-ggaggaaaactcaccctcagttgattaaaaagtcaaccaatcatcatgaacactgtagat
-cgaaattcaagcattatagtactttcaatatttactgggaaacaacaaacaagtttttgt
-aaaagagttagcgtttatgccggccggaactgtcatacctaatttctttcattttaaacc
-accatttaacattaaggaattggataatgaaactcttaagcaactacattttaatcatca
-gaaaattaacggattggactggtcagctggagatattccgtatacatgtcttgaagaaat
-actttcaccgctaaacaaataccgtacagttatcgttcgtggtgaaattaagaaaatctt
-tttaagcaagtatttaacagcaaacataattgatatagatattggaaaaagtttaactca
-gctacccaatttttttaccaattgtagaatacataagaaaaaacttccacttcgctgttc
-attaaataatttgtttaagttatttgtattcctagaaaactcgaattatgaaatatacag
-taatggtgacacatatgtctaaacttaaataaaaaataatttgtaaaccatttagatcgt
-ctactatggattccgttaaaaagttgtttggtaataatcctgagaaaaaaggatactctc
-gacttatatattgtaattattgcggatctgatacgcatttcgagaagaactgcgccaaga
-aacgcgaccaggaaaatcataaaaaagcatagtatatttcataacaaatatacaataaat
-aacggaaaaatatacattttatagtttatcttgtataaaataaatcagtgaatatacatt
-taaaatgtttcgacaatttatacatccttacacaatgttaatttgcggaccttcaggatc
-gggaaaaacaacatttctagaaaatctgataaacaagaagaatgatctttttaatgtttc
-aattgatcgaattatttggtgttatggggaggagagtgctaagccaaattttaataacat
-tgaatactttaaaggagttcctgaaaccatcgaaaatgaaactaatgagcctattctctt
-gatattggacgatttgatgatgggagcctttaacaaaaatgtatgtgaactctttactaa
-aggttcccaccaccgaaatttatctgttattgttgttactcaaaatatatttcacaaatc
-atcgcataccagagatatttcacttaacactaaatatataattgcatttaaaaatcctcg
-tgacaaactgcaatttcaatgcctggcaagacaaatttatccggaaaaccccatggagtt
-atttagaatatataaagaagtaacagaacaaccacacgggtatttacttattgatcttac
-tcagggaataaacgatctcttgagatttagatcagacatttttaattcggaatatacagt
-gtgctattctgacgaatatggtttacaaaaagagcctaaatcgcttgaaagcgaacaaac
-atatattgtatgttctcaaaagggccaacaacaaactacggaaggcaattataagcaatg
-gtgataatgagctggtaaaaacaatagtagaaatagttttaaatacattacgaggaaatc
-agacagtcaataaagcgcatctaagtgctttaaaaaagtataaaaatgcattgcgatata
-tttcatgtccaaagcgtacattaaactctaagagaaaagtcctaattcaaaaaggtggtt
-ttttaccaattctaattagttcgttgctttcaggaatttttggaaaaattttaaaaaatg
-atcaaaaataagcataatttaaataaagtaattttaatgaacccgaataccttacaaaaa
-ttacttaataatgatcgagggaatgaattaataattacaaaatttttaccaattttaaat
-aataacaaaataagtgattttgataaatggattaagattcgtcaagaactaagtttctat
-caaaataaaaaacgtagtaaatcatggaatacttcaaatgaacaaaaatcatacttaaat
-tcaacgagaacagctgaatctcaaacaatagaatcgattgatataagtcctaacacttca
-aaattaaattcaaagttttcaccgaacatgtcggagctctcggatttacctcaaaaaact
-gatgaagaagattttaaatcaaaagaaactgctaagttattgaatgttaaaaaaaaggta
-aaatccggtattttactttcaagaaacgaagagattcctgacttacctccagaaagtgat
-gatgaaattccaaataaaattatcaataaacgaaagataagcaacacttcgttttcagat
-gataaagaagatataaaaaaacaagcagtagtaagagtaaagcttactgaaaaacaacgc
-aggttaagagaaaagttaaataaaattaaagcaacggaaacattaccatatcaaaattta
-aattatataacaggtcgtgaaaaattgcgaagatcaactagaaaaaatttagtgcaaata
-gggaaaaacaaacttaattggatatcttaccaatagcagaaatttaaatataaaaatgaa
-ttatgtaaatgatttctttattacattgctcagtaatgactcattgaatgtatttcctga
-taatgtaaagtgtgcatttacaaacattgtaaatatccccgaagacatgaatgatgactg
-ggaagtaggcattacagatatgtatctgaataattatattagcaaaacaactgcaaaaga
-aacaaatttatctgaagaagcagagtttgtgagtttagtaaatgctgaaacatttagata
-taaaaacgtcgctgtcgaatcgaaaatatctgaatgtggattgatttttatttacactga
-cataattaaacccaggtctgttggtagtatgagaccccgatgtcttcgtgtaatgcatta
-taacggaaaagaaaaaaatattcattttaaaaatattgaatattatcctttggatatatg
-gtctccaaatgaaatctcaatattaattactgattcaagtggatataaagtacctttcga
-gacttccgcagtgccgatttttgttactcttcactttagaaaaaggagaaggtcaaatct
-ataaataatacatacccaaataatgcttacttagaacactaatagtcatcatggtgaaat
-cttatcaggattattatgtaaatcagtgtggagcaggtttgtccaatataggaaccctat
-atgtaaccccgcgaattattcaacaaggtcgaggaatcggaaacttttttagtggacttt
-ttaattacataaaaccacttttcatttcgggtttaaatgctataaaaaatcaagctgcag
-agactggaaaagctgtaattaatgaatttggtagaaagccattaagaaatattattcaag
-aacagagtaaaattgctttacaaaacctatcaaataaagcaataaataaaatgacacggt
-ttcaaaatggcagtggaaaaagaaataaaaagcgaggtggtagaaaaaaacgaaatcatt
-taacatctaaacgacaacgtaaacatacccaaccgtctcataaaaraaaaaaatcatcaa
-ggaaattaaatattacggatattttttctaacacaaaatgagtaaccatatagaatgtat
-gaaaggcgaattggatttgtttgcaccacaccctacgcaaagttcaattctacgaaccga
-agaggtttcttataatccaattgcatccttggatggtgcctcctcaatcgaatttgtttg
-tttaggaaatggtgaaacatatcgagatctatcaagtgtttatttacgacttgtggtgca
-attgaaaaaaaatgataacagcgtcattgaaggaaatgctgtcggtgtagtaaacaatat
-cttacattcaatatttagaagttcatcagtatatttaaataacatattagtttcgcagag
-tgataataattatcattatagagcatatctgcaaacagttttaaactatgggagtgacgc
-ctcggaaagccacttggcctcgcaaggttattttccaaatttcggacgattaacatcagg
-aaaatacgtttatccgagctctaatgaaactctgaaaaatatatttcaaaatagtaataa
-ggtagaactatttggaaaaattcatggtgatatatttaatcaaacgaaacttcttgtcaa
-taatgttgacttaagaattaattttaatattgaaaaaactgcattttatttaatggaaaa
-ggatagcgaatcaaatttaaagatattagaagcacaacttttcatgaatcatgtaactgt
-gaacccaagcattttattggctcatcatcatgttttacaaacaaaaaatgctctttaccc
-attcagtaaagtagaagtaaaatcgtttacaatttacccaggaaacaatacgctatcaat
-agacaatgctgtaattggacaattaccaaattttctagctttttgtatgattaaaaaccg
-ttcatactcaggcaacagaggactagatccatttaattttgaacattttaaaatgcaacg
-ctttaatctaatggtgaatggagttcaagttccttcgcaagctctggaatttgactactc
-gaactctgaaaacgttcaaagctcaagaggctataatatgctattcagatcaagcggaat
-aaaacattatgatcggggtcttcaaattaccaaggaaatgtttgatacgaacagttttat
-attagcctttgatttaactgctgatcagtcaaataccaccatatgttcaaatttgatgtc
-gcaaggcacaataagaatcgaaggaagattttcagaacctcttagtgaagccgttacttg
-tctggtatattgtgaatacgattccatgattgatattgataagcatagaaatattcgaac
-ccttttttaaaatgaatactttacaaattcacaatttgcttacaaaacatatatacacaa
-aatcaatttttaaaggagttttcccttcagaccagcttccaaaaactatttcaaagtatc
-cggctttaattattgcaaacaccgacacttcagatcaaccaggaactcattggattgcat
-tctatttcgaaagtcgcaaatcagcagaattttttgattcctatggacaatttccccaaa
-acaaggaattcgtgacatttttaaaatctaacgcaaataaatattgctataacaagcaac
-aactacaaggatatttttctaatacgtgtggtcattattgcataatgtatggtcttttta
-aatgtaaaaagaaaacgctaaaatatttattaacaaattttaagagaaatgacttttcat
-ataacgataaattaatacttaaaatgtttaagtctaattttaaaaaataaaatgcaagat
-atttaagaaaatcaatgtagtttatttattaagtcgtttgtttagcttataatattttaa
-cataatattgaaggcctcgtctcttaaaattggaagcctatgacactggcacgtatcggg
-tccttccgaagcgtcatcatcactccagggacaaagcttgtagtggaatccatatttaga
-atggatcagttctttatcctctaagtcctccagagtgctcttcaaatatataagctgcgt
-tacgtgctcctcaaatatcatgtcttcgaactgcatcaagaagagctcaatttgtttgga
-gtccattttcgttatggttcttttaaggttttttaaagactgatgttggatttagaaaac
-tcaaacctttatattggaaaatttcatttacttatttatttactgataaaaattcaattc
-gtgcagaactatatctatttacatccttccccttatataccatatgggtaataccattct
-catttaatttcctaaaaggtgtcttagtacagaatttgtttacataactcttaggtagaa
-aaatccaaacatctttttcgtccttgtctgctaaataaagagctaccttagttccataag
-gtgtctttttcagcttacaaccagtgatcttatactcaaatccaatacatagatcttcag
-tttttgtataaccaatcacaggcttcgattcattcagagtctctaggaaatcctagaaat
-tcaataaaatttgaacaggatttatttattaatgtcctatatgcataccatttctgacca
-acgtgagatttgattcgttatgctcttgtaactattcgtattatactaatgcatttactt
-acaattacgagacttttatactgttcagcactacatatatatatatatatatatatatta
-caagaacaaaatactacgtgaaagagataccaatatatctgttatgctctttatatacat
-aaactcagttaagcctatgtagaatatttttatatacttgagtatatctatctcattttg
-tataaatatataacttcatatgaaataaaaggttactacaaacctaatataagacagcac
-ttttctcgaaaactcagattcaatttttactctcagaatgacaaagttgtattgtgagtt
-gtgttcggaaacaaaatcgtttgcttcacgcagcggtttaaaaaaacataccttaaaagt
-gcataacttcagctatcaaaaatcaaaatcttcttattattgttgctttttctgtcccaa
-tgaacgaaaattctggttgcgatataattacaatgttcatctcttgctgatgcacgatgc
-agaattaaagagtatgcgtaaatcaatggaaagttatcaaataaagataaaacaagtttg
-agaatttaattttgtaaaatagttttatttaataaatttctgtataatatagacaaatta
-aaaacctagatcaaataaaacgtctagtaatgaatggtcatcttcatccttcattattcg
-taaataaatgttgggttgacttggctcgatgaactgatcaaaaatatgatcatcatcagg
-aaactcatagattataggatctgtgtgcagtatatccatatcgaaatgctgtgcacattg
-catttcttgatcgtctccattgcctcgtataagatcatttaaaacgtcctgcgttgccgc
-tccaaaaggaaaatcgctccactcaagagacgcaaattcacttccaatttttgtagtggg
-ggtagatgacatagaagggtcaaatactcctcttaagaagcgatctatcgaatcctctgt
-gtcgatagcctccacataaccttccttcgagccttcaattatttcgacatcagagtcttg
-agttaatggaacatttattccatttactgagtcaacaaactctacagtaagatccattgg
-tatgcagtgctgaggtattataagaactgatcctgagcaatttaaggggatccattttta
-tacacgaggattagagagtttgacatctacagggggtgtctactcttagaatccacctga
-ttggttctcgatttaaggagccttcacagactgcagactgcacagactgcaatggggaag
-tcagaaaaggagggcgagctatgggtttggatgcaggtaaatagccgcttgactttctcg
-ataataggttcaaagagtcataaatatttgattttatggggtctcctagcataatgaaaa
-tggagacagatcacagataatctgaaatacatatctctgtagggaattatttcggatgac
-cgcagtcagggatcatgaaattattggtgactactagtcattgttactttataagtaaca
-ttttgcaaggcatacatttaaaacgtgggtagccttaagctgaaagtcgctatgacttca
-gattgtttagattttcttctcaacggctccatagcttttagctgaaagtagctggaatat
-acgggaacgacggttttttaacggttttatgattatatgattttttatatatacgtatac
-acgaccctataaccagtttgtttgatatttctaaatatttctcaactaataatccaacca
-ccagttaccttcccagaaaattgaggacacagtaaggtgcatagccttgaacagaaatct
-cacccccacccttgcgatcatc
->INV2j_DB:classII:TIR
-aaaaaaaaatacctactaattgtagggccctcaaaatgattccaaacttcagtgattttt
-aattaatgacattcgcggtaagaaaaaatggaaacgataacttttcgaacgcaaattgag
-aagaacgcaaaatgagccatacgagcaagttagcaaaaatgatctagtcaacctaactga
-gcaagtgagccaaaatgagcaagtgagccatatcactaaccatacaacacatagactgga
-caactagaacaaacttttttcacgaagcagattatgatttcccgtcctagtcatcttcgt
-atttgctcggctctttaatttactgttcgggcagcgactcgcggacaaatttcaattttt
-gtgagctgctggcttgtgcctgtgtagacacacatacgtacatacatatatatatatgag
-aggcatagagagagtgagtgagtaaagaaagaatagcacacagcggacttcatatgagaa
-taaaatcatttcgttcgagcgctggcagcgaactgaatatcaactgctgtattttcgctg
-tccgaacagtaaattaaagatccgagcaaatacgaagatgactaggacgagaaatcataa
-tctgcttcgtgcaaaaagtttgttctagttgtccagtctatgtgttgtatggttagtgca
-tatatacatatgtgtacgtctgtgatgtgataataattatcgtcgagtatcacttgtata
-ggcgtttgaatgaatactctgccttgggcatttgcatatttcttgcatgggtctcaaata
-ttgggcgtgttcatacctcaacttaagattttgggttcaaattgcaggagaggtcaataa
-atttgtattacataatttgacactatggctaaaatgggacatgttattt
->TELSAT_PG:satellite:satellite
-aaaaaacgttaaattcaaatgatttaagacgtttggctaagaaattagaataatattcac
-gttagtttaataaaaacaaataaaaaacatcgactttcgcatgattttagcattatttta
-gtcaatttatcactaaatcgctctaaaaacgttaaattagcatgatttaagacgtttggc
-taagaaattagaataatactcgcgttaatttactaaaaaaagctaaataacgtcgaattt
-tgcttgattttagcacaaatttagtcaatttaacgctaaattgctttaagaaaattaaat
-ttgcttgttttaagacgtttggctaagaaattagaataatactggcgttagtttaataaa
-agcagctaaaaaacattgactattgcttgattttagcattattttggtcaatttatcgat
-aaatcgcttt
->Neptune2_Ap:classI:LINE
-gcgaatactcgccctgtggtggattcagaaaatatcgacaaataccgtaataccgcaaaa
-aaaatcggcaaatatcgaaataccgcatcgaaagtcgatgaaataccgaaattgcaaaaa
-cgtggtataaggcgcaaccttttaaaagactttgacctttttgcaagacgaatgcgcctc
-aaagacattttttcacgggaaagaaacaaacaacaccctttccacgttaaatcaacatgg
-gaaccaccggttcaacagtcagtggccttggaaaccttcctagaggaggtggaatttgaa
-ctggcgaacagccctagtaagaggccaaaagacaacctatcacccggtgaaaggcgtgca
-ttacataacctattaggtgacaaaactatcattgtaaagaaagccgataaaggaaccact
-accgtaataatgagcagagaacaaaaaattaaagagggtcaaattctgttgaacgatctg
-gataactacaggcccttagaaaaacaaatggctgacgaaacagttgaaaaaataaaacaa
-ctaacaacgtctatgctcacagaaagccacattgacgaaatgacagtaaaatggctctcc
-caaacaccaaatccacctagaattccagaattctatacactaacaaagattcacagacct
-actttagtaggcagacctataatctctgggtgtgacggccccacagagagaatttcatgc
-tttgtcgaccgcctcatacagccgatagcacaacaacaagaatcttatctgaaagattca
-aaagattttataaacttcattgaaaacacaaaactgccaaagaacactatccttgcctca
-aaggacgttactagcttatacacaaacattcctcaagaagaagggattacaactgtatgc
-aaagcatacgaagacttctataaaaaccgtttaccaatccctactaatttcttgaggcga
-atgctctgcctaatacttaaagagaattcatttcaatttaataaacgacattatctacaa
-acccacggaacggctatgggaaccaaaatggccgtggcctttgcaaatattttcatggca
-aaaatagaaaaaggcattatcagcaagagcataattaaaccgctagtttggaagagatat
-attgacgatgtcttctgtctgtgggacacaaacgaagacaatatcaaggaatttgttaca
-agggcaaaccactaccacgataatataaaatttacggctgaaatatcagactcagaaatt
-gcattcttgggacacaaaagtgtacaaaggcgagagattcaacagagactcccaccctcg
-atgtgcaaacgcattataaacaaacagagacctttcaatacacgaaatttttattcgtgt
-catccaccaggcgtaaagaaaggattcataaaaggagaggcgctgcacctgctaagaaca
-aattcgtcacactcgacgtttaacaaaaacatgcagagtttcaaaacacgcctaaagaac
-agaggatacccaaatgagtttttagagaaaaaaggcccttgaaacaaagacaaaagcaca
-aaaaataaaatattgcctt
->REP2-2_TT:classI:LINE
-aaaaaactttccaaaaactttaattaagattcgaaaaaaacgaagcttaaaagtaaaaca
-gagaagtacaaattaattaaaaaatcagaggaaaaacaagaaaaagtcaaacaaactatt
-aaaagatatctaaataacgagcaaaacctactgaaaatgtctcaaagaagataaagcaat
-aagaagcaagagagcttagcaaacaagcaaaaacaggaccaaacaatcaccatatctcct
-aggaatgcatcagcggacacttaaaacatagaactcaaccgaaacatcttagaaaaccac
-acaaccaagcaccaatcaaaaacctaatccagaaatttctgaaaagaaggtagatggcag
-gaagagaggtttcagatcggcctacaagaataaggtagaaaaacaatatgaagaacagca
-accagtgtcaactccactcccatctgaagagaattgtttaaatctgctgtaggagcccca
-aatggtcataaataagtagccaagacccgaagccaaggaggttccaatcagcagcaatac
-atcaatctcgtaaagatcaaatagcaatgatagtagcagtctaaaacagaaccacaacca
-ctagcatcgacactcaagcatctctagacaagaaagtaaaccagccttgcaagaaccgaa
-accggaacttccaacctccatcgatatcggcaataaaatctggaaattgtgtagatttga
-cgcaggcatgaatggatgcagaaacagttcctaggattgcaagtttatccatttggactt
-gatagaacaggtagctctaagcgacaaaaagaagctagccaatgtagcaatctggaactg
-ggactaagctaagctagacagcaagtatcaaccttctgacaaggaccttctcaactcctg
-ggtaaactcaaattcaaacgagggaaatcccctcttcatcaaatacaaaacaatgattga
-ggagaaggatcctgaattcgtctaactcactaaagatctcacagctgagtaaatggaact
-tgaagaactctaaaacgcattccaagtcaagaagcagcgctacatgtcggagctttcttc
-aagactaagacagaaaattctattcaaaagcaggcaaaaggcctttgataaattgctttc
-agaatcagcccagaagagaacagcagcatctgaagcagcattatctcaagaaagtagcag
-catagaatatctcccaccatcccagtagaagtactcaaatcgatatcagatgataccaca
-tcacaaggaacaatatctaccctttgaaaattcacagtattcctcactccagtagtagcc
-aaaatctccaatacgaacttctcagcagcaacattattactagcaaaacaatactcaaag
-ctaccagccacagcactaagcccataactggaatccaacttattagcactagcaatctaa
-caattagagatttgaacccagctacaagccgtcctactactgaagaaatacatatgaaaa
-ctccttgaaatgaaatattaacatctcatgcatcaataaggaagtgttttacctctacta
-gagatgagttttgagtaaactcttatttaaagaatttggaaagttttaaaaagaacgtat
-caaacaaaaaccctgtgtcttcttcatatttacatattgtagtccctcaacacgcttaaa
-tatagctcattctctatccccaataattagcaccagcaaattacaataggctttgctctt
-attataataatatatcacagatataaaatttattattactattttttaggtatattctaa
-aaggaattaagaaggccataaaataaagcaaacaactaaagaacatctatataatgatta
-gaccaaatcctatttatagatcaagcaagaagtcacaaacacaaacctcacagacaataa
-agctagatttaagactcatctagtaaattaactcacacctcaactaacatgattctaacc
-taaaaagtagctcctgctcaaatcaatcaatgtcctccaaacgacgtattaacaaagact
-cgatgaacaaagtaaatcaataccttggctctaacaaaacttctccccctcaatattcac
-cacaacaacatttaaaaagcaaaattattggctcttagctcacaattacaggcttcaata
-ctcaaggagtagcaaaagctaacaaaagaaataagcaatactctacgctttacctccaaa
-agcttttcgctgaaagcgatgctaccatactcttggagacaaattgcaaagaaaatatga
-gagtggatatccataatccggactatattcaaatgaacaatcactgcaaagtacgctaaa
-tgggtgcaggaacagcctctatccaccacaaggaaatcaaacttgcaccatacgtcgcaa
-gcctcaataatgaaaaagtccttgcccaagtattaattcttgagaatcaatagagagttc
-taatcatgggactacatctccaactctaggccaaccctattgaagaataagctctactcg
-aagaaatcatctcgtaagtgctgcaagacaacaggctcaaccatatacttatctacgggg
-acttcaacctcgatatctcaacctccaactcctcacacgcagatgtaaggaaagccggac
-aaatcagaaggctcaaggacttcttgaaatcaaagaacttatacatacacagcacaaata
-ggcacactagagaagcattcaagcagaacaaaatcataaaaactcaagtggacttcttca
-taagctcgtttgctcctaattgcattctcaagattgaaacaattacacaggacgaaagca
-acagaggcagtgatcattatcccatccgaattcaaattgacttgcaagttgcaaaggcta
-gagaaatcaaaaaagtcatcaacttaaagtagctagatctcctatcctagaagcttcaaa
-aattcattcgcagcagtccatagaatgacacagaaatcagagataaaattaacagcatta
-aaggcaaacttgatctcaaataacaaaactcttaacagctaaggcgaaacataaaccaaa
-gaataaatgtagttatcagggcaatccacaaacatgaaaaggtgctaatgattgattaaa
-actcagcaaaaactagagcagaacatatgaaaacgcgtagaaaaatcatacagagcaaag
-acaccataatccagcataaggtcagtgaaatactcaaagaatactatgccgaatcaacga
-aaaaagtccaatcactctttaaaacaaacattaagcgatattattagaacatcaagagag
-tatgcagcttaggcaacaagtcaaatgttctaaacacctcaagcggaccagttgaaaact
-cgaacaaagaactcttatttgatagtaaagatatctaaaacgaaataagcaaatacttca
-aagaacactataaatgtgaaacacacgtcaattactatcacaccattgggcaacttagca
-gcagcgaaatagacactctcattcagtcttcagaaactctctacagcagcaggaacaagg
-ccttctccaacgattatatcaaagataagtgctttttcccaccaaattacagcgaaatct
-ctaacgccatgcaaagcattccttgctccaaaactaccaagaagcaaatgatttctgaga
-aaatgctctctcaatagtagcatagagacacaaacctcagaacactcctcaaagacatcc
-tcactaacccagactccttcagacagaccttcaatgcgaggtaaatctacctcctaaaga
-gcgaaagcagataaattatcaactgtagacccatcacgattcagtcctcagctattaaaa
-tcctggaaaatgcaatgctccagcatgtccaaaagctcaaagatgaagggaaggttaaag
-attttcacatcagccaatgtggcttccaaaagaatcgaagcacaatcatcaacatttgca
-gaactattgctctcatccaaagtacagtagccaagaaagaaaacagagttgccatcttcg
-tagatgtcaagagtgctttcgatagcgtcaaccacgaacagctgttctaagcactgcgaa
-atcaaggctttgacgatattttcatcaaatctgtcgcctttctctactagcactgtcgca
-tcaatgggtaccaaatcgggagaggagtcatccagggaggaaaattatcgcctatcctgt
-tcaattacctctatgaagaagtcagagtgaaaatccttgaaatctggaagagtaagaagt
-tggattgtcaagacctccactttgagctcttcgccgatgacatgctaatcattctcaaaa
-agtacaagctcacagcaaccctccttgaagtcctcaagcaagcgtatagagacataaatc
-tccaaatcaatgaatccaagacgaaaatcatgctaatcggcaagcaggaaacctacataa
-aggactcactcaaactaaggcaagcgaagggcatagatcttgtcatggagttcaagtacc
-ttggcttagtcatcaacaatgtgggcaaaatccacaaagatgtagctaagaaagtagaaa
-aggcaaagaatctcacacaaatgctcaagaggtggcgctacaacaagctaggtgttatcc
-cttgcctccttctctggtagctctttataaaatcgcagctataatacgcttcagcaatca
-tgatcacatcagcctaaagcgaaaaatgcatgagaagtcttcgaaacatgtacaactctt
-cccttagggacatacttggactcaacaggaacacttcaatctcaactatctgtgcagttc
-ttggcatcgaaaacattgagtctatgattctcaactgctacaacaacctaatgagccaaa
-ttaacgctgataaacgaatctaaatgtagttcaaagtcttcactaaaaacattaaattag
-acatggctagcaggcatcaacagctgctacaagcagctactcataaggacagcagagtca
-aacaaagattttggtggtagttcaacaacaagtacgatgatctcattaaactcaacatat
-atctctagaaccctgctggacaattctgctggaaatgttaaaggttctacaagggcggca
-gttggctctactgtcagcacaaaaaagaagcttggatggaactccaaaagatattaaata
-ctacctccaaggcagaaatagtcagtgtgctcaatcttagaaacacggattggcaaaagt
-tttctatagacataaaaaaaagtattcaagagtgggctagactcctggtctattaagaca
-tttctaaggtcagatgaaagaaaaaatcagctcccaaaatttaaaattctcactcaaaaa
-aaaaaaaaacttaaagaatcattcaagaatttgcaggcccttttcaatgtgagccaagta
-ttgaacaaacgcccttcatgtttgttcaaatggaagaaatagtgaggagtttctttaata
-accatgaagttactgtcttatacaatgtgagtcatgtatagtatatgtacatccataact
-attaaaaaaaaactgaaagaatcacccatgaagtttaagccctatacaatgtgagtcatg
-tatagaacaagcccttcatgtttgttcaaagtggaggcaatagtgaggagtttctttaat
-aaccatgaagttactgtcctatacaatgtgagtcatgtatagtatatgtacatccatact
-attaaataaatttaaagaatcacccatgaagtttaagccctatacaatgtgagtcatgta
-tagaacaagcccttcatgtttgttcaaagtggaggcaatagtgaggagtttctttaataa
-ccatgaagttactgtcctatacaatgtgagtcatgtatagtatatgtacatccataacta
-ttaaaaaaaactgaaagaatcacccatgaagtttaagccctatacatgtatagaacaagc
-ccttcatgtttgttcaaaagtaagaataaattatttttcatgttaagcgcaaataaataa
-ttaaaaataataaacaataaattaaataaattaattgactcggaacaataaatagaaaaa
-ggttattaaattaccaaattgttctggaattaatgagaaaaagaggaaactgggtgtata
-ttaaatattcaaaaatcagatattgattgaattattaaaaattaataatttggaaaatac
-ctaaaaataaataaaaattatctatataaatataataaaaataaattttaagatgtattc
-tgagtgcatttatatgtgcgagtttttctattctattctatc
->GYPSY10_I:classI:LTR_retrotransposon
-gacgcccaacgcgcttaagtgtcgtaataacgtaaactccgtaataaaaatatctaaaaa
-tcaaggtctcgtaaccgggttttctttgaaaacgcttcggactcgcacgctgcacaacaa
-cagtgaacatcaacacacaaacaaaaatatctaatgcaaaagtaaaacaacgccgcacaa
-gcaacagtgaaaaccgctgcatatcaacagtaaacagctaaaacgacagccagaggataa
-acggtcaaccagcaaccgtcttcgctgcattttaatataccaatataacatgtaagtgag
-atctttattttcaatttacctcttttaacgtcaaccagatatgtgtgccatttttgaaaa
-aaatacaaaactcataataaataacgaataaaacaaataaaaagagtgaatacaattaaa
-actttaagtatagtgattttaatttacaaattgattagaaaaaaaaaaatgaagaatgaa
-aatttaagtctttcctaagaagtaattctttctcatacaaagatatcattgtccgatgta
-tagaaatagtatcgaaaacaacgacagtgacgaggacttaatacagagctataaagacat
-aagaaacaataaccaacatgggggttacattgacggtactgagaccgacgaagatataga
-attaaaaaacttaatagacggctttacagacagagtaaaaatggttaacgatcaagaatt
-tcaaaatcaacctcaggaccttcaacaagaggcaacaccaacacaggaacaggcgaaaac
-ctcaggtaccattagtaataaagatgtaattagactcatggaagcggccgtaaatggtgc
-actagtgcaccagcatcaacaaaaaatattctcagacaagcttaaagaggttgaaaatag
-gcagagaataaacgatggtggacccttagtggtatacgagcaaataccacataatgctgc
-tattccttgtaatgaaccactagacttggtaaagtccatacccagttttgacggaaaaca
-agatgaatatgtggtatgaagaaccgcagcagttaacgcctacgaaatctaccataataa
-tataataatatataatagctagaatgggctgcgcatgtgcagaacaaactccaatcgagg
-tgacgcagcagcaaatggttactatgcgtcagggagatcttcctctaatgacttttataa
-tgagattgagagaaagctaactcttattattagtaggacttttttgtcttatgagacaaa
-tactgccgctatcttaaaaaatagatcacggcaggacgctttgaacgcttttgtgaccgg
-gctaaaaaaatcagtccgaaatgtagttctctcagctgcgcccaaagatttgccatcagc
-attggccgtggctcaacggacagagtcctgcaatgaacgagcctggttcgttgcaagctt
-taataaaaatgtagaagaaaaatcttacaattcagaaaaccgtcgccaaggtaaccgttt
-tcataacaccccacaaagtaataaccacaacaactcccagggtgctttccagagaaacta
-aaacaataatccaccgtgcactagtaatcaagctaatggctctcaattttctaaaaacca
-aagataaaaaggccaagcgcatcagaacaatgaatcaaaaaatcttcgataaggttatac
-gcaaaacctaggtcctgaacccatggacgtcgatcccacatcacgttctaaattcaggag
-cgaacggagagctcgcagtagtcaacggttgaaccagaacaagagcagtcaaatgaccag
-gagtatagggtaaagtcatcctacgaagcagcggaaatcgaggctgataacacgtccgat
-tccgaatcatgtaattttttaggggacgtccctgctcccccaaataattcgttcgatagc
-ggggcgagaaattaggttactgttggatacagaagcctccaaaaattacataaaacctct
-aacagaattaaaacacttcaaaccggtggaaacaccatttgaagtcacatcaatccatgg
-tcatacaaaaatagaacaaaagtgtctgatccatctattcaatgttaagtcatacttctt
-cttgttaaacaacctgaacgaatatgaaggaattgttagactggatttgccaaaaaaggt
-caatgcaaaaattgatctaacaaaaaacatcatcgagcatgatcatggtacggagcaaat
-tttttactcaaaatgcaggaatggtaactttattaacatcgatgacgtggacgtgccgaa
-agccataaacgaaaatttcaaaaagatgatcaaaaacagatcaaaagcctttgcggaccc
-aaacgattccctccccttcaaaatgaatacggtcgccacgatccgcactgacggggaacc
-cgtatattcaaaactttacccatatccgatgggtgtagccgatttcgtcaatacggaggt
-taagcaacatctagcagacggaataataaggccatcccggtcgccttacaataacccaat
-ttgggttgttgataagaagggttttggcggagaaggtcataggaagaaacgtctcgttat
-taacttcaggaaactgaatcaaaaaacaattgatgacaagtatcctataccattcatatc
-gaccatactgtcgaactttggaaaagctcagtacttcacgactcttgatctgaagtcggg
-cttccatcaaattgagccctcggagcgctttcgagaaaagacagctttttagtagtatga
-attctgcagacttccctttgctttaaaaaatgcgcctagtattttccaatagacgatgtt
-ctgagagaacacatcggcaaaactcgctatgtctacgtcgatgacgtaatatttttctcc
-caaacaatggagagtcatgccaacgatataaacacggttctgaaaactttgtgcgatgca
-ggtatgagagtgtctgtagaaaaatctatgttctttaaagagaacgtagaatatttggga
-ttcatagtgtcccgagggggaattaaaacttcacccgaaagggttaaggctataaaacaa
-tttaaacctccatcgacattgttaagtctcaggtcatttctgggattggccagttattat
-ataatagatgtttcataaaggggctttttagcatcgcaagacctctgacgaatattctaa
-aaggtgacaacggaaaaattggtgctaccactcaaagaaagtcaaactggaacgagcagc
-gaaaatcattcgaaaaactaagaaacaccctggagtctgaggatgtcattttggcatacc
-cagattccactcagccatttgacttgaaaactgacgcctctggaagcggcctaggggctg
-ttcttttacagatttaatcggcagcggcagaaatcaccgcaaattgcagaacgtgttccg
-aagcaaaacaccaatcgtcacccagtgcaacaaaccatagcggaaacatcaattcctggt
-tacactggggaaagtatccacatagatatattttggactgatcaaaagcattttctaacc
-tgtatcgacaagttttcaaaatccgctatagtccaaccaatcgattcaagagcaatcgta
-gatatcaaaactccgatactacaactaataaatctgttcaccaaaataaaaacagtttac
-tgcgacaatgaaagatctatcaattcacaaaccatacgaaccatcctagaaaataggtat
-ggtatacgggtctcaaatgcgcacccgttgcacagcacatctaatggccaagttgagaga
-tttcatagcaccctaggggaaatcgcacggtgcatcaagatagatcaaaacataaccgag
-acgagcgaccttattctattcggaacaatagaataggacagaactgtccactcggttaca
-attaaaaagggtcatgaaatagttcacgctattccaccagattttacgagcaccataaga
-gacaaaatcaaagaggcccaagagaaaacacttaggtactcaaatgcacacaaatgcaat
-aaacagtaccaaataggcgaaaaaatctggttaaaaaaccaacagacgcctgggtaccaa
-attaacgccactctgctcagaagaggtcatcgaggctgatctcggcacgacagtgcttat
-tatggagcaacgaacattacatcgtacgagacttacgcggacgagacgaaacacgcgatg
-gatttcttcgagaaggagcacatgagacgggtacttgaaacggactaggaacgaatagag
-actcttctggacacactaaaggtacgtcacagacatgcccgtagtcttaatttctcttaa
-ttttctcttaatttctcttaatttgctttgaaagcaatagagtggacacctgactctgac
-ggctgagaccaggtgaggttttgacaggaacagctaacggactcggtaaacggacagata
-gatttaaacaacaaaatacaattgcaattaaacacaatgacctcgtccatgaattctatt
-ttaaaatcggacgacttagacacagaacatttgtacgagacgattttggcaaaaaaccgt
-attgtaattcaagaacttgaaaatttaatacttgcaatcaccctttccaaattaaacgta
-ataagtccaataatcttgaatgacgttgacgtaagggagattgaaaaaacttttcaaaat
-cgagacctattgtactttttaataaaatttccgaagcctttgttaacttgtagaaaaata
-agaatattcccggtacagcatgaaaatagaatcttagatttcgaggacggtagcacggtc
-gcggattgcgggacggaaaccttcgccgtcaaggactgcaatgtatcaccaccttctgca
-ggagatcgaaagcgccaacctgcgcacaacaactcatctctggcatggtcgcccactgca
-acacccagcctggacacttggacccactcaccatgatcgactagggaatgctcatcacga
-acgatgtaacgataaatatcaccgacgaaaagggaataagccggataatatcaggaactt
-acccggtatgatataccgaaaaaattaaaataaacggcacccttttacgttaacaatatc
-ggaacatcaaagaagaaagccgcagtttcagctatggcccaagtaaacgttctgagacat
-atagagcgccttactctgtcctggaaagaaagatgatgatctttcttatctaccgtttga
-aagccaaaccaactaagaccattgaatccgaggacgaattcatcttaagacaaggagg
->blumeria_Grouper_14770_3
-GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA
-AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG
-CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT
-TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/hmmbank_test	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19248 +0,0 @@
-HMMER2.0  [2.3.2]
-NAME  DUF234
-ACC   PF03008.6
-DESC  Archaea bacterial proteins of unknown function
-LENG  100
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  19
-DATE  Tue Apr 22 17:16:17 2008
-CKSUM 5535
-GA    15.0000 15.0000;
-TC    15.4000 15.4000;
-NC    14.9000 14.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.994637   0.724738
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -138      *  -3458
-     1  -4805  -3913  -5457  -5685   -185  -5282  -1653  -3657  -5166  -3035   1529  -4003  -5160  -4085  -4629  -4531  -4683  -3846   5759   2382     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -8474  -9516   -894  -1115   -701  -1378  -1138  -7629 
-     2  -4703  -3842  -5413  -5626   4193  -5234   1199  -3686  -5187  -3174  -3160  -3955  -5117  -4054  -4635  -4458  -4581     97   -875   1388     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -8474  -9516   -894  -1115   -701  -1378  -7767  -7622 
-     3  -2371  -3264  -2698  -1965  -4162  -3111  -1597  -3684   -469  -3509  -2752  -2006  -3258    923   3603    330     86  -3304  -3493  -3205     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -8474  -9516   -894  -1115   -701  -1378  -7767  -7615 
-     4  -2617  -2306  -4759  -4273   3096  -4141  -2245    160  -3894    547   -831  -3607  -4045  -3290  -3615  -3271  -2541    365  -1682   3149     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -8474  -9516   -894  -1115   -701  -1378  -7767  -7607 
-     5  -2826  -2347  -5502  -5177  -3043  -5232  -5201   2131  -5110  -1855  -1760  -4940  -5049  -5047  -5246  -4584      0   3252  -4681  -4169     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8475  -9517   -894  -1115   -701  -1378  -7767  -7601 
-     6   -257  -1279  -2599  -2020    892  -2638   1046   -810  -1792    542   -474    -22   -338  -1580  -1919   -385  -1175   -710  -1648   3385     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9516   -894  -1115   -701  -1378  -7767  -7592 
-     7  -3058  -3845  -2245  -2210  -4348  -3380   1529  -4491    177  -4262  -3625  -2331   3930  -1887  -1298  -2975  -3059  -4092  -3954  -3528     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9516   -894  -1115   -701  -1378  -7767  -7585 
-     8  -1984  -3171  -1772  -1234  -3094  -2795   1043  -3212   -431  -3092  -2294   3505  -2878    756    909  -1867  -1870  -2866  -2958   1283     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9516   -894  -1115   -701  -1378  -7767  -7577 
-     9   -240  -1075  -3406  -2780    332  -2753  -1615   1091    271    498   2206  -2344  -2804  -2064   1759  -1830  -1164    299  -1530   1319     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9516   -894  -1115   -701  -1378  -7767  -7570 
-    10    616  -2550   1188   1102  -2868  -2053   -714  -2618    554  -2565  -1640   -689  -2148    885   -804   1393    566   -649  -2734  -2053    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9516   -894  -1115   -701  -1378  -7767  -7562 
-    11   -284  -2271    386   1985     43   -622   -796  -2159   -435    345  -1391   -812  -2212   -384    552  -1042  -1037  -1833  -2524   1710    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9517   -894  -1115   -701  -1378  -7767  -7555 
-    12  -3169  -2650  -5783  -5388  -2350  -5577  -5088   3385  -5289   1338  -1100  -5248  -5144  -4803  -5218  -4932  -3130    777  -4096  -3944    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -8474  -9517   -894  -1115   -701  -1378  -7767  -7547 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7767      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF1414
-ACC   PF07208.3
-DESC  Protein of unknown function (DUF1414)
-LENG  44
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  20
-DATE  Tue Apr 22 22:18:01 2008
-CKSUM 126
-GA    25.0000 25.0000;
-TC    65.9000 65.9000;
-NC    14.6000 14.6000;
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-EVD    -8.196627   0.666528
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -126      *  -3584
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -8634  -9677   -894  -1115   -701  -1378  -6552  -5729 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37  -8638  -9680   -894  -1115   -701  -1378  -6552  -5556 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -38  -8639  -9681   -894  -1115   -701  -1378  -6552  -5493 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -39  -8640  -9682   -894  -1115   -701  -1378  -6552  -5460 
-    44  -2898  -2432  -5520  -5129  -2851  -5219  -4799   1824  -5001    990  -1634  -4874  -5008  -4807  -5038  -4512   -170   2979  -4303  -3897    45
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -6552      0 
-//
-HMMER2.0  [2.3.2]
-NAME  CPW_WPC
-ACC   PF09717.2
-DESC  Plasmodium falciparum domain of unknown function (CPW_WPC)
-LENG  65
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  45
-DATE  Wed Apr 23 04:57:54 2008
-CKSUM 4547
-GA    20.0000 20.0000;
-TC    22.2000 20.4000;
-NC    19.2000 19.2000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -7.988613   0.756730
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -44      *  -5045
-     1  -7831   5874  -7883  -8268  -8316  -6799  -7490  -9351  -8422  -8760  -8675  -8123  -7272  -8288  -7847  -8267  -8109  -8877  -7099  -8312     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13 -10173 -11215   -894  -1115   -701  -1378  -1044  -7000 
-     2  -2354  -3687   -893   1820  -3953  -3351  -2016    464   1625  -1795  -2791  -2010  -3442   2102  -2117   -370   -354    365    515   -575     2
-     -   -149   -500    233     43   -381    400    105   -627    210   -466   -721    277    393     45     96    360    117   -370   -295   -245 
-     -   -119  -4292  -5617   -991  -1009   -701  -1378  -7044  -6989 
-     3  -2320  -3772  -2176    955     72  -3297    868    357   1573  -3784   1176  -1936    169    708   2073   -457   -697  -3389  -3960  -3283     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13 -10143 -11186   -894  -1115  -1225   -806  -7044  -6977 
-     4  -4525  -6480   3138   -895  -6652   -700  -3764  -1278  -4139  -6468  -5869   3071  -4910  -3451  -5103  -4156  -4620  -1219  -6688  -5600     6
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21 -10180 -11222   -894  -1115   -701  -1378  -7044  -6248 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21 -10180 -11223   -894  -1115   -701  -1378  -7044  -6229 
-    55  -2342  -3802    393   -124  -4118  -3318  -1977    224   2095   -923  -2893   1331  -3411   1093   -815    140   -721  -1472   1371   1003    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -10182 -11224   -894  -1115   -701  -1378  -7044  -6210 
-    56   -990  -3763   -958    834   -126  -3330  -1991   1274   2146    305  -2859    874  -3422  -1538   -237    204  -2286  -3373  -3961  -3292    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -10181 -11223   -894  -1115   -701  -1378  -7044  -6190 
-    57  -7831   5874  -7883  -8268  -8316  -6799  -7490  -9351  -8422  -8760  -8675  -8123  -7272  -8288  -7847  -8267  -8109  -8877  -7099  -8312    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -10181 -11223   -894  -1115   -701  -1378  -7044  -6170 
-    58  -2342  -3808   1421   -248    138   -488   1548  -1099   1033   -266  -2898   2359  -3410    994  -2064  -1205  -2281  -3428  -3993   -622    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -10182 -11224   -894  -1115   -701  -1378  -7044  -6150 
-    59    667  -2666  -5240  -4624     81  -4476  -3386   1915  -4237   -784  -1890  -4124  -4513  -3874  -4052   -535   1102   2447  -3241  -2893    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -10183 -11225   -894  -1115   -701  -1378  -7044  -6130 
-    60   -989  -3815    391    830   1322  -3315  -1974  -3886   1306  -3831  -2904   1708    552    799      2    695  -2280  -3437    928  -3315    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -10182 -11224   -894  -1115   -701  -1378  -7044  -6109 
-    61  -6831  -5738  -7192  -7555   1756  -7075  -3254  -5713  -7110  -5014  -5113  -5682  -6929  -5824  -6468  -6327  -6679  -5871   5923   1458    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -10182 -11225   -894  -1115   -701  -1378  -7044  -6087 
-    62  -2347  -3819   -889   1125  -4140  -1372  -1979  -3890   -460  -1233  -2909    224   3275   -348   -545   -402  -2287  -1343  -4003  -3320    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -10184 -11226   -894  -1115   -701  -1378  -7044  -6067 
-    63  -7831   5874  -7883  -8268  -8316  -6799  -7490  -9351  -8422  -8760  -8675  -8123  -7272  -8288  -7847  -8267  -8109  -8877  -7099  -8312    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -10183 -11225   -894  -1115   -701  -1378  -7044  -6044 
-    64  -2486  -2817   -856    649   -472  -3757  -2511   1693   2080     79    735   -754  -3829  -2392  -2827    -83  -1051   -271  -3216    534    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -10183 -11225   -894  -1115   -701  -1378  -7044  -6022 
-    65  -2341  -3813    988    141  -4133   -159    358  -1329   1242  -2057   1090   2609   -272   -228  -2062    129  -2280  -1575  -3996  -3314    77
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7044      0 
-//
-HMMER2.0  [2.3.2]
-NAME  HECT
-ACC   PF00632.17
-DESC  HECT-domain (ubiquitin-transferase)
-LENG  355
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  64
-DATE  Tue Apr 22 15:38:44 2008
-CKSUM 49
-GA    18.4000 18.4000;
-TC    19.7000 18.5000;
-NC    17.2000 18.2000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.957989   0.640935
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -32      *  -5524
-     1   -431  -3047  -1564   -315   1677  -4371  -3174   -400  -3476     85    823     32  -4434   1565  -3628    308   1336   -102  -3479   1308     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11699   -894  -1115   -701  -1378  -1032  -9468 
-     2  -4071  -3782  -1069   -362  -3845  -5851  -4893    272  -5587   2777  -2878  -5454  -5822  -5239  -5474  -5005     42   1032  -4688  -4346     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11699   -894  -1115   -701  -1378  -9499  -9466 
-     3  -4588   1291  -7048  -6503   -961  -6488  -5512   1212  -6213   2435    127  -6144  -6308  -5732  -6029  -5662  -1450   1883  -5028  -4808     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11699   -894  -1115   -701  -1378  -9499  -9464 
-     4    338   2298  -1671  -4688  -2822  -1671  -3442   -125  -4296   -361    -63  -4200  -1065  -3930  -4116   2235    926   1054  -3324  -2981     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11700   -894  -1115   -701  -1378  -9499  -9461 
-     5   -425  -4242   -391   -290  -4563  -3743   2753  -4314   1650  -4258   -457    -61  -3836   1459   1992    -93  -1100  -3864  -4426   -744     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11700   -894  -1115   -701  -1378  -9499  -9459 
-     6    -31  -4243    961   2854  -4564  -3743      4  -4314    665  -2456  -3332   -833  -1431    905  -2490   -533  -1457  -1935  -4426  -3743     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33 -10657  -5600   -894  -1115   -701  -1378  -9499  -9457 
-     7    103  -2836  -1232  -4712   -924  -1719  -3427   2113  -4309   1403   2446    329  -4606  -3933  -4111  -3640  -1016    837  -3294  -2952     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34 -10628  -5557   -894  -1115  -1400   -687  -9499  -9455 
-     8  -2920  -3039   -610  -1204   3553  -4287  -3080  -2580   -400    846    961  -3489  -4353    844  -3498  -3308  -1071   -391  -3465  -3076     8
-     -   -149   -500    237     42   -381    399    111   -627    211   -467   -721    275    393     45     95    358    118   -370   -295   -250 
-     -   -171  -4016  -4373  -1088   -917   -270  -2550  -9499  -9453 
-     9  -1707  -4238   2087  -2045  -4559  -3722    766  -4310   -156  -4253  -3328   3185  -3822   -537    135    -42   -217  -3860  -4419  -3736    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9451 
-    10   -750  -4165   -411   -871  -4478  -1357    265  -1584   -429  -4178  -3256  -2327   3480  -1890   -937   -673    283   -775  -4353  -3675    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9449 
-    11  -1595    467   1984   -143   -527  -1128   -392   -234    701  -1966   1477   1629  -3779      9  -1109   -224  -1288  -3789  -4356   1214    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9447 
-    12   -919  -3778  -1007    124   1233  -1825    797  -1736  -2175    -28  -2911   1342  -3904   -333   -238  -2743  -2697  -1214  -4064   3418    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9445 
-    13    866   2349   -807   -220  -1079   2458  -2353  -4188  -1940  -1383  -3239   -302   -514    127   -859   -722   -983  -2149  -4339  -3666    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9443 
-    14  -3622  -3412  -5950  -5327    463  -5191  -3969   -367  -4933   2656   3144  -1170  -5174  -4480  -4708  -1595  -3555  -2712  -3686   -564    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10589 -11632   -894  -1115  -1970   -425  -9499  -9441 
-    15  -6416  -5678  -7390  -7515   4234  -7128  -3661  -1345  -7082  -1016  -4979  -1163  -7028  -6012  -6559  -1469  -6306  -5538   2595     44    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -121 -10589  -3677   -894  -1115  -1970   -425  -9499  -9439 
-    16  -2826   1013  -4362   1580   -480  -4263  -3084   1298   -802     16    888  -3615  -4323   -416    675    348   1043    300  -3260  -2892    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -116 -10472  -3732   -894  -1115  -2931   -203  -9499  -9437 
-    17  -2513   1702  -2369   -268  -1028  -3490  -2149  -4018   -441  -3974  -3054   -562    762   1211    374     49    642  -3580  -4151   3396    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -741 -10360  -1324   -894  -1115  -3448   -139  -9499  -9435 
-    18    985    972    877   -342  -3310  -2958  -1637  -2986  -1278   -949  -2223    910  -3050  -1226  -1759   2155   -220    -29  -3358  -2751    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1206  -9624   -827   -894  -1115  -4761    -54  -9499  -9433 
-    19  -1083  -2484   1760   -402  -2789     85   -734  -2521   -331  -2501  -1595   -707    700   -285    372    439   1452  -2101  -2697   1329    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -185  -8426  -3109   -894  -1115  -5351    -36  -9499  -9430 
-    20  -1482  -2776   2410   -594  -3129    482  -1152    517   -918  -2886  -2047   2174  -2463   -755  -1462  -1372    819  -2446  -3137  -2455    25
-     -   -148   -501    237     42   -378    398    105   -627    209   -463   -721    277    393     44     95    358    118   -370   -295   -250 
-     -  -3414   -147  -9292    -24  -5892  -5394    -35  -9499  -9428 
-    21   -975  -2327   -863   -319  -2607    111   1301  -2324    979  -2325  -1433    988    407   -183   -702   -879   1963  -1928   2585  -1889    27
-     -   -148   -501    234     44   -382    398    109   -624    211   -467   -721    274    393     44     95    360    116   -368   -295   -247 
-     -  -3414   -147  -9292    -24  -5892  -5394    -35  -9499  -9426 
-    22    279  -2498   1436   1016  -2811  -1960   1986  -2562   -250  -2511  -1592   1016  -2073   -195   -763   1029   -968  -2116  -2683   1234    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -329  -8250  -2327   -894  -1115  -5394    -35  -9499  -9424 
-    23    835   -747  -3107  -2484   -711  -2441  -1312   1171  -2113    297   2217  -2041  -2492  -1765  -1966    385    868   1268  -1219   -873    30
-     -   -149   -500    232     44   -381    398    105   -627    211   -466   -721    277    393     50     95    359    117   -370   -295   -250 
-     -  -3096   -797  -1709    -47  -4969  -5456    -33  -9499  -9422 
-    24   -750  -1280  -1278  -1030  -1736  -1748  -1108   2081  -1033  -1594   -916   2511  -2106   -925  -1344   1016   -859   -900  -2094  -1615    32
-     -   -149   -500    233     43   -381    401    105   -623    210   -466   -721    275    393     45     95    360    117   -370   -295   -250 
-     -  -1791   -501  -8450    -54  -4757  -4656    -58  -9499  -9420 
-    25   -671  -1955   -560   1674  -2215  -1655   -321    717     94  -1941  -1069    980  -1752    110   1287   -587    954  -1542  -2176  -1547    34
-     -   -152   -504    240     49   -385    400    101   -627    209   -467   -717    277    391     46     95    360    115   -370   -299   -249 
-     -  -2004   -421  -8663  -2959   -199  -5503    -32  -9499  -9418 
-    26   -799  -1457  -2519  -2613  -3751   1983  -2632  -3549  -2816  -3751  -2845  -1978   2255  -2491  -2929   2190  -1221  -2476  -3922  -3667    43
-     -   -147   -502    231     41   -382    398    104   -625    213   -466   -722    276    397     43     97    357    116   -369   -296   -243 
-     -  -2004   -756  -2670  -1964   -427  -5503    -32  -9499  -9416 
-    27  -1116  -2075   2428   -449  -2815   1954  -1154  -2310  -1153  -2630  -1898   -706  -2170   -844  -1701  -1103  -1252   1161  -2988  -2354    48
-     -   -149   -500    233     43   -381    398    105   -623    210   -466   -721    275    393     45     96    360    117   -370   -295   -242 
-     -  -2543   -615  -2525    -60  -4624  -5533    -32  -9499  -9414 
-    28  -1748  -1556  -3206  -2950    351  -2955   -899   -491  -2568   -963   -723  -2320  -3065  -2200  -2461  -2180  -1754   1825   -371   3862    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -421  -7108  -2033   -894  -1115    -19  -6237  -9499  -9412 
-    29    512  -4173     29    447     65    -79    868   -780   -748  -1274  -3268    547   -465   -765  -2481    176    860    270  -4368   1538    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10627 -11670   -894  -1115   -388  -2084  -9499  -9409 
-    30   -748  -4242   -718   1196  -4563    -69   1488  -4314   1196  -2015   -935   1112    -27    440   -382    -21    903  -1583  -4425    -29    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11700   -894  -1115   -701  -1378  -9499  -9407 
-    31    234  -4249   2743    817  -4570  -3747  -2407  -4321     74  -4265  -3338   1343   -573   -235     76   -141   -184  -3871  -4432  -3749    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11700   -894  -1115   -701  -1378  -9499  -9405 
-    32  -1877  -4241    935     52  -4561   -466  -2402   -506    330  -4257   -848   1541   -312  -1942    600   1507   1026   -799  -4424  -3742    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -10657 -11700   -894  -1115   -701  -1378  -9499  -9403 
-    33  -1674   1136    441  -1133   -968   -242   1906  -4305    508  -2014  -3327   1427  -3837   -586    347   -552    234  -1328  -4422   2655    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -     -5 -10659 -11701   -894  -1115   -701  -1378  -9499  -8547 
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-     -     -5 -10659 -11701   -894  -1115   -701  -1378  -9499  -8543 
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-     -     -5 -10659 -11701   -894  -1115   -701  -1378  -9499  -8539 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10659 -11701   -894  -1115   -701  -1378  -9499  -8535 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -     -5 -10659 -11701   -894  -1115   -701  -1378  -9499  -8512 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1300 -10659   -760   -894  -1115   -701  -1378  -9499  -8508 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -212  -9366  -2917   -894  -1115    -86  -4112  -9499  -8504 
-   347  -1776    -10   -227   2981  -4449  -3644     34  -4197  -1886  -1187  -3223   1384  -3738    943  -2393   -798   -284  -1528  -4318  -3638   556
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -129 -10543  -3610   -894  -1115  -2454   -291  -9499  -8500 
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-     -     -5 -10549 -11591   -894  -1115   -578  -1599  -9499  -8492 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10627 -11669   -894  -1115  -1457   -653  -9499  -8488 
-   351  -3173  -4450   -857  -2490  -4861   3233  -2897  -2069  -2558  -4601  -3729    338  -4239  -2476   -153    238     15  -4167  -4827  -1432   561
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10627 -11669   -894  -1115  -1457   -653  -9499  -8484 
-   352  -7237  -6176  -7592  -1394   4423  -7509  -3718  -6085  -7525  -5378     25  -6129  -7368  -6265  -6902  -6764  -7092  -6268  -2965   1028   562
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10627 -11669   -894  -1115  -1457   -653  -9499  -8480 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10627 -11669   -894  -1115   -373  -2134  -9499  -8476 
-   354  -3031  -2865  -5326  -4693   2051   -989  -3442    574  -1383   2078   1888   -129  -1065    413  -4117  -3656  -1516   -830  -3322  -2979   564
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10659 -11702   -894  -1115   -701  -1378  -9499  -8472 
-   355    923  -3214  -3773   1435  -3224  -4226  -2989   -607   -584    132     91    166  -4298  -2905   -352   1168  -2874    993    715    486   565
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9499      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF46
-ACC   PF01864.9
-DESC  Putative integral membrane protein DUF46
-LENG  182
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  4
-DATE  Wed Apr 23 03:44:13 2008
-CKSUM 4942
-GA    18.2000 18.2000;
-TC    18.7000 18.7000;
-NC    18.1000 18.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.986970   0.699731
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -263      *  -2585
-     1   -918   -809  -2745  -2140   1856  -2425  -1236   1631   1251   -123   2744  -1879  -2441  -1519  -1752  -1497   -855    -21  -1209   -850     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8488   -894  -1115   -701  -1378  -1263  -8500 
-     2  -1562  -1304  -3835  -3223   -559  -3201  -1994   1766  -2863   1519   2882  -2819  -3077  -2339  -2639  -2317  -1486   -291  -1580   2236     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8488   -894  -1115   -701  -1378  -8763  -8496 
-     3  -1348  -2888   1942    -72  -3202  -1788   -794  -3001   -543  -2920  -2101   2819  -2125   -400   1679  -1145  -1338  -2544  -3072  -2317     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8488   -894  -1115   -701  -1378  -8763  -8492 
-     4  -1832  -1634  -3533  -2966   -757  -3420  -2207   1797  -2513   2156    307  -2827  -3262   1960  -2478  -2548  -1753   -366  -1938  -1739     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8488   -894  -1115   -701  -1378  -8763  -8488 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1457  -7446   -673   -894  -1115   -701  -1378  -8763  -8484 
-     6  -1100  -2035   3420    265  -2470  -1135   -635  -2476   -811  -2543  -1992    -73  -1634   -393  -1400   -942  -1209  -2101  -2362  -1884     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37  -6026  -7068   -894  -1115  -2319   -323  -8763  -8480 
-     7   -680   -650  -2307  -2103   -853  -1943  -1698   1114  -1830    -88     40  -1822  -2264  -1762  -1889  -1343   -804   2908  -1793  -1338     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37  -6026  -7068   -894  -1115   -193  -2996  -8763  -8476 
-     8  -3057  -2523  -5066  -4649   2234  -4760  -2707   -365  -4353   2767    294  -4250  -4187  -3332  -3921  -4078  -2931  -1092  -1743  -1113     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8489   -894  -1115   -701  -1378  -8763  -8472 
-     9    984  -1962   -461   1423  -2220  -1611   -288  -1934   1566  -1950  -1083   -276  -1724    140   -304   -576   -607  -1562  -2165   1820     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8489   -894  -1115   -701  -1378  -8763  -8468 
-    10   1471  -1029  -2391  -1987  -1937  -1614  -1646  -1392  -1800  -1806  -1090  -1596  -2137  -1598  -1965   1420   1787   1498  -2318  -1962    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8489   -894  -1115   -701  -1378  -8763  -8464 
-    11  -2428  -1999  -4764  -4212   2159  -4315  -2992   2717  -3929   1593    326  -3936  -3891  -3153  -3623  -3526  -2333   -327  -2149  -1899    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7446  -8489   -894  -1115   -701  -1378  -8763  -8459 
-    12  -3973  -3059  -4457  -4697    703  -4307   -752  -2990  -4191  -2378  -2423  -3085  -4232  -3178  -3688  -3641  -3861  -3124   5543   2996    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8763      0 
-//
-HMMER2.0  [2.3.2]
-NAME  POC4
-ACC   PF10450.1
-DESC  POC4 chaperone
-LENG  280
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  2
-DATE  Wed Apr 23 02:43:39 2008
-CKSUM 4598
-GA    14.0000 14.0000;
-TC    14.1000 14.1000;
-NC    10.1000 10.1000;
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -    -24  -6676  -7718   -894  -1115   -701  -1378  -9539  -8775 
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-     -    -24  -6676  -7718   -894  -1115   -701  -1378  -9539  -8771 
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-     -    -24  -6676  -7718   -894  -1115   -701  -1378  -9539  -8765 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6676  -7718   -894  -1115   -701  -1378  -9539  -8762 
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-     -    -24  -6676  -7718   -894  -1115   -701  -1378  -9539  -8758 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8755 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8752 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8748 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8745 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8741 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8738 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8735 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8731 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8728 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8725 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8721 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8718 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8714 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8711 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8707 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8704 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8700 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8697 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8690 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8687 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8683 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8679 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8676 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8672 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6676  -7718   -894  -1115   -701  -1378  -9539  -8665 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8281 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8276 
-   250  -2228  -1908  -3555  -3373   -604  -3255  -2515    -62  -2963   2976    358  -3207  -3275  -2644  -2802  -2988  -2232   -567  -1904  -1643   250
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8271 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8267 
-   252  -1504  -1181  -3518  -3077   2714  -3146  -1536   2450  -2771    462    445  -2639  -3017  -2265  -2612  -2339  -1453    437   -970   -215   252
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8262 
-   253   -922  -2235    -30   2103  -2629  -1500   -236  -2310   2245  -2216  -1420   -154  -1726    172    132   -763   -854  -1927  -2307  -1746   253
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8257 
-   254   -145   -822  -1232  -1197  -2475   -984  -1343  -2257  -1289  -2457  -1648   -938   2573  -1138  -1524   2213   -487  -1514  -2653  -2253   254
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8253 
-   255    -23   -665  -1554  -1408  -2317   -922  -1375  -1952  -1343  -2242  -1442  -1006  -1572  -1193  -1538   2192   2445  -1278  -2554  -2187   255
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8248 
-   256   -978  -2138   -392   2087  -2570  -1625   -245  -2231    552  -2133  -1357   -323  -1799    161   2412   -852   -890  -1881  -2194  -1720   256
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8243 
-   257  -2742  -2290  -3014  -3139    701  -3008   -615  -2258  -2836  -1879  -1835  -2399  -3220  -2421  -2640  -2733  -2781  -2314     18   4561   257
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8238 
-   258   -425  -1013  -1661  -1792  -2558  -1187  -1802  -2565  -1897  -2800  -2098  -1367  -1878  -1746  -1993   3270   -814  -1808  -2742  -2368   258
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8234 
-   259   -711  -1282   -482   1995  -1525  -1624   -677   -227   -477  -1098   -591   -568  -1882   -404   -852   -858   -724   2009  -1942  -1415   259
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8229 
-   260  -1279  -3054   2666   2403  -3264  -1297   -599  -3155   -759  -3060  -2359     97  -1798   -259  -1541   -971  -1332  -2660  -3234  -2299   260
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8224 
-   261  -1668   5611  -3406  -3571  -2843  -2114  -2801  -2423  -3306  -2880  -2568  -2847  -2716  -3192  -3058  -1988  -2033  -2131  -2810  -2873   261
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8219 
-   262  -1229  -1727  -1084   -807    215  -2029   -229  -1530   -383  -1435   -967   -870  -2181   2701   -588  -1226  -1178  -1405   -380   3151   262
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8214 
-   263  -2176  -2415  -2504  -1923  -3054  -2403  -1269  -3053   -167  -2856  -2350  -1844  -2662   -997   3887  -2228  -2131  -2807  -2501  -2452   263
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8209 
-   264  -1969  -1609  -3949  -3396   -179  -3705  -2482    427  -3020   2223   3555  -3268  -3302  -2409  -2821  -2923  -1873   -151  -1699  -1632   264
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8205 
-   265  -3232  -2594  -3508  -3648   -882  -2917  -1886  -3060  -3237  -2665  -2615  -3229  -3282  -3161  -2996  -3457  -3341  -3103   6081   -495   265
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8200 
-   266  -2176  -2415  -2504  -1923  -3054  -2403  -1269  -3053   -167  -2856  -2350  -1844  -2662   -997   3887  -2228  -2131  -2807  -2501  -2452   266
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8195 
-   267   -985   3856  -3039  -2604   -554  -2301  -1691    332  -2185   1898    332  -2179  -2506  -1921  -2105  -1576  -1051    205  -1504  -1141   267
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8190 
-   268  -2059  -2867   3860   -532  -3452  -1877  -1516  -3665  -1847  -3616  -3145   -882  -2414  -1318  -2469  -1872  -2198  -3236  -3167  -2847   268
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8185 
-   269    -84   -748  -1385  -1442  -2705   2248  -1577  -2502  -1649  -2709  -1859  -1043  -1617  -1406  -1840   2270   -470  -1609  -2876  -2539   269
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8180 
-   270   3260   -995  -2154  -2261  -2604  -1267  -2060  -2035  -2233  -2502  -1934  -1631  -1961  -2058  -2240   -724   -871  -1499  -2817  -2619   270
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8175 
-   271   3260   -995  -2154  -2261  -2604  -1267  -2060  -2035  -2233  -2502  -1934  -1631  -1961  -2058  -2240   -724   -871  -1499  -2817  -2619   271
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8170 
-   272  -1608  -1307  -3432  -3238  -1179  -3095  -2687   3474  -2941   -191   -206  -2987  -3216  -2818  -2915  -2635  -1653    832  -2363  -1952   272
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8165 
-   273  -1814  -2025  -2478  -2748  -3577   3650  -2700  -3847  -3052  -3864  -3354  -2492  -2699  -2874  -2984  -2040  -2187  -3148  -3081  -3439   273
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8160 
-   274   3260   -995  -2154  -2261  -2604  -1267  -2060  -2035  -2233  -2502  -1934  -1631  -1961  -2058  -2240   -724   -871  -1499  -2817  -2619   274
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8155 
-   275  -1762  -2287  -1132  -1144  -2520  -2040  -1289  -2773   -740  -2625  -2183  -1302  -2433   4141   -881  -1765  -1840  -2519  -2457  -2076   275
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8150 
-   276   -425  -1013  -1661  -1792  -2558  -1187  -1802  -2565  -1897  -2800  -2098  -1367  -1878  -1746  -1993   3270   -814  -1808  -2742  -2368   276
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8145 
-   277  -1814  -2025  -2478  -2748  -3577   3650  -2700  -3847  -3052  -3864  -3354  -2492  -2699  -2874  -2984  -2040  -2187  -3148  -3081  -3439   277
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8140 
-   278  -2228  -1908  -3555  -3373   -604  -3255  -2515    -62  -2963   2976    358  -3207  -3275  -2644  -2802  -2988  -2232   -567  -1904  -1643   278
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8134 
-   279  -2742  -2290  -3014  -3139    701  -3008   -615  -2258  -2836  -1879  -1835  -2399  -3220  -2421  -2640  -2733  -2781  -2314     18   4561   279
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -6677  -7719   -894  -1115   -701  -1378  -9539  -8129 
-   280  -1608  -1307  -3432  -3238  -1179  -3095  -2687   3474  -2941   -191   -206  -2987  -3216  -2818  -2915  -2635  -1653    832  -2363  -1952   280
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9539      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Amino_oxidase
-ACC   PF01593.16
-DESC  Flavin containing amine oxidoreductase
-LENG  482
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  86
-DATE  Thu Jun 12 16:59:13 2008
-CKSUM 9581
-GA    14.7000 14.7000;
-TC    14.7000 14.7000;
-NC    14.6000 14.6000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -11.621656   0.638325
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -21      *  -6109
-     1   -879  -3440  -5962  -5326   1363  -5165  -4037   2098  -4922   1732   2496  -4811   -942  -4543  -4721  -2381  -3556    453  -3899   -962     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -1021  -9910 
-     2   2577   -174  -7680  -8030  -7603   -581  -6944  -7430  -7633  -7692  -6711  -5998  -2236  -7050  -7217   2396    697  -6086  -7825  -7821     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9908 
-     3  -9325  -8016  -8995  -9382  -9561   3867  -8643 -10645  -9576  -9967  -9932  -9344  -8440  -9454  -8996  -9819  -9545 -10244  -8234  -9579     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9907 
-     4  -6837  -6181  -9247  -8670  -4254  -9136  -7774   1218  -8509   3096    544  -8875  -8014  -7168  -7947  -8577  -6669  -1220  -6140  -6412     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9905 
-     5   1930    341  -5676  -5058  -3419  -5100  -3966   -120    -26  -3311    347  -4664  -5157  -4379  -1022   1738   1245    863  -3914  -3566     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9904 
-     6   3046   2318  -6649  -6218  -4451  -2698  -4972  -1235  -5818  -2021  -3685  -5345  -5585  -5411  -5588   -263   1170  -1052  -4943  -4622     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9902 
-     7   3604  -4865  -7589  -7942  -7589  -1377  -6926  -7427  -7609  -7687  -6709  -5985  -5965  -7029  -7208  -2016  -1790  -6088  -7814  -1132     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9901 
-     8  -1114  -4419  -3399  -1503  -1375  -4404   -846   -538    697   -324  -3548    189  -4493    834   2102    -34    763   -447   1175   1671     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9899 
-     9   -515   -278    -33   1196  -5092  -4285   2363  -1819   -209   -372   -782   -125  -4378   1621   1153  -1746    169   -964  -4960    919     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9898 
-    10  -6948  -6281  -9311  -8704   -622  -2204  -7697   -194  -8522   3212    641  -8925  -8008  -7118  -7912  -8613  -6758  -4620  -6067  -6338    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9896 
-    11    794   -402  -4345   -222  -3764  -4784   -524   -829    496   1336   -462  -3852  -4854   1673  -3891    325   1274  -1265  -4162  -1049    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9895 
-    12   -311  -4782   1322    753  -5103   -143   1146  -2360   -190  -4798   -653    402  -4376   1585   1518    529   -431  -1987  -4965  -1595    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -147   -488    232     42   -381    398    105   -627    210   -467   -721    275    398     44    101    358    116   -370   -295   -250 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9890 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1621 -11254   -570   -894  -1115   -701  -1378  -9931  -9889 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9883 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9881 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9880 
-    22  -5769  -7695  -1347   3887  -1395  -5503  -5007  -8026  -5497  -7845  -7325  -4122  -6114  -4721  -6544  -5390  -1919  -7426  -7901  -6762    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9878 
-    23   2942  -4715  -3206  -1378  -1446    911  -2972  -4731   -634  -4717   -544  -2960  -1658  -1744    -32     22  -3264  -4320  -4918  -1063    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9877 
-    24  -1363  -4782    362    382  -5103   -259  -2941  -4854   -218  -2555  -3871    -41  -1565    604   2567   1380   -102  -1997  -4965  -4283    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9875 
-    25  -1587  -5332   3064    659  -5637    633    -11  -5405  -1494  -5342  -4437   1169    780    -44  -3596   -914  -3763  -4948  -5511  -4792    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9873 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9872 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9870 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -14 -11254  -6901   -894  -1115   -701  -1378  -9931  -9869 
-    29  -5478  -5937  -7945  -8316  -8391   3837  -7615  -8499  -8347  -8586  -7781  -7002  -6904  -7869  -7952  -2180  -5947  -7260  -8025  -8508    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -11242 -12285   -894  -1115   -472  -1842  -9931  -9867 
-    30  -3038  -6589  -6998  -5326  -7496  -6485    461  -6745   1223   -875  -5721   -519  -6386  -3858   3728  -5873  -1832  -6544   1219  -6146    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9866 
-    31    811    931  -5987  -5354  -3423  -2146  -4071   2260  -4952    199   1490  -4840  -5242  -4577  -4754   -919   -937   2122  -3935  -3592    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9864 
-    32    -21   -586  -3743  -1874    350   -619   2410  -2525   -917  -1546   -637    299  -4641    215   1687   -527  -1338   -505   3033   1600    49
-     -   -147   -500    233     43   -381    398    105   -626    210   -466   -721    275    394     45     96    359    117   -370   -295   -244 
-     -    -25  -5987 -12296   -987  -1013   -701  -1378  -9931  -9863 
-    33   -557  -4570  -1590  -2880  -4866  -1215  -3151  -4550  -1438  -2748  -3768  -3155  -1856  -2736  -1944   2293   2865   -881  -4898  -4289    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9861 
-    34  -3366  -4349    675    458   1472  -2142   1283    410   -118  -1325    107  -3171  -1670   -417    221  -1112   -818   1030   2643    788    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9860 
-    35  -1337  -4778  -1450    683   -654  -2654     33   -761    806  -2172    867    277    633    797   2012   -548   -854  -1303  -4963   1131    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9858 
-    36  -3324  -4654   1149   -122   1578   -363  -2986  -1866    -97    331    -56  -1327  -4413   -672    731    686    203    214  -4873    212    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -337 -11254  -2272   -894  -1115   -701  -1378  -9931  -9856 
-    37   -213  -4477   1365    501   -782    829  -2636  -4549   1523  -2248   -348   -336    406    248     16    684  -2943  -4099  -4660   -777    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -584 -10920  -1593   -894  -1115  -4107    -86  -9931  -9855 
-    38  -2497  -3947   1919  -1803  -1017   1967    242  -4002   -593   -788  -3038   1678  -1498   1024  -2224   -460  -2436  -1097  -4136  -3459    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -729 -10339  -1341   -894  -1115  -4518    -64  -9931  -9853 
-    39  -1935    582    -93  -1288   -586   1988    279  -3254  -1201  -3266  -2377    589  -3023    -88  -1698   1328   1456  -2866  -3490    -84    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -848  -9650  -1177   -894  -1115  -4177    -82  -9931  -9852 
-    40  -1443  -2917   1918    392  -3237    972   1494  -2988    487  -2932  -2006    120   1342   -615  -1166   -363   -203  -2538  -3100     83    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -470  -8993  -1864   -894  -1115  -2466   -288  -9931  -9850 
-    41   1220  -3227   -166   1029     65   1082  -1394  -3293    789  -3242  -2317    343  -2829   -935    332   -842     42   -416  -3412   -253    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -62  -9444  -4660   -894  -1115  -1525   -616  -9931  -9849 
-    42  -2461  -3920   2647    -32  -4235  -1203  -2096  -1430  -1679   -388  -3010  -1107   1483    119    213   -217    594  -1390  -4107  -3428    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -33 -10302  -5578   -894  -1115  -1002   -998  -9931  -9847 
-    43  -1408  -4396   -368      6  -4717   2820  -2556  -4468   -873  -4412  -3486   1085  -3990   -589   -148     95  -1161   -693  -4580   -704    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -10829 -11871   -894  -1115  -1189   -833  -9931  -9845 
-    44   -154  -3785   -378   -248   1936  -1781     37   -204  -2974    266  -2951   -505  -4479    348   -500   -901  -1319    846   1213   2082    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -374  -2132  -9931  -9844 
-    45  -3518   -722  -5253   -768    819  -4987    219   1053   -424    498   -655   -588    147  -1224   -392   -596   1022    206   1901   1737    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11210 -12252   -894  -1115   -252  -2640  -9931  -9842 
-    46    536    230  -1780  -2018   1125  -2257  -4005   1713  -1894    661    356  -4777  -5184  -1380  -4688  -2019  -1631   1394   1963   1249    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9841 
-    47  -4482  -6107   2783   2801  -6378  -2158   -747  -6183  -3799  -2573  -5249   -109  -5291   -499  -4413   -644  -4466  -2013  -6279  -5482    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9839 
-    48   -352  -4109  -3715   -218    -80  -2033   -430   -387   -301   1180   2694     16  -4630  -1074    640  -1091    711    207  -4453  -3952    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9838 
-    49  -2116  -5166  -7358  -7413  -1198   3726   -504  -2072  -7059  -2444  -5007  -6117  -6424  -6492  -6754  -5168  -5196  -5273  -4785  -3765    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -45 -11254  -5098   -894  -1115   -701  -1378  -9931  -9836 
-    50   2378   -241  -5716  -5091    959    954  -3933  -2892  -4724   -475  -2598   -552   1614  -1329  -4585  -1929  -1520   -772  -3851   -843    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -11212 -12254   -894  -1115   -258  -2608  -9931  -9834 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9833 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9831 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -276 -11254  -2532   -894  -1115   -701  -1378  -9931  -9830 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -200 -10981  -2970   -894  -1115  -3873   -102  -9931  -9828 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -10784 -11826   -894  -1115  -1472   -645  -9931  -9827 
-    56    745   1419    -62  -2603  -1129     35   -212    444   -653  -2207    779    395    870     40   -280    226    -12    427  -4405   -753    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -30 -10962  -5716   -894  -1115  -2542   -272  -9931  -9825 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -3 -10973 -12016   -894  -1115   -169  -3179  -9931  -9823 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -50 -11235  -4951   -894  -1115   -388  -2084  -9931  -9822 
-    59   -201    451   -349    612  -1329    331    798  -1256  -1530   -997    409   1706    739     28  -3081    488   -750   -487    235    124    78
-     -   -150   -501    232     42   -382    399    111   -624    209   -467   -712    274    395     44    100    360    118   -371   -296   -251 
-     C   -219  -2843 -12250    -21  -6146   -244  -2683  -9931  -9820 
-    60    843    859  -1853  -1312   -335  -1309  -3646  -1063   -575   1125   -155    208    442  -1552  -4048   -976    321   1448  -4086   -991    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -11254 -12296   -894  -1115   -701  -1378  -9931  -9819 
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-   215  -3315   -363   -793   -281   -604  -4298   2592   -554    861    558  -3826  -1297  -4390   1287   1649     -2   -950  -1058  -4928    -64   386
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -34 -11255  -5551   -894  -1115   -701  -1378  -9931  -9547 
-   216  -1299  -3401  -5767  -2593   1051  -5087    319    -56  -1270   2077     17  -4689  -1764  -1221     93  -1987   1026  -1000   -445   1294   387
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11224 -12266   -894  -1115  -1687   -536  -9931  -9545 
-   217  -3287  -1362    423   -285  -1467   1403   -744  -4820  -2503  -4768  -3844   2693  -4355   -925   1123    157  -3227    856  -4939  -4257   388
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-   218    942   1222  -1436     50  -5073  -2603    285  -4823   1076  -2564   -948    241  -4348   1209    343   -234   1557   -864   1602   -961   389
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -11224 -12266   -894  -1115  -1687   -536  -9931  -9541 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -11224 -12266   -894  -1115   -952  -1049  -9931  -9539 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9537 
-   221    -14   -217    -36   -174  -4609  -1673    469    303    669   -227    -51  -3090  -4468  -2662   1737     15   1234    143  -4696  -1157   392
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9535 
-   222    -38  -4766  -1688   1087  -5087   -445   -531  -4838   1192  -4782  -3855    -42  -4359    846   1589   1264   -465  -1963     67    531   393
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9533 
-   223  -3569  -3404  -1684  -1034  -1136   -920  -3978   2828  -4832    880    299  -1575  -5161  -4466  -2182  -2130  -1322   1657  -3861  -3518   394
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9531 
-   224     15  -4766    942    685  -5087  -1458   1133  -4838    394  -1452  -3855    586  -4359    188   1299    660   1088   -788  -4949  -1571   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9529 
-   225  -1801   -775    261  -1100    358  -2618    450   -931    731   -121  -3827    101   -279   1561    523   -852    574  -1071   2352    968   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -48 -11237  -5009   -894  -1115  -1354   -716  -9931  -9527 
-   226   -196  -4724    879   1264  -1360    730    240  -1772      9  -1622  -3813   1151  -1698    542   -183    994   -574  -2108  -4907  -4224   397
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -261 -11191  -2612   -894  -1115  -2280   -333  -9931  -9526 
-   227    442    541    824    743  -4811   1588    405  -4561   -855  -4505  -3579    296   1315  -2189     75    509   -710  -2335  -4673  -3990   398
-     -   -145   -495    239     44   -384    398     99   -633    206   -465   -719    276    397     43     89    364    118   -370   -301   -251 
-     T   -805  -1996  -2511  -1761   -505  -4058    -89  -9931  -9524 
-   228  -1382  -4240   2142  -1169   -868   1220    -99  -1819    114  -4256  -3329   1654  -1580   -425     82    426   -155  -1560  -4424  -3741   412
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -3 -10655 -11698   -894  -1115   -872  -1140  -9931  -9522 
-   229  -1122  -4559    827    725  -4880   1750  -2718  -4631   1340  -2370    179    177     25   -317    841   -792   -857  -1744  -4742  -1195   413
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11011 -12053   -894  -1115   -179  -3101  -9931  -9520 
-   230    525   1261    519  -4659  -1160    615  -3842    620   -995  -1152  -2686   -783  -1807  -4113  -2135  -2387  -1098   2561  -3933  -3572   414
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115   -405  -2031  -9931  -9518 
-   231   -780   -746  -1596   -309  -1288   -182  -3347   -514    563   -665    122     18  -4700  -3113    923   -272   1825     38   1386   1174   415
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9516 
-   232    149  -3678  -1720  -1653  -3674   -914  -1938    450  -3796    850   -466  -1635  -4916  -1248   -689    124   -380   2465    219  -3700   416
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-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9514 
-   233   -607   -280   -693   -571   -752  -1362   1199   -152   -436    432  -3725   -467  -4424    342    307    -53   1751    545    236  -1362   417
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-   234   -189   2583   -766  -1779    472  -1286      2    324   -133    165   -500  -3945  -4894    -95  -1153  -1213   1631    689  -4120    570   418
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-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9510 
-   235  -1138   -269   -226   1100  -5087   -146  -1202  -1827    925    -40  -3861  -1677  -4379    372    147    581    143    982    681    -85   419
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-     T     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9508 
-   236    379  -4781   2518   -351    413   -383    131  -4852  -1668  -1863  -3870   1960   -813  -1046   -666  -2171    434  -2620  -4965  -2092   420
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-     T     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9506 
-   237   -363  -4783   -322   -622  -5104   2927  -2942  -4854     26  -1559  -3872     63  -4376   -552  -1060     -8   -374  -4405  -4966  -1082   421
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-     S   -264 -11255  -2598   -894  -1115   -701  -1378  -9931  -9504 
-   238   -990  -4543    840   1270  -4864   -453   -201  -1153   -277   -641  -1008  -1524    824    508   1457    179    380  -1710  -4727   -852   422
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S  -2293 -10994   -333   -894  -1115  -3815   -106  -9931  -9502 
-   239   -405  -2687   1373   -538  -3000     85   2442   -514   -451   -910  -1778    752    329   1050    561  -1116    219  -2305  -2875  -2197   423
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-     .   -535  -8709  -1709   -894  -1115  -6002    -23  -9931  -9500 
-   240  -1186  -1081  -3280  -2696  -1102   2098  -1672    689  -2362   1037   -312  -2300  -2779  -2047  -2274    444  -1157   1016  -1638  -1289   424
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-     .   -179  -8184  -3160   -894  -1115  -5005    -46  -9931  -9498 
-   241  -1032  -1037  -2549  -1961  -1012  -2460  -1291    361  -1708    772   -237    331  -2526  -1481  -1792   1305   1734   -464   2843  -1107   425
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-     .   -202  -8204  -2990   -894  -1115  -3797   -108  -9931  -9496 
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-     S     -8  -8586  -9628   -894  -1115  -3129   -175  -9931  -9494 
-   243   -517  -3023   -189    -53  -3327   2126   1066  -3067    867   -656  -2116  -1210  -2662   -775  -1321   -308   1061  -2636   1747  -2543   427
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S   -293  -9212  -2469   -894  -1115  -5067    -44  -9931  -9492 
-   244    208  -2874   1584    -89    644  -2409  -1069  -2925   -654  -1472  -1966   1019  -2502   1156    804    612   -115     69  -3065  -2390   428
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -6  -8996 -10038   -894  -1115  -3852   -104  -9931  -9490 
-   245  -1647  -3119   1400   1827  -3438  -2613  -1277  -3189     -6  -3134  -2209  -1248   -119   1499  -1370    813    140    745  -3303  -2619   429
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -5  -9266 -10308   -894  -1115  -4282    -76  -9931  -9488 
-   246  -1750  -3004    -40    386    881   -408  -1430    700    -94  -2983    824  -1436  -2852    297    627    915    945     43  -3240    166   430
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B     -5  -9409 -10452   -894  -1115  -2377   -308  -9931  -9486 
-   247   -276    653  -2070   1944   -739  -3172  -1835  -3554   1016   -514    103    -44  -3264    205    293    623    -39    112  -3761  -3104   431
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -4  -9962 -11004   -894  -1115   -160  -3255  -9931  -9484 
-   248   -755  -4409  -3269    875   -917  -4302   -402     -3    162   -533  -3532  -1577  -4392    316   -406    861   1628   1398  -4670  -1313   432
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11172 -12214   -894  -1115   -906  -1101  -9931  -9482 
-   249   -319  -3395  -1013   -627   1639  -1171   -428   1373  -4734    520    321  -4666  -1756  -4387   -733  -1154  -1167   1063  -3850   2108   433
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -65 -11214  -4565   -894  -1115   -781  -1259  -9931  -9480 
-   250   -376  -4710     64   1299  -1463  -4210   1182  -4781    610  -1232  -3799    -88    216    292    725    598   1095   -170  -4893  -4210   434
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11176 -12218   -894  -1115  -1687   -536  -9931  -9478 
-   251   2642   2024  -2414  -2022   1414    785   -505  -2920  -4525  -3269  -2617  -4519  -5068  -4223  -4468  -4078   -201    -49  -3866    381   435
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11191 -12233   -894  -1115   -553  -1651  -9931  -9476 
-   252   -798  -4820   3573   -796  -5140  -2104   -427  -4890    554  -4834  -3910  -2940  -4405  -2514    739  -1731  -3286  -1969  -5001  -1159   436
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9474 
-   253   1819  -4603   -785  -2686    131  -1972   2420  -4556    -84   -823   -134  -2983  -1626    798    175     98  -1465   -870  -4830   1542   437
-     -   -147   -501    232     42   -382    399    105   -627    209   -467   -721    274    393     48     95    358    116   -361   -295   -245 
-     E   -160  -3270 -12279    -27  -5760  -1354   -716  -9931  -9472 
-   254   -272    694  -6755  -6183  -4211  -6065  -5068    793  -5838   -514  -3329  -5718  -6069  -5506  -5686  -2157  -4281   3326  -4894    883   439
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9470 
-   255  -1333  -5002  -8222  -7909  -5588  -8098  -8163   3060  -7893   -374    -55  -7752  -7793  -7818  -8063  -7492  -5515   2587  -7415  -6939   440
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9468 
-   256   -534   2957  -5917  -5281  -1882  -2124  -3990    883  -4876    628   1129  -1475  -5169  -4499  -4676    667  -3512   2303  -3856   -864   441
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9466 
-   257   2292   1382  -7644  -7979  -7536  -2055  -6902  -7351  -7587  -7617  -6648  -1194  -5944  -7011  -7180   -612   3068  -1978  -7766  -7750   442
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9464 
-   258    731   1431  -1771  -5236  -3357   -995   -472   1293  -4841    516    -31  -4743  -2068  -4473  -1709    380   1004   1714  -3860  -3517   443
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -3 -11237 -12279   -894  -1115  -1354   -716  -9931  -9461 
-   259  -3144  -6791   1059   -255  -7117    -87  -4487  -6986  -4567  -6883  -6122  -2013   3553  -4127  -5311    771  -1190  -6463  -7071  -1031   444
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -11237 -12279   -894  -1115   -405  -2031  -9931  -9459 
-   260    351  -3547  -1718  -1929    736  -1288   -498    132  -4216   1650    410  -1362   1282     75  -4302     39  -3485    643  -3986  -3617   445
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9457 
-   261   -317   -793    231  -2609  -5100   1796   1138  -4849  -1289  -4795   -307    295    988   -908    533   1008   -701  -4401   1028    938   446
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9455 
-   262    941   -437   -991    -51  -1304  -1373    529   -343   -776  -1117  -3266     -8  -1319  -2964  -3458   -584    922   2185  -4453   -355   447
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9453 
-   263   1224  -3418  -5903  -1973  -3372  -5131  -4001    145  -4870   2230   1127   -967  -1703  -4499  -1823   -128  -1790    198    240  -1061   448
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9451 
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-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9390 
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-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9388 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9386 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9384 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9382 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9379 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9373 
-   301  -1818    707  -1463   -220   3191  -1353   -461  -1518    112  -2449  -3830  -1176    553   -346   1106  -1120  -1509  -1954   1589  -1004   498
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9371 
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-     S   -533 -10788  -1704   -894  -1115  -3410   -143  -9931  -9362 
-   306  -1278  -3557    620  -1996  -3732   1214   1786    215    706    234   -451   -407   -760  -1842   -531   -196   -878    539   1587  -3255   503
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-   312   1416  -2331   -881    605  -2644  -1947   -558  -2349    795    549  -1432   -598  -2031   1125   1474   -878   -909  -1951  -2497  -1877   513
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-   313  -1324  -1707    526   -156  -1734  -2574  -1320    384  -1288   -101   -884  -1563  -2648    349     70   -157  -1264   1167   2735   2254   514
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B     -7  -8713  -9755   -894  -1115  -4929    -48  -9931  -9344 
-   314    710  -2803   1379    205  -3123  -2305   -964  -2871   2252  -2817  -1893   -941  -2400   -505    550    238  -1275  -2425   2221  -2305   515
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -7  -8831  -9873   -894  -1115  -3840   -104  -9931  -9342 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -6  -9143 -10185   -894  -1115   -353  -2203  -9931  -9340 
-   316  -1753  -4546   1651    517  -4866   1075   -890    850   -991  -1236  -3635     20   -454    257   -109     82    581  -1111  -4729   -962   517
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -10998 -12040   -894  -1115   -660  -1446  -9931  -9338 
-   317  -1257   -273   -638    212    -12    -46    236    193  -1337   1215   -711   -720  -4481    444    565   -386  -1717   -245    244   1496   518
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11166 -12209   -894  -1115   -483  -1813  -9931  -9335 
-   318  -1244  -4762   1065   -322   2095    374   1198  -4834   -450   -492  -1023     71   1247    263   -861     40   -276  -4384  -4945  -4263   519
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11233 -12276   -894  -1115   -374  -2131  -9931  -9333 
-   319   -842  -4752  -3173    -76   -143   2535   1021   -167  -1277  -3089  -3845   -213     70    220    166   -681   -625   -569  -4944  -4269   520
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9331 
-   320   -802   1990  -1826   -490   1801  -4964   1093   1213    187    973    755  -4284  -1318  -1411  -1104   -697   -799  -1128   1201   -978   521
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9329 
-   321   -708   -130  -1914  -5263   -332    342  -4000   1208  -1854   1558    778  -4765   -809   -603  -4678    172   -710   1286  -3876  -3533   522
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9326 
-   322   -588  -3520  -5192  -1918   1135    270  -3836    495  -1340    432   -431   -304   -179    219    -93  -2074    244   1054   1846   1077   523
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9324 
-   323    161  -4757    653     76  -5066    293  -2950  -1059  -1283    154  -1273  -1477    883   -952  -1386    647   1735   -603  -4947  -1016   524
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9322 
-   324    345   -366   1732     56  -1484   -490   1002  -2492  -1559  -1232  -3867    370    307  -1318    351    732    682   -287  -4962  -4281   525
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9320 
-   325  -1113  -4782    356    681  -5103   1203   1274  -4853    -78    -23  -3871   -442    812  -2482   -156    937    372   -624  -4965  -4282   526
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S  -1000 -11255  -1006   -894  -1115   -701  -1378  -9931  -9317 
-   326   -403  -3901    786   1514  -4221     69  -2061  -3971  -1642     77  -2990    886   1522  -1601    691    478   -742  -3522  -4084  -3402   527
-     -   -149   -507    232     54   -383    395     99   -628    213   -457   -717    273    391     45    104    357    114   -374   -287   -256 
-     S  -1265  -1643  -1932  -2171   -362  -5292    -37  -9931  -9315 
-   327   -957  -3520   1749   1484  -3836   -729  -1693   -546    436    282   1701  -1671    286    954   -175  -1941  -1997  -3139  -3706  -3026   540
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G     -5  -9821 -10863   -894  -1115   -893  -1115  -9931  -9313 
-   328    -71  -3904    451    611    360  -3973  -2658   1203  -2341    578  -3039   -813  -1183   -262   1050    -92  -1281   -788  -4195   1554   541
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10756 -11798   -894  -1115   -881  -1130  -9931  -9311 
-   329    417  -4587   -166  -1194    741    103   -194  -4657   -208  -1182   -387  -1409    363    305    570   1404    777   -367  -4771  -4089   542
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -26 -11045  -5999   -894  -1115   -631  -1498  -9931  -9308 
-   330  -1730   1393  -1473   -370   -400   -538   -822   -829    646   -361    420    -53   1099   -107   1493  -1780   -749     20   2366   -261   543
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11165 -12207   -894  -1115   -419  -1988  -9931  -9306 
-   331    269   -193  -3999    -88    975   1216   -492    713   -847   -277  -3065    -46  -4728  -1245   -835    676    -22   -593    222    579   544
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -32 -11237  -5647   -894  -1115   -404  -2033  -9931  -9304 
-   332    495  -4539    184   1080   -543   1172   -366  -1247  -2620    -51     93  -1295   -170    -56   -650  -1261   -755    425  -4780   1002   545
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -11227 -12269   -894  -1115   -325  -2309  -9931  -9301 
-   333    -53    602   1004   -116  -1682  -2340  -3164    520   -532    383   -965  -1292  -1859   -238  -1453    147    -26   -181   1107   2179   546
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9299 
-   334  -1983   2268  -5931  -2038   1660  -5135  -4006   1127  -1857   -299   1363   -559   -443  -4514  -4691  -1184    889   1340   2158    410   547
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9297 
-   335   -138    570   -903  -4689   1476  -2119   -212   -314  -1882   1298   1133    753  -1836  -1353  -1682    233    111   -671   1252    436   548
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9295 
-   336  -3376   -236   1984   -282   1301    309    317  -1873  -2858   -914   -510   1634  -1654  -1314   -148   -480  -1210   -235    220    577   549
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9292 
-   337  -1154   -180   -907  -1730   1084  -1367   -646   -182   -818  -1263   -631   -706   1113  -3269   -757    188   1609   -710   2738   1462   550
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9290 
-   338   -752   2384  -1030    397   1058  -1982    871    209  -2787  -1319  -3506    520  -1651   -183  -3251   1423   1035  -1856  -4660    594   551
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9288 
-   339   -776    745  -1547    -14   1276   -450   -565  -2251   1037  -2797   -963  -2966   1264    307   1074   -451    136   -406    753    764   552
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -115 -11255  -3742   -894  -1115   -701  -1378  -9931  -9285 
-   340    378  -4447    541  -2646    894   -745    144  -2036    131   -515   -523   -372    552   -422  -1861    966   1145    198    275  -4074   553
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11143 -12185   -894  -1115  -1027   -974  -9931  -9283 
-   341   -626  -4716   1783    540  -5032  -4231   -366    -34   -505  -2415  -3807   -878    866  -1146  -2979   1580    651  -1862    256    869   554
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11195 -12237   -894  -1115  -1381   -699  -9931  -9281 
-   342  -3298    346   -730    507  -1401   1777  -2990  -4403  -2622  -1140    565   -500   1645    156  -1678   -139    349  -2128    935   1352   555
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -915 -11211  -1096   -894  -1115  -1960   -429  -9931  -9278 
-   343   -397  -3883  -1135    685    355   -303    443  -3918  -1694   -186    617     83   -840    577    542    977   -658    460  -4079    845   556
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -124 -10300  -3642   -894  -1115  -4185    -82  -9931  -9276 
-   344   1377  -2486    933  -4205   2081   1301  -3030    558  -3833   -392     57  -1605  -4218  -3484   -624  -3245  -2576    449  -2941  -2595   557
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -202 -10223  -2963   -894  -1115  -5326    -36  -9931  -9274 
-   345   1816  -3692   -971     68  -4009   -916    579  -3757  -1442  -3706  -2782   -136   2574   -373   -395  -2108   -481   -977   1303  -3196   558
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C  -1183 -10026   -844   -894  -1115  -5487    -33  -9931  -9271 
-   346  -1333  -2777   1249   -642  -3086  -2310   -970  -2827    634   -481  -1869   1560   1294   -515    610    937  -1272     12  -2967  -2292   559
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -246  -8849  -2706   -894  -1115  -4904    -49  -9931  -9269 
-   347  -1337   1990  -1971    434  -1780     41  -1318  -1357  -1265    -69   1667    724  -2651    998  -1603    217  -1277    393   3238  -1695   560
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7  -8736  -9778   -894  -1115   -441  -1924  -9931  -9267 
-   348   -100  -4464   1169   -445  -1158   1322    201  -1499   1050  -2096  -3553    612    925    673  -1579   -231    255  -4086  -4647  -3964   561
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -10906 -11948   -894  -1115   -336  -2265  -9931  -9264 
-   349    186  -4727   -657   -245  -5048    799   1549  -4799    -40  -4743  -3816    288   1236    343   1649    311  -1572   -655  -4910    337   562
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -103 -11195  -3903   -894  -1115   -700  -1379  -9931  -9262 
-   350    700  -4670  -1291   -166  -1459   1072      3  -4740   -639   -223   -885    693    948   -798    408     21    686   -208  -4854  -4172   563
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11135 -12177   -894  -1115  -1101   -906  -9931  -9260 
-   351  -1933  -3405  -5434  -4824  -3367  -2052  -3851    670  -2157    406   1341  -1453   1352  -1288  -1021   -207   1079   2167  -3856  -3502   564
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11187 -12230   -894  -1115   -636  -1488  -9931  -9257 
-   352  -2038  -3527  -5028  -1252  -3500  -2021   1101    342  -3012   2368    608  -1509   -377  -3961    206   -628   -433   -449  -3966    -32   565
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11232 -12274   -894  -1115  -1490   -635  -9931  -9255 
-   353    170    724  -2319  -1618    188   1059  -3917    408  -4626   1402   1517   -837  -5117   -843  -1625  -1207    166    713  -3885  -3535   566
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -11232 -12274   -894  -1115  -1490   -635  -9931  -9253 
-   354   1025   -447  -3443   -645  -1374    361   2136  -1093  -1497  -2716  -3459  -3154  -1567      5    -14   1636   -392    876  -4617   -657   567
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11232 -12274   -894  -1115  -1490   -635  -9931  -9250 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11232 -12274   -894  -1115  -1490   -635  -9931  -9248 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11232 -12274   -894  -1115   -363  -2167  -9931  -9246 
-   357    473  -3510  -1928  -1945   -118    584  -3851    522  -1821    995    954   -768  -1633  -1331  -4398     -2   -344    749   2698   -581   570
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9243 
-   358    993  -4754   -238    118  -5062   2088  -2951  -2211  -1294   -109  -3847  -1237  -1605  -2495  -1360    891    577  -1957    219  -4270   571
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11255 -12297   -894  -1115   -701  -1378  -9931  -9241 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -45 -11255  -5119   -894  -1115   -701  -1378  -9931  -9238 
-   360    974    173   1165    -47   -248    986   1432   -347   -669  -2084  -3805  -1173  -1540   -927   -221   -750   -419  -1624    202   1522   573
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -46 -11213  -5100   -894  -1115  -1919   -443  -9931  -9236 
-   361   1644   -298    786  -1896     93   -620   -473   -423   -697  -1034  -3556     48    377   -563  -1316    140  -3204    164   1826    597   574
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C  -2254 -11171   -343   -894  -1115  -2562   -268  -9931  -9234 
-   362  -1604  -2954    548   -908  -3339   1929  -1299  -3072   -940   -472  -2172   2150    362   -863  -1451    151    382  -2642  -3270  -2602   575
-     -   -147   -503    230     40   -384    401    103   -629    210   -465   -723    275    393     52     95    358    127   -372   -297   -252 
-     C  -2910   -793  -1796  -1402   -686  -3922    -98  -9931  -9231 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11255 -12297   -894  -1115   -701  -1378  -9931  -9101 
-   415  -3578    699  -1805   -129   1590  -5096    927    921  -1815    333   -397    842  -1652  -4370  -4589  -1267    313   -893   2809   2126   645
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11255 -12297   -894  -1115   -701  -1378  -9931  -9098 
-   416   1530  -4139  -1760  -1607    537  -2588  -3238   -872  -1663  -1562  -3294  -3348   1923  -1055   -567    841    465  -1101   1775    907   646
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11255 -12297   -894  -1115   -701  -1378  -9931  -9095 
-   417   -673  -4781  -1399   -837    579    681    294  -4851    638    224    -54  -1205  -1749   1482   2085  -1762  -1564  -4402  -4964    960   647
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11255 -12297   -894  -1115   -701  -1378  -9931  -9093 
-   418    531  -4241  -1572  -3010   -411   2798   1001  -1849  -2903  -4169   -662  -3256  -1586  -1074  -1418    431  -1833  -3753  -4558   1497   648
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -63 -11255  -4633   -894  -1115   -701  -1378  -9931  -9090 
-   419    850   1132  -1429  -2716  -4681   1198  -2986  -4360  -1305   -251  -3588  -1592  -1578     27  -3106   1652   1207    432  -4721  -4111   649
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11196 -12238   -894  -1115  -2218   -349  -9931  -9087 
-   420  -2134    -75  -5785  -1637   2358   -243   -998   -468  -4770  -1434  -2571   -523  -1767  -4410   -739  -1416  -1507     71   2464   3329   650
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11196 -12238   -894  -1115  -2218   -349  -9931  -9085 
-   421    927  -4726  -3102   -390  -1430    795    693  -4797    618  -4742  -3816   -842    920  -1331   -212   1382   1052  -1126  -4910  -1010   651
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11196 -12238   -894  -1115   -208  -2895  -9931  -9082 
-   422   1155  -3721  -4432  -1173    950  -2072   1694   -589  -1659    168   -474  -1465   -728    334  -3945   -892    556  -1066  -4134   2630   652
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9079 
-   423   -420    803   -254  -1730   1361  -1388  -3550    197  -1671   -194   1199    144   1209   -419  -1105   -689     20    206   1157   1195   653
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-     H     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9077 
-   424    552  -4696  -1069   -139   -590  -2307  -2971  -2354  -2568  -1590   -739     19   1888    151   1376    925    343   -861  -4903    411   654
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9074 
-   425   -610  -4654   -709   -633     49    318  -2986   -542   -653  -1165     62   -787   1368    921    328  -1035    463   1453    132  -4226   655
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-     C     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9071 
-   426   -601    736  -1501  -2853  -4586   2171   -413  -2253  -1379    617    220   -234   -325   -243    619   -881   -804   -572  -4690    768   656
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-     C     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9069 
-   427    649  -4782   1104    715  -1458    753   -420  -4854   -826  -4798     26    788   -397   1701  -3029     84    465  -2004  -4965   -192   657
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-     H     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9066 
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-     H     -4 -11255 -12298   -894  -1115   -701  -1378  -9931  -9050 
-   434   1006  -4614    594   -328    -16    329   1037     38  -2616  -1070     89   -790   -820    538    872     37     96   -721     26  -1419   667
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-   435   -500  -4279  -1562   -203   -460  -4463    743  -1254  -1540   2006    852   -161  -1406   1645   -874  -1788  -3317  -1093   1077    442   668
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-   436   1324   -240  -1856  -1072   -871   -402  -2988  -2563   1054  -2101   -763  -2222    296  -2549   1975    775     43   -657  -4870  -4224   669
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-     C    -33 -11255  -5637   -894  -1115   -701  -1378  -9931  -9039 
-   438   -557  -4755   -578  -2582  -5076  -1115  -2915  -4826    346  -4771   -637   -658   3251   -909   1046    -77    -31  -4377  -4939   -999   671
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-     T     -4 -10500 -11542   -894  -1115   -490  -1795  -9931  -9003 
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-     T     -4 -11079 -12121   -894  -1115    -90  -4045  -9931  -9000 
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-     E     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8997 
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-     E     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8994 
-   454  -1881   -171  -6091  -5456   3373  -5300  -4166   -336  -5053   1630   -381  -4946  -5336  -4662  -4849  -4387  -3684    660   1633   -273   701
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-     E     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8992 
-   455   3264   1711  -7635  -7940  -7433   -442  -6867  -7220  -7550  -7496  -6555  -5979  -5956  -1458  -7156  -1187    250   -413  -7683  -7640   702
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8989 
-   456  -4245   -293  -7581  -7879  -7364   3639  -6834  -1960  -7508  -7435  -6508  -1578  -5955  -6957  -7125    -64  -1718  -5976   -643  -7557   703
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-     S     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8986 
-   457    685   1761   1764   2402  -5094  -4295   -396  -4840  -2542  -3121   -568    788  -4390  -2500  -3049    526   -417  -4398  -4967  -4288   704
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8983 
-   458   1239  -4022    425   -526   -885   -566   3349  -1944  -3153  -3924   -528  -3471  -4678  -3063  -3545    511  -1523  -3501   2170   2361   705
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8980 
-   459  -2174   1526  -5922  -5287  -1160  -5134   -489    144  -1250   -878   -529  -1891  -5184  -4509   -570   -883   3051    414   1174    897   706
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8977 
-   460   1236    512    337   -737  -1408   -923   2108   -268   -877  -4793   -294   -819  -4377   -862   -181   1643    826  -4398  -4962  -1026   707
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S   -137 -11256  -3504   -894  -1115   -701  -1378  -9931  -8974 
-   461   -639   -166  -1423  -1308  -4940   1083   -415  -4682   -792   -279    851  -2809    797   1242    809    840    861  -2302    349    -33   708
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11123 -12165   -894  -1115   -114  -3724  -9931  -8972 
-   462  -1222   -199   -312    959    545   1099    839  -4847    383   -783  -3868    607  -1768  -1169   -262     38   -396    969    170  -4281   709
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -370 -11256  -2161   -894  -1115   -701  -1378  -9931  -8969 
-   463  -2086  -3118  -5221   -871    644   1113   2455  -2619  -4277   -194    536    694  -4791  -3966  -4202  -1105     36  -1141   3012   2475   710
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -209 -10890  -2921   -894  -1115  -3217   -164  -9931  -8966 
-   464   -697    433  -4438  -3852    937    916   1576   -410  -3620   -263  -2264  -1015   2110  -1261   -279   -717    109  -2498  -3506   1726   711
-     -   -149   -488    232     45   -381    400    105   -627    210   -466   -721    275    393     45     95    359    117   -367   -295   -250 
-     T   -171  -3505  -5520    -45  -5038  -1611   -572  -9931  -8963 
-   465   1502  -4307    -51  -2556  -4644   2453  -2849  -1442  -2480  -4392  -3527  -2834  -4224   1081   -251    658  -3068   -545  -4650  -4029   713
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10875 -11918   -894  -1115   -453  -1891  -9931  -8960 
-   466   -530    864  -5836  -5201    224    193   -598  -2825  -4799  -1243  -2536  -4692  -5100  -4424  -4604   1153   2430  -1429   3669    875   714
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11166 -12209   -894  -1115   -155  -3297  -9931  -8957 
-   467   -330  -3428  -5949  -5314    439  -5152   -490   2030  -4909   -225   2918  -4798  -5201  -1354  -4709  -4237    -12   2119  -3889  -3547   715
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8954 
-   468   -666  -4783   1309   2031  -5103   -147   2655  -1980  -2524  -4799  -3872    444    926   1275  -1369  -3191  -3250  -1337  -4966  -1082   716
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8951 
-   469  -2269  -4987    973  -1470  -5315   3206  -3129  -5067   -479  -5009   -587  -3065  -4551  -2676   -121   -324   -687  -4616  -5176  -4489   717
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8948 
-   470   3196   2507  -7635  -7939  -7426   -559  -6865  -7212  -7549  -7488  -6549  -5978  -5956  -1458  -7154   -485   -914    -35  -7677  -7633   718
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8945 
-   471  -1119  -3415  -5934  -5298    672  -5136  -4007   2085  -4893   1009   -599  -4782  -5186  -4516  -1345  -2219   -995   1915   1111   1665   719
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8943 
-   472   -831  -4768   -661   1693  -2343  -1708    346   -565   -315    927    714   -505  -4380    707   1393   -564  -1006  -1084  -4955  -1138   720
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8940 
-   473    623  -6041  -1408  -1627  -6440  -1325  -1053  -6246  -3894  -6174  -5322  -3652  -5336   -386  -4506   3101   1266  -5749  -6352  -5563   721
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8937 
-   474   1283  -4880  -7575  -7931  -7617   3500  -6938  -7449  -7622  -7708  -6729  -5996  -5978  -7039  -7222  -1104  -4752  -6106  -7830  -7827   722
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8934 
-   475  -1975   1592  -2180     55  -1319  -2005   -709    818    971    983   -799  -1903  -4724     83   1652  -3614   -371   -162    713    376   723
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8931 
-   476   -554   -254  -1086    -34  -2345  -2018   -421   -962   -132   -232  -1151    438  -4378   -238   2907   -301    284  -4395  -4960  -1082   724
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8928 
-   477   2734   -272  -4478   1457  -4507  -2070  -3898  -2942  -3813  -4362  -3630  -4020  -5032  -1229  -4156   -321    417    740  -4833  -4389   725
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8925 
-   478   3360   1183  -7680  -8026  -7576  -5147  -6938  -7331  -7627  -7650  -6683  -5998  -5965  -7047  -7212    269  -2506    333  -7807  -7798   726
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8922 
-   479    929   1388   1098    720  -5100   -941  -2942  -2897   -975  -4796  -1246    411  -4377   1684   1427   -809   -265    -32   -689  -1432   727
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8919 
-   480   1200    337   1133   1040  -5092  -1953   -490  -1167  -1285   -548  -3865   -386  -4378    754   1891  -2293  -1573   -284  -4960   -405   728
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8916 
-   481   -222    210  -7778  -7354  -5235  -7395  -6829   2587  -7179    880   1061  -7045  -7247  -6983  -7182  -6645  -2467   2357  -6473  -6046   729
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11256 -12298   -894  -1115   -701  -1378  -9931  -8913 
-   482   -184    -89  -1779  -4504  -1425  -2037    191   1650  -1748   1925    630    489  -1681  -1785  -1140   -778   -863    -74  -3979  -3611   730
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     H      *      *      *      *      *      *      *  -9931      0 
-//
-HMMER2.0  [2.3.2]
-NAME  TrbL
-ACC   PF04610.6
-DESC  TrbL/VirB6 plasmid conjugal transfer protein
-LENG  285
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  37
-DATE  Thu Apr 24 20:13:05 2008
-CKSUM 7909
-GA    16.4000 16.4000;
-TC    16.8000 16.8000;
-NC    15.7000 15.8000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.984805   0.666494
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -37      *  -5286
-     1   1046  -2737  -5268  -4635    341  -4478  -3354   2002  -4234   1457   1201  -4124  -4520   -543  -4034  -3565   -752   1255  -3208  -2870     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -1037  -9150 
-     2    509  -3178  -3190  -2630  -3226   1064  -2610    827    -63  -1443  -2348    234  -3957    362  -2865   1036   1408   -193   1973  -3093     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9147 
-     3   1988  -2649  -5144  -4511  -2606   -482  -3238    918  -4111    -82  -1854  -4003  -4413  -3738  -3918   1059   1116    408  -3110    760     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9145 
-     4   1875   2116  -5166  -4531    515    792  -3242    586  -4126    507   2878  -4014  -4417  -3749  -3926  -1336  -2761  -2058  -3107  -2765     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9142 
-     5  -1088  -2638  -5156  -4520    466   -366  -3230   1169  -4115   2088    338  -4004  -4408  -3738   -876  -1284  -2752   1314   1846  -2753     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9140 
-     6  -1140  -2647  -5125  -4492  -2603    167  -3230   1176  -1077    -60    409  -3994  -4410  -3725  -3908   -331   2573   1439  -3106  -2763     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9137 
-     7  -5276  -4709  -7875  -7462  -3917  -7754  -7136   2057  -7386   2752  -2654  -7441  -7099  -6627  -7193  -7166  -5214    847  -5789  -5822     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9134 
-     8  -1037  -2869  -4076  -1029   1310  -1380    131  -2405  -1052  -2730  -2062  -3431  -4247  -3083  -3433  -1226  -2736   -846   2579   4100     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9132 
-     9  -3798  -3554  -6145  -5526   1338  -5418  -4230   2715  -5148    375   1249  -5061  -5346  -4653  -4913  -4528  -3727   1695   2641   -224     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9129 
-    10    796  -3078  -5670  -5055   -505  -4921  -3826   1845  -4674    822   3089  -4568  -4931  -4287  -4481  -4022   1161    783  -3638  -3312    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9127 
-    11  -1166  -2772  -5301  -4666   1680  -4510  -3381    912  -4264   1916   2088  -4157  -4547  -3875  -4061  -3598    -98    -73  -3224   1987    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9124 
-    12   -329  -2647  -5062  -4432   1666  -4345    278    144    297    -40    360  -3961  -4396    855    551  -3425    -40    -12   2512   2349    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9122 
-    13    640    709  -6767  -7050  -6572   3310  -6007  -6355  -6674  -6631  -5694   -846  -5117  -6119  -6297  -1287    -58   -165  -6824  -6773    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9119 
-    14   -429  -3473  -5995  -5398   1390  -5261  -3877   1699  -5005   1349    245  -4861  -5224  -4514  -4765  -4364  -3634  -2755    979   3354    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9116 
-    15    430  -3997  -2418      3  -4304    133  -2197  -4045    141   1008   1572   1213  -3630    495    190    522  -2497  -3611   1011    516    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9114 
-    16  -2810  -2637  -5153  -4517   1853  -4357    344   1678  -4112  -1166   2698   -782  -4407   -562  -3913  -1302    -47   1257   2494    674    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9111 
-    17   -315  -2637  -5156  -4519   -503  -1289    108    925  -4114   1682   2846  -4004  -4408  -3737  -3914   -418   -790    487    979    775    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9109 
-    18   -363  -2639  -5138  -4503   1806  -1330  -3226    100  -4102   1353    336  -3996  -4405   -617   1473   -317    857   -726   1063   -271    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9106 
-    19   -346  -4376  -2922  -2372  -4798   3291  -2580  -4496   -553  -4426     17    292  -4066   -189   -682  -1078  -2976  -4074  -4561  -3969    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9103 
-    20    986  -3574  -2713   -762   -684    148    340    392    890     84    225   -528   -945  -1998   1261   -341    -67   -232  -3870  -3311    20
-     -   -143   -503    233     40   -379    399    103   -625    210   -464   -713    275    393     43     93    360    115   -369   -283   -252 
-     -   -307  -3635  -3192  -2646   -251   -701  -1378  -9187  -9101 
-    21   -272  -2505  -4856   -113   -230  -1160  -3051   1773  -3856     84    411  -3785  -4239   1100  -3708    972   -762   1596  -2960  -2615    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10246 -11288   -894  -1115   -885  -1125  -9187  -9098 
-    22  -2487  -3960    673   1127  -4281    218    286  -4032    150  -3976  -3049   1251     79   1410    604    259    543  -1073  -4143   -167    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10335 -11377   -894  -1115   -256  -2622  -9187  -9095 
-    23    149  -3787   1227   1484  -4008    141  -2272    350  -1903    392   1054  -2285   -798   -324   -624  -1045    449   -372  -4034  -3418    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9093 
-    24  -1162  -3964     71  -1887  -4257  -1279  -2208  -3987  -1800   -272  -3061    848   2899    583   -581    503    -29  -1303    967  -3500    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9090 
-    25   -349  -2639  -5135  -4501   1620  -4355    217   1791  -1042    274    328  -3995     47    848   -968  -3439  -2750   1065   2567    -55    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10413 -11455   -894  -1115   -701  -1378  -9187  -9087 
-    26    478  -4027   -623    403  -4347   -410   1174    391     92  -4042     60   -392   -869    509   1278    540    -16    151  -4210   -419    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -115  -8988  -3809   -894  -1115  -4809    -52  -9187  -8219 
-   272    155   1918    243  -2156    870    -92  -1668  -1109  -1944    -55   1555  -2105    452  -1752    473    119    468    539  -2001  -1617   450
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -380  -8882  -2146   -894  -1115  -4864    -50  -9187  -8214 
-   273  -1217  -1583  -1986  -1431  -1657  -2455  -1286  -1225  -1272  -1515   2632  -1527    694   1134  -1582    469   2091    660  -2029  -1601   451
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11  -8513  -9556   -894  -1115  -5018    -45  -9187  -8209 
-   274  -1263  -1092  -3586  -2952   1195    269  -1678    889  -2553   1090   -293  -2448  -2859  -2180  -2361    341  -1204   1576  -1548   1350   452
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11  -8513  -9556   -894  -1115  -5018    -45  -9187  -8205 
-   275    656  -2078  -3333  -3034  -3541   2486  -2842  -3211  -2909  -3464  -2663  -2562  -3058  -2702  -3101    708   1755  -2613  -3825   1619   453
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11  -8513  -9556   -894  -1115  -5018    -45  -9187  -8200 
-   276    502  -1221  -3012  -2424  -1199   2135  -1596   -749  -2138    351   1953  -2174    681  -1873  -2148  -1777  -1216   -658  -1682   1336   454
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -523  -8513  -1748   -894  -1115  -5018    -45  -9187  -8195 
-   277   2492  -1512  -3096  -2779  -2653   1051  -2362  -2228  -2579  -2549   2521  -2202  -2625  -2347  -2679  -1300   1277  -1802  -3023  -2697   455
-     -   -147   -501    235     42   -381    398    105   -627    210   -467   -712    275    393     44     95    360    119   -370   -295   -244 
-     -  -3168   -179  -9046    -30  -5625  -5160    -41  -9187  -8190 
-   278   -894  -1140  -1791  -1223  -1153    637   -969   1119    997  -1012   2101   1276  -2271   -905  -1300  -1201   -835   1080  -1558  -1147   457
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -8004  -9046   -894  -1115  -5160    -41  -9187  -8185 
-   279   1987  -1496  -3202  -2922   1739   1921  -2417  -2202  -2734  -2523  -1794  -2267  -2645  -2462  -2788  -1319   1383  -1785  -2976  -2635   458
-     -   -150   -501    232     45   -381    399    105   -627    210   -467   -721    275    393     48     98    360    116   -370   -295   -245 
-     -  -3168   -179  -9046    -30  -5625    -25  -5837  -9187  -8180 
-   280   2024  -3991   -726    449  -4298    180  -2263  -1063  -1863  -4013  -3110   -402  -3684  -1816  -2366   2016    -89  -1243  -4214  -3551   460
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10415 -11458   -894  -1115   -701  -1378  -9187  -8175 
-   281   1670  -4004   -626   -681   -813   1238  -2194  -4057  -1779  -1599  -3096    359  -3628    996    647   1071  -2496  -1155  -4194   -314   461
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10415 -11458   -894  -1115   -701  -1378  -9187  -8170 
-   282    127  -2643  -5162  -4526   -457  -4365  -3237   2109  -4121   1823   1248   -869  -4415  -3745  -3922   -399     19    388  -3103  -2760   462
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10415 -11458   -894  -1115   -701  -1378  -9187  -8165 
-   283   2097  -2960  -4092   -203  -3019    528  -3077   -852  -3324  -2897   2026  -3460  -4272  -3136  -3502   1637    516   -837  -3457  -3072   463
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10415 -11458   -894  -1115   -701  -1378  -9187  -8160 
-   284   1079  -5309   -553  -2868  -6137   3149  -3769  -5962  -3798  -1900  -5132    922  -4855   -458  -4459  -1287  -4112  -5371  -6130  -5330   464
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10415 -11458   -894  -1115   -701  -1378  -9187  -8155 
-   285   -321  -3883  -6171  -6162   -515   3405  -5391  -1011  -5936  -5577  -4787    800  -5035  -5513  -5768  -1183   -815  -4585  -5969  -5743   465
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9187      0 
-//
-HMMER2.0  [2.3.2]
-NAME  TNV_CP
-ACC   PF03898.5
-DESC  Satellite tobacco necrosis virus coat protein
-LENG  204
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  3
-DATE  Tue Apr 22 18:35:33 2008
-CKSUM 926
-GA    25.0000 25.0000;
-TC    341.6000 341.6000;
-NC    12.4000 12.4000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.992213   0.710576
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -322      *  -2322
-     1  -1576  -1321  -3770  -3314   -951  -3278  -2537    645  -2971    118   3953  -2998  -3258  -2651  -2894  -2509  -1576   2174  -2172  -1891     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -1322  -8665 
-     2   1805   -920  -2226  -1991  -2736  -1205  -1832  -2401  -1871  -2659  -1817  -1432  -1877  -1663  -2046   1993   2054  -1642  -2966  -2650     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8662 
-     3  -2077  -2778  -2642  -1393  -3606  -2611   -552  -2955   2978  -2621  -1949  -1304  -2566   -133   2555  -1958  -1775  -2720  -2467  -2355     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8658 
-     4  -1724  -2636  -2029  -1019  -3345  -2386   -445  -2769   2348  -2486  -1760  -1043  -2362   2373   2314  -1600  -1483  -2487  -2392  -2176     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8655 
-     5  -1268  -2125   -747   -803  -3095   1947  -1271  -3003   -903  -3003  -2271   -985  -2275   3443  -1194  -1272  -1431  -2468  -2987  -2520     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8651 
-     6   -668  -1478   -757   -861  -2928  -1379  -1374  -2842  -1305  -2957  -2143   2287  -1980  -1104  -1677   2702   -961  -2094  -3061  -2494     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8647 
-     7  -1011  -2316   -530   -145  -2736  -1753   -329  -2403   1912  -2281  -1451   1975  -1890   2395    173   -874   -919  -2013  -2358  -1826     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8644 
-     8  -1121  -2214  -1045   -455  -2708  -1918   -378  -2323    547  -2213  -1421   -632   1941   2258   2080  -1029  -1013  -1980  -2276  -1849     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -433  -7112  -2003   -894  -1115   -701  -1378  -8987  -8640 
-     9   2338   -629  -1811  -1729  -2520   -890  -1620  -2178  -1695  -2470  -1643  -1145  -1587  -1476  -1834   2163   -380  -1389  -2758  -2442     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -24  -6703  -7745   -894  -1115   -384  -2097  -8987  -8637 
-    10   -711  -1856   -573   -170  -2452  -1557   -399  -2159    187  -2140  -1295   1958  -1773     15   1870   1552   -711  -1728  -2293  -1729    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8633 
-    11  -2071  -2775  -2624  -1387  -3600  -2607   -552  -2952   3070  -2620  -1947  -1301  -2564   -134   2398  -1953  -1771  -2716  -2467  -2353    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8629 
-    12   -827  -2094   -576   -101  -2523  -1667   -270  -2198   1853  -2120  -1274   -350  -1791   2333    143   1306   -752  -1804  -2237  -1689    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8626 
-    13   1495  -1766   2179   -198  -2740  -1391   -797  -2483   -649  -2542  -1701   -433  -1823   -430  -1176   1550   -837  -1925  -2773  -2123    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8622 
-    14   -944  -1028  -3105  -2838  -1693  -2240  -2330    475  -2571  -1002   -695  -2311  -2668  -2405  -2593  -1533   1831   2888  -2540  -2156    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8618 
-    15   1254  -1298  -1000   -447  -1521  -1671   -439  -1039   1847  -1249   2640   -606  -1811   -132   -252   -709   -584   -841  -1719  -1258    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8615 
-    16   -891  -2057   -815   -258  -2533  -1746   -309  -2186    481  -2112  -1285   -470  -1860   2366   1963   1327   -814  -1811  -2217  -1720    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8611 
-    17   1366  -1005  -1266   -819  -1342  -1641   -775   -572   -619  -1091   -448   -880  -1894   2074   -915   -750   -580   1729  -1713  -1272    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8607 
-    18  -1771  -1603  -3750  -3689  -2037  -3050  -3231    403  -3479  -1154  -1076  -3246  -3399  -3383  -3437  -2628  -1917   3536  -3074  -2677    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8604 
-    19  -2071  -2775  -2624  -1387  -3600  -2607   -552  -2952   3070  -2620  -1947  -1301  -2564   -134   2398  -1953  -1771  -2716  -2467  -2353    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8600 
-    20   -863  -1630  -1473  -1068  -2727  -1673   -957  -2475   -172  -2500  -1728  -1047  -2077   -614   2130   2599  -1014  -1962  -2572  -2169    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8596 
-    21  -1885  -1507  -4178  -3694   -880  -3807  -2903   3020  -3382    332   3083  -3452  -3572  -2937  -3254  -3046  -1840    528  -2291  -2091    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8592 
-    22  -1790  -1359  -4287  -3823  -1188  -3926  -3178   2288  -3620   1634    -19  -3566  -3679  -3222  -3536  -3170  -1750   2160  -2597  -2350    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8589 
-    23  -1231  -2766    311   1931  -3156   1708   -728  -2975   -672  -2917  -2129   2214  -1965   -358  -1305  -1017  -1267  -2490  -3105  -2289    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8585 
-    24   -499  -1478   -659   -286  -2236  -1403   -558  -1925   -189  -2015  -1178   -469  -1712   2358   -592   1442   1680  -1481  -2272  -1710    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8581 
-    25   -548  -1104  -1024   -564  -1117  -1629   2739   -915   -335  -1129   2684   -686  -1819   -329   -645   1481   -550   -720  -1464   -906    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8577 
-    26   1508  -1248  -2927  -2615   -971  -2338  -1997   -153  -2300   2370     10  -2241  -2654  -2067  -2288  -1614  -1266   -314  -1982  -1695    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8574 
-    27  -2641  -3308   -896   3732  -3966  -2458  -2043  -4105  -2128  -4016  -3555  -1531  -2959  -1842  -2560  -2479  -2750  -3722  -3563  -3385    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8570 
-    28  -1551  -2496   -766   -632  -1919  -2059   4205  -2642    -45  -2505  -1855   -834  -2308   2407   -219  -1439  -1496  -2346  -2066  -1309    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8566 
-    29  -2620  -2961  -2461  -2046  -3743  -2791  -1570  -3603   3784  -3387  -2839  -2048  -3039  -1260   -465  -2604  -2536  -3331  -3001  -2988    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8562 
-    30  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8558 
-    31   1818  -1223  -2786  -2597   3368  -2039  -1358   -938  -2395  -1065   -763  -1994  -2490  -2061  -2356  -1339  -1209   -867  -1115   -224    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8555 
-    32   2580  -1302  -1116  -1177  -2856  -1359  -1540  -2578  -1492  -2814  -2022   2500  -1983  -1304  -1798   -725   -896  -1889  -3029  -2561    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8551 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8547 
-    34  -2338  -1877  -4643  -4129   -648  -4329  -3241   2154  -3845   2530    526  -3986  -3834  -3104  -3580  -3607  -2251     49  -2266  -2229    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8543 
-    35   -559  -1034  -1117   -730  -1219  -1646   -708   -717   -587   1181   -380   1879  -1881   -529   -884   -761   1640   -559  -1607  -1145    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -19  -7112  -8154   -894  -1115   -701  -1378  -8987  -8539 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8535 
-    37   -370  -1036  -1802  -1694  -2833   1755  -1743  -2534  -1734  -2753  -1912  -1323   2344  -1541  -1957   -568   2045  -1762  -3021  -2675    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8531 
-    38   -706  -1485   -832   -880  -2750  -1440  -1308  -2485  -1154  -2697  -1931   3185  -2004  -1038  -1487   -808   2159  -1896  -2895  -2365    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8527 
-    39   -786   -992  -2857  -2600  -1723  -1965  -2122    148  -2330  -1132   -772  -2065  -2454  -2169  -2370  -1258   2774   2159  -2461  -2088    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8524 
-    40   -897  -1219  -1644  -1577  -1707  -1913  -1579   -257  -1592  -1408   -957   2125  -2350  -1510  -1792  -1235  -1062   2799  -2280  -1758    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8520 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8516 
-    42  -1213  -1674  -2755  -2906  -3163  -1922  -2659  -2698  -2788  -3105  -2612  -2311  -2600  -2708  -2753  -1463   3819  -2197  -3286  -3157    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8512 
-    43   2672   -923  -2519  -2463  -2802  -1245  -2152  -2236  -2320  -2688  -1925  -1650  -1962  -2081  -2357   -582   2292  -1558  -3103  -2841    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8508 
-    44  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8504 
-    45   -671  -1424   -928   -957  -2705  -1429  -1339  -2424  -1187  -2651  -1885   2469  -1998  -1079  -1505   -788   2865  -1841  -2865  -2354    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8500 
-    46  -1753  -1297  -4326  -3965  -1769  -4049  -3747   2525  -3836   -621   -545  -3725  -3875  -3695  -3913  -3366  -1745   2915  -3274  -2826    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8496 
-    47   -896  -1016  -1828  -1324   -158  -2161   -630   1713   -946   -622   -117  -1269  -2223   2046  -1102  -1225   -834   -353   -744   2659    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8492 
-    48   -785   3974  -2050  -2043  -2559  -1599  -1953  -2388  -1976  -2741  -2045   3338  -2236  -1890  -2099  -1002  -1125  -1837  -2813  -2386    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8488 
-    49  -2871  -2457  -4231  -4103  -1033  -3803  -3165   -541  -3734   3130    -31  -3935  -3797  -3286  -3484  -3713  -2869  -1136  -2394  -2220    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8484 
-    50   -342   -976  -2178  -2130  -2924  -1229  -2010  -2609  -2075  -2891  -2061  -1512  -1936  -1873  -2191   2695   2284  -1781  -3154  -2844    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8480 
-    51  -1311  -2551    -89   -171  -2897  -1712   -782  -2865   -386  -2796  -2056   3108  -2095   2573   -742  -1159  -1341  -2431  -2813  -2131    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8476 
-    52   -772  -1355   -978   -834   2431   1484   -827  -1504   -997  -1683  -1020   2099  -2033   -821  -1341   -901   -884  -1235  -1454   -633    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8472 
-    53  -1759  -1303  -4330  -3968  -1750  -4051  -3742   3033  -3837   -596   -527  -3729  -3875  -3688  -3909  -3368  -1751   2429  -3258  -2819    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8468 
-    54  -1760  -1306  -4326  -3963  -1738  -4044  -3729   3119  -3830   -582   -517  -3723  -3870  -3676  -3899  -3361  -1752   2302  -3244  -2808    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8464 
-    55  -1347  -2795     87   2076  -3101  -1691   -705  -2905   -365  -2813  -2055   -340  -2051   3237   -787  -1138  -1336  -2486  -2929  -2233    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8459 
-    56  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8455 
-    57  -2784  -3432   4016  -1200  -4140  -2466  -2197  -4505  -2621  -4365  -3956  -1551  -3014  -2039  -3232  -2593  -2938  -4046  -3710  -3552    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8451 
-    58  -1738  -2966   3199   -299  -3803   1997  -1380  -3798  -1661  -3735  -3085   -646  -2361  -1095  -2413  -1547  -1903  -3196  -3693  -3006    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8447 
-    59  -2117  -1673  -4474  -4001   -850  -4163  -3231   3039  -3732   1696    310  -3813  -3789  -3164  -3558  -3442  -2058    457  -2404  -2262    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8443 
-    60   -455  -1114  -1103   -808  -1867  -1416   -938  -1375   -801  -1724   -981   2049  -1830   -690  -1147   1716   -614   1571  -2140  -1662    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8439 
-    61  -1301  -2524   -137   -195  -2874  -1725   -765  -2833   -327  -2761  -2019   2216  -2094   3373   -663  -1155  -1325  -2405  -2774  -2107    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8435 
-    62  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8430 
-    63   -347   -973  -2195  -2157  -2892  -1234  -2021  -2564  -2097  -2859  -2038  -1526  -1942  -1896  -2201   1838   3091  -1758  -3133  -2825    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8426 
-    64  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8422 
-    65  -1496  -2778   3018   -239  -3183  -1827   -900  -3046   -554  -2964  -2220   -560  -2198   -541   2279  -1315  -1503  -2621  -2980  -2370    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8418 
-    66  -1019  -1451  -1441  -1144  -1584  -2005  -1088   -593   -679  -1172   -771  -1208  -2277   3169   -871  -1242  -1069   1909  -2057  -1558    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8414 
-    67  -1760  -1306  -4326  -3963  -1738  -4044  -3729   3119  -3830   -582   -517  -3723  -3870  -3676  -3899  -3361  -1752   2302  -3244  -2808    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8409 
-    68  -1401  -2470  -1393   -665  -3056  -2131   -390  -2586   2106  -2376  -1605   2226  -2167     39   2200  -1279  -1229  -2259  -2350  -2015    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8405 
-    69  -1271  -1039  -3372  -2821   -746  -2956  -1954   2085  -2506   1611    268  -2529  -2908  -2168  -2436  -2093   1651    532  -1730  -1449    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8401 
-    70  -1129  -1043  -2382   1602  -1280  -2726  -1713   2125  -1793   -609   -269  -1949  -2753  -1666  -2011  -1835  -1095   2040  -2075  -1654    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8397 
-    71   -732  -1944   -349    -15  -2194  -1556   2770  -2037    154  -2034  -1202   -286  -1744   2316   -225   1327   -698  -1655  -2158  -1516    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8392 
-    72   -779  -1538   -883   -378  -1389  -1773   2750  -1267    132  -1342   2859   -569  -1873   2092   -131   -816   -706  -1080  -1618  -1030    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8154   -894  -1115   -701  -1378  -8987  -8388 
-    73   -635  -1151  -1229   -693  -1428  -1748   -623   -578   1654  -1146   -486   -802  -1915   -366   -494   -816   1596   1678  -1720  -1278    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8384 
-    74  -2871  -2457  -4231  -4103  -1033  -3803  -3165   -541  -3734   3130    -31  -3935  -3797  -3286  -3484  -3713  -2869  -1136  -2394  -2220    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8379 
-    75  -1166  -1763  -1594   -856  -1595  -2115   2912  -1492    395    986   -885   -927  -2153   -172   2227  -1224  -1039  -1341  -1706  -1192    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8375 
-    76   -646   -645  -2289  -1770   -455  -2034   -960    103  -1479   -470     93  -1523  -2173  -1260  -1525  -1143   1622   1714  -1016   2546    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8371 
-    77  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8366 
-    78   -615   3515  -1900  -1423  -2268   1618  -1198  -1899   -700  -2102  -1348  -1243  -2012   -953   2262   -797   -822  -1467  -2388  -2036    78
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-    79  -1213  -1674  -2755  -2906  -3163  -1922  -2659  -2698  -2788  -3105  -2612  -2311  -2600  -2708  -2753  -1463   3819  -2197  -3286  -3157    79
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-     E    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8358 
-    80   1598   -835  -1948  -1621  -1480   1525  -1316   -938  -1461   1368   -650  -1333  -1958  -1289  -1619   -723   -631   -703  -1920  -1548    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8353 
-    81  -1392  -1721   2195   -979  -1835  -2221  -1498   2859  -1606  -1277   -980  -1217  -2552  -1319  -2033  -1664  -1434   -116  -2506  -1947    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7112  -8155   -894  -1115   -701  -1378  -8987  -8349 
-    82  -1213  -1674  -2755  -2906  -3163  -1922  -2659  -2698  -2788  -3105  -2612  -2311  -2600  -2708  -2753  -1463   3819  -2197  -3286  -3157    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8344 
-    83   -499   -990  -1342   -980  -1523  -1559   -963   -710   -883  -1308   -643   1974  -1911   -782  -1180   -726   1931   1623  -1896  -1455    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8340 
-    84   -897  -1462  -2333  -2543  -3185  -1640  -2474  -3294  -2686  -3497  -2780  -1973  -2360  -2483  -2703   3465  -1316  -2413  -3310  -3025    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8335 
-    85   1762  -1583   -889   -741  -2535  -1544  -1002  -2219   -585  -2340  -1610   -838  -1987   3264   -865   -834   -933  -1764  -2605  -2101    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8331 
-    86   -454  -1303   -899   -682  -2550  -1315   -993  -2264   -775  -2391  -1545   2338  -1796   -657  -1177   1619   1860  -1668  -2643  -2119    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -1016  -7113  -1014   -894  -1115   -701  -1378  -8987  -8326 
-    87     55   -556   -935   -973  -1848   -729  -1049  -1737  -1029  -2004  -1322   -708  -1370   -930  -1202   2867   -288  -1129  -2083  -1629    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -35  -6132  -7174   -894  -1115  -1898   -451  -8987  -8322 
-    88   -889  -1218  -1459  -1647  -2605   3392  -1709  -2674  -1891  -2802  -2245  -1471  -1892  -1754  -1945  -1091  -1230  -2077  -2314  -2429    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -36  -6132  -7174   -894  -1115  -1898   -451  -8987  -8317 
-    89  -1726  -1441  -2629  -2593   3818  -2406   -441   -600  -2363   -279   -303  -1978  -2597  -1898  -2197  -2007  -1774   -811    162   1215    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -36  -6132  -7174   -894  -1115   -265  -2575  -8987  -8313 
-    90  -2592  -2120  -4387  -4051   3376  -4079  -1780   -262  -3715   1922    314  -3437  -3733  -2862  -3365  -3346  -2493   -855   -983   -117    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8308 
-    91  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8304 
-    92  -3605  -2699  -4175  -4419   3662  -4045   -396  -2519  -3997  -1925  -1968  -2748  -3929  -2852  -3447  -3293  -3484  -2672    347   3430    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8299 
-    93  -2091  -1746  -3971  -3840  -1676  -3532  -3289   3684  -3581   -659   -693  -3562  -3674  -3445  -3521  -3194  -2146    449  -2877  -2493    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8295 
-    94  -1537  -1405  -3306  -2952   -257  -2774  -1387   -259  -2449   -681   -470  -2429  -2944  -2232  -2354  -2072  -1569   2091   4960   -115    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8290 
-    95  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8285 
-    96  -1718  -2027  -2526  -1687  -1660  -2584   -993  -1270     19   1506   -768  -1617  -2641   -719   3033  -1889  -1604  -1399  -2041  -1685    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8281 
-    97  -2784  -3432   4016  -1200  -4140  -2466  -2197  -4505  -2621  -4365  -3956  -1551  -3014  -2039  -3232  -2593  -2938  -4046  -3710  -3552    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8276 
-    98   -706  -1485   -832   -880  -2750  -1440  -1308  -2485  -1154  -2697  -1931   3185  -2004  -1038  -1487   -808   2159  -1896  -2895  -2365    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8271 
-    99   -576  -1175   -991   -484  -1288  -1668   -492   -835   -181   -987   2643   -640  -1814   2204   -489   -708   1549   -684  -1605  -1143    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8267 
-   100  -2171  -2655  -1458  -1748  -3334  -2364  -2267  -3943  -2365  -3936  -3437   4205  -2932  -2205  -2608  -2224  -2439  -3392  -3253  -2909   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8262 
-   101  -1828  -2631  -1980  -1140  -3268  -2415   -574  -2807    683  -2546  -1859  -1150  -2451   2612   3090  -1726  -1614  -2542  -2444  -2219   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8257 
-   102  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8253 
-   103  -1213  -1674  -2755  -2906  -3163  -1922  -2659  -2698  -2788  -3105  -2612  -2311  -2600  -2708  -2753  -1463   3819  -2197  -3286  -3157   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8248 
-   104  -1053  -1202  -2650  -2305  -1031  -2237  -1773   -191  -1929   1625   -106  -2019  -2549  -1812  -1975  -1495   2728   -287  -1922  -1576   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8243 
-   105  -2931  -2878  -3420  -3706  -4181  -2925  -3468  -4621  -3859  -4490  -4165  -3491   4225  -3781  -3695  -3182  -3279  -4087  -3594  -4064   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8238 
-   106   2778   -923  -2528  -2479  -2813  -1244  -2164  -2247  -2337  -2700  -1937  -1656  -1963  -2095  -2369   -583   2095  -1564  -3114  -2854   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8234 
-   107  -1753  -1297  -4326  -3965  -1769  -4049  -3747   2525  -3836   -621   -545  -3725  -3875  -3695  -3913  -3366  -1745   2915  -3274  -2826   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8229 
-   108  -1021  -1195  -2600  -2263  -1081  -2184  -1755   -230  -1888   1445   -171  -1977  -2517  -1787  -1943  -1447   2849   -305  -1946  -1587   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8224 
-   109  -1716  -3565   2497   2847  -3761  -1632   -991  -3694  -1237  -3572  -2913   -234  -2166   -664  -2082  -1378  -1785  -3176  -3735  -2752   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8219 
-   110  -1771  -1603  -3750  -3689  -2037  -3050  -3231    403  -3479  -1154  -1076  -3246  -3399  -3383  -3437  -2628  -1917   3536  -3074  -2677   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8214 
-   111  -2871  -2457  -4231  -4103  -1033  -3803  -3165   -541  -3734   3130    -31  -3935  -3797  -3286  -3484  -3713  -2869  -1136  -2394  -2220   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -20  -7113  -8155   -894  -1115   -701  -1378  -8987  -8209 
-   112  -1169  -2684   2147    158  -3122  -1517   -718  -2952   -682  -2898  -2097   2204  -1937   -346  -1338   1703  -1215  -2450  -3089  -2265   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8205 
-   113   -343   -977  -2182  -2140  -2936  -1228  -2020  -2624  -2088  -2906  -2074  -1517  -1937  -1885  -2201   2804   2088  -1789  -3166  -2858   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8200 
-   114   2424  -1127  -2650  -2357  -1192  -2029  -1837   -332  -2066   1598   -276  -1969  -2439  -1888  -2105  -1308  -1079   -373  -2034  -1693   114
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8195 
-   115  -1198  -2731   2327    162  -3158  -1522   -732  -2992   -711  -2934  -2139   2213  -1949   -363  -1377   1518  -1246  -2489  -3125  -2292   115
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8190 
-   116  -1500  -1139  -3919  -3420   2157  -3443  -2490   2238  -3159   -157    -39  -3064  -3321  -2799  -3057  -2628  -1460   2260  -2102  -1688   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8185 
-   117   -391   -839  -1673  -1231  -1399  -1472  -1027   -921  -1038  -1230   2890  -1095  -1865   -917  -1274   1684   1786   -677  -1782  -1382   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8180 
-   118   -897  -1462  -2333  -2543  -3185  -1640  -2474  -3294  -2686  -3497  -2780  -1973  -2360  -2483  -2703   3465  -1316  -2413  -3310  -3025   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8175 
-   119  -1268  -2125   -747   -803  -3095   1947  -1271  -3003   -903  -3003  -2271   -985  -2275   3443  -1194  -1272  -1431  -2468  -2987  -2520   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8170 
-   120  -3482  -2868  -3701  -3919    238  -3552  -1112  -3000  -3638  -2516  -2526  -3027  -3772  -3101  -3341  -3418  -3527  -3071   -441   4711   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8165 
-   121  -1517  -3098    332   2171  -3409  -1637   -901  -3304   -911  -3229  -2513   3174  -2115   -559  -1545  -1257  -1570  -2823  -3357  -2511   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8160 
-   122   -874  -1199  -2534  -2422  -1974  -1870  -2091   -571  -2228  -1524  -1151  -1969   3081  -2111  -2286  -1235  -1137   2139  -2571  -2198   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8155 
-   123  -1271  -1039  -3372  -2821   -746  -2956  -1954   2085  -2506   1611    268  -2529  -2908  -2168  -2436  -2093   1651    532  -1730  -1449   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8150 
-   124   -671  -1424   -928   -957  -2705  -1429  -1339  -2424  -1187  -2651  -1885   2469  -1998  -1079  -1505   -788   2865  -1841  -2865  -2354   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8145 
-   125   1514   -936  -2964  -2422   2190  -2527  -1355     83  -2113   1483    394  -2085  -2562  -1744  -2040  -1648  -1022    -62  -1133   -644   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8140 
-   126  -2562  -2904  -1886  -1971  -3251  -2661  -2079  -3690  -1565  -3469  -3081  -2107  -3091   4371  -1665  -2586  -2674  -3411  -3077  -2821   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8134 
-   127  -2562  -2904  -1886  -1971  -3251  -2661  -2079  -3690  -1565  -3469  -3081  -2107  -3091   4371  -1665  -2586  -2674  -3411  -3077  -2821   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8129 
-   128  -1409  -2516   -702   -483  -3060  -1954   -610  -2751   2812  -2606  -1855   2347  -2176   -215    106  -1280  -1337  -2379  -2592  -2144   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8124 
-   129  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8119 
-   130  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8114 
-   131  -1021  -1846  -1209   -791  -2625  -1811   -732  -2166   2159  -2253  -1518   -882  -2091   -364    -57  -1048   2695  -1808  -2425  -2026   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8109 
-   132  -1497  -1141  -3902  -3399   2367  -3419  -2435   2226  -3131   -116     -4  -3038  -3297  -2759  -3022  -2600  -1455   2109  -2041  -1619   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8103 
-   133  -2607  -2130  -4562  -4141   2460  -4247  -2232   -108  -3828   2577    509  -3710  -3790  -2932  -3464  -3520  -2495   -765  -1361   -680   133
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8098 
-   134  -1064  -1978  -1150   -505  -2207  -1951   -370  -1797   1949   1081  -1063   -669  -2008   2207    343  -1027   -943  -1579  -2050  -1627   134
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8093 
-   135  -2784  -3432   4016  -1200  -4140  -2466  -2197  -4505  -2621  -4365  -3956  -1551  -3014  -2039  -3232  -2593  -2938  -4046  -3710  -3552   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8155   -894  -1115   -701  -1378  -8987  -8087 
-   136   -747   -913  -1546   1578   1993  -2038   -821    -21  -1012   -515    -23  -1163  -2133   -853  -1253  -1111   -704   1639  -1215   -660   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8082 
-   137   -876   -771  -2845  -2309   -820  -2402  -1526    541  -2005   -282   2873  -2008  -2507  -1753  -2001  -1537   1640   2049  -1534  -1188   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8077 
-   138  -1430  -1891   -997   1943  -1407  -2232  -1211   -856  -1028   2166   -495  -1166  -2456   -991  -1319  -1576  -1412  -1000  -2129  -1684   138
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8071 
-   139  -1169  -2684   2147    158  -3122  -1517   -718  -2952   -682  -2898  -2097   2204  -1937   -346  -1338   1703  -1215  -2450  -3089  -2265   139
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8066 
-   140   -633   3273  -2717  -2211   -772  -1961  -1349     37  -1862   1436     73  -1775  -2222  -1600  -1823  -1139   1717     83  -1400  -1059   140
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8061 
-   141   -354   3968  -2987  -2999  -2850  -1257  -2393  -2537  -2724  -2899  -2106  -1841  -2005  -2431  -2625   2749   -779  -1738  -3152  -2893   141
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7113  -8156   -894  -1115   -701  -1378  -8987  -8055 
-   142   1505   -993  -3296  -2756   -792  -2864  -1913   2087  -2457   1427    208  -2457  -2855  -2133  -2401  -2006  -1172    581  -1733  -1434   142
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8050 
-   143   -378   -821  -2113  -1746  -1706  -1425  -1436   -946  -1562  -1526   -851  -1381  -1942  -1382  -1726   1808   1901   1742  -2115  -1749   143
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8044 
-   144   2071  -1050  -2379  -2525  -3265   2793  -2380  -2989  -2649  -3274  -2425  -1725  -2038  -2320  -2657   -670   -868  -2016  -3445  -3261   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8039 
-   145   -727  -1975   -459   1602  -2347  -1592   -256  -2020    334  -2001  -1156   -284  -1728    168   1811   -632   1710  -1643  -2175  -1599   145
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8033 
-   146   -461  -1123  -1084   -795  -1871  -1419   -933  -1376   -793  -1728   -984   2248  -1831   -682  -1142   1534   -617   1569  -2143  -1662   146
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8028 
-   147  -2150  -1703  -4501  -4020   -812  -4187  -3228   2939  -3750   1854    352  -3838  -3794  -3151  -3559  -3464  -2086    395  -2376  -2254   147
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8022 
-   148   -564  -1318   -924   -427  -1714  -1577   -497  -1192   1699  -1482   -736   -584  -1783   -172   -379   1511   -577   1384  -1875  -1388   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8017 
-   149   -924  -2398   1900    149  -2675  -1551   2845  -2460   1940  -2388  -1539   -178  -1794     22   -458   -755   -882  -2029  -2526  -1828   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -8011 
-   150   1781  -1642  -1799  -1285  -2726  -1776  -1005  -2310   -123  -2396  -1677  -1200  -2163   -670   3029  -1063  -1095  -1878  -2550  -2226   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -435  -7114  -2005   -894  -1115   -701  -1378  -8987  -8006 
-   151    -41   -683  -1588  -1448  -2358   -938  -1412  -1997  -1384  -2285  -1482  -1035  -1592  -1231  -1576   2298   2360  -1311  -2593  -2228   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -609  -6705  -1596   -894  -1115  -1420   -675  -8987  -8000 
-   152   -119   -620  -1272  -1224  -1670   -932  -1144   -973  -1064  -1461   -973   -934  -1524  -1048  -1189   -353   3160   -658  -1988  -1640   152
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -37  -6133  -7175   -894  -1115   -265  -2575  -8987  -7994 
-   153   1314  -1018  -3354  -2812   -775  -2912  -1952   2090  -2510   1593    233  -2508  -2888  -2172  -2442  -2055  -1204    561  -1743  -1454   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7989 
-   154  -1331  -1033  -3624  -3149  -1382  -3208  -2506   2274  -2910   -585   -325  -2845  -3205  -2692  -2920  -2401   1867   2193  -2370  -1976   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7983 
-   155  -1091  -2254   2022     -7   2307  -1631   -590  -2177   -610  -2224  -1514   2121  -1961   -345  -1175   -965  -1094  -1867  -1997  -1103   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7977 
-   156   -854  -1829   -742   -266  -2039  -1748   -347  -1678   1829    822   -992   2092  -1864     32     62   -817   -776  -1417  -2003  -1492   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7972 
-   157  -1014  -2229   -731   -251  -2679  -1801   -332  -2322   1937  -2215  -1397   -477   1678   2400    260   -900   -918  -1951  -2297  -1805   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7966 
-   158  -1396  -2406  -1485   -733  -3031   1368   -424  -2557   2258  -2367  -1603   -839  -2185      1   2209  -1295  -1239  -2232  -2351  -2031   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7960 
-   159   -956  -1729  -1220   -563  -1980  -1909   -402  -1484    409  -1625   -912   -705  -1983   2175   1981   -978   -858   1572  -1930  -1509   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7954 
-   160   1282  -1147  -1092   -621  -1207  -1720   -605   -725   -353    999   -300   -754  -1884   2230   -650   -786   -607   -617  -1604  -1153   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7948 
-   161  -1750  -1296  -4320  -3959  -1766  -4040  -3736   2391  -3828   -620   -544  -3718  -3870  -3687  -3904  -3356  -1743   2997  -3266  -2819   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21  -7114  -8156   -894  -1115   -701  -1378  -8987  -7943 
-   162  -1557  -1925  -1528  -1273   2498  -2437   3324  -1733  -1206  -1657  -1198   2113  -2565  -1049  -1476  -1568  -1515  -1612   -270    823   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7938 
-   163  -3482  -2868  -3701  -3919    238  -3552  -1112  -3000  -3638  -2516  -2526  -3027  -3772  -3101  -3341  -3418  -3527  -3071   -441   4711   163
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7931 
-   164  -1079  -1894   -638   -875  -3323   2010  -1585  -3303  -1636  -3372  -2614   3328  -2223  -1339  -2053  -1134  -1370  -2548  -3342  -2836   164
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7925 
-   165  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222   165
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7919 
-   166   3438  -1472  -2846  -3040  -3287  -1726  -2735  -2840  -3028  -3257  -2662  -2236  -2447  -2798  -2944  -1216  -1387  -2183  -3405  -3320   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7913 
-   167   2778   -923  -2528  -2479  -2813  -1244  -2164  -2247  -2337  -2700  -1937  -1656  -1963  -2095  -2369   -583   2095  -1564  -3114  -2854   167
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7907 
-   168   1495  -1766   2179   -198  -2740  -1391   -797  -2483   -649  -2542  -1701   -433  -1823   -430  -1176   1550   -837  -1925  -2773  -2123   168
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7901 
-   169   1775   -997  -3102  -2890  -1831  -2024  -2366    280  -2664  -1179   -841  -2234  -2536  -2444  -2662  -1333  -1052   2797  -2635  -2270   169
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7895 
-   170   3438  -1472  -2846  -3040  -3287  -1726  -2735  -2840  -3028  -3257  -2662  -2236  -2447  -2798  -2944  -1216  -1387  -2183  -3405  -3320   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7889 
-   171   2672   -923  -2519  -2463  -2802  -1245  -2152  -2236  -2320  -2688  -1925  -1650  -1962  -2081  -2357   -582   2292  -1558  -3103  -2841   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7883 
-   172   -897  -1462  -2333  -2543  -3185  -1640  -2474  -3294  -2686  -3497  -2780  -1973  -2360  -2483  -2703   3465  -1316  -2413  -3310  -3025   172
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7877 
-   173  -2171  -2655  -1458  -1748  -3334  -2364  -2267  -3943  -2365  -3936  -3437   4205  -2932  -2205  -2608  -2224  -2439  -3392  -3253  -2909   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7870 
-   174  -1497  -2107  -1935  -1658  -3324   2771  -1482  -3136   -643  -3095  -2386  -1612  -2536  -1182   2519  -1589  -1657  -2617  -2943  -2764   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7864 
-   175  -1657  -2262  -2018  -1580  -3182  -2250  -1270  -2964   -298  -2882  -2213  -1564   3179   -945   2523  -1713  -1720  -2571  -2771  -2563   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7858 
-   176  -1051  -1842   -709   -951  -3332   2743  -1643  -3311  -1706  -3391  -2630   2613  -2227  -1407  -2105  -1123  -1357  -2535  -3357  -2872   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7852 
-   177   3438  -1472  -2846  -3040  -3287  -1726  -2735  -2840  -3028  -3257  -2662  -2236  -2447  -2798  -2944  -1216  -1387  -2183  -3405  -3320   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7845 
-   178  -1362  -1048  -3685  -3215  -1415  -3271  -2583   2287  -2982   -598   -347  -2911  -3255  -2767  -2991  -2469   1667   2332  -2429  -2031   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8156   -894  -1115   -701  -1378  -8987  -7839 
-   179  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8157   -894  -1115   -701  -1378  -8987  -7833 
-   180  -1387  -1123  -3602  -3030   2410  -3049  -1834    367  -2696    386   3020  -2643  -2945  -2218  -2519  -2181  -1324   1837  -1430  -1038   180
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8157   -894  -1115   -701  -1378  -8987  -7827 
-   181  -2871  -2457  -4231  -4103  -1033  -3803  -3165   -541  -3734   3130    -31  -3935  -3797  -3286  -3484  -3713  -2869  -1136  -2394  -2220   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8157   -894  -1115   -701  -1378  -8987  -7820 
-   182   -683  -1822   -253   1770  -2047  -1539   -316  -1613     60  -1769   -983   -239  -1712   2084   -374   -616   -636   1242  -2094  -1488   182
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8157   -894  -1115   -701  -1378  -8987  -7814 
-   183  -2150  -1703  -4501  -4020   -812  -4187  -3228   2939  -3750   1854    352  -3838  -3794  -3151  -3559  -3464  -2086    395  -2376  -2254   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7114  -8157   -894  -1115   -701  -1378  -8987  -7807 
-   184   -446  -1090  -1996  -2160  -3283   2774  -2224  -3123  -2430  -3335  -2463  -1572  -2017  -2113  -2525   2071   -869  -2091  -3449  -3188   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7801 
-   185  -1307  -2585   3174    -69  -3390  -1557  -1071  -3300  -1229  -3293  -2567   -398  -2100   -754  -1931   1637  -1465  -2706  -3438  -2615   185
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7794 
-   186   -837  -2035   -620   -149  -2399  -1682   2790  -2121   2004  -2072  -1242   -389  -1813    121    117   1316   -767  -1749  -2185  -1633   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7788 
-   187   1335   -890  -3130  -2616   -925  -2631  -1823    656  -2327   1318     36  -2286  -2719  -2049  -2301  -1788  -1042   2123  -1752  -1415   187
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7781 
-   188   1777   -797  -2482  -2107  -1558  -1610  -1626   -334  -1885  -1255   -679  -1637  -2100  -1668  -1974   -855   1871   1840  -2077  -1725   188
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7775 
-   189   -497  -1111  -2184  -2286  -3154   2779  -2229  -2856  -2381  -3142  -2325  -1659  -2063  -2135  -2449   -723   2336  -1984  -3326  -3099   189
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1018  -7115  -1016   -894  -1115   -701  -1378  -8987  -7768 
-   190   -889  -1218  -1459  -1647  -2605   3392  -1709  -2674  -1891  -2802  -2245  -1471  -1892  -1754  -1945  -1091  -1230  -2077  -2314  -2429   190
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -38  -6134  -7176   -894  -1115  -1898   -451  -8987  -7762 
-   191  -1077  -1341  -1504  -1619  -2337  -1430  -1611  -2341  -1664  -2436  -2002  -1516   3831  -1645  -1732  -1276  -1365  -1949  -2170  -2176   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -38  -6134  -7176   -894  -1115   -265  -2575  -8987  -7755 
-   192  -1481  -1881  -1664  -1314  -1173  -2402  -1126   -898   -612   1389   -389  -1418  -2538   3337   -756  -1655  -1442  -1115  -1890  -1382   192
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7748 
-   193  -1538  -1429  -2767  -2359    604  -2716   -515  -1060  -1999  -1137   -682  -1887  -2775  -1678  -1987  -1830   1999  -1003   3929   2918   193
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7741 
-   194  -1496  -2778   3018   -239  -3183  -1827   -900  -3046   -554  -2964  -2220   -560  -2198   -541   2279  -1315  -1503  -2621  -2980  -2370   194
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7735 
-   195   -727   -720  -2519  -2006   -747  -2135  -1292    271  -1719   1398    108  -1734  -2299  -1487  -1751   1285   -741   1798  -1391  -1026   195
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7728 
-   196   -307   -969  -2046  -1917  -2936   1979  -1874  -2661  -1909  -2877  -2007  -1404  -1888  -1686  -2097   1822   2066  -1796  -3129  -2810   196
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7721 
-   197   1338   -635  -2333  -1826   -532  -2000  -1024    114  -1550   -501     66  -1552  -2169  -1315  -1588  -1124   -632   1887  -1089   2351   197
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -22  -7115  -8157   -894  -1115   -701  -1378  -8987  -7714 
-   198  -1341  -2823    136   2701  -3119  -1670   -707  -2930   -413  -2838  -2077   -312  -2039   2546   -867  -1124  -1334  -2502  -2963  -2244   198
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7707 
-   199   1314  -1018  -3354  -2812   -775  -2912  -1952   2090  -2510   1593    233  -2508  -2888  -2172  -2442  -2055  -1204    561  -1743  -1454   199
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7700 
-   200  -1178  -1483  -1895  -1388  -1814  -2239  -1084   -312   2039  -1304   -847  -1392  -2421   -830   -457  -1469  -1171   2593  -2162  -1766   200
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7693 
-   201  -3623  -2708  -4178  -4427   3051  -4051   -395  -2540  -4005  -1942  -1988  -2750  -3935  -2856  -3452  -3300  -3500  -2692    349   4032   201
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7687 
-   202  -1021  -1195  -2600  -2263  -1081  -2184  -1755   -230  -1888   1445   -171  -1977  -2517  -1787  -1943  -1447   2849   -305  -1946  -1587   202
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7679 
-   203  -2784  -3432   4016  -1200  -4140  -2466  -2197  -4505  -2621  -4365  -3956  -1551  -3014  -2039  -3232  -2593  -2938  -4046  -3710  -3552   203
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -7115  -8157   -894  -1115   -701  -1378  -8987  -7672 
-   204   2567   -984  -2446  -2151  -1454  -1708  -1697   -657  -1861   -906   3082  -1717  -2200  -1714  -1931   -984   -868   -562  -2109  -1761   204
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8987      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Peptidase_S29
-ACC   PF02907.7
-DESC  Hepatitis C virus NS3 protease
-LENG  149
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  9
-DATE  Thu Apr 24 22:36:31 2008
-CKSUM 7420
-GA    25.0000 25.0000;
-TC    26.6000 25.9000;
-NC    21.1000 21.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.924948   0.629218
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -263      *  -2585
-     1  -3196  -3194  -3915  -4259  -4867   3789  -4005  -5414  -4591  -5241  -4823  -3935  -3840  -4374  -4341  -3455  -3585  -4634  -4094  -4784     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -1263  -8209 
-     2   -868  -2282   -192   2166  -2665  -1619   -503  -2418   -199  -2389  -1511   1806  -1849    -79   -732    449   1117  -1970  -2583  -1880     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8205 
-     3  -2033  -1555  -4661  -4321  -2097  -4413  -4239   2851  -4228   -908   -842  -4097  -4210  -4117  -4333  -3757  -2027   2763  -3698  -3228     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8200 
-     4   -921   -870  -2514  -1931   1569  -2386  -1175    -71  -1644   -159   2002  -1757  -2410   2557  -1691  -1446   -860   1400  -1223   -826     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8195 
-     5  -1036   -855  -3092  -2502    693  -2647  -1538   1059  -2135   -402     30  -2174  -2663  -1873   1084  -1745   -984   2671  -1465  -1087     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8190 
-     6  -2674  -2256  -4913  -4449   -858  -4495  -3519      7  -4124   2959    305  -4273  -4080  -3359  -3831  -3824  -2613    628  -2499  -2467     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8185 
-     7   -743  -1376  -2493  -2714  -3708   2701  -2700  -3572  -3000  -3787  -2896  -1979  -2337  -2630  -3021   2398  -1184  -2452  -3867  -3664     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8180 
-     8   -636  -1252  -2729  -2807  -3379  -1514  -2567  -3085  -2752  -3387  -2546  -1957  -2262  -2498  -2759   1322   3457  -2164  -3620  -3368     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8175 
-     9   2015   -831  -2264  -1757  -1098  -1885  -1232   -448  -1530    690   -283  -1525  -2171  -1322  -1651   1110   -713    717  -1572  -1203    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7447  -8489   -894  -1115   -701  -1378  -8472  -8170 
-    10   1331  -1226  -3008  -3075  -3311  -1531  -2673  -2760  -2930  -3221  -2446  -2058  -2283  -2646  -2875   -888   3460  -1984  -3603  -3392    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8472      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF1301
-ACC   PF06979.4
-DESC  Protein of unknown function (DUF1301)
-LENG  145
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  8
-DATE  Tue Apr 22 21:57:56 2008
-CKSUM 5186
-GA    25.0000 25.0000;
-TC    275.6000 275.6000;
-NC    14.1000 14.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.124557   0.661501
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -222      *  -2808
-     1    458  -1085  -2557  -2091  -1296   2627  -1530   -735  -1835    377   1766  -1816  -2423  -1634  -1924  -1283   -982   -634  -1827  -1472     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -1222  -8170 
-     2   1128  -1566  -4013  -3923  -2565  -2672  -3382    -29  -3709  -1742  -1492  -3055  -3221  -3463  -3636  -2021  -1693   3308  -3555  -3188     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8165 
-     3  -2768  -3358  -3517  -2082  -4283  -3215  -1090  -3581   3548  -3200  -2554  -1926  -3157   -675   1605  -2646  -2424  -3367  -3000  -2948     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8160 
-     4  -1385   2974  -3780  -3192   2035  -3094  -2042   1678  -2840    672   -118  -2739  -3069  -2456  -2666  -2214  -1332   1633  -1809  -1484     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8155 
-     5  -3471  -2881  -5046  -4890   3959  -4750  -2008  -1042  -4543   1248   -434  -3983  -4410  -3530  -4086  -4096  -3369  -1678  -1191   -197     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8150 
-     6  -1644  -2173  -3321  -3615  -4077  -2357  -3411  -4307  -3792  -4459  -3725  -2859  -3095  -3512  -3692   3619  -2088  -3285  -4091  -3959     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8145 
-     7  -3351  -2810  -4588  -4497     67  -4377  -1480  -1529  -4018   2252   -967  -3478  -4227  -3269  -3670  -3677  -3266  -1991   -755   3645     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8140 
-     8   1459  -1468  -3324  -3507  -3903  -1728  -3101  -3677  -3478  -3955  -3050  -2337  -2512  -3087  -3362   3205  -1305  -2550  -4127  -3966     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8134 
-     9   -878  -1493  -3146  -3292  -3762  -1753  -2970  -3504  -3238  -3799  -2935  -2284  -2521  -2935  -3178   1361   3530  -2490  -3997  -3786     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8129 
-    10  -1644  -2173  -3321  -3615  -4077  -2357  -3411  -4307  -3792  -4459  -3725  -2859  -3095  -3512  -3692   3619  -2088  -3285  -4091  -3959    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8124 
-    11  -1530  -1248  -3897  -3347  -1303    378  -2350   1933  -3033   1482   -341  -2945  -3282  -2701  -2914  -2451  -1488   2057  -2139  -1798    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8119 
-    12   1889   -734  -2866  -2275   1174    847  -1278    952  -1951   -583     32  -1907  -2413  -1642  -1880  -1414   -796    902  -1262   -908    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8114 
-    13  -1044  -1786  -1596  -1793  -3847   2868  -2302  -3677  -2431  -3818  -2949   1311  -2491  -2076  -2758   1586  -1423  -2689  -3981  -3548    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8109 
-    14    910  -1456  -4181  -3644  -1358  -3634  -2703   1933  -3353   1972   -317  -3275  -3544  -2979  -3228  -2796  -1735   1219  -2383  -2086    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7719  -8761   -894  -1115   -701  -1378  -8392  -8103 
-    15   1098   -746  -3124  -2513   1186  -2470  -1376     60  -2153    567     73  -2079  -2519  -1809  -2016  -1561    621   2115  -1275   -929    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8098 
-    16   1546  -1027  -3445  -2837   1844  -2797  -1677   1215  -2477   -188   3143  -2411  -2798  -2081  -2317  -1897  -1160   -106  -1476  -1152    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8093 
-    17    507   -852  -2512  -1920   -749  -2355  -1190   -181  -1644    944   2017  -1740  -2400   2213  -1694  -1410   -833   1282  -1304   -954    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8087 
-    18  -4077  -3791  -4518  -4858  -5206  -3818  -4460  -5898  -5053  -5602  -5343  -4628   4289  -4938  -4749  -4364  -4429  -5313  -4385  -5119    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -879  -7719  -1159   -894  -1115   -701  -1378  -8392  -8082 
-    19  -2722  -2327  -2878  -2828   1098  -3297   3115  -2227  -2394  -1788  -1679  -2101  -3316  -2027  -2304  -2565  -2644  -2265    392   4065    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6864  -7906   -894  -1115   -675  -1419  -8392  -8077 
-    20  -2130  -1667  -4681  -4245  -1510  -4364  -3713   2898  -4076   1453   -310  -4016  -4068  -3673  -4005  -3642  -2092   1684  -3028  -2794    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -18  -7460  -8502   -894  -1115   -382  -2105  -8392  -8071 
-    21  -2646  -2238  -4991  -4384   1207  -4477  -3244   -282  -4081   2452   2284  -4140  -4030  -3255  -3736  -3668  -2536   1343  -2379  -2359    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8066 
-    22  -1006  -1270  -2930  -2628  -1630  -2121  -1991  -1061  -2321   2611   -785  -2130  -2578  -2122  -2322    468    757   -967  -2246  -1909    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8061 
-    23   -963  -2426   -478   2224  -2757  -1796   -510  -2498   1042  -2429  -1534   -428  -1947   1871   -513    938   -905  -2058  -2582  -1912    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8055 
-    24   -859  -2126   -625   -247  -2644  -1739   -623  -2374   -244  -2372  -1488   1667  -1947   2373   -722    984   1569  -1923  -2573  -1926    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8050 
-    25   1154  -1713  -1141   -890  -2261   1914  -1147  -2074   -988  -2247  -1468   1768  -2194   -861  -1402  -1004  -1038  -1698  -2501   1989    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8044 
-    26    362   -738  -2968  -2356   -646  -2403  -1281   1081  -2009   1380   2631  -1971  -2449  -1674  -1901    895   -820    -43  -1207   -870    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8039 
-    27   -776  -1011  -1704  -1119  -1007   1092   -819    668   1720   -867   1633  -1166  -2143   -757  -1041  -1085   -714   -451   2982   -997    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8033 
-    28   -820   -750  -2559    850   1825  -2307  -1158   1566  -1695   -574     50  -1739  -2362  -1431  -1710    191   -764   1524  -1235   -869    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8028 
-    29    912  -2755   1168    919  -3049   1971   -750  -2829   -508  -2770  -1898   -457  -2098   1445  -1083  -1034  -1183  -2372  -2952  -2199    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8022 
-    30   1367  -1446  -3261  -3360  -3901   2044  -3011  -3687  -3342  -3926  -2997  -2273  -2477  -2954  -3288   2517  -1265  -2537  -4107  -3945    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1356  -7719   -735   -894  -1115   -701  -1378  -8392  -8017 
-    31   2092   -474  -1969  -1665  -1216  -1289  -1325    342  -1461   -727   -294  -1269  -1778  -1300  -1583   -555   -385   1835  -1844  -1464    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -6394  -7437   -894  -1115  -2465   -288  -8392  -8011 
-    32   -719  -1926    385   2402  -2369  -1201   -333  -2119   -126  -2153  -1394     21   1684     25   -616   -593   -751  -1721  -2330  -1693    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -6394  -7437   -894  -1115   -173  -3142  -8392  -8006 
-    33   -871   -819  -2544  -1944   1226  -2336  -1158   -224    990   1404   1747  -1739  -2378  -1395  -1669  -1391   1378   -194  -1243   -892    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -8000 
-    34    889  -1344  -2585  -2352   1288    647  -2069  -2119  -2269  -2406  -1670  -1890   3187  -2034  -2413  -1083  -1125  -1671  -2788  -2385    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7994 
-    35  -1446  -1196  -3778  -3180   -943  -3125  -2044   1155  -2830   1231   3217  -2755  -3080  -2418  -2654  -2240   1240   1208  -1785  -1497    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7989 
-    36    461  -1064  -2104  -1542  -1002  -2305  -1138   1440  -1273   -644   2383  -1523  -2377   2753  -1455  -1348   -897   -284  -1536  -1160    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7983 
-    37   1302  -1288  -3966  -3434  -1467  -3416  -2515   1379  -3143   -803   2506  -3050  -3389  -2843  -3054  -2569  -1551   2483  -2321  -1960    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7977 
-    38   1543   -851  -3370  -2748   1173  -2639  -1522   1028  -2366    531   2473  -2274  -2653  -1975  -2179  -1733   -989   1109  -1343  -1023    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7972 
-    39  -2323  -1939  -4703  -4149   3504  -4190  -3010   1152  -3857    960     28  -3823  -3897  -3221  -3609  -3375  -2246    932  -2336  -2081    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7966 
-    40   1190   4307  -3346  -3059  -1233  -2112  -1872  -1468  -2707  -1820  -1216  -2269  -2627  -2402  -2614  -1386  -1271  -1233  -1804   3006    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7960 
-    41   -950  -1372  -2950  -2809  -2465   2913  -2384   1487  -2639  -2202  -1612  -2177  -2567  -2420  -2670  -1267    974  -1156  -2945  -2615    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8761   -894  -1115   -701  -1378  -8392  -7954 
-    42  -2064  -1676  -4546  -4036   1871  -4054  -3142   1976  -3779    738   -324  -3701  -3863  -3344  -3636  -3251  -2015   2485  -2648  -2373    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8762   -894  -1115   -701  -1378  -8392  -7948 
-    43   1743   -761  -2935  -2340   -777    185  -1338   1135  -2013   -583   2541  -1973  -2472  -1704  -1938  -1488   -838   1115  -1310   -958    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8762   -894  -1115   -701  -1378  -8392  -7943 
-    44  -1736  -2433  -1602  -1933  -4223   3321  -2631  -4323  -2861  -4387  -3641   1915  -2952  -2468  -3193  -1851  -2107  -3376  -4175  -3845    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8762   -894  -1115   -701  -1378  -8392  -7937 
-    45   -956  -1336  -2909  -2666   3414  -1982  -1903  -1719  -2477  -1997  -1370  -2074  -2529  -2205  -2507   1330   1482  -1422  -2070  -1386    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8762   -894  -1115   -701  -1378  -8392  -7931 
-    46  -4350  -3618  -4843  -5137   4483  -4245  -2206  -3493  -4990  -2887  -3007  -4147  -4512  -4243  -4506  -4433  -4439  -3737  -1500   -417    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7719  -8762   -894  -1115   -701  -1378  -8392  -7925 
-    47  -1572  -1816  -3432  -3252  -1836  -2621  -2648  -1010  -2820   1009   -944  -2731  -3094  -2717  -2792  -1971   3413  -1091  -2765  -2414    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7720  -8762   -894  -1115   -701  -1378  -8392  -7919 
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-     -    -20  -7723  -8765   -894  -1115   -701  -1378  -8392  -7219 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7723  -8765   -894  -1115   -701  -1378  -8392  -7209 
-   142   1362  -1652  -3253  -3536  -4100   3318  -3254  -3906  -3698  -4170  -3287  -2477  -2669  -3271  -3562  -1294  -1510  -2764  -4229  -4163   142
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7723  -8765   -894  -1115   -701  -1378  -8392  -7200 
-   143  -4356  -3341  -4796  -5119   2367  -4668   -930  -3246  -4685  -2582  -2665  -3328  -4542  -3457  -4078  -3932  -4222  -3409   -179   4452   143
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7723  -8766   -894  -1115   -701  -1378  -8392  -7190 
-   144  -3832  -4189   4132  -2236  -5073  -3341  -3194  -5633  -3716  -5365  -5035  -2584  -3886  -3102  -4252  -3662  -4000  -5151  -4434  -4544   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7723  -8766   -894  -1115   -701  -1378  -8392  -7180 
-   145  -2233  -3610   1743   -725  -4063  -2369  -1472  -3904   3388  -3751  -3052  -1058  -2787  -1120  -1439  -1991  -2239  -3461  -3728  -3115   145
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8392      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Toxin_18
-ACC   PF08087.3
-DESC  Conotoxin O-superfamily
-LENG  55
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  7
-DATE  Tue Apr 22 23:21:53 2008
-CKSUM 1977
-GA    14.7000 14.7000;
-TC    15.9000 15.9000;
-NC    14.6000 14.6000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.941043   0.590357
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -322      *  -2322
-     1  -2406  -2296  -3638  -3594  -1525  -3105  -2824  -1047  -3121   -596   5043  -3293  -3425  -3046  -2996  -2911  -2552  -1398  -2513  -2207     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -7121  -8163   -894  -1115   -701  -1378  -1322  -6755 
-     2   -420  -1753   -291    241    629    -14   2245  -1736    998  -1744   -859   1197  -1496   1224   -132   -325   -358  -1349  -1959  -1313     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -7121  -8164   -894  -1115   -701  -1378  -7077  -6741 
-     3   -481   -336  -2608  -1990   1071  -2009   -854   1552  -1630    558    507  -1579  -2054  -1290    800  -1086   -421    991   -765   1446     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -7122  -8164   -894  -1115   -701  -1378  -7077  -6728 
-     4   -845  -1836   -818   -303  -1798  -1748   -330  -1805   2652  -1836  -1061   -507  -1868     22     54    463   -778  -1508  -1854   1576     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -7122  -8164   -894  -1115   -701  -1378  -7077  -6714 
-     5    963   -923  -2237  -2029  -2777  -1203  -1870  -2440  -1918  -2704  -1860  -1449  -1883  -1706  -2082   2221   2431  -1665  -3006  -2696     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7123  -8165   -894  -1115   -701  -1378  -7077  -6701 
-     6    460   -661  -2708  -2174   -853  -2243  -1399   2283  -1902   -506     11  -1862  -2381  -1646  -1910    639   -743   1744  -1462  -1095     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7122  -8164   -894  -1115   -701  -1378  -7077  -6687 
-     7  -1366  -1240  -2973  -2381   1523  -2814  -1351    -94  -1809   2261    408  -2161  -2748  -1662   1081  -1921  -1290   -379  -1141   -583     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7122  -8164   -894  -1115   -701  -1378  -7077  -6672 
-     8  -1030   2502  -3316  -2712   1150  -2654  -1528    383  -2353   1931    489  -2281  -2617  -1921  -2169  -1764   -970   1248  -1256   -944     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7122  -8164   -894  -1115   -701  -1378  -7077  -6658 
-     9   1272   -771  -3149  -2549   1152  -2584  -1461   1752  -2211   1387    469  -2170  -2558  -1816  -2072  -1685   -915    309  -1248   -940     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7122  -8165   -894  -1115   -701  -1378  -7077  -6644 
-    10    730   -542  -2848  -2250   1920  -2274  -1179    417  -1910    -62   1861  -1859  -2308  -1569  -1799  -1368   -656   1971  -1067   -718    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7123  -8165   -894  -1115   -701  -1378  -7077  -6629 
-    11   1485   2016  -2987  -2397   -606  -2387  -1335   1353  -2059    759    239  -1989  -2417  -1733  -1945  -1490   -711   1432  -1228   -876    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30  -7123  -8165   -894  -1115   -701  -1378  -7077  -6615 
-    12    631   -401  -2165  -1571   -380  -1918   -774    174  -1293    471   1760  -1347    345  -1033  -1318   -977    685   1595   -872   -512    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -7124  -8166   -894  -1115   -701  -1378  -7077  -6601 
-    13    970   -695  -1828  -1353   2330  -1515   -985   -668  -1171   -992   -302  -1163  -1867   -985  -1358    776   1551   -460  -1506  -1108    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -449  -7123  -2001   -894  -1115   -701  -1378  -7077  -6585 
-    14   2240   -660  -2372  -2102  -1463  -1509  -1685    228  -1888   -945   -530  -1597  -2023  -1701  -1963   -793   -613   2045  -2127  -1759    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -6710  -7752   -894  -1115  -1425   -672  -7077  -6570 
-    15   2756   -617  -1853  -1799  -2514   -886  -1664  -2159  -1767  -2468  -1649  -1174  -1591  -1539  -1882   1459   -383  -1376  -2764  -2456    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -6710  -7753   -894  -1115  -1425   -672  -7077  -6555 
-    16    631   -711  -2760  -2239   -583  -2386  -1511    774  -1953   1830    393  -1976  -2454  -1681  -1956  -1531   -827   1644  -1457  -1141    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -6711  -7753   -894  -1115   -382  -2102  -7077  -6539 
-    17    478   -789  -1139   -599   1161  -1646   -464   -423   -456    324    -11   1905  -1756   -334   -771    387   -376   -274  -1205   -755    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -7124  -8166   -894  -1115   -701  -1378  -7077  -6524 
-    18   3007   -956  -2782  -2665  -2211  -1517  -2209   -781  -2448  -1772  -1312  -1875  -2169  -2220  -2451   -847   -860    959  -2793  -2467    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -7125  -8167   -894  -1115   -701  -1378  -7077  -6509 
-    19   -578  -1790   -300    109  -1881  -1490   -200  -1739    184  -1779   -942    988    802   2585   -262   -498   -525  -1394  -1936   1223    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -231  -7124  -2948   -894  -1115   -701  -1378  -7077  -6492 
-    20  -1376  -1849  -1607  -1053    138  -2279   3192  -1670   -181  -1596  -1063  -1056  -2327   -509   1185  -1372  -1272  -1526   -432   3135    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -219  -6927  -3043   -894  -1115  -1117   -892  -7077  -6476 
-    21    997   2943  -2230  -1806  -1003    713  -1150   -312  -1550   -850   -192  -1290  -1729  -1290  -1583   -496   -315   1779  -1465  -1123    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37  -6745  -7787   -894  -1115   -395  -2061  -7077  -6459 
-    22   2385  -1131  -2664  -2367  -1174  -2045  -1841   -318  -2075   1652   -255  -1981  -2449  -1894  -2112  -1323  -1086   -365  -2026  -1688    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -7125  -8167   -894  -1115   -701  -1378  -7077  -6443 
-    23   1770   -772  -1989  -1594  -1273  -1531  -1215   -731  -1391   1582   -450  -1320  -1951  -1219  -1539    829   -588   -536  -1733  -1358    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -7125  -8167   -894  -1115   -701  -1378  -7077  -6426 
-    24   3438  -1472  -2846  -3040  -3287  -1726  -2735  -2840  -3028  -3257  -2662  -2236  -2447  -2798  -2944  -1216  -1387  -2183  -3405  -3320    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -7126  -8168   -894  -1115   -701  -1378  -7077  -6410 
-    25  -2476   5735  -4102  -4358  -3712  -2763  -3545  -3518  -4167  -3859  -3569  -3631  -3363  -4030  -3832  -2793  -2860  -3158  -3464  -3718    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -7125  -8167   -894  -1115   -701  -1378  -7077  -6392 
-    26   2072   -927  -2496  -2439  -2787  -1250  -2138  -2212  -2298  -2669  -1911  -1644  -1965  -2065  -2339   -587   2950  -1545  -3090  -2824    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -7125  -8167   -894  -1115   -701  -1378  -7077  -6375 
-    27  -1712  -3554   2325   2948  -3753  -1633   -990  -3684  -1230  -3564  -2903   -236  -2165   -662  -2071  -1376  -1781  -3168  -3726  -2747    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -7126  -8168   -894  -1115   -701  -1378  -7077  -6358 
-    28  -1213  -1674  -2755  -2906  -3163  -1922  -2659  -2698  -2788  -3105  -2612  -2311  -2600  -2708  -2753  -1463   3819  -2197  -3286  -3156    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -7127  -8169   -894  -1115   -701  -1378  -7077  -6341 
-    29  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -7126  -8168   -894  -1115   -701  -1378  -7077  -6322 
-    30   1837  -1632  -1792  -1281  -2717  -1769  -1008  -2302   -134  -2391  -1671  -1196  -2158   -674   2991  -1054  -1087  -1869  -2549  -2223    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -7126  -8168   -894  -1115   -701  -1378  -7077  -6304 
-    31   -854  -1314  -1344  -1295  -1841  -1772  -1422   -691  -1364  -1644  -1144   3057  -2234  -1288  -1613  -1100  -1035   2055  -2329  -1775    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -7126  -8169   -894  -1115   -701  -1378  -7077  -6285 
-    32  -2476   5735  -4102  -4358  -3712  -2763  -3545  -3518  -4167  -3859  -3569  -3631  -3363  -4030  -3832  -2793  -2860  -3158  -3464  -3718    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -7127  -8169   -894  -1115   -701  -1378  -7077  -6267 
-    33   -884  -1803   -949   -367  -2079  -1814   -343  -1581   1870  -1718   -969   -558  -1899   2079    189   -864   -792   1573  -1992  -1530    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -35  -7128  -8170   -894  -1115   -701  -1378  -7077  -6249 
-    34  -1287  -1583  -1687  -1309    229  -2303   3312  -1339  -1018  -1398   -867  -1266  -2425   -963  -1230  -1406    952  -1215   -393   3181    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -35  -7127  -8169   -894  -1115   -701  -1378  -7077  -6229 
-    35   -664  -1470   -771   -876  -2929  -1377  -1385  -2843  -1317  -2961  -2146   2190  -1981  -1117  -1686   2749   -960  -2093  -3064  -2499    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -35  -7127  -8170   -894  -1115   -701  -1378  -7077  -6209 
-    36    670  -1874   2154   -105  -1581  -1594   -570  -1807   -524  -1939  -1213   -386  -1895   -317  -1032   -845   -906  -1519  -1918   2872    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -7129  -8171   -894  -1115   -701  -1378  -7077  -6191 
-    37  -1128  -2299    -43   3032  -2909  -1606   -854  -2560   -676  -2672  -1932   -441  -2023   -503  -1167  -1024   1176  -2143  -2912  -2244    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -7128  -8170   -894  -1115   -701  -1378  -7077  -6170 
-    38  -1368   5163  -2991  -2539  -2629  -2123  -1865  -2316  -1204  -2559  -1981  -2125  -2616  -1747   1633  -1609  -1599  -1984  -2686  -2451    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -7128  -8170   -894  -1115   -701  -1378  -7077  -6150 
-    39  -2476   5735  -4102  -4358  -3712  -2763  -3545  -3518  -4167  -3859  -3569  -3631  -3363  -4030  -3832  -2793  -2860  -3158  -3464  -3718    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -7129  -8171   -894  -1115   -701  -1378  -7077  -6129 
-    40   -897  -1462  -2333  -2543  -3185  -1640  -2474  -3294  -2686  -3497  -2780  -1973  -2360  -2483  -2703   3465  -1316  -2413  -3310  -3025    40
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
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-//
-HMMER2.0  [2.3.2]
-NAME  ABC_transp_aux
-ACC   PF09822.1
-DESC  ABC-type uncharacterized transport system
-LENG  287
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  56
-DATE  Wed Apr 23 02:18:46 2008
-CKSUM 6761
-GA    19.1000 19.1000;
-TC    19.1000 19.1000;
-NC    18.1000 18.1000;
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-     -     -6 -10842 -11884   -894  -1115   -701  -1378  -9188  -8170 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -10842 -11884   -894  -1115   -701  -1378  -9188  -8165 
-   287   -565  -4735   3522     40  -5034   -426  -2872  -4785  -2512  -2377   -386    756  -4278    319  -3037  -3133  -3214  -1842  -4926  -4229   404
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9188      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF1602
-ACC   PF07673.6
-DESC  Protein of unknown function (DUF1602)
-LENG  39
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  4
-DATE  Tue Apr 22 22:48:23 2008
-CKSUM 9246
-GA    15.0000 15.0000;
-TC    15.0000 15.0000;
-NC    14.9000 14.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -7.011845   0.849240
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -263      *  -2585
-     1  -3196  -3194  -3915  -4259  -4867   3789  -4005  -5414  -4591  -5241  -4823  -3935  -3840  -4374  -4341  -3455  -3585  -4634  -4094  -4784     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -7461  -8503   -894  -1115   -701  -1378  -1263  -6248 
-     2  -1298  -1844  -2875  -3136  -3678  -2026  -2995  -3857  -3302  -4033  -3306  -2458  -2758  -3055  -3253   3563  -1733  -2892  -3744  -3541     2
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-     -    -32  -7462  -8505   -894  -1115   -701  -1378  -6511  -6230 
-     3  -1298  -1844  -2875  -3136  -3678  -2026  -2995  -3857  -3302  -4033  -3306  -2458  -2758  -3055  -3253   3563  -1733  -2892  -3744  -3541     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -7462  -8504   -894  -1115   -701  -1378  -6511  -6209 
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-     -    -33  -7463  -8505   -894  -1115   -701  -1378  -6511  -6171 
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-     -    -33  -7463  -8505   -894  -1115   -701  -1378  -6511  -6150 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -7463  -8505   -894  -1115   -701  -1378  -6511  -6129 
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-     -    -33  -7463  -8505   -894  -1115   -701  -1378  -6511  -6109 
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-     -    -35  -7465  -8507   -894  -1115   -701  -1378  -6511  -5977 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36  -7466  -8508   -894  -1115   -701  -1378  -6511  -5931 
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-     -    -37  -7467  -8509   -894  -1115   -701  -1378  -6511  -5883 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37  -7467  -8509   -894  -1115   -701  -1378  -6511  -5858 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -38  -7468  -8511   -894  -1115   -701  -1378  -6511  -5834 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -39  -7469  -8511   -894  -1115   -701  -1378  -6511  -5782 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -39  -7469  -8511   -894  -1115   -701  -1378  -6511  -5755 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -43  -7473  -8515   -894  -1115   -701  -1378  -6511  -5586 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -6511      0 
-//
-HMMER2.0  [2.3.2]
-NAME  zf-P11
-ACC   PF03854.6
-DESC  P-11 zinc finger
-LENG  50
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  3
-DATE  Tue Apr 22 18:49:02 2008
-CKSUM 2670
-GA    25.0000 25.0000;
-TC    25.1000 81.0000;
-NC    20.1000 20.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
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-EVD    -8.886599   0.692147
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -415      *  -2000
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7030      0 
-//
-HMMER2.0  [2.3.2]
-NAME  V-ATPase_G
-ACC   PF03179.7
-DESC  Vacuolar (H+)-ATPase G subunit
-LENG  105
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  34
-DATE  Tue Apr 22 17:22:48 2008
-CKSUM 5949
-GA    25.0000 25.0000;
-TC    26.1000 25.7000;
-NC    20.2000 17.0000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
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-EVD    -8.957211   0.669611
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -70      *  -4392
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7771      0 
-//
-HMMER2.0  [2.3.2]
-NAME  XhoI
-ACC   PF04555.5
-DESC  Restriction endonuclease XhoI
-LENG  202
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  4
-DATE  Tue Apr 22 19:35:36 2008
-CKSUM 1869
-GA    25.0000 25.0000;
-TC    48.0000 48.0000;
-NC    16.4000 10.6000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
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-EVD    -9.990635   0.682481
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -263      *  -2585
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8914      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Endomucin
-ACC   PF07010.4
-DESC  Endomucin
-LENG  267
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  3
-DATE  Thu Apr 24 20:53:30 2008
-CKSUM 1726
-GA    25.0000 25.0000;
-TC    26.2000 26.2000;
-NC    10.0000 10.0000;
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9470      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF1798
-ACC   PF08807.2
-DESC  Bacterial domain of unknown function (DUF1798)
-LENG  114
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  15
-DATE  Wed Apr 23 02:14:02 2008
-CKSUM 1086
-GA    25.0000 25.0000;
-TC    157.6000 157.6000;
-NC    14.0000 13.2000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.714548   0.634826
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -93      *  -4000
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -121  -9072  -3826   -894  -1115   -701  -1378  -7913  -6907 
-   108  -1492  -2321  -1694   1050  -2442  -2590  -1275   -170   1177   1566  -1469  -1372  -2673    741    506  -1534  -1429   -233  -2635    761   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -8967 -10009   -894  -1115  -1476   -643  -7913  -6895 
-   109     51  -3058   2081   2140  -3374    -38  -1181  -3131   -793  -3072  -2154  -1102  -2599    831    388     24  -1513  -2678  -3241  -2545   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -414  -8967  -2064   -894  -1115  -1476   -643  -7913  -6883 
-   110  -1184  -2658   1550   1400    752     39   1770  -2726   -402  -2672  -1749    844  -2240   1213   -913  -1061    509  -2278  -2842  -2156   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -18  -8571  -9613   -894  -1115  -2692   -242  -7913  -6870 
-   111  -2389  -2069  -4808    192  -1937  -4228  -3250   2625  -3950   1129   1938  -3867  -4134  -3560  -3802  -3379  -2338   1620  -2928  -2635   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -145  -8571  -3571   -894  -1115  -2692   -242  -7913  -6858 
-   112    369  -2526    834   1944  -2843  -2037   -696  -2590    954   -270  -1617   -673  -2131   -238    871   -946    576  -2146  -2711  -2032   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1091  -8445   -946   -894  -1115  -2895   -208  -7913  -6845 
-   113  -1674  -2477  -2062  -1127  -2989  -2449   -626  -2405   2616  -2354  -1641  -1168  -2452   -221   2065  -1620  -1484   1341  -2418  -2145   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7379  -8421   -894  -1115    -71  -4379  -7913  -6833 
-   114  -1528  -2989  -1358   1807  -3311   -299  -1149  -3056   -714  -1015  -2080    491  -2588   2368   1730  -1409    270  -2612  -3168  -2493   114
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7913      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF881
-ACC   PF05949.4
-DESC  Bacterial protein of unknown function (DUF881)
-LENG  237
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  86
-DATE  Tue Apr 22 20:40:31 2008
-CKSUM 3639
-GA    21.8000 21.8000;
-TC    21.8000 23.4000;
-NC    21.7000 21.7000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.432429   0.608424
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -19      *  -6267
-     1    758  -5056  -8159  -7774  -5496  -7872  -7478   1340  -7655   1230    201  -7525  -7653  -7470  -7700  -7172  -1091   2784  -6970  -6557     1
-     -   -145   -501    232     42   -378    397    105   -627    209   -462   -722    274    393     44     95    359    116   -368   -285   -250 
-     -    -35  -5539 -12459  -2240   -343   -701  -1378  -1019  -8883 
-     2    237   3823  -6087  -5451   1470    189  -4161  -1730  -5046    931   1618  -4935  -5339  -4669  -4846    770   -960   -548  -4026  -3684     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8880 
-     3   1696   1436  -6136  -5502   -527   -647  -4218    852  -5099   1701    277  -4988  -5390  -4723  -4901  -4428  -1191   1284  -4081  -3738     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8877 
-     4    406   -438  -6408  -5791    661   -628  -4551   1777  -5403   1629  -3050  -5290  -5678  -5039  -5217  -4739  -1670   1985  -4404  -4057     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8873 
-     5    876    635  -6109  -5474   1445  -5313  -4185    213  -5070   2373    -45  -4959  -5361  -4692  -4870   -986   -532   -158  -4049  -3707    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8870 
-     6   -526  -5047  -7720  -8077  -7782   3737  -7100  -7616  -7783  -7874  -6896  -6160  -6144  -7200  -7386  -1374  -4920  -6274  -7991  -7990    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8867 
-     7   -455  -3593  -6116  -5480   2939  -2499  -4192   1538  -5076   1405   -539  -4966  -5368  -4698  -4876  -4405  -1178    915  -4055   -356    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8864 
-     8   1020  -3630  -6158  -5528  -3593     -1  -4244   -962  -5125   1979   3362  -5008  -5406  -4748  -4926  -2100  -1858    413  -4108  -3767    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8861 
-     9  -1005   -344  -6099  -5463   1450  -2323  -4174   2005  -5059   1987   -669  -4948  -5351  -4682  -4859  -4387  -1872   1228  -4038   -374    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8858 
-    10   2175  -3588  -6102  -5470  -1463   -149  -4186  -1481  -5067  -2351   -700  -4953  -5357  -4691  -4869   1729   1246   1074  -4054  -3712    15
-     -   -147   -501    233     41   -379    401    104   -628    209   -465   -722    274    396     44     94    359    118   -365   -296   -251 
-     -    -54  -4875 -12459  -2181   -359   -701  -1378  -8902  -8855 
-    11    -86  -3567  -6085  -2282   1084  -5288   -806    377  -5044   -498   1401  -4933  -5338  -4667  -4844   -430   1986   1848   1625    557    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8852 
-    12    571  -4602  -1164  -2970   -708   -535   -517  -1796  -2874  -1657   -994    723  -4630   3523  -3349    660   -635  -4151  -4871  -4280    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8849 
-    13    582  -3567  -6086  -5450   2745  -5288    -13    420  -5044     -9    849  -4934  -2175  -4667  -2167  -4372  -1965   1426   2272   1534    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8845 
-    14    198  -4931  -1018  -1637  -5252  -1530    249  -2146   1465  -4947  -4020    852  -4525   1244   2824  -1195  -1054  -1238  -5114  -4431    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8842 
-    15  -3510  -4536  -1532  -1934   1029  -1641   -774    -36  -2924  -1261  -1156    660  -1920   1830  -1024   1321   1738    598  -4821  -4247    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8839 
-    16   1382  -4909  -1597  -1456  -5219  -1291   -552   -253  -1458   -739  -4001    835  -2084    103  -1512     28   2060    363  -5098    289    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8836 
-    17   -607  -4930    283     22  -1761    428    226  -1881   1440  -1236   -925   -669  -4525    611   1786    749  -1815   -315  -5113  -4431    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -98 -11417  -3987   -894  -1115   -701  -1378  -8902  -8833 
-    18    -73  -4843    609    810   -618    636    147  -1033   -431  -1893  -3932   1245  -1931    477  -1573    921    692   -270  -5027  -4344    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -85 -11323  -4200   -894  -1115  -2794   -225  -8902  -8830 
-    19    -80  -4768     -7    529  -5089    -31   -540   -190   -245  -2370    809    831    576   1276   -540   -125    714    273  -4952  -1206    29
-     -   -142   -511    231     50   -392    391    104   -632    226   -467   -724    285    387     46     98    356    114   -370   -294   -250 
-     -   -954  -1055 -12284  -1333   -730    -83  -4166  -8902  -8827 
-    20   1350  -4924    557   1109  -1877  -1101  -3092  -2092    511  -2738   -788    941  -1103  -1081  -3181    959    529    -91  -5109  -4429    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8823 
-    21    906  -4707    709  -2893   -523    217   -527   -352   -426   -397  -3822   -876   1006   -437  -1750   -488   1353    560  -4950  -1210    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8820 
-    22     75  -3724  -2061   -636  -1500   -196  -3913    183  -4273   1187  -2918  -1729    266  -4059   1253    371   -210    688   -273    619    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8817 
-    23   -184  -4930   1133    989  -5251  -2189  -3090  -2000  -1523  -2585  -4020   1196    669    965   1181    147    177    331  -5114  -1062    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36 -11417  -5502   -894  -1115   -701  -1378  -8902  -8814 
-    24   1278  -4897    -87   -956  -1892  -1380   -557   -267    -20  -2621  -3986    115    370  -1001     40    396   1730   -922   2018  -4400    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11385 -12427   -894  -1115  -1796   -490  -8902  -8811 
-    25   1239  -4900   -509    473  -1484  -1349  -3061  -4971    742   -315   1024  -1296  -4495   1573   1596   -582  -1659  -4522  -5084    949    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11385 -12427   -894  -1115  -1796   -490  -8902  -8807 
-    26   -136  -4901   1166    718  -5222  -2405  -3060  -4973    222  -1395  -3990    519  -4495    156   2548    113   -520   -781  -5084  -1331    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11385 -12427   -894  -1115  -1796   -490  -8902  -8804 
-    27   -277  -4883   -304    590  -5195  -4407  -3067   -221   -848  -1430    536  -1213   1233   1124   1456   -433    199    285  -5071   1267    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -92 -11385  -4074   -894  -1115  -1796   -490  -8902  -8801 
-    28   1381  -4820    783   1397  -1548  -1420  -1029  -4891   -187  -2618  -3909    -80   -803   2011  -1417   -695   -799  -4442   1846    496    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11297 -12339   -894  -1115   -112  -3741  -8902  -8798 
-    29   -198  -4931   2560   1443  -5252   -539  -3090  -1881   -848   -935  -4020    -51  -4525   1131    -40   -376   -497  -1959  -5114  -4431    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8794 
-    30   -116  -3588  -6107  -2029  -3536  -5312  -4183    939  -5067   2836   -101  -4957  -5360  -4689  -1708  -4397   -563  -1161  -4047  -1257    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8791 
-    31   1427  -3621  -5647  -5038  -3583  -5219  -4066    265  -1982   -252   -709  -1801  -5273      6   1591   -231    549   1636  -4071    646    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8788 
-    32    857  -4931   1372    746  -5252  -1529  -3090  -1934    -55  -2739  -4020    980  -4525   1218    738     45    539    167  -5114  -4431    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8785 
-    33   -838  -4894   -134   1762  -1491  -4442   -482   -243    -85    730    198   -888  -4535   1747    372   -437  -1893    -62  -5087  -1181    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8781 
-    34  -3756  -3582  -6101  -5465  -3531  -5305  -4175   1866  -2059   2240   -433  -1659  -5353  -4681   -436  -4390  -3697   1692    179  -1179    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8778 
-    35   -483  -4930   1447    930  -5251  -1059    185   -261   1173   -693   -745    719  -4525    691    871   -856    139  -2124  -5114  -1322    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8775 
-    36    587  -4931    855   1250  -5252   -839  -3090  -5003    310  -2738   -625    542  -4525   1822   -132   1308   -531  -2123  -5114  -4431    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8771 
-    37    401  -4191  -3957   1386  -4260  -1422  -3454  -1055  -1872   1753    514  -3600  -4817    512   1185  -1636    163  -1260  -4548  -1302    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8768 
-    38   -299  -4931    -59   1070  -5252  -1365   -711  -1885   1066  -1724  -4020    633  -4525   2233   -410    727     95   -871  -5114   -296    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11417 -12459   -894  -1115   -701  -1378  -8902  -8765 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11370 -12412   -894  -1115  -1066   -937  -8902  -7907 
-   234   2943  -3547  -6067  -5431  -1467  -2831  -4141    496  -5026    403   1737  -4916  -5319  -4649  -4826  -1242  -3662   -451  -4006  -1071   325
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11390 -12432   -894  -1115   -299  -2418  -8902  -7901 
-   235   -985  -4948  -3326   1142  -5271  -4450   -732  -1951   2585  -4963  -4037  -1368  -4542   1879   1604  -1138     91  -4571  -5128  -4448   326
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -57 -11420  -4883   -894  -1115   -701  -1378  -8902  -7895 
-   236  -1271  -4866  -1518   -492  -5178  -1222  -3050  -1984   -854   -864  -3958  -3029   3393    353    254   -442  -1004   -347  -5055  -4377   327
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11370 -12412   -894  -1115   -217  -2840  -8902  -7889 
-   237   1087  -4882    350   -963  -5180   -457   -483    838   -787    214   -107   -198  -1772  -1142   -470   -203  -3402   1788  -5079  -4410   328
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8902      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Jun
-ACC   PF03957.5
-DESC  Jun-like transcription factor
-LENG  303
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  8
-DATE  Tue Apr 22 18:34:54 2008
-CKSUM 5089
-GA    17.1000 17.1000;
-TC    19.5000 19.5000;
-NC    14.6000 16.4000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.746502   0.736470
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -222      *  -2807
-     1  -3457  -3250  -4578  -4682  -2595  -3839  -3833  -2264  -4294  -1708   5248  -4331  -4225  -4184  -4072  -3938  -3655  -2653  -3435  -3236     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -1222  -9238 
-     2  -2158  -3524   -582   3298  -3978  -2358  -1318  -3723   1470  -3555  -2845  -1019  -2729   -948  -1034  -1923  -2126  -3313  -3559  -2987     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9236 
-     3  -1080  -1949  -1247  -1026  -2936  -1903  -1292  -2625   -884  -2720  -1921  -1143    707   2400  -1202  -1136   2873  -2136  -2966  -2456     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9234 
-     4  -1235  -1818  -3027  -3219  -3898  -2041  -3060  -3637  -3229  -3906  -3152  -2469   3734  -3029  -3204  -1471   1762  -2747  -4023  -3880     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9231 
-     5  -2641  -2319  -4532  -4373   3950  -3950  -1907   -663  -4056   -856   -909  -3499  -3996  -3379  -3771  -3267  -2670   1382  -1223   -196     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9229 
-     6  -2327  -2517  -3180  -3315   -151  -3049  -1364  -3049  -3228  -2780  -2544  -2650  -3500  -2840  -3154   1108  -2573  -2835   -842   4411     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -308  -7716  -2430   -894  -1115   -701  -1378  -9461  -9226 
-     7   1376  -1517  -1341  -1250  -2737   1450   3962  -2552  -1350  -2716  -1915  -1216  -2162  -1248  -1665   -915  -1041  -1962  -2920  -2416     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7423  -8466   -894  -1115   -362  -2170  -9461  -9224 
-     8    951  -3821   3190   1635  -4084  -2057  -1379  -3970  -1562  -3869  -3165   -667  -2567  -1039  -2369  -1730  -2099  -3453  -4069  -3102     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9222 
-     9    951  -3826   3210   1589  -4089  -2058  -1383  -3976  -1568  -3876  -3172   -668  -2570  -1043  -2377  -1734  -2104  -3458  -4075  -3107     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -205  -7716  -2989   -894  -1115   -701  -1378  -9461  -9219 
-    10   2190  -1311  -1672  -1280  -2302  -1618  -1333  -1900  -1204  -2157  -1373   1732  -2080  -1078  -1544   1023   -842    722  -2544  -2102    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7525  -8567   -894  -1115  -1280   -766  -9461  -9217 
-    11  -2881  -2442  -4385  -4135    -68  -4154  -1716   -879  -3671   2825   -302  -3432  -3952  -3029  -3390  -3440  -2797  -1404  -1000   2237    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7525  -8567   -894  -1115   -430  -1957  -9461  -9214 
-    12   1008  -1589  -2172  -2200  -3660  -1739  -2383  -3434  -2436  -3618  -2734   1056  -2436  -2174  -2668   3059  -1279  -2482  -3818  -3464    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7716  -8758   -894  -1115   -701  -1378  -9461  -9212 
-    13   1709   -867  -2771  -2247   1339   1495  -1392   1366  -1965   -814   -204  -1883  -2410  -1682  -1950  -1335   -870   -264  -1467  -1086    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -583  -7716  -1618   -894  -1115   -701  -1378  -9461  -9209 
-    14   1855   -804  -2020  -1629  -1335  -1543  -1257   -798  -1428   1516   -511  -1348  -1974  -1256  -1578    900   -615   -593  -1789  -1414    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1083  -7151   -946   -894  -1115   -833  -1189  -9461  -9207 
-    15  -2048  -1653  -3858  -3452   2913  -3572  -1527    129  -3122   2098    663  -2968  -3281  -2401  -2857  -2797  -1958   -402   -792      6    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6702  -7744   -894  -1115  -2292   -329  -9461  -9205 
-    16   2800   -697  -1820  -1850  -2659   1384  -1771  -2320  -1918  -2622  -1804  -1240  -1656  -1661  -2019   -304   -477  -1503  -2868  -2607    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6702  -7744   -894  -1115  -1286   -762  -9461  -9202 
-    17    754  -1540   -504   -140  -2263    540   -470  -1968   -129  -2029  -1171   -359    951   2652   -580   -467   -540  -1508  -2272  -1678    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -18  -7096  -8138   -894  -1115  -1959   -429  -9461  -9200 
-    18   -671  -1922   -125     85  -2359   1310   2096  -2114    -84  -2132  -1281   1931    930     10   -577   -582   -676  -1690  -2341  -1676    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -18  -7096  -8138   -894  -1115  -1959   -429  -9461  -9197 
-    19   2267  -2617   1577   1386  -2952  -1512   -634  -2729   -555  -2710  -1907   -165  -1894   -257  -1188   -916  -1132  -2279  -2927  -2135    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -18  -7096  -8138   -894  -1115  -1238   -795  -9461  -9195 
-    20   1112  -1095  -2575  -2583  -3377   2261  -2401  -3140  -2601  -3368  -2463  -1767  -2084  -2284  -2664   2283   -878  -2097  -3576  -3346    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -7303  -8345   -894  -1115   -846  -1172  -9461  -9192 
-    21   -623  -1206  -2473  -2162  -2603   1462  -1953  -2197  -2022  -2504  -1720  -1699  -2201  -1821  -2209   2317   1018   1074  -2902  -2558    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7523  -8565   -894  -1115   -428  -1963  -9461  -9190 
-    22   -806  -1433  -2720  -2541  -3238   2573  -2387  -2918  -2472  -3173  -2336  -1965    865  -2239  -2631   1766  -1176    438  -3483  -3171    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -141  -7716  -3533   -894  -1115   -701  -1378  -9461  -9187 
-    23    364  -1415  -2823  -2419   1574   1011   -983  -1118  -2193  -1311   -763  -2022  -2788  -1852  -2210  -1754  -1415  -1017   -667   3614    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1518  -7589   -635   -894  -1115  -1119   -890  -9461  -9185 
-    24   2047   -315  -1008   -946  -1954   1750   -997  -1559  -1012  -1869  -1086   -599  -1200   -825  -1217    115    -27   -904  -2176  -1830    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -6105  -7147   -894  -1115  -2581   -264  -9461  -9182 
-    25   1776   -411   -880   -731  -1732   -661   -798  -1268   -710  -1586   -862   -523   2180   -595   -955     32    -69   -764  -1978  -1586    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -6105  -7147   -894  -1115  -2581   -264  -9461  -9180 
-    26    -98   -600  -1242  -1190  -1640   -914  -1112   -939  -1029  -1428   -940   -906  -1503  -1014  -1157   -332   3134   -627  -1961  -1609    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -6105  -7147   -894  -1115  -2581   -264  -9461  -9177 
-    27    286   -399   -713   -681  -2033   1715   -871  -1783   -835  -1993  -1175   -461  -1190   -656  -1097   2003    -48  -1059  -2215  -1807    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34  -6105  -7147   -894  -1115  -1723   -520  -9461  -9175 
-    28   1603   -635  -1562  -1618  -2573   2719  -1624  -2235  -1746  -2535  -1725  -1093  -1566  -1499  -1872   -228   -403  -1427  -2770  -2494    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6573  -7615   -894  -1115  -2371   -310  -9461  -9172 
-    29   -313  -1290   -522    -44  -1944  -1231   -189  -1616    357  -1677   -854   -221   1143    199   1872   1201   -350  -1214  -1899  -1377    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6573  -7615   -894  -1115  -2371   -310  -9461  -9170 
-    30     -9   -679  -1258  -1285  -2565   1445  -1427  -2352  -1466  -2558  -1715   -926  -1531  -1243  -1675   2670   -384  -1498  -2737  -2382    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6573  -7615   -894  -1115  -1742   -512  -9461  -9167 
-    31   -783  -1361  -1679  -1822  -3174   2905  -2021  -3068  -2126  -3217  -2457  -1555   2278  -1909  -2286   -973  -1155  -2247  -3105  -2992    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -2210   -351  -9461  -9165 
-    32   -869  -1262  -1855  -1760  -1679   2844  -1580  -1276  -1625   1060  -1063  -1562  -2212  -1568  -1752  -1127  -1097  -1119  -2145  -1719    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -2210   -351  -9461  -9162 
-    33   -207   -760  -1119   -652  -1276    733   -615   -859   -524    627   -396   -665  -1607   -413   -848   1334   1199   -591  -1591  -1154    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -2210   -351  -9461  -9160 
-    34  -2207  -1787  -4080  -3662   2720  -3777  -1769     82  -3337   2308    647  -3203  -3431  -2562  -3041  -3015  -2110   -495   -991   -244    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -1204   -822  -9461  -9157 
-    35   2579  -1012  -2206  -2054  -2955  -1263  -1959  -2667  -2007  -2895  -2033  -1498   1441  -1784  -2179   1471   -740  -1823  -3162  -2851    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7186  -8228   -894  -1115  -1855   -467  -9461  -9155 
-    36   -453   -561  -1738  -1171   1280  -1811   -682   -122   -957    761    220  -1101    573   -766  -1120    471   1425    -14  -1017   -627    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7186  -8228   -894  -1115  -1855   -467  -9461  -9152 
-    37   1438  -1375   -977   -731  -2157  -1486   2606  -1926   -685  -2089  -1309   -812   2509   -649  -1029   -701   -760  -1498  -2342  -1807    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7186  -8228   -894  -1115  -1855   -467  -9461  -9150 
-    38   -909  -1722   1624   -321  -2097   2038   -854   1576   -804  -1894  -1207   -574  -1997   -569  -1292   -942   -969  -1233  -2363  -1789    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -592  -7186  -1608   -894  -1115  -1855   -467  -9461  -9147 
-    39  -1211  -2128  -1236   -535  -2637  -1898   -186  -2236    939  -2056  -1336   -624  -1960   2632   2599  -1119  -1047  -1950  -2038  -1718    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -6618  -7661   -894  -1115  -2344   -316  -9461  -9145 
-    40    872   -700  -2852  -2319   -586  -2551  -1590   2349  -2036   1137    407  -2080  -2549  -1766  -2038  -1685   -861    945  -1496  -1172    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8855 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8852 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8849 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8845 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8842 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8839 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8836 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8833 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115  -2671   -246  -9461  -8830 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -42  -5820  -6862   -894  -1115   -149  -3348  -9461  -8827 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1781  -7717   -510   -894  -1115   -701  -1378  -9461  -8823 
-   153   -646  -1003  -1185  -1348  -2333   3269  -1433  -2351  -1572  -2505  -1938  -1197  -1673  -1447  -1655   -842   -975  -1784  -2095  -2147   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -38  -5974  -7016   -894  -1115  -2625   -255  -9461  -8820 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -38  -5974  -7016   -894  -1115   -154  -3303  -9461  -8817 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8814 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8811 
-   157  -1216  -2648   2247   1156  -2943  -1850   -795  -2677   -576  -2684  -1838   -501  -2124   -390  -1146   1576  -1198    860  -2908  -2182   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8807 
-   158  -3777  -4125  -1925   3871  -4984  -3355  -3125  -5379  -3371  -5156  -4796  -2611  -3875  -3007  -3762  -3630  -3916  -4960  -4357  -4463   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8804 
-   159  -2128  -3614   -351   2081  -3946  -2254  -1393  -3819  -1121  -3677  -2983   -910  -2691   3669  -1546  -1872  -2144  -3376  -3729  -3016   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8801 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8798 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7717  -8759   -894  -1115   -701  -1378  -9461  -8794 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8791 
-   163   3225  -1599  -3356  -3607  -4039   1290  -3237  -3824  -3680  -4097  -3209  -2466  -2631  -3256  -3531  -1243  -1456  -2697  -4194  -4117   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8788 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8785 
-   165  -3681  -3593  -4389  -4747  -5281   3812  -4419  -5908  -5071  -5671  -5288  -4417  -4223  -4850  -4766  -3952  -4069  -5125  -4424  -5214   168
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8781 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8778 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8775 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8771 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8768 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8765 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8762 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8758 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8755 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8752 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8748 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8745 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8741 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1781  -7717   -511   -894  -1115   -701  -1378  -9461  -8738 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -38  -5974  -7016   -894  -1115   -154  -3303  -9461  -8735 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9461      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Jun
-ACC   PF03957.5
-DESC  Jun-like transcription factor
-LENG  303
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  8
-DATE  Tue Apr 22 18:34:54 2008
-CKSUM 5089
-GA    17.1000 17.1000;
-TC    19.5000 19.5000;
-NC    14.6000 16.4000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.746502   0.736470
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -222      *  -2807
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -2210   -351  -9461  -9162 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -2210   -351  -9461  -9160 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -6819  -7861   -894  -1115  -1204   -822  -9461  -9157 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7186  -8228   -894  -1115  -1855   -467  -9461  -9155 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7186  -8228   -894  -1115  -1855   -467  -9461  -9150 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -191  -7523  -3098   -894  -1115  -1286   -762  -9461  -9129 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    398    110   -626    210   -465   -721    275    394     45     96    359    117   -369   -295   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14  -7717  -8759   -894  -1115   -701  -1378  -9461  -8741 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1234  -6069   -843   -894  -1115  -1744   -512  -9461  -8658 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -618  -7718  -1555   -894  -1115   -701  -1378  -9461  -8271 
-   297   -906  -1471  -2346  -2557  -3197  -1649  -2486  -3307  -2701  -3510  -2792  -1984  -2369  -2496  -2716   3468  -1326  -2424  -3320  -3037   308
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7121  -8163   -894  -1115  -1935   -437  -9461  -8267 
-   298   -724  -1160  -1439   -931   2722  -1813   -590   -978   -480  -1169   -521   -957  -2005   -565   1498   1064   -732   -804  -1158   -428   309
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7121  -8163   -894  -1115   -804  -1226  -9461  -8262 
-   299  -2188  -3284   2573   -821  -4311   2917  -1920  -4378  -2277  -4295  -3680  -1156  -2810  -1661  -3028  -2025  -2392  -3716  -4129  -3552   310
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7474  -8516   -894  -1115  -1397   -689  -9461  -8257 
-   300    780   2406    946   2328  -2495  -1631   -518  -2205   -226  -2240  -1383   -345  -1852   -105   -751   -730   -813  -1802  -2479  -1808   311
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -7474  -8516   -894  -1115   -391  -2075  -9461  -8253 
-   301   -866  -1488  -3133  -3250  -3779  -1744  -2946  -3533  -3198  -3812  -2936  -2264  -2509  -2894  -3159   2902   2425  -2498  -4004  -3793   312
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7718  -8760   -894  -1115   -701  -1378  -9461  -8248 
-   302  -4077  -3791  -4518  -4858  -5206  -3818  -4460  -5898  -5053  -5602  -5343  -4628   4289  -4938  -4749  -4364  -4429  -5313  -4385  -5119   313
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15  -7718  -8760   -894  -1115   -701  -1378  -9461  -8243 
-   303  -1248  -1829  -3028  -3227  -3912  -2051  -3072  -3655  -3242  -3923  -3171  -2479   3794  -3043  -3215  -1483   1549  -2762  -4032  -3893   314
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9461      0 
-//
-HMMER2.0  [2.3.2]
-NAME  SLT
-ACC   PF01464.12
-DESC  Transglycosylase SLT domain
-LENG  137
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  39
-DATE  Thu Apr 24 19:36:04 2008
-CKSUM 2764
-GA    16.1000 16.1000;
-TC    16.2000 16.2000;
-NC    16.0000 16.0000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.686005   0.638888
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -41      *  -5170
-     1    330  -3843   1410   1063    133   -458  -2111  -1111  -1707  -1038    981    246    940   -203   -613    272   -585  -1055  -4048   -693     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -1041  -8087 
-     2    383   3238  -4925  -4297  -2500  -4233  -3098    175  -1477   1371    112    255      6   -951  -3761  -1536   -919   -688  -3000   2172     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8082 
-     3   -325  -2650  -4253   -371   2284  -4114  -2939   2002   -378  -2506    300   -576    158  -3158   -734   -490  -2609    355   2403   -198     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8077 
-     4    623  -3913     -8      9    829   -405  -2088   1266    499    445  -3004    612  -3522   1042    487  -1006  -2392  -3532  -4100  -3420     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8071 
-     5    996  -3754  -2397   1061    380  -1240  -2142   -133   1704  -1688     55   1016  -3566    838   -615  -1317  -2409   -320  -3983   -330     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8066 
-     6   2182  -3734  -2409    104  -3974    304  -2150   -158    144  -1487  -2846   -466   -832    -95   -509  -2396    -41   -939   1860    610     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8061 
-     7   1425  -3725  -2415   1112   -759   1234  -2153    130    193   -828    136  -2159  -3575   -224   -510    461    -66  -3301  -3962  -3334     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8055 
-     8    365   2115    -37    960  -4239  -1233  -2086  -3988    820   -325  -3010   -294  -3520   1336    -15    100   -870   -383   1042    737     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8050 
-     9   1324  -3924   -698    -13  -4244  -1233  -2084  -1133   2087  -3940    884   -431   -345    537   1419  -2332   -839  -1085  -4107  -3425     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8044 
-    10  -2454  -3907   -674    240    682  -1557  -2090  -3965    531   -730  -2999   1260    630  -1632    115   -936    218  -3525    816   2958    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8039 
-    11   -360    747    496    629  -4246   1663    323  -3997   -547  -3941     32   1794  -3519    471    566   -862   -125  -3547  -4108   -276    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8033 
-    12  -2702  -2536   -934  -4360     66  -1287    219   2281  -3967    473  -1739    126  -4294  -3600  -3787     56  -2642   2053  -2993   -471    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8028 
-    13   -947  -3908   2006   1679  -4221  -3430  -2090  -3967  -1673   -329     94   -456   1538   -227   -168    289  -2393  -1211    808  -3418    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8022 
-    14   -391  -3430  -2650    867  -3566  -3595  -2285  -3199     90   -732  -2571  -2352   2980   -261  -2442   -443  -2452    428   2050   -113    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8017 
-    15    760  -3901    139    -24   -739  -1077  -2092  -1144   -816   -321     95    326    -35    497    670   1443   -770  -1209  -4091   -313    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8011 
-    16  -1155  -2536  -4991    934   -396  -1414  -3111    165   -579   2222    492  -3871  -4294  -3600  -3786  -3325    637     72  -2993   -151    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8006 
-    17    130  -3459  -6063  -5438    444  -5336  -4196   1947  -5061   2261    520  -4989  -5256  -4564  -4826  -4447  -3633    752    950  -3614    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -8000 
-    18   1442  -2615  -1088  -3836    393  -4152  -2988  -2124    971   1016   2059  -3590  -4208  -3276    434  -3208    -74   -743  -3061   1679    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7994 
-    19   2864  -2718  -4189  -3608    383     75  -2964  -2266   -113   -598  -1936  -3461  -4182  -3137  -3455   -328   -878  -2164  -3175    794    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7989 
-    20  -4657  -4150  -7303  -6935  -4299  -7098  -6781   3088  -6855   1005    971  -6756  -6766  -6568  -6886  -6445   -497   1797  -5992  -5694    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7983 
-    21   2178  -2998  -5586  -5033  -3149  -4616  -3840   2180  -4657  -2899   2003  -4446   1012  -4294  -4476    -63  -3131    455  -3724  -3379    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7977 
-    22    457  -3531  -2557    -35  -3700  -1123  -2234   -150    338   -861    165  -2276  -3640   2198   1532   -832   -674  -1098   2825    221    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7972 
-    23   -368  -3885  -2323  -1774  -4188  -1352   1210   -276    798  -3893  -2979   -440  -3531   2640    585   -966   1046   1153  -4079  -3408    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7 -10297 -11339   -894  -1115   -701  -1378  -8128  -7966 
-    24  -8228  -7103  -6788   3978  -8485  -6892  -7278  -9521  -8039  -8876  -8815  -7418  -7352  -7720  -7820  -8447  -8372  -9169  -7241  -8359    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -51 -10297  -5075   -894  -1115   -701  -1378  -8128  -7960 
-    25  -5419  -5656  -7297  -7669  -7703  -5817  -6986  -8194  -7765  -8089  -7486  -6731  -6489  -7413  -7341   3779  -5866  -7108  -7058  -7711    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8 -10254 -11296   -894  -1115   -370  -2143  -8128  -7954 
-    26    428  -3892   -690  -1768   -580   1744   1889  -3938    102   -855    165    217  -3528  -1640   1049   1180  -2394  -3506  -4084  -3411    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7948 
-    27   -925    646  -5092  -4463   3164   1407  -3132  -2082  -4060   -112    241   -617  -4355  -3678  -3860  -3391  -2704  -2005   3027   1241    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7943 
-    28  -2458  -3931   1357      0  -4252   -211  -2090  -4003   1117   -800  -3020   2965  -3524   -170     62   -972  -2397  -1057  -4114  -3431    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7937 
-    29    524  -4256  -3437   -993  -5493  -4111  -3566  -5211   1148  -5245  -4387  -3360   3620  -3192  -3509   -333  -3478  -1270  -5426  -4891    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7931 
-    30   -960  -3897   -141  -1765   -668    470    980  -3946    994  -1562    126   1647  -3526    381    866    111   -646   -979    840   1434    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7925 
-    31   3045  -2685  -5132  -4523  -2696  -4344  -3316     93  -4136  -1060  -1928  -4023  -4435  -3781   -777   -397   -949    800  -3212  -2868    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7919 
-    32  -2939  -2910  -4601  -3898  -2901  -4347  -3061   2292   1225  -2760  -2108  -3684  -4390    801  -1215  -3425    883   1884  -3331   1290    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7913 
-    33  -3695  -4460  -3700  -4086  -6661    136    417  -6635  -5325  -6747  -5911   2330  -5062  -4727  -5736   3147  -4106  -5485  -6828  -6308    33
-     -   -150   -501    234     42   -382    399    104   -623    211   -464   -722    276    393     44     95    358    121   -370   -296   -250 
-     T  -2312  -2071   -846    -23  -6011   -701  -1378  -8128  -7907 
-    34  -1686  -1663  -3285  -2689  -1634  -3133   1075   1523    835   -112   -860   1314  -3192  -2178  -2468  -2181    186    145   4124  -1739    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -10  -9118 -10160   -894  -1115  -4538    -63  -8128  -7901 
-    35  -3334  -4867   2005  -1699  -5689   1012  -2905  -5641  -3281  -5536  -4894   3311  -3930  -2601  -4192  -3084   1212  -4960  -5731  -4716    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -9118 -10160   -894  -1115  -4538    -63  -8128  -7895 
-    36  -1522  -2988    463   -821  -3308  -2495  -1153   -517   1863  -3003  -2078    388     30   -694   1890   1054    278  -2610  -3172  -2492    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -10  -9118 -10160   -894  -1115  -4538    -63  -8128  -7889 
-    37  -1603  -2926   1842   -938  -3204   -154  -1268      8   -886  -2934  -2051   2751  -2682   -833    514     88  -1548   -260  -3162  -2514    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -10  -9118 -10160   -894  -1115    -39  -5215  -8128  -7883 
-    38    267  -3926  -2301   -518  -4247   1685    295  -3998   1351  -3942  -3016  -2063   1352    -66   1487   -275   -806  -3548  -4109   -630    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -8 -10297 -11339   -894  -1115   -701  -1378  -8128  -7877 
-    39    849  -3896  -2315  -1766  -4203  -1276  -2094  -3944   1041  -1562  -2988    904   -894   -229   -850   1556   1483    402  -4087  -3413    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -55 -10297  -4957   -894  -1115   -701  -1378  -8128  -7870 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .  -2311 -10251   -334   -894  -1115  -1517   -620  -8128  -7864 
-    41  -1983  -3066   -947  -1026  -3448   2869   2586  -3575  -1069  -3502  -2773  -1281  -2825   1841  -1354  -1880  -2049  -3117  -3407  -2742    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7955  -8997   -894  -1115  -5031    -45  -8128  -7858 
-    42   -827  -2137    749   -181  -2392  -1815   2808    296   1072  -2123  -1244   -477  -1908   1614   -530   -737   -764  -1730   2788  -1706    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7955  -8997   -894  -1115  -5031    -45  -8128  -7852 
-    43    849  -2092  -1754  -1765  -3652  -2100  -2086  -3389  -1805  -3506  -2709  -1724   3450   1830  -2062  -1459  -1625  -2690  -3713  -3271    44
-     -   -142   -504    231     46   -385    394    101   -630    210   -464   -714    274    390     52     97    357    118   -359   -299   -254 
-     .  -3119  -1721   -793  -3767   -110  -3396   -144  -8128  -7845 
-    44   1129  -2354   1694     80  -2671  -1613   -441  -2432   1615  -2380  -1492   1606  -1820     -9   -648   -714   -825  -1983  -2558  -1843    60
-     -   -149   -500    232     43   -381    398    105   -624    210   -464   -721    278    393     45     98    359    117   -370   -295   -250 
-     .  -2601   -272  -8479    -46  -4996  -4184    -82  -8128  -7839 
-    45  -1346  -2510  -1117   -651  -2957  -2136   2635  -2677   2285  -2583  -1768   -864  -2278   -309   -145   1853  -1274  -2295  -2639  -2128    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -17  -7668  -8710   -894  -1115  -5090    -43  -8128  -7833 
-    46   -949  -1575  -2835  -3085  -3975   1529  -3005  -3853  -3359  -4069  -3168  -2250  -2555  -2960  -3330   3184  -1399  -2688  -4128  -3960    63
-     -   -149   -500    232     42   -376    400    105   -627    210   -463   -721    275    393     45     95    359    119   -370   -295   -250 
-     .  -2832   -230  -8710    -38  -5254    -27  -5768  -8128  -7827 
-    47   2727  -4024   2165  -5203  -6468   -180  -5337  -6274  -5719  -6487  -5566  -4551   -657  -5231  -5803    391  -3808   -126  -6662  -6432    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7820 
-    48   -351  -2538  -4976  -4345   -188  -4241  -3108    749    188    809   2207  -3864  -4291   -663    632     91   -828   1327  -2994   1104    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7814 
-    49  -7735  -6862  -7916  -8296  -7837   3828  -7444  -9369  -8453  -8778  -8665  -8091  -7356  -8294  -7911  -8121  -8032  -8856    969  -7653    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7807 
-    50  -5999  -5330  -8376  -7775  -3275  -8260  -6809   1848  -7600   2842   2188  -8009  -7083  -6202  -6997  -7704  -5814  -3610  -5159  -5446    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7801 
-    51   -400  -4223  -6710  -6279   -193  -5924  -4194  -2970  -5897  -2528   4905  -5543  -5892  -5220  -5582  -5110  -4460  -1092   3348  -2740    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7794 
-    52  -6268  -6240  -6505  -6620  -6354  -6289  -6129  -7022  -5772  -6327   1342  -6460  -6773   4529  -5709  -6470  -6512  -7038  -6424  -6244    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7788 
-    53  -4629  -4162  -7196  -6750   1439  -6855  -6160   2602  -6579   1570  -2709  -6515  -6536  -6123  -6474  -6129    617   1308  -5432  -5230    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7781 
-    54  -2717  -2650     19  -3871  -2623  -4194  -3034   1292  -1130  -1215   3533   2263  -4250  -3317  -3592  -3252   1272   -300  -3110  -2750    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7775 
-    55  -1106  -3925    415  -1753   -560  -1535  -2087  -3996    829  -3941  -3015  -2064   2703    852    509   1288   -670  -3547  -4109  -3427    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7768 
-    56    663  -3826  -2354  -1804    732   -432   1555  -3823  -1716  -3823      3   1025    743   1055    655   1519   -872  -1018  -4036  -3381    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7762 
-    57   -187  -3820  -4847  -4659  -5342  -4137   2945  -1086  -4620  -5261  -4457    965  -4773  -4413  -4815   -190   3275  -4388  -5613  -5267    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7755 
-    58   2459  -2536  -4992  -4360   1748  -1354    474    486  -3967   -458    249   -610  -4293  -3600   -736   -520  -2642   -602   1153  -2650    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7748 
-    59  -1056  -3925     48     86  -4246    364  -2084  -3997   2017  -1579  -3014   1289   -122    214    975    385   -770  -1075  -4108  -3425    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -10298 -11340   -894  -1115   -701  -1378  -8128  -7741 
-    60    627  -3923     72    499  -4243   -335   1571  -3993    467   -376  -3012   -454    203  -1625   1436    446  -2391  -1075   1864   -345    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -232 -10298  -2808   -894  -1115   -701  -1378  -8128  -7735 
-    61  -2458  -2510    421  -3230    634  -3864    353    708   -796   1884  -1703  -3142  -3926    -73  -3138   -988    737  -1938  -2943   1975    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10075 -11117   -894  -1115  -2841   -217  -8128  -7728 
-    62   1424  -2683  -3381  -2808  -2697   1806  -2532    203   1559  -2564    633  -2859  -3829  -2480   -742   -181  -2390    737  -3102  -2694    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S   -114 -10075  -3831   -894  -1115  -2841   -217  -8128  -7721 
-    63  -2206  -3354  -2202    195    835  -3238    268  -3227   1824   1111    428   -298   -622  -1505    928   -623   -310   -867  -3613    -95    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -64  -9970  -4737   -894  -1115  -3246   -161  -8128  -7714 
-    64   -311  -3558  -2002    389   -388  -3117  -1777   -750   1480  -3566   2197   -115    116    832   1780   -558  -2074  -3169   1490    -37    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -189  -9916  -3093   -894  -1115  -3411   -142  -8128  -7707 
-    65  -2207  -2058  -4397  -3771     90   1189  -2600    562  -3400    781    601   1294  -3789   -107   -496     16  -2148   1307  -2513    474    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -79  -9736  -4395   -894  -1115  -3819   -106  -8128  -7700 
-    66  -1998  -2774  -2241  -1687     59   1109  -1819   1237    402  -2693    667    790  -3201    869   -127    687    571   -585  -3105    120    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -670  -9666  -1452   -894  -1115  -3941    -97  -8128  -7693 
-    67  -1602  -1531    217  -2788    774    954  -1919   1550    -18   -124   1553  -2530  -3136  -2218  -2488   1096  -1542    460  -1979  -1621    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -561  -9007  -1665   -894  -1115  -4615    -60  -8128  -7687 
-    68  -1428  -2894    951   -566  -3201  -2251  -1000  -2957   2158  -2902  -2008   1945   1546   -560  -1093  -1290  -1376  -2519   2366  -2378    86
-     -   -151   -502    233     45   -383    404    103   -628    208   -468   -723    276    392     46     96    361    117   -371   -297   -242 
-     .  -1992   -652  -3220  -1343   -723   -621  -1516  -8128  -7679 
-    69   -560  -3317    399  -1474  -3549   -699    701    274    446   1447   1052  -1766   1157    195   -246   -587  -2015  -2891  -3556     71    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -9  -9824 -10866   -894  -1115    -74  -4318  -8128  -7672 
-    70  -2454  -3923    629    969   -741   1669  -2087  -3991    438  -3938  -3012   -455     78  -1627  -2175   1235      4  -3544   1861    664    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -9 -10298 -11340   -894  -1115   -701  -1378  -8128  -7665 
-    71   -958  -3731    144   1273  -3969  -3482   1448    809   -661   -791     58   -480    664  -1723    546  -2397    341    693  -3966   1156    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10298 -11340   -894  -1115   -701  -1378  -8128  -7658 
-    72  -2452  -3924   2315    155  -4245   -562    280  -3996   -436  -3940    -35   1291  -3519    474      5    242    171   -986    838   1133    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10298 -11341   -894  -1115   -701  -1378  -8128  -7651 
-    73  -1070  -3920   2125   1084  -1036   -343    543  -3983  -1677    751  -3011   1823  -3527   -172  -2184   -289  -2398  -3539  -4106   -629    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10298 -11341   -894  -1115   -701  -1378  -8128  -7644 
-    74     -9  -2555  -4845  -4221  -2512  -4222  -3083   1561   -970   1617    488  -3802    359  -3519   1961  -1064   -841   -698  -3009  -2663    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10298 -11341   -894  -1115   -701  -1378  -8128  -7637 
-    75  -2480  -3678     68  -1899   2031  -3501  -2173  -3579     32    745  -2795   -469  -3591    436    889  -1100   1476  -3244    852   1639    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7629 
-    76  -4230  -5959   3356  -2599  -6211  -4376    124  -1155    471  -5913  -5164   2311  -4814    658  -3985  -3947  -4244  -5564  -6061  -5213    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7622 
-    77    506  -3918  -6575  -6923  -6623    546  -5960  -6378  -6630  -6695  -5734  -5028   3815  -6058  -6243  -3569  -3791    300  -6850  -6832   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7615 
-    78   -628   3615   -848   1728  -3119  -3776  -2506    410   -805   -705  -2242   -477  -3853   -765  -2761  -2743    504   -174    948   1259   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7607 
-    79   -389  -3902   1330   -838   -574  -3432    239   1063    930    344     78    178  -3525   1273   -659  -1175    925  -3518  -4092  -3415   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7600 
-    80    244  -4583   -839  -3678  -6520  -4304  -4575   -842  -4917  -6463  -5655   3611  -4994  -4332  -5478   1906  -4094  -5396  -6661  -6062   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7592 
-    81   -352  -2886  -5486  -4878  -2919  -4738  -3663   2782  -4499   1180    277  -4386  -4765  -4139  -4319  -1314    846   1128  -3508  -3160   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7585 
-    82  -1111  -3917   -201    436  -4234  -3428   1629    356    720   -140   -383    849  -3521   -179   1004    798    -43  -1213  -4102    500   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7577 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7570 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7562 
-    85   1945  -2595  -4613  -4005  -2561  -1323  -3040   1345  -3688   -561  -1799   -615  -4243   -411  -3638    -41   1783    644  -3049  -2696   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7555 
-    86    650  -3922  -2300   -170  -4242  -1313    251  -3992   1502   -765  -3012   1346  -3519   -436    546     52     35  -3544   2455   1568   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7547 
-    87  -2715  -2546  -5031  -4398    411  -4259    232   1658  -1126    285    358  -3895  -4309   -415  -3807  -3343   -609  -1959  -2992   3789   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9 -10299 -11341   -894  -1115   -701  -1378  -8128  -7539 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -10 -10299 -11342   -894  -1115   -701  -1378  -8128  -7459 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -897  -9584  -1133   -894  -1115  -4067    -89  -8128  -7443 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -504  -8701  -1801   -894  -1115  -4784    -53  -8128  -7435 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -227  -8212  -2871   -894  -1115  -4964    -47  -8128  -7426 
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-     -   -149   -500    235     43   -381    398    105   -623    210   -466   -721    279    393     45     96    359    117   -370   -295   -250 
-     .   -879  -1157  -9043    -57  -4698  -5020    -45  -8128  -7418 
-   103  -1081  -2567    846   1700  -2889  -1923   -650  -2640    906  -2572  -1669   -551   2132   -205   1060   -942  -1026  -2192  -2732  -2044   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -17  -8001  -9043   -894  -1115  -3918    -99  -8128  -7409 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -16  -8198  -9240   -894  -1115  -3993    -94  -8128  -7401 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -8345  -9387   -894  -1115    -30  -5600  -8128  -7392 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10300 -11342   -894  -1115   -701  -1378  -8128  -7384 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10300 -11342   -894  -1115   -701  -1378  -8128  -7375 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -12 -10302 -11344   -894  -1115   -701  -1378  -8128  -7098 
-   137   -889  -3229  -2864   -686   1569  -3687  -2397   1087    -67   -722  -2387   1262   -844    599   -745    -77   -680    880  -3575   1451   163
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     H      *      *      *      *      *      *      *  -8128      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF2346
-ACC   PF09803.1
-DESC  Uncharacterized conserved protein (DUF2346)
-LENG  85
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  4
-DATE  Wed Apr 23 11:37:31 2008
-CKSUM 3285
-GA    25.0000 25.0000;
-TC    75.0000 75.0000;
-NC    18.3000 18.3000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.353738   0.654674
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -322      *  -2322
-     1  -2406  -2296  -3638  -3594  -1525  -3105  -2824  -1047  -3121   -596   5043  -3293  -3425  -3046  -2996  -2911  -2552  -1398  -2513  -2207     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -1322  -7392 
-     2  -2594  -2690  -3304  -3623  -4328   3747  -3462  -4761  -3953  -4671  -4212  -3320  -3352  -3748  -3779  -2839  -2981  -4004  -3668  -4222     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -7714  -7384 
-     3   -509  -1122  -2185  -2309  -3189   3004  -2259  -2898  -2421  -3184  -2367  -1674  -2074  -2170  -2482   -734   1898  -2011  -3356  -3137     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -7714  -7375 
-     4  -4114  -3274  -4214  -4453  -1722  -3496  -2681  -4109  -4149  -3619  -3615  -4044  -3885  -4032  -3816  -4355  -4248  -4133   6191  -1329     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -7714  -7366 
-     5    799   -814  -1301   -734   -872  -1762   -550   -235   1486   -661   2104   -821  -1851   -420   -751   -774   -450   1283  -1272   -852     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -7714  -7358 
-     6  -2621  -2150  -4779  -4219   -461  -4494  -3220     96  -3870   2769   2743  -4144  -3872  -3010  -3534  -3778  -2499   -607  -2129  -2177     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -7117  -8159   -894  -1115   -701  -1378  -7714  -7349 
-     7  -2641  -3308   -896   3732  -3966  -2458  -2043  -4105  -2128  -4016  -3555  -1531  -2959  -1842  -2560  -2479  -2750  -3722  -3563  -3385     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7341 
-     8  -1353  -1046  -3665  -3193  -1401  -3248  -2558   2516  -2958   -586   -336  -2889  -3238  -2741  -2967  -2445   1714   2060  -2409  -2013     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7331 
-     9   1670  -1068  -2356  -2522  -3292   3016  -2397  -3020  -2673  -3306  -2459  -1734  -2052  -2340  -2677   -688   -888  -2041  -3464  -3286     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7322 
-    10  -2094  -2785  -2682  -1412  -3620  -2623   -554  -2963   2657  -2626  -1956  -1316  -2575   -136   2950  -1975  -1788  -2730  -2468  -2362    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7313 
-    11  -2181  -1846  -4016  -3616   2507  -3644  -1766   -192  -3261    453   4167  -3118  -3453  -2613  -3018  -2875  -2117   -683  -1079   -288    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7304 
-    12   1903   -837  -1939  -1608  -1507   1291  -1314   -970  -1448   1218   -676  -1322  -1949  -1279  -1612   -710   -626   -724  -1938  -1564    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7295 
-    13  -2608  -2141  -4766  -4204   -460  -4476  -3205     97  -3856   2695   3003  -4125  -3863  -3001  -3522  -3757  -2487   -604  -2124  -2169    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7285 
-    14  -2505  -2094  -3669  -3495    642  -3542   -786  -1112  -3019   1517   -667  -2637  -3481  -2467  -2795  -2783  -2437  -1389   -126   3938    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8159   -894  -1115   -701  -1378  -7714  -7276 
-    15  -1935  -1579  -4147  -3649   -752  -3770  -2800   2196  -3305    474   4085  -3414  -3529  -2828  -3155  -3003  -1884    302  -2168  -1994    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8160   -894  -1115   -701  -1378  -7714  -7267 
-    16   1629   -934  -2493  -2453  -2801  -1255  -2155  -2210  -2315  -2678  -1928  -1654  -1972  -2085  -2350   -596   3203  -1547  -3107  -2843    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7117  -8160   -894  -1115   -701  -1378  -7714  -7257 
-    17  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7248 
-    18  -2931  -2878  -3420  -3706  -4181  -2925  -3468  -4621  -3859  -4490  -4165  -3491   4225  -3781  -3695  -3182  -3279  -4087  -3594  -4064    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7238 
-    19  -1771  -1603  -3750  -3689  -2037  -3050  -3231    403  -3479  -1154  -1076  -3246  -3399  -3383  -3437  -2628  -1917   3536  -3074  -2677    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7229 
-    20   2812  -1031  -2417  -2539  -3226   1919  -2364  -2941  -2626  -3229  -2380  -1721  -2026  -2302  -2634   -654   -848  -1983  -3415  -3226    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7219 
-    21   1363  -1012  -2948  -2391   -529  -2600  -1586    171  -2073   1390   3306  -2147  -2620  -1752  -2044  -1722  -1080    -16  -1460  -1199    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7209 
-    22  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -7118  -8160   -894  -1115   -701  -1378  -7714  -7200 
-    23  -2869  -2566  -3159  -3012    482  -3346   4459  -2567  -2250  -2185  -2020  -2429  -3457  -2223  -2192  -2817  -2819  -2573   4286    940    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7119  -8161   -894  -1115   -701  -1378  -7714  -7191 
-    24  -1593  -1309  -3750  -3173   -294  -3234  -1864   1811  -2794   1716    532  -2792  -3068  -2279  -2593  -2370  -1514   -130   4136   -923    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7180 
-    25  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7170 
-    26  -2171  -2655  -1458  -1748  -3334  -2364  -2267  -3943  -2365  -3936  -3437   4205  -2932  -2205  -2608  -2224  -2439  -3392  -3253  -2909    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7160 
-    27  -2562  -2904  -1886  -1971  -3251  -2661  -2079  -3690  -1565  -3469  -3081  -2107  -3091   4371  -1665  -2585  -2674  -3411  -3077  -2821    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7150 
-    28  -2931  -2878  -3420  -3706  -4181  -2925  -3468  -4621  -3859  -4490  -4165  -3491   4225  -3781  -3695  -3182  -3279  -4087  -3594  -4064    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7140 
-    29  -1056  -2198    -90   2762  -2807  -1589   -814  -2450   -614  -2570  -1818   -439  -1988   -459  -1095   -967   1850  -2039  -2820  -2167    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8160   -894  -1115   -701  -1378  -7714  -7129 
-    30  -1968  -1663  -3449  -3179    425  -3234   -909   2056  -2760   -727   -585  -2488  -3235  -2324  -2604  -2442  -1927   -510   -325   3834    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8161   -894  -1115   -701  -1378  -7714  -7119 
-    31  -3342  -2776  -4026  -4232   4354  -3545  -1431  -2315  -4038  -1801  -1900  -3299  -3780  -3350  -3645  -3490  -3420  -2566   -739    349    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7118  -8161   -894  -1115   -701  -1378  -7714  -7109 
-    32  -1333  -2680   -200   2722  -3090  -1792   -603  -2792   1985  -2673  -1897   -444  -2067   -206   -274  -1149  -1277  -2396  -2740  -2167    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7119  -8161   -894  -1115   -701  -1378  -7714  -7098 
-    33  -1322  -2652   -257   2542  -3073  -1807   -580  -2764   2244  -2639  -1860   -459  -2065   -180   -195  -1143  -1258  -2372  -2700  -2144    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7119  -8161   -894  -1115   -701  -1378  -7714  -7087 
-    34  -3385  -2605  -4132  -4289   2898  -3917   -510  -2270  -3852  -1702  -1731  -2784  -3847  -2843  -3367  -3234  -3291  -2460   5254   1394    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -7119  -8161   -894  -1115   -701  -1378  -7714  -7077 
-    35  -1559  -1267  -3827  -3378  -1101  -3355  -2652    803  -3065    -61   3067  -3063  -3324  -2776  -3009  -2589  -1555   2846  -2308  -1995    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -458  -7119  -1957   -894  -1115   -701  -1378  -7714  -7066 
-    36   -676  -1158  -2054  -2114  -2456  -1434  -1951  -1867  -1973  -2321  -1832  -1659  -2082  -1927  -2017   -920   3615  -1459  -2685  -2441    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -6692  -7734   -894  -1115  -1442   -662  -7714  -7055 
-    37   -749  -2322   1834   1689  -2602  -1267   -227  -2387   1797  -2314  -1468    119  -1569    181   -553   -552   -726  -1931  -2488  -1725    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -6692  -7734   -894  -1115  -1442   -662  -7714  -7044 
-    38   -650  -1507   -774   -350  -2135  -1486   -366  -1675   1998  -1798  -1055   -484  -1733      2    169   -669   2338  -1348  -2029  -1585    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -6692  -7735   -894  -1115  -1442   -662  -7714  -7033 
-    39  -1569  -2366  -1930   -894  -3087  -2179   -229  -2509   2901  -2237  -1540   -875  -2165    189   2259  -1460  -1319  -2252  -2132  -1951    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32  -6692  -7735   -894  -1115   -378  -2119  -7714  -7022 
-    40  -2957  -3022  -3318  -2735  -3796  -2998  -1968  -3912   -846  -3631  -3157  -2611  -3280  -1724   4056  -3026  -2913  -3650  -3096  -3185    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27  -7119  -8161   -894  -1115   -701  -1378  -7714  -7011 
-    41  -1023  -2495    142   1645  -2834   1427   -524  -2604   -258  -2551  -1723   -191  -1856   2572   -771   -845  -1012  -2162  -2727  -1999    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27  -7119  -8161   -894  -1115   -701  -1378  -7714  -7000 
-    42  -1501  -1232  -3584  -3033   -175  -3101  -1605   1572  -2672   1963    433  -2613  -2979  -2179  -2489  -2228  -1427    -98  -1135   2582    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27  -7119  -8162   -894  -1115   -701  -1378  -7714  -6989 
-    43  -2096  -2299  -2511  -1940   -102  -2789   -660  -2221   -502  -2032  -1638  -1740  -2878  -1080   2241  -2107  -1995  -2130   -679   3875    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7714      0 
-//
-HMMER2.0  [2.3.2]
-NAME  LBP_BPI_CETP
-ACC   PF01273.17
-DESC  LBP / BPI / CETP family, N-terminal domain
-LENG  209
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  37
-DATE  Wed Apr 23 15:04:47 2008
-CKSUM 8171
-GA    15.3000 15.3000;
-TC    16.3000 16.3000;
-NC    12.5000 12.5000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.901358   0.674794
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -51      *  -4858
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-     H     -6  -9971 -11013   -894  -1115   -701  -1378  -1051  -8700 
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-     H     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8697 
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-     H     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8693 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8690 
-     5   1627  -3277    901   -113  -3449   1029   1136  -3102  -1649    385  -2412  -2010  -3378  -1590  -2117   -725   -544   1030  -3562  -2985     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -197  -9971  -3006   -894  -1115   -701  -1378  -8751  -8687 
-     6    437   1758   -500  -1434  -3532    570  -1722    105   1225  -1653  -2407   1528  -3144  -1295   -148    672   -447    122  -3531  -2904     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -6  -9780 -10822   -894  -1115  -2451   -291  -8751  -8683 
-     7    -70  -3480    895   1321   -301  -1216    834  -1269   -515   -812    493    -55  -3094   2515   -610  -1908   -301  -1046  -3667  -2989     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -6  -9780 -10822   -894  -1115  -1552   -601  -8751  -8679 
-     8  -1022  -3054   -401   1349  -3198  -1054  -1876    938  -1574   1216  -2194   -280  -3274   1108  -2030   -954     92    452  -3355     58     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -6  -9825 -10867   -894  -1115  -1239   -795  -8751  -8676 
-     9    -11  -2294  -4441  -3847  -2307   2581  -2815    397  -3513    381  -1546   -672  -3944  -3194  -3426    937   -365   -333  -2799  -2450     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -6  -9873 -10915   -894  -1115   -878  -1133  -8751  -8672 
-    10   -699  -2218  -4577  -3950    456   -944  -2766    975   -257   1333   2503  -3502  -3954    160   -629   -841   -130   1002  -2674  -2328    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -484  -9922  -1828   -894  -1115  -1415   -678  -8751  -8669 
-    11   1031  -3226    746  -1063  -3543    295  -1395  -3291   1684   -343  -2316    950  -2829   1407     57  -1643  -1700   -333  -3411  -2730    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7  -9444 -10486   -894  -1115  -3471   -136  -8751  -8665 
-    12   1388  -2588  -2079   -477     54  -2948  -1651    563    659  -2506    422    131    347    365  -1839   -440   -552   1448  -2921  -2407    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7  -9444 -10486   -894  -1115  -3471   -136  -8751  -8662 
-    13   -636  -2958  -5837  -5337  -3017  -5297  -4479   1398  -5077   2646  -1937  -4965  -5186  -4731  -4967  -4490    178    856  -4118  -3799    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -7  -9444 -10486   -894  -1115  -3471   -136  -8751  -8658 
-    14  -1773  -3240  -1612    844  -3559  -2744  -1404    404    523  -3255  -2330   1057   -113   3122  -1490    170   -427  -2861  -3424  -2743    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9444 -10486   -894  -1115  -2507   -279  -8751  -8655 
-    15    293  -3301  -1691     62  -3625  -2810  -1461  -3370   1612  -3314  -2391  -1447  -2902   1724   1126     60   1484  -2925   2731  -2805    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9507 -10549   -894  -1115  -3342   -150  -8751  -8651 
-    16    964  -3222  -1683   2030  -3518  -2795  -1456   -402    468  -1493    245  -1441    167   1147  -1550    771   -175  -2831  -3421  -2754    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -9507 -10549   -894  -1115    -92  -4019  -8751  -8647 
-    17  -1201  -2257  -4771  -1056    -32  -3979  -2851   1212  -3732   2481    619  -3623  -4029  -3356  -3535   -362   -575    122  -2717  -2375    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8644 
-    18     94  -3635   -438   1384  -3948   -344  -1817    -34   1106      1  -2726    605  -3251   2104  -1906  -2065   -601   -912  -3823   -797    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -129  -9971  -3605   -894  -1115   -701  -1378  -8751  -8640 
-    19   -212  -3552  -1925    780  -3873    737    156  -3623   1573  -3568  -2641   1350    320    648    629     58    260  -3174  -3735  -3052    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9848 -10890   -894  -1115   -235  -2733  -8751  -8637 
-    20     -8  -2519      9  -2824  -2514  -1224  -2472   1928  -1079   1128   1352   -812   -834   -294   -581   -915  -2287    236   1214     -4    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8633 
-    21  -2184    713  -2051  -1503  -3904  -1153    539  -1046    450  -1396  -2700   -180   1098   1874   1099    850   1318  -1388  -3801  -3132    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8629 
-    22  -4070  -3690  -6533  -5997  -3192  -6000  -5013   2560  -5717   2262  -2092  -5657   -556  -5200  -5523  -5188  -4011    828  -4456    133    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8626 
-    23   -851  -3676  -2162   -409  -3957  -3302  -1984  -3668  -1570   1273  -2793   -229   3113   -104   -420   -156  -2287  -3280  -3892  -3250    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8622 
-    24  -2190  -3664   2981    451  -3984    325    270  -3735   -281  -3680  -2753   1115   -543  -1361   -373   -898   -729  -3286  -3847   -139    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8618 
-    25    190  -2259  -4636  -4009   1538  -3948  -2812   1951     53    597  -1461  -3553  -3999    523   -672  -1460   -181    972  -2715    360    25
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-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8615 
-    26  -2201  -3435   -893    212  -3666  -3215    461  -1592   -326   1236   2001   -586  -3306  -1462    400   1228    573    304  -3676  -3053    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8611 
-    27   -125  -3655    413    980  -3976   2086  -1814  -3727    583  -3671    411   1522  -3248    141     18  -2062   -452  -3277  -3838  -3155    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8607 
-    28   -817    820    729   1195  -3971  -3154  -1812  -3721    889  -3666  -2740   -625   1192    731  -1900    591   1344   -378    783  -3152    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8604 
-    29  -1138  -2522  -3389   1695   1406   -264  -2468    818     73  -1494   1941  -2834  -3755  -2467  -1282    566    -19    419  -2941  -2542    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -6  -9971 -11013   -894  -1115   -701  -1378  -8751  -8600 
-    30    756  -3652    110    149  -3973   1593  -1812  -3724   1388   -587  -2742  -1789    167     68    436     47   -660  -3274  -3836  -3153    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -286  -9971  -2503   -894  -1115   -701  -1378  -8751  -8596 
-    31   -760  -3250   -204    725  -3496     51  -1641   1856    -45    115   1629   -571  -3065    268  -1749    347   -310   -774  -3479  -2845    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -6  -9691 -10733   -894  -1115  -2824   -220  -8751  -8592 
-    32    228  -3421   -237   -413  -3741  -1002  -1585  -3490   1993  -1388    713   -367    777    316    229  -1009    110    921  -3606  -2924    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -300  -9691  -2444   -894  -1115  -2824   -220  -8751  -8589 
-    33    450  -2670  -1926    -44   1179   -794   2130  -2432     45   1021  -1813     53    746  -1203  -1717   -314  -1714   -325  -2980   -159    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -304  -9399  -2426   -894  -1115  -2290   -330  -8751  -8585 
-    34  -1778  -1652  -3834  -3217    711   -287  -2148   1321  -2873   1731   -853    647    -47    143  -2775  -1000     95    279  -2105  -1756    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9217 -10259   -894  -1115  -2978   -196  -8751  -8581 
-    35  -2315  -2932  -5202  -5544  -5633   3537  -4874  -5459  -5493  -5713  -4744  -3953   -155  -4935  -5185   -203    100  -4140  -5848  -5805    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -1021  -9279   -991   -894  -1115  -2755   -231  -8751  -8577 
-    36  -2227  -1956  -4583  -3976  -1415    214  -2804    822  -3622   2495   1989  -3561  -3806  -3124  -3403  -3037  -2159    635  -2424  -2200    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -10  -8411  -9453   -894  -1115  -4463    -67  -8751  -8574 
-    37  -2062  -1803  -4404    324    894  -3749  -2655   1029  -3455   2144   -477  -3383  -3681  -3014  -3265  -2868  -2000   1658  -2351  -2080    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -10  -8411  -9453   -894  -1115  -4463    -67  -8751  -8570 
-    38  -2840  -4456   1157  -1067  -5134   3096  -2305  -5137  -2721  -5009  -4411   2077  -3347  -2008  -3669  -2551  -3006  -4478  -5162  -4134    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -252  -8411  -2695   -894  -1115  -4463    -67  -8751  -8566 
-    39    420   -906  -2981  -2369   -867    320  -1368   1038  -2043    454   -107    887  -2571  -1736  -1976   -232   -955   1386   2631  -1006    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -187  -8171  -3117   -894  -1115  -4565    -62  -8751  -8562 
-    40  -1811  -1518  -4207  -3659  -1504    366  -2655   1494  -3345   1920   -517  -3254  -3562  -2992  -3214  -2754  -1769   2017  -2401  -2077    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -429  -7997  -1996   -894  -1115  -4625    -60  -8751  -8558 
-    41  -1463  -1293  -3531  -3038  -1054   1459  -2138   2395  -2710   1468    -95  -2689  -3079  -2392  -2627  -2195  -1449    107  -1959  -1647    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7583  -8625   -894  -1115  -4736    -55  -8751  -8555 
-    42   -801  -1643  -1026   -576  -2071   2051   -730  -1704    936    328  -1078   -760  -2002   -388   -697   1001   -820  -1400  -2200  -1688    42
-     -   -149   -500    232     43   -381    400    105   -627    215   -465   -721    275    393     45     95    359    117   -370   -295   -250 
-     .  -1967   -436  -8625    -46  -4979  -4736    -55  -8751  -8551 
-    43  -1084   -909  -3253  -2655   -729    610  -1577    108  -2304   1372   2495  -2260  -2678  -1947  -2177  -1758  -1033   1918  -1431  -1116    44
-     -   -149   -500    232     42   -381    402    105   -627    210   -463   -721    275    393     45     95    360    117   -370   -295   -246 
-     .   -246  -2725  -8625  -2620   -256  -1522   -618  -8751  -8547 
-    44  -1423  -1791  -2119  -1555  -1817   -317  -1428    -80  -1406   1098   1365   1971  -2752    728  -1728    665    791  -1247  -2187  -1753    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -9  -8847  -9889   -894  -1115  -4199    -81  -8751  -8543 
-    45  -1423  -1829  -2065  -1501    596   -316  -1404  -1437    627   1063  -1005  -1637   1131  -1240    368   1220  -1363    264  -2218  -1777    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -9  -8847  -9889   -894  -1115  -4199    -81  -8751  -8539 
-    46     24  -1885  -1956  -1395  -1928    713  -1356    864     25     54  -1056    172  -2699    760  -1619    172    340   1352  -2264  -1809    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -9  -8847  -9889   -894  -1115  -4199    -81  -8751  -8535 
-    47  -1334  -2635   1335   -704   1232   -520  -1003    173    393  -2622   1217   1279    246    902  -1108   -162   -244   -768  -2861  -2221    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -9  -8847  -9889   -894  -1115   -487  -1803  -8751  -8531 
-    48  -1989  -3458   -303  -1289    168  -2963    734  -3527   1669  -1250  -2548     72    531   1845    408    427    281  -3079  -3642   1210    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -119  -9737  -3728   -894  -1115  -2647   -251  -8751  -8527 
-    49   -972  -1974  -4483  -3850    134   1689  -2574   -220  -3449    957  -1178  -3341   -388  -3075  -3255  -2782    681   2049  -2442  -2099    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9625 -10667   -894  -1115  -3042   -187  -8751  -8524 
-    50  -1907   1109  -1799    -41  -3549   -701   1077   -598   1280    496  -2373   -283   -762    927    358    400  -1846    578  -3482    190    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9625 -10667   -894  -1115  -3042   -187  -8751  -8520 
-    51  -1995  -2564  -2433   -454   -124  -3176  -1898  -2215   1195   -549    752   1348   -339     50  -2132  -2137  -1934    421  -2929   3186    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9625 -10667   -894  -1115   -558  -1641  -8751  -8516 
-    52  -2121  -3596    356    630  -3916    801   1222  -3668    270  -3611  -2685   2329  -3184   1132    428    931  -2060  -3218  -3778  -3094    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -6  -9874 -10916   -894  -1115   -272  -2541  -8751  -8512 
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-     E   -226  -7222  -2887   -894  -1115  -4805    -53  -8751  -8308 
-   101   1854  -1269  -2482  -2259   -925  -1872  -1423  -1467  -1872  -1639  -1154  -1819  -2358  -1803  -1909  -1229  -1173  -1255   5068   -688   114
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -431  -7017  -2014   -894  -1115  -4836    -51  -8751  -8304 
-   102  -2610  -1985  -3539  -3553   3171  -3341    -98  -1559  -3136  -1098  -1059  -2260  -3280  -2265  -2750  -2601  -2524  -1718   4657   1772   115
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -27  -6613  -7655   -894  -1115  -4884    -50  -8751  -8299 
-   103  -2610  -1985  -3539  -3553   3171  -3341    -98  -1559  -3136  -1098  -1059  -2260  -3280  -2265  -2750  -2601  -2524  -1718   4657   1772   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -27  -6613  -7655   -894  -1115  -4884    -50  -8751  -8295 
-   104  -1603  -1358  -2899  -2552    763  -2831   -564   -313  -2128   1893     92  -2030  -2792  -1751  -2033  -2009  -1538   -548    -20   3167   117
-     -   -149   -500    235     43   -381    400    105   -626    210   -466   -721    275    394     45     96    359    117   -369   -295   -250 
-     .  -1777   -515  -7655    -92  -4024   -331  -2287  -8751  -8290 
-   105    347  -2571   -423  -2027  -2624   1878  -2007    407   1845   -172  -1746  -2194  -3351  -1794  -2261    -71  -2009    208  -2952  -2492   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .  -1786  -9694   -503   -894  -1115  -2818   -221  -8751  -8285 
-   106    123  -2051   1314   -616  -2521    674  -1009  -2182   -790    341  -1518   -860   2501   -654  -1272  -1078  -1115  -1834  -2654  -2072   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -14  -7922  -8964   -894  -1115    -36  -5326  -8751  -8281 
-   107  -1185  -3652   -343   1200  -3973    823  -1812  -3724   -521     57  -2741    686    675    832   -777    850    -31  -3274  -3835    769   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11014   -894  -1115   -701  -1378  -8751  -8276 
-   108  -2427  -2257  -4752  -4118   2677  -3973  -2846   1847  -3719    340  -1459   -533   1429  -3346  -3527   -863    905   -591  -2717  -2375   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11014   -894  -1115   -701  -1378  -8751  -8271 
-   109  -2418  -2246  -4749  -4114    347  -3964  -2834   1951  -3712   1674   1298   -531  -4014   -819  -1144  -1059    249   1137  -2704  -2361   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11014   -894  -1115   -701  -1378  -8751  -8267 
-   110    410  -3652   1632   1678   -582  -3153  -1812  -3724   1816  -3668  -2742   -197   -543    376   -239  -2060   -513  -3274   1197  -3153   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11014   -894  -1115   -701  -1378  -8751  -8262 
-   111  -1237  -2256  -4770   -898    617  -3978  -2850   1980  -3731   2031    126  -3622  -4027  -3355  -3534   -389      7    372  -2716  -2374   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -2730  -9972   -243   -894  -1115   -701  -1378  -8751  -8257 
-   112  -1028  -1899  -1095   -865  -2947  -1765   -988  -2669   1715  -2677  -1895   -959  -2158   -629   -478   2765  -1153  -2156  -2761  -2309   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -19  -7261  -8303   -894  -1115  -4798    -53  -8751  -8253 
-   113  -3037  -3621   4053  -1443  -4372  -2676  -2438  -4787  -2889  -4616  -4227  -1794  -3225  -2294  -3488  -2849  -3196  -4320  -3891  -3795   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -19  -7261  -8303   -894  -1115  -1924   -441  -8751  -8248 
-   114  -1152  -2598  -1008   -454  -2924    372   2801  -2663    503  -2608  -1691   -758  -2211   1597    348   1373    639  -2224  -2772  -2108   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -11  -8488  -9530   -894  -1115  -3200   -166  -8751  -8243 
-   115  -2989  -3540  -3324  -3703  -5552   3705  -4215  -5796  -4640  -5817  -5096    266  -4212  -4183  -4793  -3161  -3406  -4715  -5298  -5319   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115  -4333    -73  -8751  -8238 
-   116   -144  -2648    551   -519  -2953   -430   1636   1045    362  -2658  -1743   1462  -2283   -399   -949   1636  -1154  -2262  -2842  -2168   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115  -4333    -73  -8751  -8234 
-   117   1758  -2338  -4818  -4610   3692  -3390  -3090  -1437  -4288  -2083  -1840  -3624  -3861  -3822  -4069  -2686  -2430    656  -2765  -1982   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115  -4333    -73  -8751  -8229 
-   118  -2719  -4536   3128   1276  -4741  -2817  -2059  -4620  -2160  -4505  -3758    516  -3288   1140  -2923   1079  -2754  -4112  -4692  -3751   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115  -4333    -73  -8751  -8224 
-   119    174  -2661  -5481  -5047  -2172  -4698  -4195   -593  -4778   2694  -1022  -4617  -4660  -4245  -4586  -3966  -2966   1725  -3579  -3428   133
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115  -4333    -73  -8751  -8219 
-   120  -1195  -2650     53   1201    903  -2171   -831  -2708    654   -384  -1741    868  -2264   1041   -921   1429  -1134  -2268  -2838    322   134
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -10  -8653  -9695   -894  -1115    -45  -5010  -8751  -8214 
-   121   1220  -2736   -632    175  -2771  -3532   1761    831   -569    248  -1910  -2490  -3608  -2094  -2549     65   -784   1582  -3121     36   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11015   -894  -1115   -701  -1378  -8751  -8209 
-   122    673  -3632   -497    628  -3944   -915    643     52    673   -313     90   -265  -3251    549   -278   -445  -2120   1612  -3821  -3144   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9972 -11015   -894  -1115   -701  -1378  -8751  -8205 
-   123   -817    707   -320    915  -3973   2049    643   -833    426  -3668  -2741   -197    -83    142   -336    563   -726  -3274  -3836  -3153   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8200 
-   124   -779  -2276  -4791  -4157  -2236  -4005  -2879   1129   -816   1425   2521  -3648  -4053  -3382  -3561   -868    113   2002  -2746  -2403   138
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8195 
-   125   -767  -3945   1822   1145  -4260  -1003  -2058  -4019  -1685  -3961  -3047   2114  -3468  -1608  -2210   1356    779  -3566  -4131    324   139
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8190 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8185 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8180 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8175 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8170 
-   130   -874  -2288  -4812  -4179   -202  -4022  -2899   1755  -3778   1769  -1494   -536  -4070  -3403  -3581   -995   -815   2015  -2764  -2421   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8165 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8160 
-   132    -75  -2809  -5406  -4790    502  -4664  -3561   1865  -4411   2163   1395  -4312  -4653  -3999  -4209  -3768   -539    734  -3334  -3030   146
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8155 
-   133  -1017  -3643    255   2045  -3960   1291  -1815  -3708    632  -1475   -481  -1792  -3249    669  -1903   -730    692    233  -3829  -3149   147
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8150 
-   134  -2231  -3600  -2122  -1569  -3886  -3217  -1869  -3606    559  -1320   1932   -228  -3307    666   2035   1289   1485  -3203  -3799    615   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8145 
-   135  -2248  -3708   3091   -238  -4021   -913  -1879   -826  -1473  -3721  -2803   1831  -3307  -1424   -569    191   -440  -1505  -3897  -3215   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8140 
-   136    792    862   -119   1574  -3981    379  -1819  -3731   -728  -3676  -2749    214   2013  -1359   -483    780  -2126  -3282  -3843  -3160   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -211  -9973  -2929   -894  -1115   -701  -1378  -8751  -8134 
-   137    166  -3484    556    418    833  -2988  -1647   -161    394  -3499  -2573     47  -3081   1742   -316    665   1351  -3105  -3668   -477   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -1563  -9770   -606   -894  -1115  -2507   -279  -8751  -8129 
-   138  -1338  -1952  -3888  -4125  -4422  -2213  -3652  -4221  -4056  -4497  -3590  -2860  -3005  -3665  -3889   2188   3309  -3062  -4642  -4501   152
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -12  -8219  -9261   -894  -1115   -109  -3780  -8751  -8124 
-   139  -4032  -5794   -463  -1138  -6050   3444    593  -5889  -1379  -5735  -5021   -170  -4551  -2915    282  -3725  -4054  -5403  -5872  -5011   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9922 -10964   -894  -1115  -1434   -667  -8751  -8119 
-   140   -696  -3606   -387  -1438  -3925    -92   2091  -3674    700   -351  -2696  -1748   -842    109   2466   -693    477  -3227  -3790    522   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9922 -10964   -894  -1115   -380  -2111  -8751  -8114 
-   141   -486  -2255  -4676  -4046  -2210  -3954  -2820    140  -3659     74    619  -3572   2961  -3298    196    -15    701     12  -2711    115   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8109 
-   142  -1130  -3601  -2057     93  -3898  -1375   1057  -1044    762  -3607  -2696  -1814  -3262    840   1801  -2078   1947    956  -3798     15   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8103 
-   143  -1008  -2900  -5537  -4935   -227  -4820  -3746    188  -4569   1942    513  -4469  -4800  -4170  -4380  -3933     12   2548  -3514  -3203   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8098 
-   144    370  -3625   -323   -647  -3934  -3161  -1820   -357    619  -3636  -2718    570  -3253  -1365    461   1058   1189   1683  -3816  -3141   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8093 
-   145    811   2104  -4762  -4126    708  -3966  -2837    815  -3722   1490   1422   -531  -4016  -3345  -3522    730  -1006    373  -2703  -2361   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8087 
-   146  -2183  -3635  -2038    658  -3948   1608  -1819  -3692   -381  -1372  -2727  -1799    167    935   -373   1780   -458    337  -3823  -3146   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8082 
-   147   -382  -3655   1435   1485  -3976    575    576  -3727     18  -3671  -2744    596  -3248  -1354   1117   1077  -2121   -877  -3838  -3156   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -7  -9973 -11015   -894  -1115   -701  -1378  -8751  -8077 
-   148  -5110   5815  -6955  -7315  -7197  -5516  -6618  -7800  -7351  -7727  -7139   -473  -6187  -7050  -6961  -5381  -5554  -6761  -6686  -7130   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -8072 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8066 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8061 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8055 
-   152  -2419  -2247  -4750  -4115    596  -1341   1323   1770  -3713    324  -1450  -3606   2052  -3339  -3518  -1245    431   1414  -2705  -2363   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8050 
-   153  -1263    -73    812    250  -3973   2175    678  -3724   -287  -3668  -2741    452  -3246   -317   -336   1103   -536   -986  -3836  -3153   167
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8044 
-   154   -789  -3653    373   -296  -3974  -1151   1939  -3725    593  -3669  -2742   1245   -931  -1352    129   2088   -962  -3275  -3836    927   168
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8039 
-   155   1373  -2514  -5091  -4476  -2524  -1109  -3240   2133  -4090   1332    585  -3978  -4364  -3725  -3905  -3428   -658   1374  -3091  -2745   169
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8033 
-   156  -2180  -3653   1356    359  -3974   -323   1905  -3725    277  -1343  -2742    443  -3247    478   1268   1538   -548  -3275  -3836  -3153   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8028 
-   157    381  -2682  -5300  -1345  -2726  -4573  -3510   2616  -4330   1476    290  -4218  -4591  -3974  -4157  -3680   -659   1309  -3347  -2999   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8  -9973 -11015   -894  -1115   -701  -1378  -8751  -8022 
-   158   -815  -3650   -258   -375   -146  -3154   2286  -3720   1236  -1737  -2739    585  -3247    676   -775   1611    405   -876  -3834     10   172
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -49  -9973  -5141   -894  -1115   -701  -1378  -8751  -8017 
-   159  -2669  -2477   -171  -4388   1994  -4243  -3118   1783  -3992   1896   1184  -3889  -4266  -3596  -3790   -396  -2609    299  -2942  -2619   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -8  -9932 -10974   -894  -1115  -1316   -741  -8751  -8011 
-   160  -2151  -3588  -2011    602   -952    614   1347  -3633  -1377   1590  -2681   -180    323    644   -251    997  -2090  -3201  -3780  -3107   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G     -8  -9932 -10974   -894  -1115  -1316   -741  -8751  -8006 
-   161  -1165  -3628    358  -1450  -3949   2250   1793  -3700    199  -3644  -2718   1792   -502  -1327   -450    266   -505  -3250  -3812  -3129   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9932 -10974   -894  -1115  -1316   -741  -8751  -8000 
-   162  -2148  -3621   -224    643  -3942   1782  -1780  -1163    665  -3637  -2710    757   -579  -1320   1554    520    279  -3243  -3804  -3121   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H  -1847  -9932   -480   -894  -1115  -1316   -741  -8751  -7994 
-   163   -970  -2234   -909    920  -2500  -1960   -593  -2188   1037    545  -1344   -629  -2046   -162   1987    642   -902   -280  -2438  -1827   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -14  -8099  -9141   -894  -1115  -2388   -306  -8751  -7989 
-   164  -1246  -2363    624   -695  -2581    640   1582  -2251   -633   1391  -1516   -974    404   -571  -1112    235    921  -1936  -2654  -2056   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -11  -8613  -9655   -894  -1115  -4358    -72  -8751  -7983 
-   165  -1653  -2379  -3001  -2902  -4474    364  -3063  -4255  -3039  -4401  -3485    839   2280  -2806  -3321   2518    716  -3274  -4585  -4214   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -685  -8614  -1430   -894  -1115  -2692   -243  -8751  -7978 
-   166  -1112  -1492  -1787  -1219   1593    325  -1079  -1097   -981   1378   -668  -1338    621   1127    892  -1340  -1050   -955  -1871  -1433   180
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -13  -8307  -9349   -894  -1115  -1879   -458  -8751  -7972 
-   167  -1536  -1508  -3154     73   1270  -2987  -1814    989    644   1556    992  -2371   1134  -2046  -2343   -577  -1476   -930  -1950  -1586   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10  -8924  -9966   -894  -1115   -750  -1303  -8751  -7966 
-   168    599  -1956  -4475  -3839    133  -3678  -2549    993  -3434   1361    919  -3323    655  -3057  -3234   -836  -2070   1873    902  -2072   182
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9633 -10675   -894  -1115  -1975   -424  -8751  -7961 
-   169   -701  -3683  -1814   -520  -4007   1915  -1804  -3763    923  -3703  -2788   2451  -3221   1085  -1920    763  -2144  -3310  -3869  -3175   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9694 -10736   -894  -1115   -370  -2143  -8751  -7954 
-   170    176    470    395   -660  -3885   -837    584  -3625    376   -198    378   -562  -3217    149   -630    920  -2083   -249   3925  -3099   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9927 -10969   -894  -1115  -1379   -700  -8751  -7948 
-   171   -849  -2219  -4740  -4104    989  -3944  -2816   1644  -3700   2127  -1417  -3590  -3993  -3323  -3500   -406    -33    722    649  -2338   185
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9927 -10969   -894  -1115  -1379   -700  -8751  -7943 
-   172   -307  -2212  -4667  -4035  -2166  -3918  -2787    645   -697   1712  -1414  -3546    726  -3275  -3462   -427   -436    925  -2669   2277   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9927 -10969   -894  -1115  -1379   -700  -8751  -7937 
-   173  -2170  -3644   2197  -1458  -3965   -941   1293  -3716    984  -3660  -2734   2339  -3232   1670   -707   -616   -629  -3266  -3826  -3143   187
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9927 -10969   -894  -1115  -1379   -700  -8751  -7931 
-   174   -153  -3350  -2145   -581   1101     97  -1865  -3241   -459   1473    411    242   -767   -123  -1985   1333   -477  -2913  -3602  -2991   188
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     49     96    359    117   -369   -294   -249 
-     H    -61  -4771 -10969   -162  -3233  -1379   -700  -8751  -7925 
-   175   -997  -2805  -5448  -4852   2917  -1080  -3672    425  -4489   1370  -1868  -4380  -4724  -4111  -4309  -3843  -2997   1998  -3466  -3136   190
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -8  -9927 -10969   -894  -1115   -397  -2056  -8751  -7919 
-   176     58  -3318   -617   -429   -600  -3255   1937    544  -1587   -280    142   -252  -3343    567    707    848   1159    -77  -3586  -2995   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7913 
-   177   -870  -3652    531    425  -3973    742  -1812  -3724    718  -3668  -2742   2482  -3247  -1352   -738    943     20  -1252  -3836   -139   192
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7907 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7901 
-   179  -5195  -4621  -7651  -7110   1263  -7421  -6266   2528  -6931   1992   1018  -7125  -6597  -5849  -6509  -6773  -5072   1121  -4892  -5055   194
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7895 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7889 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7883 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7877 
-   183  -4751  -4295  -7164  -6584   -885  -6711  -5551   2096  -6317   2423   1501  -6390   -960  -5457  -5969  -5940  -4646    945  -4577  -4609   198
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7870 
-   184   -936    574  -2346  -1793  -3328  -3306    521    130   1155   -992  -2321  -2053   1708    562   1460    564    197      6  -3482  -2926   199
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7864 
-   185   -381  -3648   -495    556    476    -36  -1813  -1309   1559   -584  -2737   1819  -3247    141  -1901   1051   -845  -3269  -3832  -3151   200
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7858 
-   186    370  -2370      7  -3357  -2342  -3826  -2650   -780  -1312   1454   1433    674   -719  -2861  -3168  -1426    -43   1893  -2811  -2444   201
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7852 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7845 
-   188  -2183  -3656  -2029    940  -3977   -205  -1814  -3728   1335  -3672  -2745   1503   1109   2423    400   -928   -963  -3278  -3838   -628   203
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7839 
-   189   -790  -3655    779   -113  -3976   1525    549  -3726   1284  -3671  -2744   1502   -543     62    106    838  -2120  -3277  -3838  -3155   204
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -8  -9974 -11016   -894  -1115   -701  -1378  -8751  -7833 
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-     -   -149   -500    232     45   -381    398    105   -627    212   -467   -721    275    393     50     95    359    117   -365   -295   -250 
-     H    -92  -4133 -11016  -1636   -560   -701  -1378  -8751  -7827 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9974 -11016   -894  -1115   -701  -1378  -8751  -7820 
-   192  -3086   5679  -6357  -6709  -6386    -72  -5717  -6247  -6392  -6497  -5532  -4804  -4779  -5831  -5995   -914  -3568  -4916  -6558  -6578   211
-     -   -149   -500    233     43   -381    400    105   -627    210   -464   -721    275    393     48     96    359    117   -370   -295   -250 
-     H    -59  -4818 -11016  -1507   -626   -701  -1378  -8751  -7814 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9974 -11016   -894  -1115   -701  -1378  -8751  -7807 
-   194   -846  -2513  -3415   -681  -2508  -3695    184    693   -154   1118   1521  -2852  -3762   -724   -583   -278    791   1762  -2934  -2537   216
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9974 -11016   -894  -1115   -701  -1378  -8751  -7801 
-   195    235    789  -6789  -6426  -4257  -6529  -6254   2837  -6330    991  -3011  -6185  -6318  -6212  -6419  -5845  -4124   2051  -5769  -5299   217
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -953  -9974  -1065   -894  -1115   -701  -1378  -8751  -7794 
-   196    378  -2908  -1305   1299  -3222  -2428  -1087    560    397  -2921  -1999    639  -2521    900    -11   -200   1375  -2526  -3095   1389   218
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -11  -9031 -10074   -894  -1115  -4041    -90  -8751  -7788 
-   197  -1469  -2943    782     38  -3264   -540   1275  -3015    538  -2959  -2033   1967  -2532    733  -1192   1692  -1409   -118  -3127  -2443   219
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    119   -369   -294   -249 
-     H   -433  -4006  -2378   -175  -3131  -4041    -90  -8751  -7781 
-   198    634  -1715  -2009    -84  -1744  -2582  -1332   1232  -1300    879   -894  -1574  -2658    430  -1627   1365    899  -1172  -2110  -1674   221
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -12  -8723  -9765   -894  -1115  -4289    -76  -8751  -7775 
-   199     32  -2340  -5245  -4877  -2943      1  -4266   2139  -4673  -2063  -1824  -4379  -4579  -4450  -4641  -3718  -2668   3025  -4056  -3639   222
-     -   -149   -500    235     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H   -136  -3567  -9765   -162  -3233   -397  -2056  -8751  -7768 
-   200  -2019  -3493    856    688  -3814   -840  -1651  -3565    735  -3509  -2582   1633  -3085   1744   1052    608    899  -3115  -3676  -2993   224
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9770 -10812   -894  -1115  -2511   -278  -8751  -7762 
-   201    996  -3326    872    640   -230    -59  -1697   -685    527  -1295  -2433  -1696  -3122   -124  -1803   1341  -1967    -21  -3551    541   225
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9770 -10812   -894  -1115  -2511   -278  -8751  -7755 
-   202  -2239  -2082   -500  -3848    617  -1164     53   1189    495   1427   1630  -3385  -3826  -3110  -3305  -1023  -2179   1673  -2538  -2193   226
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H  -1789  -9770   -504   -894  -1115  -2511   -278  -8751  -7748 
-   203  -1599  -2312  -1827  -2102  -4072  -2260  -2647  -4002  -2699  -4191  -3429   3987  -2951  -2464  -2957  -1740   1185  -3135  -4202  -3735   227
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7996  -9038   -894  -1115  -4626    -60  -8751  -7741 
-   204    298  -1208  -1679    730  -1254  -2158   -955   1033   -975  -1105   -413  -1218    737   -845  -1276    679   -841   1719  -1644  -1219   228
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7996  -9038   -894  -1115  -4626    -60  -8751  -7735 
-   205  -1065  -2314   -883   -391  -2586    463   3226  -2282   1224    152  -1441   1570  -2106   -221   -533   -978   -997  -1924  -2502  -1901   229
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -15  -7996  -9038   -894  -1115    -37  -5303  -8751  -7728 
-   206  -5257  -4659  -7733  -7211    413  -7569  -6434   1158  -7061   2834  -1886  -7276  -6679  -5943  -6633  -6963  -5136   1054  -4967  -5137   230
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -9  -9974 -11017   -894  -1115   -701  -1378  -8751  -7721 
-   207  -2190  -3662  -2034   1278  -3984    559    549  -3734   -331  -3678  -2751    917  -3255   1669     55   2028  -2129   -986  -3844  -3162   231
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -9  -9974 -11017   -894  -1115   -701  -1378  -8751  -7714 
-   208    284  -3645    737  -1481  -3963   -293  -1814  -3711   -288   -978  -2735   1449   1251     65   -913    416   1471  -1126  -3830   -102   232
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -9  -9974 -11017   -894  -1115   -701  -1378  -8751  -7707 
-   209  -3729  -3442  -6104  -5492  -2768  -5425  -4294    460  -5136   2411   2548  -5080  -5280  -4590  -4890  -4553   -795    544  -3849   2004   233
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     S      *      *      *      *      *      *      *  -8751      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF258
-ACC   PF03193.8
-DESC  Protein of unknown function, DUF258
-LENG  305
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  75
-DATE  Mon May 19 14:40:20 2008
-CKSUM 4641
-GA    40.0000 40.0000;
-TC    41.2000 41.2000;
-NC    39.3000 39.3000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.842202   0.641016
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -25      *  -5882
-     1   -469  -4557  -1441   1021    537  -4076    475    429    337   -737  -3648   -579    797   1158    416  -1043    857    -64  -4745  -1022     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -1025  -9248 
-     2    931   -420  -7194  -1824  -1080   3509  -6628  -7069  -7296  -7338  -6387  -5723  -5732  -6726  -6932  -4286  -1755  -5811  -7501  -7450     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9246 
-     3  -3529  -3404  -5602  -4909  -3366  -5019  -3808   1050    473    621    743  -4529  -5062    816   2652  -4107    991    221  -3846  -3506     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9243 
-     4  -5284  -4764  -7967  -2355  -5546  -7855  -8055   2873  -7685  -4280  -4210  -7518  -7591  -7699  -7902  -7262  -5280   3086  -7396  -6821     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9241 
-     5   -125   -100  -5718  -5082  -1154  -2307  -3791   2507  -4677    446  -2402  -4566  -4970  -4299   -405  -1692    403   1878    478   -795     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9238 
-     6   1606  -4556  -1332   -633  -1390  -1059  -2736  -2054   1760  -2516    301  -2715  -4170    620    848    757    610  -1783  -4744  -4065     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9236 
-     7    885  -4520  -2974    -51  -1406   -407    765  -1665   -163   -909  -3615   -492  -4180    456   1239    466  -1364   1803  -4717  -4049     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9234 
-     8  -3178  -3994     66   -801   1316  -4286   3186    829  -1419    636  -3143   -282  -1842   1366  -3162  -3226   -271  -1703  -4318   1351     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9231 
-     9   1849  -5235  -5214  -4698  -6839   2014  -4442  -6446    143  -6319  -5509   -339  -5621  -4054   1858   1028  -4586  -5782  -6310  -6022     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9229 
-    10   -864  -4572    422   -169  -4893   1995   -507  -1053   -307  -2200  -3661   1919  -4165    699    441   -107   -284  -1998  -4755  -4072    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -3 -11025 -12067   -894  -1115   -701  -1378  -9273  -9226 
-    11  -3304    876   -832  -3910   2600   -551   2212  -1518  -3707  -3284    467  -1370  -4740   1121    855   -609  -1694   -567   1103   1983    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21 -11025  -6308   -894  -1115   -701  -1378  -9273  -9224 
-    12    176   1398  -5704  -5068    873  -4906  -3776  -1271  -4663   -250    181  -4552  -4956  -4286  -4463   -429  -3299   -760   1002   4039    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11007 -12049   -894  -1115  -1276   -768  -9273  -9222 
-    13  -3102  -4384   1332    571  -1223   -357  -2775    779    467   -392  -3493  -2776  -4199    696    646  -1694   -287  -1347   1071   2307    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3 -11007 -12049   -894  -1115  -1276   -768  -9273  -9219 
-    14  -5237   1386  -7935  -7623  -5449  -2224  -7838   1192  -7597   -289  -4133  -7435  -7513  -7568  -7776  -7146  -5231   3474  -7214  -6678    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -25 -11007  -6060   -894  -1115  -1276   -768  -9273  -9217 
-    15   -161   -467   -999   2147     13  -4171    502    504    314   -610  -3270  -2897  -4258    976    445  -3098  -3053   -149  -4422   1417    15
-     -   -150   -501    242     43   -382    397    104   -628    209   -458   -722    274    392     44     95    358    116   -371   -296   -251 
-     E   -263  -2602 -12028    -20  -6164  -1748   -510  -9273  -9214 
-    16    680   1361  -1089  -1810  -1090  -1004   -837   -613  -3967    639  -2490   -966   -976  -3736   -836    604   1717    923    259   -832    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -3 -10986 -12028   -894  -1115  -1748   -510  -9273  -9212 
-    17   -590  -4536   1908   2486  -4857  -1110  -2695  -1787   -693  -4552  -3625    751     51    469  -1395   -791   -787  -1696  -4719  -4036    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -52 -10986  -4920   -894  -1115  -1748   -510  -9273  -9209 
-    18  -1134  -4492   2165    801  -4813   1406   -160  -4564   -325  -2292   -744   1353  -1646    431  -1235   -954    470  -4114  -4676  -3993    19
-     -   -149   -500    232     44   -381    399    105   -627    210   -467   -721    275    393     47     99    360    117   -368   -295   -250 
-     T   -152  -6127  -3569  -2614   -257  -2437   -295  -9273  -9207 
-    19  -1109  -4272  -2815    903  -1478   2692  -2575  -1669    657  -4267  -3374  -2567  -4003   1379   -882  -1582  -2858    -60  -4484   -675    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -10811 -11853   -894  -1115  -3393   -144  -9273  -9205 
-    20  -1077  -4309  -1462   1367   -239   -823   -490    745  -1004    198    420    130   -288   -165   -728   -216   1028    437  -4511  -3848    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S   -824 -10811  -1208   -894  -1115  -3393   -144  -9273  -9202 
-    21  -2199  -3648   -534    460    357    163  -1836   1621   -226    527  -2740   -464   -915   1055   -381   -315    893  -3265  -3837  -3161    29
-     -   -157   -501    242     47   -384    396    104   -628    215   -462   -723    273    393     40     91    363    113   -359   -295   -260 
-     C   -640  -1619  -5005  -3001   -193   -368  -2151  -9273  -9200 
-    22  -3190  -3025  -5485  -2468   1513  -4732   -124   1256   -681   1259  -2227  -4361  -4783  -1765   -688  -3815  -1647    661  -3481   3019    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10831 -11873   -894  -1115  -1764   -503  -9273  -9197 
-    23   -151  -4437   -731    802  -4757  -3939  -2598  -4507    216    961   -592   -408  -1432   1924   1826   -436  -1363  -1114  -4620   -999    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10878 -11920   -894  -1115  -1477   -642  -9273  -9195 
-    24   1396   4872  -5221  -4675  -3665   -372  -3944  -3217  -4406  -1879  -2887  -4372  -1762  -1237  -1753  -1818    747   -855  -4128  -3771    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10922 -11965   -894  -1115  -2595   -261  -9273  -9192 
-    25   -948  -4452  -1435    352    881  -3987    595   -200   1226  -2297   -600    685  -4080   -209   1671  -1667    959    769  -4643  -3967    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10922 -11965   -894  -1115  -1059   -944  -9273  -9190 
-    26   1372  -3289  -1894  -4150   -941   -185  -3514    512   -299    402  -2484  -4021    929  -3685   1214  -1372   -249   1143  -3727  -3355    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10967 -12010   -894  -1115  -2050   -399  -9273  -9187 
-    27  -1121  -4276  -3215  -2652  -4475  -4215  -2870  -1609    956  -1781  -3403  -2923  -1386    671   3464  -1124   -257   -921  -4531  -3953    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10968 -12010   -894  -1115   -236  -2727  -9273  -9185 
-    28    135  -4568  -1371  -1304  -4887   2855  -2733  -1170    620  -4583  -3658  -2710   -329   -700    413  -1697    208  -1956  -4752  -4071    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9182 
-    29  -1960  -4563  -1399  -1487  -4879   -469  -2734   -468   2118   -422  -3653   1925  -4168  -1061   1640  -1549    436   -316  -4748  -4068    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9180 
-    30   -691  -3200  -5715  -5079   2811  -4920  -3791    235  -1039   1772    550  -4565  -4970  -1328   -361  -4004   -784     79   1632  -3315    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T  -1244 -11025   -797   -894  -1115   -701  -1378  -9273  -9177 
-    31    -24  -2435  -3050  -2482   -132  -3477   1230   -264    405   -798   1884  -2552  -3547   1495   2019    542  -2116   -354  -2844    175    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -109  -9786  -3838   -894  -1115  -5273    -38  -9273  -9175 
-    32  -1962  -3271  -1878    539  -3528    105   3000  -3234   -116    635  -2377  -1626  -3054  -1192   1152    327    -84   -726  -3493   1073    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -123  -9682  -3668   -894  -1115  -5342    -36  -9273  -9172 
-    33   1956  -3317  -1704   1316  -3634   -572  -1488  -3381    575   -951  -2407    -94   -639    221   -282  -1736    597   -391  -3502  -2822    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -146  -9565  -3421   -894  -1115  -5410    -34  -9273  -9170 
-    34   1646  -1966  -3391  -2807  -1959   1118  -2189   -193  -2566    609  -1177  -2679    662  -2348   1402   -299  -1882   -258  -2419  -2047    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -6  -9424 -10466   -894  -1115   -421  -1982  -9273  -9167 
-    35   -718    216  -1316   -152   -614  -3843   1034   -224   1288  -2154   -261    432  -1355     67   2480   -872   -483  -1788   1358  -3825    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10763 -11805   -894  -1115  -2618   -256  -9273  -9165 
-    36   -822  -4358  -1158   -999  -1057  -1020   1714  -4430   2371    178  -3448    467   -829    564   -446    365  -1355  -1574  -4542    -66    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10789 -11832   -894  -1115  -3499   -134  -9273  -9162 
-    37  -1720  -4359   -527    126  -4680    183   -141    303   1145  -2108   -538    409    665    646   1601    443   -577   -958  -4542  -3860    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10790 -11832   -894  -1115  -3499   -134  -9273  -9160 
-    38   -979  -4359    464    204  -4680   1596    981  -4431   1214  -2440   -393    865  -3953   -175   1324   -800    262  -3981  -4543   -625    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10790 -11832   -894  -1115    -82  -4176  -9273  -9157 
-    39   -701  -4568     80    624    241  -1983   1122    901    244   -207  -1084    755   -395    984    557   -250    -64  -1220  -4752  -4070    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9155 
-    40   -390  -4564    133  -1374    368  -1193  -2733   -636   1260  -1499  -3654    347    569    209    -32   1003    922   -955  -4749    445    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9152 
-    41   -832   -221  -5779  -5145   -224  -4986  -3860    921  -4743    703    192  -4632   2784  -4364  -4543  -4072  -3372   1795  -3721   -127    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9150 
-    42   1439   1377  -5715  -2200   -989  -4919    142  -1481  -4675    807   1771  -1456  -4969  -4298  -4475  -2006    287   2013  -3657    558    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9147 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9145 
-    44  -6817  -6872  -7623  -8011  -8811   3838  -7819  -9387  -8574  -9143  -8671  -1364  -7539  -8199  -8274  -7074  -7229  -8428  -7920  -8782    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9142 
-    45  -9219  -7872   4234  -8289  -9297  -7715  -8179 -10383  -9031  -9697  -9673  -8495  -8164  -8744  -8687  -9541  -9351 -10061  -7997  -9224    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9140 
-    46  -3107  -4531   -280    151    349  -4088   -825    312    948  -1438  -3626   -146  -4180   -416   2292  -2996  -3045  -4143   4018    203    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9137 
-    47  -2213  -4773  -7999  -7701  -5491  -7845  -8034   -853  -7694  -2104  -4160  -7526  -7582  -7676  -7893  -7245  -5286   3822  -7338  -6797    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9134 
-    48  -1106   -216    417   1797  -3430  -2237  -3445    703  -3651    989  -2628  -3839  -4723   -414     18  -2252   -876   1286   1802  -1043    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9132 
-    49  -1588   -101  -5723  -5087   2448  -1040  -3797   1808  -4682    594   -620  -4571  -4975  -4305  -4482  -4010  -3318   1799   2405   -197    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9129 
-    50  -1792  -4570    314   2089  -4891  -1395  -2731  -1935   -735  -1093  -3660   -435  -4166   1418   1311    443   -362     34  -4754     64    74
-     -   -150   -501    232     42   -382    399    109   -627    209   -461   -721    274    396     44     97    359    116   -370   -295   -250 
-     E   -245  -6214  -2826  -3106   -178   -701  -1378  -9273  -9127 
-    51   1141  -4339  -1136    246   -918   -136   -333     92    546   -999  -3432  -2526   1895   -561  -1266    334   -855     92  -4532  -3859    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10806 -11848   -894  -1115  -3418   -142  -9273  -9124 
-    52   -194  -4373   1355    782  -1088     -5   -233   1211    196  -4389  -3462   -329   -685   1081    -37   -407  -1367    201  -4556   -639    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10806 -11848   -894  -1115  -3418   -142  -9273  -9122 
-    53   -202  -4375   2081   1046  -4695  -1856  -2538  -1952  -2120   -286  -3465   2141  -1339      3  -2627    288    547  -3997  -4560  -3877    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10806 -11848   -894  -1115  -3418   -142  -9273  -9119 
-    54   -450  -4372   -197    677  -1219    279    630  -2019   -636   -941  -3461    647    228   1193    106    686   -694  -1831   2900   -796    88
-     -   -146   -503    232     43   -384    401    102   -630    207   -463   -711    272    394     56     93    359    116   -365   -298   -253 
-     C  -5970  -2463   -320  -1409   -682  -1849   -469  -9273  -9116 
-    55     -4  -2694     47   -536  -3010   1318   -867  -2757   1356   -499  -1785    499    280   -409   1109  -1116    503  -2313  -2880  -2201    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -312  -8708  -2396   -894  -1115  -2343   -317  -9273  -9114 
-    56   1056  -3117    817      8  -3424  -2657  -1317   -367    180  -3127  -2210  -1298   1052   1225  -1408    427    -90   1113  -3309  -2635    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -6  -9334 -10376   -894  -1115  -2815   -221  -9273  -9111 
-    57   -635  -3423   1505   1156  -3744   1882  -1583  -3494   -414  -1217    691     28   -646    110   -590    210  -1889  -3045  -3606  -2924    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5  -9688 -10730   -894  -1115   -390  -2077  -9273  -9109 
-    58   -348  -4376   1113    856  -4697    965  -2535   -394    809  -4392  -3465   1087  -3970    362    313    349    367   -967  -4559  -3877    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10809 -11851   -894  -1115   -597  -1560  -9273  -9106 
-    59  -1897   -418    947   1474  -4831  -1377   -533   -922    784   -420  -3599   -609   -145   1346   1218     54    152  -4132  -4693  -4010    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -10957 -11999   -894  -1115  -1164   -852  -9273  -9103 
-    60   1211      5  -4171  -1608  -1137   2922  -3326  -3045  -1834  -3350  -2663  -3654  -4627   -568   -218  -3559  -3185   -307   1413     25    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10982 -12024   -894  -1115   -870  -1142  -9273  -9101 
-    61    193  -3191  -5583  -1789  -1194  -4883  -3748    937  -2124   -849   1013  -4493  -4934    -70    570  -1848   -324   2003  -3647   2649   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11003 -12045   -894  -1115   -396  -2058  -9273  -9098 
-    62  -5439  -4905  -8119  -7792   -727  -8006  -7927   3672  -7770   -960  -3839  -7663  -7626  -7535  -7866  -7408  -5419   1529  -6982  -6645   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9095 
-    63   -391     95   -533   2155  -4814  -2163   1077   -994   -746    564    -61  -1215  -4180   -290  -1308  -1111    170   1107  -4716  -4048   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9093 
-    64   1267  -4572    593   1227  -1492   -847   -741  -4644   1483  -4588  -3661    596  -4166   -319   1636   -666   -753  -4194  -4755  -4072   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9090 
-    65  -1936  -3220  -5742  -5107  -1256  -4947  -3820   2579  -4703     90  -2422  -4592  -4996  -1411    561  -4032   -806   2448  -3685   -898   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9087 
-    66  -1224   -165  -1755   1584   1028  -2536   2425  -1214  -1319   1992    159  -4459  -4938  -4175  -4388  -3961  -3304  -1305  -3679    300   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9085 
-    67   -908  -5827    534   2365  -6111  -4733    305  -5912  -1464  -5833  -4976  -3345   3107  -3305  -4135   -664  -1748  -5438  -6009  -5220   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9082 
-    68  -8439  -7615  -8562  -8569  -9118  -7595  -7725  -9858  -7275  -9294  -9046  -8417  -1682  -7937   4251  -8747  -8580  -9431  -7862  -8897   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9079 
-    69  -3100   -504  -2950   -129   -496  -4075     56  -4631   2409  -2650  -3655   -480  -4168    980   1967   -358   1065  -2192  -4750   -993   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9077 
-    70  -2160  -4669  -6723  -6994  -7346  -1758  -6483  -7170  -6948  -7409  -6443   3313  -5726  -6492  -1579   2144   1559  -5865  -7542  -7470   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9074 
-    71   -234    -48  -5457   1502   -121  -4881  -3739   -508   -653    772   -149  -4443  -4934   1017  -1857    356  -1556   1276    943    500   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9071 
-    72  -6619  -5964  -9021  -8443   1242  -8905  -7513   1249  -8279   2971  -2781  -8639  -7784  -6934  -7712  -8343  -6450  -1253  -5894  -6144   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9069 
-    73   -775  -3936  -1661   -354  -1439  -4315   -550   1311   -242  -1284  -3090   -488  -4398  -2711    443   1089    810   1488    425    810   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12067   -894  -1115   -701  -1378  -9273  -9066 
-    74  -6170  -6757   -540  -5127  -7746  -6349  -4481  -7088   -719  -6673  -6059  -5098  -6428  -4084   4146  -6000  -5859  -6862  -6414  -6386   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T  -4378 -11025    -75   -894  -1115   -701  -1378  -9273  -9063 
-    75  -1331  -1739  -1699  -1097   -134  -2155   -277  -1581    125  -1520  -1006  -1054  -2240   -397   2478  -1367  -1233  -1450   -634   3156   114
-     -   -149   -500    233     45   -381    398    105   -627    210   -466   -721    275    393     45     98    359    117   -367   -295   -250 
-     .  -1836  -1500  -1456  -1507   -625  -1891   -453  -9273  -9061 
-    76  -1788  -3193  -1674  -1098  -3538    861  -1345  -3256   1916  -1141  -2290  -1385  -2827    558   1807    592   1154  -2831  -3339  -2711   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -81  -9183  -4287   -894  -1115  -4629    -59  -9273  -9058 
-    77   2284  -3018  -1434    151  -3329  -2553  -1213  -3070    409  -3030  -2112    471  -2647   -757   1011   -196    694   -359  -3209  -2535   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -6  -9186 -10228   -894  -1115  -2065   -394  -9273  -9055 
-    78   1655  -3471    725  -1454  -3757  -3096  -1771  -3478    -24  -3478    450   1263   1925  -1328  -1873    433  -2054    398  -3692  -3037   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5  -9848 -10890   -894  -1115  -2505   -280  -9273  -9053 
-    79  -2312  -3785   1955  -1604  -4106   1848  -1942  -3856   -287  -3801  -2875   1206  -3376    998   -388    926   -491  -1193  -3968  -3285   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5 -10107 -11150   -894  -1115  -4994    -46  -9273  -9050 
-    80  -2295  -3767   1680    366  -4088   -445  -1928  -3838   1047    212  -2856   -395  -3362  -1468    440   1075    371  -3389  -3951   1282   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5 -10107 -11150   -894  -1115  -4994    -46  -9273  -9047 
-    81   -223  -3766    912    903  -4087   -312    938  -1058    835  -3782  -2855  -1903   -990   -150   1817   -259  -2233   -981  -3950   1789   123
-     -   -151   -504    240     41   -377    402    101   -628    211   -470   -717    271    395     44     94    359    119   -372   -277   -246 
-     .  -5272    -41 -11150     -6  -7819  -4994    -46  -9273  -9044 
-    82    430  -3766   1127   1025   -850   1459    123  -3837    915  -1426  -2855  -1903  -3361    553   1029  -2174   -824  -3387  -3949   -274   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5 -10107 -11150   -894  -1115  -4994    -46  -9273  -9042 
-    83   -340  -3614  -2226   2059  -3870   -363  -1977   -695  -1587   -332  -2721  -1975   -821    988    819    576    571    -80  -3838  -3198   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5 -10107 -11150   -894  -1115  -4994    -46  -9273  -9039 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5 -10107 -11150   -894  -1115    -29  -5671  -9273  -9036 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9033 
-    86   -742  -3212  -5600  -4972  -1237  -4903   -491   2108    617     80   -754  -4512   2349  -1556  -1678  -1267  -1720    819  -3668   -897   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9031 
-    87   2338    186  -7770  -7583  -5655  -2254  -7340   1238  -7457  -4534  -4393  -6832  -6881  -7274  -7461  -5893  -5012   2745  -7140  -6681   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9028 
-    88   3280   -529  -7449  -7794  -7343  -4917  -6706  -7126  -7395  -7421  -6452  -5768  -5735  -6815  -6981   1243  -1010   -465  -7573  -7562   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9025 
-    89  -7762  -7293  -7291  -7671  -5449  -7361  -6426  -8725  -8279  -8124  -8077   4430  -7815  -7781  -8059  -7836  -7993  -8490  -5932   -827   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9022 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9020 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9017 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9014 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9011 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9008 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9006 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9003 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -9000 
-    98   2100  -4633  -7415  -7768  -7377    476  -6711  -7204  -7398  -7466  -6485  -5764  -5736  -6815  -6987   2827     88  -5860  -7598  -7593   141
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -8997 
-    99   1224   -139  -5786  -5153   -353  -4994  -3870    897  -4751   1964   -544  -4640  -1750  -4374  -4552  -4080    -67   1591  -3732  -3390   142
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -8994 
-   100    301  -4479   1784    115  -4758  -1908  -2763  -1844   1335   -427     31   1435  -4191  -2317  -2860  -1028   -901   1326  -4688  -4031   143
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -683 -11025  -1416   -894  -1115   -701  -1378  -9273  -8992 
-   101  -2521  -3994   2069   1947   -627  -3487  -2152  -4064   -635  -4009    952    460  -3584   2322  -2244    -10  -2461  -3615  -4178   -531   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10347 -11389   -894  -1115    -36  -5362  -9273  -8989 
-   102   -806  -5514   -632  -1446  -5804   -394    868  -5587  -1484  -5517  -4637  -1153   3853  -1213  -3794  -3773  -3916  -2017  -5690  -4938   145
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -8986 
-   103  -1192   -505   2375   1744  -4893  -1055  -2731  -4644    607  -4588  -3661    511    644   -192  -2819    -72   -167  -1352  -4755  -4073   146
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11025 -12068   -894  -1115   -701  -1378  -9273  -8983 
-   104  -1943   -117  -5746  -5110   3380  -4948  -3819    824  -4705   1012   -174  -4595    850  -4325  -4504  -4034    154  -2632  -3680    515   147
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8980 
-   105  -1854  -4643    800   -138  -4963  -4118   -480  -4715     50  -4659  -3734   3092  -4222  -2333   -245   1799   -499  -4265  -4826  -4139   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8977 
-   106   -561  -3751   -631   -121  -1482  -4420  -1128  -1600  -3021   1198  -2919   -367   1904  -2924  -1479    105   1362    370   1152  -3657   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8974 
-   107    -51  -4550    736   -750    395     -2   -530  -1011  -1112  -1264  -3641   1909  -4171    379   1875   -632  -3040  -1133    -26    809   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8972 
-   108  -3352  -3369  -4818  -4221    899  -2009  -3578    566  -1710   2001  -2563  -4091  -1797   1612   1939  -1879   -548  -2796  -3804  -3433   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8969 
-   109   -476  -4798  -7964  -7615  -5159  -7747  -7555   2365  -7548   2500  -3885  -7420  -7464  -7352  -7626  -7100  -1961    624  -6848  -6471   152
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8966 
-   110  -3564  -5078   2954   1872   -406   -725  -3151  -5148  -2810  -2501  -4183    922  -4547  -1105  -3348    166   -170  -4694  -5260  -4544   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8963 
-   111  -5998  -6501  -7181  -5303  -7528  -6392  -4133  -6711   1538  -6284  -5654  -1442  -6285  -3714   3947  -5863  -5586  -6525  -6063  -6064   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8960 
-   112   -423   1814  -5732  -5097   3319  -4935  -3798  -2705  -4692  -1271   1077  -4580  -4985  -1488  -4492  -2068  -3330  -1273  -3658   3228   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8957 
-   113  -6713   -540  -9090  -8488  -3985  -8967  -7519    -87  -8313   3275   -213  -8720  -7793  -6912  -7708  -8410  -6527  -4333  -5868  -6157   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8954 
-   114   1104  -3224  -5748  -5113  -1049  -2078  -3827   1352  -4710    257   -399  -4599  -5001  -4334  -4511  -1224     38   2671  -3691  -3349   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8951 
-   115   1462  -3518  -1883  -1231    493  -2143    816    658   -946   1312  -2703  -3679  -4658    109  -3713   -318     55    227  -3929     14   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8948 
-   116   2739   2101  -5755  -5121    237  -4960  -3834    503  -4717   -328  -2433  -4606  -5008  -4341  -4519  -1341  -3348    836  -3698    551   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8945 
-   117  -1142  -4386  -3096   3155   -403  -1447   1521  -4307   -694  -4360   -429   -454  -4254  -2410  -2943  -3082  -3091  -3960   2853    749   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8943 
-   118   1285  -4570    113   1289   -566  -1352   1076  -1194   -681  -4585  -3659  -1480  -4166    358  -1475   1205    250   -638  -4753   1078   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8940 
-   119    734     17  -2953     78  -1385    110   -732  -2137    389   -294  -3649    970  -4169   1020   -254   1006    783  -4177  -4745    566   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -464   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -29  -5826 -12068   -158  -3268   -701  -1378  -9273  -8937 
-   120  -2264  -4582   1056   -475  -4903   2712    640  -4654    642  -2438  -1419   1395  -4174   -210   -250  -2988  -3048  -4204  -4764  -4082   164
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8934 
-   121    889  -4555  -7571  -7139  -1182  -7179  -6580   3064  -6958    798  -3770  -6832  -7019  -6725  -6941  -6426   -737   1281  -6187  -5793   165
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8931 
-   122   -788  -4572     67   1830  -4893  -2005   1185  -4644   1104  -2486   -726    532    971   1369   -175  -1235    489  -1737  -4755  -4072   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8928 
-   123   -260  -3219  -5576  -2002  -1342  -4903  -3768   -369  -4575  -1304  -2422   -543   3543  -4225  -1677  -3982  -1516   1263  -3676  -3331   167
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8925 
-   124  -3372  -3210  -5637  -5005  -3166  -4910    293   1597  -1132   1118   -759  -4529  -4961   -622  -1167  -1146    -26   2581  -3667  -3323   168
-     -   -149   -500    232     43   -381    398    105   -623    210   -464   -721    275    395     45     95    359    117   -367   -295   -250 
-     E    -94  -4035 -12068    -52  -4833   -701  -1378  -9273  -8922 
-   125  -5674  -5123  -8314  -7941  -4742  -8200  -7824   3256  -7891   1307   -466  -7872  -7667  -7346  -7823  -7609  -5633   1594  -6612  -6525   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8919 
-   126   -941   2984  -6299  -5703  -3741  -2076  -4517    492  -5334    718  -2906  -5218  -5588  -4983  -5162  -4676  -3850   2854  -4358   1342   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8916 
-   127  -6492  -5855  -8930  -8380   2220  -8809  -7523   1881  -8228   2548  -2833  -8532  -7768  -6963  -7715  -8239  -6344   -541  -5942  -6161   172
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8913 
-   128  -2093  -4659  -6942  -7305  -7381  -4923  -6625  -7211  -7279  -7466  -6492   3353  -5738  -6693  -6952   1234   2567  -5876  -7598  -7561   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8910 
-   129  -9209  -7823  -8656  -8830  -9255  -7767  -8050 -10217   4070  -9548  -9441  -8826  -8181  -8474  -7730  -9635  -9270  -9925  -7933  -9126   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8907 
-   130   1417    746  -4702  -2053  -3341  -2281   -880   1871  -1015   -631   1751  -1460  -4792  -1402   -876    -89    121   1030  -3798   -873   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     G     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8904 
-   131  -5573  -7624   4129   -620  -7802  -5271  -4764  -7832  -5249  -7649  -7126  -3866  -5880  -4467  -6318  -2226  -5694  -7242  -7835  -6678   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8864 
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-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8861 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -28 -11026  -5921   -894  -1115   -701  -1378  -9273  -8855 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11002 -12044   -894  -1115  -1419   -676  -9273  -8852 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11002 -12044   -894  -1115  -1419   -676  -9273  -8849 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11002 -12044   -894  -1115  -1419   -676  -9273  -8845 
-   150   1200  -4551    685   -133  -4872    -71    509  -4623    566  -4567  -3640   1281  -4144   1925   -369    499    377  -4173  -4734  -4051   207
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11002 -12044   -894  -1115  -1419   -676  -9273  -8842 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -27 -11002  -5985   -894  -1115   -384  -2096  -9273  -8839 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11004 -12046   -894  -1115  -1384   -697  -9273  -8836 
-   153   -853     69  -5689  -5054  -1092  -1073  -3770   -760  -4651  -1990  -2383  -4542   -855  -4275   -154  -2210  -3292    -52  -3637   4360   210
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -148   -500    232     42   -381    398    105   -627    210   -461   -721    276    393     45     95    358    117   -368   -295   -246 
-     .   -225  -3338  -4527    -33  -5449   -274  -2530  -9273  -8830 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10964 -12006   -894  -1115  -2110   -380  -9273  -8827 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10964 -12006   -894  -1115  -2110   -380  -9273  -8823 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10964 -12006   -894  -1115  -2110   -380  -9273  -8820 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -10964 -12006   -894  -1115  -2110   -380  -9273  -8817 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -94 -10964  -4050   -894  -1115  -2110   -380  -9273  -8814 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -10874 -11917   -894  -1115  -3005   -192  -9273  -8811 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H  -1437 -10874   -671   -894  -1115  -3005   -192  -9273  -8807 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -62  -9444  -4704   -894  -1115  -4563    -62  -9273  -8804 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -6  -9448 -10490   -894  -1115   -170  -3165  -9273  -8801 
-   164  -1807  -4479   1393    698   -343  -3982   -413  -1790   -469  -1640  -3568   1161   -142    664  -1482    425   2056  -2257  -4663  -1332   222
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -10926 -11968   -894  -1115  -2571   -266  -9273  -8798 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -10926 -11968   -894  -1115   -160  -3248  -9273  -8794 
-   166     43  -4567    920   2160  -1939  -1250   -380   -166     68  -2726    751   -335  -1826   1224  -1191  -1822    363  -1370    -27   -956   224
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8791 
-   167    145   -201    360  -2809  -4138   2614  -2971  -1999  -2701  -1098  -3166   1068   -436   -911  -3142    618   -835  -1844  -4338  -1681   225
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8788 
-   168   -814  -3199  -5716  -5080    836  -4920    276   2085   -247   1331   1512  -4565  -4970  -2130  -1662  -4004   -382   1155    106   -795   226
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8785 
-   169    678  -4572   1874   2199  -4893  -1314  -2731  -4644   -129   -625  -3661  -1309   -185    573   -454   -345  -1496  -4194  -4755  -4073   227
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8781 
-   170   1611  -4569    397   1798  -4889  -4073   -828  -1151    848  -2371  -3659  -2709   -301   -998    310   -317     48   -675  -4753   -802   228
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8778 
-   171  -6554  -5919  -8945  -8368   -665  -8783  -7368   1470  -8188   2932  -2782  -8498  -7735  -6890  -7642  -8186  -6390    163    802  -6019   229
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8775 
-   172    629  -4566  -1713    396  -4885  -4074  -2733  -1146   1835     25   -876  -1059  -1948   1311   1548    -21   -841  -1271  -4751  -1356   230
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8771 
-   173   1027  -4572    373   1299   -841  -4072  -2731  -1684    734  -4588  -3661    617   1950    217   -874    481  -1598  -2504  -4755  -4072   231
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -81 -11026  -4275   -894  -1115   -701  -1378  -9273  -8768 
-   174   -809  -4241   -625   -280   -113  -4085   1291  -1603    255    765    129   -101  -4175    118    162   -961  -1593   -138   3026   2076   232
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -10950 -11992   -894  -1115  -2303   -327  -9273  -8765 
-   175  -6224   1244  -8690  -8158    723  -8515  -7354    824  -8001   2978  -2810  -8225  -7617  -6866  -7560  -7903  -6099   -483  -5888  -6069   233
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -10950 -11992   -894  -1115  -2303   -327  -9273  -8762 
-   176    993  -4503    683    702  -1194   -652    698  -4575   1783  -2620  -3592   -426  -1719    385    375    264    442  -4125  -4686  -4003   234
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -4 -10950 -11992   -894  -1115  -2303   -327  -9273  -8758 
-   177  -1018  -4540   1642    -33  -4860   2215   -542  -4612    275  -4556  -3630   1265    755  -1133  -2788     62  -1479  -4162  -4723  -4038   235
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T  -1766 -10950   -508   -894  -1115  -2303   -327  -9273  -8755 
-   178  -2187  -3594    294  -1263  -3949   2985  -1800  -3695    277  -3674    978    417  -3150  -1382  -2027  -2053    592  -3262  -3875  -3176   236
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -7  -9191 -10233   -894  -1115    -47  -4954  -9273  -8752 
-   179  -3082   -629  -1333   -240  -1368   -261   1749  -4627   2472  -4571  -3644    305  -4149   1553   1882   -870  -3021  -4177  -4738  -4055   237
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -4 -11005 -12047   -894  -1115   -407  -2024  -9273  -8748 
-   180  -3375     69  -5720  -5084  -1154  -4923  -3794   2007  -4679    348    -80  -4568  -4972  -1087  -1460   -713   2609   1059  -3659  -3317   238
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8741 
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-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8738 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8735 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8731 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8718 
-   189   1082  -4747  -7752  -7704  -5822  -6119  -7333  -2778  -7537  -4674   1199  -6643  -6647  -7256  -7445  -5494  -4982   3552  -7284  -6909   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8714 
-   190  -9012  -7763  -8749  -9136  -9317   3867  -8401 -10389  -9331  -9723  -9677  -9082  -8194  -9205  -8754  -9491  -9245  -9968  -7999  -9333   248
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8711 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8707 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -4 -11026 -12068   -894  -1115   -701  -1378  -9273  -8704 
-   193  -4171  -4771  -7338  -7694  -7457  -5044  -6773  -7330  -7442  -7573  -6614  -5869  -5855  -6885  -7058   2567   3282  -6001  -7613  -7639   251
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -5 -11027 -12069   -894  -1115   -701  -1378  -9273  -8701 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8697 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8693 
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-     H     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8690 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8687 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8683 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8679 
-   200  -4683  -5914  -1611  -3627  -7006   2014  -4602  -6858  -4734  -2475  -6054  -1194   3359   -950  -5425    617  -1761  -6178  -7025  -6213   258
-     -   -147   -500    232     43   -381    398    105   -627    210   -466   -721    275    393     48     95    360    117   -367   -295   -250 
-     T    -47  -5080 -12068   -992  -1008   -701  -1378  -9273  -8676 
-   201  -1308    -84    418   1982  -4893    699    826  -1964   -195  -4588  -3661   1083  -2178    992    225    559   -235  -4194  -4755  -4072   262
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -51 -11026  -4961   -894  -1115   -701  -1378  -9273  -8672 
-   202    577  -4483    372    739  -4782  -4043   -632    298  -1168   1569  -1035  -1275  -1754   1057  -1292   -513    -25   -443  -4679  -1299   263
-     -   -159   -494    234     53   -363    397    108   -623    219   -467   -710    278    391     42     86    353    110   -368   -266   -248 
-     -   -101  -3943 -12021  -4229    -79   -269  -2556  -9273  -8669 
-   203   -341  -4572   1581   1004  -4893  -1160    739   -939    421  -1724  -3661    676  -1623    781   -211   -544    -64   1061  -4755  -4072   304
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8665 
-   204    249  -3205  -5695  -5060  -1043  -4919  -3789    590  -4661   1880   1925  -1341  -4969   2585   -378  -4003  -1605  -1036  -3662  -3319   305
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8662 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8658 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8655 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8651 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8647 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8644 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8640 
-   211    437  -4571    857   2212  -4892    429    981  -1542    461  -2280  -3660  -1324  -4166   1005  -2819     -1   -823  -1040  -4755  -4072   312
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8637 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -86 -11026  -4184   -894  -1115   -701  -1378  -9273  -8633 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -10945 -11987   -894  -1115   -187  -3043  -9273  -8629 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8626 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8622 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     X     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8618 
-   217  -5954  -6472  -7225  -5269  -7480  -6373  -4097  -6660   2768  -6240    239  -5036  -6254    784   3139  -5820  -1938  -1923  -6029  -6023   318
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8615 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8611 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8607 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8604 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8600 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -5 -11026 -12068   -894  -1115   -701  -1378  -9273  -8596 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12069   -894  -1115   -701  -1378  -9273  -8592 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11026 -12069   -894  -1115   -701  -1378  -9273  -8589 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -5 -11026 -12069   -894  -1115   -701  -1378  -9273  -8585 
-   226  -4809  -4526  -7068  -6499   2844  -6392   1241   1996  -6122    972    161  -5962  -6271  -5534  -5847  -5515  -4729   -873  -4338   2382   327
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -5 -11026 -12069   -894  -1115   -701  -1378  -9273  -8581 
-   227   -102  -4571    589     60  -4892  -4072   2783  -1542    145   -144   -877    132   2248   -197   -737    112  -3038  -4193  -4755  -4072   328
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-//
-HMMER2.0  [2.3.2]
-NAME  SOCS_box
-ACC   PF07525.8
-DESC  SOCS box
-LENG  42
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  62
-DATE  Tue Apr 22 23:09:05 2008
-CKSUM 9714
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -30 -10837 -11879   -894  -1115   -701  -1378  -6386  -5673 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -    -34 -10841 -11883   -894  -1115   -701  -1378  -6386  -5493 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -39  -8869  -9911   -894  -1115    -21  -6099  -6386  -5427 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -36 -10843 -11885   -894  -1115   -701  -1378  -6386  -5393 
-    42   -341  -4378    262   1282    240   -949   1559  -1581    981   -341  -3467   -837   -965   1289   1193   -188  -1310  -4000  -4561  -3878    46
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -6386      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DUF1289
-ACC   PF06945.5
-DESC  Protein of unknown function (DUF1289)
-LENG  56
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  27
-DATE  Thu Apr 24 21:10:17 2008
-CKSUM 838
-GA    25.0000 25.0000;
-TC    25.1000 25.1000;
-NC    23.5000 23.5000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.784554   0.652248
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -67      *  -4459
-     1   1056  -3317    529   1811  -3638  -2818  -1477  -3388   1147  -3333  -2406  -1454    380    243   1055  -1725   -111   -249  -3500  -2818     1
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-     -    -16  -9563 -10605   -894  -1115   -701  -1378  -1067  -6781 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -9565 -10608   -894  -1115   -701  -1378  -6848  -6508 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -9566 -10608   -894  -1115   -701  -1378  -6848  -6492 
-    22  -7256  -6212  -7081  -7066  -7533  -6172  -6204  -8374  -5729  -7775  -7568  -6976  -6573  -6418   4266  -7573  -7311  -8055  -6331  -7280    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -9566 -10608   -894  -1115   -701  -1378  -6848  -6476 
-    23  -2155  -3275  -2096  -1612     34  -3118   2317  -3270    347  -3338  -2503   -257  -3258  -1461  -1858    713   3086  -2930  -3568  -2963    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -9566 -10608   -894  -1115   -701  -1378  -6848  -6459 
-    24     21  -1937  -4147  -3523  -1894  -3582    920    659    286   1639   1075  -3135  -3634  -2838   1898  -2656  -2007    683  -2389  -2041    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -9567 -10609   -894  -1115   -701  -1378  -6848  -6444 
-    25   -263  -3340   2697   1687  -3660  -2833    973  -3411  -1082  -1111  -2430  -1468    399     90     34   -760  -1807  -2962  -3524  -2840    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -9566 -10609   -894  -1115   -701  -1378  -6848  -6426 
-    26  -4435  -6252    711   3791  -6541  -4087  -3603  -6643  -4086  -6433  -5937  -2728  -4686  -3321  -5102  -4037  -4550  -6073  -6404  -5482    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -9567 -10609   -894  -1115   -701  -1378  -6848  -6409 
-    27  -3838  -3380  -6464  -6059  -3984  -6131  -5890   3645  -5396  -2779  -2714  -5809  -5978  -5671   1243  -5507  -3840    889  -5584  -5102    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -9567 -10609   -894  -1115   -701  -1378  -6848  -6392 
-    28   1217   2154  -4110  -3492   1554    687  -2422    780   -417   -573  -1127  -3115  -3619  -2825    898   -597     43    -91  -2379  -2029    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -9567 -10609   -894  -1115   -701  -1378  -6848  -6375 
-    29   1606  -3361  -1737    288  -3688   -756    975  -3434    447  -3374  -2451   1924  -2955   1393   1569  -1774  -1832  -2986  -3536  -2861    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -9568 -10610   -894  -1115   -701  -1378  -6848  -6359 
-    30  -7875  -6321  -7259  -7641  -6426  -6309  -6538  -8612  -7781  -7895  -7930  -7574  -6736  -7627  -7209  -8364  -8007  -8416   6311  -6122    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -9567 -10610   -894  -1115   -701  -1378  -6848  -6340 
-    31    111  -3177  -1766  -1216  -3438   -405    706  -3148   1082   -135   1355    815  -2946  -1082   1465   1211   -531   -579  -3397  -2753    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -9568 -10610   -894  -1115   -701  -1378  -6848  -6322 
-    32     70  -3285    701  -1158   -126    877  -1485  -3332    625   -798  -2378    143  -2918  -1030   1159   1679  -1785  -2899  -3477   -162    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -9568 -10610   -894  -1115   -701  -1378  -6848  -6304 
-    33    187  -1929  -4361  -3731   -144  -3632  -2494  -1409   -403    658   4054  -3252  -3680  -2976  -3165  -2714   -208  -1338  -2374   2148    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21  -9568 -10610   -894  -1115   -701  -1378  -6848  -6285 
-    34  -2207  -3717   1067   -188  -4027  -3035  -1799  -3791    380  -3730  -2821    859   -420  -1355  -1980   2049   2115  -3335  -3899  -3188    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -9569 -10611   -894  -1115   -701  -1378  -6848  -6268 
-    35  -2232  -3746   2651   1471  -4055  -3051  -1819  -3820     -1  -3757  -2850   1345    764  -1375    412     99  -2184  -3364  -3925  -3213    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -9569 -10611   -894  -1115   -701  -1378  -6848  -6248 
-    36    907  -3378   2241    879  -3702    529  -1569  -3448  -1167  -1022  -2489  -1523    270  -1115  -1678    -50    874  -3007  -3583  -2902    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -9569 -10611   -894  -1115   -701  -1378  -6848  -6229 
-    37   -614  -3475     -8   3015  -3796  -2918  -1605  -3548    -41  -3488  -2569  -1551  -3034   1889    -72  -1867   -567  -3098  -3652  -2966    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22  -9569 -10611   -894  -1115   -701  -1378  -6848  -6209 
-    38  -4559  -5070  -5803  -3863  -6087  -4964  -2686  -5262   2215  -4836  -4204  -3628  -4847   1832   3398  -4422  -4141  -5079  -4620  -4618    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -9570 -10612   -894  -1115   -701  -1378  -6848  -6191 
-    39    154  -3220  -1743    656  -3498  -2843   1299  -3219  -1104    379   1276    146  -2935    969   2368   -396  -1792   -745  -3429  -2773    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -9570 -10612   -894  -1115   -701  -1378  -6848  -6170 
-    40   2074  -3316   -392   1158  -3637  -2818   1383  -3387  -1057  -3332  -2406    726  -2911    373    -95     28    627  -1143  -3500  -2817    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -9570 -10612   -894  -1115   -701  -1378  -6848  -6150 
-    41   -872   1258  -5064  -4478  -2517  -4358  -3327   2412  -4121   -628  -1660  -4005  -4369  -3780  -3960  -3474   -570   2707  -3162    343    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -9571 -10613   -894  -1115   -701  -1378  -6848  -6130 
-    42  -2192  -2012  -4537  -3902    268  -3746  -2611   1628  -3499   1505   2737  -3391  -3783  -3108   -364  -2832  -2131    315   3132    442    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -9570 -10613   -894  -1115   -701  -1378  -6848  -6109 
-    43    788  -3302    -32    639  -3617   -403  -1479   -626    749   -269  -2393  -1458  -2913   1998   1329  -1727   -182   -572  -3489  -2810    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -9571 -10613   -894  -1115   -701  -1378  -6848  -6087 
-    44    470  -3344  -1739    458  -3667  -2856  -1506  -3411    715   1025  -2434    826  -2948   1572   1826  -1767   -242  -2967  -3521  -2849    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -9572 -10614   -894  -1115   -701  -1378  -6848  -6067 
-    45    514   3676  -4548  -3920  -1965  -3763  -2648    789  -3522   1901    978  -3411  -3806  -3145  -3325   -577  -2138    -77  -2504  -2164    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -9571 -10614   -894  -1115   -701  -1378  -6848  -6044 
-    46   1217  -3287    391     23   -739  -2825   1243  -3335     98    199  -2379  -1466   2018  -1030    889  -1733   -111  -2901  -3478  -2804    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25  -9572 -10614   -894  -1115   -701  -1378  -6848  -6022 
-    47   1324  -3307  -1702   1544  -3621   -566  -1489   -486    104  -3321  -2400  -1467   -349   2620  -1577  -1737    418  -2926  -3496  -2818    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -9573 -10615   -894  -1115   -701  -1378  -6848  -6001 
-    48   -796  -4681  -3957    528  -5535  -4475  -2757  -4936  -1467   -997  -4049  -3297  -4595  -2359   3870  -3891  -3799  -4674  -4657  -4487    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -9572 -10615   -894  -1115   -701  -1378  -6848  -5977 
-    49    599  -2895    -67  -1407  -3057   -661    667  -2704   1352   1037   1896  -1675   -452  -1249    639  -1873  -1824   -566  -3183    815    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -26  -9573 -10615   -894  -1115   -701  -1378  -6848  -5954 
-    50   1710  -3310   -205    801  -3628  -2819  -1477  -3377   1127  -1622    451  -1455  -2912    353   1465    354  -1783   -554  -3495  -2814    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27  -9574 -10616   -894  -1115   -701  -1378  -6848  -5932 
-    51   1292  -3314  -1691    845  -3634   -731    886  -3384    109  -1174  -2403     65   -447    471   1213   -590    792     98  -3498  -2815    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27  -9574 -10616   -894  -1115   -701  -1378  -6848  -5907 
-    52    877  -2102  -3254  -2674    969  -3394    951   -321    646    690    790    -27  -3458    718    372  -1019  -1951    739   1412  -2147    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -28  -9575 -10617   -894  -1115   -701  -1378  -6848  -5884 
-    53     70  -3270    549   1049  -3570    984  -1489    265    101   -156   1282     81  -2921    637  -1582    303  -1786   -563  -3466  -2796    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -28  -9574 -10617   -894  -1115   -701  -1378  -6848  -5858 
-    54    429   1241  -2212    374      6   -691  -1761   -391    315    854  -1789  -1878  -3136    239   1190   -415    631   -445  -2975  -2470    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -28  -9575 -10617   -894  -1115   -701  -1378  -6848  -5833 
-    55   1328  -3309    582   -478  -3626   -707  -1477  -1109   1755   -395    113    156   -194   -135   -347   -436   -273  -1141  -3494  -2813    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -9576 -10618   -894  -1115   -701  -1378  -6848  -5808 
-    56    328  -3313    -91     43    -80   -143  -1476  -3383    637  -1489    113    -33   1582    373    390    -66    903  -2934    823  -2815    56
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -6848      0 
-//
-HMMER2.0  [2.3.2]
-NAME  TRAP_alpha
-ACC   PF03896.8
-DESC  Translocon-associated protein (TRAP), alpha subunit
-LENG  327
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  3
-DATE  Tue Apr 22 18:33:16 2008
-CKSUM 6808
-GA    25.0000 25.0000;
-TC    35.3000 35.3000;
-NC    19.0000 19.0000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.948719   0.710292
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -415      *  -2000
-     1  -1621  -1355  -3403  -2944   2238  -3105  -1433    197  -2607    752   3913  -2566  -2959  -2079  -2451  -2291  -1559   -223   -855   -141     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -1415  -9349 
-     2  -1056  -1999   -842   -416  -2515  -1728   -317  -2242    638  -2142  -1400   1920  -1908     70   2880   -988   -986  -1900  -2126  -1713     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -468  -6674  -1911   -894  -1115   -701  -1378  -9764  -9347 
-     3  -1492  -1186  -3178  -2740   2556  -2980  -1103    454  -2421   1977    905  -2354  -2785  -1862  -2266  -2167  -1416     22   -485    301     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -6237  -7279   -894  -1115  -1292   -757  -9764  -9344 
-     4   -334   -696  -1193   -946   -870   1703   -775   -366   -765   1467   -157   -873  -1681   -715   -953   -601   -463   -268  -1380   -927     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -6237  -7279   -894  -1115  -1292   -757  -9764  -9342 
-     5    133   -564   -734   -625  -1958   -718   -803  -1696   -680  -1901  -1111   -491   2176   -564   -962   1921   -160  -1077  -2145  -1699     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31  -6237  -7279   -894  -1115   -425  -1969  -9764  -9340 
-     6  -1201  -2188  -1363   -517  -2733  -1943   2940  -2269   2066  -2070  -1316   -608  -1951    293   2136  -1093  -1010  -1971  -2037  -1727     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -9764  -9338 
-     7  -1848  -1445  -4035  -3518   -369  -3747  -2662   2061  -3209   2389    775  -3350  -3372  -2615  -3023  -2984  -1772    424  -1883  -1772     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -9764  -9335 
-     8  -2012  -1638  -4015  -3459   -174  -3768  -2537    425  -3090   2419   3210  -3338  -3337  -2447  -2875  -2990  -1912   -171  -1715  -1667     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -9764  -9333 
-     9  -1293  -1007  -3440  -2881   2235  -2981  -1704    627  -2568   1613    724  -2538  -2828  -2065  -2403  -2121  -1225   1739  -1236   -819     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -9764  -9331 
-    10  -2228  -1908  -3555  -3373   -604  -3255  -2515    -62  -2963   2976    358  -3207  -3275  -2644  -2802  -2988  -2232   -567  -1904  -1643    10
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-     -    -23  -6674  -7717   -894  -1115   -701  -1378  -9764  -9329 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9039 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9036 
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-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9033 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9031 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9022 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9020 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24  -6675  -7717   -894  -1115   -701  -1378  -9764  -9017 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9764      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DGOK
-ACC   PF05035.4
-DESC  2-keto-3-deoxy-galactonokinase
-LENG  298
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  3
-DATE  Thu Apr 24 19:21:09 2008
-CKSUM 8061
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-TC    25.4000 27.3000;
-NC    24.7000 24.7000;
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8253 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8248 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8243 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8238 
-   294   -559  -1155  -1272   -736  -1584  -1607   -651  -1067   -235  -1379   -663   -800  -1856   -386   1895   1446   -606   1537  -1810  -1369   294
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8234 
-   295   -564  -1527   -403   1619  -1779  -1498   -357  -1410    -60  -1557   2641   -311  -1687      1   -501   1350   -545  -1131  -1926  -1357   295
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8229 
-   296   1527  -1082  -3221  -2918  -1500  -2529  -2381   2994  -2668   -711   -484  -2481  -2848  -2480  -2685  -1809  -1234    682  -2443  -2062   296
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8224 
-   297   2746   -923  -2525  -2473  -2809  -1244  -2160  -2243  -2331  -2696  -1933  -1654  -1963  -2090  -2365   -582   2158  -1562  -3110  -2850   297
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20  -7113  -8155   -894  -1115   -701  -1378  -9536  -8219 
-   298  -1907  -2604  -2099  -1284  -2657  -2476   3258  -2795    540  -2560  -1901  -1273  -2532   -306   3182  -1827  -1709  -2547  -2258  -1843   298
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9536      0 
-//
-HMMER2.0  [2.3.2]
-NAME  RVT_1
-ACC   PF00078.19
-DESC  Reverse transcriptase (RNA-dependent DNA polymerase)
-LENG  242
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F --prior PRIOR HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  156
-DATE  Mon Jun  2 18:30:00 2008
-CKSUM 7481
-GA    35.2000 35.2000;
-TC    35.2000 35.2000;
-NC    35.1000 35.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.513688   0.618327
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -13      *  -6834
-     1    254   -362  -1116     20   -891   -782   -593  -1348    663  -2265  -4560    682    522    340    223   2070  -1876  -2798   -263  -4972     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26756 -26756      0 -19932      0 -19932  -1013  -8913 
-     2   -419   -233   -396  -1108   1220  -2792  -3751   -250   -584  -1669  -4321  -1660   2448   -323   -379  -1635   -527  -1337   3626    168     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -26767  -7314      0 -19932      0 -19932  -8926  -8910 
-     3  -3036   1124  -1949  -2086   -484  -1024   1155   -973   1367  -1738   -250   1015   -902    -89   1143   -814   -125  -1397   2962   1591     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932   -781  -1259  -8926  -8907 
-     4    516   -987   -771   -323  -5789  -1603   1192   -740     80  -1399    452   1966   1252   -961    178    229    252  -1273   -632  -4972     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932   -781  -1259  -8926  -8904 
-     5   1343  -1132  -6596  -5963  -4077   -340  -4703    201  -5567  -2165   -675   -770  -2432  -5197   -287   1192   2065    481  -4580    975     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932      0 -20712  -8926  -8901 
-     6  -1152  -5367  -3923  -1459  -2119   -869   -642  -1019    908  -1501  -4470    334   2500  -1749   1764  -1025    141    -13   -594  -1817     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26767 -26767      0 -19932      0 -19932  -8926  -8898 
-     7    414  -4522  -2360  -2529  -4542  -1623  -4197   1934   -816    267    417  -4460  -2354  -1999   1302  -1950    186   1758  -4919  -4490     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -26767  -7603      0 -19932      0 -19932  -8926  -8895 
-     8  -1232    249  -2517  -1894   2481  -2907  -1402   1076   -826   -485   -144  -5476  -2696  -5208  -3149  -1959    -20   2026   1351    503     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26760 -26760      0 -19932      0 -20598  -8926  -8892 
-     9   -326   -780  -6569  -1098   1014  -1723  -4705    257  -1888   1172   1075  -2521   1316  -1495  -2370  -1038    150   1000   -840    905     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26767 -26767      0 -19932      0 -19932  -8926  -8889 
-    10  -2023  -4161  -6677  -6043  -4122  -5889  -4763   3113    421    347  -3366  -5532  -3033  -2495  -5439  -2044  -4278   1853  -4631  -2367    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8886 
-    11  -1532   -925   -861   -558  -2142  -2848     -1  -5538   1673   -830  -1756  -1740   2989   -728    420  -1491  -1524  -1544   -391   -323    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8883 
-    12  -2479   -934   -756  -1673  -5967  -1045  -3780  -5717   3714  -3186  -4737   -136  -5213  -3325  -2083  -1082  -4109  -5267  -5820  -5139    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8880 
-    13    262  -5481  -2457   -738  -2834    -90    720  -1046   2411  -3136  -1998    109   1725  -1947    385  -1398    -19  -1750  -5664  -4982    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -96 -26768  -4007      0 -19932      0 -19932  -8926  -8877 
-    14   -918  -5393   1629  -1647  -5714   1663   -577  -3044   -693  -3398   -280   1674     78  -1243  -1281    870    271   -974  -5577  -4894    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2177 -26675   -364      0 -19932  -3019   -190  -8926  -8873 
-    15  -1990  -3463    642   -164  -3784     52  -1621  -3535   2750  -3479  -2553   -358  -3056  -1162    689    419    372  -1466  -3646  -2964    15
-     -   -143   -502    237     40   -383    396    103   -622    215   -466   -719    273    395     43     93    358    119   -369   -297   -252 
-     -   -924  -1279  -4083   -890  -1119  -2512   -278  -8926  -8870 
-    16  -2532  -4006   2703    176  -4327   -878  -2164  -1084    732  -4022  -3095    368    430    314    286    176    120  -3628  -4189  -3506    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -43 -25156  -5202      0 -19932  -3031   -188  -8926  -8867 
-    17   1343  -4235  -2613    765  -4556  -1612   -394  -4306   1265  -1925  -3325   -878   2045   -425   1462  -2645  -2704  -2105  -4419    367    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25420 -25420      0 -19932  -4332    -73  -8926  -8864 
-    18  -1649    181    202   1708  -1424  -1681    780   -351     84  -1465  -3393    250  -3900   -746    687    719   1544  -3925  -4487  -1140    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25498 -25498      0 -19932  -6082    -21  -8926  -8861 
-    19  -2832   -484   1177    998  -4624   -380  -2465   -534   1269   -880  -3393   1194  -3900    479   1395   -249  -1257   -365  -4488  -3805    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25498 -25498      0 -19932  -2441   -294  -8926  -8858 
-    20    371    932  -4615  -4033  -3389  -2690  -1260    663   1010    284   1483   -781   1309  -3621    824   -590    932   -521  -3837  -3455    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25811 -25811      0 -19932      0 -25745  -8926  -8855 
-    21   -493   -956   -637   -811  -5799   2603  -3642  -1792    630  -3039  -1303    131  -1710    210  -1664    396    149  -2130  -5663   -820    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8852 
-    22  -1421  -5482    948    444  -5803    745  -3641  -5554   2185  -1905  -4571    861  -5076    133  -1579   1184   -273  -2650  -5666  -4983    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8849 
-    23   -872  -4789  -1840   -921   1402  -2863   -300   -311    510   -812    717  -4109  -1336  -1121  -1444   -444  -1402  -1505   3760   2812    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11 -26768  -7603      0 -19932      0 -19932  -8926  -8845 
-    24  -5704  -6056  -7996  -6825  -2108  -6586   -497  -2732  -4517  -6550  -5948  -6246  -6944  -5403   4157  -2861  -1824  -2714  -6359  -5766    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26760 -26760      0 -19932      0 -20598  -8926  -8842 
-    25  -4300  -4130  -6619  -5984  -1190  -1378  -1903   -399  -1669    974   2714  -1891   3079  -1530  -5395  -3025   -851   -422  -4587  -1770    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1169 -26768   -854      0 -19932      0 -19932  -8926  -8839 
-    26  -4627   3553  -7174  -6703  -4570  -6691  -5964    280  -6466   1189  -3479  -6346  -6585  -6211    -24  -5900  -1593   2736  -5656  -5269    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25601 -25601      0 -19932  -3759   -111  -8926  -8836 
-    27   -827  -3116  -5634  -4998    639  -1775   2199   2166  -4593   -123   -100  -4482  -4887    846  -4393  -3921   -197   1919  -3574   -894    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -4838 -25704    -55      0 -19932    -14  -6685  -8926  -8833 
-    28  -5481  -4951  -8165  -7838  -5232  -8041  -7994   3162  -7814   1830  -3929  -7702  -7677  -7600  -7919  -7440  -1403    945  -7080  -6741    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25860 -25860      0 -19932  -5761    -27  -8926  -8830 
-    29    232    955  -5770  -5354  -5068   1877   -688  -4661  -5146  -4968  -4248  -1321  -5406  -4919  -5270   2593    677  -1772  -5461     11    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25860 -25860      0 -19932  -4806    -53  -8926  -8827 
-    30   -675   2153  -5851  -5219  -3295  -5057  -3940   2173  -4818   2005  -2537  -1414  -5109     73  -4621   -619  -3448    731  -3806  -3463    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25882 -25882      0 -19932  -4713    -56  -8926  -8823 
-    31   -401   2962  -1678  -4937  -3314   -855  -3855  -1291  -4590   1544    769   -597   2580  -4263  -4486  -2011   -211  -2771  -3808  -3460    36
-     -   -150   -501    232     42   -381    398    105   -627    215   -467   -721    275    395     47     95    360    117   -368   -295   -250 
-     -    -23  -6212 -25906  -1908   -447  -4149    -84  -8926  -8820 
-    32   -839   1267   -696  -2543  -5033  -1917   -333  -4783   -286  -4729   -860   2270    643  -2417  -1526   1875   1628  -4334  -4897  -4215    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25950 -25950      0 -19932  -4709    -56  -8926  -8817 
-    33  -1879   1901   -906  -1823    481  -2316  -3633    175  -1846  -1477    580  -1433   1406  -1323    381   -344    342   1822    313    346    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25971 -25971      0 -19932      0 -25557  -8926  -8814 
-    34  -1810   -947   2715   -705   -757  -2054  -3700    462   -434    478   -253    387  -2383  -1147    993  -1639  -1679  -1230  -5549  -1865    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8811 
-    35   -504    919   1586  -1388   1751    139  -4568  -3729  -5099    674  -1102  -1595  -2366  -2430  -5120   -627  -4209  -1387  -1195   2893    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8807 
-    36  -6789  -7381  -7791  -6094  -8347  -7249  -5026  -7567   3106  -7162  -6514  -2261  -2426  -2058   2867   -723  -1453  -7364  -6965  -1151    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8804 
-    37   1020    -74    -53    123  -5289  -1494  -3790   1906    342    175   -867  -3828  -1361    490   -775  -2007  -1174    679  -5393   -826    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8801 
-    38  -1239  -4172  -6697  -6062    983  -5902  -4775   1651  -2374   1965   1322  -5548  -5948  -5280  -5458  -4988   -774   1583  -4636      7    50
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7931 
-   240  -1534   -471  -6646  -6010   1634  -5848   1551    395  -2992    459    536  -5494  -2838   -389  -2391  -1937    236   1344    897   2624   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7925 
-   241  -2622  -5466   -752    857  -2292  -2207    995    364   -165  -1444  -1749    756    498    828    311  -1262   1250    763    439   -121   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7919 
-   242  -4303   -182  -2660  -6012   1335  -5850  -1410   2547  -5607   1628  -1427  -1351  -5900  -2315  -5407  -4935  -4243   1497  -4587  -2045   397
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8926      0 
-//
-HMMER2.0  [2.3.2]
-NAME  rve
-ACC   PF00665.18
-DESC  Integrase core domain
-LENG  169
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  244
-DATE  Tue May 13 16:19:14 2008
-CKSUM 4196
-GA    18.8000 18.8000;
-TC    18.8000 18.8000;
-NC    18.7000 18.7000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.945397   0.640242
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-           -8      *  -7555
-     1   -197  -1909   -799    748  -2861  -3201   1326   -121    651   -977  -1324    367  -1690   1232   1292   -391    257    -46    594   -661     1
-     -   -114   -519    222     36   -395    401    108   -633    195   -474   -737    271    418     51     98    351    116   -351   -321   -253 
-     -  -7883    -11 -13761     -1 -10451   -701  -1378  -1008  -8392 
-     2   -865  -2124    371    556   -357  -3053   1182  -2321    520   -674     80    472    408   -877    643    796   1087  -1490  -1719   -926     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8388 
-     3    649    292  -1080    566   -678   -541   1387  -1418   1072  -1993   -241   -457  -1485   1061   1788  -1063  -1458  -1794    644  -1130     4
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-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8384 
-     4    -83    146  -1895   -786  -1987  -1493  -4393   -496   -383  -1385  -1747  -1222   3264   -937   -343   -335  -1551   -360  -6227  -1446     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -12719  -6658   -894  -1115   -701  -1378  -8400  -8379 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12704 -13747   -894  -1115  -1876   -459  -8400  -8375 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12704 -13747   -894  -1115   -870  -1143  -8400  -8371 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115  -1413   -679  -8400  -8366 
-     8  -1592   -934  -2227  -1850    -92  -1848  -2494   1094  -6285    557  -1131  -2392  -6585  -1795  -2384  -5619  -2850    806   5050    162     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115  -1413   -679  -8400  -8362 
-     9   -823    989  -2737   1003   -235  -2308   2877  -6170  -2578  -1478  -1601  -2192  -5766   2514  -1305    274    -26    549  -6320   -485    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12712  -8236   -894  -1115  -1413   -679  -8400  -8358 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12707 -13749   -894  -1115   -996  -1004  -8400  -8353 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115  -1413   -679  -8400  -8349 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115   -386  -2090  -8400  -8344 
-    13  -1033   1445  -7341  -6705     36  -1380  -5414    367      0  -1211   -667  -6189  -6593  -1152  -6100   -737   2672   1059   2402   -237    14
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-     -  -1561 -12719   -604   -894  -1115   -701  -1378  -8400  -8340 
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-     -   -310  -2394 -12206   -397  -2056    -71  -4375  -8400  -8335 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12676 -13718   -894  -1115   -123  -3617  -8400  -8331 
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-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8326 
-    17    173   -685    247    212  -6490    -87   -131  -2534   1089  -1679  -5258   -461   1763   -503   1500    -10  -1377  -2148   1395  -5670    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -796 -12719  -1248   -894  -1115   -701  -1378  -8400  -8322 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -11928 -12970   -894  -1115  -1454   -655  -8400  -8317 
-    19   -382  -5709   -490    595    881   -304  -1632   -163    748   -129   -128   -390   1050   -100   -447    172     58   -517  -1171  -1939    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -105 -12265  -3907   -894  -1115   -882  -1129  -8400  -8313 
-    20    530  -5899    -39  -1538  -1038   1154   -375  -1664     53   -884  -1336    273  -2656  -2388   -133   1223   1697  -2121  -6084  -5403    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12445 -13487   -894  -1115  -5228    -39  -8400  -8308 
-    21  -1341  -5882  -1193   -960  -1504    359    246    -87   1596   -823   -340    285    730     -8   1041  -1123   -746    -42    744    509    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11 -12445  -7858   -894  -1115  -1115   -893  -8400  -8304 
-    22   -330  -1058   1228    777   -928   1970  -4185  -6095    369  -1993  -2250    677  -3373    851   -830  -1527   -651  -1743   1736  -5525    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -657 -12571  -1464   -894  -1115  -4454    -67  -8400  -8299 
-    23  -3928   -253   -832  -1978  -5721   2706  -3560  -1353     11  -5416  -4489    693  -2211    563   1226     -4   -362  -2789   -525  -4901    26
-     -   -153   -530    215     29   -395    432    139   -619    213   -473   -729    264    378     43    138    340    129   -367   -302   -252 
-     -   -457  -1932  -7292  -2912   -206  -1696   -532  -8400  -8295 
-    24  -1186  -5669  -1872   -775   1498  -5174    433  -5737   1789  -3721  -1897   1109   -326  -1206   1058  -2350    -84  -1466   2750   1780    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25 -12204  -6211   -894  -1115   -275  -2528  -8400  -8290 
-    25    113    698   -903  -2060  -3453  -5639    471   -292   1301   -187   -425   -360   -191    343    932    411   -474    543   -297    574    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12630 -13672   -894  -1115   -497  -1779  -8400  -8285 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12695 -13737   -894  -1115  -1201   -823  -8400  -8281 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12703 -13745   -894  -1115   -818  -1208  -8400  -8276 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115   -384  -2098  -8400  -8271 
-    29   -287  -4932  -3125  -5965   -185  -1293     53   -199  -5702  -1212  -4129  -1342   -675  -1995   -374   -271   2263   2271  -5374  -5009    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11 -12719  -7936   -894  -1115   -701  -1378  -8400  -8262 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12713 -13755   -894  -1115  -1299   -752  -8400  -8257 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27 -12719  -6019   -894  -1115   -701  -1378  -8400  -8248 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17 -12711  -6904   -894  -1115   -364  -2164  -8400  -8238 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12707 -13749   -894  -1115  -1739   -514  -8400  -8234 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12707 -13749   -894  -1115  -1739   -514  -8400  -8229 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12707 -13749   -894  -1115   -951  -1051  -8400  -8224 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12712 -13754   -894  -1115   -395  -2062  -8400  -8219 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8214 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8209 
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-     -     -5 -12719 -13761   -894  -1115   -701  -1378  -8400  -8205 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -12722 -13764   -894  -1115   -701  -1378  -8400  -7531 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -175 -12707  -3207   -894  -1115  -1927   -440  -8400  -7484 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12065 -13107   -894  -1115   -202  -2939  -8400  -7468 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1012 -12609  -1005   -894  -1115  -2707   -240  -8400  -7443 
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-     -   -149   -470    233     41   -383    397    111   -629    206   -464   -716    269    408     41    106    357    113   -373   -301   -256 
-     -   -123  -3727 -12668  -2753   -232   -743  -1313  -8400  -7435 
-   165   -745    732  -6892  -6262   -750  -6177  -5044   -638  -3232  -1792  -1367  -3221    199  -1139  -1950   1785   2946   -955  -4937  -4593   266
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12362 -13404   -894  -1115   -238  -2716  -8400  -7426 
-   166   -322  -6588  -6322  -5642  -7454  -4139  -5484  -7061  -1661  -3401  -6259  -5708   3978   -780     -2  -1264  -2286  -2716  -7208  -6810   267
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12662 -13704   -894  -1115   -530  -1701  -8400  -7418 
-   167   1055   -280  -6713   -269   1485   -996    637    543  -1046   -820    427   -717  -6471  -1478   -358   -759  -2863    602   1052   2103   268
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12694 -13736   -894  -1115   -958  -1044  -8400  -7409 
-   168    -34  -1728   1000   2766   -728  -2371  -2092  -2450   -113  -3881  -1883  -1088  -5740   1783   -589   -730  -4612  -1830  -1693  -5645   269
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12699 -13741   -894  -1115   -387  -2089  -8400  -7401 
-   169    114   -627  -7319  -2591   1095  -6526  -5397   1121     83    657    437  -6170  -6576  -2100   1723  -1147  -2475   1240    239    603   270
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8400      0 
-//
-HMMER2.0  [2.3.2]
-NAME  zf-CCHC
-ACC   PF00098.15
-DESC  Zinc knuckle
-LENG  18
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  182
-DATE  Tue May 13 14:21:32 2008
-CKSUM 3531
-GA    19.8000 19.8000;
-TC    19.8000 19.8000;
-NC    19.7000 19.7000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -6.952779   0.647275
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -19      *  -6229
-     1   -913    876   -121   -409  -1294    318  -3066    579    526  -1019   -322    160    236    825   1355   -275  -1007    456  -5054  -4381     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -44 -11418 -12460   -894  -1115   -701  -1378  -1019  -5088 
-     2    -24   -988  -1419   -268  -2693    862   -475   -926   1474   -996  -3757    -55  -1148    101    762   -435   1099     44  -4336  -1265     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -45 -11419 -12461   -894  -1115   -701  -1378  -5107  -5045 
-     3  -9552   5878  -9150  -9537  -9669  -8130  -8775 -10782  -9717 -10094 -10074  -9513  -8579  -9603  -9129 -10070  -9755 -10412  -8353  -9679     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -47 -11421 -12464   -894  -1115   -701  -1378  -5107  -5002 
-     4  -2463  -3648  -3632  -2286   2681  -4423    870  -3781  -2184  -1895  -3132   -837  -1910  -1113     53  -2466  -2220  -3613   2900   3579     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -48 -11422 -12464   -894  -1115   -701  -1378  -5107  -4955 
-     5  -1416  -4420  -3232  -1573  -1332  -2403    558  -1184   2100  -2684  -3770   2805  -4365  -1198    930   -379   -452  -1732  -4416     48     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -50 -11424 -12466   -894  -1115   -701  -1378  -5107  -4909 
-     6  -8755   5871  -9072  -9454  -8118  -7963  -8293 -10229  -9567  -9644  -9557  -9141  -8442  -9350  -9000  -9118  -9053  -9786  -7820  -3000     6
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-     -    -51 -11425 -12467   -894  -1115   -701  -1378  -5107  -4859 
-     7  -2444  -4374  -2105  -2120  -4921   3287   -256  -4782    584  -3355  -3761    668  -4335   -253   -737  -2351  -3299  -3315  -4339  -4177     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -53 -11428 -12470   -894  -1115   -701  -1378  -5107  -4809 
-     8   -658  -4895   -851   1465  -5217    -96  -3054  -3238   2285  -4911  -3984  -1094  -4489   2190    471     30  -2445  -2140  -5079  -4396     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -55 -11429 -12472   -894  -1115   -701  -1378  -5107  -4757 
-     9   -712  -4440  -1806   1466   -633  -1548  -1315   -160   -363  -1082   1001   -933   2065  -1793   -142   -432    819   -302  -4473   -746     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -57 -11431 -12474   -894  -1115   -701  -1378  -5107  -4702 
-    10  -3621  -7917   -257   -766  -2799   3663  -5030  -8037  -3067  -7859  -7302  -1529  -6174  -4722  -2416  -5451  -5952  -7471  -8058  -6924    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -60 -11435 -12477   -894  -1115   -701  -1378  -5107  -4647 
-    11  -9856  -8225  -9114  -9499  -9330  -8179   5478 -10798  -9690 -10071 -10090  -9535  -8612  -9585  -9118 -10419  -9988 -10522  -8262  -9210    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -62 -11436 -12478   -894  -1115   -701  -1378  -5107  -4587 
-    12  -3703  -3532  -6027  -5393   1774  -5248  -2191   1429   -354    717   1833  -2455  -5298    579    398  -2082   -829    470   2225   1129    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -65 -11439 -12482   -894  -1115   -701  -1378  -5107  -4527 
-    13   2405  -4466  -3571  -1766  -2533  -1812  -3231  -1681    967  -2690   1010  -3283  -4633    469   -140   1477  -3419   -962  -4758  -4194    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -68 -11442 -12484   -894  -1115   -701  -1378  -5107  -4462 
-    14    466  -4892  -1785  -2120  -1083  -4397  -1037  -1763   1748  -4907  -3981     48  -1842  -1695   2893    306   -581  -1839  -5076  -1979    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -71 -11445 -12487   -894  -1115   -701  -1378  -5107  -4395 
-    15  -1558  -4443   2798   1932  -1194  -2341  -2946  -2873   -635  -4816  -1016    749  -4357   1472  -1620  -1163  -2311  -2885  -4430  -2016    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -75 -11449 -12492   -894  -1115   -701  -1378  -5107  -4326 
-    16  -8641   5869  -9075  -9458  -2879  -7931  -8315 -10103  -9573  -9532  -9450  -9114  -8419  -9344  -9000  -9002  -8953  -9678  -7851  -7886    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -79 -11453 -12495   -894  -1115   -701  -1378  -5107  -4252 
-    17  -1345  -4887   -463  -2725  -1179  -3060   -573  -4952    927  -2822  -1697  -2003   2836   -351   1498   -851   1103  -4507    661   -796    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -83 -11457 -12499   -894  -1115   -701  -1378  -5107  -4174 
-    18    172  -4895  -1008   1064  -5216  -1138    569  -1324   1288  -2109   -325   1475  -4489   1525  -1288    838    -27  -1150  -5078  -4395    18
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -5107      0 
-//

--- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/hmmpfamOut.align.clean_match.path	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-1	blumeria_Grouper_28830_3	2424	2882	RVT_1	242	23	4.1e-39	132	0
-10	blumeria_Grouper_4152_12:NoCat	428	478	DUF1602	23	39	0.0013	5	0
-11	blumeria_Grouper_4152_12:NoCat	382	407	V-ATPase_G	2	10	0.017	2	0
-12	blumeria_Grouper_4152_12:NoCat	136	228	XhoI	202	172	4.3e-05	9	0
-13	blumeria_Grouper_4152_12:NoCat	479	497	DUF1798	40	35	0.011	1	0
-14	blumeria_Grouper_4152_12:NoCat	294	365	DUF881	237	214	0.0052	4	0
-15	blumeria_Grouper_4152_12:NoCat	84	131	LBP_BPI_CETP	209	191	0.012	1	0
-16	blumeria_Grouper_4152_12:NoCat	230	247	SOCS_box	6	1	0.031	2	0
-2	blumeria_Grouper_28830_3	786	1229	rve	169	1	1.4e-23	77	0
-3	blumeria_Grouper_28830_3	4061	4108	zf-CCHC	18	3	1.7e-09	29	0
-4	blumeria_Grouper_590_20:NoCat	271	324	DUF234	5	22	0.0047	3	0
-5	blumeria_Grouper_590_20:NoCat	331	357	DUF1414	1	9	0.02	2	0
-6	blumeria_Grouper_590_20:NoCat	90	113	CPW_WPC	1	9	0.024	1	0
-7	blumeria_Grouper_590_20:NoCat	119	148	DUF46	182	173	0.00034	6	0
-8	blumeria_Grouper_4152_12:NoCat	337	381	Peptidase_S29	1	15	0.0034	4	0
-9	blumeria_Grouper_4152_12:NoCat	62	79	Toxin_18	50	55	0.014	4	0

--- a/commons/pyRepetUnit/hmmer/tests/TestAcceptanceHmmpfamAndParse2alignInparallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-import os
-import sys
-import unittest
-import pyRepet.seq.fastaDB
-from sets import Set
-import ConfigParser 
-from pyRepet.launcher.programLauncher import *
-from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
-from pyRepet.sql.RepetJobMySQL import *
-from pyRepet.util.file.FileUtils import *
-import commons.pyRepetUnit.dbSplit.LauncherDbSplit
-import commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align
-
-CONFIG_FILE = "datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg"
-CURRENT_DIR = os.getcwd()
-
-class TestAcceptanceHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase):
-
-    def setUp(self):
-        self._config = ConfigParser.ConfigParser()
-        self._config.readfp( open(CONFIG_FILE) )
-        self._batchFilesList = []
-        self._batchFilesBatchesList = []
-        self._inputFile = self._config.get("dbSplit_config", "input_file")
-        self._programLauncherInstance = programLauncher()   
-        self._outputFileNotInparallel = self._config.get("hmmer_config", "output_file")
-        self._hmmpfamOutput2align = commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align.HmmpfamOutput2align()
-        os.chdir(CURRENT_DIR)
-
-    def _launchHmmpfamAndParseNotInParallel(self):
-        self._programLauncherInstance.reset(self._inputFile)
-        self._programLauncherInstance.setOutputFileName(self._outputFileNotInparallel)
-        self._programLauncherInstance.launchHmmpfam(evalFilter=self._config.get("profil_search", "Evalue"), inputFormat=self._config.get("profil_search", "InputFormat"), profilDatabank=self._config.get("profil_search", "ProfilDatabank"))
-        self._hmmpfamOutput2align.setInputFile(self._outputFileNotInparallel)
-        self._outputFileParsingNotInparallel = self._config.get("hmmpfam2align_config", "output_file")
-        self._hmmpfamOutput2align.setOutputFile(self._outputFileParsingNotInparallel)
-        self._hmmpfamOutput2align.run()
-
-
-    def _countNblinesInAllResultsFilesInParallel(self, fileUtils):
-        result_dir = self._config.get("hmmer_config", "result_dir")
-        dirFiles = fileUtils.listFilesInDir(result_dir)
-        listPath = []
-        for file in dirFiles:
-            listPath.append(file)
-        
-        nbLinesInAlignFilesInparallel = fileUtils.countLinesInFiles(listPath)
-        return nbLinesInAlignFilesInparallel
-
-
-    def _launchHmmpfamAndParseInParallel(self):
-        user = self._config.get("db_config", "user")
-        host = self._config.get("db_config", "host")
-        passwd = self._config.get("db_config", "passwd")
-        dbName = self._config.get("db_config", "dbname")
-        jobDb = RepetJob(user, host, passwd, dbName)
-        params = {"param": "--informat " + self._config.get("profil_search", "InputFormat") + " -E " + self._config.get("profil_search", "Evalue"), "profilDB": self._config.get("profil_search", "ProfilDatabank"), "outputDir": self._config.get("hmmer_config", "result_dir"), "query": self._config.get("hmmer_config", "query_dir"), "job_table": "jobs", "queue": self._config.get("sge_config", "queue"), "groupid": self._config.get("sge_config", "groupid"), "tmpDir": self._config.get("hmmer_config", "tmp_dir"), "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"), "cDir" : "."}
-        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
-        self.hmmpfamAndParse2align.run()
-
-
-    def _splitInputFile(self, dbSplit):
-        dbSplit.setInFileName(self._inputFile)
-        dbSplit.setIsNewDir(True)
-        dbSplit.setNbSequences(3)
-        dbSplit.run()
-
-    def testAcceptanceHmmpfamAndParse2alignHasRunInparallel (self):
-        
-        dbSplit = commons.pyRepetUnit.dbSplit.LauncherDbSplit.LauncherDbSplit()
-        self._splitInputFile(dbSplit)         
-        self._launchHmmpfamAndParseInParallel()
-        fileUtils = FileUtils()
-        nbLinesInAlignFilesInparallel = self._countNblinesInAllResultsFilesInParallel(fileUtils)
-        dbSplit.clean()
-        self._launchHmmpfamAndParseNotInParallel()
-        nbLinesInAlignFileNotInparallel = fileUtils.countLinesInAFile(self._outputFileParsingNotInparallel)
-        self.assertEqual(nbLinesInAlignFilesInparallel,nbLinesInAlignFileNotInparallel)
-        self._clean()
-
-    def _clean(self):
-        
-        dirToClean = self._config.get( "hmmer_config", "tmp_dir" )
-        os.system("rm  " + dirToClean + "/*")
-        dirToClean = self._config.get( "hmmer_config", "result_dir" )
-        os.system("rm  " + dirToClean + "/*")
-        os.system("rm  HmmpfamJob*.e*")
-        os.system("rm  HmmpfamJob*.o*")
-        os.remove(self._outputFileNotInparallel)
-        os.remove(self._outputFileParsingNotInparallel)
-
-
-if __name__ == "__main__":
-        unittest.main()

--- a/commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamAndParse2alignLauncherInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-import os
-import sys
-import unittest
-from sets import Set
-import ConfigParser 
-from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
-from pyRepet.sql.RepetJobMySQL import *
-from pyRepet.util.file.FileUtils import *
-
-CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg"
-CURRENT_DIR = os.getcwd()
-
-class TestFunctionalHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase):
-    
-    def setUp(self):
-        self._config = ConfigParser.ConfigParser()
-        self._config.readfp( open(CONFIG_FILE) )
-        os.chdir(CURRENT_DIR)
-
-    def testHmmpfamAndParse2alignHasRunInparallel (self):
-        user = self._config.get( "db_config","user" )
-        host = self._config.get( "db_config","host" )
-        passwd = self._config.get( "db_config","passwd" )
-        dbName = self._config.get( "db_config","dbname" )
-        jobDb = RepetJob(user , host , passwd , dbName)
-        params = {"param":"--informat FASTA -E 10", 
-                  "profilDB": self._config.get("profil_search", "ProfilDatabank"), 
-                  "outputDir": self._config.get("hmmer_config", "result_dir"),
-                  "query": self._config.get("hmmer_config", "query_dir"),
-                  "job_table":"jobs", 
-                  "queue" : self._config.get("sge_config", "queue"), 
-                  "groupid" : self._config.get("sge_config", "groupid"),
-                  "tmpDir": self._config.get("hmmer_config", "tmp_dir"),
-                  "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"),
-                  "cDir" : "."}
-        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
-        self.hmmpfamAndParse2align.run()
-        fileUtils = FileUtils()
-        dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir"))
-        dirSet = Set(dirFiles)
-        alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut.align", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut.align"])
-        self.assertTrue( alignFileSet.issubset(dirSet))
-        self._clean()
-
-    def _clean(self):
-        
-        dirToClean = self._config.get( "hmmer_config", "tmp_dir" )
-        os.system("rm  " + dirToClean + "/*")
-        dirToClean = self._config.get( "hmmer_config", "result_dir" )
-        os.system("rm  " + dirToClean + "/*")
-        os.system("rm  HmmpfamJob*.e*")
-        os.system("rm  HmmpfamJob*.o*")
-
-
-if __name__ == "__main__":
-        unittest.main()

--- a/commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-import os
-import sys
-import unittest
-from sets import Set
-import ConfigParser 
-from pyRepet.sql.RepetJobMySQL import *
-from pyRepet.util.file.FileUtils import *
-import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
-
-CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg"
-CURRENT_DIR = os.getcwd()
-
-class TestFunctionalHmmpfamClusterComponent(unittest.TestCase):
-    
-    def setUp(self):
-        os.chdir(CURRENT_DIR)
-        self._config = ConfigParser.ConfigParser()
-        self._config.readfp( open(CONFIG_FILE) )
-        self._hmmer = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
-
-    def testHmmpfamHasRunInparallel (self):
-        user = self._config.get( "db_config","user" )
-        host = self._config.get( "db_config","host" )
-        passwd = self._config.get( "db_config","passwd" )
-        dbName = self._config.get( "db_config","dbname" )
-        jobDb = RepetJob(user , host , passwd , dbName)
-        self._hmmer.setJobDb(jobDb)
-        self._hmmer.loadConfig(self._config)
-        self._hmmer.run()
-        fileUtils = FileUtils()
-        dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir"))
-        dirSet = Set(dirFiles)
-        alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut"])
-        self.assertTrue(alignFileSet.issubset(dirSet))
-        self._hmmer.clean()
-        
-if __name__ == "__main__":
-        unittest.main()

--- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-import unittest
-import os
-import sys
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
-from pyRepet.sql.RepetJobMySQL import *
-
-class TestHmmpfamAndParse2alignLauncher(unittest.TestCase):
-    
-    def testConstructor(self):
-        
-        params = {
-                  "query" : "toto",
-                  "job_table":"fakeTable", 
-                  "queue" : "fakeQueue", 
-                  "groupid" : "fakeId",
-                  "tmpDir" : "fakeDir",
-                  "cDir" : "."
-        }
-      
-        hmmpfam = HmmpfamAndParse2alignLauncher("toto", params)
-        
-        self.assertEquals("toto", hmmpfam.query)
-        self.assertEquals("fakeTable", hmmpfam.job_table)
-        self.assertEquals("fakeQueue", hmmpfam.queue)
-        self.assertEquals("fakeId", hmmpfam.groupid)
-        self.assertEquals("fakeDir", hmmpfam.tmpdir)
-       
-       
-    def testCmd_start(self):
-        
-        fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
-        expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut"
-
-        user = "oinizan"
-        host = "pisano"
-        passwd = "oinizan"
-        dbName = "repet_oinizan"
-        jobDb = RepetJob(user , host , passwd , dbName)
-        params = {"param":"--informat FASTA -E 10",
-                  "query" : "toto",
-                  "job_table":"fake", 
-                  "queue" : "fake", 
-                  "groupid" : "fake",
-                  "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms",
-                  "tmpDir" : "fakeDir", 
-                  "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas",
-                  "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", 
-                  "cDir" : "."
-        }
-        self.hmmpfam = HmmpfamAndParse2alignLauncher(jobDb, params)
-        self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName ))    
-        
-        
-    def testCmd_finish(self):  
-        
-        fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
-        user = "oinizan"
-        host = "pisano"
-        passwd = "oinizan"
-        dbName = "repet_oinizan"
-        jobDb = RepetJob(user , host , passwd , dbName)
-        params = {"param":"--informat FASTA -E 10",
-                  "query" : "toto",
-                  "job_table":"fake", 
-                  "queue" : "fake", 
-                  "groupid" : "fake",
-                  "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms",
-                  "tmpDir" : "fakeDir", 
-                  "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas",
-                  "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py",
-                  "cDir" : "."
-        }
-        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
-        expectedCmdFinish = "os.system( \"/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py -i /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut -o /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut.align -c\" )\n"
-        self.assertEquals(expectedCmdFinish, self.hmmpfamAndParse2align.cmd_finish ( fullInFileName ))
-
-
-
-if __name__ == "__main__":                 
-	unittest.main()
-

--- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-import os
-import unittest
-import ConfigParser
-import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
-from pyRepet.sql.RepetJobMySQL import *
-from pyRepet.util.file.FileUtils import *
-
-class TestHmmpfamClusterComponent(unittest.TestCase):
-
-     def setUp(self):
-         
-        self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
-        
-     def testLoadConfig(self):
-        config = open("tmpConfig.cfg", "w")
-        config.write("[profil_search]\n")
-        config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n")
-        config.write("[hmmer_config]\n")
-        config.write("result_dir: /repet_results\n")
-        config.write("query_dir: /repet_datas/hmmer_in_parallel\n")
-        config.write("tmp_dir: /repet_tmp\n")
-        config.write("[sge_config]\n")
-        config.write("queue: main.q\n")
-        config.write("groupid: fake\n") 
-        config.close()
-        config = ConfigParser.ConfigParser()
-        config.readfp( open("tmpConfig.cfg") )
-        self.component.loadConfig(config)
-        self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() )
-        self.assertEquals( "/repet_results", self.component.getResultDir() )
-        self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() )
-        self.assertEquals( "/repet_tmp", self.component.getTmpDir() )
-        self.assertEquals( "main.q", self.component.getSGEQueue() )
-        self.assertEquals( "fake", self.component.getSGEGroupId() )
-        os.system("rm tmpConfig.cfg") 
-        
-     def testClean (self):
-        fileUtils = FileUtils() 
-        if (fileUtils.isRessourceExists("dummyTmpDir")):
-             os.system("rm -r dummyTmpDir")
-         
-        if (fileUtils.isRessourceExists("dummyResultDir")):
-             os.system("rm -r dummyResultDir") 
-         
-        os.mkdir("dummyTmpDir")
-        os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")
-        os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py")
-        os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py")
-        os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py")
-        
-        os.mkdir("dummyResultDir")
-        os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut")
-        os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut")
-        os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut")
-        os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut")
-
-        self.component.setTmpDir("dummyTmpDir")
-        self.component.setResultDir("dummyResultDir")
-        
-        self.component.clean()
-        
-        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut"))
-        self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut"))
-        
-        os.system("rm -r dummyTmpDir")
-        os.system("rm -r dummyResultDir")
-       
-
-if __name__ == "__main__":
-	unittest.main() 

--- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-import unittest
-import os
-import sys
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-from pyRepet.launcher.Launcher import HmmpfamLauncher
-from pyRepet.sql.RepetJobMySQL import *
-
-class TestHmmpfamLauncher(unittest.TestCase):
-    
-    def testConstructor(self):
-        
-        params = {
-                  "query" : "toto",
-                  "job_table":"fakeTable", 
-                  "queue" : "fakeQueue", 
-                  "groupid" : "fakeId",
-                  "tmpDir" : "fakeDir",
-                  "cDir" : "."
-        }
-      
-        hmmpfam = HmmpfamLauncher("toto", params)
-        
-        self.assertEquals("toto", hmmpfam.query)
-        self.assertEquals("fakeTable", hmmpfam.job_table)
-        self.assertEquals("fakeQueue", hmmpfam.queue)
-        self.assertEquals("fakeId", hmmpfam.groupid)
-        self.assertEquals("fakeDir", hmmpfam.tmpdir)
-       
-       
-    def testCmd_start(self):
-        
-        fullInFileName = "/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
-        expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut"
-        user = "oinizan"
-        host = "pisano"
-        passwd = "oinizan"
-        dbName = "repet_oinizan"
-        jobDb = RepetJob(user , host , passwd , dbName)
-        params = {"param":"--informat FASTA -E 10",
-                  "query" : "toto",
-                  "job_table":"fake", 
-                  "queue" : "fake", 
-                  "groupid" : "fake",
-                  "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms",
-                  "tmpDir" : "fakeDir", 
-                  "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", 
-                  "cDir" : "."}
-        self.hmmpfam = HmmpfamLauncher(jobDb, params)
-        self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName ))    
-        
-    def testCmd_finish(self):  
-        
-        fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
-        expectedCmdFinish = ""
-
-        user = "oinizan"
-        host = "pisano"
-        passwd = "oinizan"
-        dbName = "repet_oinizan"
-        jobDb = RepetJob(user , host , passwd , dbName)
-        params = {"param":"--informat FASTA -E 10",
-                  "query" : "toto",
-                  "job_table":"fake", 
-                  "queue" : "fake", 
-                  "groupid" : "fake",
-                  "tmpDir" : "fakeDir",
-                  "cDir" : "." 
-                  }
-        self.hmmpfam = HmmpfamLauncher(jobDb, params)
-        self.assertEquals(expectedCmdFinish, self.hmmpfam.cmd_finish ( fullInFileName ))
-
-
-if __name__ == "__main__":                 
-	unittest.main()
-

--- a/commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.hmmer.LaunchPreProcessHmmpfamPostProcessNotInParallel import *
-from pyRepet.util.file.FileUtils import *
-import ConfigParser 
-
-if (not os.environ.has_key("REPET_PATH")):
-    print "*** Error: no environment variable REPET_PATH"
-    exit =1 
-          
-if (not os.environ.has_key("PYTHONPATH")):
-    print "*** Error: no environment variable PYTHONPATH"
-    exit =1
-    
-if (exit == 1):    
-    sys.exit(1)
-
-CONFIG_FILE = "datas/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg"
-CURRENT_DIR = os.getcwd()
-
-class TestLaunchPreProcessHmmpfamPostProcessNotInParallel(unittest.TestCase):
-  
-    def setUp( self ):
-        os.chdir(CURRENT_DIR)
-        self._LaunchPreProcessHmmpfamPostProcess = LaunchPreProcessHmmpfamPostProcessNotInParallel()
-        self._configFile = CONFIG_FILE
-        config = ConfigParser.ConfigParser()
-        config.readfp(open(self._configFile))
-        self._InputFile = config.get("hmmer_config", "input_file")
-        self._OutputFile = config.get("hmmer_config", "output_file")        
-        self.fileUtils = FileUtils()
-        
-    def testRun(self):
-        #Normal launch
-        self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile )
-        self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( self._OutputFile )
-        self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile )
-        self._LaunchPreProcessHmmpfamPostProcess.run()
-        self.assertTrue(self.fileUtils.isRessourceExists(self._OutputFile))  
-        self.assertFalse(self.fileUtils.isFileEmpty(self._OutputFile)) 
-        os.system("rm " + self._OutputFile)
-        #without config file
-        configFile = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/configdummy.cfg"
-        self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( configFile )
-        self._LaunchPreProcessHmmpfamPostProcess.run()
-        self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) 
-        #without input file
-        InputFile = ""
-        self._LaunchPreProcessHmmpfamPostProcess.setInputFile( InputFile )
-        self._LaunchPreProcessHmmpfamPostProcess.run()
-        self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile))
-        #without output file
-        self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile )
-        self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile )
-        OutputFile = ""
-        self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( OutputFile )
-        self._LaunchPreProcessHmmpfamPostProcess.run()
-        self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile))
-        
-        
-        
-if __name__ == "__main__":
-        unittest.main()        

--- a/commons/pyRepetUnit/hmmer/tests/TestProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-import os
-import unittest
-from pyRepet.launcher.programLauncher import *
-from pyRepet.util.file.FileUtils import *
-import ConfigParser 
-
-if (not os.environ.has_key("REPET_PATH")):
-    print "*** Error: no environment variable REPET_PATH"
-    exit =1 
-          
-if (not os.environ.has_key("PYTHONPATH")):
-    print "*** Error: no environment variable PYTHONPATH"
-    exit =1
-    
-if (exit == 1):    
-    sys.exit(1)
-
-CONFIG_FILE = "datas/config.cfg"
-CURRENT_DIR = os.getcwd()
-
-class TestProgramLauncher(unittest.TestCase):
-  
-    def setUp(self):
-        os.chdir(CURRENT_DIR)
-        self._programLauncherInstance = programLauncher()
-        self._configFile = CONFIG_FILE
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(self._configFile) )
-        self._configFile = CONFIG_FILE
-        config = ConfigParser.ConfigParser()
-        config.readfp(open(self._configFile))
-        self._inputFile = config.get("hmmer_config", "input_file")
-        self._outputFile = config.get("hmmer_config", "output_file")
-        self.fileUtils = FileUtils()
-    
-    def testLaunchHmmpfam(self):
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(self._configFile) )
-        self._programLauncherInstance.reset( self._inputFile )
-        self._programLauncherInstance.setOutputFileName( self._outputFile )
-        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
-                              inputFormat=config.get("profil_search","InputFormat"),
-                              profilDatabank=config.get("profil_search","ProfilDatabank"))        
-        self.assertTrue(self.fileUtils.isRessourceExists(self._outputFile))  
-        self.assertFalse(self.fileUtils.isFileEmpty(self._outputFile))        
-        os.system( "rm " + self._outputFile)
-        self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa2.fa"
-        self._programLauncherInstance.reset( self._inputFile )
-        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
-                              inputFormat=config.get("profil_search","InputFormat"),
-                              profilDatabank=config.get("profil_search","ProfilDatabank"))
-        self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
-        #No output file
-        self._outputFile = ""
-        self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa.fa"
-        self._programLauncherInstance.reset( self._inputFile )
-        self._programLauncherInstance.setOutputFileName( self._outputFile )
-        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
-                              inputFormat=config.get("profil_search","InputFormat"),
-                              profilDatabank=config.get("profil_search","ProfilDatabank"))
-        self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
-        os.chdir(CURRENT_DIR)
-    
-if __name__ == "__main__":                 
-    unittest.main()

--- a/commons/pyRepetUnit/hmmer/tests/datas/Outputhmmpfam	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,148 +0,0 @@
-hmmpfam - search one or more sequences against HMM database
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-HMM file:                 myhmms
-Sequence file:            7LES_DROME
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Query sequence: 7LES_DROME
-Accession:      P13368
-Description:    SEVENLESS PROTEIN (EC 2.7.1.112).
-
-Scores for sequence family classification (score includes all domains):
-Model    Description                                    Score    E-value  N 
--------- -----------                                    -----    ------- ---
-pkinase  Protein kinase domain                          314.6      6e-95   1
-fn3      Fibronectin type III domain                    176.6      2e-53   6
-rrm                                                     -40.4       0.72   1
-
-Parsed for domains:
-Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------- ------- ----- -----    ----- -----      -----  -------
-fn3        1/6     437   522 ..     1    84 []    48.3  8.8e-15
-fn3        2/6     825   914 ..     1    84 []    13.4  2.2e-06
-fn3        3/6    1292  1389 ..     1    84 []    15.9  1.2e-06
-fn3        4/6    1799  1891 ..     1    84 []    63.5  2.3e-19
-fn3        5/6    1899  1978 ..     1    84 []    15.2  1.5e-06
-fn3        6/6    1993  2107 ..     1    84 []    20.3  4.3e-07
-pkinase    1/1    2209  2483 ..     1   294 []   314.6    6e-95
-rrm        1/1    2223  2284 ..     1    77 []   -40.4     0.72
-
-Alignments of top-scoring domains:
-fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 8.8e-15
-                CS    C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
-                   *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
-                      P saP   + +++ ++ l ++W p +  ngpi+gY++++ +++ g+ 
-  7LES_DROME   437    PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482  
-
-                CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                   + e+ vp    sy+++ L++gt+Y++ +  +n +G+Gp     
-  7LES_DROME   483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA    522  
-
-fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 2.2e-06
-                CS    CCCCCEEEEEECCTTCCEEEEECCC       CCCCCCCEEEEE.EC
-                   *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
-                       ++P  l++   ++  + +sW+ p++++ ++ + +   +Ye+++  +
-  7LES_DROME   825    GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869  
-
-                CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC  CCCC   
-                   knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*
-                   + +++ ++++++ g+   + l+ L+P+  Y++rV+A+n +G++G+++   
-  7LES_DROME   870 VASQSAFSIRnIRGPI--FGLQRLQPDNLYQLRVRAINVDGepGEWT    914  
-
-fn3: domain 3 of 6, from 1292 to 1389: score 15.9, E = 1.2e-06
-                CS    CCCCCEEEE      EEC  CTTCCEEEEECCC    CCCCCCCEEE
-                   *->PsaPtnltv......tdv..tstsltlsWsppt....gngpitgYev
-                      Ps+P++l+v  ++  t++++   s++l+W++p+++++       Y +
-  7LES_DROME  1292    PSQPRRLRVfverlaTALqeANVSAVLRWDAPEqgqeAPMQALEYHI 1338 
-
-                CS EE.ECCCCCCCCCCEEECCCC CECECCEEEEECCCCEEEEEECCC    
-                   tyRqpknggewneltvpgttt.sytltgLkPgteYevrVqAvnggG....
-                   ++ +   g e +e    +++  ++ ++ L+P+ +Y+++V A+ ++++   
-  7LES_DROME  1339 SC-W--VGSELHEELRLNQSAlEARVEHLQPDQTYHFQVEARVAATgaaa 1385 
-
-                CS CCCC   
-                   GpeS<-*
-                   G++S   
-  7LES_DROME  1386 GAAS    1389 
-
-fn3: domain 4 of 6, from 1799 to 1891: score 63.5, E = 2.3e-19
-                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC 
-                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
-                      Ps+P+n++v+ +++ +l +sW pp++ +++  +Y++++ q++ +ge+
-  7LES_DROME  1799    PSPPRNFSVRVLSPRELEVSWLPPEqLRSESVYYTLHW-QQELDGEn 1844 
-
-                CS        CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   .......wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                    +++++ + + +   t+ ++ ltg kPg+ Y+++VqA+ + +++  S   
-  7LES_DROME  1845 vqdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTkSNSS    1891 
-
-fn3: domain 5 of 6, from 1899 to 1978: score 15.2, E = 1.5e-06
-                CS    CCCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCCC
-                   *->PsaPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggewn
-                        +   l+  +++++sl+l+W       p+ + ++++R   ++ e  
-  7LES_DROME  1899    FAELPELQLLELGPYSLSLTWAGT--PDPLGSLQLECR---SSAEQL 1940 
-
-                CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
-                   eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
-                   +++v g+ t ++++ L+P t+Y+ r+    ++++G++    
-  7LES_DROME  1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL    1978 
-
-fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 4.3e-07
-                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC 
-                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
-                      Ps+P+ ++ + + +  ++++W++++++++pi  Y+++   ++++  +
-  7LES_DROME  1993    PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038 
-
-                CS                            CCCCEEECCCC CECECCEEEEE
-                   ...........................wneltvpgttt.sytltgLkPgt
-                   +++++++++++++ ++ +  +++   ++++l+  +tt  s++++ L   +
-  7LES_DROME  2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088 
-
-                CS CCCCEEEEEE CCC CCCC   
-                   eYevrVqAvn.ggG.GpeS<-*
-                      +rV+A++ ++G Gp+S   
-  7LES_DROME  2089 LLLFRVRARSlEHGwGPYS    2107 
-
-pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 6e-95
-                   *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
-                      ++ll+ lG+G+fG+Vy++++k+++++  ++VA+K l+k+++++ e  
-  7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253 
-
-                   flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
-                   +l E+q++ +++H+NIvrl g++  + +++ l+mE+me GdL++ylr+ +
-  7LES_DROME  2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302 
-
-                   ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
-                    +++++++++  ls  e++ ++ ++++G +YL+++++vHRDL+ +N+L++
-  7LES_DROME  2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352 
-
-                   en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
-                   e +++++++ tvKi+DFGLAr++++++++++ + +  p+++m+PE  l +
-  7LES_DROME  2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401 
-
-                   rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
-                     +++++DvW++Gv+++E+lt g                         ++
-  7LES_DROME  2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426 
-
-                   PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
-                   P+         ++ +e+++++k+ g+rl +p+ c e l++Ll  c++ DP
-  7LES_DROME  2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468 
-
-                   skRpGsatakeilnhpwf<-*
-                   ++Rp   +++ + n +     
-  7LES_DROME  2469 WERP---SFRRCYNTLHA    2483 
-
-rrm: domain 1 of 1, from 2223 to 2284: score -40.4, E = 0.72
-                   *->lfVgNL.......ppdvteedLkdlFskfGpi.vsikivkDhkektk
-                      ++ g L+++++++p+ v  + L++  s+f +   +++++ +      
-  7LES_DROME  2223    VYEGQLktedseePQRVAIKSLRKGASEFAELlQEAQLMSN------ 2263 
-
-                   etgkskGfaFVeFeseedAekAlealnGkelggrklrv<-*
-                               F+     e+ ++ l G+ ++   +     
-  7LES_DROME  2264 ------------FKH----ENIVR-LVGICFDTESISL    2284 
-
-//

--- a/commons/pyRepetUnit/hmmer/tests/datas/config.cfg	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-[profil_search]
-
-Evalue: 10
-InputFormat: FASTA
-ProfilDatabank: ./datas/myhmms
-
-[hmmer_config]
-input_file: ./datas/test_input_aa.fa
-output_file: ./datas/hmmpfam_output
-        
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/tests/datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-[db_config]
-user: oinizan
-host: pisano
-passwd: oinizan
-dbname:repet_oinizan
-
-[profil_search]
-Evalue: 10
-InputFormat: FASTA
-ProfilDatabank: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/datas/myhmms
-
-[hmmer_config]
-output_file: ./datas/hmmpfam_output
-result_dir: /home/oinizan/repet_integration/repet_results
-query_dir: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/batches
-tmp_dir: /home/oinizan/repet_integration/repet_tmp
-
-[sge_config]
-queue: main.q
-groupid: fake
-
-[parse_config]
-scriptToLaunch: /home/oinizan/repet_integration/repet_pipe/repet_base/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py
-
-[dbSplit_config]
-input_file: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/datas/test_input_aa.fa
-
-[hmmpfam2align_config]
-output_file: ./datas/hmmpfam_outputNotInParallel.align

--- a/commons/pyRepetUnit/hmmer/tests/datas/configTestFunctionalHmmpfamLauncherInparallel.cfg	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-[db_config]
-user: oinizan
-host: pisano
-passwd: oinizan
-dbname:repet_oinizan
-
-[profil_search]
-Evalue: 10
-InputFormat: FASTA
-ProfilDatabank: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/datas/myhmms
-
-[hmmer_config]
-input_file: ./datas/test_input_nt.fa
-output_file: ./datas/hmmpfam_output.align
-result_dir: /home/oinizan/repet_integration/repet_results
-query_dir: /home/oinizan/repet_integration/repet_datas/hmmer_in_parallel
-tmp_dir: /home/oinizan/repet_integration/repet_tmp
-
-[sge_config]
-queue: main.q
-groupid: fake
-
-[parse_config]
-scriptToLaunch: /home/oinizan/repet_integration/repet_pipe/repet_base/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py

--- a/commons/pyRepetUnit/hmmer/tests/datas/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-[profil_search]
-
-Evalue: 10
-InputFormat: FASTA
-ProfilDatabank: ./datas/myhmms
-
-[hmmer_config]
-input_file: ./datas/test_input_nt.fa
-output_file: ./hmmpfam_output.align
\ No newline at end of file

--- a/commons/pyRepetUnit/hmmer/tests/datas/myhmms	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1433 +0,0 @@
-HMMER2.0  [2.3.2]
-NAME  rrm
-LENG  77
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -A myhmms rrm.sto
-COM   hmmcalibrate myhmms
-NSEQ  90
-DATE  Thu Jan  8 17:50:18 2009
-CKSUM 8325
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -45.953121   0.233439
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -16      *  -6492
-     1  -1084    390  -8597  -8255  -5793  -8424  -8268   2395  -8202   2081  -1197  -8080  -8115  -8020  -8297  -7789  -5911   1827  -7525  -7140     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378    -16      * 
-     2  -2140  -3785  -6293  -2251   3226  -2495   -727   -638  -2421   -545   -675  -5146  -5554  -4879  -1183  -2536  -1928    267     76   3171     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     3  -2542    458  -8584  -8273  -6055  -8452  -8531   2304  -8255   -324    101  -8104  -8170  -8221  -8440  -7840  -5878   3145  -7857  -7333     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     4  -1505  -5144  -1922   -558  -1842   2472  -3303  -2213   1099  -5160  -4233    372  -4738   -530   1147    168    498  -4766  -5327  -1476     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     5  -3724  -5184    300  -3013  -1655   1803  -3353  -5245  -1569  -2686  -4276   3495  -1963  -1331  -1054  -1472  -3664  -4803  -5369     -2     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     6  -1569  -6106  -8967  -8363    555  -8531  -7279    654  -8092   2953    -94  -8220  -7908  -1643  -7682  -7771  -6460    -59  -6191  -6284     6
-     -   -151   -504    230     45   -380    399    101   -621    211   -470   -713    278    399     48     91    360    113   -364   -299   -254 
-     -   -178  -3113 -12684  -1600   -578   -701  -1378      *      * 
-     7   -409  -5130   -215  -2987  -1709   -956    690  -5188   -395  -5144  -4224    729   3054  -2862  -3409    354   1293  -1381  -5321  -4644    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     8  -3674  -5118  -1004    639    420  -4652    176  -2050    404  -1039   -935     16   1755    168    147   -275    198  -1472   1889   1977    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     9   -408  -5134   2415   1299   -950    -66   -767  -1296  -2889  -1843  -4224   1084   -968  -1439  -1854    540   -314  -2304  -5320    -60    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    10    586   1804  -6294   -631  -1627  -1671  -4374   1029  -2223   -162   1172  -5147  -5554  -1870  -5058  -2327   1741   1687  -4242    687    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    11  -2134  -5144    845  -1187  -1652  -1667  -3303  -5216   -513   -801  -4233   1026  -1873   -543   -619    575   2956  -4766  -5327  -4644    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    12  -3671  -5144   1091   2489  -1652  -2234   -613  -2170    736  -1364  -4233   -448   -197   1030   -116   -639  -1349  -4766   1408   -424    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    13   -139  -5144   1642   2051  -5465  -1429    503  -5216    530  -3223  -1447   -672  -4738   1875     73    318  -2111  -4766  -5327  -4644    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    14   -122  -5142   2117   1851  -5462  -1085   -933  -2288     33   -526   -556   -741  -4738   1222  -3392   -175    -13  -2228   -370  -4643    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    15  -7175  -6527  -9596  -9028   -232  -9481  -8154   1635  -8870   2831   -816  -9215  -8388  -7557  -8326  -8917  -7014    705  -6536  -6798    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -11642  -6295   -894  -1115   -701  -1378      *      * 
-    16   -654  -5013  -1860    729    726  -2316   -688  -1184   1801   -277  -4115   -790  -4754  -2885   1825   -463  -1784   -442   -227   1362    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11624 -12666   -894  -1115  -1520   -619      *      * 
-    17    156  -5127   2136   1476  -5448  -1504  -3286  -5199    301  -1955   -539   -894  -1057   1509    524   -467    301  -4749  -5310  -4627    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11624 -12666   -894  -1115   -355  -2197      *      * 
-    18    -49  -3785  -6295   -490   1591  -5504    920   1218  -2312   1810     49  -5147  -5554  -4880  -2068  -1575   -764   -207    -54   1201    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    19  -1516    962  -6738  -6118   4230  -2323  -4741  -1819  -5718   -295    162  -5595  -5977  -5294  -5502  -5054  -4347  -3561  -4499   -386    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    20     66  -5142  -3519    977  -5463   1170  -3304  -2365   1047  -2653  -4232   -150  -4738    557    447   1868  -1288  -2163  -5326  -1696    26
-     -   -147   -500    232     42   -381    398    105   -627    212   -464   -721    275    393     45     95    360    117   -367   -295   -250 
-     -    -19  -6287 -12684  -2206   -352   -701  -1378      *      * 
-    21  -1055  -5144    363    870  -1814   -295     89  -2404   1817  -5160  -4233    811   1390   1737  -1607   -671   -664  -2375  -5327  -1696    32
-     -   -149   -500    232     45   -377    398    105   -627    212   -467   -721    278    393     45     98    358    117   -370   -295   -250 
-     -    -90  -4053 -12684    -35  -5398   -701  -1378      *      * 
-    22   -394   1434  -6258  -2307   2972  -2526     19    850  -2195  -1152  -2991  -1854  -5549   -851  -5045  -2352  -3896   -124   -189   2914    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    23   -684  -7735  -1742   -712  -8352   3518  -5400  -8353  -5878  -8206  -7641   -311    -59  -5105  -6910  -1500  -6163  -7684  -8410  -7291    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    24  -1107  -5144    202    908  -1788     -8    -90  -1263   1342  -1905  -4233   -889   1908    171     58    -98   -246   -190  -5327  -4644    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    25  -3958   -549  -6303  -1346    278  -5505  -4377   2725  -2224   -925   -752  -5151  -2076  -4885  -5062  -2366  -1362   2524  -4242   -488    37
-     -   -147   -500    232     45   -381    398    105   -627    212   -466   -721    275    396     45     95    359    117   -370   -295   -250 
-     -   -170  -4711  -3774   -436  -1938   -701  -1378      *      * 
-    26  -1474   -441  -3586   1371  -4982  -2413  -3303    -26   1319    143     14    194  -4719   -534   -232   -509    586   1466  -5027  -4420    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -11533  -6292   -894  -1115   -978  -1022      *      * 
-    27   -251  -5076   1198   1096  -5397     75    696  -1292   -903  -5092  -4165   1381  -4669  -1297    629   1609   -628  -2391  -5259   -408    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11569 -12611   -894  -1115   -146  -3377      *      * 
-    28   1071   1843  -6303  -5667    723  -2647  -4376   2229  -2340    234    705  -1807  -5555  -4884  -5062  -1098  -1942   1556  -4241  -1380    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    29  -3674  -5121    815    520   -935  -4651   -961  -1319   1431   -350   -888    798  -4744    589   1471   -312     16    -53   -490     25    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    30  -1650  -3784  -6302  -5666   -659  -5505   -883   2172  -2226   1327   2112  -5150  -2048  -4884  -1866  -1552  -1875   1962  -4242  -3899    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    31  -1062   1015  -6187  -2355    288  -5488   -892   1176    271     -7   1951  -1951   1337  -4822   -157    104  -2109   1363  -4252   -388    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    32  -2112   -485   -886   -668   -313  -2330      4    217   1142   -767   -209    692    319  -1357   1259   -193    786   -575   -384   1141    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -396 -11642  -2062   -894  -1115   -701  -1378      *      * 
-    33  -3688  -5186   3392   -313  -5499     -6   -454  -5258    433  -1458  -4287   1354  -4689  -2831  -1676  -3548  -3635  -1045  -5362  -4662    47
-     -   -149   -500    233     43   -381    398    105   -627    210   -466   -710    275    396     48     96    359    117   -370   -295   -250 
-     -  -6411  -5987    -40  -1512   -623  -2885   -210      *      * 
-    34  -1469  -1564  -2202  -1918   -552  -2529   4215   2006  -1348   -996   -690  -1802  -2714  -1483  -1429  -1805  -1473   -636  -1202   -358    51
-     -   -149   -500    233     43   -381    398    112   -626    210   -466   -721    275    394     49     96    359    117   -370   -295   -250 
-     -  -1128   -892  -8229    -81  -4198  -5423    -34      *      * 
-    35   -751  -1651   -818   1403  -1742  -1787   -442   1180   1551  -1566   -793   -538  -1879    -93   -423   -761   -684  -1159  -1892   1944    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -7536  -8578   -894  -1115  -4803    -53      *      * 
-    36   -910  -2356   1159   1228   1231  -1845   -535  -2402   1262  -2363  -1453   1307  -1959    -86   -651   -790   -852  -1969  -2539   1518    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8  -8039  -9081   -894  -1115  -4804    -53      *      * 
-    37  -1099  -2524   -937    888  -2834  -2064   2027  -2568   1720   -117  -1620   1180  -2160   -267   -765   -986   1530  -2141  -2708  -2044    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -8399  -9441   -894  -1115  -4767    -54      *      * 
-    38    235  -2729    703    788  -3049    223   -886  -2800   -475  -2746  -1822   -850   1424   1228   -985    385   1396  -2351  -2915  -2230    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8686  -9729   -894  -1115  -1069   -935      *      * 
-    39   -700  -4332   -848   -249  -4652  -1581  -2493  -1503   1869  -4348    556  -2470   1337    695   1753    213    248  -1559  -4516   -771    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -35 -10758  -5421   -894  -1115  -1195   -828      *      * 
-    40    261  -4711   -766   1352   -381   -593  -2877   -409    129   -553  -3801   1185   -530   1096   -444   -107   -230    125  -4896  -1159    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11181 -12223   -894  -1115  -2259   -338      *      * 
-    41  -3332  -4804   -266  -1352  -1285   -573   1070  -1856     94  -1034  -3893    693  -1621  -1012   -796    -42   3040  -4426  -4988  -4305    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11278 -12320   -894  -1115  -2412   -300      *      * 
-    42   -700  -4863    333   -363  -5184   2525   -526  -1783   1384  -1745  -1075    844  -4458  -1045   -288  -1109  -1656  -4485  -5047  -1079    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11341 -12383   -894  -1115  -1798   -489      *      * 
-    43  -1172  -4941  -1557   -978   -603  -1467    369  -5013   1954  -1803    139    307    133    945   2036    160   -396  -2174  -5125  -1379    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11425 -12467   -894  -1115  -2153   -367      *      * 
-    44   -766    548  -4072  -3514    -30  -1388    708  -1753   -535   -693   -216   1222   1100  -3294   -286   2283    209  -3672  -4562  -4089    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11466 -12509   -894  -1115   -924  -1080      *      * 
-    45  -2030  -5056   -425  -2898   -209  -2289   -317  -5120   2371  -1002     10    254   -677   -468   2287   -733   -566  -1327  -5243  -1405    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11559 -12601   -894  -1115   -133  -3508      *      * 
-    46  -3709   -478  -1486  -3139  -1677   3251   -865  -2175   -901  -2798  -4003    413    402  -1330     -1  -3653  -3648  -2158  -5137  -4528    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    47  -3901    493  -2084  -1422   3079  -5305    100   -845   -824  -1161     47  -1681  -5367     76  -1853   -895   -625    157   -197   2653    65
-     -   -147   -500    232     45   -381    398    111   -627    210   -467   -721    275    393     45     98    359    117   -367   -295   -250 
-     -    -18  -6390 -12684  -2198   -355   -701  -1378      *      * 
-    48   2530   2195  -7363  -7063  -5396   2351  -5852   -623  -6670  -2653  -4603  -5982  -6144  -6243  -6417  -2409  -2154   -359  -5898  -5593    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    49  -2230  -3786  -6302  -5666   4039  -5506  -4377   -645  -2108  -1078  -2988  -5151  -5556  -4884  -1886  -2366  -1143   -672  -4243   1796    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    50  -1604    877  -8576  -8264  -6059  -8440  -8511   1855  -8244   -398   -860  -8092  -8163  -8212  -8428  -7826  -5871   3314  -7851  -7323    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    51   -579  -5144    386   2160  -5465  -4645   -873  -1018    675  -3028  -4233    266  -4738    601    424    -82   1330   -935  -5327  -1448    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    52  -7789   -427  -8717  -8877   4014  -8544  -4968  -5804  -8476  -2590    903  -7303  -8291  -7255  -7885  -7792  -7647  -1406  -4199   2905    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    53    294  -5144   1172   1874   -905  -1521    942  -1481    949  -2782  -4233   -271   -458   -130   -424   -618    572   -932  -5327  -4644    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    54  -3672  -5145   1936     61  -5467  -4646   -792  -5217    217  -5161  -4234   1953  -4739    -97    -14   1514   1249  -2329  -5329  -1477    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    55  -1001  -5136  -1209   1440  -1655  -2269   1514   -739   1051   -828     10  -1549   1185    501   -508    130  -1281    403  -5321     14    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    56   -141  -5143   1634   2313  -5463  -1920   -847  -1167  -1176  -2873  -1144   -776   -609  -1383   1036    197  -1750   -566   -388  -1420    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    57    397   -642   2370    782  -1819     93   -852  -2167  -2927  -2706  -1040   -291  -2126    423  -3428   1295   -683  -1543  -5268   -636    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    58   3056  -3783  -6299  -5663   -617  -5503  -4375  -1074  -5258  -1171   1496  -5148  -5553  -1855  -2149   -500   -304     33  -4241  -1297    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    59    209   -573   1016   1604  -5465  -1966   -792   -304   1162  -1412  -4233    571  -1837   1303   -111  -2225    743  -2280  -5327  -4644    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    60    994  -5141    565    -83  -1740  -4645    693  -2288   2342  -1443  -1038    178  -4739   -566    596    -97  -1094  -1488  -5325   -377    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    61   3262   2020  -6694  -6082   -687  -5927  -4850   -126  -5698  -2502   -659  -5582  -5963  -5332  -5512  -1610  -4263   -114  -4698  -4352    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    62  -1537  -3785  -6300  -5664   -786  -5505  -4376   2171    652   1595    833  -5150  -5555   -869  -1636  -2574  -3898   1605  -4242  -1298    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    63     57  -5144   1387   1323  -5465  -2264  -3303   -780    812  -1898  -4233    131  -4738   1747   1061    108  -1766   -907  -5327   -793    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -310 -11642  -2372   -894  -1115   -701  -1378      *      * 
-    64   1233    705    139   1044  -1390   -413   -504  -4926    814  -1849   -873    617  -4450    473   -254    605    234  -2178    137  -4356    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11332 -12374   -894  -1115   -123  -3612      *      * 
-    65   -375    873  -6218  -1441    516  -5480  -4348  -3270   -294   2247   2716  -5104  -5531   -342  -2306  -4562  -1171   -333  -4233    564    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11626 -12668   -894  -1115   -382  -2105      *      * 
-    66  -2168  -5145   1778  -1715  -5466  -1556   1110  -5217   -347  -5161  -4234   3166   -102   1100   -928   -613  -1766  -4767  -5328   -411    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    67  -1458  -5144  -1823    270   -984   2973    159  -5216    311  -5160  -4233    841  -4738  -1432   -954   -817   -981  -4766  -5328   -609    90
-     -   -148   -501    232     42   -379    397    104   -627    216   -467   -722    274    395     48     95    358    116   -365   -296   -251 
-     -   -157  -3284 -12684    -21  -6140   -701  -1378      *      * 
-    68   -674  -5080  -1101   -628    453  -1645   1133    200   1615  -1341    445  -3310  -4756    953   1117    -19    662  -1560  -5281    955    92
-     -   -149   -500    232     43   -381    398    105   -627    210   -466   -721    275    396     45     95    359    120   -366   -295   -250 
-     -    -20  -6226 -12684  -1519   -619   -701  -1378      *      * 
-    69  -3696   -785    -17   1147    150  -1499  -3377    543   1044   -698    461   -736   -351    445   -584   -975    753     89    793    475    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    70  -3956  -3787  -1147  -2465   2321  -2554  -4371   1615  -2185   1495   -817  -5139  -2093  -4870  -2110  -2380  -1415   1282  -4244    800    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    71  -1015   -904    926    188   -880   1152   -650  -5215    677   -786    923   1723   -676    247    421  -1028  -1335  -4766  -5327    275    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    72  -2168  -5150    604  -1054  -5471   2761   -702  -5222   -918  -2141  -4239   1981  -4742   -142  -1740    262  -2027  -4772  -5333  -4650    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    73  -1412    853  -3523  -1169   -883  -4647   1925  -5199   1786  -1944   -937    588  -4740    633   2507   -312   -306  -4755  -5321   -528   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    74   -301   -498  -1749   1022   -866  -4653  -3313  -1356   1140  -1447  -4209    233   1336   -200    701  -1399   1158    451  -5307   -378   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    75  -1685    926  -1227  -5667  -1443  -2425  -4376   2317  -5261   1910    668  -5151  -2133  -1673  -5061  -2536  -2110   1189     -5  -3899   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    76  -2255  -5128   -302    363   -784  -2353   1398  -2058   1512   -314   -275  -1693  -1200   -571   1806   -524    252   -175   -255    793   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    77   -633    879  -2198  -5620  -1457  -5498  -4367   1846  -2705   -311  -2992  -5128  -1361  -1689   -695  -1593     53   2770  -4246  -3903   104
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  fn3
-ACC   PF00041
-DESC  Fibronectin type III domain
-LENG  84
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -A myhmms fn3.sto
-COM   hmmcalibrate myhmms
-NSEQ  108
-DATE  Thu Jan  8 17:50:26 2009
-CKSUM 6130
-GA    7.8 -1.0
-TC    7.9 0.1
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -45.973442   0.237545
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -13      *  -6756
-     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1
-     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 
-     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * 
-     2   -614  -5389   1600   -869  -5707    554  -3557  -5456  -3139   -894  -4479   -526   1870  -1543  -2008   1941   -583  -1300  -5575  -1474     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11909 -12951   -894  -1115   -701  -1378      *      * 
-     3   1995  -5396  -2039    116  -5717  -1669  -3555  -5467    258  -3094  -4485  -1086   2220    798   -677     -2   -956   -578  -5579  -1715     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11909 -12951   -894  -1115   -701  -1378      *      * 
-     4  -1912  -4661  -2736  -6706  -4806  -6475  -5572   -132  -6339  -1660  -3954  -6200   3827  -6009  -1350  -5615  -2249   1184  -5436  -5082     5
-     -   -148   -501    232     42   -382    397    104   -620    209   -460   -713    274    394     44     98    358    116   -371   -296   -251 
-     C   -126  -3586 -12977    -21  -6130   -701  -1378      *      * 
-     5  -1300   -687  -1378    378   -144    668   -265  -5487     14  -1261  -1302  -1797   -370   1178   1071   1001   1362  -1715   -318  -1774     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -14 -11935  -6732   -894  -1115   -701  -1378      *      * 
-     6   -940  -5407   1505   -576  -2047    913   -229   -576  -1226  -1234  -4497   2715   -753    558    130  -1654  -1045  -5029  -5591  -1769     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11921 -12963   -894  -1115   -373  -2136      *      * 
-     7  -1897  -4171  -1391   -671    567  -5914  -4791    411  -5670   2172    671  -5560    677  -5290  -5471  -5002  -4294   1827  -4646  -4308     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -23 -11935  -6029   -894  -1115   -701  -1378      *      * 
-     8  -1831   -846  -1308   -316  -1878  -1626   2028   -992    850  -3178  -4487   -515  -4994   1363   1296    945   1383    130  -5581  -4899    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11913 -12955   -894  -1115   -288  -2468      *      * 
-     9   1403    203  -6582  -5946   1720   -612  -4657    930  -2532    -51   -163  -5431  -2233   -508  -2411  -1893  -2433   2083   -257  -4180    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    10  -1199   -964   -117    123  -5708  -2832   -152    395    364   -765    243  -1202  -2253   -353    210   1235   1816    -79   -372  -1628    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    11    369  -5421   1596   1205   -476    497  -1028  -5492  -1937  -5437  -4510   1521    432   -395   -711      3   -529   -199  -5604  -1530    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -55 -11935  -4751   -894  -1115   -701  -1378      *      * 
-    12   -172   -860  -1215   -801  -5280  -4965  -3640   1669  -1233     51   -266     83   -719    327    227   -864    377   1823  -5339  -4737    14
-     -   -147   -503    232     43   -379    402    103   -625    210   -467   -723    275    395     42     93    360    117   -369   -297   -247 
-     C   -245  -2679 -12922   -347  -2227   -156  -3286      *      * 
-    13  -1709  -5420   -448   -619  -5741    996  -3580  -5492  -1898  -2294  -1324   1287  -5014    770     65   1101   2339  -5042   -449   -671    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    14    557  -5421    996    818  -5742   -274   -121  -5492  -1312  -3064  -4510   -279   1606  -1495  -1316   1523    650  -2689    269  -1603    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -13 -11935  -6826   -894  -1115   -701  -1378      *      * 
-    15  -3943  -5416   1390  -1433  -5737   -521   -114  -5488  -1246  -5432  -4506   1786  -5009  -3115    -78   1199   2391  -1872  -5600    210    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -1 -11922 -12964   -894  -1115   -384  -2097      *      * 
-    16   -608  -5420  -1172    108  -2035   -373  -1142  -5492   -242  -5436  -4509    357  -5014   -374   -668   2462   1185  -1222   -441    383    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    17    558  -4068  -6587  -5951    992  -2729  -1149   1701  -5546   1788   1281  -5435  -5839  -5169  -5346  -4874  -2289   1515  -4526  -1448    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    18   -933   -827  -1427   -266  -1123  -2663    326   -350  -1355    -51   -412   -200  -2224    686    473    560   1711   1050   -544   -656    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    19  -1888   -657  -6942  -6325    201  -2610  -5088   1651  -5939   1947   -224  -5827  -6212  -5572  -5752  -5278  -2376   2336  -4936  -4591    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    20   -929  -5421  -2266     84  -5742  -1769   1077  -5492   -417  -1270   -355    696  -5014    948    666   2138   1348  -5043   -456  -4921    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    21  -8216  -7316  -9156  -9322     91  -9004  -5417  -2436  -8936  -2051  -5172  -7772  -2396  -7636  -8307  -8288  -8065  -6554   6180  -3487    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    22  -1346  -5419    317    824  -2006  -2602   -264   -991    524   -814  -1291     53  -2064   1082    -69   1315   1519  -1271  -5603  -1682    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    23   1030  -5384  -3815   -335  -5688   -765    631   -926     42  -1595  -4478  -1903   2752   -932    121   -525   -280   -486    486  -1747    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    24     20  -5351  -1334  -1374  -5640  -1245  -3604  -2376   -447   -714  -1287   -993   3325  -1489  -3699    571  -1376   -142  -5553  -4891    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -636 -11935  -1489   -894  -1115   -701  -1378      *      * 
-    25   -313  -4824    738    903    489  -1961   -319  -1743    600   -730  -3913   -512   1182  -1049    456     69   1061  -1200  -5008  -1017    29
-     -   -149   -513    256     52   -380    388    111   -628    204   -474   -734    271    397     57     90    357    118   -370   -308   -236 
-     C  -2828   -458  -2930   -849  -1169  -4426    -69      *      * 
-    26  -1035   -178    227  -2617  -4671   2074    534  -1574  -1120   -142   -607    230   1117    -92     -7    -60  -1463   -921    262   -829    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11120 -12162   -894  -1115   -170  -3167      *      * 
-    27   -844  -5358    807    -90  -5679   1010    444   -968   -772  -3028  -4447   2041    -30    361    367    805   -592  -1669   -300  -1468    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11869 -12911   -894  -1115   -135  -3482      *      * 
-    28    598  -5412    -68    -40  -5729   2274  -3582   -979  -1438  -2130  -1237   -611  -2305  -1455      8   1107   -928   -265  -5598  -1593    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    29   -198  -5420   1001   1041  -5741  -1104    365  -1001    184  -3104  -1165   -263   2128   -388   -817   -491    330    124  -5603  -1626    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    30  -1055  -4065   -347  -5945   1276  -1786  -4657   2523  -5541    289   -897  -2216   -363  -1931  -5342  -2542  -2178   1499    562    787    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    31   -967   -668   1478     53   -533  -5043  -3723   -660   -547    -75  -1257   -546  -5132    295    -78    232   2008    -34   -405  -1682    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    32  -1289  -5416   -428   -607  -1226   2233   1325  -2385    447  -3088  -1092    818  -5016   -421    121    608  -1015  -1904   -552    535    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    33  -8249  -7313  -8871  -9139   2077  -8699  -1001  -1545  -1643  -2150  -6647  -7381  -8569  -7497  -8103  -7930  -8116  -1723   -286   4502    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    34  -1279  -5417   -134   1350   -543  -2801   -194   -359    427   -185  -4507    178  -5015    291   1530    265    393   -291  -5601   -249    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    35  -2842  -5745  -8966  -8648  -6155  -8853  -8876   2516  -8633   1028  -1220  -8509  -8508  -8481  -8771  -8255  -6260   2811  -8011  -7616    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -86 -11935  -4117   -894  -1115   -701  -1378      *      * 
-    36   -727   -855    134   1149  -1104  -4850    469   -317    612  -1220  -4399  -3492  -4943   1518    899    134   1469  -1101  -5498    -88    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11849 -12891   -894  -1115   -109  -3778      *      * 
-    37   -919   1849  -6583  -5947    -78  -5786   -316   -279   -394      5  -3268  -5431  -5836  -5165   -783  -2538   -975    515   2753   3639    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -1980 -11935   -422   -894  -1115   -701  -1378      *      * 
-    38  -4510  -5545  -3323   -676  -6286  -4728   2257  -5750  -2040  -5420  -4762   -420  -4944  -2779   3841   -989  -4331  -5444  -5302  -5022    46
-     -   -149   -489    232     45   -381    398    105   -627    210   -467   -711    277    393     48     95    359    117   -370   -295   -250 
-     .  -1797  -3160   -736   -733  -1328    -10  -7198      *      * 
-    39   -133    378  -1993    318   -904  -1088  -3465   -146   1095   -700  -4031  -1603  -2036   2018  -3588    429   -687   -306   2892    659    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -16 -11696  -6532   -894  -1115   -359  -2184      *      * 
-    40   -842   -917    563   1105  -5685  -1640    299  -2487    565  -1697    239    359   1961    355  -1190    286    442   -781  -5547  -4864    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11875 -12917   -894  -1115  -2701   -241      *      * 
-    41    194   -140    529    476  -5651  -1649  -1025    -35   1058   -241   -181  -3511   -102    569  -1132     74    739    807  -5531  -4855    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -117 -11875  -3684   -894  -1115   -146  -3378      *      * 
-    42  -3842  -5314   1613   -195  -1914   1700  -1086  -5385  -1826  -1539  -4403   2308  -4909   -723    276     26   -350   -751  -5497  -1525    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11823 -12865   -894  -1115    -87  -4088      *      * 
-    43   -626  -5420   1257    862  -5742   1052    748  -2386    534  -1327  -1382    504  -5014    -67   -724    909    706  -1767  -5604  -4921    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    44   -960  -5398  -1350    633  -2318   1625   -956  -1630   -939   -994    235   1507    831   1105  -3677    -17   -314   -640  -5588   -673    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -142 -11935  -3421   -894  -1115   -701  -1378      *      * 
-    45  -2194  -5287   1087   1415  -5608    870   -907  -2395    349   -427  -4376   -492    291   1176   -317    355    -70  -2410    771  -4787    55
-     -   -148   -444    225     63   -389    400    108   -622    197   -475   -727    259    408     43    103    350    102   -361   -222   -237 
-     C  -1290   -759 -12836  -1725   -520  -1099   -907      *      * 
-    46   -157    337    519    798  -1912  -1225    -68   -653    114   -297   -291  -1697    725   -732  -1940   -255     36    -19   3575  -4816    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11858 -12900   -894  -1115   -119  -3655      *      * 
-    47   -342  -5028   -807  -3514    413  -5058   1265    -38    982   -213  -1333   1448   -681   1545    500  -1182    191    127   -692  -1745    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    48  -1332  -5420  -1211   1830  -5741  -2545   2195  -2506  -1309  -5436  -1184    473   -397    559    487    489    809    -73   1534   -190    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    49   -723   -908   -854    -86   1437  -1366   -957    813    137    381   -284  -1081  -5126   1056    499  -1688   -640    833  -5352    508    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    50  -2535  -5405    488   -913   -774  -4926   -190    346   -730  -1313    232   1785   -479    314    404    559   1718   -315  -5593  -4914    70
-     -   -146   -501    231     42   -382    399    104   -628    211   -467   -722    274    394     47     94    361    116   -362   -296   -251 
-     E    -55  -4758 -12977  -1430   -669   -701  -1378      *      * 
-    51   -112  -4491   -192   -433  -1967  -1809  -4106   1489  -2323    501  -1098   -148  -2213  -3956   -431  -1276     -3   2236  -4883  -4446    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    52   -188   -867   1259   -506  -1086   -884   -221  -5486     13  -2134  -4507  -1033   2226  -3121   -710   1236    300    -54  -5601  -4919    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    53    -38  -5420   -774    -50  -5740   1398  -3580  -2557    497  -1087  -4509   1165   1212  -1491   1386    411  -3886  -2629   1114  -1704    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    54   -920  -5420    805   -572  -5741   -897   1041  -2557  -3160  -5436  -4509   1517    869    197   -752   1055   1687    273  -5603  -1603    77
-     -   -148   -501    231     42   -382    401    104   -628    209   -460   -722    276    392     47     94    358    122   -371   -296   -251 
-     C    -48  -4927 -12977  -1667   -546   -701  -1378      *      * 
-    55    540  -5417  -2058   1449  -5737  -4922    -14  -1594    207   -756  -4507  -3558   -134   1030   -427    194   1990   -278  -5602  -4920    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -537 -11935  -1688   -894  -1115   -701  -1378      *      * 
-    56  -1224  -4911    173   -396    -20   -696   1167   -519   -782  -2435    170   1440  -1034   -413    525    371   1659  -1244  -5096    752    83
-     -   -149   -490    230     45   -378    398    103   -621    208   -466   -723    273    391     43    104    358    121   -372   -297   -252 
-     C   -353  -2204 -12441   -101  -3887   -730  -1332      *      * 
-    57  -1089  -5230  -3621    543   -958   -947     54  -2267   -700  -1972  -1130    237  -1105    775    826   1902   1424  -2256  -5416    -93    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11745 -12787   -894  -1115    -56  -4726      *      * 
-    58    917   1372  -2400  -5948   1183  -2657   1045   -570  -5543   -207    697  -5432  -5836  -5166  -2244  -4870    -66   1482   -485   2853    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    59  -1727  -5372   -530     74  -2004  -4936    218    671    -46   -927    317    346  -2296     81   -674   -607   2399    703  -5569  -1950    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    60  -4299  -4122   -680  -6010   1503  -5851  -4724   1768  -5607   1770   -994  -5497  -5897   -439  -2266  -2656  -4239   1982  -4583  -4244    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    61  -1194  -5420    -55    570  -1167  -1802    702  -5492    441  -3071   -267    303   -123    727    117    856   1924   -610   -463  -1603    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    62  -2500  -5421   1801   -319  -5742   2398   -103  -2430   -195  -5437  -1130   1999  -2064   -939  -2013   -537  -3887  -5043  -5604  -1643    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    63  -2648  -4734  -2418  -6668   -914  -6542  -5402  -1252  -6279   3190   -215  -6192  -6513  -2081  -6056  -5641  -2421  -1067  -5136  -4863    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    64  -1252  -5420   -773    708  -5740  -2561   -177   -696   1132   -424  -1267     14   -857   1130   1213   -170    967    135  -5603   -223    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    65    680  -5349  -3837    246  -5636  -4944  -3606  -5364  -1398  -5350  -1237  -1116   3633   -932  -3701  -1668   -269  -2586   -311  -1663    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    66   -878  -5418    654  -1315   -625   2683   1459  -5488  -1208  -3181  -4507   1018  -5015  -1522  -1172    -93  -2240  -2527   -441    731    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    67   -329   -911  -3925   -296  -5440  -4989   -278  -1599   -486  -2271    688  -1087  -5079   -875   1192     93   2762    681  -5449  -4826    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    68   -715  -5420    613   1359  -1160  -1216    -61   -999   1010  -1064   -286    512    256    691    198   -142    563  -1715   -332  -4921    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    69  -8584  -7494  -8947  -9309   -410  -8831  -5010  -7468  -8866  -3134  -6868  -2232  -8685  -7581  -8225  -8081  -8433  -7626  -4256   4884    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    70  -1815  -5406  -2090   1238  -1053  -2697    642   -683    206   -981  -1214   1027  -5018    797    -56    458   1323    686  -5593   -187    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    71  -1772   -576  -6691  -6059   2751  -2721  -4781   1861  -5659    107    276  -5548  -5946  -5283  -5462  -4990  -4280   2105  -4641    656   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    72  -1774    157   -771   -126  -5740  -2696   -247  -1555    925  -5435   -361   -242  -5015   1187   2154    813    923  -1324   1141    185   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    73  -1859  -5823  -9013  -8663  -1043  -8868  -8653   1700  -8616    373  -1223  -8529  -8476  -8301  -8657  -8252  -6326   3293  -7705  -7445   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    74    339   -912  -2304  -1480   -161  -4982    242    328    485  -1007  -4340  -1086  -5073   1886   1206  -1252    451    493  -5463   1681   103
-     -   -149   -500    233     43   -381    398    105   -626    210   -462   -721    275    394     45     96    359    117   -369   -295   -250 
-     E    -43  -5729  -6603    -86  -4119   -701  -1378      *      * 
-    75   3003  -4642  -7089  -2701  -4985   -369  -5478  -2243  -6266  -1473  -4220  -5882  -6177  -5887  -6084    548   1259   -953  -5472  -5145   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11920 -12962   -894  -1115   -357  -2190      *      * 
-    76   -890   -701  -6337   -456   -128  -5749    302    444   -435    294   -981  -5315  -5801    452   1013  -1812  -1348   2281  -4547   1032   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    77  -2363   -782    199  -2083  -5740  -2662   -943  -1132    147  -3104  -4508   2805   -755  -1553   -765   1511   1258  -2796  -5603   -104   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -14 -11935  -6734   -894  -1115   -701  -1378      *      * 
-    78    349   -725    812    169  -2094   1817   -228  -2472   -192  -5424  -4497    321  -2426    905     63   -120    421   -272  -5591  -4908   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11921 -12963   -894  -1115   -373  -2135      *      * 
-    79    763   -866    480    290  -2215    944    426    219    379  -1687   -278    514  -2124    507    130  -1212   -544     72  -5596   -747   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -733 -11935  -1329   -894  -1115   -701  -1378      *      * 
-    80  -1112  -4529  -1625   -701  -1337   3244  -3171  -4384  -2854  -2219  -3676  -1217  -4563  -2782  -3334   -608    476  -4085  -4818    474   110
-     -   -153   -500    231     50   -364    398     93   -624    206   -464   -733    283    383     46     94    356    116   -368   -250   -237 
-     C  -6367    -18 -12245   -485  -1807  -3912    -99      *      * 
-    81  -5380  -6068  -5956  -5194  -7389   3194   -752  -6799  -1418  -2482  -5840  -5063   -706  -4120  -1351   1839  -5344  -6386  -6417  -6291   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11248 -12290   -894  -1115   -277  -2516      *      * 
-    82     68  -5329   -386    943  -1053    -34   1308  -2479    103  -1629    757   -877   1926   1130    381  -1141   -878  -1038  -5513  -1828   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11840 -12882   -894  -1115   -101  -3893      *      * 
-    83    102  -5296  -3867   1691     21  -1212  -3624  -1510   -259   -602  -1204  -1862   1786  -1626    665   -353   -181  -4888   2391    466   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    84  -1211  -5433  -3815  -1455  -5755   -850   -140  -2313  -1280  -5448  -4523  -3575  -2241  -1598   -412   3271    384  -5056  -5615  -4936   119
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     C      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  pkinase
-ACC   PF00069
-DESC  Protein kinase domain
-LENG  294
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -A myhmms pkinase.sto
-COM   hmmcalibrate myhmms
-NSEQ  67
-DATE  Thu Jan  8 17:50:39 2009
-CKSUM 4536
-GA    -57.9 -57.9
-TC    -57.7 -57.7
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -194.939484   0.145939
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -21      *  -6109
-     1  -3588  -3415  -5932  -2068   2209  -1198  -4007   1029  -4891    889  -2618  -4781  -5186  -4515  -1612  -2029  -1657   -333   1774   3270     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378    -21      * 
-     2  -1103   -137  -1497   1525  -5095  -4284   1704    -69    423  -1097  -3867   -503  -4377   1172   1017  -1013    975    769  -4962  -4280     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     3  -3460   -131   -785   -393   1050  -4703  -3447   1378    306   1185   -596   -562  -1734   -284    173  -1848     58    960  -4250  -1088     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     4  -3367  -4343   -251    -58  -1421   1411    919    542    574    989   -604    -23  -4523   -994  -3271  -1049  -1512    847  -4637   -148     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     5  -1098  -4782   -183   1680  -5103    503   -434  -4854   1124  -4798   -647  -1288  -1568   1359   1836   -240  -1526  -1059     97  -4283     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     6  -1811   -238   -680    526   -557  -4309    481    726   1770   -409  -3794  -2960    209    272    290  -1047    576    765  -4901  -4244     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     7  -6084  -5527  -8663  -8230  -4683  -8506  -7801   2582  -2005   2411   -444  -8189  -7866  -7357  -7914  -7892  -6017    898  -6516  -6551     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     8  -1162  -4907  -7014  -7375  -7618   3734  -6813  -7450  -7402  -7698  -6730  -5890  -5975   -453  -7118  -4539  -1742  -6121  -7823  -7778     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     9     21  -4782  -1460   1735  -1488  -2091  -2941  -1034    378  -4798   -702   -451  -1594   1320   1488   1403   -804  -2034  -4965  -4282     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    10  -9325  -8016  -8995  -9382  -9561   3867  -8643 -10645  -9576  -9967  -9932  -9344  -8440  -9454  -8996  -9819  -9545 -10244  -8234  -9579    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    11   1482   -366  -1515   -623  -1509    750    367  -4853   -639  -4797  -3871    397  -4376   -316   -611   1560   1138   -595  -4965  -4282    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    12  -3528  -3640  -4717   -983   3576   -666  -3694  -3183  -3938  -3506    429   -575  -4965  -3756  -1463    310   -886  -1665  -4065   2502    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    13    303  -4863  -7632  -7986  -7606   3448  -6938  -7434  -7625  -7696  -6714  -5992  -5965  -7041  -7216    899  -1607  -6089  -7827  -7822    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    14  -1086   2001   -620    718  -5095  -1992    493  -1038   1420  -2482  -3866  -2921  -4377    200    493    575   1303    928  -4961  -4280    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    15  -1356    755  -8169  -7898  -5798  -7710  -8130     18  -7871  -4555  -4472  -7586  -7648  -7843  -8040  -7096  -1974   3721  -7582  -7028    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    16  -3578   -158  -5677   -557   2092  -5098  -3955  -1494    705   -517  -2646  -1470  -5150  -4374    149  -1247  -3519   -369   1758   3515    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    17  -3311  -4764  -1417    525  -5076  -2045   1000   -427   2116   1135    223  -2927  -4381    303   1113   -167  -1542  -1123  -4952  -4275    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    18   2118   3534  -6025  -5409  -3498   2043  -4127  -1439  -5006  -2062  -2745  -4861  -5247  -4627  -4805  -1994  -1655    223  -4002   -858    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    19  -3543   -185  -5023    219  -1266  -4971    330   1223   1347  -1328   -458  -4300  -5031    540   1105  -1143    884    884    180   1134    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    20  -1194   -320    747    506  -5101  -4283   2862  -4852   -146    447  -3870   1539  -4376   -286    544  -1766  -3248  -4403   3098    408    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    21   -309  -4771   -186   -672  -5087  -4286   1935    775   1613    102    432  -1231   -703   -249   1435  -1070  -1560    120  -4958  -4278    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2119 -11253   -378   -894  -1115   -701  -1378      *      * 
-    22   -107  -3005   2005   -836  -3323   -312   1271  -3072   1151  -3020   1085   1327    980   -712  -1261  -1419    163  -2625  -3190  -2509    22
-     -   -156   -495    251     56   -388    395     99   -630    214   -469   -727    277    393     49     92    359    113   -370   -301   -250 
-     -  -3044   -188 -10179  -1816   -482   -467  -1854      *      * 
-    23   -416  -4471   1004    318  -4792    826   -147  -1359   1106  -1202  -3560    963    132   -684   -368    424   -435   -755  -4654    158    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10912 -11954   -894  -1115  -1138   -874      *      * 
-    24  -1682  -4615   1757   -661  -4935   -427    520  -1584    312  -4630  -3704    639  -4210  -2316  -1263    866   2334  -1008  -4798   -935    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11071 -12113   -894  -1115    -88  -4074      *      * 
-    25  -1145   -281    187    523  -5103   2336  -2941  -4853    106  -2370  -3871   1500   -802    200   -578   -191  -3248   -610  -4965  -1037    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    26  -1091    788   -244   1592  -1536  -2091  -2948    -88   1743  -1612    221  -1236  -1595   1121    984  -1655   -277   -562  -4951  -1009    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    27  -1886  -4706   -690     97   -588  -4305    957   1554    380    259   -673   -468    530   1124    271  -1749    300   -181  -4910   -191    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    28  -1208   -195  -5934  -5297   1615  -5136  -4007   -272   -890  -3263    384  -4782  -5186  -4515  -1665  -4220  -1578   2938    187   2163    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    29   3436   -240  -7292  -6870  -1443  -6199  -5909  -1316   -960  -4324  -3966  -6219  -6445  -6242  -6403  -5441  -4707    364  -5768  -5389    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    30  -1900   -234  -5942  -5306  -3379  -2158  -4018   2542   -986    331    885  -4792  -5196  -4525  -1762  -2083  -3538   2511  -3884  -3542    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    31  -6181  -6227  -7911  -6341  -5278  -7070  -5185  -4471   3970  -2148   -640  -6080  -6949  -4791  -3803  -6514  -5992  -1936  -6206  -6162    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    32   -327    703  -4460    659   -413  -4820   -456   1575   1396  -1956    367  -3933  -4889    193    -99   -337    588    858  -4126   -874    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    33  -1154  -3437  -5959  -1813   1336  -5163  -4035   1984  -4919   1660    417  -4809  -5211  -1331  -4720  -1830  -3553   1845  -3899  -3557    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -92 -11253  -4020   -894  -1115   -701  -1378      *      * 
-    34  -1041   -132    238   -186  -1315  -4205    593   -921   2082   -572  -3769   1251    233  -2407    820    192  -1519  -1897  -4866    476    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1554 -11161   -602   -894  -1115  -2645   -251      *      * 
-    35  -1979  -2616    600  -1789  -2689  -3138    917   -262   1783    813  -1778    212    701  -1583  -2068  -2093  -1919    409  -2970   1920    42
-     -   -150   -503    239     47   -384    400    102   -626    207   -465   -724    275    393     42     93    362    116   -369   -298   -252 
-     -  -1002  -1000 -10653  -1035   -966  -1861   -464      *      * 
-    36  -2419  -3891    679   1238   -598    232  -2052  -3962   -399   -689  -2981   1316   -775   1132    761   -903    593    330  -4075  -3392    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10253 -11295   -894  -1115    -23  -5973      *      * 
-    37    412  -4781    488   1427  -5102   -222  -2942   -361   2029  -1668  -3871  -2918   -162   -877    973   -574   -836  -1888  -4965  -4282    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    38   -678   -137   -210   1427  -1398  -4286   1671   -384   1154  -2518  -3862  -1162  -4379    894   1614    249  -1509   -483    197  -1118    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    39   -267  -4782    693    699  -1490  -4283   -508  -4854    809   -957  -3871    707    241   1159    519    994     44  -2057  -4965    442    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    40  -1182    -72    921    502   1029  -1156  -3293    951    402    104   1219     -6  -1620  -3023   -615  -1908    661    177  -4410  -1040    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    41  -1051  -4776    457     54  -1510  -1190   -243    -88   1940  -1673   -501    113    206    593  -3032   1547  -3249   -655  -4961  -4280    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -183 -11253  -3077   -894  -1115   -701  -1378      *      * 
-    42    406   1421    611   1061  -1312    -43    546  -4677    532   -534   -514  -1084     17    -29  -1122    292    214   -978    300   -772    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -425 -11071  -1974   -894  -1115  -3398   -144      *      * 
-    43  -2764  -4221   -153   1053  -4535  -1485   1520     90   1494   -131    -48   -671   -128  -1941    400   -407    604  -1460   2315  -3729    57
-     -   -142   -510    239     64   -403    385     95   -622    235   -461   -723    267    376     51    101    353    107   -365   -302   -244 
-     -  -2565   -268 -11690  -2050   -399  -2023   -408      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10806 -11848   -894  -1115   -123  -3615      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    55  -3588    778  -5934  -2096    797  -2154  -4007    159  -4893   2424   1320  -4782  -5186  -4516  -4693   -346  -1581    896  -3872    -85    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    56  -1884    764    906  -1443  -5103   -188   1312  -4854    809  -4798    279   1929  -4376    884   1300   1258  -3248  -4404  -4965  -1122    91
-     -   -153   -504    236     41   -384    403    108   -630    213   -468   -724    272    397     53     95    359    121   -373   -298   -253 
-     -   -399  -2052 -12295   -717  -1352   -701  -1378      *      * 
-    57  -4352   -210  -6980  -7327  -1361   -967   5242  -7335  -7366  -7491  -6640  -1620  -6023  -6814  -7093   -250  -4823  -6121  -6864  -6133    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    58  -1173   -216    245   1204  -5103  -1809  -2941  -4854    620  -4798   -545  -1224   3079   -272   -672   -439  -1509  -1128  -4965  -4283    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    59  -1852    -77  -4160  -3595    422  -2007   1972  -3460   -814  -3742  -3036   3674  -4802  -3324  -1558  -3710  -1482  -1517  -4249   1576    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    60  -5621  -5100  -8287  -7944  -1270  -1991  -7944   3577  -7896    340  -4034  -7788  -7778  -7646  -7966  -7505  -5600   1263  -7086  -6756    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    61  -3675    717  -6027  -5396  -3463  -5238  -4119   2327  -4996    517   -394  -4885  -1663  -4622  -1582  -2054   -833   2711  -3982  -3638   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    62  -1178   1286  -3156    313  -5103  -1183   -408  -4853   1393  -2436   -677     14   -122    883   2214   -185    985  -4404  -4965   -903   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    63  -1976   -183  -6001  -5366   2192  -5206  -4078    676  -4962   2130   1643  -4853  -5251  -4581  -4761  -4292   -286     32  -3935   1196   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    64  -1822  -3432  -5776  -2112    643  -5113    393   1723    887   1018   -388  -4708  -5164   -395   -262  -2058  -1656   -366    329   2505   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    65   -276   -189   2087    898  -5103   2182    893  -4854  -2523  -4798   -507  -1182  -4377   -928    -69   -525  -3249  -4404  -4966    370   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    66   1071   -123  -5934  -5298    884  -5136  -4007   1473  -4893   -796   1351  -4782  -5186  -4515  -4692    650    324   1711   1346      6   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    67  -1874   3490   -804   -451   2702  -5115   -515   -716  -4788   -850    431   -572  -1625  -1375  -4637  -1919  -3523      7   1286   1956   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    68   -519   -292  -1523   1548  -1530  -1060    375   -412   -187   -696    822   -442  -4421    557    492  -1702   1121   -118    303   1118   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1500 -11253   -630   -894  -1115   -701  -1378      *      * 
-    69   -561  -3477   1784   1293    -31  -2981  -1639  -3547  -1220  -1130  -2567     56   1133    276   1610   -418   -236  -3099  -3661  -2979   108
-     -   -153   -497    234     42   -381    398    113   -616    215   -467   -731    275    398     42     91    361    121   -376   -305   -254 
-     -  -1804   -656  -3664  -2224   -347   -150  -3344      *      * 
-    70   -486  -4664   1357   1085  -4985   -532    560  -1808   -124  -1513  -3753   -323  -4258   -857    689    801   1256   -403  -4847    -32   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11124 -12166   -894  -1115   -343  -2242      *      * 
-    71  -1858  -4763   1193    898   -529    564    909  -4835   1010  -2351  -3852   1168   1013   -944   -517    695   -813  -4385  -4946  -1086   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12274   -894  -1115   -380  -2110      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    73   -651  -4782   -168    750   -578  -2047   2645  -4853     97  -2362  -3871    924    471   -251    537    474   -748  -1103    200   1429   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    74  -1178    880  -5933  -5297    136  -2001   -595   1808  -4892   1524   1344   -420    242  -4515   -726  -4220   -778    458    172    878   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    76  -5531  -5173  -7904  -2040    823  -7303  -6128   2057  -6964   2030   2806  -6970  -6988  -1364  -6658  -6465  -5436    671  -5433  -5361   133
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    77  -1279    704  -6522  -1998   -434  -5796  -4741   2404  -5557   -580  -3125  -5443  -5814  -1174  -5386  -4905  -4074   2919  -4581  -4228   134
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    78  -3589  -3420  -5900  -1855   1657  -5133  -4002  -1255  -4869   1532   3646  -1319  -5183     81  -4681  -1944   1306  -1569  -3877  -3535   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    79  -2223  -7725    285   3557  -7843  -5438   -536  -7828  -5262  -7661  -7076  -4019    830    173  -6251  -2036  -5764  -7268  -7864  -6740   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    80  -1960    -21  -5934  -5298   2086  -5136    965  -1405  -1868    792    371  -4782  -5186  -4516  -1638  -4221  -3529  -1458   1188   3749   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -346 -11253  -2233   -894  -1115   -701  -1378      *      * 
-    84  -4093  -4778  -5475  -5209  -6710   3477  -4989  -6385  -1530  -6450  -5617  -1206  -5539  -4693  -1363   -750    464   -678  -6565  -6305   141
-     -   -149   -490    235     41   -383    398    103   -621    210   -462   -723    273    391     46     93    360    117   -366   -297   -246 
-     -   -209  -3130  -5579  -1553   -601    -52  -4818      *      * 
-    85  -1064   -309   2847   1153  -5078  -4262  -2921  -4828  -2502  -2463  -3848    -19   -143   -981  -1323   1598  -1440  -1955  -4942  -4260   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11229 -12271   -894  -1115   -357  -2189      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    87     65  -4715   -633   -683   2397  -4302   1674  -4734    106    256    293    400  -4395   -982    175   -586  -1543  -1923     84   1800   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    88   -244  -4782   2096    691  -1564   -655    356  -4854    362  -1051  -3871    418  -4376    310   1132    103     85  -2000  -4965  -1119   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    89   -192  -3415  -5929  -5293   1681  -5135   1886    155   -443    842    377  -1607  -5185  -4513     79  -4219  -3528    502    353   2774   152
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    90  -3694  -3515  -1855  -5404    238  -5246  -4114   2100  -1935   2342   1019  -4893  -5287  -4614  -4798  -4333  -3634    529    376   -853   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    91  -1140  -4769   -713   -285  -1372  -4287   1385  -1034    442   -724    377   -361  -1676    907   1756    527   1005    112  -4956   -958   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    92    432  -4782    135    936  -1402   -557   -432  -4854    633  -2451    296    904  -1592   1082   1316     68   -298  -1942  -4965    493   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    93   -255   1350  -1412      8  -5103   -673   1861  -4854   1303  -1545  -3871   1796   -783    596   1588  -1069   -279  -4404  -4965  -1089   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -150   -489    236     49   -389    397    112   -631    207   -469   -713    278    404     38     91    361    117   -369   -308   -253 
-     -  -1831  -1995  -1095  -2447   -292   -701  -1378      *      * 
-    95  -1080  -3937    182   -657    243   1157    313    398   -566   -222  -3030    354   -753   -190    303   -169    866   -320  -4129   -218   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10343 -11385   -894  -1115   -442  -1921      *      * 
-    96    161    805  -3172   -664  -1324   -499    507   -210    761   -208  -3441    187   1533    381    470    -56  -3114     25    291    106   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11067 -12109   -894  -1115   -270  -2553      *      * 
-    97  -3566  -3393  -1784  -5272   2324  -2052  -3984   1346  -1923   1790   1918  -4758  -1734  -1383  -4669  -4198  -1576     -4  -3851    816   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -46 -11229  -5024   -894  -1115  -1501   -629      *      * 
-    98   -573  -4721    583    376  -5043    109  -2880  -4793   -122  -4738  -3811    450    794   -124   -488   1914   1370  -4343  -4905  -4222   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11185 -12227   -894  -1115   -189  -3026      *      * 
-    99  -1028  -3904    124   2654    138  -4673   -512   -770  -3327   -335   1334  -3619    749  -1209  -1508  -1131   -714  -1749   1225    -45   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   100   -594   -305    921    761   -475   -189    958  -1005   1123  -1604   -581     20    250    202    916   -608   -818  -1956   1257   -967   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   101   -288  -4776   1376   1776  -5095  -1923   1385    -92  -1241   -114  -3866  -1259  -1603   1656  -1447  -1739   -258   -206    343  -1032   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   103   -311    808  -1654  -3848   -281   -270  -3577    405   1931    468  -2911  -3904  -4877    558   1705  -1197  -3434    448  -4139  -3729   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   104    -26   1340    244   -781   1400  -2057   1319  -4839   1543   -712    384    932  -4378  -1028    246    332   -782  -1932  -4960   -145   182
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   105  -1214    774  -5976  -5341   1650  -5180  -4051   2169  -4937     40   1853  -4826  -5227  -4557  -4736  -4266  -3570   1080   1714   2407   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   106   1686    753  -5934  -5298   1553  -1286  -4007   1034  -4893   -199   2436  -4782  -5186  -4515  -4692   -260     57    657    354  -3530   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   107   -329  -4076  -3758   -905  -1389  -1199    339   -927   1302    805  -3236  -1389  -4648  -3000   1305     15    366  -1029   1191   1974   185
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   108  -1131   -335    172    908  -5104  -1136   -419  -4854  -2523  -4799   -668  -1124  -4377   3782  -1397   -607   -347  -4405  -4966  -4283   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   109  -5639  -5117  -8302  -7952  -5272  -8144  -7935   2597  -7900    836   1936  -7803  -7778  -7622  -7955  -7519   1191   1991  -7052  -6759   187
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   110   1484   2123  -5947  -5311   -235  -1115  -4022   -201  -4907   1978   -379  -4796  -5199  -4530  -4707   -310  -3541   1030  -3887  -3545   188
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   111   -671   1330   -647   1060  -5102  -1994  -2941  -1909   1295   -153   -695     41  -4376    877   1727    855   -765  -4403  -4965  -4282   189
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   112   2243  -4861  -7644  -7983  -7589   3019  -6925  -7411  -7584  -7674  -6697  -5990  -5964  -7026  -1546  -1067  -1841  -2167  -7810  -7801   190
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   113  -2201   -281  -7971  -7452  -1406  -7501  -6570    952  -7203   2152   2957  -7163  -7211  -6648  -7009  -6716  -5421   1875  -5905  -5754   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   114    777  -4782    718   1515  -5103  -4283   -340   -991   1157  -1577  -3871   1333  -4376    385   -492    662  -3248  -1111  -4965   -155   192
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   115   -360  -6644  -7694  -2051   1433  -7828   2559  -6632  -7848  -6039  -6064  -6593  -7806  -6748  -7364  -7112  -1819  -6729  -3620   4368   193
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   116  -2172   2767  -9105  -8531  -4252  -8881  -7599   1439  -8345   2749   1681  -8628  -7916  -7096  -7825  -8265  -6539  -4267  -6093  -6326   194
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   117   -416  -7356  -3349    266  -7495  -2140   5143  -7872  -5379  -7711  -7155  -1371  -6074  -4694  -6292  -5305  -5780  -7254  -7669   -182   195
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   118    -13   -306    733    907  -5103     93   -360  -1867   -241  -2549  -3871     30  -4376   -206    743   2216  -3248  -2034  -4965  -4282   196
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   119   -672    716  -1446    516  -1522  -4311   1363   -950   1016  -1159   1883   1645  -4404   1679   1321  -3222  -3259  -1108    116  -4240   197
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   120  -1862   -163   -618  -1440   -568   2279   1298   -961    792  -2520  -3868   1125  -4377   -991    749    191   -831  -4400  -4963  -1118   198
-     -   -149   -504    231     41   -380    401    113   -627    215   -466   -725    274    403     45     92    355    116   -371   -283   -253 
-     -   -179  -3102 -12295  -1872   -460   -701  -1378      *      * 
-   121  -5411    727  -8000  -7587   1790  -7672  -7025   2905  -7434   -152  -3911  -7314  -7433  -7129  -7406  -6949  -5382   2179  -6446  -1162   209
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   122   -618    840  -5935  -5299  -1214  -5137  -4008   2237  -4894    666   1335  -4783  -5187  -4516  -1766  -1187  -1501   2326  -3873   -906   210
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   123  -8407  -7275  -8450  -8809  -3793  -8053   5359  -7648  -8566  -6951  -7039  -7461  -8186  -7592  -7995  -8098  -8340  -7763  -4475   1186   211
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   124  -5094    -99  -6822  -5503  -6155  -1963  -4473  -5623  -1567  -1569   -400  -5194  -6119  -4158   4040  -2036  -1702  -5399  -5873  -5700   212
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   125  -6923  -7890   4200  -5000  -8686  -6482  -6170  -9053  -6698  -8760  -8346  -1338  -7059  -5964  -7524  -6617  -7065  -8485  -8135  -7889   213
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   126  -6540  -5924  -9034  -8525  -4401  -8921  -7834   1903  -8399   2803    425  -8636  -7981  -7257  -7969  -8350  -6420    556  -6283  -6487   214
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   127    752      8  -7399  -6507  -7582  -5487  -5445  -7170   3745  -7106  -6303  -5655  -6103  -5131  -1542  -2121  -1851  -6239  -7053  -7025   215
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   128    744   -225   -806  -5038  -3547   -641  -4037  -1521  -4712    -20   -468  -4668   3197  -4402  -4641    680    105  -2996  -4036  -3686   216
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   130  -9229  -8006  -8715  -9103  -9439  -7953  -8550 -10587  -9451  -9925  -9876   4461  -8411  -9287  -8946  -9659  -9447 -10180  -8207  -9396   218
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   131  -5687   2300  -8350  -8002    207  -8210  -8001   3253  -7958    805  -3949  -7870  -7814  -7644  -8002  -7596  -5662   1231  -7044  -6779   219
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   132  -6956  -6284  -9325  -8719   1416  -9211  -7739  -1549  -8543   2946   2123  -8959  -8021  -7132  -7931  -8654  -6766   -521  -6086  -6376   220
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   133  -5440    745  -7858  -7282    552  -7294  -6203   2301  -6978   2043   -260  -6956  -7014  -6345  -6720  -6469  -5362   1537  -5557   -212   221
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   134  -1083   -301   2506     21  -5100   -558    393  -4850    423  -2499   -658    933  -4376  -1003  -3030    708    343    411  -4964  -4282   222
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   135  -1846  -4782    467   1295  -5103  -1155   1373  -4854    833  -2408   -624    940   -735    879    357    505    762  -1029  -4965    -77   223
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   136  -1769  -4782    926    565  -5103   -161    908  -1978    983  -2502  -3871   2098    726    267    224   -199   -260  -1060  -4965  -4283   224
-     -   -157   -500    246     44   -384    394     93   -614    211   -477   -722    284    397     36    103    361    118   -368   -307   -245 
-     -  -2910  -2055   -675  -2460   -289   -701  -1378      *      * 
-   137   -497    939   1358   -204  -3859    731    895  -3609  -1283  -3555  -2629   1390   1009    363    608  -1950    447   -695  -3723    233   243
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2  -9833 -10875   -894  -1115    -55  -4733      *      * 
-   138   -244   -254   -598   -313   -479   2144    387   -871  -1338   -383    292    950   -584   -997   -597   -165   -811  -1046  -4875  -1035   244
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11229 -12271   -894  -1115   -359  -2181      *      * 
-   139  -1671   -330    766   -286    152  -4301   1876   -443    106  -1110   -517    409  -1724   1474   -631   -610   1022    776  -4920   -219   245
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   140   -691   1386  -6334  -5723  -3772  -5578  -4498   2087  -5341   1399   -559  -5227  -1618  -4979  -5158  -1025  -3901   2349  -4347  -3999   246
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   141  -5615   1796  -6263   -306  -7053  -6235   -297  -6425   3658  -6155   -761  -4908  -6173  -3754    311  -5513  -5324  -2136  -6057  -1058   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   142  -2324     -4  -8046  -1864  -5464  -7795  -7522   3094  -7591   1907  -4214  -7450  -7571  -7458  -7677  -7116  -5380    678  -7004  -6550   248
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -69 -11253  -4436   -894  -1115   -701  -1378      *      * 
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-     -   -153   -484    239     41   -390    398    113   -626    219   -472   -700    272    392     40     90    367    123   -389   -285   -237 
-     -  -2058   -691  -2833  -1765   -503  -2348   -315      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10967 -12009   -894  -1115    -61  -4600      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   161     -7   3604  -1703  -1952  -1279     20  -3751   -241   -967  -1274  -2774  -4228  -5005  -1297   -183  -3975    111   2386  -4015  -3638   286
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   163  -3463   -231  -4104  -1583  -3901  -4703   -285  -3477  -3393   -668   -567  -1427  -1763  -3282  -1601   1567   3275  -3329    138  -3817   288
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   164  -1054  -4447  -1448   -799  -1483  -4394   -504    568   -717    269  -3573  -1209   2638  -2674   1632     35  -3291   -894  -4717    -97   289
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   165  -1148   -188    195    688     59     28    447   -345  -1520  -1501  -3412    402    235  -2812    568  -3404    134    567   3104   1134   290
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   166  -7087  -6552  -7865  -7298    906  -7610   -394  -6464    -71  -5974  -5863  -6312  -1544  -5805    222  -6878   -916  -6520   3392   4239   291
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   167   -223    717  -5916  -5281  -3370  -5133  -4004    236  -1798   -289   3511   -585  -5183  -4506   1713  -1968  -1689    674   3286  -3531   292
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2663 -11253   -249   -894  -1115   -701  -1378      *      * 
-   168  -1615  -1432  -3894  -3271  -1190  -3170  -2004   1005  -2881    340   3898  -2792  -3191  -2488  -2695    455  -1554   -744  -1818   2200   293
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -8595  -9637   -894  -1115    -14  -6700      *      * 
-   169   3331  -4866  -7603  -7958  -7608  -1940  -6935  -7436  -7620  -7697  -6716  -5989    604  -7036  -7215    952  -4738  -6092  -7827  -7821   294
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   170  -5719  -5989  -8212  -8414  -6061  -6510  -7452  -5461  -8195  -1053  -5125  -7267   4235  -7661  -7816  -6091  -6099  -1808  -7128  -7038   295
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   171  -5844  -7649  -3465   3879  -7964  -5599  -4859  -7816  -4663  -7563  -7007  -1205  -6142  -1082  -1705  -5462  -5891  -7329  -7621  -6774   296
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   172  -1140   2074  -5903  -1972  -3372  -2210  -4001   1453  -4870    805  -2620  -4768  -5182  -1229   -302   -350  -1427   2455   1276  -3532   297
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2385 -11253   -307   -894  -1115   -701  -1378      *      * 
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-     -   -147   -508    232     44   -380    394     97   -634    213   -465   -707    273    393     41    103    365    119   -372   -303   -247 
-     -  -1167   -853  -9914  -2962   -198    -41  -5143      *      * 
-   174  -3569  -3395  -5913  -1783  -1209  -2028   -312   2012  -4872   2363    985  -4762  -5166  -4496  -4673  -1049  -1621    557  -3853  -3511   318
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21 -11253  -6175   -894  -1115   -701  -1378      *      * 
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-     -   -151   -496    236     48   -375    395    115   -627    213   -472   -719    275    387     51     93    363    116   -369   -303   -247 
-     -   -723  -1344 -12275  -1185   -836   -388  -2085      *      * 
-   177  -1854   -365    250   -270  -1451   -695  -2942  -1670    829  -1506  -3870   1446    994   1339   1305    316     71  -2013  -4964  -1132   327
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   178  -1183  -4781    479    337   -476   1157    920  -4851    811  -1706    863     91    780   -251  -1348   -518  -1627   -249  -4964   1628   328
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   179   -641  -3679    186  -1774   1732  -4848   1886    417  -3794  -1978  -2867  -1484  -4915  -1042   -659  -1931  -3446   -785    351   3626   329
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   180  -4456  -5182   1171  -4993   -329   1754  -5512  -6689  -5796  -6852  -6053  -4925    -79  -5350  -6183   1886   2183  -5902  -6901   -135   330
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   184  -2185  -7763   4161  -1526  -8064  -5545  -5059  -8102  -5545  -7921  -7396  -4164  -6155  -4765  -6600  -5444  -5959  -7498  -8066  -6964   334
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   185  -3763  -3574  -6119  -5491  -3529  -5337  -4222   1931  -1751   -459   2285  -4984  -5377  -4717  -4898  -4427  -1556   2841   2093  -1035   335
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   191  -5172  -4754  -7738  -7288  -5043  -7312  -6644   2449  -7086    995   1643  -6965  -7162  -6821  -7043  -2325   1223   2054  -6259  -5887   341
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   192  -1076   1328  -5938  -5302    836  -5140   -325   1005  -4897   2425   1260  -4786  -5190  -4519  -4697  -4225   -335    240  -3876   -892   342
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   195  -1952  -3418  -5937  -5301   -272  -5139  -4011   1021  -1684   2216   3270  -4785  -5189  -4519  -4696  -2001   -778      8  -3875   -822   345
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   196    806   1503  -5937  -5301   1069  -5139  -4010   -159  -4896   2118   1853  -4785  -5189  -4518  -1647  -4224   -704    488  -3875    -12   346
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -68 -11253  -4450   -894  -1115   -701  -1378      *      * 
-   197   -244   1762  -1486   -304    176  -4478  -3186  -1620  -1279   -221  -3216    398  -4561  -2888   -637    521   2695  -1689  -4401     88   347
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -11185  -6108   -894  -1115  -2339   -318      *      * 
-   198  -3245  -4700  -1285  -2549   -491   2810   -331  -4760    938  -1086  -3791   -321  -4313   -924    849   -991  -3184  -4319  -4885   1151   348
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1315 -11165   -743   -894  -1115  -2606   -259      *      * 
-   199  -2173   1967  -2528  -1972     17   2076  -2043   -457    979  -2731    717    -64   -376    170   1038  -2282   -340   -523  -3176  -2686   349
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -599  -9852  -1561   -894  -1115  -5598    -30      *      * 
-   200    585  -2946    192    327    320  -2642  -1313  -2906    368  -2934  -2055  -1307   2663   -879  -1420  -1559    970   -222  -3173  -2532   350
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -273  -9256  -2548   -894  -1115  -4647    -59      *      * 
-   201     -7  -1595    298  -2960  -1558  -3177  -2022   1183  -2650    990   -794  -2662   1216  -2358  -2612    727    308    444  -2044    901   351
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -110  -9104  -3800   -894  -1115  -5907    -24      *      * 
-   202     57  -1583  -4065  -3442   2875  -3303  -2112   1403  -3043    674   -733    458  -3345  -2657  -2848  -2389  -1701   -972   3227  -1515   352
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8998 -10040   -894  -1115  -5935    -24      *      * 
-   203  -1548  -2953    474   -828   1541    -89  -1185  -2981    576  -2962  -2061  -1137   2705    902  -1297  -1437    354  -2564  -3160  -2490   353
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -632  -8998  -1503   -894  -1115  -5935    -24      *      * 
-   204    949  -1873  -3594  -3310  -3215   2567  -2867    956  -3113  -3131  -2370  -2617  -2976  -2850  -3187    780   1132  -2303  -3567  -3260   354
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -360  -8372  -2199   -894  -1115  -6061    -22      *      * 
-   205    726  -1828  -1018   -467  -2006    573   2223  -1643   -310    410   -995   -717    992   -285   1111   -896   -833  -1380  -2145  -1598   355
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -541  -8020  -1695   -894  -1115  -6108    -21      *      * 
-   206  -1455  -3002   2743   -124  -3339  -1838   -906  -3139   1668  -3063  -2255   -476   1698   -520  -1270  -1244  -1458  -2675  -3223  -2453   356
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -375  -7491  -2162   -894  -1115  -5060    -44      *      * 
-   207   -746  -1560   1425   -341  -1356  -1795   -444  -1289   -170    682   -700   -571  -1893   -160   1517   -779   -684  -1075  -1644   1953   357
-     -   -149   -500    232     45   -381    400    111   -627    210   -466   -721    275    393     45     98    359    117   -370   -295   -250 
-     -  -2633   -258  -8511    -45  -5040  -6160    -20      *      * 
-   208  -1767  -3401   2107   -139  -3802  -1858  -1202  -3699  -1354  -3615  -2897   2073   2793   -864  -2119  -1501  -1847  -3169  -3794  -2874   359
-     -   -150   -501    232     42   -377    397    105   -627    211   -463   -722    277    393     48     95    360    116   -370   -282   -250 
-     -  -1435  -1255  -2242  -1944   -434  -4946    -48      *      * 
-   209   2138  -1310  -3697  -3171  -1088  -3181  -2298   1866  -2865   1275    -74  -2834  -3185  -2520  -2785  -2341  -1503    291  -2073  -1786   364
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -7515  -8557   -894  -1115  -4020    -92      *      * 
-   210  -1233  -1057  -3502  -2875   2324  -2779  -1614   1177    721    798   2162  -2397  -2809  -2101  -2304  -1865  -1171   -427  -1448   1579   365
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -8194  -9237   -894  -1115  -4002    -93      *      * 
-   211  -1302   2115  -2420    350   1052  -2659  -1447    663  -1647     92   -633    792  -2725  -1476   1471  -1674   1486   -879  -1868  -1474   366
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8636  -9678   -894  -1115  -4368    -72      *      * 
-   212  -1500  -1493  -3073  -2485  -1475   1806   1631  -1021  -2227    -15   1601  -2312    308  -1989  -2294    905  -1446   1296  -1944  -1577   367
-     -   -150   -501    231     44   -378    400    104   -628    211   -463   -722    274    397     47     94    358    116   -365   -296   -251 
-     -  -4031    -93  -9909    -16  -6545  -3062   -184      *      * 
-   213   -308   3406  -2790  -2223    329   1927   1217  -1722  -2052  -2025   1176  -2281   -140  -1909    100    454  -1826  -1593  -2560  -2148   369
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9403 -10445   -894  -1115  -4745    -55      *      * 
-   214    497  -3267   2280  -1089  -3587    302   1113  -3338    180  -3283  -2356    257    698    544  -1514   -236    711  -2888  -3450  -2767   370
-     -   -150   -501    231     42   -382    399    104   -628    209   -467   -722    282    394     44     94    364    118   -368   -296   -251 
-     -  -3424   -847  -1511    -17  -6404  -5781    -26      *      * 
-   215    126   1810   1788   1660  -3167     24  -1012  -2917   -604  -2866  -1944    757  -2441   1048  -1115  -1263  -1325  -2471  -3038   1028   372
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8855  -9897   -894  -1115  -4219    -80      *      * 
-   216  -1659  -1606   1126  -2775  -1573  -3126   1339   1650  -2494    568   1451  -2548  -3183    578  -2513     17  -1600   1517  -2052  -1691   373
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9076 -10118   -894  -1115  -5914    -24      *      * 
-   217  -1495  -2943   2280   1499  -3254  -2470  -1131    -17   -716   -641  -2035  -1109  -2564    944    544    118    299  -2560  -3133  -2456   374
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9076 -10118   -894  -1115  -4783    -53      *      * 
-   218  -1591  -3032   1083   1465  -3339  -2560  -1226  -3080   -812    730  -2126  -1201  -2658   2356    399  -1477    268  -2647  -3222    680   375
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9175 -10217   -894  -1115  -5886    -25      *      * 
-   219  -1742  -1646  -3647   -173  -1608   -321   1411   1597  -2724   1305   1373  -2730  -3291  -2428    236   -122  -1683    373  -2096    857   376
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9175 -10217   -894  -1115  -5886    -25      *      * 
-   220  -1721  -1749  -3148    754   1397  -3140   1240   1590  -2325   -145   -943  -2447  -3201    511    276   -102  -1661   1010  -2185    836   377
-     -   -149   -502    231     43   -383    396    103   -624    212   -466   -713    276    392     43    102    360    115   -366   -297   -251 
-     -  -4339    -74 -10217    -12  -6866  -4187    -81      *      * 
-   221    585  -2351  -2208     71  -2412  -2955  -1677   2453     99  -2250   1246  -1839     12   1339  -1909  -1915     53    -32  -2715  -2240   379
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9346 -10388   -894  -1115  -5830    -26      *      * 
-   222   -185   1537  -4239  -3604   2205  -3447  -2319    312    744    864   1396  -3091  -3497  -2824  -3003  -2532    911    887  -2186  -1843   380
-     -   -151   -502    233     45   -383    398    103   -625    214   -466   -723    273    391     50    101    358    115   -366   -297   -252 
-     -  -4510    -66 -10388    -11  -7043  -3687   -117      *      * 
-   223    431  -2579   -112   -147     32    338  -1823    594    -73    500  -1741  -1965  -3188  -1555     80   -423    -49   1384  -2934  -2448   382
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9573 -10615   -894  -1115  -4704    -56      *      * 
-   224  -2022  -2478    612   -287  -2518   1276   1865    -81  -1896   1098    904  -2188   -169  -1790   -128  -2216  -1962  -1942   1522   1336   383
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9636 -10678   -894  -1115    -47  -4966      *      * 
-   225   -253   -342    241    943  -1550    511    416  -1901   1300  -1037    261   -423   -738   1137    593   -947    117  -1919  -4945  -1082   384
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12275   -894  -1115  -1421   -675      *      * 
-   226  -1092  -4749   -606    581   -564  -1870   -440    343  -1335    619  -3840   -387   1504    244   -647    265   1309   -569  -4936  -4258   385
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12275   -894  -1115   -384  -2098      *      * 
-   227  -5705  -7606   -601     32  -7987  -5466  -4991  -8006  -5466  -2585  -7299  -4094   4121  -4694  -6511  -2244  -5847  -7381  -8039  -6892   386
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   228  -3576   -202  -5624  -2094   3261  -5089   -616  -2951  -1896   -127   -464  -1572  -5142  -1385  -1692  -1955    348   -801   2793   2371   387
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   229   -675   -230    195    293  -5097  -1215    985   -443    145  -2453   -681  -1107   1491    688    497    985  -3248  -2026     82   1781   388
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -137 -11253  -3475   -894  -1115   -701  -1378      *      * 
-   230   -191  -4658   1917    454  -1407   1496   1095  -4730  -1106  -2385  -3747   1039   -543    738    348    -76  -3124  -4280  -4841  -4158   389
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1242 -11117   -794   -894  -1115  -3068   -183      *      * 
-   231    125  -3514    984   1532   -304  -3096   1711   -630  -1349  -3518    667  -1742    485    271    549    602  -2050   -736  -3715    242   390
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -536  -9877  -1693   -894  -1115  -4485    -66      *      * 
-   232  -1923  -1930  -3418   -248  -1905  -3354  -2172   1427   -236    734   1293   1008    902  -2354  -2673   -304  -1864     70   3345  -1999   391
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -169  -9424  -3199   -894  -1115  -5801    -26      *      * 
-   233   -177  -3080   1072    307  -3395   -302   1306    752    341  -3093    992  -1237   1877   -801   1122  -1506  -1562  -2699  -3267  -2589   392
-     -   -149   -500    232     43   -381    398    105   -627    210   -466   -711    277    393     52     95    359    117   -370   -295   -250 
-     -   -400  -2049 -10301    -45  -5039  -3694   -116      *      * 
-   234   -377  -3122   1282    735     41  -2823   1070   -384   1371   -727  -2229  -1488  -2914  -1054  -1594    959    724   -463  -3347  -2707   394
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9503 -10545   -894  -1115  -3327   -151      *      * 
-   235    130   1019   -202   -129  -3730   -752  -1662  -3464    739   -271    708    836    572  -1210   1162  -1909   1062   -690  -3631    333   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2  -9764 -10806   -894  -1115  -2310   -325      *      * 
-   236    -58  -3831    759   -412  -4150  -3336    462   -824   -379   -632  -2921   1020    238   1173   1239    716   -637   -940   1081   -137   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10185 -11228   -894  -1115  -1418   -677      *      * 
-   237  -2832   1269    712    563   -861  -3892  -2576   1496    656   -533    842    558   -205   -410    -69  -1296    302   -548    658   -557   397
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10670 -11712   -894  -1115   -170  -3173      *      * 
-   238  -1058  -4740   1414    765   -505   -595   1409   -449    226  -1087    894    747   -692    900      1    369   -643  -2020  -4923  -4240   398
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115   -870  -1143      *      * 
-   239  -3290  -4745   -186   -313  -1388    289  -2926    291    186   -589    254   1668   1599    315    -90   -180    386  -1937  -4933  -1011   399
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -366  -2158      *      * 
-   240   -597  -3523   -247  -4579   1041   -239   -634    180   -870    649   1849   -639   -164  -1356  -4363   -295   1168   -437    214   1209   400
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   241     24  -4780   1113   1177    464  -1969  -2942  -1715    359  -1612    289     33  -1527   1156   1155     43   -331  -1938  -4964   -108   401
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   242    242  -4780   -209   1327   -510  -1162    503  -1003    465  -1135   1207    936  -4376   1386    762   -217   -847  -1164  -4964  -4282   402
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   243   -331  -3415  -5931  -5295   -356  -5135   -422   1682     -8   1115    434  -4780  -5185  -4514   -720   -670   -339   1301    471   1689   403
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   244   -296  -3807   -160   -358   1602   -658   1942   -290  -1591    308   1232   -534   -809  -3375  -3810   -232   -346    497  -4206   1378   404
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   245    645   1246    171    325  -1565   -246  -2950  -1914    109   -424   -644     22   -730    238   1783     20  -1585  -1951     91    356   405
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   246   -287  -3957  -3935  -1604   -375   1032    978   1813   -377    425   1292    -24  -1671   -330   -784  -1105   -805   -488  -4329    -31   406
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   247   -315  -4676    531  -1367  -1473  -2022   -415   1100    963    214   -409    682  -4406    637    -75  -1766     67    581  -4889    867   407
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   248   -667   -245   -660    757   -571  -1911  -2960  -1964   1281     94    254     30  -1661   1539    220   -532   -816   -542   1187   1076   408
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   249  -1120  -4782    476    511   -524     59   1681  -1888    841  -2553    212   1135   -697    617   1196   -148    307  -2032  -4965  -4283   409
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1035 -11253   -967   -894  -1115   -701  -1378      *      * 
-   250  -2422   1649  -2415   -463    385  -1084   1415    -55    201  -1508  -2696    926   2305  -1718    332   -877    585  -3132   1189  -3229   410
-     -   -159   -489    230     48   -393    391    106   -623    208   -470   -723    279    401     36    106    362    114   -367   -264   -229 
-     -  -1907   -448 -11262  -1831   -476  -1095   -911      *      * 
-   251  -1337    300    199   -985    473   1252  -2522    -11    852  -1939  -3443      4   1241   -508    726   -186    467  -3973  -4538   -749   422
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10789 -11831   -894  -1115   -205  -2918      *      * 
-   252  -3278  -4644    482    537   1408     82    473  -1832   -601    349   -629  -1201   1239   -976    601   -147  -3217   -110    247    426   423
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115  -1984   -420      *      * 
-   253    286    -35   -649    327  -1315  -1967    472  -1932    118    449   -662    521    902  -2448   1699   -196    411  -4342  -4912   -976   424
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115   -870  -1143      *      * 
-   254  -1072  -4374   -669   -329     78  -2066  -3076    298   -238    849    793  -1238    981   -953   1064    324   -798    -92    233    424   425
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115  -1481   -640      *      * 
-   255  -1157  -4745    460   1205   -545   -662   -388   -825   1032   -684   -579  -1144   1754   -996    220   -870   -287   -488    293  -1067   426
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -366  -2158      *      * 
-   256  -1133    675  -3596   -353   1466  -1233    347     10    323    289  -3359     46    554   1055    771  -1097  -3329    288   1117   -152   427
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   257  -1790  -4723    147   -649    460  -2044  -2961   -960  -1300  -1584  -3820    405   2753    391   -111  -1764  -1419  -1995   3263    479   428
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   258  -1133  -4774    919    289  -1472  -4285    510    -76    364  -1072   -506   -466   1480    246    187    969   -220   -998  -4960    487   429
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   259   -628  -4735  -1504    267  -5035   -673    421    268   -650    195   -713   1874   -715  -2504    282    699    318  -1878    176   1059   430
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   260  -1175   3614  -5930  -5294    516  -5135   -538   1325   -983    925   -380  -4780   -704  -1274  -1768  -1016   -812   1047   1179   -985   431
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   261  -1076  -4800   -682   -725  -5121  -2088  -2956  -4872  -1209  -4816  -3890   -471   1956    -73  -1338   2811   -348  -4422  -4983  -4299   432
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   262  -1037  -4782   1535   1680  -5103   -510  -2942   -924    405  -1698  -3871   -529   1595  -2482    233    976  -3248  -4404  -4965  -1079   433
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -51 -11253  -4857   -894  -1115   -701  -1378      *      * 
-   263     84  -4736    971   2258  -5057  -1922  -2895  -4808   -213  -1467   -574     15    534   -116  -1288    303    398  -4358    128    -67   434
-     -   -149   -502    231     48   -378    396    110   -628    208   -463   -712    273    394     43     97    359    120   -371   -297   -251 
-     -   -125  -3594 -12244  -1472   -645   -232  -2751      *      * 
-   264   1731   2547  -5934  -5298    640   -263  -4007   -247  -1801   1576    924  -4782  -5186  -4516  -4693  -4220  -1553    458    192  -3530   439
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   265   -241   -198  -3682   -794   -427  -1936  -3240    612   2124    111  -3291   -475  -4617    956    498  -3480   -202  -1841  -4474   1903   440
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   266   -289   -331   2577    958  -1430  -1196   1052  -1871    140  -1667   -735   -379  -4376    573   -654    661  -3248  -4402  -4964  -1037   441
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   267  -5570  -5207  -7943  -7332   2492  -7349  -6163    426  -7006   2460   -530  -7015  -7020  -6282  -6695  -6514   -964    748  -5450   -851   442
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   268  -1228   -132  -7186  -6649  -4539  -2083  -5657   2368  -6345   1703   2977  -6230  -6527  -6019  -6218  -5733  -4672   1093  -5411  -5058   443
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -11253  -5950   -894  -1115   -701  -1378      *      * 
-   269   -233    733    496    538  -1512   -556   -483  -1871   1194   -153  -3846     49  -4356   -914    979    500    853  -1866  -4941    -84   444
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -360  -2177      *      * 
-   270  -1879    740    708     42  -5102    499  -2941  -4853   1925  -1686  -3871   -478  -4376    840   1351    531  -3248  -1765   1733    -65   445
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   271  -1078   4527  -6001  -5369  -3424  -5188  -4083    473  -4965   1280   2971  -4849  -5245  -1263  -4765  -2003  -1635  -2877  -3945  -3606   446
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   272  -6032   1306  -8380  -7761    165  -7863  -6566    202  -1775   2623   -272  -7537  -7346  -6544  -7063  -7064  -5909  -4318   4168  -5617   447
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   273     16   1673    924    771  -5103  -4283   2109  -1011    386  -4798  -3871   1377  -4376    855    547  -1066    354   -205  -4965  -1058   448
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   274  -1190  -4283  -1596   -753    779  -4462   -457  -1758   1515    461    303  -3221    581    211    534  -1081   -360    361   1085   1460   449
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   275  -1788   -192   3257   -772  -5108  -4287  -2947  -4859   -129  -4804  -3877   2093  -4381   -992  -1328  -1034  -1521   -207  -4971  -4288   450
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   276      9   -212  -3967   -984  -1118  -2024   -395  -3569  -3273  -3831    325  -3573   3646  -1156   -648  -1930  -1495   -116  -4315  -3856   451
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   277    468  -4779   -133   1101  -1427  -1979    368  -1871    610  -1046   -655    948  -1568    259   -674    967    318  -1112     68    403   452
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   278   -657   -189    933   1062  -5103  -4283  -2941  -4854   2011   -701    218    391  -4376   1360    303     74     67  -4404  -4965  -4283   453
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   279  -7207  -7306  -8076  -6588  -8459  -7223  -5448  -7982  -1500  -7531  -6953  -6369  -7277  -5081   4236  -7139  -6862  -7777  -7053  -7277   454
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   280   -694   -163  -5922  -5286  -1204  -2048   -610   1082  -1800   1434  -2618  -4776   2951  -4509  -4688  -1216  -1648  -2829    202     21   455
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -3168 -11253   -171   -894  -1115   -701  -1378      *      * 
-   281  -1412  -2132  -2007  -2293  -4366   3113  -2847  -4225  -3107  -4377  -3503   1660  -2881  -2661  -3396    961  -1821  -3134  -4516  -4119   456
-     -   -150   -489    232     42   -382    400    104   -627    211   -465   -722    274    393     51     95    359    116   -370   -296   -245 
-     -  -2121   -637  -2975   -831  -1191  -6099    -21      *      * 
-   282   -968  -1818  -1787  -1351  -3112    953  -1494  -2818  -1122  -2911  -2044  -1365  -2340  -1133   1510   1816   2121  -2205  -3137  -2649   459
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -228  -7899  -2816   -894  -1115  -4964    -47      *      * 
-   283    840  -1663   -994    969   1159    503   -604  -1413   -325  -1594   -814   -688  -1996   -267   1103   -851   -755  -1179   2900  -1437   460
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9  -7938  -8980   -894  -1115    -89  -4060      *      * 
-   284  -3257  -4642   -697  -2590  -1218   -252  -2907  -4655  -1306  -2353   -529    482  -1607  -2459  -1398   2112   2745  -4246  -4848  -4187   461
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11183 -12226   -894  -1115   -186  -3045      *      * 
-   285   2163    763  -1619  -5296   2250  -2060  -4007   1241  -4891   -489    484  -4781   -226  -4515  -4692   -678  -1688   -813    264  -3530   462
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   286   -268   -329   -158    917   -541  -1990    350  -4851   1273  -1075    388  -1130    233    840    993   -602    801   -595  -4964   -857   463
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   287    109   -243    672   2304  -5103  -4283    488  -4854  -1317  -2269   -656   -492  -1519   2679   -655   -618  -3248  -4404  -4965  -1114   464
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   288   1312   1294  -6215  -5593   -206  -1244  -4339   2188  -5201   1409    395  -5091  -5478  -4828  -5009  -4538  -3794   1162  -4188  -3846   465
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -11253  -6022   -894  -1115   -701  -1378      *      * 
-   289  -3562    799  -5767  -2054  -1235  -2075    318    138    237   2164   1713  -1454  -5145  -1272   -730  -4172  -1640   1071  -3865    -34   466
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115  -1470   -646      *      * 
-   290     73   1351   -674   1236  -1549  -2008   1350  -4834   1049  -2498  -3851   1801  -4356   1813   -115   -223  -1582  -1052  -4945  -4262   467
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
-   291  -1739   -320    777  -2654  -1419  -2051   4360  -4707  -1358  -2412   -689  -1300  -4399   -224    537    531   -289  -2010  -4905  -1057   468
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   292  -3345  -4494   -233   -332   -563  -1986  -3051    333     99   1063  -3616  -3072   2953  -1026  -1490   -943  -1528  -1070  -4753  -4151   469
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10815 -11857   -894  -1115   -701  -1378      *      * 
-   293  -6409  -5751  -7614  -7636   2593  -7311  -4003  -5084  -7219   -150   -151  -6210  -7172   -849  -6723  -6510  -6299  -1387   4881   2807   470
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10749 -11791   -894  -1115   -701  -1378      *      * 
-   294  -4057  -3817  -6415  -5791   3203  -1638  -4541   1679  -5412    765   1434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//

--- a/commons/pyRepetUnit/hmmer/tests/datas/test_input_aa.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,258 +0,0 @@
->blumeria_Grouper_28830_3_1
-CGF*LISL*SQ*FHVGVSWLRLINNIMRVELETNKT*IXFYNTGSPTYLNIPPHHVSQST
-AHNLHGRVSINWDPQTIPLLKTSCPQLI*ITS*LEILLWYHSN*ILAEFLSVFLSCSSIR
-RLPYHRLRTGCPSRTYAGNRFVPLYLLPNLYPPGDIKE*VLLL*QAATAHGPS**GSILC
-LRWRTRSTQSPGA*VRISAFSSWR*ARILSLVAFILLT*ERAIGAGCFLPSSSAQRRSSD
-SVASRVYTG*EFSSSGG*VPKSKK*GLYPLGETLRLKFITASERAPASVILGESRRTLTS
-MAFRTPFACSTLPFPLGLAGVVWTTCSCWLA*NRCASMPPKQPALSLIICFGFPKFWIIY
-VSRGTVLAKSALGTKRDSSQPVAYSIALSKTWGPT*V*SIPHRVRGGAGTIGVKLPSNGS
-GGFMS*QDLHFRTAS*AARISSGCQNLRPNSRIVLPIDAWPWPS*TFTAVDTRSSYSKIS
-SRVAAPDGPGASPTCCDGFFLMRCNLELYIAKLSRTQVAAIFRGSASPKVRNSVMHCRSM
-RLSSCGCFISSISSSLSAPLWILEFSLSSVATFPSPSSLERNRTSQGRERKSARTFAFPR
-R*IILILKCSIASKKRTILTGCSALV*IVRRDSWSVITVTSPPSTQ*RQCCSDSKIPSNS
-LSCAE*RCWVSFSFLEK*AMGCSTERSELLEHRMYGWSMTAPTNFWEASVSNMTGSLQSN
-FFTTGDVVSASLILFHD*IDWSVRMTGQFLGPEDWSVSGPASWEKFLMRQRR*PAAFTNP
-LISEVVVGIGLSLIAETFSGSAAMPCLEIWKPRKIPSETNSLHFEALRRRP*EANLEKIS
-INRECNSAIESAQTATSSRSPATNGRNGSRTSSIKHWKVAGALHRPKGITSHS*TPKGVT
-NAVFSEESLCIRICQNPFSRSRNA*KLCPAAR*ISS*AFGRGWACFFVILLSSL*STQIR
-QTVWLVWVSVFFWC**QRCSPWSLTFAYELSRSCVAQESPRMACCCAGAISPRRGVLNWV
-DNYPVSMRVFLSWESFIPFGGRDLSKS*RGI*L*YCREKL*CGMKGGLGAI*PLEYLK**
-RLFGLGEY*L*D*ELVGQLS*EVAVCHLINIVAPVHGIKFVQVSHLLGMCHLGQLLETL*
-IPESRMIQGDSSKETVQLKLHP*KLLGQGHQCLTF*K**MYYKKSNI*RKTVKHNMLKSR
-SQKKLKIGHRENELFVQKTFCVACHILPVEVVLLGVAQICPFLRPQSRYSGCPIHKFLHF
-AFDIEWLQFRHRAAHLLFGLQGLFALDPNLLAQQGK*K*QALMNDRVVLQVLHIFYFSLI
-GKFS*IYR*NATRCI*RLVHIPFVLLIPPALFSSTGSLSPSGLSFRN*SIRNACRELGMI
-YLFLQCLVTQRRLAHTTLDQLWMRQMLEAFRLLTLRSELVHWTRNV*IHHPQVSTL*YRV
-*LEPLDPQAPRW*VWGDYWK*WSRYVEVRVEYAASVYL*SEALP*HPKVG*RKLSGVVAQ
-IVIESRRFLQLFVQMLSKATRVHHCRTVF*GYSLQLLPNRGVD**LFFAPR*NLHPFPLQ
-F**PKQNMEAYVESSMIACGIIYSLCSHQQSAISIVVGIPRVFFYLPLLKGRADFQLRNA
-KRNLGSTALFFALVQ*HSMVR*LTGGIN**SHLCFAHHCLGWALFHRIAPR*RVFS*AET
-RLAWLRVARRCLLKSQIAPPGMVFYFQMALLPKVERGLNFSKKFLFPRLHFYLLVWKLSR
-SLQTFV*LEEKFVIGSLQTFDRFSWRDLLSLPLQLH*LRKNFRWLWFARQCDPSSSFPTE
-HYSGRP**LNRW*NA*KIWRRLKLG*PRIVRFSQQKYIILWLLVDQFMITMISRRCLVAP
-TNQQYNASRA*D**NVNFIL*YRTANLFKYSPAPREPINSTQFARSGFHQLGST
->blumeria_Grouper_28830_3_2
-VASS*SVYDHNDFT*VSRGSD*STI*CE*SLRLIKREFXSIIQDRQLI*IFPRTT*ANQQ
-RTICTVGFPSIGIHKLSPFSKLAVHSLFKLQVN*KFYYGITQTKSLLNF*VSFYPAPAYG
-GYHTIDYELGVLHVHMPGIGLCRCTCCLICIHPVILRSRYYYYDKLLRPMARHSRAPSCV
-FAGVLAVPSLRGRKYV*VPFLPGGKPVFYP*LLSYY*RRSVLLVRGVSFRVLRPRGAPLI
-LWLHGYILDKNFPPPGAECRRVRSKGYTRWVRLFD*NSLPRVRERQLV*F*ENPGEL*PV
-WLSERHLPVRLCHFLLA*LVWYGQPAVVG*LEIVVLLCLRSSQHCH**SALAFQSSG*YT
-*AEAQC*RSLHWELSGIPASLLRTQLH*ARLGVLLEYDLYPTVSEEVLVL*ELSFPVTGL
-EVS*ADRTCIFGQLREPRGSVRGAKTYALIPA*YCRLTHGLGPHEHLRPSILDPHIPRFL
-VGLRRQMDQVHRLLVATGSF**DAIWNCTSQNYLGPKWQLYLGEVPLLRLEIR*CTAGRC
-G*VRVGALFPPSQVLFLHHFGF*SFRCRQ*LHSLPLLP*REIEHHRDGRENQREHLLFRD
-GR*S*Y*NAL*HLKNGPF*RAARLWSE*FVEIHGQLSPLRRRLLPSDANVVVTVKSQVIP
-SLVLNNAAGYRLVFLRSKLWDAALNDRNCWSIACTVGV*LHPRTFGKRQFPI*REVSNQI
-FLQLVML*ALV*YFSMIESIGPSE*QGNF*VQRIGP*VALLVGRNF**DNVGNQLHLQIL
-LFPR*LLA*ACL*SLKLFRGLLQCHV*KYGNQGRFPLKQIACTLKH*GGDHRKRI*KK*V
-STVSAILPLSLPRQLHRPGALRQMDGMALELLP*NTGK*LVRCIGRKA*LAIHRHRKESQ
-MLFSLKSLCAYVSAKIRFPGRGMHRSYVLLRAEFHLEHLVGDGRVSS*SC*ALYSQHKYA
-KRFG*SGLASFFGVNNRGAAHGPLHLRMN*AGHVLHKKVPGWLVVAPGLYRLGGEF*IGL
-TITPFLCGCFCLGRVLSHLAGEIYRKVEGEFNFDIVGKNCNAE*RVGWVPFDHWNI*SSE
-DFSVWESINYRIKNWLVN*VEKLQFAI**TS*PQFME*SLSKCHICWECAIWDNS*RHCE
-FLSPE*FKVIRAKKLCS*NCILRNCWARATNA*HFRNNRCIIRSQIFRERL*NITC*RAV
-VKKN*KLDIGKMSYSCKKHSVWLAISFP*RLSFWGWLKFALSYGHKVGIRAVLFINFFIS
-HSI*NGFNFVIELLIFYLAFRAYLLLIQIFWLNKESRSDRL**TIVWCYRFYIFFIFH*L
-VSFPEFIAETRRGVFSVWCIFPLFF*FHRRCFHQPAVFRPVACLSAIEAFVTLVVNWV*F
-ICFCNVL*RKDVLPIRPWISYGCVKCWKLFAF*R*DRNWCIGLGMFEYIILKCPPCNTAC
-DLNHSIRKLRAGEFGEIIGNDGPGTWK*ESNMLPQYISSLRPYHDIRR*AKESFPESSRK
-L*LSLVVSCSYSCKCCQRRPEYIIVEQYFKDTVYSSCPIEVLTDDCSSRRDEIFIHFHCN
-SDSPSRIWKHMLNHQ*LHVV*YIHYVLISKVQFPLWWEYRACFSICLF*RAVRIFSFGTR
-KEIWEVPLYFSLLFSNIQWFVN*LAV*INSPIFVLLIIA*VGRCFIELRRGKGSFLRLKH
-DWPGCGSRGAAC*KVK*LLPVWFFIFRWPCFRKLKGD*IFRRSFCFHVFISTY*FGN*VV
-HCRHLFD*KRNL*LGLFKPLIDSLGEIFCHCLCSFISFGKIFVGFGLPGNVILHQAFQLS
-IIQADHDD*IGGEMRKKFGDVLNWDDLEL*GSLNKNI*FCGF*LISL*SQ*FHVGVSWLR
-QINNIMRVELETNKT*ISFYNTGPPTYLNIPPHHVSQSTAHNLHGRVSINWDP
->blumeria_Grouper_28830_3_3
-WLLVDQFMITMISRRCLVAPTNQQYNASRA*D**NVNXIL*YRIANLFKYSPAPREPINS
-AQFARSGFHQLGSTNYPPSQN*LSTAYLNYKLIRNFIMVSLKLNPC*IFECLSILLQHTA
-ATIP*TTNWVSFTYICRE*VCAVVLVA*FVSTR*Y*GVGIIIMTSCYGPWPVIVGLHLVS
-SLAYSQYPVSGGVSTYKCLFFLEVSPYFIPSCFHTTNVGACYWCGVFPSEFFGPEALL*F
-CGFTGIYWIRIFLLRGLSAEE*EVRAIPAG*DSSIEIHYRE*ESAS*CNFRRIQENSDQY
-GFQNAICLFDFAISSWPSWCGMDNLQLLASLKSLCFYASEAASIVTDNLLWLSKVLDNIR
-EQRHSVSEVCIGN*AGFQPACCVLNCIEQDLGSYLSMIYTPPCQRRCWYYRS*ASQ*RVW
-RFHELTGLAFSDSFVSREDQFGVPKPTP*FPHSIAD*RMALALMNIYGRRY*ILIFQDF*
-*GCGARWTRCIAYLLRRVLFDEMQFGIVHRKIISDPSGSYI*GKCLS*G*KFGDALQVDA
-VEFVWVLYFLHLKFSFCTTLDSRVFVVVSSYIPFPFFPREK*NITGTGEKISENICFSAT
-VDNPDIKMLYSI*KTDHSDGLLGFGLNSS*RFMVSYHRYVAAFYPVTPML**Q*NPK*FP
-LLC*ITLLGIV*FS*EVSYGMQH*TIGIVGASHVRLEYDCTHELLGSVSFQYDGKSPIKF
-FYNW*CCKR*FDTFP*LNRLVRQNDRAIFRSRGLVREWPC*LGEIFNETT*VTSCIYKSS
-YFRGSCWHRPVSDR*NFFGVCCNAMFRNMETKEDSL*NK*PAL*SIEEETIGSESRKNKY
-QP*VQFCH*VCPDSYIVQEPCDKWTEWL*NFFHKTLESSWCVA*AERHN*PFIDTERSHK
-CCFL*RVFVHTYLPKSVFQVEECIEVMSCCALNFILSIW*GMGVFLRNLVKLSIVNTNTP
-NGLVSLG*RLFLVLITEVQPMVPYICV*IEPVMCCTRKSPDGLLLRRGYIASEGSFKLG*
-QLPRFYAGVSVLGEFYPIWRERFIEKLKGNLTLIL*GKTVMRNEGWAGCHLTIGIFEVVK
-TFRFGRVLIIGLRIGWSIKLRSCSLPFDKHRSPSSWNKVCPSVTSAGNVPSGTTPRDTVN
-S*VQNDSR*FEQRNCAVKIASLEIVGPGPPMPDILEIIDVL*EVKYLEKDCET*HAEEP*
-SKKTENWT*GK*VIRAKNILCGLPYPSRRGCPFGGGSNLPFPTATK*VFGLSYS*ISSFR
-IRYRMASISSSSCSSSIWPSGLICS*SKSSGSTRKVEVTGFDERSCGVTGFTYFLFFIDW
-*VFLNLSLKRDEVYLAFGAYSLCSFDSTGAVFINRQSFAQWPVFPQLKHS*RLS*IGYDL
-SVSAMSCDAKTSCPYDLGSAMDASNAGSFSPFDAEIGIGALDSECLNTSSSSVHLVIPRV
-T*TTRSASSALVSLGRLLEMMVQVRGSESRICCLSISLV*GPTMTSEGRLKKAFRSRRAN
-CN*VSSFLAVIRANVVKGDPSTSLSNSILRIQSTAPAQSRC*LMIVLRAEMKSSSISIAI
-LIAQAEYGSIC*IINDCMWYNIFIMFSSAKCNFHCGGNTARVFLFASFKGPCGFSASERE
-KKSGKYRFIFRSCSVTFNGSLTDWRYKLIVPSLFCSSLLRLGVVS*NCAEVKGLFLG*NT
-IGLVAGREALPAEKSNSSSRYGFLFSDGPASES*KGTEFFEEVFVSTSSFLLTSLEIKSF
-IADICLTRREICDWVSSNL*SILLERSFVTAFAASLASEKFSLALVCPAM*SFIKLSN*A
-LFRPTMMIE*VVKCVKNLETS*IGMT*NCEVLSTKIYNFVASS*SVYDHNDFT*VSRGSD
-KSTI*CE*SLRLIKREFHSIIQDRQLI*IFPRTT*ANQQHTICTVGFPSIGIH
->blumeria_Grouper_28830_3_4
-CGSQLMETRPCKLCAVDWLTWCGGIFK*VGGPVL*NEIHVLLVSSSTRIILLICRSHETP
-T*NHCDHKLIN*KPQNYIFLLREPHNSRSSQFKTSPNFLRISPPIQSSWSA*IMLSWKA*
-*RITLPGKPKPTKIFPKLMKLQRQ*QKISPRESIKGLKRPNHKFLF*SNKCLQ*TT*FPN
-**VEMKTWKQKLLRKIQSPFNFRKQGHLKIKNHTGRSYLTFQQAAPRDPQPGQSCFSLRK
-DPLPRRNSMKQRPT*AMMSKTKMGLLIYTASQLTNH*MLLNKSEK*SGTSQISFRVPKLK
-IRTAL*KRQIEKHARYSHHNGNCTLLMRT**IYYTTCNH**FNICFHILLGLSELQWKWM
-KISSRREEQSSVNTSIGQEL*TVSLKYCSTMMYSGRL*QHLHE*LQETTRLNYNLRDDSG
-KLSLAYLRMSW*GLRLEIY*GSIFDSHFHVPGPSFPIISPNSPARSLRIEWFKSHAVLQG
-GHLRMMYSNIPSPMHQFRSQRQKAKSFQHLTHP*LIQGRMGKTSLRHKTLQKQINHTQFT
-TSVTNASIAERQATGRKTAG**KQRRWNQKNKGNMHQTLNTPRRVSAINSGKLTNQ*KIK
-NM*NL*HHTIVHQSLSLLLSLLSQKIWIKSK*ALKAK*KMSSSMTKLKPFYIECEMKKFM
-NRTARIPTLWP*ERANLSHPQKDNLYGKDMASHTECFLHE*LIFPMSNFQFFLTTALQHV
-MFHSLSLNI*LLIIHLLFLKCQALVALAQQFLRMQF*LHSFFARITLNHSGLRNSQCL*E
-LSQMAHSQQM*HLDKLYSMNWGYDVYQMANCNFST*LTNQFLIL*LILSQTEKSSLLQIF
-QWSNGTQPTLHSALQFFPTISKLNSPSTFR*ISPAKWDKTLPRQKHPHRNGVIVNPI*NS
-PPRRYSPGATTSHPGTFLCNT*PAQFIRKCKGPWAAPLLLTPKKDANPD*PNRLAYLC*L
-*RA*QDYEETRPSPTKCSR*NSARSRT*LLCIPRPGKRILADTYAQRLFRENSICDSFRC
-L*MASYAFRPMQRTSYFPVFYGRSSRAIPSICRRAPGRCSCLGRLNGRIALTVDTYFF*I
-RFLWSPPQCFKVQAICFRGNLPWFPYF*TWHCSRPRKSFSDQRQAYANNYLGNKRICKCS
-WLPTLSH*KFLPTSRATHGPILWT*KLPCHSDGPIDSIMEKYQTSAYNITSCKKI*LETS
-RHIGN*RFPKVRGCSHTPTVHAMLQQFRSFSAASHSLLLKKTKRYPAALFSTREGITWDF
-TVTTTLASLGRRRRRNGDN*P*ISTNYSDQSRAARQNGPFFRCYRAF*YQDYLPSRKSKC
-SR*FSLPSL*CSISL*GRRGRECSY*RQRKL*NPKWCRKRT*DGGNKAPTRTQPHRPAVH
-HRISNLRRGTSPKYSCHLGPR*FCDVQFQIASHQKEPVATSRRCTWSIWRRNPTRNLGI*
-GSSIDGRKCS*GPRPCVNRQYYAGIRA*VLAPRTDPRGSRSCPKMQVLSAHETSRPVTGK
-LNSYSTSTSSDTVGYRSYSSRTPSLAQCN*VRNRLAGIPLSSQCRLR*HCASAHVYYPEL
-WKAKADYQ*QCWLLRRHRSTTISS*PTTAGCPYHTS*AKRKWQSRTGKWRSESHTGQSSP
-GFS*NYTSWRSLTRGNEFQSKSLTQRV*PLLLTLRHSAPGGGKFLSSIYP*SHRIRGAPL
-GRRTRKETPRTNSTLLR**YESN*G*NTGLPPGRKGTYTYLRPRRLGTASTPAKTQDGAL
-L*RAMGRSSLS***YLLLNITGWIQIRQQVQRHKPIPGICT*RTPSS*SMVW*PPYAGAG
-*KDTQKFSKDLV*VIP**NF*LTCNLNKLWTASFEKGDSLWIPIDGNPTVQIVRC*LAHV
-VRGNI*ISWRSCIIEXNSRFISLKLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT
->blumeria_Grouper_28830_3_5
-VDPN*WKPDRANCVLLIGSRGAGEYLNKLAVLYYRMKFTFY*SQALLALYC*FVGATRHL
-REIIVIIN*STRSHKIIYFC*ENLTILGHPNLRRLQIFYAFHHLFNHHGRPE*CSVGKLD
-EGSHCRANQSQRKFFRS**SCKGSDKRSLQENRSKV*RDPITNFSSSQTNVCNERLNFQT
-SK*K*RRGNKNFFEKFSPLSTFGSRAI*K*KTIPGGAI*LFSRQRLATRNQANRVSA*EK
-TLYLGAIL*NNAQPKQ**AKQRWDY*FIPPVS*RTIECY*TRAKNKAVLPRFLFAFRS*K
-SARPFKRGK*KNTRGIPTTMEIALC**EHNEYIIPHAIIDDSTYASIFCLGYQNCNGNG*
-RFHLGAKNNHQSTPRLGRSCRLYP*NTVRQ*CTRVAFDNICTNNCKKRRDSITICATTPE
-SFL*PTFGCHGRASD*RYTEAAYSTLTSTYLDHHFQ*SPQTHQRGACGSSGSSHTRYYKV
-DT*G*CIQTFRVQCTNSDLSVKRRKASSI*RIHS*SKVVWARRLCVTRHCRNR*IIPNSR
-QALRMLQLRKDRPLGERLPVDENSAGGIKRTKGICTKR*IHLVAFQR*IQENLPINEK*K
-ICKTCNTTRSFIKACHFYFPC*ARRFGSRANKP*RPNRR*AAR*RN*SHSISNAK*RNL*
-IGQPEYLLCGRRKGQI*ATPKRTTSTGRIWQATQNVFCTNNSFSLCPIFSFF*LRLFSML
-CFTVFL*IFDFL*YIYYF*NVRHWWPWPNNF*GCNFNCTVSLLESP*IILDSGIHSVSRS
-CPRWHIPSRCDTWTNFIP*TGATMFIKWQTATSQLN*PTNS*SYN*YSPKPKSLHYFKYS
-NGQMAPSPPFIPHYSFSLQYQS*IPLQLFDKSLPPNGIKLSQDRNTRIETG*LSTQFKTP
-LRGDIAPAQQQAIRGLSCATHDRLNSYANVRDHGLHLCY*HQKKTLTQTNQTVWRICVDY
-RELNKITKKHAHPLPNAQDEIQRAAGHNFYAFLDLENGFWQIRMHKDSSEKTAFVTPFGV
-YEWLVMPFGLCNAPATFQCFMEEVLEPFRPFVAGLLDDVAVWADSMAELHSRLILIFSRF
-ASYGLLLNASKCRLFVSEGIFLGFHISKHGIAADPEKVSAIRDRPMPTTTSEIRGFVNAA
-GYLRCLIKNFSQLAGPLTDQSSGPKNCPVILTDQSIQSWKSIKLALTTSPVVKKFDWRLP
-VILETDASQKFVGAVILQPYMRCSNNSDRSVLHPIAYFSRKLNDTQQRYSAQERELLGIL
-LSLQHWRHWVEGGDVTVITDHESLRTIQTKAEQPVRMVRFLDAIEHFNIRIIYRRGKANV
-LADFLSRPCDVLFLSREEGEGNVATDDNENSRIQSGAERELEMEEIKHPHELNRIDLQCI
-TEFLTLGEALPLNIAATWVRDNFAMYNSKLHLIKKNPSQQVGDAPGPSGAATLLEILEYE
-DLVSTAVNVHEGQGHASIGNTMRELGRRFWHPELILAAHEAVRKCKSCQLMKPPDPLLGS
-LTPIVPAPPLTRWGIDHTQVGPQVLLNAIEYATGWLESRLVPNADFANTVPLLTYIIQNF
-GKPKQIISDNAGCFGGIEAQRFQASQQLQVVHTTPARPRGNGKVEQANGVLKAILVRVLL
-DSPKITLAGALSLAVMNFNRRVSPSGYSPYFLLFGTQPPEEENSYPVYTREATESEERLW
-AEELGRKHPAPIARSYVSSMKATRDKIRAYLQEEKALIRTYAPGDWVLRVRQRRHKMEPY
-YDGPWAVAACHNNNTYSLISPGGYKLGNKYNGTNLFPAYVREGHPVRSLWYGSRRMLEQD
-RKTLKNSARI*FE*YHNKISN*LVI*ISCGQLVLRRGIVCGSQLMETRPCKLCAVDWLTW
-CGGIFK*VGDPVL*NXIHVLLVSSSTRIILLISRSHETPT*NHCDHKLIN*KP
->blumeria_Grouper_28830_3_6
-WIPIDGNPTVQIVCC*LAHVVRGNI*ISWRSCIIE*NSRFISLKLYSHYIVDLSEPRDTY
-VKSL*S*TDQLEATKLYIFVERTSQF*VIPI*DVSKFFTHFTTYSIIMVGLNNAQLESLM
-KDHIAGQTKANENFSEANEAAKAVTKDLSKRIDQRFEETQSQISLLVKQMSAMNDLISKL
-VSRNEDVETKTSSKNSVPFQLSEAGPSENKKPYREELFDFSAGSASRPATRPIVFQPKKR
-PFTSAQFYETTPNLSNDEQNKDGTINLYRQSVNEPLNVTEQERKIKRYFPDFFSRSEAEN
-PHGPLKEANRKTRAVFPPQWKLHFADENIMNILYHMQSLMIQHMLPYSAWAIRIAMEMDE
-DFISARRTIISQHLDWAGAVDCILKILFDNDVLGSPLTTFARITARNDETQLQFARRLRK
-AFFSLPSDVMVGPQTRDILRQHIRLSLPRTWTIISNNLPKLTSAELADRVVQVTRGITRW
-TLEDDVFKHSESNAPIPISASKGEKLPAFDASIADPRSYGQDVFASQDIAETDKSYPIHD
-KRYECFNCGKTGHWAKDCRLMKTAPVESKEQREYAPNAKYTSSRFSDKFRKTYQSMKNKK
-YVKPVTPHDRSSKPVTSTFLVEPEDLDQEQISPEGQIEDEQLDDEIEAILYRMRNEEIYE
-*DSPNTYFVAVGKGKFEPPPKGQPLREGYGKPHRMFFARITHFPYVQFSVFFDYGSSACY
-VSQSFSKYLTSYNTSIISKMSGIGGPGPTISKDAILTAQFLCSNHLESFWTQEFTVSLGV
-VPDGTFPADVTLGQTLFHELGLRCLSNGKLQLLNLIDQPILNPIINTLPNRKVFTTSNIP
-MVKWHPAHPSFRITVFPYNIKVKFPFNFSINLSRQMG*NSPKTETPA*KRGNCQPNLKLP
-SEAI*PRRNNKPSGDFLVQHMTGSIHTQM*GTMGCTSVINTKKRR*PRLTKPFGVFVLTI
-ESLTRLRRNTPIPYQMLKMKFSAQQDITSMHSSTWKTDFGRYVCTKTLQRKQHL*LLSVS
-MNG*LCLSAYATHQLLSSVLWKKF*SHSVHLSQGSWTM*LSGQTQWQNCTHG*YLFFLDS
-LPMVSSSMLQSAGYLFQRESSLVSIFLNMALQQTPKKFQRSETGLCQQLPRK*EDL*MQL
-VTYVVSLKISPN*QGHSRTNPLDLKIALSF*RTNRFNHGKVSN*RLQHHQL*KNLIGDFP
-SYWKLTLPKSSWVQSYSNRTCDAPTIPIVQCCIP*LTSQEN*TIPSSVIQHKRGNYLGFY
-CHYNIGVTG*KAAT*R**LTMNLYELFRPKPSSPSEWSVF*ML*SILISGLSTVAEKQMF
-SLIFSPVPVMFYFSLGKKGKGM*LLTTTKTLESKVVQKENLRWRK*STHTNSTASTCSAS
-PNF*P*ERHFP*I*LPLGSEIILRCTIPNCISSKRTRRNK*AMHLVHLAPQPY*KSWNMR
-I*YRRP*MFMRAKAMRQSAILCGN*GVGFGTPN*SSRLTKLSENASPVSS*NLQTRYWEA
-*LL*YQHLL*HGGV*IILK*DPKSCSMQLSTQQAGWNPA*FPMQTSLTLCLCSRILSRTL
-ESQSRLSVTMLAASEA*KHNDFKLANNCRLSIPHQLGQEEMAKSNRQMAF*KPYWSEFSW
-ILLKLH*LALSHSR**ISIEESHPAGIALTSYSSALSPRRRKILIQYIPVKPQNQRSASG
-PKNSEGNTPHQ*HAPTLVV*KQLGIKYGLTSRKKRHLYVLTPPETGYCEYASEDTRWSPT
-MTGHGP*QLVIIIIPTP*YHRVDTN*ATSTTAQTYSRHMYVKDTQFVVYGMVAAVCWSRI
-ERHSKIQQGFSLSDTIIKFLINL*FK*AVDS*F*EGG*FVDPN*WKPDRANCALLIGSRG
-AGEYLNKLAILYYRXKFTFY*SQALLALYC*LVGATRHLREIIVIIN*STRSH
->blumeria_Grouper_14770_3_1
-G*TDTVSLV*SCGRKN*LETSVLRCMVLSKTELIRVRLRVRISYQLRFLTSIYQSPWIIS
-YDPCRCKSIYVQIYEPEI*S*IHVCR**IRETFNLHLIHNHLMEC*CEINANVR*TFREE
-CADDNDIGR*I**PN*PDLQMSYPWHSRIYNISTPLLTLHRG*IHK*KTVSIFIVISHLM
-LVW*TRQWLY*YQKLKCINRCALVSVSLLYIYLRDF*LKEHVIV*ASRLQFFPL*NDKRC
-RYV*KHHLVLDCEQVQWQPYCQSRLLLGCCLQGIGEVRAKSRYIVWMRALLPCTQLRRLN
->blumeria_Grouper_14770_3_2
-VRPIQ*VSYEVVEGRIDWKQVY*DVWF*VKLS**E*DCVCAYLIN*GF*PVFINLHGS*V
-MIPVDVNLYTYRYMSQKYKAKYMCVGNRSEKPLTCI*YIII*WNASVK*MPMYVKLSVRN
-VLMTMI*EGEFDNLISRTYK*VILGIPGYTIFQHPSSLCIEDRYISEKLLVYLLSFLI*C
-WYGRHASGCTSTKN*SA*IGVPWSR*AFCTYICEIFS*RNM**CKRAVFNSFPCKMISDV
-DMFRSII*FWIVSKFNGSRIVSRDCCWDAVSKESVKSAQNPDILFGCERYCHVLSFAG*M
->blumeria_Grouper_14770_3_3
-LDRYSKSRMKLWKEELTGNKCIEMYGSE*N*ADKSEIACAHILSTEVFDQYLSISMDHKL
-*SL*M*IYIRTDI*ARNIKLNTCVSVIDPRNL*PAFDT*SSDGMLV*NKCQCTLNFP*GM
-C**Q*YRKVNLIT*LAGLTNELSLAFQDIQYFNTPPHFASRIDT*VKNC*YIYCHFSSNA
-GMVDTPVVVLVPKTEVHKSVCLGLGKPFVHISARFLAEGTCNSVSEPSSILSLVK**AMS
-ICLEASFSFGL*ASSMAAVLSVEIAAGMLSPRNR*SPRKIQIYCLDASAIAMYSASQVE
->blumeria_Grouper_14770_3_4
-HSTCEAEYMAIALASKQYIWILRGLHRFLGDSIPAAISTDNTAAIELAHNPKLNDASKHI
-DIAYHFTRERIEDGSLTLLHVPSAKNLADICTKGLPRPRHTDLCTSVFGTSTTTGVSTIP
-ALDEK*Q*IY*QFFTYVSILDAK*GGVLKYCISWNAKDNSFVSPAN*VIKFTFLYHCHQH
-IPHGKFNVHWHLFHTSIPSDDYVSNAG*RFLGSITDTHVFSFIFLAHISVRI*IYIYRDH
-NL*SMEIDKYWSKTSVDKICAHAISLLSAQFYSEPYISIHLFPVNSSFHNFIRDLLYRSN
->blumeria_Grouper_14770_3_5
-IQPAKLSTWQ*RSHPNNISGFCADFTDSLETASQQQSRLTIRLPLNLLTIQN*MMLLNIS
-TSLIILQGKELKTARLHYYMFLQLKISQIYVQKAYRDQGTPIYALQFLVLVQPLACLPYQ
-H*MRNDNKYTNSFSLMYLSSMQSEEGC*NIVYPGMPRITHL*VRLIRLSNSPSYIIVIST
-FLTESLTYIGIYFTLAFHQMIMYQMQVKGFSDLLPTHMYLALYFWLIYLYVYRFTSTGII
-TYDPWRLINTGQKPQLIRYAHTQSHSYQLSFTQNHTSQYTCFQSILPSTTSYETYCIGLT
->blumeria_Grouper_14770_3_6
-FNLRS*VHGNSARIQTIYLDFARTSPIPWRQHPSSNLD*QYGCH*TCSQSKTK*CF*TYR
-HRLSFYKGKN*RRLAYTITCSFS*KSRRYMYKRLTETKAHRFMHFSFWY*YNHWRVYHTS
-IR*EMTINILTVFHLCIYPRCKVRRGVEILYILECQG*LICKSG*LGYQIHLPISLSSAH
-SSRKV*RTLAFISH*HSIR*LCIKCRLKVSRIYYRHTCI*LYISGSYICTYIDLHLQGS*
-LMIHGD**ILVKNLS**DMRTRNLTLISSVLLRTIHLNTLVSSQFFLPQLHTRLTVSV*
->blumeria_Grouper_1717_12_1
-ISSILP*RASKS*SNSFRSLSSVTGSNSLQNPMMKRSACAERVWNILPCSARNLVATI*G
-DGVCWCGELR*LAS*IGSTNCCVGCCDGGCGPLRTISTS*RVEH*VGRGGQEPASAEDWG
-GMSE*GLWQCEIVDGIRRA*R
->blumeria_Grouper_1717_12_2
-FPVSCPEGPVSPDRIVFEVSRQ*LVPTACRTQ**SALLVRSASGISCPVRRGIWSRRFEA
-TEFVGAVSFDDSPRRLALQIVVWVVVMAVVAR*GPFRRLDASNIELGGGAKSQPLRRTGA
-A*VSEVCGSVRS*MVYGALEG
->blumeria_Grouper_1717_12_3
-FQYLALKGQ*VLIE*FSKSLVSDWFQQLAEPNDEALCLCGARLEYPALFGEEFGRDDLRR
-RSLLVR*ASMTRLVDWLYKLLCGLL*WRLWPVKDHFDVLTRRTLSWEGGPRASLCGGLGR
-HE*VRFVAV*DRRWYTARLK
->blumeria_Grouper_1717_12_4
-PFKRAVYHLRSHTATNLTHSCRPSPPQRLALGPPSQLNVRRVKTSKWSLTGHNRHHNNPH
-NNL*SQSTRRVIEAHRTNKLRRLKSSRPNSSPNRAGYSRRAPHKQSASSLGSASCWNQSL
-TRDFENYSIRTYWPFRARYWK
->blumeria_Grouper_1717_12_5
-PSSAPYTIYDLTLPQTSLTHAAPVLRRGWLLAPPPNSMFDASRRRNGP*RATTAITTTHT
-TICRANLRGESSKLTAPTNSVASNRRDQIPRRTGQDIPDALRTSRALHHWVLQAVGTSH*
-RETSKTIRSGLTGPSGQDTGN
->blumeria_Grouper_1717_12_6
-LQARRIPSTISHCHKPHSLMPPQSSAEAGSWPPLPTQCSTRQDVEMVLNGPQPPSQQPTQ
-QFVEPIYEASHRSSPHQQTPSPQIVATKFLAEQGRIFQTRSAQAERFIIGFCKLLEPVTD
-ERLRKLFDQDLLALQGKILE

--- a/commons/pyRepetUnit/hmmer/tests/datas/test_input_nt.fa	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
->blumeria_Grouper_28830_3
-TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC
-CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC
-TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA
-GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC
-AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT
-CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG
-CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG
-TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA
-TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT
-CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT
-TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG
-CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT
-TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG
-AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC
-GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT
-ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT
-GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG
-AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC
-GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG
-CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA
-CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT
-GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC
-AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG
-CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT
-AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT
-TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT
-ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG
-CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT
-TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG
-AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA
-CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG
-GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG
-TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC
-CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG
-GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT
-GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT
-TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT
-TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT
-GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT
-CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG
-TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT
-AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT
-ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC
-CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT
-GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA
-AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG
-TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT
-AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC
-CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC
-CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC
-CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT
-GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC
-GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG
-TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA
-AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT
-TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT
-GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA
-ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG
-CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG
-TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT
-AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC
-TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC
-CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC
-GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT
-CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG
-GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT
-GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT
-ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC
-AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT
-TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG
-CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG
-CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG
-TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA
-TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT
-GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA
-ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC
-CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA
-GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA
-TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT
-ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG
-CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG
-AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT
-CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA
-GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA
-CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC
-GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT
-TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT
-TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT
-GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA
-AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG
-CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA
-CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG
-TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG
-ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA
-TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC
-ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA
->blumeria_Grouper_14770_3
-GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA
-AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG
-CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT
-TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC
-TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT
-CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA
-TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA
-ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT
-CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG
-CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG
-TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA
-CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT
-CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT
-TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA
-TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT
-G
->blumeria_Grouper_1717_12
-ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC
-TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG
-GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC
-GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT
-TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA
-CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC
-GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA
-AGGG
-

--- a/commons/pyRepetUnit/profilesDB/CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils
-import re
-import sys
-
-
-class CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber(object):
-    '''
-    Check if profiles from a profiles list are present in profiles DB, if not you can generate the getz command to add them.
-    By default the profiles list is a list of profiles names    
-    '''
-
-    def __init__(self):
-        '''
-        Constructor
-        '''
-        self.profilesDBUtils = ProfilesDatabankUtils()
-        self.profilesToAddNotInDB = []
-        self._pfamAccNumber = False
-
-    def setProfilesDBFile ( self, profilesDBFile ):
-        self._profilesDBFile = profilesDBFile
-        
-    def setProfilesToAdd ( self, profilesFile ):
-        self._profilesToAdd = profilesFile
-        
-    def setPfamAccNumberKeys ( self ):
-        self._pfamAccNumber = True
-
-    def _IsProfilInDB(self, pfamDBList, profil):
-        IsProfilInDB = False
-        for profilInstance in pfamDBList.getList():
-            if (self._pfamAccNumber == False and profilInstance.name == profil) or (self._pfamAccNumber == True and re.match(profil + "\.\d+", profilInstance.accNumber)):
-                IsProfilInDB = True
-                break 
-        return IsProfilInDB
-    
-    def _generateProfilesList(self):
-        f = open(self._profilesToAdd)
-        profilesToAddList = f.readlines()
-        return profilesToAddList
-
-    def generateNotExistingProfilesList ( self ):
-        '''
-        generate the profiles list of profiles not in profiles DB among profiles in a list of name or accession number
-        '''        
-        self.profilesToAddNotInDB = []
-        profilesToAddList = self._generateProfilesList()
-        pfamDBList = self.profilesDBUtils.read( self._profilesDBFile )
-        if pfamDBList.getList( ) != []:           
-            for profil in profilesToAddList: 
-                if profil != "\n":
-                    sys.stdout.flush()
-                    profil = profil.rstrip( )
-                    IsProfilInDB = self._IsProfilInDB(pfamDBList, profil)
-                    if ( IsProfilInDB == False):
-                        self.profilesToAddNotInDB.append( profil )
-        return ( self.profilesToAddNotInDB )    
-      
-    def generateGetzCmdProfilesList ( self, profilesList ):
-        '''
-        generate the getz command to retrieve profiles list of name or accession number
-        ''' 
-        getzCmd = "getz -e \'"
-        if (self._pfamAccNumber == False):
-            for profileName in profilesList:
-                getzCmd += "[pfamhmm-Id:\"" + profileName + "*\"] | "
-        else:
-            for profileAccNumber in profilesList:
-                getzCmd += "[pfamhmm-AccNumber:\"" + profileAccNumber + "\"] | "
-        getzCmd = getzCmd[ 0:len( getzCmd )-3 ]
-        getzCmd += "\'"
-        return getzCmd
-    
-    def CmdToCompleteProfileDB (self):
-        '''
-        generate the getz command to retrieve profiles list of name or accession number if the profile is not yet in profiles DB
-        ''' 
-        profilesList2Add = self.generateNotExistingProfilesList()
-        return self.generateGetzCmdProfilesList ( profilesList2Add )

--- a/commons/pyRepetUnit/profilesDB/InsertProfilesMapFileInDB.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-from commons.core.coord.Map import Map
-from pyRepet.sql.TableAdaptator import TableMapAdaptator
-
-class InsertProfilesMapFileInDB(object):
-    '''
-    Insert a map File in a database
-    You have to specified the input file name, the table name and the repetDB object when you create the object
-    '''
-
-    def __init__(self, inputFileName, tableName, db):
-        '''
-        Constructor
-        '''
-        self.inputFileName = inputFileName
-        self.tableName = tableName
-        self.db = db
-        
-    def createAndLoadTable(self):
-        '''
-        Create the table and load the map data from input table
-        '''
-        self.db.createTable(self.tableName, "map", overwrite = True)
-        f = open (self.inputFileName, "r")
-        iMap = Map()
-        lMap = []
-        while iMap.read( f ):
-            lMap.append(iMap)
-            iMap = Map()
-        f.close()
-        self._tMapA = TableMapAdaptator( self.db, self.tableName )
-        self._tMapA.insMapList( lMap )
-        
-        
-if __name__ == "__main__":                 
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/Profiles.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-import re
-
-#------------------------------------------------------------------------------
-
-class Profiles:
-    '''
-    Hmm profile Class
-    Attributes are name, desc, length, accNumber, GA_cut_off and retrieve
-    '''
-    
-    #--------------------------------------------------------------------------
-
-    def __init__( self, name="", desc="", length=0, accNumber = "", GA_cut_off = 0, retrieve = False ):
-        self.name = name
-        self.desc = desc
-        self.length = length
-        self.accNumber = accNumber
-        self.GA_cut_off = GA_cut_off
-        self.retrieve = retrieve
-        self.tab_profile = []
-        
-    #--------------------------------------------------------------------------
-
-    def _noProfileInFile(self):
-        self.name = None
-        self.desc = None
-        self.length = None
-        self.accNumber = None
-        self.GA_cut_off = None
-
-    #--------------------------------------------------------------------------
-
-    def _initialisation(self):
-        self.name = ""
-        self.desc = ""
-        self.length = 0
-        self.accNumber = ""
-        GA_cut_off = 0
-        self.tab_profile = []
-        
-    #--------------------------------------------------------------------------
-
-    def read( self, hmmFile ):
-        '''
-        Read a profile and characterize the object profile
-        attributes name, length, desc, accNumber and GA_cut_off are specified
-        '''
-        line = hmmFile.readline()
-        if line == "":
-            self._noProfileInFile()
-            return
-        self._initialisation()
-        if self.retrieve:
-            self.tab_profile.append(line)        
-        while not re.match("\/\/.*", line):            
-            line = hmmFile.readline()
-            if self.retrieve:
-                self.tab_profile.append(line)                  
-            name = re.match("NAME\s*(.*)", line)
-            if name:                    
-                self.name = name.group(1)
-            desc = re.match("DESC\s*(.*)", line)
-            if desc:                    
-                self.desc = desc.group(1)
-            length = re.match("LENG\s*(.*)", line)
-            if length:                    
-                self.length = int(length.group(1))
-            accNumber = re.match("ACC\s*(.*)", line)
-            if accNumber:                    
-                self.accNumber = accNumber.group(1)
-            GA_cut_off = re.match("GA\s*\d*\.\d*\s*(.*);", line)
-            if GA_cut_off:                    
-                self.GA_cut_off = float(GA_cut_off.group(1))
-            else : 
-                if (self.GA_cut_off == 0):
-                    self.GA_cut_off = "NA"
-        if self.retrieve:
-            return self.tab_profile
-        else:
-            return 1
-            
-    #--------------------------------------------------------------------------
-
-    def readAndRetrieve( self, hmmFile ):  
-        '''
-        Read a profile and characterize the object profile
-        attributes name, length, desc, accNumber and GA_cut_off are specified
-        And a list of each line of profile is returned
-        '''
-        self.retrieve = True
-        return self.read(hmmFile)

--- a/commons/pyRepetUnit/profilesDB/ProfilesDB2Map.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils
-
-
-class ProfilesDB2Map ( object ):
-    """
-    write a file in map format from a ProfilDatabank object
-    You have to set an input File and an Output File names
-    """
-
-    def __init__(self):
-        self.profilesDBUtils = ProfilesDatabankUtils()
-        self._inputFile = "" 
-        self._outputFile =  ""    
-        
-    def setInputFile(self, input):
-        self._inputFile = input
-         
-    def setOutputFile(self, output):
-        self._outputFile = output   
-         
-    def _readProfilesDB( self ):
-        pfamDB = self.profilesDBUtils.read( self._inputFile )
-        return pfamDB
-    
-    def _writeMapFile( self, pfamDBList ):
-        """
-        write a file in map format from a ProfilDatabank object
-        """
-        if pfamDBList.getList() != []:
-            f = open( self._outputFile , "w")
-            for ProfilInstance in pfamDBList.getList():
-                f.write(ProfilInstance.name + "\t" + ProfilInstance.desc + "\t1\t" + str(ProfilInstance.length) + "\n")
-            f.close()   
-    
-    def run( self ):
-        """
-        read a profiles DB file, parse it and, write the corresponding .map file
-        """
-        pfamDBList = self._readProfilesDB()
-        self._writeMapFile(pfamDBList)

--- a/commons/pyRepetUnit/profilesDB/ProfilesDB4Repet.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,226 +0,0 @@
-#!/usr/bin/env python
-
-import re
-import getopt
-import sys
-from commons.pyRepetUnit.profilesDB.Profiles import Profiles
-from commons.core.LoggerFactory import LoggerFactory
-
-LOG_DEPTH = "commons.pyRepetUnit.profiles"
-
-## Format a profiles DB for pipelines in REPET
-#    
-class ProfilesDB4Repet( object ):
-    
-    def __init__(self):
-        self.profile = Profiles()
-        self._inputFile = "" 
-        self._outputFile =  ""
-        self._verbosity = 2
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-        
-    def _help( self ):
-        print
-        print "usage: %s.py [ options ]" % ( type(self).__name__ )
-        print "options:"
-        print "     -h: this help"
-        print "     -i: name of the profiles DB to format for Repet"
-        print "     -o: name of the output profiles DB for Repet"
-        print
-        
-        
-    def _setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
-        except getopt.GetoptError, err:
-            print str(err); self._help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self._help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputFile( a )
-            elif o == "-o":
-                self.setOutputFile( a )
-                
-    #TDOD: add nb of each domain in log file, verbose...
-    def _searchCurrentDomain(self, profile):
-        currentDomain = ""
-        #TODO: pattern GAGA and GAGE should be excluded !
-        #TODO: add new tag like "ORF1_LTR" for ATHILA as key word in Pfam
-        #TODO: add new tags from GypsyDB (MOV etc...)
-        if (re.search("[gG][aA][Gg]", profile[1]) or re.search("[gG][aA][Gg]", profile[3])):
-            currentDomain = "GAG"
-        elif (re.search("Zinc knuckle", profile[1]) or re.search("Zinc knuckle", profile[3])):
-            currentDomain = "GAG"
-        elif (re.search("PF02813", profile[2]) or re.search("PF01021", profile[2])):
-            currentDomain = "GAG"
-        elif (re.search("GAG_", profile[1])):
-            currentDomain = "GAG"
-        elif (re.search("GAGCOAT_", profile[1])):
-            currentDomain = "GAG"
-            
-        elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]aspartic", profile[3])) and (re.search("[pP]roteinase", profile[1]) or re.search("[pP]roteinase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[rR]etrotransposon", profile[1]) or re.search("[rR]etrotransposon", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[eE]ndopeptidase", profile[1]) or re.search("[eE]ndopeptidase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]roteinase", profile[1]) or re.search("[pP]roteinase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[eE]ndopeptidase", profile[1]) or re.search("[eE]ndopeptidase", profile[3]))):
-            currentDomain = "AP"
-        elif ((re.search("AP_", profile[1])) and not (re.search("[eE]ndonuclease", profile[3]))):
-            currentDomain = "AP"
-            
-        elif ((re.search("[iI]ntegrase", profile[1]) or re.search("[iI]ntegrase", profile[3])) and not (re.search(" C ", profile[1])) and not (re.search(" C ", profile[3]))):
-            currentDomain = "INT"
-        elif (re.search(".*[Cc]hromo.*", profile[1]) or re.search(".*[Cc]hromo.*", profile[3])):
-            currentDomain = "INT"
-        elif (re.search("INT_", profile[1])):
-            currentDomain = "INT"
-            
-            
-        elif ((re.search("[rR]everse", profile[1]) or re.search("[Rr]everse", profile[3])) and (re.search("[tT]ranscriptase", profile[1]) or re.search("[tT]ranscriptase", profile[3]))):
-            currentDomain = "RT"
-        elif (re.search("RT_", profile[1])):
-            currentDomain = "RT"
-            
-            
-        elif ((re.search("R[nN]ase", profile[1]) or re.search("R[nN]ase", profile[3])) and (re.search("H", profile[1]) or re.search("H", profile[3]))):
-            currentDomain = "RH"
-        elif ((re.search("R[nN]ase", profile[1]) or re.search("R[nN]ase", profile[3])) and (re.search("H ", profile[1]) or re.search("H ", profile[3]))):
-            currentDomain = "RH"
-        elif (re.search("RNaseH_", profile[1])):
-            currentDomain = "RH"
-            
-            
-        elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[pP]rotein", profile[1]) or re.search("[pP]rotein", profile[3]))):
-            currentDomain = "ENV"
-        elif ((re.search("ENV", profile[1]) or re.search("ENV", profile[3])) and (re.search("[pP]olyprotein", profile[1]) or re.search("[pP]olyprotein", profile[3]))):
-            currentDomain = "ENV"
-        elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[pP]olyprotein", profile[1]) or re.search("[pP]olyprotein", profile[3]))):
-            currentDomain = "ENV"
-        elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[gG]lycoprotein", profile[1]) or re.search("[gG]lycoprotein", profile[3]))):
-            currentDomain = "ENV"
-        elif (re.search("PF07253", profile[2]) or re.search("PF03811", profile[2])):
-            currentDomain = "ENV"
-        elif (re.search("ENV_", profile[1])):
-            currentDomain = "ENV"
-            
-        elif ((re.search("[tT]yrosine", profile[1]) or re.search("[tT]yrosine", profile[3])) and (re.search("[rR]ecombinase", profile[1]) or re.search("[rR]ecombinase", profile[3]))):
-            currentDomain = "YR"
-            
-        elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and not (re.search("AP ", profile[1]) or re.search("AP ", profile[3])) and not (re.search("[aA]purinic", profile[1]) or re.search("[aA]purinic", profile[3]))):
-            currentDomain = "EN"
-            
-        elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and (re.search("AP ", profile[1]) or re.search("AP ", profile[3]))):
-            currentDomain = "APE"
-        elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and (re.search("[aA]purinic", profile[1]) or re.search("[aA]purinic", profile[3]))):
-            currentDomain = "APE"
-            
-        elif ((re.search("[tT]ransposase", profile[1]) or re.search("[tT]ransposase", profile[3])) and not (re.search("DDE ", profile[1]) or re.search("DDE ", profile[3]))):
-            currentDomain = "Tase"
-        elif (re.search("DUF659", profile[1])):
-            currentDomain = "Tase"
-        elif (re.search("PF01695", profile[2])) or (re.search("PF02316", profile[2])) or (re.search("PF09039", profile[2])) or (re.search("PF04827", profile[2])) or (re.search("PF05699", profile[2])):
-            currentDomain = "Tase"
-            
-        elif ((re.search("[tT]ransposase", profile[1]) or re.search("[tT]ransposase", profile[3])) and (re.search("DDE ", profile[1]) or re.search("DDE ", profile[3]))):
-            currentDomain = "Tase*"
-            
-        elif ((re.search("[rR]eplication", profile[1]) or re.search("[rR]eplication", profile[3])) and (re.search("[pP]rotein", profile[1]) or re.search("[pP]rotein", profile[3])) and (re.search("A ", profile[1]) or re.search("A ", profile[3]))):
-            currentDomain = "RPA"
-        elif (re.search("[rR]epA ", profile[1]) or re.search("[rR]epA ", profile[3])):
-            currentDomain = "RPA"
-        elif (re.search("RPA", profile[1]) or re.search("RPA", profile[3])):
-            currentDomain = "RPA"
-            
-        elif (re.search("[cC]-integrase", profile[1]) or re.search("[cC]-integrase", profile[3])):
-            currentDomain = "C-INT"
-            
-        elif ((re.search("[pP]ackaging", profile[1]) or re.search("[pP]ackaging", profile[3])) and (re.search("ATPase", profile[1]) or re.search("ATPase", profile[3]))):
-            currentDomain = "ATP"
-            
-        elif ((re.search("[cC]ysteine", profile[1]) or re.search("[cC]ysteine", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))):
-            currentDomain = "CYP"
-        elif ((re.search("[cC]ysteine", profile[1]) or re.search("[cC]ysteine", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))):
-            currentDomain = "CYP"
-        elif (re.search("[pP]eptidase_C", profile[1]) or re.search("[pP]eptidase_C", profile[3])):
-            currentDomain = "CYP"
-        elif (re.search("PF00559", profile[2])):
-            currentDomain = "CYP"
-            
-        elif (re.search("[pP]ol\S*_*B", profile[1]) or re.search("[pP]ol\S*_*B", profile[3])):
-            currentDomain = "POLB"
-        elif ((re.search("[pP]olymerase", profile[1]) or re.search("[pP]olymerase", profile[3])) and (re.search("B ", profile[1]) or re.search("B ", profile[3]))):
-            currentDomain = "POLB"
-            
-        elif (re.search("[hH]elicase", profile[1]) or re.search("[hH]elicase", profile[3])):
-            currentDomain = "HEL"
-            
-        else :
-            currentDomain = "OTHER"
-        return currentDomain
-    
-    
-    ## Replace the old profile name by accession number, name, domain and gather cut off
-    #  
-    # @param fout file handle
-    # @param profile Profiles instance
-    # @param currentDomain string
-    #
-    def _writeModifiedProfile(self, fout, profile, currentDomain):
-        for i in xrange(0, len(profile), 1):
-            if i != 1:
-                fout.write(profile[i])
-            else:
-                fout.write("NAME  " + self.profile.accNumber + "_"\
-                            + self.profile.name + "_"\
-                             + currentDomain + "_"\
-                              + str(self.profile.GA_cut_off) + "\n")
-                
-                
-    ## Set input file name
-    #  
-    # @param inputFileName string
-    #
-    def setInputFile(self, inputFileName):
-        self._inputFile = inputFileName
-        
-        
-    ## Set output file name
-    #
-    # @param outputFileName string
-    #
-    def setOutputFile(self, outputFileName):
-        self._outputFile = outputFileName   
-        
-        
-    ## Read a profiles DB file, parse it and, write a new profiles DB with TE domain information and GA score cut_off placed side by side of the name
-    #    
-    def run( self ):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        fileIn = open( self._inputFile )
-        fout = open( self._outputFile, "w" )
-        profile = self.profile.readAndRetrieve( fileIn )
-        while profile != None:
-            currentDomain = self._searchCurrentDomain(profile)
-            if currentDomain == "OTHER":
-                self._log.warning(self.profile.accNumber + " " + self.profile.name + " has no associated domain")
-            self._writeModifiedProfile(fout, profile, currentDomain)
-            profile = self.profile.read( fileIn )
-            
-            
-if __name__ == "__main__":
-    i = ProfilesDB4Repet()
-    i._setAttributesFromCmdLine()
-    i.run()

--- a/commons/pyRepetUnit/profilesDB/ProfilesDatabank.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-class ProfilesDatabank:
-    
-    """
-    List of profiles objects.
-    """
-    
-    list;
-    
-    def __init__( self ):
-        self._profilesDatabank = []
-    
-    def append( self, list ):
-       self._profilesDatabank.append(list)
-       
-    def len (self):
-        return len(self._profilesDatabank)
-    
-    def get(self, index):
-        return self._profilesDatabank[index]
-    
-    def getList(self):
-        return self._profilesDatabank
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-"""
-Utility to handle a databank of HMM profiles.
-"""
-
-import sys
-from commons.pyRepetUnit.profilesDB.Profiles import Profiles
-from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank
-from commons.core.utils.FileUtils import FileUtils
-
-class ProfilesDatabankUtils:
-    """
-    Utility to handle a databank of HMM profiles.
-    """
-    
-    def read( inFileName, verbose=0 ):
-        """
-        Read a file in Pfam format and return a L[ProfilesDatabank<commons.core.ProfilesDatabank>} instance.
-        @param inFileName: name of the input file
-        @type inFileName: string
-        @param verbose: verbosity level
-        @type verbose: integer
-        """ 
-        if verbose > 0: print "reading file '%s'..." % ( inFileName ); sys.stdout.flush()
-        
-    
-        if FileUtils.isEmpty(inFileName):
-            return (None)
-        profilesInstance = Profiles() 
-        profilesDBInstance = ProfilesDatabank()
-        f = open( inFileName , "r")
-        while profilesInstance.read( f ):
-            profilesDBInstance.append( profilesInstance )
-            profilesInstance = Profiles()
-        f.close()
-        if verbose > 0: print "file '%s' is loaded" % ( inFileName ); sys.stdout.flush()
-        return (profilesDBInstance)
-    
-    read = staticmethod( read )

--- a/commons/pyRepetUnit/profilesDB/tests/InsertProfilesMapFileInDBTestRessources.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-'''
-Created on 24 juin 2009
-
-@author: choede
-'''
-
-class InsertProfilesMapFileInDBTestRessources(object):
-    '''
-    Put here ressources not present in config file
-    '''
-    REPET_DB_USER = "ochoede"
-    REPET_DB_HOST = "pisano"
-    REPET_DB_PW = "ochoede"
-    REPET_DB_NAME = "repet_ochoede"
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-'''
-Created on 18 mai 2009
-
-@author: choede
-'''
-import unittest
-import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber
-
-
-class TestCompleteProfilesDBFromProfilesNameListOrAccNumber(unittest.TestCase):
-
-
-    def setUp(self):
-        self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt"
-        self._filePfamList = "./datas/ListpfamAccNumber.txt"
-        self._profilesDB = "./datas/profilesDBTest.hmm"
-        self.CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber()
-        self.CompleteProfilesDB.setProfilesDBFile ( self._profilesDB )
-        self._expectedList = ["zf-CCHC", "InvE", "Chromo", "TLV_coat"]
-        self._expectedList2 = ["PF00075", "PF00424", "PF00469"]
-        self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'"
-        self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'"
-        
-        
-    def tearDown(self):
-        pass
-
-
-    def testListNotExistingProfiles(self):
-        #with name
-        self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList )
-        profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( )
-        i = 0
-        if profilesNotInDBList != []:
-            for profil in profilesNotInDBList:
-                self.assertEquals(profil, self._expectedList[i])
-                i = i + 1
-        #with pfam accession number
-        self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList )
-        self.CompleteProfilesDB.setPfamAccNumberKeys ()
-        profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( )
-        i = 0
-        if profilesNotInDBList != []:
-            for profil in profilesNotInDBList:
-                self.assertEquals(profil, self._expectedList2[i])
-                i = i + 1
-    
-    def testCreateGetzCommand(self):  
-        getzCmd = self.CompleteProfilesDB.generateGetzCmdProfilesList( self._expectedList )
-        # pour le moment je cherche dans les fs ou les ls si je ne veux que les fs specifier type = fs ce sera surement le cas a terme
-        self.assertEqual (getzCmd, self._expectedGetzCmd)
-        
-    def testCmdToCompleteProfileDBFromList(self): 
-        #names list
-        self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList ) 
-        getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB()
-        self.assertEqual (getzCmd, self._expectedGetzCmd)  
-        #pfam accession Number list
-        self.CompleteProfilesDB.setPfamAccNumberKeys ()
-        self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList ) 
-        getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB()
-        self.assertEqual (getzCmd, self._expectedGetzCmd2)
-        
-    
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/TestInsertProfilesMapFileInDB.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-import unittest
-import time
-import os
-from commons.core.sql.TableMapAdaptator import TableMapAdaptator
-from commons.core.coord.Map import Map
-#from commons.pyRepetUnit.profilesDB.tests.InsertProfilesMapFileInDBTestRessources import InsertProfilesMapFileInDBTestRessources
-from commons.pyRepetUnit.profilesDB.InsertProfilesMapFileInDB import InsertProfilesMapFileInDB
-from commons.core.sql.DbMySql import DbMySql
-
-
-class TestInsertProfilesMapFileInDB(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFileName = "./datas/profiles.map"
-        self._createProfilesMapFile()
-#        self._host = InsertProfilesMapFileInDBTestRessources.REPET_DB_HOST
-#        self._user = InsertProfilesMapFileInDBTestRessources.REPET_DB_USER
-#        self._passwd = InsertProfilesMapFileInDBTestRessources.REPET_DB_PW
-#        self._dbname = InsertProfilesMapFileInDBTestRessources.REPET_DB_NAME
-#        self._db = DbMySql( self._user, self._host, self._passwd, self._dbname )
-        self._db = DbMySql( os.environ["REPET_USER"],
-                            os.environ["REPET_HOST"],
-                            os.environ["REPET_PW"],
-                            os.environ["REPET_DB"] )
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-        self._table = "dummyMapTable_%s" % ( self._uniqId )
-
-    def tearDown(self):
-        os.remove(self._inputFileName)
-        self._deleteDBtables()
-        self._db.close()
-
-    def testInsertProfilesMapFileInDB(self):
-        resultFromFileMapUtils = self._readMapResultsFromFileAndFillList()
-        InsertProfilesMapFileInDBinstance = InsertProfilesMapFileInDB(self._inputFileName, self._table,  self._db)
-        InsertProfilesMapFileInDBinstance.createAndLoadTable()
-        resultFromTableMapUtils = self._readMapResultsFromTableAndFillList() 
-        self.assertEquals(resultFromFileMapUtils, resultFromTableMapUtils)
-    
-    def _createProfilesMapFile(self):
-        f = open(self._inputFileName, "w")
-        f.write("rrm\t\t1\t77\n")
-        f.write("fn3\tFibronectin type III domain\t1\t84\n")
-        f.write("pkinase\tProtein kinase domain\t1\t294\n")
-        f.close()
-        
-    def _readMapResultsFromTableAndFillList(self):
-        tableMapAdaptatorInstance = TableMapAdaptator (self._db, self._table)
-        return tableMapAdaptatorInstance.getListOfAllMaps()
-
-    def _readMapResultsFromFileAndFillList(self):
-       mapInstance = Map()
-       lMap = []
-       f = open( self._inputFileName , "r")
-       while mapInstance.read( f ):
-            lMap.append (mapInstance)
-            mapInstance = Map()
-       f.close()
-       return lMap
-   
-    def _deleteDBtables(self):
-        self._db.dropTable(self._table)
-        
-if __name__ == "__main__":
-    unittest.main()

--- a/commons/pyRepetUnit/profilesDB/tests/TestProfiles.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,151 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.profilesDB.Profiles import Profiles
-from commons.core.utils.FileUtils import FileUtils
-
-
-class TestProfiles(unittest.TestCase):
-
-    def createInputDBFile(self):
-        f = open(self._inputDBFile, "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  fn3\n")
-        f.write("ACC   PF00041\n")
-        f.write("DESC  Fibronectin type III domain\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 2.0;\n")
-        f.write("TC    7.9 2.1;\n")
-        f.write("NC    7.0 1.1;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  truc\n")
-        f.write("ACC   PF00042.012\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0;\n")
-        f.write("TC    7.9 0.1;\n")
-        f.write("NC    7.8 0.1;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.close()
-        
-        
-    def setUp(self):
-        self.profiles = Profiles()
-        self._inputDBFile = "dummy.hmm"
-        
-        
-    def testRead(self):
-        # atomic profiles file
-        self.createInputDBFile()
-        file = open( self._inputDBFile )
-        profile = self.profiles
-        profile.read(file)
-        self.assertEqual("fn3",profile.name)
-        self.assertEqual("Fibronectin type III domain", profile.desc)
-        self.assertEqual(84, profile.length)
-        self.assertEqual("PF00041", profile.accNumber)
-        self.assertEqual(2.0, profile.GA_cut_off)
-        profile.read(file)
-        self.assertEqual("truc",profile.name)
-        self.assertEqual("", profile.desc)
-        self.assertEqual(123, profile.length)
-        self.assertEqual("PF00042.012", profile.accNumber)
-        self.assertEqual(-1.0, profile.GA_cut_off)        
-        os.system("rm " + self._inputDBFile)        
-        # empty file
-        f = open(self._inputDBFile, "w")
-        f.close()
-        file = open( self._inputDBFile )
-        profile = self.profiles
-        profile.read(file)
-        self.assertEqual(None, profile.name)
-        self.assertEqual(None, profile.desc)
-        self.assertEqual(None, profile.length)
-        self.assertEqual(None, profile.accNumber)
-        self.assertEqual(None, profile.GA_cut_off)
-        os.system("rm " + self._inputDBFile)
-        
-        
-    def testReadAndRetrieve(self):
-        # atomic profiles file
-        self.createInputDBFile()
-        file = open( self._inputDBFile )
-        profile = self.profiles
-        myProfile = profile.readAndRetrieve(file)
-        self.assertEqual("fn3",profile.name)
-        self.assertEqual("Fibronectin type III domain", profile.desc)
-        self.assertEqual(84, profile.length)
-        self.assertEqual("PF00041", profile.accNumber)
-        self.assertEqual(2.0, profile.GA_cut_off)
-        myProfile2 = profile.readAndRetrieve(file)
-        self.assertEqual("truc",profile.name)
-        self.assertEqual("", profile.desc)
-        self.assertEqual(123, profile.length)
-        self.assertEqual("PF00042.012", profile.accNumber)
-        self.assertEqual(-1.0, profile.GA_cut_off)
-        #I check if retrieve work like I want
-        f = open("retrieveResult", "w")
-        for item in myProfile:
-            f.write(item)
-        for item in myProfile2:
-            f.write(item)
-        f.close()
-        self.assertTrue(FileUtils.are2FilesIdentical("retrieveResult", self._inputDBFile))
-        os.system("rm " + self._inputDBFile) 
-        os.system("rm retrieveResult")       
-        # empty file
-        f = open(self._inputDBFile, "w")
-        f.close()
-        file = open( self._inputDBFile )
-        profile = self.profiles
-        myProfile3 = profile.readAndRetrieve(file)
-        self.assertEqual(None, profile.name)
-        self.assertEqual(None, profile.desc)
-        self.assertEqual(None, profile.length)
-        self.assertEqual(None, profile.accNumber)
-        self.assertEqual(None, profile.GA_cut_off)
-        self.assertEqual(None, myProfile3)
-        os.system("rm " + self._inputDBFile)    
-    
-        
-if __name__ == "__main__":                 
-    unittest.main()            
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/TestProfilesDB2Map.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,199 +0,0 @@
-import os
-import unittest
-from commons.pyRepetUnit.profilesDB.Profiles import Profiles
-from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank
-import commons.pyRepetUnit.profilesDB.ProfilesDB2Map
-from commons.core.utils.FileUtils import FileUtils
-
-
-class TestProfilesDB2Map(unittest.TestCase):
-    
-    def setUp(self):
-        self.profilesDB2Map = commons.pyRepetUnit.profilesDB.ProfilesDB2Map.ProfilesDB2Map()        
-        
-        
-    def testWriteProfilesDB(self):
-        # atomic hmmerpfam file
-        profilesDB = ProfilesDatabank()
-        profiles1 = Profiles()
-        profiles1.name = "fn3"
-        profiles1.desc = "Fibronectin type III domain"
-        profiles1.length = 84
-        profilesDB.append( profiles1 )
-        profiles2 = Profiles()
-        profiles2.name = "truc"
-        profiles2.desc = ""
-        profiles2.length = 123
-        profilesDB.append( profiles2 )
-        file = open( "expectedFile", "w" )
-        file.write( "fn3\tFibronectin type III domain\t1\t84\n" )
-        file.write( "truc\t\t1\t123\n" )
-        file.close()
-        self.profilesDB2Map.setOutputFile("testOutput.map")
-        self.profilesDB2Map._writeMapFile(profilesDB)
-        self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map"))
-        os.remove("expectedFile")
-        os.remove("testOutput.map")
-        #empty profileDB object
-        profilesDB = ProfilesDatabank()
-        self.profilesDB2Map._writeMapFile(profilesDB)
-        self.assertFalse(FileUtils.isRessourceExists("testOutput.map"))
-        
-    def testReadProfilesDB(self):
-        # atomic hmmerpfam file
-        f = open("dummy.hmm", "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  fn3\n")
-        f.write("ACC   PF00041\n")
-        f.write("DESC  Fibronectin type III domain\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  truc\n")
-        f.write("ACC   PF00041\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")        
-        f.close()
-        self.profilesDB2Map.setInputFile("dummy.hmm")
-        pfamDB = self.profilesDB2Map._readProfilesDB()
-        expectedProfiles1 = Profiles()
-        expectedProfiles1.name = "fn3"
-        expectedProfiles1.desc = "Fibronectin type III domain"
-        expectedProfiles1.length = 84
-        expectedProfiles2 = Profiles()
-        expectedProfiles2.name = "truc"
-        expectedProfiles2.desc = ""
-        expectedProfiles2.length = 123
-        self.assertEqual(expectedProfiles1.name, pfamDB.get(0).name)
-        self.assertEqual(expectedProfiles1.desc, pfamDB.get(0).desc)
-        self.assertEqual(expectedProfiles1.length, pfamDB.get(0).length)
-        self.assertEqual(expectedProfiles2.name, pfamDB.get(1).name)
-        self.assertEqual(expectedProfiles2.desc, pfamDB.get(1).desc)
-        self.assertEqual(expectedProfiles2.length, pfamDB.get(1).length)
-        os.remove("dummy.hmm")
-        #empty pfamDB file
-        file = open( "pfamDBEmpty", "w" )
-        file.close()
-        self.profilesDB2Map.setInputFile("pfamDBEmpty")
-        pfamDB2 = self.profilesDB2Map._readProfilesDB()
-        self.assertEquals(None, pfamDB2)
-        os.system("rm pfamDBEmpty")
-        
-    def testRun(self):
-        f = open("dummy.hmm", "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  fn3\n")
-        f.write("ACC   PF00041\n")
-        f.write("DESC  Fibronectin type III domain\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  truc\n")
-        f.write("ACC   PF00041\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")        
-        f.close()
-        self.profilesDB2Map.setInputFile("dummy.hmm")
-        self.profilesDB2Map.setOutputFile("testOutput.map")
-        self.profilesDB2Map.run()
-        file = open( "expectedFile", "w" )
-        file.write( "fn3\tFibronectin type III domain\t1\t84\n" )
-        file.write( "truc\t\t1\t123\n" )
-        file.close()
-        self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map"))
-        os.remove("expectedFile")
-        os.remove("testOutput.map")
-        os.remove("dummy.hmm")
-        
-        
-if __name__ == "__main__":                 
-    unittest.main()         
-        
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/TestProfilesDatabankUtils.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-import unittest
-import os
-from commons.pyRepetUnit.profilesDB.Profiles import Profiles
-from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils
-
-
-class TestProfilesDatabankUtils( unittest.TestCase ):
-    
-    def setUp( self ):
-        self.profilesDBUtils = ProfilesDatabankUtils()        
-        
-        
-    def test_read_emptyFile( self ):
-        file = open( "pfamDBEmpty", "w" )
-        file.close()
-        pfamDB2 = self.profilesDBUtils.read( "pfamDBEmpty" )
-        self.assertEquals( None, pfamDB2 )
-        os.remove( "pfamDBEmpty" )
-        
-        
-    def test_read( self ):
-        f = open("dummy.hmm", "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  fn3\n")
-        f.write("ACC   PF00041\n")
-        f.write("DESC  Fibronectin type III domain\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  truc\n")
-        f.write("ACC   PF00041\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    7.8 -1.0\n")
-        f.write("TC    7.9 0.1\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")        
-        f.close()
-        pfamDB = self.profilesDBUtils.read("dummy.hmm")
-        expectedProfiles1 = Profiles()
-        expectedProfiles1.name = "fn3"
-        expectedProfiles1.desc = "Fibronectin type III domain"
-        expectedProfiles1.length = 84
-        expectedProfiles2 = Profiles()
-        expectedProfiles2.name = "truc"
-        expectedProfiles2.desc = ""
-        expectedProfiles2.length = 123
-        
-        self.assertEqual( expectedProfiles1.name, pfamDB.get(0).name )
-        self.assertEqual( expectedProfiles1.desc, pfamDB.get(0).desc )
-        self.assertEqual( expectedProfiles1.length, pfamDB.get(0).length )
-        self.assertEqual( expectedProfiles2.name, pfamDB.get(1).name )
-        self.assertEqual( expectedProfiles2.desc, pfamDB.get(1).desc )
-        self.assertEqual( expectedProfiles2.length, pfamDB.get(1).length )
-        
-        os.remove("dummy.hmm")
-        
-        
-if __name__ == "__main__":                 
-    unittest.main()         
-        
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_CompleteProfilDB(unittest.TestCase):
-
-    def setUp(self):
-        self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt"
-        self._filePfamList = "./datas/ListpfamAccNumber.txt"
-        self._profilesDB = "./datas/profilesDBTest.hmm"
-        self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'"
-        self._expectedFile(self._expectedGetzCmd)
-        self._outputFileName = "./datas/outputFile"
-        self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'"
-        
-    def tearDown(self):
-        os.remove(self._outputFileName)
-        os.remove(self._expectedGetzCmdFile)
-
-    def testCompleteProfilesDBScriptByName(self):
-        Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._fileProfilesList + " -o " + self._outputFileName + "\n"
-        os.system (Cmd)
-        self.assertTrue (FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile))
-    
-    def testCompleteProfilesDBScriptByAccession(self):
-        self._expectedFile(self._expectedGetzCmd2)
-        Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._filePfamList + " -o " + self._outputFileName + " -n\n"
-        os.system(Cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile))
-
-    def _expectedFile(self, expectedGetzCmd):
-        self._expectedGetzCmdFile = "./datas/expectedCmdFile"
-        f = open(self._expectedGetzCmdFile, 'w')
-        f.write(expectedGetzCmd)
-        f.close
-
-
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB2Map.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-from commons.pyRepetUnit.profilesDB.ProfilesDB2Map import ProfilesDB2Map
-
-class Test_F_ProfilesDB2Map(unittest.TestCase):
-    
-    def setUp(self):
-        self.profilesDB2Map = ProfilesDB2Map()
-        self._inputFile = "./datas/myhmms"
-        self._outputFile = "./datas/outputFile.map"
-        self._expectedFile = "./datas/profiles.map" 
-        self._createProfilesMapFile()
-        
-    def tearDown(self):
-        os.remove(self._outputFile)
-        os.remove(self._expectedFile)
-        
-    def testRun(self):
-        self.profilesDB2Map.setInputFile(self._inputFile)
-        self.profilesDB2Map.setOutputFile(self._outputFile)
-        pfamDB = self.profilesDB2Map.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile))
-        
-    def _createProfilesMapFile(self):
-        f = open(self._expectedFile, "w")
-        f.write("rrm\t\t1\t77\n")
-        f.write("fn3\tFibronectin type III domain\t1\t84\n")
-        f.write("pkinase\tProtein kinase domain\t1\t294\n")
-        f.close()   
-                   
-        
-if __name__ == "__main__":                 
-    unittest.main()       
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB4Repet.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-class Test_F_ProfilesDB4Repet(unittest.TestCase):
-
-    def setUp(self):
-        self._inputDBFile = "%s/Tools/ProfilesDB4Repet_v2.hmm" % os.environ["REPET_DATA"]
-        self._outputDBFile = "output.hmm"
-
-    def tearDown(self):
-        os.remove(self._outputDBFile)
-
-    def test_run_as_script(self):
-        cmd = "python ../ProfilesDB4Repet.py -i " + self._inputDBFile + " -o " + self._outputDBFile
-        os.system(cmd)
-        self.assertEqual(FileUtils.getNbLinesInSingleFile(self._outputDBFile), 375854)
-        
-if __name__ == "__main__":
-    unittest.main()

--- a/commons/pyRepetUnit/profilesDB/tests/Test_ProfilesDB4Repet.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,442 +0,0 @@
-import unittest
-import os
-from commons.pyRepetUnit.profilesDB.ProfilesDB4Repet import ProfilesDB4Repet
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_ProfilesDB4Repet(unittest.TestCase):
-
-    def setUp(self):
-        self._inputDBFile = "./datas/dummy.hmm"
-        self._expectedDBFile = "./datas/expected.hmm"
-        self._outputDBFile = "./datas/output.hmm"
-        self._profilesDB4Repet = ProfilesDB4Repet()
-
-    def tearDown(self):
-        os.remove(self._expectedDBFile)
-        os.remove(self._outputDBFile)
-        os.remove(self._inputDBFile)
-
-    def testFormateProfilesDB4Repet(self):
-        self._createHmmFile()
-        self._createExpectedHmmFile()
-        self._profilesDB4Repet.setInputFile(self._inputDBFile)
-        self._profilesDB4Repet.setOutputFile(self._outputDBFile)
-        self._profilesDB4Repet.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
-
-    def test_formateProfilesDB4Repet_GypsyDB(self):
-        self._createHmmFile_GypsyDB()
-        self._createExpectedHmmFile_GypsyDB()
-        self._profilesDB4Repet.setInputFile(self._inputDBFile)
-        self._profilesDB4Repet.setOutputFile(self._outputDBFile)
-        self._profilesDB4Repet.run()
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
-   
-    def _createExpectedHmmFile(self):
-        f = open(self._expectedDBFile, "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  PF07582.4_AP_endonuc_2_N_APE_20.9\n")
-        f.write("ACC   PF07582.4\n")
-        f.write("DESC  AP endonuclease family 2 C terminus\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    20.9000 20.9000;\n")
-        f.write("TC    21.2000 21.2000;\n")
-        f.write("NC    20.8000 20.8000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  PF01606.8_Arteri_env_ENV_25.0\n")
-        f.write("ACC   PF01606.8\n")
-        f.write("DESC  DESC  Arterivirus envelope protein\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    21.0000 25.0000;\n")
-        f.write("TC    306.0000 406.0000;\n")
-        f.write("NC    10.3000 11.3000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  PF01606.8_Dummy_name_OTHER_25.0\n")
-        f.write("ACC   PF01606.8\n")
-        f.write("DESC  Dummy Description\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    21.0000 25.0000;\n")
-        f.write("TC    306.0000 406.0000;\n")
-        f.write("NC    10.3000 11.3000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.close()
-
-    def _createHmmFile(self):
-        f = open(self._inputDBFile, "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  AP_endonuc_2_N\n")
-        f.write("ACC   PF07582.4\n")
-        f.write("DESC  AP endonuclease family 2 C terminus\n")
-        f.write("LENG  84\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    20.9000 20.9000;\n")
-        f.write("TC    21.2000 21.2000;\n")
-        f.write("NC    20.8000 20.8000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  Arteri_env\n")
-        f.write("ACC   PF01606.8\n")
-        f.write("DESC  DESC  Arterivirus envelope protein\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    21.0000 25.0000;\n")
-        f.write("TC    306.0000 406.0000;\n")
-        f.write("NC    10.3000 11.3000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  Dummy_name\n")
-        f.write("ACC   PF01606.8\n")
-        f.write("DESC  Dummy Description\n")
-        f.write("LENG  123\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    yes\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -A myhmms fn3.sto\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("NSEQ  108\n")
-        f.write("DATE  Thu Jan  8 17:50:26 2009\n")
-        f.write("CKSUM 6130\n")
-        f.write("GA    21.0000 25.0000;\n")
-        f.write("TC    306.0000 406.0000;\n")
-        f.write("NC    10.3000 11.3000;\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 \n")
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 \n")
-        f.write("EVD   -45.973442   0.237545\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    \n")
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("COM   hmmcalibrate myhmms\n")
-        f.write("          -13      *  -6756\n")
-        f.write("     1  -1698  -4236  -5399   -847  -4220  -2885  -1259   -930  -2438    406  -3428  -4768   3631  -1835  -4773  -1187  -1331   -120  -4666  -1510     1\n")
-        f.write("     -   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 \n")
-        f.write("     C   -144  -3400 -12951    -19  -6286   -701  -1378    -13      * \n")
-        f.write("//\n")
-        f.close()
-        
-    def _createExpectedHmmFile_GypsyDB(self):
-        f = open(self._expectedDBFile, "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  _AP_17_6_AP_NA\n")
-        f.write("LENG  97\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
-        f.write("COM   hmmcalibrate output/AP_17_6.hmm\n")
-        f.write("NSEQ  7\n")
-        f.write("DATE  Tue Nov  3 12:11:06 2009\n")
-        f.write("CKSUM 7992\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -62.517647   0.206604\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -193      *  -2999\n")
-        f.write("1  -2855  -2358  -5336  -4935  -1676  -5061  -4339   3600  -4729    809   -490  -4773  -4645  -4163  -4574  -4431  -2811     -4  -3348  -3185     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-     -9  -7942  -8984   -894  -1115   -701  -1378   -193      *\n") 
-        f.write("2  -3852  -3208  -4863  -4900    -13  -4670  -1533  -2120  -4409   1711  -1558  -3673  -4546  -3569  -4004  -4001  -3768  -2552   -797   4153    97\n")
-        f.write("-      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *\n") 
-        f.write("-      *      *      *      *      *      *      *      *      0 \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  _ENV_athila_ENV_NA\n")
-        f.write("LENG  647\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
-        f.write("COM   hmmcalibrate ENV_athila.hmm\n")
-        f.write("NSEQ  3\n")
-        f.write("DATE  Fri Sep  9 13:24:44 2005\n")
-        f.write("CKSUM 3522\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -12.496953   0.641902\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -576      *  -1603\n")
-        f.write("1   -995  -1009  -2161  -1884   -298  -2046  -1336    348  -1429    591   4179  -1738  -2255  -1394  -1460  -1476  -1060     98  -1303   -906     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378  -1576 -10335\n") 
-        f.write("2     95   -518   -873   -904  -1785   -691   -984  -1664   -955  -1934  -1254   -652  -1327   -861  -1134   2815   -243  -1070  -2024  -1564     2\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378 -10911 -10334\n") 
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  _ENVathila_OTHER_NA\n")
-        f.write("LENG  647\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
-        f.write("COM   hmmcalibrate ENV_athila.hmm\n")
-        f.write("NSEQ  3\n")
-        f.write("DATE  Fri Sep  9 13:24:44 2005\n")
-        f.write("CKSUM 3522\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -12.496953   0.641902\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -576      *  -1603\n")
-        f.write("1   -995  -1009  -2161  -1884   -298  -2046  -1336    348  -1429    591   4179  -1738  -2255  -1394  -1460  -1476  -1060     98  -1303   -906     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378  -1576 -10335\n") 
-        f.write("2     95   -518   -873   -904  -1785   -691   -984  -1664   -955  -1934  -1254   -652  -1327   -861  -1134   2815   -243  -1070  -2024  -1564     2\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378 -10911 -10334\n") 
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  _MOV_cavemovirus_OTHER_NA\n")
-        f.write("LENG  302\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
-        f.write("COM   hmmcalibrate output/MOV_cavemovirus.hmm\n")
-        f.write("NSEQ  2\n")
-        f.write("DATE  Tue Nov  3 11:25:12 2009\n")
-        f.write("CKSUM 1918\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -135.876633   0.154850\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -585      *  -1585\n")
-        f.write("1  -1028  -1686   -800   -442  -2171  -1521   -263  -1873   3103  -1859  -1251   -547  -1750     74    599  -1004   -972  -1620  -1812  -1528     5\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378   -585      *\n") 
-        f.write("2  -1016   -805  -2637  -2367   -591  -2470  -1853   3039  -2040    329    346  -2180  -2589  -1943  -2070  -1879  -1051   1184  -1698  -1261     6\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378      *      *\n") 
-        f.write("3  -1016   -805  -2637  -2367   -591  -2470  -1853   3039  -2040    329    346  -2180  -2589  -1943  -2070  -1879  -1051   1184  -1698  -1261     7\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378      *      *\n") 
-        f.write("//\n")
-        f.close()
-
-    def _createHmmFile_GypsyDB(self):
-        f = open(self._inputDBFile, "w")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  AP_17_6\n")
-        f.write("LENG  97\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
-        f.write("COM   hmmcalibrate output/AP_17_6.hmm\n")
-        f.write("NSEQ  7\n")
-        f.write("DATE  Tue Nov  3 12:11:06 2009\n")
-        f.write("CKSUM 7992\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -62.517647   0.206604\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -193      *  -2999\n")
-        f.write("1  -2855  -2358  -5336  -4935  -1676  -5061  -4339   3600  -4729    809   -490  -4773  -4645  -4163  -4574  -4431  -2811     -4  -3348  -3185     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-     -9  -7942  -8984   -894  -1115   -701  -1378   -193      *\n") 
-        f.write("2  -3852  -3208  -4863  -4900    -13  -4670  -1533  -2120  -4409   1711  -1558  -3673  -4546  -3569  -4004  -4001  -3768  -2552   -797   4153    97\n")
-        f.write("-      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *\n") 
-        f.write("-      *      *      *      *      *      *      *      *      0 \n")
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  ENV_athila\n")
-        f.write("LENG  647\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
-        f.write("COM   hmmcalibrate ENV_athila.hmm\n")
-        f.write("NSEQ  3\n")
-        f.write("DATE  Fri Sep  9 13:24:44 2005\n")
-        f.write("CKSUM 3522\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -12.496953   0.641902\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -576      *  -1603\n")
-        f.write("1   -995  -1009  -2161  -1884   -298  -2046  -1336    348  -1429    591   4179  -1738  -2255  -1394  -1460  -1476  -1060     98  -1303   -906     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378  -1576 -10335\n") 
-        f.write("2     95   -518   -873   -904  -1785   -691   -984  -1664   -955  -1934  -1254   -652  -1327   -861  -1134   2815   -243  -1070  -2024  -1564     2\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378 -10911 -10334\n") 
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  ENVathila\n")
-        f.write("LENG  647\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
-        f.write("COM   hmmcalibrate ENV_athila.hmm\n")
-        f.write("NSEQ  3\n")
-        f.write("DATE  Fri Sep  9 13:24:44 2005\n")
-        f.write("CKSUM 3522\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -12.496953   0.641902\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -576      *  -1603\n")
-        f.write("1   -995  -1009  -2161  -1884   -298  -2046  -1336    348  -1429    591   4179  -1738  -2255  -1394  -1460  -1476  -1060     98  -1303   -906     1\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378  -1576 -10335\n") 
-        f.write("2     95   -518   -873   -904  -1785   -691   -984  -1664   -955  -1934  -1254   -652  -1327   -861  -1134   2815   -243  -1070  -2024  -1564     2\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6075  -7117   -894  -1115   -701  -1378 -10911 -10334\n") 
-        f.write("//\n")
-        f.write("HMMER2.0  [2.3.2]\n")
-        f.write("NAME  MOV_cavemovirus\n")
-        f.write("LENG  302\n")
-        f.write("ALPH  Amino\n")
-        f.write("RF    no\n")
-        f.write("CS    no\n")
-        f.write("MAP   yes\n")
-        f.write("COM   hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
-        f.write("COM   hmmcalibrate output/MOV_cavemovirus.hmm\n")
-        f.write("NSEQ  2\n")
-        f.write("DATE  Tue Nov  3 11:25:12 2009\n")
-        f.write("CKSUM 1918\n")
-        f.write("XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4\n") 
-        f.write("NULT      -4  -8455\n")
-        f.write("NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644\n") 
-        f.write("EVD   -135.876633   0.154850\n")
-        f.write("HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y\n")    
-        f.write("         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e\n")
-        f.write("         -585      *  -1585\n")
-        f.write("1  -1028  -1686   -800   -442  -2171  -1521   -263  -1873   3103  -1859  -1251   -547  -1750     74    599  -1004   -972  -1620  -1812  -1528     5\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378   -585      *\n") 
-        f.write("2  -1016   -805  -2637  -2367   -591  -2470  -1853   3039  -2040    329    346  -2180  -2589  -1943  -2070  -1879  -1051   1184  -1698  -1261     6\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378      *      *\n") 
-        f.write("3  -1016   -805  -2637  -2367   -591  -2470  -1853   3039  -2040    329    346  -2180  -2589  -1943  -2070  -1879  -1051   1184  -1698  -1261     7\n")
-        f.write("-   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249\n") 
-        f.write("-    -33  -6045  -7087   -894  -1115   -701  -1378      *      *\n") 
-        f.write("//\n")
-        f.close()     
-
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/completeProfilesDBFromAFileWithProfilesList_script.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-'''
-Created on 19 mai 2009
-
-@author: choede
-'''
-
-import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber
-import user, os, sys, getopt, exceptions
-from pyRepet.util.file.FileUtils import *
-
-#------------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the command-line parameters.
-    """
-
-    print ""
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -d: name of profiles databank (format='pfam')"
-    print "     -l: name of the profiles list file (name or accession number, default=profiles name)"
-    print "     -o: name of the output file (default=profiles list file+'.getz')"
-    print "     -v: verbose (default=0/1/2)"
-    print "     -n: pfam accession number (default=Not set)"
-    print ""
-
-#------------------------------------------------------------------------------
-
-def main():
-
-    DBFileName = ""
-    outFileName = ""
-    verbose = 0
-    listFileName = ""
-    accNumber = False
-
-    try:
-        opts,args=getopt.getopt(sys.argv[1:],"hd:l:o:v:n")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-d":
-            DBFileName = a
-        elif o == "-l":
-            listFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-        elif o == "-n":
-            accNumber = True
-        
-            
-    if DBFileName == "" or listFileName == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "beginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    if outFileName == "":
-        outFileName = "%s.getz" % ( listFileName )
-     
-    CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber()
-    CompleteProfilesDB.setProfilesDBFile ( DBFileName )
-    CompleteProfilesDB.setProfilesToAdd ( listFileName )
-    if accNumber == True:
-        CompleteProfilesDB.setPfamAccNumberKeys ()
-        if verbose > 0:
-            print "The profiles list is in Accession number"
-            sys.stdout.flush()
-    getzCmd = CompleteProfilesDB.CmdToCompleteProfileDB()
-    f = open( outFileName , 'w')
-    f.write ( getzCmd )
-    f.close()
-
-    if verbose > 0:
-        fileUtils = FileUtils( )
-        if fileUtils.isRessourceExists( outFileName ) and not(fileUtils.isFileEmpty( outFileName )):
-            print "%s finished successfully" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-        else:
-            print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-
-    return 0
-
-#------------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/pyRepetUnit/profilesDB/tests/datas/ListPfamProfilsInRepbase.txt	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-RVT_1
-RVT_2
-rve
-zf-CCHC
-DDE
-hATC
-Hermes_DBD
-MULE
-Exo_endo_phos
-Peptidase_C27
-Transposase_mut
-InvE
-Retrotrans_gag
-Chromo
-TLV_coat
-
-

--- a/commons/pyRepetUnit/profilesDB/tests/datas/ListpfamAccNumber.txt	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-PF00075
-PF00077
-PF00078
-PF00424
-PF05407
-PF00469

--- a/commons/pyRepetUnit/profilesDB/tests/datas/myhmms	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1433 +0,0 @@
-HMMER2.0  [2.3.2]
-NAME  rrm
-LENG  77
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -A myhmms rrm.sto
-COM   hmmcalibrate myhmms
-NSEQ  90
-DATE  Thu Jan  8 17:50:18 2009
-CKSUM 8325
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -45.953121   0.233439
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -16      *  -6492
-     1  -1084    390  -8597  -8255  -5793  -8424  -8268   2395  -8202   2081  -1197  -8080  -8115  -8020  -8297  -7789  -5911   1827  -7525  -7140     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378    -16      * 
-     2  -2140  -3785  -6293  -2251   3226  -2495   -727   -638  -2421   -545   -675  -5146  -5554  -4879  -1183  -2536  -1928    267     76   3171     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     3  -2542    458  -8584  -8273  -6055  -8452  -8531   2304  -8255   -324    101  -8104  -8170  -8221  -8440  -7840  -5878   3145  -7857  -7333     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     4  -1505  -5144  -1922   -558  -1842   2472  -3303  -2213   1099  -5160  -4233    372  -4738   -530   1147    168    498  -4766  -5327  -1476     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     5  -3724  -5184    300  -3013  -1655   1803  -3353  -5245  -1569  -2686  -4276   3495  -1963  -1331  -1054  -1472  -3664  -4803  -5369     -2     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     6  -1569  -6106  -8967  -8363    555  -8531  -7279    654  -8092   2953    -94  -8220  -7908  -1643  -7682  -7771  -6460    -59  -6191  -6284     6
-     -   -151   -504    230     45   -380    399    101   -621    211   -470   -713    278    399     48     91    360    113   -364   -299   -254 
-     -   -178  -3113 -12684  -1600   -578   -701  -1378      *      * 
-     7   -409  -5130   -215  -2987  -1709   -956    690  -5188   -395  -5144  -4224    729   3054  -2862  -3409    354   1293  -1381  -5321  -4644    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     8  -3674  -5118  -1004    639    420  -4652    176  -2050    404  -1039   -935     16   1755    168    147   -275    198  -1472   1889   1977    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-     9   -408  -5134   2415   1299   -950    -66   -767  -1296  -2889  -1843  -4224   1084   -968  -1439  -1854    540   -314  -2304  -5320    -60    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    10    586   1804  -6294   -631  -1627  -1671  -4374   1029  -2223   -162   1172  -5147  -5554  -1870  -5058  -2327   1741   1687  -4242    687    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    11  -2134  -5144    845  -1187  -1652  -1667  -3303  -5216   -513   -801  -4233   1026  -1873   -543   -619    575   2956  -4766  -5327  -4644    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    12  -3671  -5144   1091   2489  -1652  -2234   -613  -2170    736  -1364  -4233   -448   -197   1030   -116   -639  -1349  -4766   1408   -424    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    13   -139  -5144   1642   2051  -5465  -1429    503  -5216    530  -3223  -1447   -672  -4738   1875     73    318  -2111  -4766  -5327  -4644    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    14   -122  -5142   2117   1851  -5462  -1085   -933  -2288     33   -526   -556   -741  -4738   1222  -3392   -175    -13  -2228   -370  -4643    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    15  -7175  -6527  -9596  -9028   -232  -9481  -8154   1635  -8870   2831   -816  -9215  -8388  -7557  -8326  -8917  -7014    705  -6536  -6798    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -11642  -6295   -894  -1115   -701  -1378      *      * 
-    16   -654  -5013  -1860    729    726  -2316   -688  -1184   1801   -277  -4115   -790  -4754  -2885   1825   -463  -1784   -442   -227   1362    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11624 -12666   -894  -1115  -1520   -619      *      * 
-    17    156  -5127   2136   1476  -5448  -1504  -3286  -5199    301  -1955   -539   -894  -1057   1509    524   -467    301  -4749  -5310  -4627    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11624 -12666   -894  -1115   -355  -2197      *      * 
-    18    -49  -3785  -6295   -490   1591  -5504    920   1218  -2312   1810     49  -5147  -5554  -4880  -2068  -1575   -764   -207    -54   1201    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    19  -1516    962  -6738  -6118   4230  -2323  -4741  -1819  -5718   -295    162  -5595  -5977  -5294  -5502  -5054  -4347  -3561  -4499   -386    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    20     66  -5142  -3519    977  -5463   1170  -3304  -2365   1047  -2653  -4232   -150  -4738    557    447   1868  -1288  -2163  -5326  -1696    26
-     -   -147   -500    232     42   -381    398    105   -627    212   -464   -721    275    393     45     95    360    117   -367   -295   -250 
-     -    -19  -6287 -12684  -2206   -352   -701  -1378      *      * 
-    21  -1055  -5144    363    870  -1814   -295     89  -2404   1817  -5160  -4233    811   1390   1737  -1607   -671   -664  -2375  -5327  -1696    32
-     -   -149   -500    232     45   -377    398    105   -627    212   -467   -721    278    393     45     98    358    117   -370   -295   -250 
-     -    -90  -4053 -12684    -35  -5398   -701  -1378      *      * 
-    22   -394   1434  -6258  -2307   2972  -2526     19    850  -2195  -1152  -2991  -1854  -5549   -851  -5045  -2352  -3896   -124   -189   2914    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    23   -684  -7735  -1742   -712  -8352   3518  -5400  -8353  -5878  -8206  -7641   -311    -59  -5105  -6910  -1500  -6163  -7684  -8410  -7291    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    24  -1107  -5144    202    908  -1788     -8    -90  -1263   1342  -1905  -4233   -889   1908    171     58    -98   -246   -190  -5327  -4644    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    25  -3958   -549  -6303  -1346    278  -5505  -4377   2725  -2224   -925   -752  -5151  -2076  -4885  -5062  -2366  -1362   2524  -4242   -488    37
-     -   -147   -500    232     45   -381    398    105   -627    212   -466   -721    275    396     45     95    359    117   -370   -295   -250 
-     -   -170  -4711  -3774   -436  -1938   -701  -1378      *      * 
-    26  -1474   -441  -3586   1371  -4982  -2413  -3303    -26   1319    143     14    194  -4719   -534   -232   -509    586   1466  -5027  -4420    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -11533  -6292   -894  -1115   -978  -1022      *      * 
-    27   -251  -5076   1198   1096  -5397     75    696  -1292   -903  -5092  -4165   1381  -4669  -1297    629   1609   -628  -2391  -5259   -408    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11569 -12611   -894  -1115   -146  -3377      *      * 
-    28   1071   1843  -6303  -5667    723  -2647  -4376   2229  -2340    234    705  -1807  -5555  -4884  -5062  -1098  -1942   1556  -4241  -1380    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    29  -3674  -5121    815    520   -935  -4651   -961  -1319   1431   -350   -888    798  -4744    589   1471   -312     16    -53   -490     25    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    30  -1650  -3784  -6302  -5666   -659  -5505   -883   2172  -2226   1327   2112  -5150  -2048  -4884  -1866  -1552  -1875   1962  -4242  -3899    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    31  -1062   1015  -6187  -2355    288  -5488   -892   1176    271     -7   1951  -1951   1337  -4822   -157    104  -2109   1363  -4252   -388    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
-    32  -2112   -485   -886   -668   -313  -2330      4    217   1142   -767   -209    692    319  -1357   1259   -193    786   -575   -384   1141    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -396 -11642  -2062   -894  -1115   -701  -1378      *      * 
-    33  -3688  -5186   3392   -313  -5499     -6   -454  -5258    433  -1458  -4287   1354  -4689  -2831  -1676  -3548  -3635  -1045  -5362  -4662    47
-     -   -149   -500    233     43   -381    398    105   -627    210   -466   -710    275    396     48     96    359    117   -370   -295   -250 
-     -  -6411  -5987    -40  -1512   -623  -2885   -210      *      * 
-    34  -1469  -1564  -2202  -1918   -552  -2529   4215   2006  -1348   -996   -690  -1802  -2714  -1483  -1429  -1805  -1473   -636  -1202   -358    51
-     -   -149   -500    233     43   -381    398    112   -626    210   -466   -721    275    394     49     96    359    117   -370   -295   -250 
-     -  -1128   -892  -8229    -81  -4198  -5423    -34      *      * 
-    35   -751  -1651   -818   1403  -1742  -1787   -442   1180   1551  -1566   -793   -538  -1879    -93   -423   -761   -684  -1159  -1892   1944    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -7536  -8578   -894  -1115  -4803    -53      *      * 
-    36   -910  -2356   1159   1228   1231  -1845   -535  -2402   1262  -2363  -1453   1307  -1959    -86   -651   -790   -852  -1969  -2539   1518    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8  -8039  -9081   -894  -1115  -4804    -53      *      * 
-    37  -1099  -2524   -937    888  -2834  -2064   2027  -2568   1720   -117  -1620   1180  -2160   -267   -765   -986   1530  -2141  -2708  -2044    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -8399  -9441   -894  -1115  -4767    -54      *      * 
-    38    235  -2729    703    788  -3049    223   -886  -2800   -475  -2746  -1822   -850   1424   1228   -985    385   1396  -2351  -2915  -2230    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8686  -9729   -894  -1115  -1069   -935      *      * 
-    39   -700  -4332   -848   -249  -4652  -1581  -2493  -1503   1869  -4348    556  -2470   1337    695   1753    213    248  -1559  -4516   -771    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  fn3
-ACC   PF00041
-DESC  Fibronectin type III domain
-LENG  84
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -A myhmms fn3.sto
-COM   hmmcalibrate myhmms
-NSEQ  108
-DATE  Thu Jan  8 17:50:26 2009
-CKSUM 6130
-GA    7.8 -1.0
-TC    7.9 0.1
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-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    11    369  -5421   1596   1205   -476    497  -1028  -5492  -1937  -5437  -4510   1521    432   -395   -711      3   -529   -199  -5604  -1530    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -55 -11935  -4751   -894  -1115   -701  -1378      *      * 
-    12   -172   -860  -1215   -801  -5280  -4965  -3640   1669  -1233     51   -266     83   -719    327    227   -864    377   1823  -5339  -4737    14
-     -   -147   -503    232     43   -379    402    103   -625    210   -467   -723    275    395     42     93    360    117   -369   -297   -247 
-     C   -245  -2679 -12922   -347  -2227   -156  -3286      *      * 
-    13  -1709  -5420   -448   -619  -5741    996  -3580  -5492  -1898  -2294  -1324   1287  -5014    770     65   1101   2339  -5042   -449   -671    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    14    557  -5421    996    818  -5742   -274   -121  -5492  -1312  -3064  -4510   -279   1606  -1495  -1316   1523    650  -2689    269  -1603    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -13 -11935  -6826   -894  -1115   -701  -1378      *      * 
-    15  -3943  -5416   1390  -1433  -5737   -521   -114  -5488  -1246  -5432  -4506   1786  -5009  -3115    -78   1199   2391  -1872  -5600    210    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -1 -11922 -12964   -894  -1115   -384  -2097      *      * 
-    16   -608  -5420  -1172    108  -2035   -373  -1142  -5492   -242  -5436  -4509    357  -5014   -374   -668   2462   1185  -1222   -441    383    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    17    558  -4068  -6587  -5951    992  -2729  -1149   1701  -5546   1788   1281  -5435  -5839  -5169  -5346  -4874  -2289   1515  -4526  -1448    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    18   -933   -827  -1427   -266  -1123  -2663    326   -350  -1355    -51   -412   -200  -2224    686    473    560   1711   1050   -544   -656    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    19  -1888   -657  -6942  -6325    201  -2610  -5088   1651  -5939   1947   -224  -5827  -6212  -5572  -5752  -5278  -2376   2336  -4936  -4591    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    20   -929  -5421  -2266     84  -5742  -1769   1077  -5492   -417  -1270   -355    696  -5014    948    666   2138   1348  -5043   -456  -4921    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    21  -8216  -7316  -9156  -9322     91  -9004  -5417  -2436  -8936  -2051  -5172  -7772  -2396  -7636  -8307  -8288  -8065  -6554   6180  -3487    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    22  -1346  -5419    317    824  -2006  -2602   -264   -991    524   -814  -1291     53  -2064   1082    -69   1315   1519  -1271  -5603  -1682    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    23   1030  -5384  -3815   -335  -5688   -765    631   -926     42  -1595  -4478  -1903   2752   -932    121   -525   -280   -486    486  -1747    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    24     20  -5351  -1334  -1374  -5640  -1245  -3604  -2376   -447   -714  -1287   -993   3325  -1489  -3699    571  -1376   -142  -5553  -4891    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -636 -11935  -1489   -894  -1115   -701  -1378      *      * 
-    25   -313  -4824    738    903    489  -1961   -319  -1743    600   -730  -3913   -512   1182  -1049    456     69   1061  -1200  -5008  -1017    29
-     -   -149   -513    256     52   -380    388    111   -628    204   -474   -734    271    397     57     90    357    118   -370   -308   -236 
-     C  -2828   -458  -2930   -849  -1169  -4426    -69      *      * 
-    26  -1035   -178    227  -2617  -4671   2074    534  -1574  -1120   -142   -607    230   1117    -92     -7    -60  -1463   -921    262   -829    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11120 -12162   -894  -1115   -170  -3167      *      * 
-    27   -844  -5358    807    -90  -5679   1010    444   -968   -772  -3028  -4447   2041    -30    361    367    805   -592  -1669   -300  -1468    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11869 -12911   -894  -1115   -135  -3482      *      * 
-    28    598  -5412    -68    -40  -5729   2274  -3582   -979  -1438  -2130  -1237   -611  -2305  -1455      8   1107   -928   -265  -5598  -1593    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    29   -198  -5420   1001   1041  -5741  -1104    365  -1001    184  -3104  -1165   -263   2128   -388   -817   -491    330    124  -5603  -1626    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    30  -1055  -4065   -347  -5945   1276  -1786  -4657   2523  -5541    289   -897  -2216   -363  -1931  -5342  -2542  -2178   1499    562    787    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    31   -967   -668   1478     53   -533  -5043  -3723   -660   -547    -75  -1257   -546  -5132    295    -78    232   2008    -34   -405  -1682    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    32  -1289  -5416   -428   -607  -1226   2233   1325  -2385    447  -3088  -1092    818  -5016   -421    121    608  -1015  -1904   -552    535    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    33  -8249  -7313  -8871  -9139   2077  -8699  -1001  -1545  -1643  -2150  -6647  -7381  -8569  -7497  -8103  -7930  -8116  -1723   -286   4502    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    34  -1279  -5417   -134   1350   -543  -2801   -194   -359    427   -185  -4507    178  -5015    291   1530    265    393   -291  -5601   -249    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    35  -2842  -5745  -8966  -8648  -6155  -8853  -8876   2516  -8633   1028  -1220  -8509  -8508  -8481  -8771  -8255  -6260   2811  -8011  -7616    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -86 -11935  -4117   -894  -1115   -701  -1378      *      * 
-    36   -727   -855    134   1149  -1104  -4850    469   -317    612  -1220  -4399  -3492  -4943   1518    899    134   1469  -1101  -5498    -88    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11849 -12891   -894  -1115   -109  -3778      *      * 
-    37   -919   1849  -6583  -5947    -78  -5786   -316   -279   -394      5  -3268  -5431  -5836  -5165   -783  -2538   -975    515   2753   3639    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -1980 -11935   -422   -894  -1115   -701  -1378      *      * 
-    38  -4510  -5545  -3323   -676  -6286  -4728   2257  -5750  -2040  -5420  -4762   -420  -4944  -2779   3841   -989  -4331  -5444  -5302  -5022    46
-     -   -149   -489    232     45   -381    398    105   -627    210   -467   -711    277    393     48     95    359    117   -370   -295   -250 
-     .  -1797  -3160   -736   -733  -1328    -10  -7198      *      * 
-    39   -133    378  -1993    318   -904  -1088  -3465   -146   1095   -700  -4031  -1603  -2036   2018  -3588    429   -687   -306   2892    659    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -16 -11696  -6532   -894  -1115   -359  -2184      *      * 
-    40   -842   -917    563   1105  -5685  -1640    299  -2487    565  -1697    239    359   1961    355  -1190    286    442   -781  -5547  -4864    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11875 -12917   -894  -1115  -2701   -241      *      * 
-    41    194   -140    529    476  -5651  -1649  -1025    -35   1058   -241   -181  -3511   -102    569  -1132     74    739    807  -5531  -4855    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -117 -11875  -3684   -894  -1115   -146  -3378      *      * 
-    42  -3842  -5314   1613   -195  -1914   1700  -1086  -5385  -1826  -1539  -4403   2308  -4909   -723    276     26   -350   -751  -5497  -1525    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11823 -12865   -894  -1115    -87  -4088      *      * 
-    43   -626  -5420   1257    862  -5742   1052    748  -2386    534  -1327  -1382    504  -5014    -67   -724    909    706  -1767  -5604  -4921    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    44   -960  -5398  -1350    633  -2318   1625   -956  -1630   -939   -994    235   1507    831   1105  -3677    -17   -314   -640  -5588   -673    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -142 -11935  -3421   -894  -1115   -701  -1378      *      * 
-    45  -2194  -5287   1087   1415  -5608    870   -907  -2395    349   -427  -4376   -492    291   1176   -317    355    -70  -2410    771  -4787    55
-     -   -148   -444    225     63   -389    400    108   -622    197   -475   -727    259    408     43    103    350    102   -361   -222   -237 
-     C  -1290   -759 -12836  -1725   -520  -1099   -907      *      * 
-    46   -157    337    519    798  -1912  -1225    -68   -653    114   -297   -291  -1697    725   -732  -1940   -255     36    -19   3575  -4816    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11858 -12900   -894  -1115   -119  -3655      *      * 
-    47   -342  -5028   -807  -3514    413  -5058   1265    -38    982   -213  -1333   1448   -681   1545    500  -1182    191    127   -692  -1745    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    48  -1332  -5420  -1211   1830  -5741  -2545   2195  -2506  -1309  -5436  -1184    473   -397    559    487    489    809    -73   1534   -190    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    49   -723   -908   -854    -86   1437  -1366   -957    813    137    381   -284  -1081  -5126   1056    499  -1688   -640    833  -5352    508    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    50  -2535  -5405    488   -913   -774  -4926   -190    346   -730  -1313    232   1785   -479    314    404    559   1718   -315  -5593  -4914    70
-     -   -146   -501    231     42   -382    399    104   -628    211   -467   -722    274    394     47     94    361    116   -362   -296   -251 
-     E    -55  -4758 -12977  -1430   -669   -701  -1378      *      * 
-    51   -112  -4491   -192   -433  -1967  -1809  -4106   1489  -2323    501  -1098   -148  -2213  -3956   -431  -1276     -3   2236  -4883  -4446    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    52   -188   -867   1259   -506  -1086   -884   -221  -5486     13  -2134  -4507  -1033   2226  -3121   -710   1236    300    -54  -5601  -4919    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    53    -38  -5420   -774    -50  -5740   1398  -3580  -2557    497  -1087  -4509   1165   1212  -1491   1386    411  -3886  -2629   1114  -1704    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    54   -920  -5420    805   -572  -5741   -897   1041  -2557  -3160  -5436  -4509   1517    869    197   -752   1055   1687    273  -5603  -1603    77
-     -   -148   -501    231     42   -382    401    104   -628    209   -460   -722    276    392     47     94    358    122   -371   -296   -251 
-     C    -48  -4927 -12977  -1667   -546   -701  -1378      *      * 
-    55    540  -5417  -2058   1449  -5737  -4922    -14  -1594    207   -756  -4507  -3558   -134   1030   -427    194   1990   -278  -5602  -4920    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -537 -11935  -1688   -894  -1115   -701  -1378      *      * 
-    56  -1224  -4911    173   -396    -20   -696   1167   -519   -782  -2435    170   1440  -1034   -413    525    371   1659  -1244  -5096    752    83
-     -   -149   -490    230     45   -378    398    103   -621    208   -466   -723    273    391     43    104    358    121   -372   -297   -252 
-     C   -353  -2204 -12441   -101  -3887   -730  -1332      *      * 
-    57  -1089  -5230  -3621    543   -958   -947     54  -2267   -700  -1972  -1130    237  -1105    775    826   1902   1424  -2256  -5416    -93    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11745 -12787   -894  -1115    -56  -4726      *      * 
-    58    917   1372  -2400  -5948   1183  -2657   1045   -570  -5543   -207    697  -5432  -5836  -5166  -2244  -4870    -66   1482   -485   2853    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    59  -1727  -5372   -530     74  -2004  -4936    218    671    -46   -927    317    346  -2296     81   -674   -607   2399    703  -5569  -1950    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    60  -4299  -4122   -680  -6010   1503  -5851  -4724   1768  -5607   1770   -994  -5497  -5897   -439  -2266  -2656  -4239   1982  -4583  -4244    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    61  -1194  -5420    -55    570  -1167  -1802    702  -5492    441  -3071   -267    303   -123    727    117    856   1924   -610   -463  -1603    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    62  -2500  -5421   1801   -319  -5742   2398   -103  -2430   -195  -5437  -1130   1999  -2064   -939  -2013   -537  -3887  -5043  -5604  -1643    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    63  -2648  -4734  -2418  -6668   -914  -6542  -5402  -1252  -6279   3190   -215  -6192  -6513  -2081  -6056  -5641  -2421  -1067  -5136  -4863    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    64  -1252  -5420   -773    708  -5740  -2561   -177   -696   1132   -424  -1267     14   -857   1130   1213   -170    967    135  -5603   -223    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    65    680  -5349  -3837    246  -5636  -4944  -3606  -5364  -1398  -5350  -1237  -1116   3633   -932  -3701  -1668   -269  -2586   -311  -1663    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    66   -878  -5418    654  -1315   -625   2683   1459  -5488  -1208  -3181  -4507   1018  -5015  -1522  -1172    -93  -2240  -2527   -441    731    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    67   -329   -911  -3925   -296  -5440  -4989   -278  -1599   -486  -2271    688  -1087  -5079   -875   1192     93   2762    681  -5449  -4826    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    68   -715  -5420    613   1359  -1160  -1216    -61   -999   1010  -1064   -286    512    256    691    198   -142    563  -1715   -332  -4921    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    69  -8584  -7494  -8947  -9309   -410  -8831  -5010  -7468  -8866  -3134  -6868  -2232  -8685  -7581  -8225  -8081  -8433  -7626  -4256   4884    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    70  -1815  -5406  -2090   1238  -1053  -2697    642   -683    206   -981  -1214   1027  -5018    797    -56    458   1323    686  -5593   -187    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    71  -1772   -576  -6691  -6059   2751  -2721  -4781   1861  -5659    107    276  -5548  -5946  -5283  -5462  -4990  -4280   2105  -4641    656   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    72  -1774    157   -771   -126  -5740  -2696   -247  -1555    925  -5435   -361   -242  -5015   1187   2154    813    923  -1324   1141    185   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    73  -1859  -5823  -9013  -8663  -1043  -8868  -8653   1700  -8616    373  -1223  -8529  -8476  -8301  -8657  -8252  -6326   3293  -7705  -7445   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    74    339   -912  -2304  -1480   -161  -4982    242    328    485  -1007  -4340  -1086  -5073   1886   1206  -1252    451    493  -5463   1681   103
-     -   -149   -500    233     43   -381    398    105   -626    210   -462   -721    275    394     45     96    359    117   -369   -295   -250 
-     E    -43  -5729  -6603    -86  -4119   -701  -1378      *      * 
-    75   3003  -4642  -7089  -2701  -4985   -369  -5478  -2243  -6266  -1473  -4220  -5882  -6177  -5887  -6084    548   1259   -953  -5472  -5145   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11920 -12962   -894  -1115   -357  -2190      *      * 
-    76   -890   -701  -6337   -456   -128  -5749    302    444   -435    294   -981  -5315  -5801    452   1013  -1812  -1348   2281  -4547   1032   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    77  -2363   -782    199  -2083  -5740  -2662   -943  -1132    147  -3104  -4508   2805   -755  -1553   -765   1511   1258  -2796  -5603   -104   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -14 -11935  -6734   -894  -1115   -701  -1378      *      * 
-    78    349   -725    812    169  -2094   1817   -228  -2472   -192  -5424  -4497    321  -2426    905     63   -120    421   -272  -5591  -4908   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11921 -12963   -894  -1115   -373  -2135      *      * 
-    79    763   -866    480    290  -2215    944    426    219    379  -1687   -278    514  -2124    507    130  -1212   -544     72  -5596   -747   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -733 -11935  -1329   -894  -1115   -701  -1378      *      * 
-    80  -1112  -4529  -1625   -701  -1337   3244  -3171  -4384  -2854  -2219  -3676  -1217  -4563  -2782  -3334   -608    476  -4085  -4818    474   110
-     -   -153   -500    231     50   -364    398     93   -624    206   -464   -733    283    383     46     94    356    116   -368   -250   -237 
-     C  -6367    -18 -12245   -485  -1807  -3912    -99      *      * 
-    81  -5380  -6068  -5956  -5194  -7389   3194   -752  -6799  -1418  -2482  -5840  -5063   -706  -4120  -1351   1839  -5344  -6386  -6417  -6291   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11248 -12290   -894  -1115   -277  -2516      *      * 
-    82     68  -5329   -386    943  -1053    -34   1308  -2479    103  -1629    757   -877   1926   1130    381  -1141   -878  -1038  -5513  -1828   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11840 -12882   -894  -1115   -101  -3893      *      * 
-    83    102  -5296  -3867   1691     21  -1212  -3624  -1510   -259   -602  -1204  -1862   1786  -1626    665   -353   -181  -4888   2391    466   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11935 -12977   -894  -1115   -701  -1378      *      * 
-    84  -1211  -5433  -3815  -1455  -5755   -850   -140  -2313  -1280  -5448  -4523  -3575  -2241  -1598   -412   3271    384  -5056  -5615  -4936   119
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     C      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  pkinase
-ACC   PF00069
-DESC  Protein kinase domain
-LENG  294
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -A myhmms pkinase.sto
-COM   hmmcalibrate myhmms
-NSEQ  67
-DATE  Thu Jan  8 17:50:39 2009
-CKSUM 4536
-GA    -57.9 -57.9
-TC    -57.7 -57.7
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -194.939484   0.145939
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -21      *  -6109
-     1  -3588  -3415  -5932  -2068   2209  -1198  -4007   1029  -4891    889  -2618  -4781  -5186  -4515  -1612  -2029  -1657   -333   1774   3270     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378    -21      * 
-     2  -1103   -137  -1497   1525  -5095  -4284   1704    -69    423  -1097  -3867   -503  -4377   1172   1017  -1013    975    769  -4962  -4280     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     3  -3460   -131   -785   -393   1050  -4703  -3447   1378    306   1185   -596   -562  -1734   -284    173  -1848     58    960  -4250  -1088     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     4  -3367  -4343   -251    -58  -1421   1411    919    542    574    989   -604    -23  -4523   -994  -3271  -1049  -1512    847  -4637   -148     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     5  -1098  -4782   -183   1680  -5103    503   -434  -4854   1124  -4798   -647  -1288  -1568   1359   1836   -240  -1526  -1059     97  -4283     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     6  -1811   -238   -680    526   -557  -4309    481    726   1770   -409  -3794  -2960    209    272    290  -1047    576    765  -4901  -4244     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     7  -6084  -5527  -8663  -8230  -4683  -8506  -7801   2582  -2005   2411   -444  -8189  -7866  -7357  -7914  -7892  -6017    898  -6516  -6551     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     8  -1162  -4907  -7014  -7375  -7618   3734  -6813  -7450  -7402  -7698  -6730  -5890  -5975   -453  -7118  -4539  -1742  -6121  -7823  -7778     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-     9     21  -4782  -1460   1735  -1488  -2091  -2941  -1034    378  -4798   -702   -451  -1594   1320   1488   1403   -804  -2034  -4965  -4282     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    10  -9325  -8016  -8995  -9382  -9561   3867  -8643 -10645  -9576  -9967  -9932  -9344  -8440  -9454  -8996  -9819  -9545 -10244  -8234  -9579    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    11   1482   -366  -1515   -623  -1509    750    367  -4853   -639  -4797  -3871    397  -4376   -316   -611   1560   1138   -595  -4965  -4282    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    12  -3528  -3640  -4717   -983   3576   -666  -3694  -3183  -3938  -3506    429   -575  -4965  -3756  -1463    310   -886  -1665  -4065   2502    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    13    303  -4863  -7632  -7986  -7606   3448  -6938  -7434  -7625  -7696  -6714  -5992  -5965  -7041  -7216    899  -1607  -6089  -7827  -7822    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    14  -1086   2001   -620    718  -5095  -1992    493  -1038   1420  -2482  -3866  -2921  -4377    200    493    575   1303    928  -4961  -4280    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    15  -1356    755  -8169  -7898  -5798  -7710  -8130     18  -7871  -4555  -4472  -7586  -7648  -7843  -8040  -7096  -1974   3721  -7582  -7028    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    16  -3578   -158  -5677   -557   2092  -5098  -3955  -1494    705   -517  -2646  -1470  -5150  -4374    149  -1247  -3519   -369   1758   3515    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    17  -3311  -4764  -1417    525  -5076  -2045   1000   -427   2116   1135    223  -2927  -4381    303   1113   -167  -1542  -1123  -4952  -4275    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    18   2118   3534  -6025  -5409  -3498   2043  -4127  -1439  -5006  -2062  -2745  -4861  -5247  -4627  -4805  -1994  -1655    223  -4002   -858    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    19  -3543   -185  -5023    219  -1266  -4971    330   1223   1347  -1328   -458  -4300  -5031    540   1105  -1143    884    884    180   1134    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    20  -1194   -320    747    506  -5101  -4283   2862  -4852   -146    447  -3870   1539  -4376   -286    544  -1766  -3248  -4403   3098    408    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    21   -309  -4771   -186   -672  -5087  -4286   1935    775   1613    102    432  -1231   -703   -249   1435  -1070  -1560    120  -4958  -4278    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2119 -11253   -378   -894  -1115   -701  -1378      *      * 
-    22   -107  -3005   2005   -836  -3323   -312   1271  -3072   1151  -3020   1085   1327    980   -712  -1261  -1419    163  -2625  -3190  -2509    22
-     -   -156   -495    251     56   -388    395     99   -630    214   -469   -727    277    393     49     92    359    113   -370   -301   -250 
-     -  -3044   -188 -10179  -1816   -482   -467  -1854      *      * 
-    23   -416  -4471   1004    318  -4792    826   -147  -1359   1106  -1202  -3560    963    132   -684   -368    424   -435   -755  -4654    158    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10912 -11954   -894  -1115  -1138   -874      *      * 
-    24  -1682  -4615   1757   -661  -4935   -427    520  -1584    312  -4630  -3704    639  -4210  -2316  -1263    866   2334  -1008  -4798   -935    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11071 -12113   -894  -1115    -88  -4074      *      * 
-    25  -1145   -281    187    523  -5103   2336  -2941  -4853    106  -2370  -3871   1500   -802    200   -578   -191  -3248   -610  -4965  -1037    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    27  -1886  -4706   -690     97   -588  -4305    957   1554    380    259   -673   -468    530   1124    271  -1749    300   -181  -4910   -191    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    28  -1208   -195  -5934  -5297   1615  -5136  -4007   -272   -890  -3263    384  -4782  -5186  -4515  -1665  -4220  -1578   2938    187   2163    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    29   3436   -240  -7292  -6870  -1443  -6199  -5909  -1316   -960  -4324  -3966  -6219  -6445  -6242  -6403  -5441  -4707    364  -5768  -5389    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    30  -1900   -234  -5942  -5306  -3379  -2158  -4018   2542   -986    331    885  -4792  -5196  -4525  -1762  -2083  -3538   2511  -3884  -3542    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    31  -6181  -6227  -7911  -6341  -5278  -7070  -5185  -4471   3970  -2148   -640  -6080  -6949  -4791  -3803  -6514  -5992  -1936  -6206  -6162    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    32   -327    703  -4460    659   -413  -4820   -456   1575   1396  -1956    367  -3933  -4889    193    -99   -337    588    858  -4126   -874    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    33  -1154  -3437  -5959  -1813   1336  -5163  -4035   1984  -4919   1660    417  -4809  -5211  -1331  -4720  -1830  -3553   1845  -3899  -3557    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -92 -11253  -4020   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1554 -11161   -602   -894  -1115  -2645   -251      *      * 
-    35  -1979  -2616    600  -1789  -2689  -3138    917   -262   1783    813  -1778    212    701  -1583  -2068  -2093  -1919    409  -2970   1920    42
-     -   -150   -503    239     47   -384    400    102   -626    207   -465   -724    275    393     42     93    362    116   -369   -298   -252 
-     -  -1002  -1000 -10653  -1035   -966  -1861   -464      *      * 
-    36  -2419  -3891    679   1238   -598    232  -2052  -3962   -399   -689  -2981   1316   -775   1132    761   -903    593    330  -4075  -3392    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10253 -11295   -894  -1115    -23  -5973      *      * 
-    37    412  -4781    488   1427  -5102   -222  -2942   -361   2029  -1668  -3871  -2918   -162   -877    973   -574   -836  -1888  -4965  -4282    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    38   -678   -137   -210   1427  -1398  -4286   1671   -384   1154  -2518  -3862  -1162  -4379    894   1614    249  -1509   -483    197  -1118    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    39   -267  -4782    693    699  -1490  -4283   -508  -4854    809   -957  -3871    707    241   1159    519    994     44  -2057  -4965    442    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    40  -1182    -72    921    502   1029  -1156  -3293    951    402    104   1219     -6  -1620  -3023   -615  -1908    661    177  -4410  -1040    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    41  -1051  -4776    457     54  -1510  -1190   -243    -88   1940  -1673   -501    113    206    593  -3032   1547  -3249   -655  -4961  -4280    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -183 -11253  -3077   -894  -1115   -701  -1378      *      * 
-    42    406   1421    611   1061  -1312    -43    546  -4677    532   -534   -514  -1084     17    -29  -1122    292    214   -978    300   -772    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -425 -11071  -1974   -894  -1115  -3398   -144      *      * 
-    43  -2764  -4221   -153   1053  -4535  -1485   1520     90   1494   -131    -48   -671   -128  -1941    400   -407    604  -1460   2315  -3729    57
-     -   -142   -510    239     64   -403    385     95   -622    235   -461   -723    267    376     51    101    353    107   -365   -302   -244 
-     -  -2565   -268 -11690  -2050   -399  -2023   -408      *      * 
-    44   -209  -4375    154   -412  -4696  -1602   1286   -625   -228  -1226   1204   1142  -3970   1548   1745   -106    467  -1483  -4559  -3876    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10806 -11848   -894  -1115   -123  -3615      *      * 
-    45    681  -3394  -5912  -5276   2096  -5115  -3986   1503  -4871    827    433   -607  -1744  -1304  -4671  -1118    609    856    272   -816    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
-    46   -626  -4647   -606   -752    805  -2069   -325    269   -194   1297   -637   -472   -676    912    961  -1066    126   -635     56  -1093    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    47     11  -4782  -1478   -265  -5103  -2017   -410  -4854   -701  -4798    856    950  -4376   -282   2794    716    530  -4404    282    -27    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    48  -1162  -7159  -5721   3926  -8826  -6736  -6972  -9200  -7516  -8992  -8497  -6330  -7351  -6908  -7907  -6775  -7061  -8358  -8133  -8426    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    49   1060   -107  -5913  -1913  -1147  -1217  -4003   2441  -4877    538    339  -1638  -5183  -1456   -854  -1108  -1595   1072  -3874    -17    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    50    239   1306  -1422   1031  -5099   -700    352  -1032    821  -1062   -599   -509  -4377   1841   1019    327  -1584  -1913  -4964    472    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    51   -985  -3415  -5933  -5297  -1248  -5136  -4007   2549  -1963   1214   1629   -583  -5186  -4515  -4692  -1195  -1579   1453  -3873    -25    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    52  -3588  -3415  -5930  -5294  -1227  -2048   1433   -663  -4890   2398   3132  -1607  -5185  -1336  -4691  -1196  -3529   -297  -3873     54    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    56  -1884    764    906  -1443  -5103   -188   1312  -4854    809  -4798    279   1929  -4376    884   1300   1258  -3248  -4404  -4965  -1122    91
-     -   -153   -504    236     41   -384    403    108   -630    213   -468   -724    272    397     53     95    359    121   -373   -298   -253 
-     -   -399  -2052 -12295   -717  -1352   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    58  -1173   -216    245   1204  -5103  -1809  -2941  -4854    620  -4798   -545  -1224   3079   -272   -672   -439  -1509  -1128  -4965  -4283    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    59  -1852    -77  -4160  -3595    422  -2007   1972  -3460   -814  -3742  -3036   3674  -4802  -3324  -1558  -3710  -1482  -1517  -4249   1576    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    60  -5621  -5100  -8287  -7944  -1270  -1991  -7944   3577  -7896    340  -4034  -7788  -7778  -7646  -7966  -7505  -5600   1263  -7086  -6756    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    61  -3675    717  -6027  -5396  -3463  -5238  -4119   2327  -4996    517   -394  -4885  -1663  -4622  -1582  -2054   -833   2711  -3982  -3638   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    68   -519   -292  -1523   1548  -1530  -1060    375   -412   -187   -696    822   -442  -4421    557    492  -1702   1121   -118    303   1118   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1500 -11253   -630   -894  -1115   -701  -1378      *      * 
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-     -   -153   -497    234     42   -381    398    113   -616    215   -467   -731    275    398     42     91    361    121   -376   -305   -254 
-     -  -1804   -656  -3664  -2224   -347   -150  -3344      *      * 
-    70   -486  -4664   1357   1085  -4985   -532    560  -1808   -124  -1513  -3753   -323  -4258   -857    689    801   1256   -403  -4847    -32   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11124 -12166   -894  -1115   -343  -2242      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12274   -894  -1115   -380  -2110      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    73   -651  -4782   -168    750   -578  -2047   2645  -4853     97  -2362  -3871    924    471   -251    537    474   -748  -1103    200   1429   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    74  -1178    880  -5933  -5297    136  -2001   -595   1808  -4892   1524   1344   -420    242  -4515   -726  -4220   -778    458    172    878   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    75   -540   2737  -1735  -5276   -383  -5132    880   -637  -1950   -184    884    -68  -5182  -4503  -4683    -25  -1513   -813   2514   3307   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    78  -3589  -3420  -5900  -1855   1657  -5133  -4002  -1255  -4869   1532   3646  -1319  -5183     81  -4681  -1944   1306  -1569  -3877  -3535   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    79  -2223  -7725    285   3557  -7843  -5438   -536  -7828  -5262  -7661  -7076  -4019    830    173  -6251  -2036  -5764  -7268  -7864  -6740   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    80  -1960    -21  -5934  -5298   2086  -5136    965  -1405  -1868    792    371  -4782  -5186  -4516  -1638  -4221  -3529  -1458   1188   3749   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    82   -280   -366   1107   1579  -5103    583  -2941  -4854   -252  -2441    199    994   1479   -196    483   -618  -1627  -2010  -4965  -4283   139
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -346 -11253  -2233   -894  -1115   -701  -1378      *      * 
-    84  -4093  -4778  -5475  -5209  -6710   3477  -4989  -6385  -1530  -6450  -5617  -1206  -5539  -4693  -1363   -750    464   -678  -6565  -6305   141
-     -   -149   -490    235     41   -383    398    103   -621    210   -462   -723    273    391     46     93    360    117   -366   -297   -246 
-     -   -209  -3130  -5579  -1553   -601    -52  -4818      *      * 
-    85  -1064   -309   2847   1153  -5078  -4262  -2921  -4828  -2502  -2463  -3848    -19   -143   -981  -1323   1598  -1440  -1955  -4942  -4260   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11229 -12271   -894  -1115   -357  -2189      *      * 
-    86  -5040  -4758  -7393  -6764   -372  -6701  -5528   -815  -6399   3096    417  -6358  -1589  -5804  -6127  -5826  -1704   -462  -5037  -1081   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    87     65  -4715   -633   -683   2397  -4302   1674  -4734    106    256    293    400  -4395   -982    175   -586  -1543  -1923     84   1800   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    88   -244  -4782   2096    691  -1564   -655    356  -4854    362  -1051  -3871    418  -4376    310   1132    103     85  -2000  -4965  -1119   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    90  -3694  -3515  -1855  -5404    238  -5246  -4114   2100  -1935   2342   1019  -4893  -5287  -4614  -4798  -4333  -3634    529    376   -853   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    91  -1140  -4769   -713   -285  -1372  -4287   1385  -1034    442   -724    377   -361  -1676    907   1756    527   1005    112  -4956   -958   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    92    432  -4782    135    936  -1402   -557   -432  -4854    633  -2451    296    904  -1592   1082   1316     68   -298  -1942  -4965    493   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    93   -255   1350  -1412      8  -5103   -673   1861  -4854   1303  -1545  -3871   1796   -783    596   1588  -1069   -279  -4404  -4965  -1089   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-    94  -1751  -4776    453   -746  -1509   1743   -243  -1869   1418  -1564  -3866     59   -690  -2484   1090   -152    385   -580  -4961   -848   157
-     -   -150   -489    236     49   -389    397    112   -631    207   -469   -713    278    404     38     91    361    117   -369   -308   -253 
-     -  -1831  -1995  -1095  -2447   -292   -701  -1378      *      * 
-    95  -1080  -3937    182   -657    243   1157    313    398   -566   -222  -3030    354   -753   -190    303   -169    866   -320  -4129   -218   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10343 -11385   -894  -1115   -442  -1921      *      * 
-    96    161    805  -3172   -664  -1324   -499    507   -210    761   -208  -3441    187   1533    381    470    -56  -3114     25    291    106   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11067 -12109   -894  -1115   -270  -2553      *      * 
-    97  -3566  -3393  -1784  -5272   2324  -2052  -3984   1346  -1923   1790   1918  -4758  -1734  -1383  -4669  -4198  -1576     -4  -3851    816   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -46 -11229  -5024   -894  -1115  -1501   -629      *      * 
-    98   -573  -4721    583    376  -5043    109  -2880  -4793   -122  -4738  -3811    450    794   -124   -488   1914   1370  -4343  -4905  -4222   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11185 -12227   -894  -1115   -189  -3026      *      * 
-    99  -1028  -3904    124   2654    138  -4673   -512   -770  -3327   -335   1334  -3619    749  -1209  -1508  -1131   -714  -1749   1225    -45   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   100   -594   -305    921    761   -475   -189    958  -1005   1123  -1604   -581     20    250    202    916   -608   -818  -1956   1257   -967   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   101   -288  -4776   1376   1776  -5095  -1923   1385    -92  -1241   -114  -3866  -1259  -1603   1656  -1447  -1739   -258   -206    343  -1032   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   102   1568   1771  -5901  -5267  -3372  -2118  -4001   1842  -1734    994   -453  -4767  -5181  -1411   -182  -1218   -875   1083  -3875  -3532   180
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   103   -311    808  -1654  -3848   -281   -270  -3577    405   1931    468  -2911  -3904  -4877    558   1705  -1197  -3434    448  -4139  -3729   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   104    -26   1340    244   -781   1400  -2057   1319  -4839   1543   -712    384    932  -4378  -1028    246    332   -782  -1932  -4960   -145   182
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   105  -1214    774  -5976  -5341   1650  -5180  -4051   2169  -4937     40   1853  -4826  -5227  -4557  -4736  -4266  -3570   1080   1714   2407   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   106   1686    753  -5934  -5298   1553  -1286  -4007   1034  -4893   -199   2436  -4782  -5186  -4515  -4692   -260     57    657    354  -3530   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   107   -329  -4076  -3758   -905  -1389  -1199    339   -927   1302    805  -3236  -1389  -4648  -3000   1305     15    366  -1029   1191   1974   185
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   108  -1131   -335    172    908  -5104  -1136   -419  -4854  -2523  -4799   -668  -1124  -4377   3782  -1397   -607   -347  -4405  -4966  -4283   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   109  -5639  -5117  -8302  -7952  -5272  -8144  -7935   2597  -7900    836   1936  -7803  -7778  -7622  -7955  -7519   1191   1991  -7052  -6759   187
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   110   1484   2123  -5947  -5311   -235  -1115  -4022   -201  -4907   1978   -379  -4796  -5199  -4530  -4707   -310  -3541   1030  -3887  -3545   188
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   111   -671   1330   -647   1060  -5102  -1994  -2941  -1909   1295   -153   -695     41  -4376    877   1727    855   -765  -4403  -4965  -4282   189
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   112   2243  -4861  -7644  -7983  -7589   3019  -6925  -7411  -7584  -7674  -6697  -5990  -5964  -7026  -1546  -1067  -1841  -2167  -7810  -7801   190
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   113  -2201   -281  -7971  -7452  -1406  -7501  -6570    952  -7203   2152   2957  -7163  -7211  -6648  -7009  -6716  -5421   1875  -5905  -5754   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   114    777  -4782    718   1515  -5103  -4283   -340   -991   1157  -1577  -3871   1333  -4376    385   -492    662  -3248  -1111  -4965   -155   192
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   115   -360  -6644  -7694  -2051   1433  -7828   2559  -6632  -7848  -6039  -6064  -6593  -7806  -6748  -7364  -7112  -1819  -6729  -3620   4368   193
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   116  -2172   2767  -9105  -8531  -4252  -8881  -7599   1439  -8345   2749   1681  -8628  -7916  -7096  -7825  -8265  -6539  -4267  -6093  -6326   194
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   117   -416  -7356  -3349    266  -7495  -2140   5143  -7872  -5379  -7711  -7155  -1371  -6074  -4694  -6292  -5305  -5780  -7254  -7669   -182   195
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   118    -13   -306    733    907  -5103     93   -360  -1867   -241  -2549  -3871     30  -4376   -206    743   2216  -3248  -2034  -4965  -4282   196
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   119   -672    716  -1446    516  -1522  -4311   1363   -950   1016  -1159   1883   1645  -4404   1679   1321  -3222  -3259  -1108    116  -4240   197
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   120  -1862   -163   -618  -1440   -568   2279   1298   -961    792  -2520  -3868   1125  -4377   -991    749    191   -831  -4400  -4963  -1118   198
-     -   -149   -504    231     41   -380    401    113   -627    215   -466   -725    274    403     45     92    355    116   -371   -283   -253 
-     -   -179  -3102 -12295  -1872   -460   -701  -1378      *      * 
-   121  -5411    727  -8000  -7587   1790  -7672  -7025   2905  -7434   -152  -3911  -7314  -7433  -7129  -7406  -6949  -5382   2179  -6446  -1162   209
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   122   -618    840  -5935  -5299  -1214  -5137  -4008   2237  -4894    666   1335  -4783  -5187  -4516  -1766  -1187  -1501   2326  -3873   -906   210
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   123  -8407  -7275  -8450  -8809  -3793  -8053   5359  -7648  -8566  -6951  -7039  -7461  -8186  -7592  -7995  -8098  -8340  -7763  -4475   1186   211
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   124  -5094    -99  -6822  -5503  -6155  -1963  -4473  -5623  -1567  -1569   -400  -5194  -6119  -4158   4040  -2036  -1702  -5399  -5873  -5700   212
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   125  -6923  -7890   4200  -5000  -8686  -6482  -6170  -9053  -6698  -8760  -8346  -1338  -7059  -5964  -7524  -6617  -7065  -8485  -8135  -7889   213
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   131  -5687   2300  -8350  -8002    207  -8210  -8001   3253  -7958    805  -3949  -7870  -7814  -7644  -8002  -7596  -5662   1231  -7044  -6779   219
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   132  -6956  -6284  -9325  -8719   1416  -9211  -7739  -1549  -8543   2946   2123  -8959  -8021  -7132  -7931  -8654  -6766   -521  -6086  -6376   220
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   136  -1769  -4782    926    565  -5103   -161    908  -1978    983  -2502  -3871   2098    726    267    224   -199   -260  -1060  -4965  -4283   224
-     -   -157   -500    246     44   -384    394     93   -614    211   -477   -722    284    397     36    103    361    118   -368   -307   -245 
-     -  -2910  -2055   -675  -2460   -289   -701  -1378      *      * 
-   137   -497    939   1358   -204  -3859    731    895  -3609  -1283  -3555  -2629   1390   1009    363    608  -1950    447   -695  -3723    233   243
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2  -9833 -10875   -894  -1115    -55  -4733      *      * 
-   138   -244   -254   -598   -313   -479   2144    387   -871  -1338   -383    292    950   -584   -997   -597   -165   -811  -1046  -4875  -1035   244
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11229 -12271   -894  -1115   -359  -2181      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   140   -691   1386  -6334  -5723  -3772  -5578  -4498   2087  -5341   1399   -559  -5227  -1618  -4979  -5158  -1025  -3901   2349  -4347  -3999   246
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   141  -5615   1796  -6263   -306  -7053  -6235   -297  -6425   3658  -6155   -761  -4908  -6173  -3754    311  -5513  -5324  -2136  -6057  -1058   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   142  -2324     -4  -8046  -1864  -5464  -7795  -7522   3094  -7591   1907  -4214  -7450  -7571  -7458  -7677  -7116  -5380    678  -7004  -6550   248
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   146  -2136  -5232   -713  -5699  -7701   3751  -6286  -1752  -6856  -7753  -6876  -5380  -6054  -6175  -7071  -4737  -4995  -6329  -7867  -7577   252
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   147   -612    -19  -1611  -5292   1276  -5135  -4006    190  -1736   2542    362  -1490  -5185  -4512  -4690   -205  -3529    -57  -3873  -3531   253
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   148   2880   1396  -7217  -7106  -5717  -1993  -5929  -5313  -6711  -2341  -4931  -5726  -5814  -6244  -6420   2072  -1794  -1875    480  -5889   254
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   149    296   1256  -3193   -232  -5009  -1223  -2964  -1957   2100  -2435  -3815   -433  -4394  -2514   2391   -515    388   -574  -4919  -4255   255
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   150   -333    765   1073    474    751  -4340   -517   -453   1037    448   -600  -1217  -4431   1337  -1436   -961   -746    141  -4829    -44   256
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   151   -659  -3507  -1669  -1079   1105  -2193   -526   1167    -24   1452   1623   -467  -1514  -1322  -4405  -4074  -1654    491    187   1198   257
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -69 -11253  -4436   -894  -1115   -701  -1378      *      * 
-   152  -1062  -4720    300    970  -1467   -166    521   -987    916  -4736  -3809    998   -728   -100    590    573   -259    159  -4903    802   258
-     -   -153   -484    239     41   -390    398    113   -626    219   -472   -700    272    392     40     90    367    123   -389   -285   -237 
-     -  -2058   -691  -2833  -1765   -503  -2348   -315      *      * 
-   153  -1547  -4521    896    -79  -1088   -371    624  -1454  -1028  -1341  -3610   1604   1464   -724    141   1099    617  -4143  -4704   -873   278
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10967 -12009   -894  -1115    -61  -4600      *      * 
-   154   -296  -4769    220  -2614  -5084    988   -473  -1826   -252  -1564   -676   1312  -1591    914   -649   1005   -203  -1012  -4956   2078   279
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   156  -1171    640   -683   -194    513  -1991   1033  -1012    956   -129    324    443    254   -236    709     38     13   -145  -4937    372   281
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   159   -645  -4731    689   -346  -1420   1043    447  -1739  -2548  -4737   -658   -491   -673    302  -3052   1138   2084   -527    231  -4260   284
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   160  -1199   -151   -702   -420   1879     28   -563    425  -3409    201   -493    337   -194   -286    767  -1166  -3401    627  -4247   1134   285
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   161     -7   3604  -1703  -1952  -1279     20  -3751   -241   -967  -1274  -2774  -4228  -5005  -1297   -183  -3975    111   2386  -4015  -3638   286
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   163  -3463   -231  -4104  -1583  -3901  -4703   -285  -3477  -3393   -668   -567  -1427  -1763  -3282  -1601   1567   3275  -3329    138  -3817   288
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   166  -7087  -6552  -7865  -7298    906  -7610   -394  -6464    -71  -5974  -5863  -6312  -1544  -5805    222  -6878   -916  -6520   3392   4239   291
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2663 -11253   -249   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -8595  -9637   -894  -1115    -14  -6700      *      * 
-   169   3331  -4866  -7603  -7958  -7608  -1940  -6935  -7436  -7620  -7697  -6716  -5989    604  -7036  -7215    952  -4738  -6092  -7827  -7821   294
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   170  -5719  -5989  -8212  -8414  -6061  -6510  -7452  -5461  -8195  -1053  -5125  -7267   4235  -7661  -7816  -6091  -6099  -1808  -7128  -7038   295
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   171  -5844  -7649  -3465   3879  -7964  -5599  -4859  -7816  -4663  -7563  -7007  -1205  -6142  -1082  -1705  -5462  -5891  -7329  -7621  -6774   296
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   172  -1140   2074  -5903  -1972  -3372  -2210  -4001   1453  -4870    805  -2620  -4768  -5182  -1229   -302   -350  -1427   2455   1276  -3532   297
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2385 -11253   -307   -894  -1115   -701  -1378      *      * 
-   173  -1542   2001  -3865  -3232  -1327    -83  -1963   2264  -2833    722   -572  -2729  -3140    745  -2643  -2176  -1483   1249  -1835   1175   298
-     -   -147   -508    232     44   -380    394     97   -634    213   -465   -707    273    393     41    103    365    119   -372   -303   -247 
-     -  -1167   -853  -9914  -2962   -198    -41  -5143      *      * 
-   174  -3569  -3395  -5913  -1783  -1209  -2028   -312   2012  -4872   2363    985  -4762  -5166  -4496  -4673  -1049  -1621    557  -3853  -3511   318
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
-   175   -287  -4778  -1431    968    438   -254  -2943  -4847    989    305    869    352  -4377    862   1100     98  -1521   -196  -4963  -4281   319
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21 -11253  -6175   -894  -1115   -701  -1378      *      * 
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-     -   -151   -496    236     48   -375    395    115   -627    213   -472   -719    275    387     51     93    363    116   -369   -303   -247 
-     -   -723  -1344 -12275  -1185   -836   -388  -2085      *      * 
-   177  -1854   -365    250   -270  -1451   -695  -2942  -1670    829  -1506  -3870   1446    994   1339   1305    316     71  -2013  -4964  -1132   327
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   178  -1183  -4781    479    337   -476   1157    920  -4851    811  -1706    863     91    780   -251  -1348   -518  -1627   -249  -4964   1628   328
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   179   -641  -3679    186  -1774   1732  -4848   1886    417  -3794  -1978  -2867  -1484  -4915  -1042   -659  -1931  -3446   -785    351   3626   329
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   180  -4456  -5182   1171  -4993   -329   1754  -5512  -6689  -5796  -6852  -6053  -4925    -79  -5350  -6183   1886   2183  -5902  -6901   -135   330
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   181   -294  -4652  -3232    -18   -493  -1889    973  -1007    354   -963  -3756  -2982    981   -155    808   1087   1407   -151  -4871   -114   331
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   182   1049  -4783  -3158    856  -5105  -1213   -419  -4855   2095  -1055  -3872  -2920   1504    205    611   -175   -804  -4405  -4966  -4284   332
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   183    694   1354  -1593  -4846  -3445  -2149  -3909    651  -4536  -1942  -2681   -470  -5116  -1270  -4499   1853   -840   2310  -3931  -3576   333
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   184  -2185  -7763   4161  -1526  -8064  -5545  -5059  -8102  -5545  -7921  -7396  -4164  -6155  -4765  -6600  -5444  -5959  -7498  -8066  -6964   334
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   185  -3763  -3574  -6119  -5491  -3529  -5337  -4222   1931  -1751   -459   2285  -4984  -5377  -4717  -4898  -4427  -1556   2841   2093  -1035   335
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   188      2   2053  -5936  -1804   2354  -5138  -4009    177  -4895   1885    427  -4784  -5188  -4517  -4694  -1967  -3531    459  -3874    878   338
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   189  -1096  -4894  -7086  -7456  -7614   3751  -6842  -7446  -7503  -7699  -6727  -1317  -5969  -6906  -7188  -2060  -4756  -6111  -7830  -7789   339
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   190  -1945   3550  -6042  -5412  -3478  -5254  -4136   1922  -5012    -23    429  -4901  -5300  -4639  -4816  -2067  -1486   2422  -3998    152   340
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   191  -5172  -4754  -7738  -7288  -5043  -7312  -6644   2449  -7086    995   1643  -6965  -7162  -6821  -7043  -2325   1223   2054  -6259  -5887   341
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   192  -1076   1328  -5938  -5302    836  -5140   -325   1005  -4897   2425   1260  -4786  -5190  -4519  -4697  -4225   -335    240  -3876   -892   342
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   193    946  -3495  -6008  -5379   1305  -5216    887   1093  -4974   -788   -375  -4852  -5263  -4589  -4771  -4302  -3613   -848   3942   3060   343
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   194   -612   -188  -1396   3179  -5077  -4288  -2947   -101  -1346  -4777  -3856   -448  -1414   -120  -3037   -525   -321  -1145  -4953     21   344
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   195  -1952  -3418  -5937  -5301   -272  -5139  -4011   1021  -1684   2216   3270  -4785  -5189  -4519  -4696  -2001   -778      8  -3875   -822   345
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   196    806   1503  -5937  -5301   1069  -5139  -4010   -159  -4896   2118   1853  -4785  -5189  -4518  -1647  -4224   -704    488  -3875    -12   346
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -68 -11253  -4450   -894  -1115   -701  -1378      *      * 
-   197   -244   1762  -1486   -304    176  -4478  -3186  -1620  -1279   -221  -3216    398  -4561  -2888   -637    521   2695  -1689  -4401     88   347
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -22 -11185  -6108   -894  -1115  -2339   -318      *      * 
-   198  -3245  -4700  -1285  -2549   -491   2810   -331  -4760    938  -1086  -3791   -321  -4313   -924    849   -991  -3184  -4319  -4885   1151   348
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1315 -11165   -743   -894  -1115  -2606   -259      *      * 
-   199  -2173   1967  -2528  -1972     17   2076  -2043   -457    979  -2731    717    -64   -376    170   1038  -2282   -340   -523  -3176  -2686   349
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -599  -9852  -1561   -894  -1115  -5598    -30      *      * 
-   200    585  -2946    192    327    320  -2642  -1313  -2906    368  -2934  -2055  -1307   2663   -879  -1420  -1559    970   -222  -3173  -2532   350
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -273  -9256  -2548   -894  -1115  -4647    -59      *      * 
-   201     -7  -1595    298  -2960  -1558  -3177  -2022   1183  -2650    990   -794  -2662   1216  -2358  -2612    727    308    444  -2044    901   351
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -110  -9104  -3800   -894  -1115  -5907    -24      *      * 
-   202     57  -1583  -4065  -3442   2875  -3303  -2112   1403  -3043    674   -733    458  -3345  -2657  -2848  -2389  -1701   -972   3227  -1515   352
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8998 -10040   -894  -1115  -5935    -24      *      * 
-   203  -1548  -2953    474   -828   1541    -89  -1185  -2981    576  -2962  -2061  -1137   2705    902  -1297  -1437    354  -2564  -3160  -2490   353
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -632  -8998  -1503   -894  -1115  -5935    -24      *      * 
-   204    949  -1873  -3594  -3310  -3215   2567  -2867    956  -3113  -3131  -2370  -2617  -2976  -2850  -3187    780   1132  -2303  -3567  -3260   354
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -360  -8372  -2199   -894  -1115  -6061    -22      *      * 
-   205    726  -1828  -1018   -467  -2006    573   2223  -1643   -310    410   -995   -717    992   -285   1111   -896   -833  -1380  -2145  -1598   355
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -541  -8020  -1695   -894  -1115  -6108    -21      *      * 
-   206  -1455  -3002   2743   -124  -3339  -1838   -906  -3139   1668  -3063  -2255   -476   1698   -520  -1270  -1244  -1458  -2675  -3223  -2453   356
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -375  -7491  -2162   -894  -1115  -5060    -44      *      * 
-   207   -746  -1560   1425   -341  -1356  -1795   -444  -1289   -170    682   -700   -571  -1893   -160   1517   -779   -684  -1075  -1644   1953   357
-     -   -149   -500    232     45   -381    400    111   -627    210   -466   -721    275    393     45     98    359    117   -370   -295   -250 
-     -  -2633   -258  -8511    -45  -5040  -6160    -20      *      * 
-   208  -1767  -3401   2107   -139  -3802  -1858  -1202  -3699  -1354  -3615  -2897   2073   2793   -864  -2119  -1501  -1847  -3169  -3794  -2874   359
-     -   -150   -501    232     42   -377    397    105   -627    211   -463   -722    277    393     48     95    360    116   -370   -282   -250 
-     -  -1435  -1255  -2242  -1944   -434  -4946    -48      *      * 
-   209   2138  -1310  -3697  -3171  -1088  -3181  -2298   1866  -2865   1275    -74  -2834  -3185  -2520  -2785  -2341  -1503    291  -2073  -1786   364
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -7515  -8557   -894  -1115  -4020    -92      *      * 
-   210  -1233  -1057  -3502  -2875   2324  -2779  -1614   1177    721    798   2162  -2397  -2809  -2101  -2304  -1865  -1171   -427  -1448   1579   365
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -8194  -9237   -894  -1115  -4002    -93      *      * 
-   211  -1302   2115  -2420    350   1052  -2659  -1447    663  -1647     92   -633    792  -2725  -1476   1471  -1674   1486   -879  -1868  -1474   366
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8636  -9678   -894  -1115  -4368    -72      *      * 
-   212  -1500  -1493  -3073  -2485  -1475   1806   1631  -1021  -2227    -15   1601  -2312    308  -1989  -2294    905  -1446   1296  -1944  -1577   367
-     -   -150   -501    231     44   -378    400    104   -628    211   -463   -722    274    397     47     94    358    116   -365   -296   -251 
-     -  -4031    -93  -9909    -16  -6545  -3062   -184      *      * 
-   213   -308   3406  -2790  -2223    329   1927   1217  -1722  -2052  -2025   1176  -2281   -140  -1909    100    454  -1826  -1593  -2560  -2148   369
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9403 -10445   -894  -1115  -4745    -55      *      * 
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-     -   -150   -501    231     42   -382    399    104   -628    209   -467   -722    282    394     44     94    364    118   -368   -296   -251 
-     -  -3424   -847  -1511    -17  -6404  -5781    -26      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8855  -9897   -894  -1115  -4219    -80      *      * 
-   216  -1659  -1606   1126  -2775  -1573  -3126   1339   1650  -2494    568   1451  -2548  -3183    578  -2513     17  -1600   1517  -2052  -1691   373
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9076 -10118   -894  -1115  -5914    -24      *      * 
-   217  -1495  -2943   2280   1499  -3254  -2470  -1131    -17   -716   -641  -2035  -1109  -2564    944    544    118    299  -2560  -3133  -2456   374
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9076 -10118   -894  -1115  -4783    -53      *      * 
-   218  -1591  -3032   1083   1465  -3339  -2560  -1226  -3080   -812    730  -2126  -1201  -2658   2356    399  -1477    268  -2647  -3222    680   375
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9175 -10217   -894  -1115  -5886    -25      *      * 
-   219  -1742  -1646  -3647   -173  -1608   -321   1411   1597  -2724   1305   1373  -2730  -3291  -2428    236   -122  -1683    373  -2096    857   376
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9175 -10217   -894  -1115  -5886    -25      *      * 
-   220  -1721  -1749  -3148    754   1397  -3140   1240   1590  -2325   -145   -943  -2447  -3201    511    276   -102  -1661   1010  -2185    836   377
-     -   -149   -502    231     43   -383    396    103   -624    212   -466   -713    276    392     43    102    360    115   -366   -297   -251 
-     -  -4339    -74 -10217    -12  -6866  -4187    -81      *      * 
-   221    585  -2351  -2208     71  -2412  -2955  -1677   2453     99  -2250   1246  -1839     12   1339  -1909  -1915     53    -32  -2715  -2240   379
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9346 -10388   -894  -1115  -5830    -26      *      * 
-   222   -185   1537  -4239  -3604   2205  -3447  -2319    312    744    864   1396  -3091  -3497  -2824  -3003  -2532    911    887  -2186  -1843   380
-     -   -151   -502    233     45   -383    398    103   -625    214   -466   -723    273    391     50    101    358    115   -366   -297   -252 
-     -  -4510    -66 -10388    -11  -7043  -3687   -117      *      * 
-   223    431  -2579   -112   -147     32    338  -1823    594    -73    500  -1741  -1965  -3188  -1555     80   -423    -49   1384  -2934  -2448   382
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9573 -10615   -894  -1115  -4704    -56      *      * 
-   224  -2022  -2478    612   -287  -2518   1276   1865    -81  -1896   1098    904  -2188   -169  -1790   -128  -2216  -1962  -1942   1522   1336   383
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9636 -10678   -894  -1115    -47  -4966      *      * 
-   225   -253   -342    241    943  -1550    511    416  -1901   1300  -1037    261   -423   -738   1137    593   -947    117  -1919  -4945  -1082   384
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12275   -894  -1115  -1421   -675      *      * 
-   226  -1092  -4749   -606    581   -564  -1870   -440    343  -1335    619  -3840   -387   1504    244   -647    265   1309   -569  -4936  -4258   385
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11232 -12275   -894  -1115   -384  -2098      *      * 
-   227  -5705  -7606   -601     32  -7987  -5466  -4991  -8006  -5466  -2585  -7299  -4094   4121  -4694  -6511  -2244  -5847  -7381  -8039  -6892   386
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   228  -3576   -202  -5624  -2094   3261  -5089   -616  -2951  -1896   -127   -464  -1572  -5142  -1385  -1692  -1955    348   -801   2793   2371   387
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   229   -675   -230    195    293  -5097  -1215    985   -443    145  -2453   -681  -1107   1491    688    497    985  -3248  -2026     82   1781   388
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -137 -11253  -3475   -894  -1115   -701  -1378      *      * 
-   230   -191  -4658   1917    454  -1407   1496   1095  -4730  -1106  -2385  -3747   1039   -543    738    348    -76  -3124  -4280  -4841  -4158   389
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1242 -11117   -794   -894  -1115  -3068   -183      *      * 
-   231    125  -3514    984   1532   -304  -3096   1711   -630  -1349  -3518    667  -1742    485    271    549    602  -2050   -736  -3715    242   390
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -536  -9877  -1693   -894  -1115  -4485    -66      *      * 
-   232  -1923  -1930  -3418   -248  -1905  -3354  -2172   1427   -236    734   1293   1008    902  -2354  -2673   -304  -1864     70   3345  -1999   391
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -169  -9424  -3199   -894  -1115  -5801    -26      *      * 
-   233   -177  -3080   1072    307  -3395   -302   1306    752    341  -3093    992  -1237   1877   -801   1122  -1506  -1562  -2699  -3267  -2589   392
-     -   -149   -500    232     43   -381    398    105   -627    210   -466   -711    277    393     52     95    359    117   -370   -295   -250 
-     -   -400  -2049 -10301    -45  -5039  -3694   -116      *      * 
-   234   -377  -3122   1282    735     41  -2823   1070   -384   1371   -727  -2229  -1488  -2914  -1054  -1594    959    724   -463  -3347  -2707   394
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3  -9503 -10545   -894  -1115  -3327   -151      *      * 
-   235    130   1019   -202   -129  -3730   -752  -1662  -3464    739   -271    708    836    572  -1210   1162  -1909   1062   -690  -3631    333   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2  -9764 -10806   -894  -1115  -2310   -325      *      * 
-   236    -58  -3831    759   -412  -4150  -3336    462   -824   -379   -632  -2921   1020    238   1173   1239    716   -637   -940   1081   -137   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10185 -11228   -894  -1115  -1418   -677      *      * 
-   237  -2832   1269    712    563   -861  -3892  -2576   1496    656   -533    842    558   -205   -410    -69  -1296    302   -548    658   -557   397
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10670 -11712   -894  -1115   -170  -3173      *      * 
-   238  -1058  -4740   1414    765   -505   -595   1409   -449    226  -1087    894    747   -692    900      1    369   -643  -2020  -4923  -4240   398
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115   -870  -1143      *      * 
-   239  -3290  -4745   -186   -313  -1388    289  -2926    291    186   -589    254   1668   1599    315    -90   -180    386  -1937  -4933  -1011   399
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -366  -2158      *      * 
-   240   -597  -3523   -247  -4579   1041   -239   -634    180   -870    649   1849   -639   -164  -1356  -4363   -295   1168   -437    214   1209   400
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   241     24  -4780   1113   1177    464  -1969  -2942  -1715    359  -1612    289     33  -1527   1156   1155     43   -331  -1938  -4964   -108   401
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   242    242  -4780   -209   1327   -510  -1162    503  -1003    465  -1135   1207    936  -4376   1386    762   -217   -847  -1164  -4964  -4282   402
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   243   -331  -3415  -5931  -5295   -356  -5135   -422   1682     -8   1115    434  -4780  -5185  -4514   -720   -670   -339   1301    471   1689   403
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   244   -296  -3807   -160   -358   1602   -658   1942   -290  -1591    308   1232   -534   -809  -3375  -3810   -232   -346    497  -4206   1378   404
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   245    645   1246    171    325  -1565   -246  -2950  -1914    109   -424   -644     22   -730    238   1783     20  -1585  -1951     91    356   405
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   246   -287  -3957  -3935  -1604   -375   1032    978   1813   -377    425   1292    -24  -1671   -330   -784  -1105   -805   -488  -4329    -31   406
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   247   -315  -4676    531  -1367  -1473  -2022   -415   1100    963    214   -409    682  -4406    637    -75  -1766     67    581  -4889    867   407
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   248   -667   -245   -660    757   -571  -1911  -2960  -1964   1281     94    254     30  -1661   1539    220   -532   -816   -542   1187   1076   408
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   249  -1120  -4782    476    511   -524     59   1681  -1888    841  -2553    212   1135   -697    617   1196   -148    307  -2032  -4965  -4283   409
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1035 -11253   -967   -894  -1115   -701  -1378      *      * 
-   250  -2422   1649  -2415   -463    385  -1084   1415    -55    201  -1508  -2696    926   2305  -1718    332   -877    585  -3132   1189  -3229   410
-     -   -159   -489    230     48   -393    391    106   -623    208   -470   -723    279    401     36    106    362    114   -367   -264   -229 
-     -  -1907   -448 -11262  -1831   -476  -1095   -911      *      * 
-   251  -1337    300    199   -985    473   1252  -2522    -11    852  -1939  -3443      4   1241   -508    726   -186    467  -3973  -4538   -749   422
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10789 -11831   -894  -1115   -205  -2918      *      * 
-   252  -3278  -4644    482    537   1408     82    473  -1832   -601    349   -629  -1201   1239   -976    601   -147  -3217   -110    247    426   423
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115  -1984   -420      *      * 
-   253    286    -35   -649    327  -1315  -1967    472  -1932    118    449   -662    521    902  -2448   1699   -196    411  -4342  -4912   -976   424
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11207 -12250   -894  -1115   -870  -1143      *      * 
-   254  -1072  -4374   -669   -329     78  -2066  -3076    298   -238    849    793  -1238    981   -953   1064    324   -798    -92    233    424   425
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115  -1481   -640      *      * 
-   255  -1157  -4745    460   1205   -545   -662   -388   -825   1032   -684   -579  -1144   1754   -996    220   -870   -287   -488    293  -1067   426
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -366  -2158      *      * 
-   256  -1133    675  -3596   -353   1466  -1233    347     10    323    289  -3359     46    554   1055    771  -1097  -3329    288   1117   -152   427
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   257  -1790  -4723    147   -649    460  -2044  -2961   -960  -1300  -1584  -3820    405   2753    391   -111  -1764  -1419  -1995   3263    479   428
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   258  -1133  -4774    919    289  -1472  -4285    510    -76    364  -1072   -506   -466   1480    246    187    969   -220   -998  -4960    487   429
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   259   -628  -4735  -1504    267  -5035   -673    421    268   -650    195   -713   1874   -715  -2504    282    699    318  -1878    176   1059   430
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   260  -1175   3614  -5930  -5294    516  -5135   -538   1325   -983    925   -380  -4780   -704  -1274  -1768  -1016   -812   1047   1179   -985   431
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   261  -1076  -4800   -682   -725  -5121  -2088  -2956  -4872  -1209  -4816  -3890   -471   1956    -73  -1338   2811   -348  -4422  -4983  -4299   432
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   262  -1037  -4782   1535   1680  -5103   -510  -2942   -924    405  -1698  -3871   -529   1595  -2482    233    976  -3248  -4404  -4965  -1079   433
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -51 -11253  -4857   -894  -1115   -701  -1378      *      * 
-   263     84  -4736    971   2258  -5057  -1922  -2895  -4808   -213  -1467   -574     15    534   -116  -1288    303    398  -4358    128    -67   434
-     -   -149   -502    231     48   -378    396    110   -628    208   -463   -712    273    394     43     97    359    120   -371   -297   -251 
-     -   -125  -3594 -12244  -1472   -645   -232  -2751      *      * 
-   264   1731   2547  -5934  -5298    640   -263  -4007   -247  -1801   1576    924  -4782  -5186  -4516  -4693  -4220  -1553    458    192  -3530   439
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   265   -241   -198  -3682   -794   -427  -1936  -3240    612   2124    111  -3291   -475  -4617    956    498  -3480   -202  -1841  -4474   1903   440
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   266   -289   -331   2577    958  -1430  -1196   1052  -1871    140  -1667   -735   -379  -4376    573   -654    661  -3248  -4402  -4964  -1037   441
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   267  -5570  -5207  -7943  -7332   2492  -7349  -6163    426  -7006   2460   -530  -7015  -7020  -6282  -6695  -6514   -964    748  -5450   -851   442
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   268  -1228   -132  -7186  -6649  -4539  -2083  -5657   2368  -6345   1703   2977  -6230  -6527  -6019  -6218  -5733  -4672   1093  -5411  -5058   443
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -11253  -5950   -894  -1115   -701  -1378      *      * 
-   269   -233    733    496    538  -1512   -556   -483  -1871   1194   -153  -3846     49  -4356   -914    979    500    853  -1866  -4941    -84   444
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11230 -12272   -894  -1115   -360  -2177      *      * 
-   270  -1879    740    708     42  -5102    499  -2941  -4853   1925  -1686  -3871   -478  -4376    840   1351    531  -3248  -1765   1733    -65   445
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   271  -1078   4527  -6001  -5369  -3424  -5188  -4083    473  -4965   1280   2971  -4849  -5245  -1263  -4765  -2003  -1635  -2877  -3945  -3606   446
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   272  -6032   1306  -8380  -7761    165  -7863  -6566    202  -1775   2623   -272  -7537  -7346  -6544  -7063  -7064  -5909  -4318   4168  -5617   447
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   273     16   1673    924    771  -5103  -4283   2109  -1011    386  -4798  -3871   1377  -4376    855    547  -1066    354   -205  -4965  -1058   448
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   274  -1190  -4283  -1596   -753    779  -4462   -457  -1758   1515    461    303  -3221    581    211    534  -1081   -360    361   1085   1460   449
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   275  -1788   -192   3257   -772  -5108  -4287  -2947  -4859   -129  -4804  -3877   2093  -4381   -992  -1328  -1034  -1521   -207  -4971  -4288   450
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   276      9   -212  -3967   -984  -1118  -2024   -395  -3569  -3273  -3831    325  -3573   3646  -1156   -648  -1930  -1495   -116  -4315  -3856   451
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   277    468  -4779   -133   1101  -1427  -1979    368  -1871    610  -1046   -655    948  -1568    259   -674    967    318  -1112     68    403   452
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   278   -657   -189    933   1062  -5103  -4283  -2941  -4854   2011   -701    218    391  -4376   1360    303     74     67  -4404  -4965  -4283   453
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   279  -7207  -7306  -8076  -6588  -8459  -7223  -5448  -7982  -1500  -7531  -6953  -6369  -7277  -5081   4236  -7139  -6862  -7777  -7053  -7277   454
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   280   -694   -163  -5922  -5286  -1204  -2048   -610   1082  -1800   1434  -2618  -4776   2951  -4509  -4688  -1216  -1648  -2829    202     21   455
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -3168 -11253   -171   -894  -1115   -701  -1378      *      * 
-   281  -1412  -2132  -2007  -2293  -4366   3113  -2847  -4225  -3107  -4377  -3503   1660  -2881  -2661  -3396    961  -1821  -3134  -4516  -4119   456
-     -   -150   -489    232     42   -382    400    104   -627    211   -465   -722    274    393     51     95    359    116   -370   -296   -245 
-     -  -2121   -637  -2975   -831  -1191  -6099    -21      *      * 
-   282   -968  -1818  -1787  -1351  -3112    953  -1494  -2818  -1122  -2911  -2044  -1365  -2340  -1133   1510   1816   2121  -2205  -3137  -2649   459
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -228  -7899  -2816   -894  -1115  -4964    -47      *      * 
-   283    840  -1663   -994    969   1159    503   -604  -1413   -325  -1594   -814   -688  -1996   -267   1103   -851   -755  -1179   2900  -1437   460
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9  -7938  -8980   -894  -1115    -89  -4060      *      * 
-   284  -3257  -4642   -697  -2590  -1218   -252  -2907  -4655  -1306  -2353   -529    482  -1607  -2459  -1398   2112   2745  -4246  -4848  -4187   461
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11183 -12226   -894  -1115   -186  -3045      *      * 
-   285   2163    763  -1619  -5296   2250  -2060  -4007   1241  -4891   -489    484  -4781   -226  -4515  -4692   -678  -1688   -813    264  -3530   462
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   286   -268   -329   -158    917   -541  -1990    350  -4851   1273  -1075    388  -1130    233    840    993   -602    801   -595  -4964   -857   463
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   287    109   -243    672   2304  -5103  -4283    488  -4854  -1317  -2269   -656   -492  -1519   2679   -655   -618  -3248  -4404  -4965  -1114   464
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   288   1312   1294  -6215  -5593   -206  -1244  -4339   2188  -5201   1409    395  -5091  -5478  -4828  -5009  -4538  -3794   1162  -4188  -3846   465
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -11253  -6022   -894  -1115   -701  -1378      *      * 
-   289  -3562    799  -5767  -2054  -1235  -2075    318    138    237   2164   1713  -1454  -5145  -1272   -730  -4172  -1640   1071  -3865    -34   466
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115  -1470   -646      *      * 
-   290     73   1351   -674   1236  -1549  -2008   1350  -4834   1049  -2498  -3851   1801  -4356   1813   -115   -223  -1582  -1052  -4945  -4262   467
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
-   291  -1739   -320    777  -2654  -1419  -2051   4360  -4707  -1358  -2412   -689  -1300  -4399   -224    537    531   -289  -2010  -4905  -1057   468
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
-   292  -3345  -4494   -233   -332   -563  -1986  -3051    333     99   1063  -3616  -3072   2953  -1026  -1490   -943  -1528  -1070  -4753  -4151   469
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10815 -11857   -894  -1115   -701  -1378      *      * 
-   293  -6409  -5751  -7614  -7636   2593  -7311  -4003  -5084  -7219   -150   -151  -6210  -7172   -849  -6723  -6510  -6299  -1387   4881   2807   470
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -10749 -11791   -894  -1115   -701  -1378      *      * 
-   294  -4057  -3817  -6415  -5791   3203  -1638  -4541   1679  -5412    765   1434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//

--- a/commons/pyRepetUnit/profilesDB/tests/datas/profilesDBTest.hmm	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7162 +0,0 @@
-HMMER2.0  [2.3.2]
-NAME  RVT_1
-ACC   PF00078.19
-DESC  Reverse transcriptase (RNA-dependent DNA polymerase)
-LENG  242
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F --prior PRIOR HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  156
-DATE  Mon Jun  2 18:30:00 2008
-CKSUM 7481
-GA    35.2000 35.2000;
-TC    35.2000 35.2000;
-NC    35.1000 35.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.513688   0.618327
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -13      *  -6834
-     1    254   -362  -1116     20   -891   -782   -593  -1348    663  -2265  -4560    682    522    340    223   2070  -1876  -2798   -263  -4972     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26756 -26756      0 -19932      0 -19932  -1013  -8913 
-     2   -419   -233   -396  -1108   1220  -2792  -3751   -250   -584  -1669  -4321  -1660   2448   -323   -379  -1635   -527  -1337   3626    168     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -26767  -7314      0 -19932      0 -19932  -8926  -8910 
-     3  -3036   1124  -1949  -2086   -484  -1024   1155   -973   1367  -1738   -250   1015   -902    -89   1143   -814   -125  -1397   2962   1591     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932   -781  -1259  -8926  -8907 
-     4    516   -987   -771   -323  -5789  -1603   1192   -740     80  -1399    452   1966   1252   -961    178    229    252  -1273   -632  -4972     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932   -781  -1259  -8926  -8904 
-     5   1343  -1132  -6596  -5963  -4077   -340  -4703    201  -5567  -2165   -675   -770  -2432  -5197   -287   1192   2065    481  -4580    975     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26758 -26758      0 -19932      0 -20712  -8926  -8901 
-     6  -1152  -5367  -3923  -1459  -2119   -869   -642  -1019    908  -1501  -4470    334   2500  -1749   1764  -1025    141    -13   -594  -1817     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26767 -26767      0 -19932      0 -19932  -8926  -8898 
-     7    414  -4522  -2360  -2529  -4542  -1623  -4197   1934   -816    267    417  -4460  -2354  -1999   1302  -1950    186   1758  -4919  -4490     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -26767  -7603      0 -19932      0 -19932  -8926  -8895 
-     8  -1232    249  -2517  -1894   2481  -2907  -1402   1076   -826   -485   -144  -5476  -2696  -5208  -3149  -1959    -20   2026   1351    503     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26760 -26760      0 -19932      0 -20598  -8926  -8892 
-     9   -326   -780  -6569  -1098   1014  -1723  -4705    257  -1888   1172   1075  -2521   1316  -1495  -2370  -1038    150   1000   -840    905     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26767 -26767      0 -19932      0 -19932  -8926  -8889 
-    10  -2023  -4161  -6677  -6043  -4122  -5889  -4763   3113    421    347  -3366  -5532  -3033  -2495  -5439  -2044  -4278   1853  -4631  -2367    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8886 
-    11  -1532   -925   -861   -558  -2142  -2848     -1  -5538   1673   -830  -1756  -1740   2989   -728    420  -1491  -1524  -1544   -391   -323    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8883 
-    12  -2479   -934   -756  -1673  -5967  -1045  -3780  -5717   3714  -3186  -4737   -136  -5213  -3325  -2083  -1082  -4109  -5267  -5820  -5139    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8880 
-    13    262  -5481  -2457   -738  -2834    -90    720  -1046   2411  -3136  -1998    109   1725  -1947    385  -1398    -19  -1750  -5664  -4982    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -96 -26768  -4007      0 -19932      0 -19932  -8926  -8877 
-    14   -918  -5393   1629  -1647  -5714   1663   -577  -3044   -693  -3398   -280   1674     78  -1243  -1281    870    271   -974  -5577  -4894    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2177 -26675   -364      0 -19932  -3019   -190  -8926  -8873 
-    15  -1990  -3463    642   -164  -3784     52  -1621  -3535   2750  -3479  -2553   -358  -3056  -1162    689    419    372  -1466  -3646  -2964    15
-     -   -143   -502    237     40   -383    396    103   -622    215   -466   -719    273    395     43     93    358    119   -369   -297   -252 
-     -   -924  -1279  -4083   -890  -1119  -2512   -278  -8926  -8870 
-    16  -2532  -4006   2703    176  -4327   -878  -2164  -1084    732  -4022  -3095    368    430    314    286    176    120  -3628  -4189  -3506    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -43 -25156  -5202      0 -19932  -3031   -188  -8926  -8867 
-    17   1343  -4235  -2613    765  -4556  -1612   -394  -4306   1265  -1925  -3325   -878   2045   -425   1462  -2645  -2704  -2105  -4419    367    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25420 -25420      0 -19932  -4332    -73  -8926  -8864 
-    18  -1649    181    202   1708  -1424  -1681    780   -351     84  -1465  -3393    250  -3900   -746    687    719   1544  -3925  -4487  -1140    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25498 -25498      0 -19932  -6082    -21  -8926  -8861 
-    19  -2832   -484   1177    998  -4624   -380  -2465   -534   1269   -880  -3393   1194  -3900    479   1395   -249  -1257   -365  -4488  -3805    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25498 -25498      0 -19932  -2441   -294  -8926  -8858 
-    20    371    932  -4615  -4033  -3389  -2690  -1260    663   1010    284   1483   -781   1309  -3621    824   -590    932   -521  -3837  -3455    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25811 -25811      0 -19932      0 -25745  -8926  -8855 
-    21   -493   -956   -637   -811  -5799   2603  -3642  -1792    630  -3039  -1303    131  -1710    210  -1664    396    149  -2130  -5663   -820    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8852 
-    22  -1421  -5482    948    444  -5803    745  -3641  -5554   2185  -1905  -4571    861  -5076    133  -1579   1184   -273  -2650  -5666  -4983    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26768 -26768      0 -19932      0 -19932  -8926  -8849 
-    23   -872  -4789  -1840   -921   1402  -2863   -300   -311    510   -812    717  -4109  -1336  -1121  -1444   -444  -1402  -1505   3760   2812    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11 -26768  -7603      0 -19932      0 -19932  -8926  -8845 
-    24  -5704  -6056  -7996  -6825  -2108  -6586   -497  -2732  -4517  -6550  -5948  -6246  -6944  -5403   4157  -2861  -1824  -2714  -6359  -5766    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -26760 -26760      0 -19932      0 -20598  -8926  -8842 
-    25  -4300  -4130  -6619  -5984  -1190  -1378  -1903   -399  -1669    974   2714  -1891   3079  -1530  -5395  -3025   -851   -422  -4587  -1770    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1169 -26768   -854      0 -19932      0 -19932  -8926  -8839 
-    26  -4627   3553  -7174  -6703  -4570  -6691  -5964    280  -6466   1189  -3479  -6346  -6585  -6211    -24  -5900  -1593   2736  -5656  -5269    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25601 -25601      0 -19932  -3759   -111  -8926  -8836 
-    27   -827  -3116  -5634  -4998    639  -1775   2199   2166  -4593   -123   -100  -4482  -4887    846  -4393  -3921   -197   1919  -3574   -894    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -4838 -25704    -55      0 -19932    -14  -6685  -8926  -8833 
-    28  -5481  -4951  -8165  -7838  -5232  -8041  -7994   3162  -7814   1830  -3929  -7702  -7677  -7600  -7919  -7440  -1403    945  -7080  -6741    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -3 -25860 -25860      0 -19932  -5761    -27  -8926  -8830 
-    29    232    955  -5770  -5354  -5068   1877   -688  -4661  -5146  -4968  -4248  -1321  -5406  -4919  -5270   2593    677  -1772  -5461     11    34
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-     -  -2102   -390 -25483  -4097    -87  -2301   -327  -8926  -7983 
-   231    377  -4605    -46   -272  -4926    372    622   -961   1077  -4621  -3695  -2743   -190    565    376    724    288    292   1619   -169   386
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -25834 -25834      0 -19932   -536  -1687  -8926  -7977 
-   232   -353   -138  -1911      1  -2593   -484   -520  -5328    927  -3180   -389    -62    -59   1427     87    951   1201    426  -5441   -633   387
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26534 -26534      0 -19932   -572  -1611  -8926  -7972 
-   233  -3935   -940   1587    949  -1696  -1834    667  -5480   1025   -660  -4497   -189    351    596    660      4    573  -1486   -854   -546   388
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26693 -26693      0 -19932  -1792   -492  -8926  -7966 
-   234  -1318   -851  -3796   1705  -5740    865  -1576  -1962    600  -2272  -1639   -630   1517    930   -134    626    247  -5042   -458  -4921   389
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26706 -26706      0 -19932  -2573   -265  -8926  -7960 
-   235    -56    502  -6585  -5948   1419   -555  -4658   1725  -5543   -382    265  -5432  -2334    -47  -1059  -1982   -919   1938    463    996   390
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26706 -26706      0 -19932  -2573   -265  -8926  -7954 
-   236  -2855  -5421    621    525  -2542  -3007   1239  -1114   2071  -1608  -4510    594  -1032    576   1627   -765    265  -2853  -5604  -2031   391
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26706 -26706      0 -19932  -1602   -576  -8926  -7948 
-   237  -7116  -6576  -8494  -8428   3402  -8105   -270  -1144  -8004  -3159  -1982  -2273  -8043  -7106  -7569  -7276  -7025    478   2514   3380   392
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26719 -26719      0 -19932      0 -22251  -8926  -7943 
-   238  -4347  -4172  -2557  -2605   -976  -5896   -430  -1241  -5649   3024   1202  -5541  -2842  -5269  -5449  -4981    269  -2237  -4626  -4287   393
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7937 
-   239  -3129  -5611  -8259  -8615  -8342   3798  -7660  -3145  -8338  -8426  -7452  -2278  -6709  -7756  -7948  -2913  -5482  -2660  -8565  -8551   394
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7931 
-   240  -1534   -471  -6646  -6010   1634  -5848   1551    395  -2992    459    536  -5494  -2838   -389  -2391  -1937    236   1344    897   2624   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7925 
-   241  -2622  -5466   -752    857  -2292  -2207    995    364   -165  -1444  -1749    756    498    828    311  -1262   1250    763    439   -121   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -26770 -26770      0 -19932      0 -19932  -8926  -7919 
-   242  -4303   -182  -2660  -6012   1335  -5850  -1410   2547  -5607   1628  -1427  -1351  -5900  -2315  -5407  -4935  -4243   1497  -4587  -2045   397
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8926      0 
-//
-HMMER2.0  [2.3.2]
-NAME  RVT_2
-ACC   PF07727.6
-DESC  Reverse transcriptase (RNA-dependent DNA polymerase)
-LENG  263
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  100
-DATE  Thu Apr 24 22:48:43 2008
-CKSUM 7668
-GA    22.7000 22.7000;
-TC    22.9000 22.7000;
-NC    22.5000 22.6000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -9.984050   0.680188
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -31      *  -5555
-     1   3503  -4299  -7019  -7349  -7016  -1725  -6347  -6838  -7014  -7099  -6125  -2116  -1913  -6443  -6627   -181  -1550  -2657  -7239  -7223     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -1031  -9033 
-     2   -814    737  -5668  -5048  -1640  -4896  -3799    977  -2359  -2914   4738  -4544  -4935  -4291  -4469  -3991   -858    534  -3655  -3309     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9031 
-     3   -659   -908   1274   1163  -4590    -17    696  -2365   1032   -893   -424   1114  -3864   1418   -711   -291  -1747  -1053  -4453   -794     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9028 
-     4    358  -4267   1596   2570  -4587  -3772     68  -2444   -533  -2453  -1238  -2408  -3865   -160  -1186    523   -473   -747  -4451  -3769     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9025 
-     5  -2751  -6054  -3823   3927  -7246  -5329  -5256  -7315  -5587  -3217  -6760  -4481  -5974  -5041  -6171  -5101  -5448  -6661  -7241  -6696     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9022 
-     6  -4946  -4604  -7299  -6677    664  -6674  -5456   2598  -2633   1609   3290  -6336  -6373  -5621  -6022  -5826  -4848  -2163  -4780    203     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9020 
-     7    130  -4270   1783   1308  -4592    215    729  -4342    737  -1917  -3360   1636  -3864   -272   -690   -204   -732  -1673  -4454  -3771     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9017 
-     8   2064  -4168  -2703  -1463  -2014  -3802  -2465  -4162   -545  -4165   -271    294  -3894  -1111  -1670   2473   -328  -1644  -4380  -3726     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9014 
-     9  -3094    225  -5439  -4803   1622  -2613   1503   1629  -4398   1773   2362  -4288  -4690   1219  -4197  -3728  -3034  -1173  -3374  -3034     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9011 
-    10  -2039  -4192  -1489   2043  -4477  -3793   1454     37   1351   -429    413  -2443  -3886    962   -266   -483   -542   -324   -544    217    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9008 
-    11   -180  -4270   -283   1058  -4591  -1652   -885  -1871   2294  -1520   -451    -78  -3864   -263   1499    471  -1853  -1694  -4453  -3771    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9006 
-    12  -2140  -4315  -3168  -2588  -4572  -4155    598  -4231  -1167  -1153  -3441   3893  -4236  -2340   -268  -1927    579  -3908  -4514   -990    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9003 
-    13  -1666   -493    942    811  -2075    840   2442  -4343   1567  -4287  -3360   1661  -3864    959   -592   -995  -2736  -3893  -4454  -3771    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -9000 
-    14  -3848  -4504  -2271  -5374  -6918  -4638  -5759  -6594  -6315  -6932  -6060  -2125  -5417  -5683  -6417  -1458   3727   1422  -7154  -6893    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8997 
-    15  -7348  -6256  -7710  -8071    993  -7593  -3771  -6232  -7620  -5533  -5632  -6199  -7447  -6340  -2273  -6843  -7196  -6389   6003   1578    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8994 
-    16  -2797  -1007   1974   2045  -4587  -1569    140  -2412   -146  -2917  -1204   -921  -3865  -1971      0    760   1204  -1211  -4452  -3770    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8992 
-    17  -3090  -2918  -5416   -444  -1547  -4639  -3510   1258  -4381   2567  -2109  -4278   -793  -1961  -2385  -3723  -2028   1181  -3378  -3037    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8989 
-    18   -231   1090  -1536    557  -2954  -2114  -3525    396  -4278  -2825   -809  -4224  -4703  -3946  -4161  -3728    558   3089  -3460  -3112    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8986 
-    19  -2007  -4268   1655   1128  -4588  -3772   -873   -820    550  -2756  -1256   -508   2230  -1181  -2518    911    324  -2385  -4452  -3770    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17 -10690  -6760   -894  -1115   -701  -1378  -9064  -8983 
-    20  -2151  -2940  -4916  -4308  -1588  -4523  -3367   -487    -64   2239  -2139  -1411   1497  -3704   1711  -2463  -1446  -2359   -398   -158    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115   -516  -1734  -9064  -8980 
-    21  -2449  -5373  -1705   -839  -5664  -4444    416  -5422   -553  -2069  -4537  -3073   3892  -2977  -3632  -3707    483  -4992  -5566  -4838    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10690 -11732   -894  -1115   -701  -1378  -9064  -8977 
-    22   -498   -109   -302   1348  -4591  -3771   -907  -4342   1978  -2870     78   -741   1847     -3    230   -451   -610  -1231  -4453  -1732    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -28 -10690  -5933   -894  -1115   -701  -1378  -9064  -8974 
-    23  -1986  -4250   1252   -142  -2058   2665     90  -4322   -293  -4266  -3339   1165  -2149    -77   -271   -515  -2716  -2217  -4434  -3751    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10667 -11709   -894  -1115   -426  -1967  -9064  -8972 
-    24     42    865  -1568  -1452  -1955  -1664   1999  -2398   2076  -4268    540  -1369  -3868   1646   1324  -1158  -1730    611  -4443  -3764    24
-     -   -149   -500    233     43   -379    398    105   -623    210   -466   -721    275    394     45     96    359    117   -367   -295   -250 
-     -    -74  -4393 -11732    -81  -4200   -701  -1378  -9064  -8969 
-    25  -3129   -778  -3123  -2535  -1243  -4118    268  -4237   2768  -2107  -3427   2068  -4195  -1359   2054  -3061  -1218  -1322  -4501  -3931    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17 -10690  -6752   -894  -1115   -701  -1378  -9064  -8966 
-    26   1621    477  -5445  -4812  -1536  -4650  -3530   1010  -4410   -872  -2126  -4298   2280  -4035  -4212  -2126   -526   1871  -3394  -3051    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8963 
-    27  -5052  -4522  -7743  -7426  -4914  -7631  -7654   3119  -7411    841  -3602  -7289  -7282  -7253  -7547  -7035  -5037   2308  -6775  -6386    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8960 
-    28  -1711  -4300    212  -1093  -4620   3093   -869  -4371   -417  -4315  -3390  -2420   -700  -1138  -1601    297    125  -3921  -4482  -3798    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8957 
-    29  -3049   4459  -5369  -4734  -1583  -1600   -970  -1228  -4335    111   -283   -191  -4644  -3963  -1879    980   1006    133  -3336   -113    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8954 
-    30  -5600  -6127  -6824  -4914  -7137  -2124  -3755  -6321   3641  -5900   -627  -4687  -5908   -884   1761  -5466  -1783  -6132  -5690  -5681    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8951 
-    31  -9201  -7519  -8444  -8831  -8263  -7482  -7921 -10022  -9010  -9286  -9320  -8844  -7910  -8885  -8420  -9772  -9318  -9786   6317  -8061    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8948 
-    32  -5014  -4485  -7710  -7399  -5005  -7598  -7673   2314  -7388  -1063  -1326  -7253  -7273  -7288  -7552  -7000  -5001   3319  -6862  -6415    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4 -10677 -11719   -894  -1115  -1059   -943  -9064  -8945 
-    33  -7333  -6241  -7694  -8056   4102  -7580   1063  -6217  -7611  -2750  -5617  -2270  -7433  -6327  -6970  -6829  -7181  -6374  -3002   2794    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -9064      0 
-//
-HMMER2.0  [2.3.2]
-NAME  rve
-ACC   PF00665.18
-DESC  Integrase core domain
-LENG  169
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  244
-DATE  Tue May 13 16:19:09 2008
-CKSUM 4196
-GA    32.0000 32.0000;
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-NC    31.9000 31.9000;
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1413   -679      *      * 
-     9   -823    989  -2737   1003   -235  -2308   2877  -6170  -2578  -1478  -1601  -2192  -5766   2514  -1305    274    -26    549  -6320   -485    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12707  -8232   -894  -1115  -1413   -679      *      * 
-    10    159   1302  -2597  -6693  -1974    879  -2447   1406  -6288   -410   2704  -6177  -6581  -2738  -3280    137   1242    384    206   -673    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12702 -13745   -894  -1115   -996  -1004      *      * 
-    11  -7245  -9332   4108  -1285  -9447  -6936  -6373  -9435  -1771  -4458  -8706  -2104  -1810  -6068  -2414  -6832  -7344  -8876  -9413  -8295    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1413   -679      *      * 
-    12  -1399   1417  -7325   -167   1917  -1494    678   1552  -6286    195   -203  -1499  -6585  -1536  -2028  -2625    615   1134   1223    454    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115   -386  -2090      *      * 
-    13  -1033   1445  -7341  -6705     36  -1380  -5414    367      0  -1211   -667  -6189  -6593  -1152  -6100   -737   2672   1059   2402   -237    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1556 -12714   -600   -894  -1115   -701  -1378      *      * 
-    14   -505  -4518  -3178    662  -4761   2938    918   -963    -97  -2018  -3628  -2923  -4344     63  -3028  -1225  -1582   -311  -4750  -4117    15
-     -   -147   -502    240     41   -379    396    103   -628    210   -466   -712    273    400     46     94    359    115   -370   -297   -252 
-     -   -306  -2390 -12201   -397  -2056    -71  -4375      *      * 
-    15  -2422  -1862  -1291    406   -349  -1163   2726   -514   -518  -1365   -708  -4436   1934   -541  -1259  -1292     -8   -562  -6083   2340    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12672 -13714   -894  -1115   -123  -3617      *      * 
-    16  -1831  -1476  -1075  -2610   1366    974  -1286   1501  -2233    849   1201  -3523  -2957  -5882  -1761   -579  -1648    992    -33    813    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    17    173   -685    247    212  -6490    -87   -131  -2534   1089  -1679  -5258   -461   1763   -503   1500    -10  -1377  -2148   1395  -5670    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -792 -12714  -1244   -894  -1115   -701  -1378      *      * 
-    18  -4211   1221  -6206  -1500   -926   -156   -357   1957  -1791  -1224  -3298  -2144   1445  -2576  -2000   -465   -601   1863   -340    626    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -11923 -12965   -894  -1115  -1454   -655      *      * 
-    19   -382  -5709   -490    595    881   -304  -1632   -163    748   -129   -128   -390   1050   -100   -447    172     58   -517  -1171  -1939    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -100 -12260  -3903   -894  -1115   -882  -1129      *      * 
-    20    530  -5899    -39  -1538  -1038   1154   -375  -1664     53   -884  -1336    273  -2656  -2388   -133   1223   1697  -2121  -6084  -5403    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12441 -13483   -894  -1115  -5228    -39      *      * 
-    21  -1341  -5882  -1193   -960  -1504    359    246    -87   1596   -823   -340    285    730     -8   1041  -1123   -746    -42    744    509    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12441  -7853   -894  -1115  -1115   -893      *      * 
-    22   -330  -1058   1228    777   -928   1970  -4185  -6095    369  -1993  -2250    677  -3373    851   -830  -1527   -651  -1743   1736  -5525    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -652 -12566  -1460   -894  -1115  -4454    -67      *      * 
-    23  -3928   -253   -832  -1978  -5721   2706  -3560  -1353     11  -5416  -4489    693  -2211    563   1226     -4   -362  -2789   -525  -4901    26
-     -   -153   -530    215     29   -395    432    139   -619    213   -473   -729    264    378     43    138    340    129   -367   -302   -252 
-     -   -453  -1927  -7288  -2912   -206  -1696   -532      *      * 
-    24  -1186  -5669  -1872   -775   1498  -5174    433  -5737   1789  -3721  -1897   1109   -326  -1206   1058  -2350    -84  -1466   2750   1780    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20 -12199  -6207   -894  -1115   -275  -2528      *      * 
-    25    113    698   -903  -2060  -3453  -5639    471   -292   1301   -187   -425   -360   -191    343    932    411   -474    543   -297    574    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12625 -13668   -894  -1115   -497  -1779      *      * 
-    26   -208    468  -7007  -6390   -829  -6472   1105     10   -768  -1800  -4035  -1234  -2930   -224   -457   -631  -1247  -1090   1900   3881    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12690 -13732   -894  -1115  -1201   -823      *      * 
-    27   -913    385  -7326  -6690   1579  -3868  -5399   1612  -3906   2080  -1762  -2962  -3083  -1815  -6085  -3379  -1714   1169  -5264     55    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12699 -13741   -894  -1115   -818  -1208      *      * 
-    28    804   1664  -3916  -6693   1117  -1350   1417    265  -3733   1477   -663  -3227  -6585  -2742  -3284   -574   -429    113    986   1385    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115   -384  -2098      *      * 
-    29   -287  -4932  -3125  -5965   -185  -1293     53   -199  -5702  -1212  -4129  -1342   -675  -1995   -374   -271   2263   2271  -5374  -5009    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    30   1247   1035  -7341  -3505   1937  -6543  -5414   1957  -6300    360    990  -1935  -6593  -2921  -6100  -1990   -895   1059    940  -2611    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -12714  -7931   -894  -1115   -701  -1378      *      * 
-    31  -1689  -4931  -2997  -2700  -4902  -3923  -5219   2233  -1752    485    737  -2451  -3623  -2963  -1132  -2953    319   2476  -5372  -1575    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12709 -13751   -894  -1115  -1299   -752      *      * 
-    32  -2652    -63   3730    784  -7916  -6474    255  -7718  -2955   -122  -2448   -897  -6816  -3034  -5985  -5828  -6034  -7256  -7835  -7032    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12709 -13751   -894  -1115   -423  -1976      *      * 
-    33     37     57   1679   -436  -6449   -648   -360   -444   -300     89  -2495  -1728  -3102  -1199   1181   -523    752    638    464  -1293    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -12714  -6014   -894  -1115   -701  -1378      *      * 
-    34    480    648  -1935   -834   2663  -1650   1897  -6001    -75   -920  -1751   -633  -5779  -1814  -1251  -2394  -1083  -2339     38   2726    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -12692  -7421   -894  -1115   -200  -2946      *      * 
-    35  -1955  -6742   -705  -5120  -7781   -698  -5645  -3549  -3220  -7540  -6647    362  -6727  -5243  -2206   3066   1900  -6937  -7708  -7047    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -12706  -6900   -894  -1115   -364  -2164      *      * 
-    36  -4969  -1994  -3000  -4266  -6752   1457    596  -6476   1696  -1769  -5490    392  -6003  -2468   3042   -996  -2509  -6040  -6535  -5902    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12702 -13745   -894  -1115  -1739   -514      *      * 
-    37   -445  -1486  -2868    785   2085  -2345  -1007  -1773    748   -471    629  -2608  -2839  -2483    560  -1630   -370  -1131   2228   2233    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12702 -13745   -894  -1115  -1739   -514      *      * 
-    38    656   1278  -7292  -2858   -847  -1351  -2037   1925  -1768   -136   -710  -6160   -956  -2883  -1593   -492   1019   1646  -5271   -660    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12702 -13745   -894  -1115   -951  -1051      *      * 
-    39  -2520  -4897   -824    234    710  -6432   1256   1006  -4099    400    -56  -3338  -2052  -1916  -2394  -1208   -487   1387   3473   1280    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12708 -13750   -894  -1115   -395  -2062      *      * 
-    40   1874    959  -1752  -2901    434   1100  -1857    703  -6180   -169  -1079  -2879  -6570  -2698  -3063   -474   -192   1169  -5295  -4949    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    41  -1438    474  -6657     89    360  -3749    631    443   -739  -1211   -280  -3271  -6483   -366    585   -983   -329    301   3298   2753    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    42    542    637  -1197   -672    557  -1949   1279     -8     19    260  -1181  -1812   1503   -190    216   -250   -969   -101  -1088   -375    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    43  -1118    904  -7337  -6701   -772  -3307    602   1488  -1823   1468   1283  -2848   -912  -1923  -1569  -1231    599   1203    247    -44    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -12714  -7603   -894  -1115   -701  -1378      *      * 
-    44   -408  -1636   -468  -1284  -1403   -196    -13  -2279   1640  -2564  -5249   -839   1245   -225    705   1052    615  -1317    614   -767    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1421   -674      *      * 
-    45  -1169  -2168    894   -203   -393    364    902  -6234    777  -1250  -1994    738  -3409     -8   1004    968   1006  -3405  -6345  -1232    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1421   -674      *      * 
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-     -   -144   -503    231     42   -384    402    107   -627    207   -469   -724    275    397     42     97    359    114   -365   -285   -248 
-     -   -537  -4580  -1895  -1573   -591  -1421   -674      *      * 
-    47     67  -1432    990    437  -2304  -2114   -836      2   -366  -2472   2095   -124    140   -706  -1478   1270   1339  -5345  -1336  -5226    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12256 -13298   -894  -1115   -141  -3423      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12681 -13723   -894  -1115  -2683   -244      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12681 -13723   -894  -1115  -2683   -244      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12681 -13723   -894  -1115   -437  -1936      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1421   -674      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115  -1421   -674      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13749   -894  -1115   -384  -2098      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-    57  -1851   -509    194   1203  -1790  -2895    702  -1436   1272    220   -399    856  -2819   1318    415  -1412  -2266    347   1105  -2670    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -212 -12714  -2874   -894  -1115   -701  -1378      *      * 
-    58    767    583   -418    155  -2590  -3610    735  -1057   1066   -965   1014    282  -2734   1395   1225   -667   -278   -499  -1119  -2654    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12503 -13545   -894  -1115    -97  -3940      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12714  -8324   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -411 -12501  -2012   -894  -1115  -4916    -49      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1465  -9777   -652   -894  -1115  -6077    -22      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -906  -8548  -1109   -894  -1115  -6757    -13      *      * 
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-     -   -150   -481    232     42   -384    400    107   -629    207   -467   -702    272    395     49     93    358    116   -368   -256   -252 
-     -  -2997   -405  -3065  -2164   -364  -4544    -63      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8812  -9854   -894  -1115   -394  -2067      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12353 -13395   -894  -1115  -2553   -270      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12467 -13509   -894  -1115    -60  -4606      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33 -12714  -5463   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12681 -13724   -894  -1115  -2659   -249      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -21 -12679  -6105   -894  -1115   -461  -1871      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12685 -13728   -894  -1115  -2524   -276      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12685 -13728   -894  -1115   -551  -1656      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -290 -12706  -2459   -894  -1115  -1498   -631      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -97  -9869  -3972   -894  -1115  -5779    -27      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10415 -11457   -894  -1115  -5759    -27      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33 -12714  -5457   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -150   -501    234     42   -382    399    105   -627    209   -467   -721    279    395     44     99    358    119   -370   -295   -250 
-     -    -48  -4932 -13757   -194  -2994   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12714  -7669   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12707 -13750   -894  -1115   -392  -2072      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -27 -12714  -5767   -894  -1115   -701  -1378      *      * 
-   111    642  -4900  -6581  -5985  -2624  -1711  -5219  -1290    641  -2328  -4098  -5785   3275  -3387    273  -1870     59    479  -5344  -4980   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -48 -12688  -4948   -894  -1115  -2439   -294      *      * 
-   112   -489   -967  -2518  -1331  -2086   2104   1800  -2704  -2175  -2574  -5119  -1832  -5714   -285    570  -1420  -2113  -3356   -199   3238   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12640 -13682   -894  -1115  -1084   -921      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12674 -13716   -894  -1115  -1235   -798      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12689 -13731   -894  -1115  -2385   -307      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12689 -13731   -894  -1115  -1262   -778      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12697 -13740   -894  -1115   -242  -2694      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -12714  -7532   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -32 -12707  -5528   -894  -1115   -375  -2127      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12683 -13725   -894  -1115   -157  -3282      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-   122   -512  -2162  -4664  -4114  -2328  -1689  -4404  -5938  -2260  -5980  -5109   1383  -5827   -307   3300   1177  -1427   -665  -6230  -2447   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-   124  -5973  -5738  -8121  -7613   1819  -7420   3449   -508  -7203  -5523   -980   3203  -3439  -2801  -6955  -6522  -5909    290   1428  -1514   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-   125  -1279  -6174  -2720  -4000  -6495   1803   -517  -6246   1026  -3461  -5263  -1479  -5768   1731   2650     92  -2271  -3289  -6356  -5674   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
-   127  -1632  -4835  -3228  -6721   -339  -6559  -5431   2086  -6316   2443    731  -6205  -6608  -5939  -6116  -2806  -1763    389  -5295   -164   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -12714  -7450   -894  -1115   -701  -1378      *      * 
-   132   -903  -1710  -2402   -884    -48  -3616  -1199    838    198    800  -1179  -1681    668  -1859   2084  -1009   -420   -550    672    526   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12706 -13748   -894  -1115  -1484   -638      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12706 -13748   -894  -1115  -1484   -638      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12706 -13748   -894  -1115  -1484   -638      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5 -12706  -8170   -894  -1115  -1484   -638      *      * 
-   136   -755   -922    609    380    663   -390    825   -910    401   -326   -707  -1482    313   -507    948    428    -68   -309    536  -5648   195
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -31 -12701  -5564   -894  -1115  -1807   -486      *      * 
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-     -   -165   -534    242     32   -348    382    107   -632    213   -448   -692    279    368     41    117    364    115   -367   -254   -241 
-     -  -3496   -391  -2748  -1740   -513  -2969   -197      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12438 -13480   -894  -1115   -175  -3130      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12689 -13731   -894  -1115   -916  -1089      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12701 -13743   -894  -1115   -284  -2484      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -134   -516    250     57   -375    374    105   -637    209   -466   -747    279    405     55     90    362    113   -375   -310   -261 
-     -  -7879     -6 -13757     -1 -10451   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12714  -7773   -894  -1115   -701  -1378      *      * 
-   150   -446   -542   -523    127   1172   -734   1884   -316   -573   -868    -52    480  -2974  -1029   -153  -1953     -2  -1407   1310   2524   234
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12708 -13750   -894  -1115  -1356   -715      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12708 -13750   -894  -1115   -404  -2033      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12714 -13757   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -24 -12714  -5942   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12691 -13733   -894  -1115  -2318   -323      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12691 -13733   -894  -1115  -2318   -323      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12691 -13733   -894  -1115  -2318   -323      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12691  -7640   -894  -1115   -643  -1475      *      * 
-   158  -1654  -6153   -712  -1845  -1516    -75   3215  -3570   1338  -1440   -659   -492    462   -130   1202    702   -744  -2027  -6337  -1610   242
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -167 -12699  -3199   -894  -1115  -1927   -440      *      * 
-   159    424    -71   -758     40  -1641    239   -809  -1008   -214   -784  -1776   -588   -586   -389    227   1772    560   -318  -6171  -5491   243
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -477 -12533  -1830   -894  -1115  -4709    -56      *      * 
-   160    380  -5306  -2547  -2591  -1516   -572   -972    353    298   1171  -4422  -2421  -1431  -1978   -320    734   1660  -3191    671    501   244
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -1 -12057 -13099   -894  -1115   -202  -2939      *      * 
-   161  -2104    622   -388   -465   -996    565    650    943    342   1547  -2196    840  -3316    621  -1715  -1670   -605  -1410  -6252  -5583   245
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19 -12647  -6236   -894  -1115  -2159   -366      *      * 
-   162  -3448   -549    201   -661    947   1989    728  -6164    892  -1532    673   1635  -3151    734   -708  -3507   -717  -3288  -6278   -744   246
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -20 -12639  -6191   -894  -1115  -3614   -123      *      * 
-   163   -589  -6076   -384  -1929   -699   1326   -869  -3857   1163  -2332   -683   -455  -2175    349    636    257    198  -5698   2053   2048   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1004 -12601   -997   -894  -1115  -2707   -240      *      * 
-   164   -475  -4649  -1814  -1455  -1287  -4791   1900    767    777   1354   1184  -1564  -4878   1589   -572  -2372   -115    -76  -4951  -1636   248
-     -   -149   -470    233     41   -383    397    111   -629    206   -464   -716    269    408     41    106    357    113   -373   -301   -256 
-     -   -114  -3719 -12660  -2753   -232   -743  -1313      *      * 
-   165   -745    732  -6892  -6262   -750  -6177  -5044   -638  -3232  -1792  -1367  -3221    199  -1139  -1950   1785   2946   -955  -4937  -4593   266
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12354 -13396   -894  -1115   -238  -2716      *      * 
-   166   -322  -6588  -6322  -5642  -7454  -4139  -5484  -7061  -1661  -3401  -6259  -5708   3978   -780     -2  -1264  -2286  -2716  -7208  -6810   267
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12653 -13695   -894  -1115   -530  -1701      *      * 
-   167   1055   -280  -6713   -269   1485   -996    637    543  -1046   -820    427   -717  -6471  -1478   -358   -759  -2863    602   1052   2103   268
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12685 -13727   -894  -1115   -958  -1044      *      * 
-   168    -34  -1728   1000   2766   -728  -2371  -2092  -2450   -113  -3881  -1883  -1088  -5740   1783   -589   -730  -4612  -1830  -1693  -5645   269
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12690 -13733   -894  -1115   -387  -2089      *      * 
-   169    114   -627  -7319  -2591   1095  -6526  -5397   1121     83    657    437  -6170  -6576  -2100   1723  -1147  -2475   1240    239    603   270
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  RVP
-ACC   PF00077.12
-DESC  Retroviral aspartyl protease
-LENG  112
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  50
-DATE  Mon Jun  2 21:10:07 2008
-CKSUM 6513
-GA    1.0000 1.0000;
-TC    1.0000 1.0000;
-NC    0.9000 0.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -64.923302   0.219530
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -42      *  -5129
-     1  -2420  -3853   -633    532  -4157     97  -2060    739   -357   -675  -2946   -384    979  -1605    288   1099    924    600  -4046  -3373     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378    -42      * 
-     2    339  -3550  -2479   -574   -334  -3496    323  -3399  -1831   1976  -2677  -2206   -251    631   -437    690    954  -3098  -3820  -3231     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     3  -2416  -3888   -115   1679  -4208   -477  -2049   -142   -497  -1004  -2977    502    116   1006   -572    673  -2355  -3510   3717  -3389     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     4    355  -3891    737  -1716  -4212  -3391    875  -3963   1229  -3907  -2980    947    164   1801   1819    142  -2357  -3513  -4074    -71     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     5  -2989  -4355  -2887   1324  -4754  -3903  -2425  -4440   -722  -1480  -3451   -309    541   1433   3206  -2867  -2897  -4025  -4431   -379     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     6  -4517  -5686  -3161     12  -6354  -1034  -3497  -5933  -2596  -1944  -5019  -3434   3978   -488   -491  -4313  -4441  -5566  -5681  -5259     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     7  -2650  -2545  -4599    218    821  -4151    -30   1107   -189    198   2107  -3660  -4205  -3361   1420     76   -140    611  -2996    631     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     8  -1280    593  -4960     53  -2452  -4206  -3075   2139   -462   1090   -195  -3836  -4257  -3566  -1757  -1718   -750   1647  -2955    922     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-     9  -1025   1607   -367   1065  -4209  -1570    943   -676   1289  -1068  -2978   -234  -1807   -414    340   -867   2084  -3510  -4072  -3389     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    10   -293   -183  -4624  -4153  -2352  -4028  -2832   2136  -3789   1023    694  -3643  -4004  -3389   -272  -3202  -2531   2378  -2559  -2475    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    11  -2425  -2502  -2805  -2327    575  -3473   1164    461   1847   -500  -1978   -392  -3450    128    803   -429    671   -942    655   1771    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    12  -2613  -2291  -4660  -4176  -2362  -4047  -2857   2377  -3808   1108  -1609  -3665  -4029  -3410  -3608  -3213  -2540   2269   1194   1268    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    13   -860  -3890   -287   1293  -4211   1645  -2049   -976     58  -3906  -2979   2061  -3484    618  -1292    695   -752  -3512  -4073  -3391    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    14  -1218  -3611   -657   -715  -3816   3013  -2158   -216  -1202   -876  -2733    374  -3572  -1748  -2282   -467   -588  -1450  -3869  -3264    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    15  -1278  -3367  -2211  -1158  -3900  -3291    421  -1291   1252  -2589   -234   1001    742   2245   1332  -1163    866  -1008  -3341   -494    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -2132 -10249   -375   -894  -1115   -701  -1378      *      * 
-    16  -1028  -1012  -2599  -2020   1393   1545  -1264   1129  -1761   -872   -217    629   1025  -1517  -1821  -1512   -973   -444   2706   -952    16
-     -   -148   -501    234     42   -377    398    105   -627    209   -465   -721    274    393     47     95    360    118   -367   -295   -250 
-     S  -3289   -159  -9167    -27  -5760  -4935    -48      *      * 
-    17   -898  -2367   -710   1051  -2685  -1860   1896  -2434   -114  -2382  -1459   1322    323   1402   -623   1225    497  -1988  -2552  -1869    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -8  -8125  -9167   -894  -1115  -4935    -48      *      * 
-    18  -1309  -1780  -3297  -3121  -2827  -2280  -2683  -2296  -2806  -2508   2469  -2496   3169  -2681  -2840  -1592   2126  -1972  -3301  -2983    19
-     -   -149   -503    230     43   -379    399    109   -625    212   -469   -723    273    396     52     98    359    117   -369   -297   -252 
-     .  -1478   -645  -9167  -1974   -424  -4935    -48      *      * 
-    19  -1151  -1742  -1534   -966  -1768  -2273   -918  -1417   -554  -1639   -911   1105  -2351   1006    706  -1270  -1080   2350  -2021   1684    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -8125  -9167   -894  -1115    -30  -5612      *      * 
-    20   -821  -3401   -896    486   -939  -3304  -1946  -1425    459   -612  -2758   -466   2149   1076   -661   -359    474  -2118   2335    751    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    21  -1054   1154  -4628  -4152   1634  -4033  -2838   1828    227    663  -1603  -3645  -4011  -3391   -737   -919     33   1534  -2571   -192    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    22  -2416  -3889   -916   1577  -4210  -3390  -2048  -3961   1673   -909  -2978   1308  -1018   1349    850   -606    699  -1056  -4072  -3390    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    23   1976   2420  -5019  -4383   1832   1038  -3093  -1987  -3978   -897   1876  -3867  -4271  -3601  -3779  -3306  -2614    579   1354  -2615    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    24  -2610  -2273  -4628  -4158  -2355  -4033  -2836    496  -3793   2977    543  -3647  -4008  -3393  -3593  -3207  -2536     52  -2562  -2480    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    25  -5573  -4970  -8034  -7497   -830  -7863  -6692   1293  -7339   2598    196  -7576  -6947  -6188  -6888  -7255  -5443   1855  -5210  -5409    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    26  -8117  -7061   4231  -6984  -8431  -6818  -7180  -9460  -7970  -8824  -8753  -7239  -7282  -7582  -7798  -8294  -8263  -9096  -7200  -8287    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    27  -3442  -4041  -6427  -6780  -6678  -4307  -5981  -6574  -6609  -6814  -5868  -5101  -5115  -6085  -6263  -1164   4041  -5263  -6826  -6828    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    28   -957  -4588   -596  -4481  -6925   3724  -5255  -6863  -5810  -6979  -6150  -4380  -5254  -5115  -6172  -4037  -4311  -5684  -6945  -6673    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    29   3614  -3941  -6530  -6885  -6643  -4217  -5960  -6497  -6629  -6750  -5783  -5040  -5031  -6064  -6247   -379  -3817  -5166  -6832  -6832    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    30   -357  -6231   3636     -9  -6497  -4371  -3718  -6413  -3939  -6286  -5594  -2978  -4896   -202  -4779   -958   1106  -5872  -6480  -5479    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    31   -363  -3712   1955   -258   -753  -3441   2278   1201    726  -1210  -2822     63  -3532  -1677   -311  -2355   -721    750  -3943  -3309    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    32  -3191    947  -5746  -5627  -5492  -4131    604  -5161  -5403  -5453  -4648    863  -4846  -5089  -5367   2005   3096   -605  -5816  -5565    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    33   -922    517  -5499  -4895  -2942  -4761  -3693   2477  -4521  -1084   1115  -4407  -4785  -4167  -4345  -3865  -1025   2721  -3539     41    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    34  -4740  -4299  -7213  -6681    -98  -6771  -5776   2762  -6437   1964    157  -6439  -6381  -5760  -6189  -6000     28    785  -4957  -4888    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    35   -423  -3890  -2264    589  -4211  -3391  -2049  -3961   1160  -1752  -2979   1298   1361   1070    432    833   1119  -3512  -4073  -3390    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    36   -583  -3888    127   1899  -4208     20  -2049   -882    264  -1744  -2977   -220   -628   1477   -347    171   -107   -907    490     81    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    37     70    470  -2709    484   -761  -3600   1597    882   -382  -2307   1074   1754    517  -1974    872   -846    -38   -810  -3621   -600    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    38   -862  -3879   2014     53  -4195  -3392   2067   -305    -78   -455   -686    338   -313   1056  -1294    171  -1543  -1515   1752   -566    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    39  -1372    299   -897   -990   1174    722  -3075    358  -3935   1295   -139  -1387  -4257  -3567   -974  -3289  -2605   -361   4048    -94    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    40  -2416    405    340   -722   -382   -923    495  -3956    488  -1470  -2976    253   2842   1289   -920   -301  -2355  -1185  -4070  -3388    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -49 -10249  -4939   -894  -1115   -701  -1378      *      * 
-    41  -1117   1824  -1375   -185    168   1225  -2580   -267   -192    928     23  -2874   -395  -2492   1109  -1341    -83     44  -3221  -2802    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10202 -11244   -894  -1115  -1504   -627      *      * 
-    42  -1173  -3848    522   -335  -4169   -790    793    235    652   -629  -2937   1688    662  -1548    264   1216    -17  -3470  -4031  -3349    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -736 -10202  -1327   -894  -1115  -1504   -627      *      * 
-    43  -1958  -2104  -3063  -2487  -2084     97  -2088    621    865  -1971  -1294   1318   -992  -2114  -2471  -2325  -1898   -398   4419   2105    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -49  -9469  -4967   -894  -1115  -4115    -86      *      * 
-    44  -1826  -2519  -2142  -1586  -2604    -60    268    -75  -1463  -2430  -1677  -1802   2647   1082   -483    811  -1766    -33  -2864   1489    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -508  -9423  -1759   -894  -1115  -2309   -325      *      * 
-    45    739  -2867  -1469    408  -3125   -196  -1221   1022   1129  -1067  -1973  -1218  -2647    811    316   -325    582    373  -3090  -2448    53
-     -   -150   -501    234     42   -382    401    105   -623    209   -467   -712    274    395     44     97    358    116   -370   -295   -250 
-     E   -566  -1627 -10196   -482  -1817  -2578   -264      *      * 
-    46   -139  -3166    321    680  -3487  -2667    936   -242    724  -3182  -2256    664   1675   1137  -1414  -1574   1530  -2788  -3350  -2667    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -3  -9354 -10396   -894  -1115    -48  -4925      *      * 
-    47   -488  -3812   -280   -216   -372  -3411  -2073  -3825   1085   -631   -119    684  -3503   -259   -224     17    236      7   3633   1229    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    48    364  -3888  -2264   -800  -4208   1066    -30  -1104   1207  -3904  -2977    504   -330    786    892    -25   1063   -374  -4071  -3389    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    49   -631  -3873    206   -671  -4186   -524  -2053   -466   -408  -1988  -2964   -415   2221  -1596   1211    720    504    301  -4060  -3382    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    50   -146    422  -2386   -548  -3911  -3451     78    724   1553  -3656    395  -2129   -856    339   -329   -107   1887    648  -3917  -3293    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    51   -483  -3315  -2688   -812   -683    177    817    803    333  -1810   1739    854      1   -261  -2463    -53   1263    -45   1206  -3108    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    52  -5149  -4599  -7699  -7238   -257  -7502  -6674   2581  -7110   1081   1767  -7187  -6851  -6281  -6850  -6865  -5072   2362  -5414  -5469    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    53   -878  -3258  -2799  -1326  -3355   1870   1141    616   -913    189  -2413  -2464  -3731   2054    863  -2597  -2460    466  -3593  -3087    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    54  -3479  -4180  -4208  -4567  -6636   3507  -5126  -6483  -5502  -6649  -5756   -335  -4984     43  -5723    -64   -115  -5276  -6792  -6464    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    55   1081  -2759  -5325  -4716  -2791  -4531  -3484   2942  -4331   -152  -1999  -4205   -656  -3967  -4147   -497   -573   1252  -3346  -2998    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    56  -3202  -3854   -947  -3220   -336   3175  -3551  -4106  -3576   -668  -3604    192  -4491  -3333  -3983   -324    924  -3788  -4762  -4273    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    57  -2671  -3072  -3401  -2881  -3194   3150  -2770  -2773  -2742  -3055    150   -483  -4018   1143  -3057   -910   -853   -470  -3557    740    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    58    404     16  -3375  -2808   1428    938  -2612    549  -2648  -2745  -2049    847    393   1848  -1307    176   -289     -7  -3272  -2850    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    59  -1205    520  -4667  -4053  -2502      4  -3020   2190   1378   -248  -1743  -3696   -976  -3404  -3637   1186    649   -144  -2994  -2644    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E  -2216 -10249   -351   -894  -1115   -701  -1378      *      * 
-    60   -934  -1041  -2190  -1614  -1053  -2301  -1142   1980  -1391   -924   -255  -1559    834  -1212    557    423   1120    891  -1497  -1113    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -8  -8041  -9083   -894  -1115    -29  -5635      *      * 
-    61   -313    237  -2215    785  -3941  -1316   -313  -1168    814  -2347    767   1723  -3353    -30   1640    649    -77   -889  -3415  -3197    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    62  -2618  -2662  -3994  -3409  -2641    804   -366   -482  -3180  -1284  -1856    859    985  -2970   -834    125   1035   2033  -3097    929    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    63  -1123  -3867  -2274    760   -652  -3396    553   -189   1934  -1829  -2959    246   -139   1367   1421  -2303   -236  -1490  -4056    531    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    64   -253  -3883   -713    578   1285    374  -2050  -1372   1243  -3898    367   -582  -3484   2262   -677   -237  -2355  -3503   2042   -298    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    65  -2450  -3580   -446  -1905   -350  -3485  -2161   -803    516   -762  -2703   -454  -3574    -93    -13   1580    883  -3133   1849   2706    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    66  -1268  -3888   1414    -94  -4208  -3390   -175    963     56   -529  -2977    518    -37    227    655    475   1098  -3509    922  -3389    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    67   -846    857    -38    119   -519   -917  -1936  -1158   1028   -222   1020   1688    -89   1642   -196  -1102  -2298   -427  -3333  -3163    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -37 -10249  -5352   -894  -1115   -701  -1378      *      * 
-    68  -1246  -2479  -4826  -4200  -2435   -186  -3024   1908  -3828    172    125  -3757  -1236    968    931   -998   -104   1772  -2934   -434    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10214 -11256   -894  -1115   -410  -2017      *      * 
-    69  -1528  -3332  -2250   1107  -1144  -1195   2186  -1018    350    788  -2701   -658    994   -647    608   -447     88  -1690    761   -765    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    70  -2662   1445  -4891  -4263  -2462  -4197   1267   1681   -347    638  -1709  -3804    853  -3528   -980  -1282    746   1841  -2963  -2618    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    71  -2416    425    137   1798  -4208  -1218   -225  -3959    987    -59  -2977    978  -3483   1732    413  -2297  -2355  -1513   2527  -3389    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    72  -2660   1526  -4835   -639  -2469  -4188    755   2294   -301    620  -1715  -3777  -4240  -3497   -758  -1279    444    417   2707    674    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    73   -798   1436    755    838  -4140   1753  -2064    515     82      1  -2936  -2047  -3495     77    954  -1130  -2360  -1535  -4037  -3368    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    74  -1025    832   1228    -70   1238   1194   1288  -3960    987  -3905    370   -413   -919    226     25   -521   -306  -3511  -4072   -708    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    75  -2367  -3381    -36   1290  -3924   -408   1574  -3782   2075    118  -2762   -475   -119     36    571  -2249   -494  -3394  -3350    236    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    76  -2418  -3871    438    125  -4183    149  -2054    104   1040   -336    833   1222    148   -690    -53  -1062    812   -146  -4059    -70    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    77   -360     53  -3942  -3359   1956  -1292    914   1087    249  -1269  -1868   -168   -884    217   -340  -3044    803   1279  -3108   -375    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    78  -2432  -3736  -2350    631  -1195  -3433  -2100   -492   1189   -929    431    120   -715   -368   1718    420   1396   -687  -3960   -632    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    79   -310  -3325  -2288   -660  -3777   2396   2911  -3574   -314  -1618    403  -2038   -917  -1613    733   -990   -902  -1009  -3351  -3143    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B  -1631 -10249   -564   -894  -1115   -701  -1378      *      * 
-    80  -1179  -2626    707    651  -2936  -2157   1254   1097    576   -744  -1718   -796    610   2043   -907  -1064    435  -2242  -2816  -2140    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -5  -8623  -9666   -894  -1115  -4757    -54      *      * 
-    81  -1384   2680  -3684  -3055   2174  -2933  -1812   1674  -2663  -1055   -421  -2566  -2984  -2299    438    327  -1326   1419  -1691  -1346    91
-     -   -149   -500    233     43   -377    400    105   -627    210   -465   -721    275    393     45     96    359    117   -370   -295   -250 
-     E   -109  -3799  -9666  -1489   -636   -203  -2929      *      * 
-    82   -435  -3785   -304  -1620  -4103  -3294   1303    508    -14  -3800  -2875     64    757    473  -2042   1292   2276  -3405  -3970  -3289    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10132 -11175   -894  -1115   -213  -2863      *      * 
-    83  -3257  -3041  -5615  -4992   2584  -4861  -3728   1251  -4606   -370   1154  -4507   2060  -4181  -4396  -3961  -3194   1738  -3492     46    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    84  -2667    439   -482  -4375    891  -1531  -3086   -575  -3970   2065    955  -3860  -4264  -3593   -595  -3299  -2608   1391  -2951   1790    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    85  -2604  -2274   -872  -4116  -2357  -2294   1095   1928  -3760    400    625   -937  -3999  -3368  -3574  -3194    562   2479  -2562  -2479    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    86   -257  -2497  -4971  -4338   -378   1595   1074   1297   -955   1467    333   -512  -4258  -3572  -3755  -3291   -842    563  -2954  -2611    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    87   -237    270    859   -949   -125  -3429  -2095  -3731  -1702  -3749    382   -317   3287  -1657   -661     69  -1022  -3348  -3977  -3332   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -586 -10249  -1586   -894  -1115   -701  -1378      *      * 
-    88   -546  -3402    943   1066   1273   -531  -1568  -3469    -14  -3417  -2492   -195  -3003     67  -1657   1444    665   -908  -3587    761   101
-     -   -150   -501    233     42   -382    398    105   -627    209   -462   -721    278    395     44     95    361    116   -368   -295   -250 
-     E   -629  -1504 -10708    -24  -5949    -65  -4498      *      * 
-    89  -1073   3109  -4363  -1235  -2578  -4105  -2959   1263  -3489    803  -1809    587  -2062  -3226  -3509    788   1976  -2030  -3056  -2695   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    90   -915  -3500  -2853   -978  -3662  -1121  -2528  -3276  -2231    161    219    194   3604  -2209   -417  -2772  -2671  -3048  -3864  -3353   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    91   -724    833   -411  -4178   1054  -1064  -2861   1001  -3810   -232    692  -3667  -4033  -3412  -3610  -3213   -135   2495  -2601   1303   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    92  -3413  -5002   2104    376  -5283  -3969  -2921   -864  -2711  -5003  -4141   3159   1300  -2508   -776  -3221   -101  -4609  -5180  -4406   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S  -2407 -10249   -303   -894  -1115   -701  -1378      *      * 
-    93   -955  -1583  -3302  -3414  -3984   2121  -3104  -3761  -3419  -4003  -3089  -2383  -2609  -3047  -3375    970   2942  -2649  -4197  -4022   107
-     -   -149   -500    233     43   -377    398    109   -627    210   -466   -721    279    393     45     96    359    117   -370   -295   -250 
-     S  -2048  -1133  -1727    -61  -4583  -5003    -46      *      * 
-    94   -825  -2138   1635     54  -2417  -1583   -463  -2144   -197    335  -1335   2202  -1810    -60   -729    825   -799  -1762  -2422  -1742   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13  -7338  -8380   -894  -1115  -5097    -43      *      * 
-    95  -1279  -2203  -1379   -702  -2533  -2140   -521   1090   2734  -2056  -1333   -852  -2192   1730    274  -1231  -1148  -1791  -2261  -1860   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -13  -7338  -8380   -894  -1115  -3954    -96      *      * 
-    96  -3120  -3192  -3100  -2901  -1216  -3459  -1812  -3384  -1847  -3039  -2773  -2756  -3711   3042  -1869  -3148  -3112  -3324   5354   -772   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -11  -7650  -8692   -894  -1115  -2192   -356      *      * 
-    97   1287  -1577  -2188  -1623  -1601  -2598  -1389  -1166  -1454    782   2532  -1689   1078    878  -1730    173    193  -1036  -2000  -1586   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -5  -8653  -9695   -894  -1115    -34  -5420      *      * 
-    98  -5058  -4498  -7670  -7269  -3827  -7546  -6999   3182  -7200   2091  -2561  -7230  -6934  -6505  -7045  -6957  -5003      6  -5694  -5692   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-    99  -3886  -3616  -6242  -5628     12  -5543  -4362   2452  -5261   2136  -1968  -5189  -5424  -4727  -5015  -1053  -3811   -582   3328  -3675   114
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   100  -7904  -6892  -7898  -8285  -8479   3864  -7575  -9502  -8489  -8886  -8791  -8163  -7355  -8344  -7931  -8329  -8183  -8999  -7205  -8490   115
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   101  -3860    913  -6321  -5315  -4587  -2411  -4170    223  -3212  -1331  -3613  -4711  -5254  -3997   3976  -4219  -3995  -3440  -4994  -4746   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   102  -1059  -6487   3322   -686  -6645  -4410  -3779  -6587   -194  -6441  -5789   2458  -4955  -3451  -4954     45  -4600  -6047  -6637  -5586   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   103    -47    663  -5137  -4507    865  -4351  -3230   2246  -4107   1707    188    980  -4393  -3730  -3909  -3439  -2726    445  -3087  -2746   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   104  -5692  -5108   -684  -7435  -3194  -7763  -6360    260  -7206   2927   2762  -7473  -6845  -5985  -6684  -7091  -5527  -3549   -292  -5152   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   105   1351   -279  -2300   -895  -4120  -3410  -2071  -1307    541  -3831  -2925  -2056  -3502   2198    942     21   1895  -1372  -4028  -3363   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   106   -739  -3425    677   -212  -3950   -766    116  -3800   2000  -2264  -2782   -462   -728   2626    463     98  -2300  -3405  -3408  -3197   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   107    923   1707  -5019  -4383    883  -1008  -3092    917  -3978   2065   1742  -3867  -4270  -3600  -3777  -3306  -2614  -1911    953      2   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   108  -2419  -3892  -1108   -439  -4213   2613    461  -3964   1158  -3908  -2981    304  -3486   1423   -842  -1061  -2359   -688  -4075      7   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   109   1959   3010  -4579   -894  -2359    -54  -2823    785  -3752   -224    623  -3620  -3998  -3362  -3570   -145   -313    650  -2563  -2479   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   110  -2433    142  -2357   -668  -3975   -166  -2104    109   1662  -1977  -2833  -2104   -619   1151    770    717   1095    421  -3952   -552   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   111  -5436  -4910  -7809  -7206     97  -7438  -6121   2172  -6954   2591    923  -7133  -6693  -5873  -6499  -6713  -5294   -438  -4902     76   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -2 -10249 -11291   -894  -1115   -701  -1378      *      * 
-   112  -2605   1170   -807  -3229   -166  -3980   1267    856  -3023  -2577    225   1866  -4045   -439   -604    706    969    927  -3140   1245   127
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     E      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  hATC
-ACC   PF05699.6
-DESC  hAT family dimerisation domain, transposase (Pace et al, 2008) 
-LENG  94
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  49
-DATE  Tue Apr 22 20:21:06 2008
-CKSUM 4922
-GA    15.6000 15.6000;
-TC    15.7000 15.7000;
-NC    15.4000 15.4000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.972273   0.665687
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -42      *  -5131
-     1   -980  -3910    973   3088   -114  -3412  -2078  -3974  -1665  -1042  -3001     86  -1672   -158  -2173   -965   -470  -3529  -4096  -3415     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10260 -11302   -894  -1115   -701  -1378  -1042  -7540 
-     2   -647  -2501  -4952  -1223   -718   -669  -3075   -102   -820   2583  -1704  -3834   -797  -3562  -3749  -3289  -2607    180  -2958   1010     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10259 -11301   -894  -1115   -701  -1378  -7581  -7531 
-     3  -1534  -3921   2280   1893  -4240  -3427    104  -1343  -1666  -3936    102    652  -3520   -684   1142   -460    329  -1641  -4105  -1163     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7524 
-     4  -1172  -3918    515    598  -1148  -3428    636   -586   1196   -627    155     -2  -3521   1745    781    258   -712    202  -4103  -3422     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7516 
-     5  -1414  -4936  -1363  -6697   1635  -6446  -3352  -4625  -6295    562  -4200  -5434  -6388    531  -5895  -5614  -5367  -4640   1227   4187     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7508 
-     6   -665  -2554  -4846  -4223    604  -1343    -52    463    443   2146   1775  -3802  -4274   -462  -1310   -548  -2637   -848  -3008   -223     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7500 
-     7   -393  -3925   1443   1211  -4246   -990  -2084  -3996   1023  -1374    221   -976  -3519    845    -54   1250    -19  -1455  -4108   -770     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7492 
-     8    -64    245    568   2822     38  -3432    303  -3955   -668  -1117    230  -2071  -3525    825   -737  -2339   -109  -3518  -4091  -3415     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1116 -10299   -910   -894  -1115   -701  -1378  -7581  -7484 
-     9   -297  -2206  -2114   1396   1163   -335  -1568    649  -1428   1124  -1373    815    125  -1334    205  -1806  -1595  -1680  -2574  -2104     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -9195 -10237   -894  -1115    -41  -5157  -7581  -7476 
-    10  -1541  -3898   1340    715   -149  -1204    391   -203    826  -1596  -2991    -87   2327  -1637  -2183   -645   -267   -773  -4089  -3414    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -10299 -11341   -894  -1115   -701  -1378  -7581  -7468 
-    11  -2588   2091   -126  -1253    181  -3831   1100    779  -1365    642  -2162    938     51  -2416      4  -1077   -142   1461  -3377  -2937    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -10299 -11342   -894  -1115   -701  -1378  -7581  -7459 
-    12    -74  -2559  -1251    436    750  -4216   -268    524  -3832   1520   1729   -821  -4268    119  -3714  -3290  -2635   1143   2065  -2665    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -34 -10299  -5920   -894  -1115   -701  -1378  -7581  -7451 
-    13   -979  -3905   1118   1070  -4226   -373  -2064  -3977    723  -3921  -2994    860   1454    435   1377    -24   -525  -1623  -4088  -3405    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -147 -10277  -3474   -894  -1115  -1172   -846  -7581  -7444 
-    14   -729  -3390   1373   -247    320  -3416  -2099   -173   -529   -979   1926  -2142    364    530   1725  -1069  -1004   -323   1979  -3100    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -77 -10140  -4467   -894  -1115  -1094   -912  -7581  -7435 
-    15  -1484  -3792   1235    591    276  -3293    949  -3864   1223   -846  -2881   1854   -904   -168   -194    247   -334   -447  -3976  -3293    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -451 -10144  -1933   -894  -1115  -2481   -285  -7581  -7426 
-    16   -577  -3404   -315    613  -3713  -1009  -1598   -183    670   -663  -2497    668    264   1043  -1689     99    929    106   1485     72    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -714  -9704  -1383   -894  -1115  -3103   -178  -7581  -7418 
-    17    -45  -2942    953   1583   1516  -2449    643  -3010    947   -143  -2032    186  -2542   -649    369   -172  -1414  -2563  -3127  -2446    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -322  -9066  -2378   -894  -1115  -4577    -62  -7581  -7409 
-    18   -159  -2551  -1202   -652   1419  -2278   1585    160    814  -2534  -1660    420   1322   -515    968    389   -131  -2132  -2781  -2147    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -622  -8758  -1547   -894  -1115  -3374   -146  -7581  -7401 
-    19  -1371  -2366  -1481   -871  -2584  -2382   -954  -2209   1340    147   1970    360  -2452   -565   2236  -1347   1192  -1935  -2578  -2063    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -171  -8395  -3280   -894  -1115  -2974   -196  -7581  -7392 
-    20  -1181  -2509  -1086   1081  -2774   1324   -843   -558    910   -316  -1615   -838    -11   -404   -945   1000    500  -2101  -2729  -2083    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -14  -8622  -9664   -894  -1115  -3361   -148  -7581  -7384 
-    21    155   1489   -375  -2244  -1457  -2851    855   1015    899    958   2236  -2144   -505  -1801  -2137   -241  -1380    -21  -1914  -1539    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -14  -8818  -9860   -894  -1115  -3861   -103  -7581  -7376 
-    22  -1357  -2825    491   1857  -3144    839   -991   -361    230   -903  -1915   -968  -2425    731    528   -260    829  -2446  -3010  -2328    22
-     -   -150   -501    233     43   -382    398    104   -622    212   -465   -717    275    392     44     94    361    120   -369   -296   -251 
-     .  -4065   -100  -9942    -15  -6571   -919  -1086  -7581  -7366 
-    23  -1112  -3501   1974   1537    270   -978    -53   -719   -263   -308  -2590   -535    659    671   -500  -1071   -321  -3122  -3685  -3002    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .    -11  -9793 -10835   -894  -1115   -789  -1248  -7581  -7358 
-    24   -939  -2363  -4829   -260   3155  -4072  -2941    182  -3801    949   1696  -3703  -4122   -444  -1181   -568  -2470   -279   1227  -2476    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -14 -10304 -11346   -894  -1115   -701  -1378  -7581  -6845 
-    73  -2463  -3824   1803   -606   -626  -3454  -2118  -3819   -371    854  -2925   1011   -535  -1674  -2217   1232   1099  -3421    950   -273    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -14 -10304 -11346   -894  -1115   -701  -1378  -7581  -6833 
-    74  -1061    115   1168   1676  -4246  -3426    563  -3997    826  -2000  -3014   -354   1402    363   1551  -1090   -690  -3547  -4108  -3425    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10305 -11347   -894  -1115   -701  -1378  -7581  -6821 
-    75  -1212  -3917  -2303   -722   1255  -3428   2150  -3983    308   -947  -3007   1098   -617    376   1128    935   -999  -3537  -4103   1886    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -15 -10304 -11346   -894  -1115   -701  -1378  -7581  -6807 
-    76  -2539  -3516  -2637  -2081   -377  -1161  -2280  -1461    879  -3457  -2652  -2341  -3689    399   3174   -499   1127  -1508    597  -3246    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -15 -10304 -11346   -894  -1115   -701  -1378  -7581  -6794 
-    77  -2686  -2588  -4605  -3995  -2549  -4183  -3030    233  -3678  -1142   2672   2223   -801  -3380   1034   1386    409   -123  -3038   -333    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -15 -10304 -11346   -894  -1115   -701  -1378  -7581  -6781 
-    78  -2496   2813  -2347     51  -4286    -75  -2117  -4031     99  -3974  -3051  -2103  -1577     17   2455   1664    -71  -3585  -4137  -3463    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10304 -11347   -894  -1115   -701  -1378  -7581  -6768 
-    79  -2949    711    970  -1986  -2647  -4476  -3335   1325  -4076   2228   2116  -4032  -4508   1334  -3959  -3559  -2888  -2144  -3241  -2915    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10305 -11347   -894  -1115   -701  -1378  -7581  -6755 
-    80   -527  -3925    997   1636  -4246   -284  -2084  -3997   1383    146  -3014   -660   -444   -114    156  -1012    949  -3547  -4108  -3426    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10305 -11347   -894  -1115   -701  -1378  -7581  -6741 
-    81  -1399  -3895     36  -1766   -729   -752   1700   -860   -162  -1706  -2988  -2074   2338    385   1546    648   -826  -3510  -4087   -208    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -15 -10305 -11347   -894  -1115   -701  -1378  -7581  -6728 
-    82  -1061  -3924    945   1599  -4245   -725    223  -3996    901    742  -3013  -2061  -3519    698   -412    671   -746  -1868  -4108    270    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10306 -11348   -894  -1115   -701  -1378  -7581  -6715 
-    83  -1212  -2845  -3558  -2987  -2848  -3936    241    513   -934  -1019   1967   2218  -4005  -2664   -773   1232   1731   -437  -3258  -2850    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10305 -11347   -894  -1115   -701  -1378  -7581  -6700 
-    84   -372  -2605    300  -3892  -2569    -48  -3003     39  -3594   1054  -1804    245  -4219  -3313  -1176  -1491   -950   2443  -3053     82    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10305 -11347   -894  -1115   -701  -1378  -7581  -6687 
-    85  -1179   1434    725   1951  -4247  -1330  -2086  -3998   -271    341  -3016    497  -1192   2126  -2174    268  -2393  -3548  -4110  -3427    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10305 -11347   -894  -1115   -701  -1378  -7581  -6672 
-    86   2527  -3833    218   -639   -944  -3451  -2114  -3836    551   -396    867  -2103  -3543    562   -962   -125  -1345  -1123  -4042  -3384    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10305 -11348   -894  -1115   -701  -1378  -7581  -6658 
-    87  -1179    409  -5036  -4401  -2485  -4249    337   1354  -3998   2541    692   -939  -4299   -596  -3803  -1290  -2643   -802  -2989     94    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10306 -11348   -894  -1115   -701  -1378  -7581  -6644 
-    88  -1071  -2534  -5022  -1432    -77  -4249  -3119   1531   -859   1277   2871  -3886  -4299    181  -3799  -3332    300   1244  -2992  -2649    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10306 -11348   -894  -1115   -701  -1378  -7581  -6629 
-    89   -181   4501  -5035  -4400   2541  -1432  -3121   -766  -3999  -1463  -1737   -683  -4300  -3624  -3804   -219  -2645   -799  -2991    723    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -16 -10306 -11348   -894  -1115   -701  -1378  -7581  -6615 
-    90    488  -2531  -5039  -4403  -2485  -4250  -3120   1660  -4000   1221   1004  -3892   -644   -765  -3804    160   1409    640    760  -2646    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -17 -10306 -11348   -894  -1115   -701  -1378  -7581  -6600 
-    91  -2465  -3937   -459   1796   -603  -3436   1072  -4009   1456  -3953  -3026   1501  -3530   1634   1608  -2345  -2404  -3560  -4119   -334    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -17 -10306 -11348   -894  -1115   -701  -1378  -7581  -6585 
-    92  -1172  -3924   1935   -146   -634   -696    150   -867    -86  -1603  -3014    583  -3519   2029    524    737  -1080  -3546  -4108   -280    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -17 -10306 -11348   -894  -1115   -701  -1378  -7581  -6570 
-    93   -853  -3854    387     44  -1135  -1481  -2108  -3871   -365  -1842   -108   1925  -3538   -195  -2203  -2355  -2399  -3459   5010   -729    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -17 -10307 -11349   -894  -1115   -701  -1378  -7581  -6555 
-    94  -1111  -2531  -5036  -1473    415  -4249  -3120   1400  -3999   2021   2092  -3891  -1453   -650  -3803     17  -1278   -252  -2989    285    98
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     H      *      *      *      *      *      *      *  -7581      0 
-//
-HMMER2.0  [2.3.2]
-NAME  hATC
-ACC   PF05699.6
-DESC  hAT family dimerisation domain, transposase (Pace et al, 2008)
-LENG  94
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  49
-DATE  Tue Apr 22 20:21:03 2008
-CKSUM 4922
-GA    5.0000 5.0000;
-TC    5.0000 5.0000;
-NC    4.5000 4.5000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -51.029842   0.246558
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -42      *  -5131
-     1   -980  -3910    973   3088   -114  -3412  -2078  -3974  -1665  -1042  -3001     86  -1672   -158  -2173   -965   -470  -3529  -4096  -3415     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10251 -11293   -894  -1115   -701  -1378    -42      * 
-     2   -647  -2501  -4952  -1223   -718   -669  -3075   -102   -820   2583  -1704  -3834   -797  -3562  -3749  -3289  -2607    180  -2958   1010     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10251 -11293   -894  -1115   -701  -1378      *      * 
-     3  -1534  -3921   2280   1893  -4240  -3427    104  -1343  -1666  -3936    102    652  -3520   -684   1142   -460    329  -1641  -4105  -1163     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-     4  -1172  -3918    515    598  -1148  -3428    636   -586   1196   -627    155     -2  -3521   1745    781    258   -712    202  -4103  -3422     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-     5  -1414  -4936  -1363  -6697   1635  -6446  -3352  -4625  -6295    562  -4200  -5434  -6388    531  -5895  -5614  -5367  -4640   1227   4187     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-     6   -665  -2554  -4846  -4223    604  -1343    -52    463    443   2146   1775  -3802  -4274   -462  -1310   -548  -2637   -848  -3008   -223     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-     7   -393  -3925   1443   1211  -4246   -990  -2084  -3996   1023  -1374    221   -976  -3519    845    -54   1250    -19  -1455  -4108   -770     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-     8    -64    245    568   2822     38  -3432    303  -3955   -668  -1117    230  -2071  -3525    825   -737  -2339   -109  -3518  -4091  -3415     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1108 -10291   -902   -894  -1115   -701  -1378      *      * 
-     9   -297  -2206  -2114   1396   1163   -335  -1568    649  -1428   1124  -1373    815    125  -1334    205  -1806  -1595  -1680  -2574  -2104     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9187 -10229   -894  -1115    -41  -5157      *      * 
-    10  -1541  -3898   1340    715   -149  -1204    391   -203    826  -1596  -2991    -87   2327  -1637  -2183   -645   -267   -773  -4089  -3414    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    11  -2588   2091   -126  -1253    181  -3831   1100    779  -1365    642  -2162    938     51  -2416      4  -1077   -142   1461  -3377  -2937    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    12    -74  -2559  -1251    436    750  -4216   -268    524  -3832   1520   1729   -821  -4268    119  -3714  -3290  -2635   1143   2065  -2665    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -25 -10291  -5912   -894  -1115   -701  -1378      *      * 
-    13   -979  -3905   1118   1070  -4226   -373  -2064  -3977    723  -3921  -2994    860   1454    435   1377    -24   -525  -1623  -4088  -3405    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -138 -10268  -3465   -894  -1115  -1172   -846      *      * 
-    14   -729  -3390   1373   -247    320  -3416  -2099   -173   -529   -979   1926  -2142    364    530   1725  -1069  -1004   -323   1979  -3100    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -68 -10131  -4459   -894  -1115  -1094   -912      *      * 
-    15  -1484  -3792   1235    591    276  -3293    949  -3864   1223   -846  -2881   1854   -904   -168   -194    247   -334   -447  -3976  -3293    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -443 -10136  -1924   -894  -1115  -2481   -285      *      * 
-    16   -577  -3404   -315    613  -3713  -1009  -1598   -183    670   -663  -2497    668    264   1043  -1689     99    929    106   1485     72    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -706  -9695  -1375   -894  -1115  -3103   -178      *      * 
-    17    -45  -2942    953   1583   1516  -2449    643  -3010    947   -143  -2032    186  -2542   -649    369   -172  -1414  -2563  -3127  -2446    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -314  -9058  -2369   -894  -1115  -4577    -62      *      * 
-    18   -159  -2551  -1202   -652   1419  -2278   1585    160    814  -2534  -1660    420   1322   -515    968    389   -131  -2132  -2781  -2147    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -614  -8749  -1539   -894  -1115  -3374   -146      *      * 
-    19  -1371  -2366  -1481   -871  -2584  -2382   -954  -2209   1340    147   1970    360  -2452   -565   2236  -1347   1192  -1935  -2578  -2063    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -163  -8387  -3271   -894  -1115  -2974   -196      *      * 
-    20  -1181  -2509  -1086   1081  -2774   1324   -843   -558    910   -316  -1615   -838    -11   -404   -945   1000    500  -2101  -2729  -2083    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5  -8614  -9656   -894  -1115  -3361   -148      *      * 
-    21    155   1489   -375  -2244  -1457  -2851    855   1015    899    958   2236  -2144   -505  -1801  -2137   -241  -1380    -21  -1914  -1539    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -5  -8808  -9850   -894  -1115  -3861   -103      *      * 
-    22  -1357  -2825    491   1857  -3144    839   -991   -361    230   -903  -1915   -968  -2425    731    528   -260    829  -2446  -3010  -2328    22
-     -   -150   -501    233     43   -382    398    104   -622    212   -465   -717    275    392     44     94    361    120   -369   -296   -251 
-     .  -4056    -91  -9934    -15  -6571   -919  -1086      *      * 
-    23  -1112  -3501   1974   1537    270   -978    -53   -719   -263   -308  -2590   -535    659    671   -500  -1071   -321  -3122  -3685  -3002    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -2  -9785 -10827   -894  -1115   -789  -1248      *      * 
-    24   -939  -2363  -4829   -260   3155  -4072  -2941    182  -3801    949   1696  -3703  -4122   -444  -1181   -568  -2470   -279   1227  -2476    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10097 -11139   -894  -1115   -431  -1954      *      * 
-    25  -2484  -3963   2517   1355  -4283  -1446  -2110  -4035    867  -1637  -3054   1950   -117  -1653   -659   -333  -2425  -3585  -4146  -3459    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10251 -11293   -894  -1115   -383  -2100      *      * 
-    26   -971  -3350  -6102  -5567  -3578  -5390  -4532   1891  -5247    501  -2643  -5098   2526  -4929  -5113  -1297  -3598   2085  -4344  -3978    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    27   -372    630  -5046  -1702   -167    -98  -3122    265  -4006   2524    797  -3896  -4301  -3629  -3807  -1244   -742   -207  -2988  -2646    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    28  -1090    115   1110   1561  -4243  -1875    768   -193    945  -1665  -3012   1119  -3519   -657   -609    804  -2391    405  -4106  -3424    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    29  -5205  -4735  -6732  -6582   1835  -1075  -3352  -1288  -1178   -592  -3969  -5367  -6247  -5339  -5757  -5452  -5121  -4380   5441   2218    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    30  -4525  -4591  -1308  -1036    161  -1045  -3528  -4174  -4971    333  -3770  -4152  -5510  -4380  -5181  -4676  -4513  -4141   5838  -2240    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    31   -393  -3922   -695   -585  -1184  -3426    114     14   2419  -3938  -3012   -742  -3520   1248    686    942  -2391    100  -4106  -3424    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H  -1896 -10291   -453   -894  -1115   -701  -1378      *      * 
-    32  -1087  -2487   -942   1547    448  -2060   -718  -2512   1558    426  -1584    930  -2155   1665   -777   -979  -1025  -2096  -2679  -2019    33
-     -   -149   -500    233     43   -381    399    111   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -166  -3220  -9444   -160  -3253  -4901    -49      *      * 
-    33   1267  -1823  -1416   -869  -1934  -2239   2286  -1541   -740    660  -1001  -1084    519    798  -1148  -1199   1426  -1335  -2184  -1683    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -6  -8402  -9444   -894  -1115    -31  -5578      *      * 
-    34   -195    286     61    898  -1040   -467  -2085  -3991    594    177  -3011    -40   -794   1552    178   -458   -211    740  -4106  -3424    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    35   -667  -3877    492   -391   -104  -3439   2163  -3912    739  -1192   -624   2781  -3531  -1647    728  -2347  -2396   -945  -4074    676    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    36  -1178   -404  -1202    644  -4243    435   1843  -1047    681  -1713  -3012   -253  -3519    897    663   1507   -303  -1106    556  -3424    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    37    280   -505    442   -587  -4232    582    477  -1427     -9   -803     14    790   -304    359  -2176   1354    663  -1220  -4101  -3421    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    38  -2456   2085   -811    458   -629  -3435  -2096  -1132   1788   -419  -2983    346  -3528  -1641   2228     94   -146  -3503  -4083  -3410    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    39  -1162    683  -5405  -4813   3015  -4634  -3274   -245  -4410  -1655  -2088  -4238  -4676  -3994  -4196  -3729  -1087  -2277  -2994   3837    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    40  -1052  -4978   -712  -3235  -6372   -612  -4171  -6177   -551  -1165  -5471  -3478   3976  -3882  -4809  -3941  -4229  -5458  -6426  -5732    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    41   -727   1107   -706    147  -3506  -3613    -97   1404   -940    369  -2528   1723  -3698  -1965     69   -835    576    709    916  -3161    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    42  -1314  -2561  -5078  -4443  -2508  -4285    496   -834  -4040   2830    816  -3931  -4334  -3662  -3842  -1621   -275    445  -3022  -2682    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    43   -125    526  -4416  -3816    431  -4148  -2983  -2129  -3531  -1030  -1817  -3578   -925    219  -1285   2590    587  -2040   2166   1250    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    44   -606  -3910  -2307   -271  -4224  -1690   -122    706   2207   -339   -183   -574  -3523   1192   1636   -268  -2393  -3528  -4097  -1048    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    45   -350  -2642  -5178  -4547    247  -4391  -3270   1671  -4147   1425   3396  -4037  -4433  -3769  -3949  -1898  -1429   1069  -3125  -2786    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    46   2935  -2552  -4919   -971   -315  -4234  -3103  -2047  -3918    427  -1755  -3840  -4288  -3565  -3764   -387  -1425   -332  -3008    737    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    47  -1586   1604  -3232  -2669    146  -3828    -63      1    777   -497   -386    811  -3903    214   2424    231    -83  -1411  -3380   -550    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    48  -1551  -3889   2865   -901  -4193  -3437  -2098   1215     83   -871  -2983    688  -3530   -466    625  -1246  -2396   -170  -4083  -3410    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    49   -769  -3183  -5805  -5197   -631  -5079  -3989   2222  -4826   1308   -327  -4727  -5058  -4417  -4630  -4188  -3363   2102  -3752   1702    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    50  -1001    720  -5591  -4975   1055  -4828   -213  -2326  -4577   2954     96  -4453  -4827  -4134  -4354  -3924  -3208  -2401   1019  -2841    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    51   1362   2817  -5487   -926  -4883  -1510  -4660    422  -4976  -4804  -4054  -4453  -4783  -4693  -5014   2374   1433  -4026  -5256  -4952    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    52  -2704   1532  -5048  -4412  -2485  -1069  -3123   2843  -4007    298    907  -3897  -4302    370  -3808  -1432   -197   1076   1587  -2647    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    53  -3299  -3207  -5461  -4917   -199  -4735  -3792  -2472  -4501   -293  -2135  -4452   3686   1486  -4363  -3878    -49   -833  -3645  -3283    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    54   1377   1607  -5066  -4432   -311  -1259  -3145   1796  -4028  -2393   1437  -3916  -4320  -3652  -3829  -1138   -896   2280  -3010  -2668    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    55   -321   -141  -4800  -4281  -3328  -4147  -3562  -2881   -808  -1669   2309  -3916  -4456  -3752  -4027   2589   2185  -2722  -3784  -3431    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    56  -1382  -3098  -3061  -2501  -3152  -1245  -2496     15   -717  -1367  -2268   -842  -3846  -2272    241   2296   2227   -323  -3471  -3006    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    57   2169    342  -5048  -4412   -167  -1842  -3122   -757  -4007  -1120   -320  -3897  -4301  -3630  -3808   -476   -718   2407  -2988   -118    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    58   2115  -3901  -2317   1330  -4210  -3438  -2101  -3952  -1687  -3913  -2996    735   -906     18  -2193   1306    343  -1165  -4095   -541    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    59    600   2383   -673  -2978   -897  -3928  -2724  -2469  -2808  -1306  -2083     91    872  -2663  -3076   2374    753   -859  -3309  -2898    61
-     -   -149   -489    234     44   -381    400    105   -627    210   -464   -721    275    393     45     95    359    117   -370   -295   -250 
-     T   -156  -3291 -11333   -426  -1969   -701  -1378      *      * 
-    60   -931  -4313     -8   3512  -4622  -3658   -191  -4383  -2051  -4325  -3417  -2287  -3817  -1967   -649  -1278  -1101  -3931  -4497   -851    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    61  -2482  -3951   -290   -729  -4273  -3451  -2108  -4022    102  -3965  -3041    200  -3545  -1649   2928   1957  -1007  -3574    601   -758    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    62   1538  -2548  -4895  -4269   -663  -4229  -3093   -738  -3897   -500  -1750    320  -4281   -534  -3749   1736    425   1534  -3003    -82    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -42 -10291  -5176   -894  -1115   -701  -1378      *      * 
-    63  -3341  -3132  -5515  -1130   4148  -4817  -3181   -645  -4568  -1110  -2338  -1038  -4851  -4121  -4349  -3912   -817  -2578   1152    359    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10251 -11293   -894  -1115   -383  -2100      *      * 
-    64  -2739    318    -17      9  -4535  -1254  -2358  -4290  -1988  -4241  -3331   -398  -1596   -209  -2511   3169  -2690   -890  -4417  -3720    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    65   1080  -3732  -2411   -584  -3971    386  -2151    375    897   -669   -290   -119   -619    356  -2260   -338   1685   -539  -3967  -3337    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -32 -10291  -5561   -894  -1115   -701  -1378      *      * 
-    66   1048    219   -415   -130   -588   1367  -2200   -745     39    819    181  -2239   -814  -1811   -561    226   -190  -3063  -3801  -3221    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T  -1809 -10261   -486   -894  -1115  -1281   -765      *      * 
-    67  -1181  -2655   -925    953  -2978  -2114   -791  -2728   2356  -2667  -1749    954    222    996   -860    980  -1122  -2279  -2831  -2150    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .   -118  -8458  -3728   -894  -1115  -4881    -50      *      * 
-    68  -1323  -1174  -3443  -2809  -1087  -2857   1468    973  -2343   1575   -293  -2415  -2894  -2091   1472  -1941  -1262   1675  -1640  -1299    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     .     -7  -8347  -9389   -894  -1115   -141  -3422      *      * 
-    69   -166  -3278  -2652  -2098  -3393   2187    142    140    655    -21  -2426  -2340  -1235   -180   -216   -238   -941    730  -3600  -3072    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10207 -11249   -894  -1115   -258  -2612      *      * 
-    70  -2530  -3989  -2385    -48  -4319  -2011   -343  -4061   2317  -1039  -3079    987  -1160    534   2536  -2410  -2465   -968  -4158  -3491    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    71  -1016  -3060  -3107    294  -3105  -3783    310   1010  -1325    346   1091   -501  -3860   -961  -1003    163   1085   1888  -3437  -2980    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    72  -2703    119  -5048  -4412   -304  -4251    266   1939  -1136   1467   1566  -3896  -1453  -3630  -3807  -1290   -821    544  -2987   2131    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    73  -2463  -3824   1803   -606   -626  -3454  -2118  -3819   -371    854  -2925   1011   -535  -1674  -2217   1232   1099  -3421    950   -273    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    74  -1061    115   1168   1676  -4246  -3426    563  -3997    826  -2000  -3014   -354   1402    363   1551  -1090   -690  -3547  -4108  -3425    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    75  -1212  -3917  -2303   -722   1255  -3428   2150  -3983    308   -947  -3007   1098   -617    376   1128    935   -999  -3537  -4103   1886    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    76  -2539  -3516  -2637  -2081   -377  -1161  -2280  -1461    879  -3457  -2652  -2341  -3689    399   3174   -499   1127  -1508    597  -3246    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    77  -2686  -2588  -4605  -3995  -2549  -4183  -3030    233  -3678  -1142   2672   2223   -801  -3380   1034   1386    409   -123  -3038   -333    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    78  -2496   2813  -2347     51  -4286    -75  -2117  -4031     99  -3974  -3051  -2103  -1577     17   2455   1664    -71  -3585  -4137  -3463    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    79  -2949    711    970  -1986  -2647  -4476  -3335   1325  -4076   2228   2116  -4032  -4508   1334  -3959  -3559  -2888  -2144  -3241  -2915    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    80   -527  -3925    997   1636  -4246   -284  -2084  -3997   1383    146  -3014   -660   -444   -114    156  -1012    949  -3547  -4108  -3426    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    81  -1399  -3895     36  -1766   -729   -752   1700   -860   -162  -1706  -2988  -2074   2338    385   1546    648   -826  -3510  -4087   -208    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    82  -1061  -3924    945   1599  -4245   -725    223  -3996    901    742  -3013  -2061  -3519    698   -412    671   -746  -1868  -4108    270    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    83  -1212  -2845  -3558  -2987  -2848  -3936    241    513   -934  -1019   1967   2218  -4005  -2664   -773   1232   1731   -437  -3258  -2850    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    84   -372  -2605    300  -3892  -2569    -48  -3003     39  -3594   1054  -1804    245  -4219  -3313  -1176  -1491   -950   2443  -3053     82    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    85  -1179   1434    725   1951  -4247  -1330  -2086  -3998   -271    341  -3016    497  -1192   2126  -2174    268  -2393  -3548  -4110  -3427    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    86   2527  -3833    218   -639   -944  -3451  -2114  -3836    551   -396    867  -2103  -3543    562   -962   -125  -1345  -1123  -4042  -3384    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    87  -1179    409  -5036  -4401  -2485  -4249    337   1354  -3998   2541    692   -939  -4299   -596  -3803  -1290  -2643   -802  -2989     94    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    88  -1071  -2534  -5022  -1432    -77  -4249  -3119   1531   -859   1277   2871  -3886  -4299    181  -3799  -3332    300   1244  -2992  -2649    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    89   -181   4501  -5035  -4400   2541  -1432  -3121   -766  -3999  -1463  -1737   -683  -4300  -3624  -3804   -219  -2645   -799  -2991    723    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    90    488  -2531  -5039  -4403  -2485  -4250  -3120   1660  -4000   1221   1004  -3892   -644   -765  -3804    160   1409    640    760  -2646    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    91  -2465  -3937   -459   1796   -603  -3436   1072  -4009   1456  -3953  -3026   1501  -3530   1634   1608  -2345  -2404  -3560  -4119   -334    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    92  -1172  -3924   1935   -146   -634   -696    150   -867    -86  -1603  -3014    583  -3519   2029    524    737  -1080  -3546  -4108   -280    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    93   -853  -3854    387     44  -1135  -1481  -2108  -3871   -365  -1842   -108   1925  -3538   -195  -2203  -2355  -2399  -3459   5010   -729    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -2 -10291 -11333   -894  -1115   -701  -1378      *      * 
-    94  -1111  -2531  -5036  -1473    415  -4249  -3120   1400  -3999   2021   2092  -3891  -1453   -650  -3803     17  -1278   -252  -2989    285    98
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     H      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  DDE
-ACC   PF03184.11
-DESC  DDE superfamily endonuclease
-LENG  242
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  20
-DATE  Tue May 13 14:50:08 2008
-CKSUM 5225
-GA    17.2000 17.2000;
-TC    17.4000 17.4000;
-NC    17.1000 17.1000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -10.513236   0.649242
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -74      *  -4322
-     1  -2743  -2515  -5078  -4458   1139  -4337  -3126   2661  -4072    401   1289  -3974  -4291  -3594  -3841  -3441   -313  -1694  -2802   2972     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -1074  -8913 
-     2    977  -3204    -78    306  -3525  -2705  -1364  -3275   1014   -876  -2293    153   1876   1244  -1452    432     27  -2826  -3388  -2705     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8910 
-     3   -322  -3182     20     25  -3493  -2710  -1370   -571    261   -992  -2274   1194   2466    516  -1460    502  -1672   -206  -3371  -2694     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8907 
-     4   -111   1162    722   2070  -3528  -2707  -1366  -3279   1515  -3223  -2297    153  -2800   1378  -1455    -29     36  -2829  -3391  -2708     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8904 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8901 
-     6  -2528  -2289  -4912  -4314  -2275  -4201  -3139   2688  -3945    129   2130  -3844  -4204  -3582   1002  -3312    700   1342  -2954  -2617     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8898 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8895 
-     8    749   1511  -5447  -5579  -5581  -3309  -4851  -5373  -5325  -5628  -4683   3602  -4105  -4871  -5114    636   1235  -4166  -5804  -5713     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8892 
-     9   1610  -1783  -4293  -3658   1716  -3503  -2372  -1266  -3255    135   2949  -3146  -3552  -2878  -3057   -204  -1896   1160  -2237    648     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8889 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8886 
-    11  -5083  -5704  -3237   3785  -6927    612  -4677  -7299  -5145  -7028  -6591  -3970  -5385  -4520  -5746  -4933  -5298  -6638  -6264  -6297    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8883 
-    12    284  -3161  -3920   -183  -5480    360  -4227  -5276  -4434  -5463  -4548  -3547  -4057  -4059  -4614   -261   3551  -4181  -5644  -5354    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8880 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8877 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8873 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8870 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8867 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8864 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8861 
-    19  -1936  -1796  -4069  -3447  -1754   1367  -2320   1242  -3088   1097   1227  -3034   1362    172  -2963   -197    -80    -52  -2251  -1904    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -9407 -10449   -894  -1115   -701  -1378  -8987  -8858 
-    20    369   2328  -2755  -2192  -2229  -3160  -1979  -1796    -99    751  -1399    391   2252  -1891  -2310    966  -1842   -277  -2621  -2204    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -183  -9407  -3111   -894  -1115   -701  -1378  -8987  -8855 
-    21   -314  -3904   2295  -1926  -5068  -3219  -2772  -4899  -2787  -4878  -4052   2820  -3737  -2421  -3410   1706    -11  -4208  -5061  -4310    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -9231 -10273   -894  -1115  -2014   -411  -8987  -8852 
-    22  -1631  -3055  -1499   -947  -3362   1428   1156  -3097    304   -561  -2149  -1251     -3   1396   1053    523  -1569  -2670  -3243   1900    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -9231 -10273   -894  -1115   -817  -1210  -8987  -8849 
-    23    895  -2350  -2176  -1618  -2414  -2934  -1653    -64     17    348   1720  -1810  -3013    429   1046    380   1708  -1828  -2711  -2233    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -939  -9328  -1075   -894  -1115  -1457   -654  -8987  -8845 
-    24  -2581  -2697  -3595  -3587  -3102  -3594  -3346  -1178  -3002  -2481  -2300  -3373  -4026   2053  -3039  -3077  -2755   3436  -3854  -3370    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -8398  -9440   -894  -1115  -3603   -124  -8987  -8842 
-    25    448  -1114  -3618  -2994  -1091  -2868  -1754    838  -2605    733   -317  -2503  -2911  -2239  -2423  -1957    971   1929  -1623   2117    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -8398  -9440   -894  -1115  -3603   -124  -8987  -8839 
-    26  -1511  -2219  -1708   1401  -2934   2000  -1852  -2374  -1747  -2747  -2007  -1668  -2808  -1583  -2147  -1630   1606   1628  -3191  -2697    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -8398  -9440   -894  -1115  -1455   -655  -8987  -8836 
-    27     20  -2105    653  -1122    694   -114  -1236  -1839  -1012    469  -1290  -1340    350   -933  -1432   1853    293  -1625  -2473  -1966    27
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -8987      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Hermes_DBD
-ACC   PF10683.1
-DESC  Hermes transposase DNA-binding domain
-LENG  68
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  4
-DATE  Thu Jun  5 22:14:57 2008
-CKSUM 1784
-GA    25.0000 25.0000;
-TC    110.1000 189.1000;
-NC    19.3000 13.5000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.006978   0.801583
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -322      *  -2322
-     1  -1032  -2095  -1079   -436  -2567  -1881   -345  -2168    557  -2097  -1303   -609  -1966   2067   2428   -958   1445  -1837  -2200  -1768     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -26  -7119  -8161   -894  -1115   -701  -1378  -1322  -7066 
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-     -    -27  -7120  -8162   -894  -1115   -701  -1378  -7388  -7056 
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-     -    -27  -7119  -8161   -894  -1115   -701  -1378  -7388  -7044 
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-     B    -27  -7119  -8161   -894  -1115   -701  -1378  -7388  -7011 
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-     -    -27  -7119  -8162   -894  -1115   -701  -1378  -7388  -6989 
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-     H    -27  -7120  -8162   -894  -1115   -701  -1378  -7388  -6954 
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-     H    -28  -7121  -8163   -894  -1115   -701  -1378  -7388  -6920 
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-     H    -28  -7120  -8162   -894  -1115   -701  -1378  -7388  -6895 
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-     H    -28  -7120  -8163   -894  -1115   -701  -1378  -7388  -6858 
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-     H    -28  -7121  -8163   -894  -1115   -701  -1378  -7388  -6845 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     H      *      *      *      *      *      *      *  -7388      0 
-//
-HMMER2.0  [2.3.2]
-NAME  MULE
-ACC   PF10551.1
-DESC  MULE transposase domain
-LENG  128
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  153
-DATE  Tue May 13 14:49:56 2008
-CKSUM 1777
-GA    16.2000 16.2000;
-TC    16.2000 16.2000;
-NC    15.9000 15.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
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-EVD    -9.794119   0.688529
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -10      *  -7219
-     1    386   1658  -2759  -2814   -512  -2979  -1881   1012  -2824   -276   -420  -5811  -2661  -1364  -2658  -1242  -1154   2452  -4960   1936     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -12382 -13424   -894  -1115   -701  -1378  -1010  -7989 
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-     -   -149   -500    233     43   -381    398    105   -627    210   -464   -721    275    393     45     96    359    117   -366   -295   -250 
-     -  -7547  -6009    -36    -77  -4269   -701  -1378  -7998  -7983 
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-     -   -147   -500    232     42   -381    398    105   -627    210   -467   -708    275    393     45     99    361    117   -370   -295   -250 
-     -  -1977  -1275  -1605  -1913   -445    -16  -6508  -7998  -7977 
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-     -   -148   -486    232     42   -381    398    105   -623    209   -464   -721    278    393     48     95    358    116   -370   -295   -250 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6 -12351 -13393   -894  -1115  -1279   -767  -7998  -7966 
-     6  -6721  -8741   4035  -1035  -2512  -1935  -5924  -8834  -2035  -8669  -8063   -725  -7090  -1461  -2884  -6341  -2814  -8287  -8862  -7777    14
-     -   -150   -501    231     42   -382    397    104   -619    214   -467   -722    274    394     44     99    358    116   -361   -296   -251 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     9  -2510  -2348  -4769  -4140   1314  -4047   2021  -1842  -3753   -926  -1551  -3663    512  -3391   -714   -589   -606    678   2402   3403    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -10063 -11105   -894  -1115  -7055    -11  -7998  -7937 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -10063 -11105   -894  -1115  -7055    -11  -7998  -7931 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -8 -10063 -11105   -894  -1115  -7055    -11  -7998  -7925 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11547 -12590   -894  -1115  -5149    -41  -7998  -7895 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23 -11564  -6430   -894  -1115  -1752   -508  -7998  -7889 
-    19   -416   1015  -1172   -822   1364    287   1295  -4719   -942   -609   -324     33  -5057  -3275   -807   -538   -995  -1777    492   3212    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -331 -11839  -2318   -894  -1115  -5733    -27  -7998  -7883 
-    20  -2184    172    321    483   -841    935    115  -1840   1547   -949    286   1490  -4614    406   1004   -287  -3485  -2343  -5200  -4518    37
-     -   -152   -503    230     49   -372    398    110   -624    215   -469   -711    272    397     42     96    356    118   -372   -297   -252 
-     -   -363  -3996  -2685  -1977   -423  -3759   -111  -7998  -7877 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11355 -12397   -894  -1115  -6415    -17  -7998  -7870 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2990 -11355   -202   -894  -1115  -5251    -38  -7998  -7864 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12  -8542  -9584   -894  -1115  -5368    -35  -7998  -7858 
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-     -    -11  -8851  -9894   -894  -1115  -4869    -50  -7998  -7852 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -9224 -10267   -894  -1115  -5972    -23  -7998  -7845 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10  -9327 -10369   -894  -1115   -309  -2373  -7998  -7839 
-    27  -2755  -1254  -1319   -699   1457  -1860   -347    -46  -1187   1863   1078  -1939  -5453    208   1016  -1318   -417  -1121  -5250    165    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -337 -12247  -2296   -894  -1115  -4036    -91  -7998  -7820 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1051 -11580   -965   -894  -1115  -1280   -766  -7998  -7807 
-    32   -992   -253  -1338   -795   1059  -1123   1183    233    693    650   1612  -1357  -4649    907    635  -1932  -3341    157    548    651    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11238 -12280   -894  -1115  -6518    -16  -7998  -7801 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11238 -12280   -894  -1115  -6518    -16  -7998  -7794 
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-     -     -7 -11238 -12280   -894  -1115  -4782    -53  -7998  -7788 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11282 -12324   -894  -1115  -2951   -200  -7998  -7781 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12318 -13360   -894  -1115  -2245   -342  -7998  -7755 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12326 -13368   -894  -1115  -3006   -192  -7998  -7748 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12326 -13368   -894  -1115  -3006   -192  -7998  -7741 
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-     -   -149   -479    231     43   -383    397    115   -621    208   -466   -722    278    392     47     94    357    115   -369   -296   -241 
-     -   -740  -7157  -1360  -3722   -114  -1162   -855  -7998  -7735 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -11648 -12690   -894  -1115  -6070    -22  -7998  -7728 
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-     -   -149   -500    239     44   -381    398    105   -627    210   -466   -721    275    393     45     95    360    117   -370   -295   -250 
-     -    -98  -5389  -4747  -1078   -926   -317  -2343  -7998  -7721 
-    45  -1551   -116   1303    756  -2218   -572   1174  -2682    545  -3413   -616    379  -1601   2351    644   -133   -121  -5320    108  -5199    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12233 -13275   -894  -1115  -4164    -83  -7998  -7714 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7 -12233 -13275   -894  -1115  -3012   -191  -7998  -7707 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11 -12387 -13429   -894  -1115   -701  -1378  -7998  -7098 
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-     -    -33 -12387  -6086   -894  -1115   -701  -1378  -7998  -7055 
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-     -   -149   -500    232     42   -381    402    105   -627    212   -467   -721    275    393     45     95    358    119   -367   -295   -250 
-     -    -30  -6287 -13398  -1542   -607   -187  -3040  -7998  -7033 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -12389 -13431   -894  -1115   -701  -1378  -7998  -7023 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -12388 -13430   -894  -1115   -701  -1378  -7998  -7011 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -12 -12388 -13430   -894  -1115   -701  -1378  -7998  -7000 
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-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7998      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Exo_endo_phos
-ACC   PF03372.15
-DESC  Endonuclease/Exonuclease/phosphatase family
-LENG  199
-ALPH  Amino
-RF    no
-CS    yes
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  162
-DATE  Thu Apr 24 23:13:42 2008
-CKSUM 1747
-GA    11.0000 11.0000;
-TC    11.0000 11.0000;
-NC    10.9000 10.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -89.894104   0.166389
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -10      *  -7237
-     1  -4685  -4512  -7031  -3738   1739  -6233  -1700   1734  -2968   1974   2366  -5879  -6283  -2770  -5790  -2448  -4626    634  -1055   -117     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378    -10      * 
-     2  -1692    195  -1188  -3625   1064  -5137    646  -2864   2209  -1310  -4452    -60  -5128  -1097   2182    139    682  -5174  -4679  -1250     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-     3  -1480   1471  -7031  -3518    745  -2992  -5104   2517  -5990    487   -473  -5879  -6283  -5612  -5789  -3224  -1447   2294   -574  -2598     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-     4    769   1252  -7031  -6395   -789   1230  -5104    916  -5990   1262   2111  -5879  -6283  -5613  -5790   -553   -821    830  -4970  -1900     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -21 -12396  -6145   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12376 -13418   -894  -1115   -814  -1214      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12387 -13429   -894  -1115   -379  -2114      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-     8    205   2182  -7033  -6397  -4467  -6235  -2102   2015  -5992     -2    996  -5881  -2899  -2849  -5791  -2956  -1121   2625  -4971  -4629     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-     9    -20  -5861   -618  -1740  -1862    544    790  -5932  -1804    433  -4950   2803  -2556    976    723  -2128  -4328  -5483   1543    -46     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    12   -482  -5858   -473  -1887    250     22     84  -1465    296  -2033   -735    -33     55   -112   1910   1332    499  -1713  -6042  -1963    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    13   1046    146    511   -362  -1431   -398  -4022  -5927   -995   -591  -1857    861   1324    535    183   -451     93  -2098  -6042   1333    13
-     -   -137   -502    232     23   -390    392     94   -632    212   -465   -719    272    408     34    117    358    130   -365   -295   -271 
-     C  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
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-     -   -151   -510    255     48   -398    389    107   -639    233   -461   -717    274    389     41    110    352    109   -374   -299   -256 
-     C  -7560    -41  -5453     -1 -10098   -701  -1378      *      * 
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-     -   -145   -502    242      9   -341    341    113   -640    217   -425   -696    290    363     65    153    327     89   -405     67   -194 
-     C  -3605   -492  -2272  -3028   -189  -2436   -295      *      * 
-    16    858   -856    -18    114  -1075     96    182  -5571    234    469   1247   -589  -2468    792    602   -370  -1415   -219   1568  -5008    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -1 -12028 -13071   -894  -1115   -120  -3643      *      * 
-    17  -3088  -5060  -1072   -522   1137  -1232  -4404    939   -887   2038   -243  -1161  -1164  -2180   -900   -664   -933    520  -5426  -2053    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12374 -13416   -894  -1115   -237  -2722      *      * 
-    18    399    366  -2572    307   -870    287    754    296   -397   1043     93  -1294  -2895    171    152   -634   -601    202   -652   -713    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    19   -301   -137    911   1064  -2428  -1483    503    364    740   -236  -1538    581  -2797   1115   -124    293   -204  -2338  -1123  -5361    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    20   -252  -1541   -181    677   1325  -2507   -681    -17  -1259    508   -902  -1670  -2740   -532  -1296   -418    -49    800   2773    601    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    21   -710    150   -287   -564    718  -3381  -1475   1156     76   1542    744   -354  -3122  -1760  -1151   -987   -333    449  -1164  -1374    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    22   -124  -5858    303   -171  -2215   -103   1092    397    929   -290   -237    119  -2878    681   1068   -119   -819  -1574  -6042    749    54
-     -   -139   -521    235     62   -397    386     98   -626    221   -447   -710    271    386     41     95    354    115   -372   -316   -254 
-     H  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-    23   -156    602  -1276    980    -91  -1783   1640  -1003    223   -328  -4937    494    397    738   -979    -35  -1844   -790    108   1629    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    24   -585  -5862   2311   -678  -1754    311    -94  -5934    180  -2716  -4951   1740  -1529    977    925     48  -1350  -5484  -6045  -5362    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    25   1212    598  -7031  -6394    458  -3071  -5104   1399  -5989   -604   -739  -1380   2355  -1295  -5789  -2390  -1103    -39   -733   1745    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -9 -12396  -7327   -894  -1115   -701  -1378      *      * 
-    26  -2204  -5379   3595  -1264  -1599  -3229    738  -1398  -2686  -2971  -1390  -2609  -5614  -1190  -4374  -1661  -1739   -517  -5682   1518    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12387 -13429   -894  -1115  -1404   -684      *      * 
-    27   -411   -597  -9230  -8855    356  -8986  -8640   2618  -8757    533   -893  -8640  -8714  -8533  -8802  -8309  -6568   2535  -8003  -7638    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12387 -13429   -894  -1115  -1404   -684      *      * 
-    28   -200    520  -7041  -6406    141  -1166  -5117   2259  -6001   1502   1061  -5891  -6294  -5625  -5802  -2140  -2151   1683  -4982  -4640    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12387 -13429   -894  -1115  -1404   -684      *      * 
-    29    467   3816  -6225  -3236   1005   1611  -4551   -979  -5579    881    -58  -1439  -5717  -5156  -5379   -348  -1913   -787  -4156  -4319    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12387 -13429   -894  -1115  -1404   -684      *      * 
-    30  -2986  -4017  -6227  -5904   1209  -5815  -4552    886  -5581   2676    685  -5398  -5717  -5157  -5380  -5089  -1194    818  -4156  -4319    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12387 -13429   -894  -1115   -389  -2082      *      * 
-    31  -1347   -503  -2709   -334  -6137  -3245  -1279  -1142  -2757  -5841     71  -1173  -5464   4070  -4123  -1083    372  -2390  -6023  -5349    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    32  -6565  -1051  -2676   3924  -9075  -3460  -6272  -9047  -6700  -8947  -8337  -5388  -7212  -5987  -3570  -6354  -6794  -3051  -9122  -8122    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    33   -184  -4528  -1931  -6250  -2514  -2249  -5073    779  -2268   -426    522  -2790   -465  -1302  -5730  -1672   2310   2261  -4984  -4638    66
-     -   -149   -488    235     43   -381    398    105   -627    210   -466   -721    275    393     45     96    360    117   -370   -295   -250 
-     E    -19  -6248 -13438   -609  -1538   -701  -1378      *      * 
-    34  -2785  -5853    675    -83    653   -719   1909  -1374   1598  -2023   -766    -88  -1214    329    613  -2119   -331    -80   2629   -617    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    35    219   1049   1099   -470    556  -2942    357  -1634  -1319    608   1395   -356   -297  -1486   -271    -55    161    424    -56  -2079    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    36   -515  -5860   -136    411  -2387   -343     54   -274    232   -380  -1874    805     22    779    372    836    336   -742  -6043   -175    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -9 -12396  -7327   -894  -1115   -701  -1378      *      * 
-    37   -316   -915   1217    646     14   -735   1118  -2016  -1012  -1060  -4938    739   1382    649      7   -318   -326  -1475    149   -197    72
-     -   -141   -521    240     57   -368    397    103   -640    207   -460   -713    288    384     43     90    353    109   -382   -290   -232 
-     T  -7551     -8 -13429     -1 -10122  -1404   -684      *      * 
-    38    -20  -5851    442    791    -78   -190   -757  -1878    253  -2054  -2347    722   -579   1359   -934    696    278   -378    225   -145    74
-     -   -142   -521    230     35   -337    382    131   -625    204   -454   -726    281    390     42     99    348    119   -363   -277   -247 
-     H  -7551     -8 -13429     -1 -10122  -1404   -684      *      * 
-    39   -794     14    -97   -329    860  -1559    -72    736    -62    147   -700  -2309    832    207   -235   -249    -62    370    593    471    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12387 -13429   -894  -1115  -1404   -684      *      * 
-    40   -485   -259    275   -205    549  -1380    141   -550    531    620   -331    307    216    164   -277    -71   -867   -935   1876     68    77
-     -   -145   -507    232     41   -388    388    127   -627    218   -437   -713    270    381     55     86    352    121   -373   -259   -265 
-     H  -7551     -8 -13429     -1 -10122  -1404   -684      *      * 
-    41    672   -188   -639   -552   -673   -174    915   -789   -584    762   -535    508    852   -376   -608   -117   -219   -252   -777  -1076    79
-     -   -141   -508    234     38   -359    391     92   -630    201   -450   -690    273    380     51    105    355    118   -357   -316   -262 
-     H  -7551     -8 -13429     -1 -10122  -1404   -684      *      * 
-    42     51  -5825    280   -213   -455   -570   1135   -307    401    260    411   1045   -334   -418   -123   -539   -468     -8    272   -187    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -10 -12387  -7255   -894  -1115  -1404   -684      *      * 
-    43   -271  -5833   -106    552   -963    584    694  -1236    559    119   -772    453   -542   -344   -387   -120   -418   -786    824   1165    82
-     -   -149   -494    233     50   -377    400     89   -628    214   -440   -713    278    387     36     84    348    106   -369   -281   -224 
-     H  -7542    -20  -6927     -1 -10101  -1894   -452      *      * 
-    44  -1182  -5808   -916    432     15    853   -894   -434    253   -591    155    960    249    562      8   -727  -1226    145   -156   1021    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -23 -12366  -5978   -894  -1115  -2337   -318      *      * 
-    45   -692  -5712   -850      3    586   1073    847   -939  -1350   -200  -2258  -2229   -529   -787   -690    312   -205   -949   1325   2422    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -32 -12343  -5530   -894  -1115  -2930   -203      *      * 
-    46   -166  -1392    334  -1046    788     89   1317  -1137   -638  -1099   -966    178    331  -2129   -560    -27   -156    530   2025   1404    86
-     -   -193   -420    183    -24   -327    303     94   -502    190   -366   -609    234    264     11    119    347     74   -191    -60    -37 
-     H  -3295   -673  -1885  -4598    -61  -3470   -136      *      * 
-    47  -1374   -680    161    -69   -142     76   -997  -1638   1063   -529  -1021    403    703  -1394    134    171   -193  -1312  -5518   2037   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11856 -12898   -894  -1115  -2065   -394      *      * 
-    48   -876   1432   -563  -2307    674   -210   -401  -1555      4   -263    202  -1095      7  -4057   -265   -228   1710    475    773    937   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11998 -13040   -894  -1115  -1370   -706      *      * 
-    49   -307    408  -1504  -1292    776   1314   1649   -795   -750   -678    505  -1689   -922  -1188    365    130   -732    208   -646   1326   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12161 -13204   -894  -1115   -919  -1086      *      * 
-    50   -273   -420   -430  -2371   1538  -1534    966    590   -278   -206    495    497   -790   -345   -718   -538    647  -1525   1532   1389   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12289 -13331   -894  -1115  -1253   -785      *      * 
-    51    -56    511    -54   -427    481    575    798   -433   -248   -637     -1   -596    559   -100   -580    256  -1967    224   -715   1164   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12332 -13374   -894  -1115   -883  -1128      *      * 
-    52    134   -458    153   -622   -640    950   1645  -1282    495  -1544  -4913    475    115  -1319    901    358  -1208    -92   -748   -600   162
-     -   -140   -510    237     39   -368    407    115   -634    205   -469   -709    266    388     51     88    355    116   -364   -315   -239 
-     E  -7530     -8 -13408     -1 -10101  -2337   -318      *      * 
-    53   -620  -5808  -1240  -1283    173   1062    722     45    209   -713  -1019    719    -61    668    435     17    474   -793    546  -1047   164
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12366 -13408   -894  -1115  -1113   -895      *      * 
-    54   -170   1237  -1956   -998  -1042   1720  -1385  -2234   1445  -1279  -2148     30   -717   -483    745    -51    194  -2074   -809   -285   165
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12378 -13420   -894  -1115   -266  -2571      *      * 
-    55  -1857  -5861   -590    129  -2314   1578   -226   -905   1003  -2693   -736   1721  -1833    524    649   -632    -41   -618  -6044   -878   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    56   -791  -5861   -418  -1383  -2426    634    923  -2767   1759  -5877   -170     58   -799   -498    563    325   -585   -824   -193   2200   167
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    57     85    536   1010  -1310  -2330   2321   1089   -233  -1578  -5742   -562     16  -5489  -3620   -794    719  -2857  -1011  -5962    299   168
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    58    313  -5859  -2666  -1725  -1561   3278  -1268  -2404  -1765  -5875  -4949    -84  -5456  -1303   -715  -1364   -883  -5481   -717  -5361   169
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    59  -1352   2047  -6962  -6330  -4474  -3313  -5091   -959  -2736    426  -3721  -1002  -2632  -1028  -2600  -3497   1443   2924  -4975  -2214   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    60   2669   1259   -871  -1940  -2074    717  -4939  -1354  -5445   -362   -116  -1651  -6166  -2438  -1136    171  -2541   -744    250  -4691   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    61  -2871  -1184  -7034  -6398     65  -6236  -5107   2618  -5993    930   -217  -5882  -6285  -5615  -5792  -1987    610   1993   -578  -1933   172
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    62  -1068    303  -7030  -3244   2198  -3095  -5104    689  -2979   1457   1093  -5878  -6282  -5612    647   -500  -1862    274    222   1495   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    63  -1206    786  -3122  -6395   2058  -2106   -495    272  -5989   -782    382  -5879  -6283  -5612  -5789   1982   -893    581   2370   1534   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    64   -831  -1382   -399  -1389  -6183  -5362   -511  -5933   2520  -1226  -1871    413  -2556    147   2471   -446  -1446  -3392  -6045  -5362   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S     -9 -12396  -7382   -894  -1115   -701  -1378      *      * 
-    65  -2180  -1524   -232    521    801  -2220     44  -1671    736    104    389    794   -215   -388    569   -373   -621    198   1149    917   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S    -10 -12387  -7255   -894  -1115  -1383   -698      *      * 
-    66   -498     64    157    -21   -440  -1713   1582  -2749    239  -1292  -2067    861   1822    210    278    523   -171  -2489  -1022   -157   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -260 -12378  -2600   -894  -1115  -1878   -458      *      * 
-    67    368  -4929  -1415  -1551    579  -5366  -1122   1239    592   1002   -497  -1914   1100  -2140    602  -1783  -2535    370  -5272    261   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -25 -12118  -5881   -894  -1115  -4944    -48      *      * 
-    68   -882  -1525    403   -160   1224  -3034     65    365    458    265  -1601    561   -570    470   -560   -269   -162    799  -5715  -1994   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12094 -13136   -894  -1115  -5049    -44      *      * 
-    69   -163    351    724    772   -118   -887   1345     26    202  -1886  -4183  -1179    275    356   -371    645   -193     70  -4398   -237   180
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -27 -12094  -5770   -894  -1115  -5049    -44      *      * 
-    70  -1046   -778  -5051    146    -79  -5534    -33   -612   1004    381    -59  -2032   -236    972  -1205    178    589   1453   -766  -1594   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -15 -12067  -6663   -894  -1115  -5152    -41      *      * 
-    71  -1799   -815   -254    -76    907   -886    819   1355   -677   -265   -184  -1294    756  -1779    832   -378    290    455   -785  -4910   182
-     -   -160   -490    229     33   -375    390    101   -611    219   -446   -726    270    388     74     91    353    113   -361   -310   -241 
-     E  -7217    -80  -4408     -2  -9717  -5204    -40      *      * 
-    72  -1269  -5465    594   -284   -692    843   1840  -2372    -54   -743  -4554     59    338    452     -8    -81   -231    235  -5649   1185   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -16 -11984  -6531   -894  -1115  -5427    -34      *      * 
-    73   -200  -1035   -148    278   1089  -2168   1164    979    323   -607    513   -599     -8   -115  -1226   -107   -258    121    512   -363   185
-     -   -179   -485    245     86   -298    375    106   -578    202   -441   -639    308    346     -1     96    302    116   -358   -319   -185 
-     C  -7132    -10 -13010  -3908    -99  -5471    -33      *      * 
-    74   -172    161   1361  -1017   -409    627    856   -337  -1341    369   -293  -1056  -1418    519   1019  -1296  -1096    514  -5548  -1920   240
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11968 -13010   -894  -1115  -5471    -33      *      * 
-    75    245  -1209   -579  -1051   1482   -657    242    617  -2487    329  -1837   -808   -776    223   -827   -308    394    528    366    808   241
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -11968 -13010   -894  -1115  -4246    -78      *      * 
-    76   -232    215   -802   1050  -2058    514  -3727   1304  -1248     79  -4323  -1048  -1446    845  -2030   -471    163    769   -722   -750   242
-     -   -151   -469    232     34   -370    407    102   -615    206   -464   -708    259    386     33    117    352    120   -372   -295   -234 
-     E  -7148    -10 -13026     -2  -9717  -2585   -263      *      * 
-    77   -212    658  -2081  -1031   -463   -344  -1063    201   -841    202   -431  -2307    137    401   1938   -343   -117    654   -434  -1646   244
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E     -1 -12053 -13095   -894  -1115  -4007    -93      *      * 
-    78   -575     17  -1174   -210  -2300  -2200   1073    668    705   -211    811  -2130  -1494   -856   1330   -529    -93   1102   -303    312   245
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12067 -13109   -894  -1115  -3995    -93      *      * 
-    79  -1371  -1039   -343  -1530   -136   -296    697   1652     21    758   -448   -709     53     59  -2051   -768  -1026   1003    550  -4819   246
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12080 -13123   -894  -1115  -3946    -97      *      * 
-    80   -573   -766   -622    302  -2444    189   -521    244    718    185  -1773    -82   -718    190    -45    453    331    186    574  -1167   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12094 -13136   -894  -1115  -3851   -104      *      * 
-    81    760   -191   -650    284  -1097   -933  -3891    833   -340   -531  -1226    219    304  -1735  -1300    247   1020    205    347   -288   248
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12107 -13150   -894  -1115  -3553   -128      *      * 
-    82   -672   -219    849    898  -5923    432    -23  -1680    225  -2691  -4691   1173  -1513    662    446    867    387   -815  -5785  -1776   249
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12125 -13167   -894  -1115    -84  -4151      *      * 
-    83  -1092   -610    551   -396   1016   1948   -193   -264   -241  -2049  -4920    600  -1660   -169   -353   -764  -1024   -111    762   -238   250
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12387 -13429   -894  -1115  -1430   -669      *      * 
-    84   -820    726    678    142   -708    728  -1660  -1549   1046  -1466  -2158    179  -1893    251   1213   -377   1132  -1702  -6034  -1204   251
-     -   -161   -521    238     49   -393    398     98   -627    209   -476   -702    283    411     36     95    370    123   -378   -286   -260 
-     E  -6441    -17 -13429     -1 -10113   -381  -2107      *      * 
-    85  -4687    226  -1042  -6397   2887  -6234  -5106   1475  -5991   1473    -27  -5881  -6284  -2240  -5791  -3119  -1447   1017  -4971      7   253
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    86   -527   2931  -1254  -2150    384  -1326   1159   -531  -5653   -565  -1370    381  -6215  -2413   -454   -268   1191   1376  -1168   1067   254
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    87  -1710  -1076  -7366  -6746   2246  -6599  -1445   1947  -6356   1273  -3960  -6243  -6629  -5978  -6163  -5694  -4946   2176  -5315  -1036   255
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    88    843  -4512  -7031  -6395    781  -1341  -1616   1633  -5989     18    583  -5879  -6283  -5612  -5789   -771  -1542   2204   -151   1176   256
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    89   -948   1726  -1881  -4216   -886      6  -4328  -4925  -4102  -2412  -4378   2905   -250  -1005  -2886    989   1158    470  -5562  -5054   257
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    90    435   1719  -2652  -6310  -2264  -1489  -5086    975  -2810   -307  -3723   -398  -6270  -1794  -5755    623   1968   1682  -4977  -2141   258
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    91  -7868  -7953  -3197  -7040  -5001  -8119   4593  -8039  -2578  -3804  -7214  -6758  -8117  -5904  -2482  -7609  -7570  -8005  -5570   3723   259
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    92    766    862  -7031  -6394   1633   -846  -5104    -37  -5989   2003    -91  -2401  -6283  -5612   -539  -1662    346    256  -4969  -4627   260
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    93    845  -4849  -1187   -754   -491  -1524   2010  -2087   -687  -1363  -4472   -865   2701   -588  -2299    285    256  -2845  -4688   -456   261
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-    94   1641  -4626  -6229  -5635   -787  -6090    998  -1628  -5376  -2305  -3822   1850   2009  -1110  -1166    774   -408  -2629   2163  -1094   262
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C    -14 -12396  -6721   -894  -1115   -701  -1378      *      * 
-    95    -67   -444    580     47  -1417   1644   2157  -3085    153  -3360  -2047   1047   -672  -1324   -381   -125    357   -984  -6031  -5349   263
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C   -647 -12382  -1470   -894  -1115  -1673   -543      *      * 
-    96   -899   -499    579   -237  -2013   1326   -924  -3254  -1984  -1186    247      4   1151   1071    494    377   -483  -1153  -5408    766   264
-     -   -153   -480    271     58   -409    417     92   -656    189   -459   -734    264    386     50     99    359    116   -376   -289   -262 
-     S  -3786   -109 -12778  -2193   -356  -2780   -227      *      * 
-    97   -821   -778    127  -1358    365    505    758  -1350    778  -2271  -1193   1354  -2540   -388   1232     35   -812  -1669   1609   1349   287
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -1 -11844 -12886   -894  -1115  -2613   -257      *      * 
-    98    146  -1040  -1991    104    905   -189  -3674   -242   -261    408  -1261    174   -412    215    138   -273   -497    716  -5439    841   288
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -1 -11941 -12983   -894  -1115  -1474   -644      *      * 
-    99    353   -968   1654   1128  -1290  -1233   -226  -1582   -235  -2046  -1400    138    923    864   -329   -388   -202   -833  -5776   -417   289
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12117 -13159   -894  -1115   -730  -1332      *      * 
-   100    -27  -1049  -1047   1342   -900  -2324    845   -369   -105  -1406  -4843  -2398   -146   1304   1018    284  -1672    420  -5938   1127   290
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12291 -13334   -894  -1115    -70  -4406      *      * 
-   101     67  -1538  -1774    485  -6178  -1509   -552  -5927   1475  -3836  -4948  -3999  -2755  -3562   3271  -1378  -1251  -2128  -1164  -1207   291
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   102   -484   -225   -345   -305  -2627   -989   1186    284  -1008    864    571   1364  -2098   -151    789  -1187   -544    749   -841  -5313   292
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   103    889  -5861    -98    897  -2840  -1566    694  -1060    494  -1015   -931    435  -5456   1387   1261    325  -1041   -469  -6044  -5362   293
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   104  -1031  -5667   1735    985   1542  -5424   -814  -2790  -3714  -1762  -4779   -383  -2579   2802  -4204  -1360  -1715  -2146   2606   -441   294
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   105    743    234    -78   -882   1620  -1288  -5029     -4   -916    719    506  -2448  -2643  -2317  -5645  -1157  -1357    443     78   2296   295
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   106    773   -446    537    273  -1595   -274  -1360  -2765   1066   -904    647    711  -2155    268    618   -686  -1108   -977   2276   -169   296
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   107    890  -5849   1273   1228  -1589  -5366    562   -212  -1337  -1067    771   -984  -1635    540    934   -527    229   -665  -6036   -500   297
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   108  -2848   -149  -2065  -2319   1615  -6230  -2048   2050  -3135   1939  -3716  -1523  -6280  -5601  -1502  -5313     71    659  -4971  -1356   298
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   109     40    639  -6575  -1711    237  -1608  -1492    102  -2396   1582    608  -1636  -6214    769    398   -476   -820    250  -5017   1570   299
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   110    -17  -5862   1780   1287  -6183  -2273    655  -5934    451  -3780  -4951   1048  -5455    728   1229    -72    730  -5484  -6045  -5362   300
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   111   -413    380   -143    345   1619  -1190   1149   -662    509   -238  -1808    270  -5495  -1288    568   -775    -21   -607    149   1264   301
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   112  -1777  -1544  -7031  -6395  -1416  -6233   -831   1556  -5989   2037   1792  -5879  -6283  -2618  -2776  -1717  -1896   1573   1327   -126   302
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   113    205   -391     -3    863     16   -534    385  -1582    732   -778  -4950    396  -1092   1001    501    801  -1051   -789  -6044  -1256   303
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -88 -12396  -4080   -894  -1115   -701  -1378      *      * 
-   114    507  -1157    930    627   1396  -1388    889  -1001    843  -1038  -4866    608  -2455    264   -596   -384    753  -5399  -5960  -1049   304
-     -   -155   -536    234     34   -388    345     96   -556    212   -427   -694    278    391     56    147    340    105   -370   -296   -249 
-     H  -4475    -67 -13350  -2653   -250   -803  -1229      *      * 
-   115     81   -391    629    132  -1529    255   -107  -1142   1049  -1225  -1850    366    619    337   1272    568  -1218  -5447  -6009  -5326   344
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12359 -13401   -894  -1115  -1333   -730      *      * 
-   116    -51  -5836    833   -919   -718    850   2309  -2742   -381  -1612  -1832    958   -818    360   -320   1217   -397  -1999  -6020  -1519   345
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12370 -13413   -894  -1115   -747  -1306      *      * 
-   117   -121  -1186   1868    883  -2830    298    -61  -1258    894  -2782  -4939    132  -1504   -590    644   -431   -260   -630    720  -1183   346
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12385 -13428   -894  -1115   -359  -2183      *      * 
-   118   -591  -1201    410   -793   -579  -2427   1755  -2150     17   -932   -355   1041   2407  -3637   -324   -750   -888   -145  -5940    559   347
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   119  -1024  -1234  -7031  -6395    606  -3192  -5104   1639  -2206    595  -1656  -5879  -2733   -462  -5789  -1342   -732   2396   2497   -150   348
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   120  -1695  -6463  -9338  -8781   2134  -8869  -7789   2578  -8517   1447    923  -8539  -8453  -7779  -8230  -8087  -6811   1083  -6942  -1052   349
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   121   -419  -1174  -7245  -6612   1447  -6459  -5330   1969  -6212   1397   -181  -6106  -6491  -5820  -6008  -5548  -4836   1089   3786  -1320   350
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   122    852   3337  -7031  -6395    871   1082  -1653    118  -5989    699   1831  -2491  -6283  -5612  -5789  -2879    109    324  -4969  -4627   351
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   123  -2300  -1150  -8984  -9338  -8876   3818  -8269  -8839  -8986  -9063  -8120  -7410  -7353  -8429  -8563  -5950  -6171  -7515   -775  -9029   352
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   124  -6844  -8445   4196  -5026  -9179  -6690  -6299  -9225  -6791  -9075  -8518  -2295  -7314  -6014  -7803  -2537  -7026  -8536  -9180  -8164   353
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   125  -2148  -5020  -7566  -6933   3549  -6794  -5642  -1656  -6537   1808    981  -6440  -6789  -6102  -6318  -5888  -1768  -1455   -103    774   354
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   126 -10001  -9011  -9562  -9948  -8172  -9029  -8795 -11006 -10360 -10358 -10334   4453  -9475 -10013  -9919 -10254 -10212 -10738  -8298  -2328   355
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   127   1392    646  -1260   -464    900  -1598   -829   1048  -5660  -1572     61  -2422  -6216  -1369   -967   -137   -125    945    347   1770   356
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   128   1110     99   -686   -156  -1482  -1442   1271   -134     71  -1258  -4937     79     81   -776   2075  -1388   -855   -960    806   -349   357
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   129   -912   1891   -583  -1563  -2291  -2259   2930    663   -594    441   -704  -2570   2111   -778  -1131  -1392  -4442   -203   -774  -1240   358
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   130   -195   -562   1307    719    275     89   -558   -605  -1442  -1724  -2084    929   -725    210    606    604    564  -1738  -6043  -5361   359
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   131   -247    586   1352   1504  -2297   -427   -992  -3222  -1186   -589     29    180   -369   -697  -1697   1085   -216  -1624   -439    459   360
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   132   -685  -5687    797   -650  -2684  -1446    -97   1281  -1647   -135   -316   -350    619  -1972    418   -356   -271     17   3258   -336   361
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   133  -1645  -5856   2225    791  -2902    273  -4022  -2152   -961  -1652   -706    452    559   -437   -714    250     88    283  -6041   -773   362
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   134   -980    378   -229   -401    579  -2053    716   -172    146    245   -875    -36   -900  -2198    334    829  -1261    361  -1083   1725   363
-     -   -131   -479    224     57   -382    386    134   -634    223   -474   -742    279    388     43    102    360    102   -378   -275   -246 
-     H  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-   135   -316  -5839    641   -325    802   -355    728   -581  -1744    104  -4931    837   -780   -407    646    194    179    546  -1211   -842   365
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   136   -166  -5657   -733   -446   -742    -75  -1386    389   -350    744    619  -2265   1251  -1571    503  -1085    456   -735   2447  -1972   366
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   137   -582   -130   -547    568  -2910   -748  -1770  -2767    954   -413  -4949    839    324    942    945    180    538   -285   -902  -1421   367
-     -   -149   -476    236     52   -371    398     90   -633    222   -468   -704    274    390     37     82    369    112   -381   -302   -250 
-     H  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-   138   -767    215  -1686  -1411    289    169    435   1259     58     98  -1660   1112   -525   -329   1313   -968   -880   -789   -445   -376   369
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   139   -517  -5858     71    354   -484   1106  -4022   -211    876   -495  -4947    -96     -4    577   1301     82  -1789  -1686   -707  -2134   370
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -12 -12396  -6944   -894  -1115   -701  -1378      *      * 
-   140   -209  -1270  -1984    150  -1505   -342   -136   -334   1207    392  -1587   1134  -2668   -239    561    480   -473    -99  -6019   -571   371
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -81 -12384  -4205   -894  -1115  -1567   -594      *      * 
-   141   -399  -1492    701     42  -1475  -1662   1024   -143   -106   -857   1100    633  -1574    750    479    502     61    221    756  -1914   372
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T    -93 -12304  -4004   -894  -1115  -3573   -127      *      * 
-   142    -27   -103    503    131  -1611  -2070    390    137    524    -64   -518     58    -28   -814   -176    354    863   -734   1124   -357   373
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H    -31 -12211  -5584   -894  -1115  -4434    -68      *      * 
-   143   -278   1017    399    618    363    497    924   -476   -564    315    426   -603  -5285   1208   -686   -316  -2310  -1630   1790   -336   374
-     -   -198   -413    302    131    -73    284    136   -630    182   -301   -530    220    221    102    150    241     46   -392   -196   -219 
-     H  -4669    -58 -13223  -4409    -70  -3718   -114      *      * 
-   144  -1523   1425   -660   1908    519  -1086    624   -282  -4048    186     46    282    220    538  -1106  -1469  -2427   -226     10    666   491
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12190 -13232   -894  -1115  -1366   -708      *      * 
-   145    266   -576   -763   -613   -906    645   1334   -302   -925    692   -776    419   1253  -1798   -118   -254   -411   -555  -5846  -1423   492
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12270 -13312   -894  -1115  -1740   -513      *      * 
-   146  -1762  -1366    105    165  -1076   -748    901    375    377   -524  -4856    464   1514    289   -443     44    195   -554  -5952    606   493
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12304 -13346   -894  -1115   -625  -1507      *      * 
-   147    130  -5823    156    252   -981    166  -1346   1078   -163   -269  -4913    881   -545   -302    946   -829    114   -273   -104  -2347   494
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H      0 -12365 -13407   -894  -1115   -185  -3052      *      * 
-   148   -919  -4854    126    662  -5573   1456    374   -907    920  -2226  -4478   -297    637  -1411  -1369   -384   1758  -3183  -4691  -1198   495
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   149  -1730  -1142    990   -755   2523    617    157   -118   -354  -1979   -292    109    449   -574  -1165   -670   -537   -932   -660   -256   496
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   150    839    898  -2411   1143  -6177    -45  -1609  -1650   -616  -1807   -324  -1263   1705    978    602   -270   -180   -289  -6042  -2510   497
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   151   -587  -1033  -2172   -737   2360  -2230  -1448  -1496  -4912  -2350  -3950  -1787   2562  -4745  -1656  -2003  -1018  -2201  -5183   2874   498
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   152  -2208  -5647  -1734  -3828    -43  -2976  -1526  -5566  -2731  -3582  -4765  -2166  -1886  -3688  -2339   1139   3574  -3287  -5892  -5271   499
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   153  -1310   1692  -1867  -1627   1608  -5506   1943  -5268  -1303  -5404  -4592   1048  -5594  -1561  -4333  -4434    -53  -1342   4005   2923   500
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   154  -1754   -435    226  -5758    825  -6117  -4950  -2443   1544  -3308   -454  -5535    439  -1584    520  -1279  -1747    401   4305   1355   501
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   155    483  -1272    -66  -4100   1477   -655  -1370  -2687  -1866    -65  -4466   -282    110  -2010   -836   1075   1078   -822  -5638   1806   502
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B    -30 -12396  -5604   -894  -1115   -701  -1378      *      * 
-   156  -1151  -5827   1001     87   -217  -1495   -111   -103    367  -1783  -1639    510    -80    975    330   -273     89  -1084    568   1934   503
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -458 -12366  -1878   -894  -1115  -2331   -320      *      * 
-   157   -447   -879   -582  -1265  -1100  -1525   -300  -1174   -863   -326    376   -182   1286   -833   2404    -44    114   -260  -5533  -2239   504
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -192 -11908  -3006   -894  -1115  -5625    -30      *      * 
-   158   -426  -5211   1191   -688  -1010   1274   1477  -1027   -337  -1100   -208   1698  -4809    519   -463    -27     26  -1644  -5395  -4713   505
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T   -183 -11717  -3074   -894  -1115  -6003    -23      *      * 
-   159   -589   -668  -1065   -588  -1447    586  -3203  -5114     18   -714  -4132   1499  -1632    615    350   1169   1606  -2202  -5226  -1978   506
-     -   -158   -519    276     41   -381    389     82   -618    209   -488   -712    287    366     40     86    345    149   -383   -239   -169 
-     T  -1683   -539 -12577  -2521   -276  -6257    -19      *      * 
-   160    932    331   -979  -1737  -5324   1255   -569  -1869  -1059  -1619  -4108   -755  -4645   -357   -981   1634    918  -2004    -66   1422   538
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     H     -1 -11535 -12577   -894  -1115  -5075    -43      *      * 
-   161  -2226  -5058    416   1530   1078   -353  -3223   -636    324  -5073   1065   -661   -454   -475   1599  -1358    -56   -243  -5242    164   539
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11554 -12597   -894  -1115  -1877   -458      *      * 
-   162   -257  -5319    280    -78  -1874  -1118   -932  -1686   1958  -1257  -1267    642   1518   -802    234   -406    346  -1334  -5503  -1578   540
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -1 -11829 -12871   -894  -1115  -1710   -526      *      * 
-   163   -792   1082    160  -1263   -953    337   2015  -5574   1487  -1261  -1536    913  -2159    557   1230   -470    375  -2686  -5686  -1949   541
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     T     -1 -12021 -13064   -894  -1115   -121  -3640      *      * 
-   164     52  -5840   -506  -1325   -854    827   -127  -5912   -759  -1894  -1800   2304   -176   -255   1917    -26   -519  -1823  -6023  -5340   542
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12374 -13416   -894  -1115  -2065   -394      *      * 
-   165   -525    372  -1660   -493    597   -733   -620    348   -280   -156  -1996  -1363   -428  -1441    614     57   1116    818    149    860   543
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12374 -13416   -894  -1115   -234  -2742      *      * 
-   166   -777    300   -923  -1937  -1236   1816    -19  -2807    348  -2043  -1513   -297   2176    272   -313   -521  -1147   -902    219   -693   544
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   167    844   2122   -358   -308  -6162    518    560  -2265     64  -1437    943   -979  -5459   -667   -322   1383  -2611  -1782   2947  -1911   545
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   168   -243   1010  -5653  -2219  -2145  -5699    168   -256  -1140   -703   -651  -1781  -1195  -2114   2669  -2842    466   -632   3583    668   546
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   169  -6129   2140  -8560  -7997   -487  -7951  -6909   2459  -7681   1945  -4364  -7602  -7811  -7207  -7486  -7105   1062   -813  -6482    889   547
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   170  -7615  -9095   4209  -3199  -9613  -7218  -6791  -9792  -7295  -9547  -9085  -5942  -2602  -6532  -8257  -7241  -7736  -9228  -9271  -8639   548
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   173  -2875   -467  -7074  -6438   2252  -6278  -5149    226  -6034   2129   -139  -5924  -6324  -5653  -5833  -5363  -1797    921   2572    984   551
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   174    839   1315  -7029  -2993    -58   -341  -1552   -979  -5988   -226   -506  -2372  -6282  -5612  -2666   -574    342   1789   2466   2253   552
-     -   -149   -502    231     41   -383    402    104   -628    212   -468   -722    273    398     43     97    360    115   -366   -281   -251 
-     E    -20  -6205 -13438  -2809   -222   -701  -1378      *      * 
-   175  -1176    359  -1258  -2695  -1571  -1024    767  -2905   1254  -5872  -1627   1521  -2478  -1322   1095   1856    642   -967  -1199  -1229   566
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   176   -541  -5862   -357    427  -6183   1661    186  -5934    638  -1366  -4951    862   1265   -202     -1    491   -631  -3057  -6045  -1144   567
-     -   -140   -521    239     53   -392    398    102   -637    210   -480   -735    283    389     41     98    372    116   -373   -315   -248 
-     S  -5685    -28 -13438     -1 -10111   -701  -1378      *      * 
-   177   -449   -194     44   -794    503   -785   1053   -294  -1247   1036  -1984    -23  -1050   -249    450    232   -253   -158   2105  -2150   569
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   178    618    679  -1714   -564  -1116  -1698    187   -313    582   1121   1101   -916   -560  -1487    235   -833    144    422  -1185  -1157   570
-     -   -147   -521    232     49   -385    381     99   -618    212   -474   -730    290    397     54    115    358    117   -361   -316   -265 
-     H  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-   179   -991   -653   -947   -903  -1788   -252   1164  -2139   -272    280  -2042    193     95   1359   1727   -506     76   -225   -893    192   572
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   180     20   1099   -348  -1533    246   -271   1046    522   -325    366  -4775  -1327  -1401   -553  -1384   -241    212   1445  -5899    -13   573
-     -   -159   -455    218     38   -387    388    103   -630    212   -472   -733    277    390     53     92    366    124   -334   -240   -253 
-     E  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-   181    -28    985    502    -69  -2946   -139   -741    619    201   -858  -4931  -1077   -263    537    -87     45   -417    261   1583   1017   575
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   182    413   1401  -1777    268  -1559  -3218    121   -249   -484    885   -227  -1229    269    247  -1914    944   -108     72    659  -1271   576
-     -   -162   -466    236     49   -384    398    103   -635    203   -476   -730    278    405     54     99    363    113   -374   -292   -228 
-     E  -7560     -8 -13438     -1 -10131   -701  -1378      *      * 
-   183   -380   -348   -317    -66   -771   -362   -212   1312   -731    272    539  -1373     61   -125   -829    207   -576    295  -4610   1057   578
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   184    329  -1134     82    410   -699   -542   1206   -961   -720    320    786    -17   -315   -782    512    231   -685     81    633   -656   579
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E    -44 -12396  -5052   -894  -1115   -701  -1378      *      * 
-   185   -795    149    792    488      7   -676    406   -140   -635    215  -1670   -618    519  -1915    131    404    412   -392   -580    323   580
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E   -237 -12352  -2725   -894  -1115  -2729   -236      *      * 
-   186   -428   1037    766   1232  -1267   -752    701   -903   -251    350  -4652  -1237    594     17  -1364  -1000    143    309   -462     -1   581
-     -   -152   -447    219     61   -321    377    100   -601    194   -428   -669    278    410     36     64    321     97   -375   -263   -178 
-     C  -2983   -417  -3004  -3334   -151  -4956    -47      *      * 
-   187  -2721    623  -1365    677   1309  -1210   1569    706    231    123  -4413   -315   -300    188     32  -2244  -2520    944  -5523    685   618
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C     -1 -11924 -12966   -894  -1115   -434  -1944      *      * 
-   188    301    -47   -817  -1492   -300   -908    506   -311    742    402   1724    169   -645  -1266    331   -391    765  -1576  -5875    666   619
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     C      0 -12289 -13331   -894  -1115    -68  -4433      *      * 
-   189    296    597   -750  -2750   1300   1477  -4850    432  -2089   -146   -496  -2406   1533  -1444  -1922   -508   -265   -336  -1011   -655   620
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   190  -5417  -6032  -8355  -8718  -8755  -2067  -8005  -8589  -8649  -8842  -7868  -7070  -7113  -2735  -8316   3728  -1831  -7252  -8967  -8937   621
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   191  -6932  -9067   4185  -2667  -9122  -6612  -6089  -9174  -6572  -8987  -8468  -5191  -3232  -2546  -7646  -6514  -7044  -8597  -9177  -2082   622
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     S      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   192  -9011  -8763  -8727  -8410  -8958  -8634   5460 -10090  -6649  -9598  -9170  -8336  -8934  -2959  -3086  -9035  -8913  -9804  -8472  -8358   623
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     B      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   193    237   2609   -565   -911   1220  -5426    235   -104    771   -162  -4775   -319  -2573  -1970   1475   -512  -2141   -954    614    934   624
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   194    237    287  -6965  -6338  -4499   -782  -1425  -4038  -5950  -1650  -1610  -5855   3794  -5588  -2639   -180  -3012  -2506  -5001   -607   625
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   195  -2959   -151  -7668  -7060  -2551  -6931  -5847   1711  -6685   1325  -1523  -6579  -6934  -1404  -6496  -6037  -5230   2963  -5650  -2091   626
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   196  -1676  -1606  -2590    423   1153   -216  -1881    -91   -810    678   1102  -1110  -5824  -1096     27   -144    513    549    523   1316   627
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   197   1909   1819  -7031  -6395   1244   -549  -5104    -41  -5990    444     45  -2779  -6283  -5613  -5790   -672    -97   1567  -4970  -4628   628
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   198   -868  -5845    764    918   -965   -994    -78   -825     59  -1374     48    247  -5460    410    172   -436   1539    324   1226   -691   629
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     E      0 -12396 -13438   -894  -1115   -701  -1378      *      * 
-   199  -4685  -4512  -7031  -6395   2815  -6233  -1895   1385  -3327   1835   -285  -5879  -3144  -5612  -2232  -2919  -2186    621  -4969    696   630
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     E      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Peptidase_C27
-ACC   PF05407.4
-DESC  Rubella virus endopeptidase
-LENG  166
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  5
-DATE  Thu Apr 24 20:52:15 2008
-CKSUM 173
-GA    25.0000 25.0000;
-TC    490.6000 490.6000;
-NC    -43.9000 -43.9000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -102.940628   0.190638
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-         -585      *  -1585
-     1  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378   -585      * 
-     2  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     3   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     4  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     5   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     6  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     7   -862  -1548   -321   -247  -1672  -1336   -419  -1721    130  -1660  -1161   -427  -1678   3540    -59   -855   -904  -1495  -1728  -1237     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     8   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-     9   -739   -638  -2403  -1903   -200  -2252  -1321   1007  -1576    760   3268  -1750  -2280  -1364  -1629  -1412   -728   1601  -1257   -943     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    10   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    11   -862  -1548   -321   -247  -1672  -1336   -419  -1721    130  -1660  -1161   -427  -1678   3540    -59   -855   -904  -1495  -1728  -1237    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    12   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    13  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    14   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    15    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    16   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    17    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    18   -637  -1349     -5   -148  -1773  -1078   -624  -1965   -499  -2112  -1514   3456  -1574   -435   -810   -661   -818  -1560  -1900  -1327    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    19   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    20  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    21   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    22   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    23  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    24   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    25  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    26    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    27   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    28   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    29   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    30   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    31  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    32   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    33    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    34    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    35  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    36   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    37   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    38   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    39  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    40  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    41   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    42   -637  -1349     -5   -148  -1773  -1078   -624  -1965   -499  -2112  -1514   3456  -1574   -435   -810   -661   -818  -1560  -1900  -1327    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    43    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    44   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    45  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    46  -1335  -1071  -2973  -2502   1355  -2866  -1288    681  -2195   2326   1102  -2271  -2665  -1713  -2104  -2053  -1264    245   -728   -113    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    47  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    48   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    49   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    50   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    51   -108   -998    231    197  -1842   -787   -312  -1705   -129  -1842  -1075   2750  -1271    -14   -522    690   -288  -1201  -1990  -1361    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    52   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    53   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    54   -862  -1548   -321   -247  -1672  -1336   -419  -1721    130  -1660  -1161   -427  -1678   3540    -59   -855   -904  -1495  -1728  -1237    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    55   2114   -296  -1481  -1184  -1098   -942   -960    197   -995   -662   -198   -864  -1451   -868  -1164   -205   -122   1203  -1656  -1261    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    56   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    57  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    58   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    59   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    60   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    61   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    62  -1667  -1473  -2001  -1964   1181  -2210    -25  -1224  -1658  -1018   -871  -1505  -2415  -1423  -1618  -1747  -1692  -1248    501   4149    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    63    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    64    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    65   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    66   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    67   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    68   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    69   -912  -1800  -1053   -263  -2351  -1619    148  -1870   2518  -1712   -987   -334  -1655    559   1966   -825   -732  -1596  -1705  -1417    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    70   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    71   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    72  -1667  -1473  -2001  -1964   1181  -2210    -25  -1224  -1658  -1018   -871  -1505  -2415  -1423  -1618  -1747  -1692  -1248    501   4149    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    73   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    74  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    75   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    76  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    77    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    78   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    79   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    80  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    81    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    82  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    83   -537  -1827    417   2082  -2154  -1114     64  -1838   1454  -1814  -1028    221  -1368    458    245   -389   -489  -1474  -1970  -1368    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    84  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915    84
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    85  -1602  -1340  -2512  -2455   3740  -2315   -379   -478  -2225   -175   -190  -1874  -2503  -1781  -2079  -1892  -1647   -683    210   1257    85
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    86   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    87   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    88  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    89    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    90   -862  -1548   -321   -247  -1672  -1336   -419  -1721    130  -1660  -1161   -427  -1678   3540    -59   -855   -904  -1495  -1728  -1237    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    91   -718  -1231  -1178   -487   -654  -1595     -1  -1049    716  -1065   -467   -528  -1681    181   2679   -787   -620   -896   2167   -243    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    92  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    93    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    94   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    95    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    96  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    97   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    98  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-    99   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   100    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   101    215   -474   -556   -464  -1769   -628   -652  -1498   -519  -1716   -947   -356   2445   -420   -797   1301    -67   -924  -1970  -1514   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   102  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   103   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   104    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   105   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   106  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   107   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   107
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   108  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   108
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   109  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   110   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   111  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   112   -965   -982  -2125  -1844   -276  -2022  -1302    373  -1390    610   4141  -1701  -2229  -1356  -1425  -1444  -1028    126  -1279   -880   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   113   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   114    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539   114
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   115   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   115
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   116   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   117   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   118   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   119   -608   5196  -2368  -2362  -1635  -1253  -1702   -987  -2034  -1540  -1191  -1745  -1831  -1953  -1922   -934   -927   -770  -1855  -1692   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   120    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   121  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   122   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   123  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   124   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   125   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   126    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   127   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   128   -578  -1512    -46    178  -1097  -1274   3376  -1477    613  -1464   -774    -39  -1482   1412    377   -513   -525  -1211  -1290   -559   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   129   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   130   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   131   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   132   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   133  -1130  -2063   3441    243  -2502  -1157   -662  -2514   -843  -2578  -2029    -96  -1658   -421  -1434   -970  -1239  -2138  -2388  -1915   133
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   134  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90   134
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   135  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   136  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   137   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   138    116   -498   -840   -867  -1751   -671   -949  -1625   -916  -1896  -1218   -622  -1304   -824  -1097   2786   -220  -1038  -1992  -1530   138
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   139  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   139
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   140  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90   140
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   141  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529   141
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   142   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721   142
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   143   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   143
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   144   -637  -1349     -5   -148  -1773  -1078   -624  -1965   -499  -2112  -1514   3456  -1574   -435   -810   -661   -818  -1560  -1900  -1327   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   145   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   145
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   146   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   146
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   147  -1926  -1577  -2416  -2370    192  -2070   -795  -1602  -1882  -1347  -1210  -2018  -2383  -1854  -1777  -2150  -1992  -1643   5696    560   147
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   148   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   149   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   150   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   151  -1369  -1199  -2542  -2295   -129  -2453  -1603    488  -1867   2607    742  -2168  -2539  -1724  -1835  -1992  -1384    130  -1284   -897   151
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   152   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742   152
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   153   -700   -665  -2337  -2135   -873  -1965  -1727   1107  -1863   -105     22  -1851  -2286  -1794  -1920  -1368   -823   2927  -1816  -1362   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   154  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   155   2806   -444  -1270  -1265  -1732   -744  -1182  -1034  -1212  -1545  -1010   -869  -1380  -1102  -1325   -156   -259   -640  -2039  -1721   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   156  -1181  -1614  -1431   -903  -2066  -1632   -446  -1944    559  -1867  -1326   -899  -1873   -156   3432  -1225  -1148  -1717  -1746  -1529   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   157   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   158   -988  -1921    379   3052  -2309  -1196   -495  -2108   -350  -2194  -1612   -103  -1621   -210   -770   -862  -1042  -1799  -2207  -1742   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   159   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   160   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   161   -637  -1349     -5   -148  -1773  -1078   -624  -1965   -499  -2112  -1514   3456  -1574   -435   -810   -661   -818  -1560  -1900  -1327   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   162   -934  -1220  -1352  -1451  -2187  -1314  -1456  -2160  -1488  -2268  -1827  -1359   3760  -1471  -1571  -1129  -1216  -1780  -2050  -2023   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   163    -52   -555  -1173  -1112  -1571   -872  -1041   -862   -950  -1353   -866   -843  -1455   -937  -1084   -285   3069   -557  -1898  -1539   163
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   164   -758  -1103  -1313  -1487  -2460   3331  -1562  -2502  -1720  -2644  -2081  -1324  -1775  -1590  -1790   -958  -1093  -1921  -2198  -2279   164
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   165  -1192  -1547   -812   -781   -520  -1557   4586  -1881   -457  -1789  -1357   -866  -1913   -669   -600  -1231  -1258  -1678   -918    -90   165
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -33  -6045  -7087   -894  -1115   -701  -1378      *      * 
-   166  -1602  -1340  -2512  -2455   3740  -2315   -379   -478  -2225   -175   -190  -1874  -2503  -1781  -2079  -1892  -1647   -683    210   1257   166
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Transposase_mut
-ACC   PF00872.10
-DESC  Transposase, Mutator family
-LENG  402
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -F HMM_ls.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_ls.ann
-NSEQ  14
-DATE  Tue May 13 14:55:02 2008
-CKSUM 8681
-GA    -160.0000 -160.0000;
-TC    -158.7000 -158.7000;
-NC    -160.3000 -160.3000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD   -345.927826   0.133743
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -93      *  -4000
-     1    -41  -1878  -3554  -3047   1043      1  -2334  -1618  -2800  -1956   4160    359  -3315  -2542  -2841  -2201   1428  -1480  -2526  -2166     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378    -93      * 
-     2   1519  -2093  -2220  -1652  -2146  -2846  -1578    168    545   -407  -1272  -1798  -2926    939  -1758  -1829   2504  -1553  -2479  -2033     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-     3  -1477  -2930    299   1638    616  -2454   1160  -2987    555    -41   1259  -1092    495   1495  -1203     60  -1416  -2547  -3118  -2441     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-     4  -1498  -2940   1608   -806  -3253  -2472  -1133  -2994   1288  -2953  -2035  -1114    906   -677   1282     57   1185    608  -3131  -2457     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-     5     66  -2909  -1353   1926  -3210  -2473   3053  -2943   -732  -2919  -2009  -1120  -2570   1371  -1235    301    474    -67  -3111  -2443     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -383  -9060  -2112   -894  -1115   -701  -1378      *      * 
-     6  -1371  -1382  -2845   1304   1688    158  -1625   -899  -2036   1262   -580  -2133  -2860  -1806  -2127    475  -1314    896  -1825  -1452     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8682  -9724   -894  -1115   -177  -3116      *      * 
-     7  -1641  -1672  -3060  -2473  -1650  -3058  -1870    342    174   1047   -866  -2362  -3119    907  -2342    996   1547   1250  -2110  -1736     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-     8    963  -2413    219  -1124    348    921  -1304     89    326    394  -1556    611    505   -954  -1467  -1546    337  -1929  -2723  -2181     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-     9    881  -2980   1193    353  -3298  -2470  -1139  -3049    433   1066  -2071    816    268   1505  -1234  -1388  -1449  -2601  -3165  -2481     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    10  -1987  -1819  -4272  -3655    961  -3529  -2430    326  -3274   1689   -812  -3178  -3569  -2882  -3092   1988   1264  -1117  -2261  -1930    10
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    11    716  -2186  -2539   2607  -2368    250  -2057  -1757  -2108    555  -1520  -2211  -3215  -1951  -2401  -2108  -1851   1005  -2775  -2353    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    12   1645  -2222  -1881    876  -2303  -2696  -1407    507  -1202    420  -1381  -1537    101   1428    453  -1648  -1488   -107  -2570  -2075    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    13    944  -1617  -3844  -3234  -1586   1352  -2158   1131  -2886   1216   -812  -2843  -3330   1671  -2781  -2354  -1696    467  -2103  -1756    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -226  -9060  -2802   -894  -1115   -701  -1378      *      * 
-    14    225  -2596   1546   -730  -2834  -2349  -1017  -2529    680    590  -1708  -1023  -2440   1641    509  -1265  -1279    348  -2830    997    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8838  -9880   -894  -1115  -1990   -418      *      * 
-    15   2100  -3058   2132  -1413  -4018   1166  -1929  -3787  -1675  -3779  -2893  -1655  -3034  -1527    685    154  -2009  -3197  -3963  -3303    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -129  -8838  -3587   -894  -1115   -981  -1019      *      * 
-    16   1020  -1368    243  -2903    666  -3000  -1857   1288  -2566   1643   -564  -2539    292  -2248  -2478  -2071    398   -774  -1823  -1474    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8823  -9865   -894  -1115  -2043   -401      *      * 
-    17  -1317  -2691    841    642    857  -2306   -969    911    514    375  -1791   -958  -2398   1012   1134    162  -1256  -2292  -2899  -2241    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2010  -8823   -416   -894  -1115  -2043   -401      *      * 
-    18  -1384  -2604   2890    -35  -3398   2153  -1059  -3341  -1265  -3309  -2624   -375  -2066   -761  -1973  -1212  -1534  -2770  -3322  -2631    18
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -6832  -7874   -894  -1115  -3867   -102      *      * 
-    19   -625  -1075  -1124  -1001  -1519  -1588  -1094   -399  -1014  -1304   -784   2677  -1998   -947  -1277   -872   -770   2116  -1997  -1457    19
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -19  -6832  -7874   -894  -1115   -347  -2225      *      * 
-    20    236  -2541    437   1734  -2764   -228  -1018    244   -648   -420  -1657    668  -2437   -598  -1134  -1264    975  -2110   2503  -2169    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8823  -9865   -894  -1115   -237  -2720      *      * 
-    21   1068  -1848  -2492     -2    894   -433  -1671  -1418    414   1465  -1032  -1988  -2974  -1609    204  -1903  -1538    169  -2257    791    21
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    22    -82  -2740   1917    430    285  -2504  -1174  -2667   -796   -520  -1853  -1179  -2595   1693  -1285    677    358    249  -2977  -2351    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    23    595  -2936    585   -819  -3268   1500  -1153  -3011   -742  -2971  -2053    667    505   -698    744   1178  -1447   -237  -3151  -2476    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    24    560  -2635  -1507   -956  -2835    587   1731   1615   1037  -2600  -1761    637    298   -809  -1339     36  -1442   -271  -2900  -2301    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -264  -9060  -2594   -894  -1115   -701  -1378      *      * 
-    25  -2418  -4071   2548    896  -4326    561  -1872  -4143  -1774   -265  -3238   1655   1557  -1480  -2420  -2191  -2416  -3668  -4249  -3423    25
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8800  -9842   -894  -1115   -225  -2795      *      * 
-    26   1154  -4812   2821   1688  -5193    926  -2517  -5080  -2659  -4973  -4237  -1835  -3697  -2168  -3439   -248  -3170  -4536  -5163  -4220    26
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    27  -1581  -1986  -2222    410    802    758  -1563  -1593  -1509   1216  -1161  -1795  -2896    614   1249  -1799    202    775  -2375  -1934    27
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    28    744  -1519  -3987  -3355   2057  -3232  -2102   1001  -2961   1410   -712  -2863  -3281    925  -2778   -211  -1628    633  -1978  -1636    28
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    29    558  -2933    295   -830  -3247   -112  -1149  -2983   1577  -2948  -2036  -1135  -2583   -696   2446  -1402     80    214  -3131  -2465    29
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    30   1294  -2981    994   1499  -3296   -190  -1147    321   -737  -2995  -2073    529  -2577    685  -1246  -1396   1111  -2600  -3168  -2485    30
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    31   1115  -1608  -3342  -2744  -1577  -3115  -1948    367  -2455   1807   -805  -2527  -3173    951    542    128  -1595    410  -2055  -1693    31
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    32   -183  -1598  -3331  -2733  -1566  -3106  -1938   1113    836   1418   1370  -2517  -3164    949  -2484    182    387    193  -2043  -1681    32
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    33    263  -3055  -1472   1085  -3397  -2573  -1204  -3131   1608  -3066  -2152  -1213  -2664   -748   2399     41    941  -2691  -3218  -2566    33
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    34   1129  -1789  -3724  -3148  -1799  -3313  -2278   1841  -2822   -305   -998  -2850  -3412    908  -2804  -2406   2583  -1023  -2329  -1977    34
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    35    203  -1512  -4005    262   1702   -437  -2103   1068  -2973    583   1401  -2869  -3281  -2601  -2783  -2316  -1624   1864  -1975  -1632    35
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    36    304  -1503  -4021  -3385   1961  -3226  -2097   1357  -2981    546   2902  -2871  -3275  -2603  -2781   -205  -1618    462  -1961    735    36
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    37   -131  -4683  -1197   2500  -4978  -3167  -2363  -4828  -2348  -4720  -3952   2524  -3610   2468  -3012  -2712  -3008  -4326  -4894  -4017    37
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    38   1460  -3031    605   1935  -3347  -2509  -1187  -3095   -775   -284  -2125  -1144  -2617   1504   1114  -1443  -1507  -2651  -3215  -2532    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    39   1309  -1940  -4498  -3907  -1920  -3722  -2729    531  -3538   2312  -1070  -3414  -3779  -3168  -3366    220  -2095    549  -2568  -2235    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    40     -2  -1952  -4476  -3857  -1716  -3722  -2627   1721  -3473   1813   2841  -3378  -3735  -3061  -3276    840  -2090  -1113  -2420  -2119    40
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    41  -1499  -2973    924   1768  -3294    607  -1128  -3045    554   -296  -2063    533  -2561   1758    696  -1378  -1438  -2595  -3155  -2472    41
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    42   2095  -2223  -1999    978  -2315    838  -1587    280  -1457    493  -1425    426  -2911  -1351  -1842  -1798  -1611  -1715  -2625  -2151    42
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    43  -3976  -5510  -1654   3679  -5912  -3718  -3143  -6013  -3243  -5783  -5257  -2406  -4280   1621  -3837  -3631  -4069  -5490  -5652  -4918    43
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    44   1126  -2663  -4736  -4014  -2083  -4190  -3026  -1577  -2948   1876   2530  -3707  -4184  -3095   2297  -3347  -2716  -1853  -3012  -2799    44
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    45  -2323  -3515   2321  -1489    974  -2954  -2136  -3845  -2000  -3891  -3073    553  -3321  -1768  -2562   1028   2498  -3395  -4117  -3417    45
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    46   1736  -4426   1529   2595  -4674  -3064   1405  -4505  -2094  -4413  -3598  -1664  -3447    709  -2756  -2493  -2739  -4020  -4593  -3746    46
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    47   1324  -1984  -3010  -2445   2137  -3218   2859  -1540  -2220   -245  -1179    818  -3278  -2040     55  -2242  -1815  -1434  -2022   1784    47
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    48  -3546   1846  -6136  -5710  -2830  -5834  -5226   2102  -5565   2512  -1609  -5503  -5489  -5113  -5479  -5135  -3507    896  -4429  -4238    48
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    49    202  -4137    512  -1336  -4523   2929  -2088  -4318    662  -4236  -3406  -1684  -3388   1571  -2447  -2393  -2597  -3835  -4404  -3629    49
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    50   2513  -1945  -3424  -2870  -2091  -3089  -2240  -1644  -2477  -1992  -1326  -2644  -3313  -2364    619  -2213    646    181  -2538   2536    50
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    51    632  -2949    464   1537  -3270    538  -1109  -3020    443  -2965   1563    527    495   -649    503    -98  -1415  -2571  -3132  -2450    51
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    52   -129  -3140  -1610    289  -3492  -2680   1776  -3208   1198  -3135  -2234  -1319   1731   -819   2405  -1614  -1656  -2782  -3274    779    52
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    53  -3372  -3454  -4096  -3514  -1355   1584   2436  -3196  -2287   -491  -2706  -3261  -4366  -2696    447  -3499  -3269  -3112  -1969   3797    53
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    54     -2  -4358   1490   3027  -4641    280  -2147  -4465  -2056  -4376  -3556  -1665  -3432  -1758    745  -2467  -2704  -3979  -4554  -3721    54
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    55    782  -4129  -4249  -3116  -5303   -175  -2288  -4654    832  -4342  -3655  -2974  -4145  -1876   3634  -3405  -3299  -4315  -4201  -4098    55
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    56   1480  -2581  -2768  -2284  -3556   -108  -2375  -3212    175  -3396  -2581  -2291  -3232  -2066  -2540   1801   2056    303  -3738  -3264    56
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    57  -2310  -3886   1231   2166  -4169   1017  -1829  -3957  -1612  -3890  -3024  -1504   1775   1108  -2201  -2123  -2286    309  -4070  -3302    57
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    58    620  -2635  -1503   1477  -2833   -397  -1210  -2503   -857  -2598   1543    491  -2624   -805    501  -1456   1403    275  -2897   1031    58
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    59    309  -3209  -3167  -3042  -5106    961  -3038  -4796  -2281  -4777  -3956   1630  -3792  -2709   3435  -2586  -2747  -3973  -4824  -4520    59
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    60  -1530  -2758  -1486   -934  -2999  -2539  -1205  -2686   -808   -513  -1878    899  -2631   1487   1657   1997     90   -303  -2998  -2381    60
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1177  -9060   -847   -894  -1115   -701  -1378      *      * 
-    61  -1200  -1921  -1863  -2051  -3964   2898  -2501  -3761  -2607  -3927  -3068   2031  -2662  -2288  -2894  -1364   1328  -2807  -4104  -3702    61
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9  -7892  -8934   -894  -1115   -238  -2717      *      * 
-    62  -1703  -3197    594    714  -3506      6  -1303  -3265   -945  -3210  -2302   2686  -2707   -858  -1474    773    902  -2815  -3384   1269    62
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8968 -10010   -894  -1115  -1400   -687      *      * 
-    63    291  -2697    231   -835  -2923  -2453   1350  -2625   -753   -180  -1811  -1128  -2548   2382  -1243   1003  -1389  -2273  -2929   2286    63
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2761  -8968   -234   -894  -1115  -1400   -687      *      * 
-    64  -1460  -1844  -1734  -1185  -2350  -1850   -667  -2258    375  -2146  -1613  -1159  -2095   -379   3603  -1504  -1421  -2026  -1959  -1787    64
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    65   2974   -591  -1518  -1543  -1976   -883  -1429  -1312  -1496  -1813  -1267  -1081  -1538  -1369  -1582   -307   -424   -880  -2260  -1972    65
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    66  -1065  -1374  -1656  -1861  -2798   3461  -1905  -2905  -2119  -3013  -2464  -1669  -2049  -1974  -2151  -1272  -1414  -2286  -2468  -2629    66
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    67   -869   -801  -2593  -2412  -1051  -2155  -1985   1034  -2146   -257   -139  -2095  -2477  -2070  -2183  -1583   -995   3075  -2020  -1573    67
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    68   -213   -712  -1409  -1380  -1808  -1017  -1285  -1128  -1222  -1611  -1122  -1061  -1620  -1201  -1334   -450   3269   -797  -2112  -1780    68
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    69  -1065  -1374  -1656  -1861  -2798   3461  -1905  -2905  -2119  -3013  -2464  -1669  -2049  -1974  -2151  -1272  -1414  -2286  -2468  -2629    69
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-    70  -1505  -1792  -1099  -1103   -742  -1790   4799  -2229   -778  -2103  -1699  -1173  -2162   -998   -901  -1547  -1584  -2022  -1131   -310    70
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115    -58  -4657      *      * 
-    71     70  -3327  -4609  -4118  -5447  -3498  -3355  -5096  -2247  -5029  -4265  -3522    847  -3051   3894  -2912  -3042  -4244  -4937  -4881    71
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    72  -3343  -5138  -1190    727  -5414  -3287   1878  -5369  -2826  -5233  -4570   3867  -3825  -2320  -3590     40  -3424  -4829  -5389  -4401    72
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    73  -4660  -4782  -5563  -5696  -6595   3695  -5243  -7004  -4849  -6756  -6236  -5325  -5414  -5307    866  -4889  -5010  -6169  -5746  -6363    73
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    74   -188  -2397  -1734    568    548  -2650   1446  -2146  -1090  -2329  -1552  -1434  -2740  -1020  -1530   2183    199  -1914  -2690   2198    74
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    75  -2773  -3465  -3239  -2374  -3726  -3653  -1926  -3345    654  -3365  -2646  -2427  -3674  -1561   2816    700  -2619    377  -3489   2916    75
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    76   -176  -2948    296    355  -3269   -118   1361  -3019    448   -300  -2037    694    997   -648    370    799    522  -2570  -3131  -2449    76
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    77  -4008  -4551  -5142  -3359  -5575  -4446  -2233  -4779   2478  -4369  -3731  -3141  -4357  -1813   3341  -3886    593  -4577  -4164  -4147    77
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    78    270  -2937    365   -783  -3253  -2455  -1114  -2999    578  -2951  -2029  -1093  -2548   1058    369   1293   2098   -372  -3124  -2446    78
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    79    219  -2550  -5307  -4744   2575  -4689  -3679    604  -4427   1518  -1235  -4342  -4576  -3986  -4245  -3840  -2815   2009  -3302  -3035    79
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    80    568  -2487    304    501  -2639    164  -1284   1025   -978    289  -1628  -1336  -2681   -916  -1436    546   1589  -2017  -2787  -2228    80
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    81  -2224  -2834  -4833  -5168  -5468    416  -4661  -5308  -5213  -5550  -4608  -3788    879  -4712  -4962  -2474   3732  -4028  -5630  -5603    81
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    82  -1495  -2903   1144   -817  -3201   -272  -1134    325    671  -2908  -2000  -1122  -2568    682   2332  -1387   1092   -357  -3100  -2435    82
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    83   1916  -1580    -11  -2817    969  -3122   1430    376  -2526  -1434   -779  -2566  -3179  -2253  -2526   -297    217   1045  -2027   1188    83
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    84    101   2079    207  -4241  -4438   3070  -3859  -4103  -4128  -4389  -3568  -3389  -3678  -3813  -4167     24  -2430    483  -4735  -4474    84
-     -   -149   -500    233     43   -381    400    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -113  -3753 -10102   -148  -3354   -701  -1378      *      * 
-    85  -1524  -2996   1411    468  -3314  -2481  -1151  -3064   1725   -730  -2087  -1115    506    945  -1244  -1403   1913  -2617  -3179  -2495    86
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    86  -3874  -3347  -6435  -5985  -2584  -6200  -5443   1558  -5849   2043   1463  -5876  -5656  -5143  -5648  -5537  -3810   2431  -4329  -4313    87
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    87  -2836  -4555   1371   2938  -4798  -3101  -2244  -4641  -2220  -4544  -3745  -1701    765   1050  -2906  -2580   1129  -4150  -4726  -3856    88
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    88  -3074  -2756  -5457  -4863    815  -4834  -3726   1938    446   2381  -1002  -4485  -4651  -3973  -4287  -3979  -3001    366  -3230  -3044    89
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    89   1310  -2945  -1330    357  -3264  -2454   1277  -3012   1020  -2959  -2035  -1091  -2547    921   1557    257    193    201  -3129  -2449    90
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    90  -3346  -2872  -5983  -5612  -3509  -5713  -5492   2922  -5274  -2339  -2245  -5376  -5525  -5354    648  -5059  -3339   2720  -5079  -4586    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    91  -5005  -5318    859  -3897  -6647  -4723  -4786  -7191  -5343  -6895  -6505  -4183   4159  -4729  -5782  -4959  -5262  -6514  -5901  -6193    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    92  -4079  -4603  -5260  -3381  -5611  -4492  -2224  -4795   2062  -4372  -3738  -3155  -4378   1813   3438  -3943  -3668  -4608  -4159  -4151    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    93    269  -2024   2429  -2095  -2166  -2923  -1903  -1699  -1966   1147  -1332  -2133  -3093  -1816  -2246    308   1005    268  -2560  -2146    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    94  -4818  -4902  -5636  -5351  -6532    452  -4608  -6712  -3628  -6376  -5845  -5060  -5384  -4450   4096  -4992  -5018  -6099  -5530  -6015    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    95    840  -2951   1040    359  -3271  -2452  -1111  -3021    357   -356  -2040   1537  -2546    856  -1200   1227     82  -2572  -3134  -2452    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    96  -2117  -2733  -4961  -5307  -5424   3507  -4661  -5255  -5270  -5509  -4544  -3745  -3809  -4722  -4969    196    685  -3940  -5637  -5589    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    97  -1516  -2954    444   -813  -3262  -2481   2237  -3003    427  -2966  -2051    814  -2582   -699  -1250   1431   1966    213  -3149  -2473    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    98  -4780  -4251  -5415  -5397   4096  -5419  -2189  -4159    558  -3727  -3630  -4269  -5411  -4230  -4471    220  -4716  -4204  -1514   1462    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-    99  -2583  -3846   1253   1338   2797  -3135  -1987  -3783  -2009  -3760  -3035  -1781  -3434  -1758  -2581   1800  -2565  -3451  -3297   1080   100
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   100  -2242  -2909  -3483  -3814  -5396    405  -4134  -5231  -4529  -5429  -4518   1004   3790  -4027  -4631  -2450    426  -4023  -5572  -5326   101
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1771  -9060   -504   -894  -1115   -701  -1378      *      * 
-   101   -774  -1741   1739   -226  -2118  -1595   -658  -1779   -463  -1928   2990   -481  -1883   -316   -945   1657   -807  -1462  -2285  -1688   102
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1096  -7303   -927   -894  -1115  -3726   -113      *      * 
-   102   -213   -712  -1409  -1380  -1808  -1017  -1285  -1128  -1222  -1611  -1122  -1061  -1620  -1201  -1334   -450   3269   -797  -2112  -1780   103
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-   103   -213   -712  -1409  -1380  -1808  -1017  -1285  -1128  -1222  -1611  -1122  -1061  -1620  -1201  -1334   -450   3269   -797  -2112  -1780   104
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-   104  -1226  -2145    216   3230  -2569  -1374   -714  -2415   -601  -2474  -1903   -296  -1814   -437  -1029  -1089  -1288  -2092  -2425  -1988   105
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-   105  -2316  -1882  -2750  -2762   -108  -2323  -1111  -2026  -2287  -1730  -1620  -2381  -2654  -2246  -2141  -2539  -2395  -2070   5856    267   106
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -29  -6236  -7278   -894  -1115  -3980    -94      *      * 
-   106  -1262  -1887  -1045   -671  -2420  -1713   -441  -2141   3276  -2091  -1488   -760  -1940   -105    475  -1235  -1199  -1883  -1990  -1746   107
-     -   -149   -500    233     43   -381    398    105   -626    210   -466   -721    275    394     45     96    361    117   -369   -295   -249 
-     -  -1400   -702  -7278   -130  -3540    -58  -4657      *      * 
-   107   1122  -2816  -1394    445  -3081  -2484  -1149  -2792    422  -2808  -1921  -1144  -2576   1094  -1250   1337    932    738   1967  -2389   109
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   108    951  -2933  -5939  -5490  -2799  -5542  -4866   2319  -5302   2212  -1616  -5217  -5292  -4895  -5210  -4802  -3339    574  -4242  -4002   110
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   109  -4102  -3575  -6570  -6043   2173  -6266  -5175   1264  -5845   2349  -1074  -5950  -5613  -4920  -5498  -5571  -4001   1375  -3998  -4049   111
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   110    626  -3141  -1368   2498  -3479    -51  -1290  -3226   -868  -3169  -2256  -1230   1466    843    710  -1556  -1627  -2779  -3333  -2654   112
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   111   1062  -4255  -4191  -2978  -5221  -4113  -2172  -4565   1888  -4241  -3550  -2885   1441  -1752   3028  -3430  -3287  -4281  -4101  -3979   113
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   112  -4002  -4289  -4641  -4194  -2577    942  -2880  -5040  -2381  -4666  -4278  -3847  -4795  -3165   2563  -4037  -4069  -4755  -3070   3976   114
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   113  -1606  -3044  -1469    325  -3379     61  -1194  -3112   1222  -3049  -2137  -1206  -2656   2772   1492  -1488    322    220  -3204  -2552   115
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   114  -6456  -5625  -6449  -6292  -6874  -5588  -5409  -7592  -4707  -7041  -6767  -6169  -5973  -5488   4258  -6707  -6489  -7272  -5739  -6531   116
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   115    -23  -2669  -1508   -956  -2879  -2541  -1214    651    721  -2637  -1793    493  -2631   -805   2461    758    332   -279  -2926  -2324   117
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   116  -1714  -2957   2305   1858   1274  -2633  -1385  -2887  -1056  -2949  -2097  -1315  -2777   -972  -1559    340    533     30  -3216  -2578   118
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   117  -1547  -2997    579   -847  -3323  -2514  -1157  -3063   1083   -344  -2088  -1151   1259   1956   1656  -1428   1041  -2622  -3169  -2503   119
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   118   2524   1414   1204  -1178  -3397   -208   1674  -3109  -1131  -3139  -2263  -1446  -2829  -1082    751  -1647  -1700  -2687  -3369  -2741   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   119    143  -2930  -5668  -5095   1544  -5038  -3951  -1138  -4775   2408  -1035  -4723  -4827  -4165  -4520  -4208  -3196   1822  -3361  -3171   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   120  -1523  -2405   2067    483    212  -2613   1148     10  -1025  -2336   1168    610  -2699   -959  -1471    318    266     80  -2717    563   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   121   2484  -3057   1093    584  -3360  -2557  -1269  -3098   -883   -547  -2170  -1204  -2684   -824    518     43  -1583  -2673  -3265  -2589   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   122   1371  -1592  -3429  -2828  -1562  -3129  -1975  -1092    833    102   1699  -2576  -3189  -2265  -2536   -189    359   2037  -2044  -1686   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   123  -3737  -3222  -6326  -5901  -2734  -6092  -5462   2253  -5779   1385   2333  -5761  -5628  -5205  -5650  -5427  -3687   2356  -4454  -4359   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   124   1785  -2110  -4657  -4044  -1814  -3928  -2838   2130  -3669    720   2681  -3582    665  -3244  -3472  -3036  -2266  -1123  -2596  -2311   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   125    -88  -2941  -1382   2461  -3261  -2502  -1181  -2996    665  -2967  -2059  -1157  -2606   -730  -1260   1372    258  -2569   2410  -2490   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   126   1072   1817  -4272  -3717  -1875  -3238  -2507  -1383  -3328   1314   3825  -3108  -3457  -2951  -3144    230  -1880  -1306  -2416  -2088   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   127  -5015  -4466  -5928  -6213  -1093  -5487  -2540  -4130  -5815  -3876  -3939  -4711  -5633  -4868  -5330  -4949  -5097    -46  -1812   4785   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   128   1247  -2103  -4695  -4108  -2064  -4033  -2989    587  -3754   1585  -1162  -3668  -4026    840  -3600  -3149  -2295   2213  -2797  -2467   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   129    220  -2958  -1373   -820  -3275  -2487   2531  -3015   1369   -650  -2050  -1126  -2578   1660   1115    684    472  -2578  -3139  -2470   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   130  -6017  -5442  -6438  -6820  -7094   3856  -6214  -7992  -7066  -7505  -7295  -6571  -5976  -6877  -6575  -6361  -6362  -7330  -5948  -7085   132
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   131  -3097  -2688  -5648  -5186  -2912  -5206  -4492   1563  -4971    -79   2291  -4857  -5057  -4684  -4912  -4428   1179   2816  -4107  -3751   133
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   132  -2170  -2814  -4021  -4315  -5348  -3012  -4303  -5188  -4698  -5410  -4478    933  -3799  -4245  -4667   3145   1922  -3955  -5542  -5358   134
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   133  -2464  -2915  -5330  -5541  -4670  -3409  -4806  -2718  -5252  -4100  -3739  -4114  -4155  -4906  -5008  -2804   3806   1007  -5324  -5106   135
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   134  -4748  -4858  -5597  -5340  -6519   1295  -4619  -6696  -3659  -6374  -5836  -5038  -5360  -4465   3968  -4926  -4965  -6059  -5536  -6017   136
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   135   -221  -3167    734   1940  -3489  -2584  -1281  -3241   1886  -3177  -2263    435  -2710   -829   1858  -1554  -1627  -2791  -3339  -2653   137
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   136  -3453  -2939  -6136  -5811  -3474  -5977  -5940   2357  -5773  -2202   2609  -5636  -5688  -5667  -5913  -5353  -3441   2975  -5234  -4779   138
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   137     66  -2948   1395    412  -3268  -2450  -1109      9    557  -2963  -2037  -1086  -2543   1502    694   1427    188  -2569  -3131  -2449   139
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   138    803  -3220   2308    683  -3537    619  -1325  -3293   1067  -3231  -2319  -1233  -2743   -875   1377  -1593  -1674  -2842  -3396  -2702   140
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   139   1081  -1523  -4027  -3394    626  -3247   2297   1774  -2994   1219   -717  -2888  -3295  -2619  -2800  -2332    209    468  -1987  -1645   141
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   140  -3038  -2682  -5503  -4964    806  -4941  -3984    886  -4674   1941  -1329  -4595  -4786  -4230  -4507  -4113    268   2415  -3547  -3295   142
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   141    895  -2963  -1334   2534  -3278   -387  -1138  -3024    349   -728  -2056  -1111  -2571    919  -1227    350  -1446  -2582  -3151  -2472   143
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   142   1457  -2817    450   1794  -3079  -2491  -1160  -2787   -767   -698  -1924  -1153  -2585   -722   1346  -1407    259    233  -3038  -2394   144
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   143  -4681  -4056  -7068  -6479  -2122  -6870  -5507  -1535  -6282   2865   3042  -6612  -5841  -4989  -5733  -6264  -4516    287  -3969  -4211   145
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   144  -1826   2711  -4111  -3502   1040   1488  -2123  -1159  -3106    790   -865  -2971  -3404  -2720  -2914  -2435    199  -1084  -1928   2871   146
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   145  -2338  -3006    310  -3183  -4923   3208  -3740  -4292  -4135  -4823  -4062  -3001  -3807  -3598  -4433  -2523     88   1411  -5206  -4813   147
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -600  -9060  -1564   -894  -1115   -701  -1378      *      * 
-   146  -1612  -3147    805   1687  -3445   1812   1993  -3220   -886  -3158  -2271   -937    832   -742  -1445  -1448    698  -2763  -3335  -2598   148
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -6  -8466  -9508   -894  -1115   -131  -3522      *      * 
-   147    689  -2884    677    458  -3176  -2465   1613    747   1100  -2888  -1981  -1112  -2558   -677  -1222    -95   1489    -36  -3085  -2420   149
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -365  -9060  -2172   -894  -1115   -701  -1378      *      * 
-   148    522  -2661    551    600  -2959   1192   1868    278   -482  -2668  -1759   -867  -2318   -437   -986   1032    438  -2271  -2860  -2191   150
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1871  -8699   -465   -894  -1115  -2397   -304      *      * 
-   149   -763  -1738   -713   -355  -2499  -1537   -452  -2178   2471  -2167  -1375   -512  -1812    -65     76   1771   -796  -1752  -2275  -1799   151
-     -   -149   -500    233     43   -381    401    105   -626    210   -466   -721    275    394     45     96    359    117   -369   -295   -249 
-     -   -800  -1247  -7889   -125  -3595    -63  -4540      *      * 
-   150  -2919  -2604  -5319  -4752    804  -4690  -3546   1605  -4421   1339  -1163  -4325  -4565  -3935  -4214  -3834  -2857   2557  -3116   1241   153
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   151  -2411  -3005  -4845  -5207  -5592    414  -4778  -5521  -5378  -5732  -4808  -3932  -4038  -4853  -5125   3575  -2885  -4227  -5671  -5694   154
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   152   1130  -2965  -3329  -3056  -4857  -3054  -3053  -4579   3036  -4626  -3752  -2854   1982  -2725  -2661    147  -2508  -3728  -4738  -4384   155
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   153    957  -4719   2064    336  -5008  -3157  -2388  -4873  -2451  -4770  -4004   1051  -3614  -2025  -3187   2448  -3026  -4360  -4958  -4048   156
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   154  -1578  -2007  -2184   1192   1862  -2808  -1550  -1619  -1485   -387  -1182  -1770  -2885   1552  -1828     34   1794    473  -2394  -1948   157
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   155  -3439  -2925  -6138  -5841  -3647  -5982  -6141   2643  -5827  -2383  -2325  -5663  -5726  -5814  -6023  -5384  -3436   3179  -5468  -4919   158
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   156  -3545  -3959  -5507  -5866  -6025  -4145  -5366  -6405  -6012  -6435  -5724  -4892  -4866  -5640  -5712   3749  -4002  -5270  -5710  -5985   159
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   157    760  -2650  -1944  -1405  -3088  -2700  -1595     80  -1227  -2865  -2045   1490  -2887  -1217   2946    -33    209  -2402  -3179  -2629   160
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   158    -35  -2151  -4845  -4270  -2210  -4171  -3159   2677  -3928   1156   1469  -3817  -4154  -3577  -3771  -3297    530   1181  -2955  -2611   161
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   159    757   2909  -2038  -1480  -2186  -2751  -1490  -1776    601  -2027   1234    568  -2837  -1256  -1727    196   1887  -1602   2397  -2028   162
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   160   1295  -3170   1670    342  -3491   -364  -1286  -3244   2258  -3182  -2267  -1215  -2712   -834    705  -1556  -1630  -2794  -3345  -2657   163
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   161    778  -2957    191    411  -3279   -401  -1115  -3029   1322  -2973  -2047  -1091  -2550   2433   1279  -1364    193  -2579  -3140  -2457   164
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   162  -2755  -2498  -5126  -4532  -1957  -4410  -3317  -1107  -4159   2339   -994  -4085  -4337  -3676  -3938  -3545    463   2050   2657  -2659   165
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   163    269  -2941   2663    341  -3234  -2495  -1168    872    705   -714  -2039  -1139  -2596   1053  -1268  -1420  -1470  -2548  -3139  -2471   166
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   164  -2821  -4490   1574   2833  -4805  -3099  -2268  -4647  -2252  -4556  -3757  -1721   1205  -1892  -2940    285    888  -4144  -4741  -3875   167
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   165    652  -2837    622   2124    261   -118  -1145   -268   -748  -2832   1092    803  -2573   -703  -1246    117  -1427  -2432  -3051  -2399   168
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   166  -1967  -1773  -4312  -3682  -1597  -3540   1770    349  -3286    723   1619  -3184  -3559  -2885  -3082  -2632  -1905   2749   2516  -1896   169
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   167   1320  -2952    633    412    240    988  -1112  -3024    557  -2968  -2042    527  -2546    947   1185  -1360  -1419  -2574  -3136  -2453   170
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   168   2389  -3232  -1447   1824  -3654  -2695  -1495  -3397  -1097  -3355  -2460    953  -2875  -1057    241  -1730    485  -2943  -3530  -2859   171
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   169  -5826  -4758  -6183  -6536   3275  -5940  -2404  -4740  -6133  -4030  -4136  -4791  -5884  -4923  -5508  -5408  -5707  -4923   5467   -470   172
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   170     28  -3009  -1460   -901  -3331  -2557   1634  -3061   -713  -3013  -2105    862  -2647   1990   2491    342  -1524  -2634   2128  -2528   173
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   171  -1551  -3032    943   1651  -3350  -2494  -1175  -3103   -768  -3046  -2123   1778  -2603    788    745    976    919  -2653  -3214  -2526   174
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   172  -6456  -5625  -6449  -6292  -6874  -5588  -5409  -7592  -4707  -7041  -6767  -6169  -5973  -5488   4258  -6707  -6489  -7272  -5739  -6531   175
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   173  -1940  -2862  -2014    587  -3563  -2833  -2055  -3233  -1805   -611  -2551  -1915   2763  -1702  -2250   1912    907  -2825  -3680  -3124   176
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   174  -5799  -5010  -6724  -6813  -3635  -5931  -5844  -3283  -6751   3380  -2571  -6759  -6037  -6040  -6237  -6793  -5781  -4086  -4884  -5095   177
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   175    219  -3558    513   2532  -3981   1211  -1721  -3758  -1445  -3701  -2813  -1474  -3049  -1295  -2002    984     45  -3276  -3877  -3146   178
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   176    813  -2970   1203   1530  -3289   -275   2001  -3040   1363   -733  -2061  -1099     99   -670  -1222  -1378  -1438  -2591  -3154  -2471   179
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   177  -1484   1461  -1386    612  -3094   -199  -1144   -266    420  -2819   1100    802    262    674  -1245    911    964    -20  -3041  -2392   180
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -786  -9060  -1258   -894  -1115   -701  -1378      *      * 
-   178  -1215  -2651   -875   1494  -2992  -2103   -798  -2728   -343  -2671  -1770   1089   1881   -351   1902  -1090    623  -2291  -2833  -2170   181
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -7  -8281  -9323   -894  -1115   -340  -2251      *      * 
-   179  -5504  -4485  -6000  -6320   2726  -5865  -2101    666  -5880  -3601  -3696  -4507  -5716  -4628  -5259  -5111  -5362  -4426  -1348   4232   182
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8954  -9996   -894  -1115   -367  -2155      *      * 
-   180   1044  -2615  -5050  -5076  -4621  -2986  -4264  -4238  -4785  -4593  -3770  -3656   3244  -4356  -4589    356    357   1412  -4947  -4765   183
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   181     68  -1663  -4094  -3479   1525  -3366  -2119  -1130  -3080   -166   -848  -2968  -3411  -2704    541  -2451  -1777   1157  -1929   3560   184
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   182  -3888  -3455  -6128  -5603    723  -5629  -3882  -1567  -5284   2252  -1037  -5171  -5220  -4429  -4915  -4825  -3779   2392   2720  -2515   185
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   183    -76  -1987  -4438  -3867   3298  -3697  -2178   1403  -3462  -1669   2267  -3258  -3726  -3020  -3238  -2792  -2132  -1400   2645    924   186
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   184    -32   1675  -4162  -3533   1453  -3380  -2264    619  -3136   2139   -795  -3026  -3420  -2759  -2940  -2470    195    713  -2117  -1778   187
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   185  -6190  -5763   4216  -4766  -6970  -5284  -5417  -7840  -6088  -7337  -7158  -5081  -5786  -5547  -6273  -6158  -6354  -7397  -5940  -6654   188
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   186   3060  -2712  -5265  -5574  -5289   1910  -4688  -4867  -5319  -5312  -4410  -3803  -3815  -4782  -4973  -2374  -2586    -18  -5547  -5491   189
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   187  -2563  -2373  -4746  -4083  -2041  -4129  -3006   1926  -3297   1437  -1080  -3705  -4113  -3239   1296  -3264   2356  -1231  -2882  -2611   190
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   188  -2415  -2295  -4189  -3534  -1351  -3787   1864  -1819  -2602  -2075   1578  -3124  -3817  -2694   1147  -2891  -2339   1187  -1930   3817   191
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   189  -1834   2458  -4165    900  -1624  -3413  -2302    485  -3153   1065   1395  -3050  -3453  -2786  -2970  -2503    613   2001  -2166  -1822   192
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   190  -3175  -4158  -3206  -2431  -4887    298  -2019  -4349   3334  -4077  -3336    326    617  -1592   1006  -3049  -2979  -4032  -3997  -3738   193
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   191   -426  -2873  -6018  -5662  -3395  -5783  -5546   1942  -5579    881  -2135  -5441  -5543  -5441  -5670  -5114  -3347   2998  -4983  -4539   194
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   192  -6456  -5625  -6449  -6292  -6874  -5588  -5409  -7592  -4707  -7041  -6767  -6169  -5973  -5488   4258  -6707  -6489  -7272  -5739  -6531   195
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    277    394     45     96    359    117   -369   -294   -249 
-     -   -356  -4143  -2624   -186  -3047   -701  -1378      *      * 
-   193  -1431  -2724   1262   2023  -2971   -202  -1087  -2671   -718    645  -1839  -1050  -2501   -660    818  -1342  -1374    707  -2953  -2311   197
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8806  -9848   -894  -1115   -228  -2776      *      * 
-   194    755  -3318   1445   1870  -3638    774  -1414  -3402  -1064  -3342  -2434   1266  -2811   -970  -1597    349     50  -2945  -3512  -2802   198
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   195   -193  -3032  -1349    672  -3356   2350   2088  -3102   -789  -3053  -2137    529  -2632   -751    700  -1459    474  -2659  -3225  -2547   199
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   196  -1836  -3108  -1788  -1189    333  -2794   1200  -3101    765  -3077  -2215    914  -2868   1570   2368  -1742  -1753   1418  -3249  -2675   200
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   197    204  -2601  -5460  -5115  -3249  -4419  -4414   1436  -4883  -2438  -2164  -4492  -4679  -4624  -4815   1126  -2874   3057  -4273  -3876   201
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   198  -1597  -2134    586  -1508  -2192  -2784  -1500  -1768    509   -439   1408  -1684  -2861  -1267   1659  -1752    543   2171  -2501  -2037   202
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -126  -9060  -3610   -894  -1115   -701  -1378      *      * 
-   199  -3018  -4399    824  -1600  -5430   1268  -2756  -5362  -3088  -5282  -4596   2213  -3730  -2450  -3937   2669  -3216  -4640  -5471  -4520   203
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8938  -9980   -894  -1115   -342  -2243      *      * 
-   200  -1511   1662  -1459    551  -2991  -2521   1158    302   1839  -2731    972  -1197  -2611   2157    519  -1439  -1449   -104  -2988  -2366   204
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   201   2504   3284  -4456  -4270  -4699    -24   1521  -4421  -4085  -4664  -3794  -3397    568  -3808  -4151   1099  -2439  -3532  -4939  -4692   205
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   202  -3048   1737  -5613  -5163  -3040  -5173  -4511   1568  -4956   1257  -1921  -4827  -5051  -4723  -4923  -4399    176   2768  -4186  -3782   206
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   203  -2310  -2092  -4591  -3997  -1490  -3866   2466    294  -3601   1937   -994  -3461  -3862  -3161  -3386  -2966  -2245    870  -2189   2825   207
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   204    -71  -2874  -6045  -5708  -3512  -5841  -5724   3011  -5648   -341  -2230  -5499  -5600  -5566  -5779  -5191  -3361   2479  -5159  -4666   208
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   205   3156  -2548  -5194  -5050  -3613   -120  -4161    820  -4754  -3082  -2647  -3934  -4055  -4381  -4572  -2775  -2597    648  -4331  -4021   209
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   206  -2393  -2130  -4811  -4242  -2238  -4129  -3144   2278  -3901   1543  -1335  -3785  -4131  -3563  -3752   -423   1477   1328  -2959  -2606   210
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   207    -33  -3174  -5133  -5495  -5745   3696  -4954  -5675  -5578  -5877  -4982  -4153  -4200  -5071  -5280  -2861  -3081  -4406  -5717  -5866   211
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   208  -3439  -2925  -6139  -5841  -3647  -5984  -6142   2820  -5828  -2383  -2324  -5664  -5727  -5814  -6023  -5385  -3436   3060  -5468  -4919   212
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   209    486  -2951   1664    468  -3268  -2458  -1120  -3016   -704   -732  -2042    597  -2553   -662   1308    -92   1709  -2571  -3137  -2456   213
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   210   2081  -2097  -2088  -1524  -2149  -2780  -1504  -1734    217   -264   1122  -1694   1449  -1284    262    -99  -1522  -1569   2140  -2008   214
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   211  -3625  -5688   3556   1945  -5840  -3344  -2818  -5853  -3274  -5677  -5135  -1933  -3945  -2516  -4319     34  -3738  -5272  -5879  -4721   215
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   212  -6017  -5442  -6438  -6820  -7094   3856  -6214  -7992  -7066  -7505  -7295  -6571  -5976  -6877  -6575  -6361  -6362  -7330  -5948  -7085   216
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   213  -1489  -2958    294   -787  -3280  -2461   1478  -3028   1352  -2972  -2047  -1097  -2554   1849   1604    628    876  -2580  -3139    732   217
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   214  -4167  -4651  -5345  -3486  -5674  -4547  -2320  -4889   2733  -4463  -3836  -3253  -4451  -1903   3403  -4038  -3763  -4701  -4230  -4238   218
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   215    174  -2972   1155   2496  -3288  -2471  -1139  -3037   -725  -2986  -2064  -1107  -2570    919    500  -1388    186    148  -3158  -2476   219
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   216  -3271  -2817  -5867  -5449  -3149  -5536  -5010   2945  -5237     74  -1953  -5182  -5333  -5051    643  -4813  -3247   2373  -4545  -4164   220
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   217  -4282  -3703  -6787  -6291  -2347  -6604  -5599    515  -6147   3055  -1106  -6315  -5804  -5125  -5777  -5993  -4180    674  -4185  -4326   221
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   218   1311  -2718  -5124  -5471  -5427   3337  -4700  -5256  -5342  -5513  -4542  -3772  -3804  -4775  -5004    198  -2584  -3931  -5644  -5611   222
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   219  -1711   1851  -4058  -3423   1916  -3263  -2135   1924  -3019    921   1596  -2909  -3309  -2639  -2819  -2349    104    463  -1994   1207   223
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   220   -179  -2955    981   1901  -3272    162  -1122  -3020    717  -2969   1078  -1096  -2555    854  -1213  -1371  -1429  -2575   3506  -2459   224
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   221     47  -1805    509  -3528  -1853  -3559  -2486   2118  -3199  -1615   1544  -3140  -3605  -2880  -3099    157  -1925   2356  -2416  -2061   225
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   222   1340  -2871  -1461    977  -3190   1901  -1287  -2899   -908  -2925   1555  -1257  -2682   1499  -1400  -1508    261  -2510  -3160  -2520   226
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2990  -9060   -197   -894  -1115   -701  -1378      *      * 
-   223  -1055  -1986    334   3108  -2384  -1246   -556  -2196   -420  -2274  -1694   -157  -1675   -273   -843   -925  -1111  -1883  -2270  -1812   227
-     -   -149   -500    233     43   -381    400    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1265   -794  -7143   -148  -3354    -58  -4676      *      * 
-   224  -1632  -3080   2206   -880  -3402    904  -1264  -3149   -879  -3108  -2197  -1194    473   1515  -1394    737    326  -2709  -3289   1170   229
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   225     45  -2821  -2312  -1836  -3975   1868  -2092  -3719  -1738  -3745  -2833    838  -3104  -1682   1521   1619   1066  -3097  -3932  -3354   230
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   226  -6234  -5752  -4492   3963  -6966  -5320  -5452  -7805  -6004  -7307  -7131  -5183  -5814  -5594  -6125  -6228  -6392  -7386  -5927  -6666   231
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   227     26  -3851   1762  -1843  -5136    833  -2780  -4992  -2900  -4970  -4170    917  -3680  -2449  -3566   2702  -2914  -4248  -5152  -4374   232
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   228   1602  -2962  -1341   1768    116    538  -1133  -3025    761  -2975  -2054    813  -2568   -675    506  -1386  -1443  -2583  -3146  -2469   233
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   229   1647  -2954    988   1167  -3268  -2464  -1130     16   1577  -2967  -2046  -1102  -2561   -673  -1223    123     81  -2572  -3142  -2462   234
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   230   1106  -2566  -3542  -3189   3036     22  -3085  -3512  -3084  -3756  -2962   1491  -3492  -2904  -3336   1257    253  -2981  -4131  -3752   235
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   231  -7240  -5775  -6720  -7095  -5539  -5783  -5867  -7902  -7198  -7201  -7237  -6973  -6208  -7031  -6643  -7679  -7381  -7739   6306  -5200   236
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   232  -1538  -2970    286   -847  -3286  -2510  -1157  -3021    562   1113  -2063  -1150  -2601   1155   2066    251    871  -2590  -3150  -2487   237
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   233   1165  -3136    490   1178  -3466   -372  -1290  -3220   -904  -3167  -2253  -1208  -2702   -840   1681  -1540   2040  -2769  -3340  -2648   238
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   234  -4176  -3645  -6528  -6068   3314  -6203  -4584  -1293  -5845   1125  -1157  -5787  -5613  -4892  -5473  -5506  -4078   2350  -3555  -3098   239
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   235  -4654  -4043  -7016  -6412   2162  -6782  -5348  -1583  -6200   2783   1560  -6498  -5789  -4924  -5653  -6141  -4484     74  -3888  -4076   240
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   236   -177  -2938   1404   1055  -3254  -2453  -1112  -3001   -695   -297  -2029   1275  -2546    788   1079  -1360    973    -81  -3125  -2445   241
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   237  -1556  -3034   2237    995  -3353   -379  -1178  -3105    666  -3048  -2126  -1132  -2607   -721    499   1494  -1497  -2655  -3216    655   242
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   238  -4912  -4242  -7000  -6575    723  -6760  -4754  -1798  -6363   3230  -1052  -6393  -5888  -5036  -5771  -6280  -4745  -2676  -3524  -3101   243
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   239  -1840  -2818  -1958  -1352  -3025  -2860  -1440    391   2407   -445  -1952    896  -2930   1033   1237  -1822  -1759    768  -3041  -2525   244
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   240   1600  -2953  -1327    353  -3271    584  -1121  -3019    717   -732  -2044   1958  -2555    788  -1210   -100  -1428  -2574  -3139  -2458   245
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   241  -4327  -4751  -4973  -3682  -5703  -4618  -2649  -5180  -1215  -4760  -4151  -3494  -4634   1092   4037  -4229  -4011  -4960  -4452  -4452   246
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   242  -6017  -5442  -6438  -6820  -7094   3856  -6214  -7992  -7066  -7505  -7295  -6571  -5976  -6877  -6575  -6361  -6362  -7330  -5948  -7085   247
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   243  -3602   1754  -6170  -5725  -2707  -5846  -5151    921  -5563   2767  -1492  -5520  -5474  -5035  -5431  -5139  -3555   1280  -4309  -4166   248
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   244   -189   1318  -1392   -840    259   -401  -1149  -2910   1680  -2895  -1993  -1142  -2583   2806    698     52  -1445  -2500  -3094  -2437   249
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   245  -2468  -3959   1839  -1325  -4369   2668  -1988  -4144  -1705  -4068  -3224  -1660  -3315   1052    712  -2291    604  -3671  -4229  -3494   250
-     -   -149   -500    233     43   -381    401    105   -626    210   -466   -721    275    394     45     96    359    117   -369   -295   -249 
-     -   -139  -3460 -10102   -125  -3595   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   248  -4743  -4100  -7090  -6512   1922  -6918  -5350   1209  -6317   2845   -892  -6609  -5859  -4989  -5748  -6317  -4569  -2404  -3868  -3940   254
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   249   1379  -2811  -5886  -5491  -3226  -5552  -5118    905  -5353    790  -2019  -5220  -5362  -5151  -5379  -4838  -3249   2940  -4644  -4240   255
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   250  -3391  -2893  -6090  -5783  -3636  -5878  -5983   2951  -5750  -2403  -2323  -5576  -5660  -5726  -5927  -5257    162   2773  -5389  -4846   256
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   251    185   2088  -5069  -5033  -4261    455  -4111  -3890  -4701  -4221  -3437  -3633  -3724  -4267  -4487   2539    617   1659  -4629  -4413   257
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   252  -6190  -5763   4216  -4766  -6970  -5284  -5417  -7840  -6088  -7337  -7158  -5081  -5786  -5547  -6273  -6158  -6354  -7397  -5940  -6654   258
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   254   1140  -2883  -4904  -4526   1155  -4379   4331  -2175  -4123   1106  -1736  -3846  -4442  -3647  -3927  -3541  -3051  -2300  -1964  -1014   260
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   256  -6017  -5442  -6438  -6820  -7094   3856  -6214  -7992  -7066  -7505  -7295  -6571  -5976  -6877  -6575  -6361  -6362  -7330  -5948  -7085   262
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   257  -4935  -4253  -6936  -6562   2358  -6707  -4424  -1858  -6335   2975  -1113  -6215  -5881  -5013  -5742  -6193  -4768  -2728  -3297  -2696   263
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   258  -1541  -2938    632    573  -3235  -2513  -1171  -2963   1099  -2939  -2037  -1159   1613   -722    265  -1433  -1478   1877   2408  -2473   264
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   269   1130  -2819  -1417   -867  -3102   -400  -1170   -118    655  -2829  -1942  -1164   1296   -731    739   1112   1042  -2426  -3055  -2410   275
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   271  -6285  -5597  -5689  -5978  -6614  -5492  -5717  -7713  -5849  -7170  -7005  -6029  -5959   4616  -5690  -6516  -6489  -7316  -5775  -6377   277
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   272  -3513  -3999  -5101  -4296  -5675  -4110  -3355  -5380  -2095  -5173  -4522  -3862  -4547  -3032   3854  -3654   1769  -4776  -4890  -4917   278
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   273  -6037   5865  -6665  -7041  -6926  -5480  -6239  -7746  -7138  -7370  -7198  -6703  -5994  -6978  -6596  -6405  -6384  -7193  -5907  -6905   279
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   284   1272  -2129  -2014  -1454   1308  -2750   2881  -1778   1131   -306  -1295  -1639  -2828    529  -1698  -1712    198  -1605  -2487    955   290
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   285   1390  -1923  -4538  -3939  -1951  -3817  -2755    583  -3571    583   1844  -3462  -3831  -3212  -3399  -2925   1133   2180  -2588  -2242   291
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   286  -2142  -3202  -2172  -1789  -4055  -2983   1246  -3749    631  -3733  -2883  -1973   3257  -1593  -1714   1354    347  -3257  -3885  -3351   292
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   287  -2288  -3544  -2279    522  -3974  -3167  -1583  -3620   2575  -3488  -2647  -1813  -3216  -1142   2383   -231  -2170  -3243   2046    768   293
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   288    175  -2960    190   -785  -3282   -400  -1118  -3032   2583  -2976  -2050  -1095    177    922    697    350  -1428  -2583  -3143  -2461   294
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   289  -1483  -2913   1661    463  -3216  -2461   2169  -2954    349    558  -2007    523  -2555   -669  -1216    666  -1422   -238  -3107    858   295
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   290   1392  -2912  -1452   -898  -3212   -109   1686  -2929   -748  -2918  -2024  -1194  -2629   1150   1736    684  -1493  -2527   3037  -2474   296
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     99    359    117   -369   -294   -249 
-     -   -110  -3790 -10102   -152  -3324   -701  -1378      *      * 
-   291    175  -2971   1627   1121  -3291    164  -1126  -3043   1564  -2987  -2061  -1097    958   -667    368     -5  -1436  -2593  -3154  -2470   298
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   292   -176  -2905   1123    625  -3206  -2460  -1120  -2943    573  -2912   1843  -1102  -2552   -667    742    685   1018     94   1960  -2429   299
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   293    218   1929  -5489  -5022    528  -4994  -4285   2144  -4791  -2162  -1899  -4655  -4910  -4554  -4742  -4202  -2914   2872  -4014  -3602   300
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   294   1454  -2003  -2201  -1637  -2038  -2814  -1553  -1614   1176    576   1142  -1779  -2889  -1381   1093     61    547    100  -2389  -1946   301
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   295   2115  -2945    299   1138  -3258  -2466  -1132  -3002   -720  -2959  -2040  -1106     99    919  -1227   -102    258    -44  -3137  -2459   302
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   296   1688  -3001   1943   1064  -3283  -2542  -1241  -3012   -858   -626    969  -1188  -2660   1754  -1367  -1495  -1548  -2603  -3206  -2537   303
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   297  -3187  -2879  -5539  -4916   1684  -4877  -3678    299  -4562   2361   1679  -4534  -4654  -3920  -4275  -4014  -3098    898  -3110   1308   304
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   298  -3690  -4428  -4324  -2982  -5291  -4237   1533  -4595   2724  -4233  -3552    879  -4166   1214   2607  -3557  -3369  -4358  -4071  -3965   305
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   299   1302  -2863    624    342  -3148   -279  -1137  -2872   -734  -2865    948  -1124    295   -690  -1234    722   1469  -2466   2062  -2413   306
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   300  -3599  -3083  -6235  -5859  -3032  -6041  -5666   3377  -5777    -18   1821  -5703  -5657  -5402  -5768  -5396  -3568   1611  -4766  -4541   307
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   301  -5675  -4621  -6102  -6442   3182  -5974  -2179    559  -5998  -3878  -3962  -4596  -5829  -4731  -5367  -5219  -5527  -4709   2855   3733   308
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   302    491  -2934   1164   -782  -3249  -2453  -1112  -2995   1068  -2947   1565    666  -2546   -655   1712    -99    355  -2553  -3121   1064   309
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   303   2839  -2998  -2331  -1740    446  -3129   1226  -2868  -1062  -2957  -2202  -1919  -3222   1512    613  -2159  -2077  -2619  -3065  -2478   310
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   304    968  -2927  -1547    551  -3401  -2565  -1353  -3134   -943  -3116  -2210  -1315   2294   -909   1215    -11   1587  -2681  -3306  -2655   311
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   305  -3168  -4991   3167    332  -5223  -3214  -2504  -5117  -2658  -4998  -4275    943  -3709  -2156  -3454    876   1526  -4596  -5190  -4224   312
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   306   2091  -1858  -3646  -3037  -1836  -3283  -2214    348  -2524   1127  -1026  -2775   1269  -2424   1426  -2379  -1844  -1244  -2353  -2008   313
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   307   1038  -4624   1365   2974  -4891  -3126  -2311  -4742  -2328  -4644  -3860    598  -3558  -1940  -3037  -2642    302  -4242  -4830  -3943   314
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   308   1044  -2848    682   2207  -3112  -2501   1150  -2824   -788    127   1464  -1161  -2600   -739  -1286     49  -1457  -2439  -3067  -2419   315
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   309   2625  -2231  -4781  -4376  -2729   -173  -3346    791  -4043  -2390  -1864  -3620  -3879  -3693  -3892  -2728    196   1841  -3342  -3004   316
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   310   1204  -2593  -1591    385  -2771  -2587   1145  -2425    492   -611  -1723  -1305  -2673   -868   1979  -1515  -1478    909  -2865   1168   317
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   311   2139  -2917  -1433   1373  -3210  -2526  -1173  -2929    442   -518  -2017  -1176  -2616   1053    518  -1442  -1480   -214  -3110  -2463   318
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   312   1920  -2910    431   -892  -3203  -2531  -1199  -2920   -777   -543  -2024  -1191  -2631   1926   1819  -1458     76  -2520  -3123  -2475   319
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   313  -2951  -2728  -4710  -4199   1291  -4275  -2133  -2277    949   2006  -1922  -3559  -4282  -3286    651  -3386  -2875  -2232   3032   2164   320
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   314    -41  -4561   2569   2341  -4800  -3101  -2239  -4643   1350  -4543  -3744    596  -3510  -1860  -2893  -2579  -2848  -4152  -4724  -3854   321
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   315   1882  -2961  -1332    489  -3281   -400   1279  -3030   -700  -2976  -2051    813  -2558    698   1787  -1373     81  -2583  -3144  -2463   322
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   316      9  -1833  -4387  -3766   3403  -3624  -2483    367  -3375    -87   -858  -3266  -3640  -2975  -3173  -2719  -1976   1439   2266  -1928   323
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   317    691  -1725     41    -68  -1713  -3007  -1804   1792  -2063   1341   -917  -2230  -3071  -1876     37  -2030    105    584  -2157  -1771   324
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   318    993  -3025   1500   1499  -3343    600   1287  -3095   -768  -3040  -2118  -1128  -2602   -718    693  -1425   1026  -2646  -3210  -2522   325
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -126  -9060  -3610   -894  -1115   -701  -1378      *      * 
-   319     65  -2642    353   -805  -2874   -188  -1089    447   2120   -430   1057  -1097  -2509   -665    323     72    181  -2216  -2882  -2258   326
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8938  -9980   -894  -1115   -342  -2243      *      * 
-   320  -2722  -2673  -3886    288  -1085  -3990   1903  -2256  -3130   1236  -1885  -3135    214  -2866  -3189  -3062  -2655  -2181   4410   2498   327
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   321   1252   1830  -3099  -2522  -1740   1186  -1936    316  -2287  -1623   -955  -2396  -3140  -2075    564     -2    288  -1183   3699  -1821   328
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   322    797   1476   1065   -960  -2838   1048  -1216  -2507   1719   -275  -1763  -1241  -2629   -811    224  -1462  -1446      6  -2902  -2304   329
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -2508  -9060   -282   -894  -1115   -701  -1378      *      * 
-   323   -965  -2497   2482    465  -2736  -1251   -397  -2602   -317  -2546  -1785    105  -1660   2657   -920   -740   -984  -2159  -2700  -1901   330
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -23  -6574  -7616   -894  -1115  -1798   -489      *      * 
-   324   -812  -1806  -1038   -655  -2673  -1721   -942  -2377   -599  -2450  -1592   -830   2434   1773  -1026   1054   1291  -1886  -2694  -2126   331
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11  -7673  -8715   -894  -1115    -79  -4238      *      * 
-   325  -2060  -3415  -1944    363  -3828  -2957  -1465  -3505   3039  -3386  -2513  -1595    375    662    664    565  -1964  -3093  -3474  -2921   332
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   326  -5671  -4620  -6098  -6435   2174  -5972   2789  -4549  -5990    463  -3957  -4595  -5827  -4728  -5362  -5217  -5523  -4709  -1427   3986   333
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   327  -2528  -3155  -4192  -4061  -5376  -3318  -3604  -5153  -2753  -5167  -4351  -3464   3691  -3352   1704    838  -2901  -4162  -5110  -4978   334
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   328   2087  -4085  -3851  -2825  -5062  -3942  -2164  -4470   2938  -4191  -3476  -2775    255  -1745    826  -3221  -3126  -4140  -4086  -3913   335
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   329   1375  -2821  -5923  -5542  -3315  -5627  -5261   2226  -5424    644  -2089  -5288  -5424  -5258  -5479  -4928  -3273   2454  -4778  -4347   336
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   330   2028   2629  -2639    -76  -2659   -318  -2054  -2253  -1980  -2517   1651  -2155  -3121  -1861  -2313   -156   1861  -2014  -2983  -2546   337
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   331    610  -2964   1846   1612  -3285  -2458  -1121  -3035   -704  -2980  -2054  -1093    -43    794    528    715     81  -2586  -3148  -2464   338
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   332  -1671  -1515  -3900  -3272  -1465  -3205   1338    414  -2892    977   2089  -2813  -3256  -2537  -2732   1734    621   -927   3178  -1623   339
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   333    -73  -2580  -5187  -4562  -1844  -4482  -3325  -1305  -4190   2374   2209  -4139  -4353  -3639  -3938  -3602  -2765    337   3777  -2697   340
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   334  -2947  -4520   2219   2474  -4863  -3250  -2209  -4617    704  -4466  -3690  -1853  -3603  -1820   2091  -2705  -2917  -4171  -4564  -3860   341
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   335  -1521  -2998    992   1858  -3318  -2477  -1147  -3070    757  -3013  -2088   1456  -2579   -689   1108    147   1060  -2620  -3180  -2495   342
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -126  -9060  -3610   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8938  -9980   -894  -1115   -342  -2243      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -95  -9060  -4011   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -8969 -10011   -894  -1115   -391  -2074      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   350  -1849  -1893  -3209  -2688  -1895  -3209   3852   2381  -2291  -1769  -1130  -2555  -3316    940  -2376   -174  -1810    245  -2361  -1969   357
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   351  -4562  -4682  -5392  -4078  -2458  -4888   2534  -4913  -1611  -4421  -4040  -3718  -4859  -2583   2676  -4422  -4253  -4820   5218  -1910   358
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   354  -3559  -3099  -6101  -5638  -2636  -5729  -4971   2890  -5446   2003  -1438  -5407    425  -4911  -5296  -5001  -3510    494  -4182  -4039   361
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   355  -3611   1980  -4619  -3277  -2982  -4320  -2146  -3854   1327  -3731  -3141  -3083  -4257  -1952   2558  -3616  -3347  -3718   4078   2584   362
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   356  -2161  -2772  -5022  -5352  -5397  -3037  -4669  -5247  -5230  -5506  -4560  -3787  -3845  -4737  -4938   2841   2898  -3964  -5601  -5536   363
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   357  -2613  -3238  -3712  -4060  -5434  -3348  -4322  -5463  -4614  -5647  -4822   1441  -4105  -4269  -4667  -2820   3832  -4339  -5517  -5286   364
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   358  -5665  -5376  -5183  -5561  -6544  -5250  -5658  -7631  -6269  -7224  -6960   4442  -5783  -6000  -6149  -5858  -5975  -6999  -5794  -6306   365
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   360  -4220  -3710  -6498  -5975  -2209  -6242  -5046   3238  -5548   1857  -1012  -5899  -5595    613  -5230  -5564  -4109  -1851  -3915  -3973   367
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   361  -6234  -5752  -4492   3963  -6966  -5320  -5452  -7805  -6004  -7307  -7131  -5183  -5814  -5594  -6125  -6228  -6392  -7386  -5927  -6666   368
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   379  -3228  -4669    646  -1698  -5645    -76  -2898  -5599  -3283  -5504  -4852   3622  -3881  -2597  -4183   1673  -3426  -4877  -5695  -4700   386
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   382   2099  -2699  -5291  -5585  -5377  -2981  -4689  -5186  -5302  -5452  -4487  -3784  -3793  -4766  -4962   2670   1642  -3894  -5601  -5564   389
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   383   1979   2823  -4425  -3811   1673  -3672  -2582   1251  -3429    639   -961  -3320  -3693  -3052  -3241  -2773  -1996    344  -2411  -2075   390
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   384    251  -1584  -3493    178  -1546  -3150  -1993   1077  -2591   2110   1386    279  -3205  -2308  -2570  -2211    210   -990  -2035  -1679   391
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   385  -3870  -4472  -4813  -3225  -5411    312  -2197  -4667   1851  -4296   1759  -3054  -4285  -1778   3435  -3754  -3524  -4454  -4120  -4066   392
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   386  -3192  -2885  -5534  -4911  -1906  -4880  -3687    409  -4556   2740   1906  -4535  -4655  -3917  -4272  -4016    299  -1823  -3120   1243   393
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   387   1282  -2477  -5273  -4732    995  -4679  -3735   1785  -4431   1217  -1425  -4329  -4592  -4060  -4287  -3837  -2762   2048  -3421  -3107   394
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   388  -1667  -1573  -3564  -2957   1037   1806  -1995  -1079  -2641  -1426   -774  -2648  -3214  -2347    298    -38    108    555   3227   1841   395
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   389   2458  -2321  -2879  -2375  -2800  -2922  -2238  -2382    590    955  -1929  -2347  -3242  -2068  -2391   -173   1244  -2134  -3124  -2710   396
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   390   -267  -3026  -5985  -5602  -2807  -5286  -4972   -740  -5399   2249  -1618  -5207  -5225  -4940  -5271  -4591  -3395   2690  -4312  -4117   397
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   391    -12  -1989  -4576  -3959    956  -3833  -2730    861  -3579   2470   -918  -3481  -3827  -3171  -3380  -2936    347    286  -2513  -2205   398
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   392   1617  -2123  -2022   1248  -2183  -2754  -1478     25  -1329  -2020   2101    417  -2833  -1241   1168  -1717  -1508    822  -2493  -2022   399
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   393  -3512  -5537   1973   2858  -5673  -3311  -2729  -5646  -3096  -5486  -4883   1488  -3883  -2413  -4061   1102  -3602  -5091  -5688  -4583   400
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -334  -9060  -2287   -894  -1115   -701  -1378      *      * 
-   394   1444  -1935  -1729  -1170  -2007    346  -1213  -1601    481   1140   1329  -1366  -2575    967  -1421  -1453    581  -1419  -2296  -1816   401
-     -   -149   -500    235     43   -381    400    105   -627    212   -466   -721    275    396     45     95    359    117   -370   -295   -250 
-     -  -3895  -3423   -252  -1899   -450   -720  -1347      *      * 
-   395   1580   -771  -2427  -2046  -1516  -1589  -1577   -294  -1826  -1212   -636  -1595  -2072  -1614  -1923   -831   2045   1825  -2033  -1679   406
-     -   -149   -500    233     43   -381    400    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -512  -1762  -8111   -148  -3354   -397  -2055      *      * 
-   396     72  -3145   1441    892  -3440  -2471   3907  -3196   -912  -3150  -2254  -1101  -2646   1132  -1445  -1519  -1613     -2  -3333  -2626   408
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -5  -8798  -9840   -894  -1115   -223  -2801      *      * 
-   397    -91  -3014   2429   1067  -3332  -2488  -1164  -3084    754  -3029  -2106  -1122  -2593   1106  -1266  -1416   1039  -2635  -3198   1017   409
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   398  -1584  -3040  -1368   2456  -3360  -2530  -1196    274   1171  -3050  -2134   1541  -2634    787  -1247  -1463    576  -2663  -3217  -2544   410
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   399  -4959  -4407  -5952  -6252   1311  -5472  -2295  -4539  -5819  -3921  -3960  -4544  -5581  -4721  -5272    231  -5034  -4610   5918   -375   411
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   400     72  -2139  -2065  -1499  -2198  -2780  -1493    967   1141   -442   2927  -1676  -2857   1806    688  -1747    202  -1614  -2503  -2038   412
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   401    550  -2810  -1401   1077  -3072   -274  -1154  -2781   -759  -2801  -1916  -1151  -2581   1045   1894  -1402    330   1143  -3031    653   413
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -4  -9060 -10102   -894  -1115   -701  -1378      *      * 
-   402   1118  -2736  -1536   -986  -3021    714  -1256    380    681  -2768  -1908  -1266  -2657   -836    517   1859     93  -2354  -3031  -2419   414
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *      *      0 
-//
-HMMER2.0  [2.3.2]
-NAME  Retrotrans_gag
-ACC   PF03732.9
-DESC  Retrotransposon gag protein
-LENG  100
-ALPH  Amino
-RF    no
-CS    no
-MAP   yes
-COM   hmmbuild -f -F HMM_fs.ann SEED.ann
-COM   hmmcalibrate --seed 0 HMM_fs.ann
-NSEQ  57
-DATE  Thu Apr 24 22:41:08 2008
-CKSUM 9950
-GA    14.8000 14.8000;
-TC    14.8000 14.8000;
-NC    14.7000 14.7000;
-XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
-NULT      -4  -8455
-NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
-EVD    -8.963948   0.670256
-HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
-         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
-          -32      *  -5492
-     1    115    130    902   -860  -4533   -379    356   -755   1837  -2221   -552    507  -3807    433   1378    319  -1096  -1449  -4396  -3713     1
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10630 -11672   -894  -1115   -701  -1378  -1032  -7629 
-     2   -665  -2831  -5338  -4703   1865  -4549    -20   1401   -371   1581   1163  -4192  -1012  -3925  -1052   -890  -2943    380  -3288    807     2
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10630 -11672   -894  -1115   -701  -1378  -7662  -7622 
-     3   2308  -3126  -5706  -5093   2778  -4949  -3863    656  -1835  -1619  -2343  -4596  -4982  -4346  -4525  -4047   -592   1118  -3715  -3367     3
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -58 -10630  -4888   -894  -1115   -701  -1378  -7662  -7615 
-     4    661  -2817  -1135  -4417   -446  -4466   1484   -583  -4067  -1290  -2018  -4025   1174  -3738  -3958   1364   1284   1739  -3271  -2922     4
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10581 -11623   -894  -1115  -1706   -528  -7662  -7607 
-     5  -2953    278  -5177    584   1348  -1840   2687     66  -1695    -35    919  -1124  -4539  -3817  -4014    552   1112    555    347   -586     5
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10581 -11623   -894  -1115  -1706   -528  -7662  -7600 
-     6    461   1338  -2607   -219   1498  -1694   2460  -4045  -1192   -158   -175    496  -3795    992   -879    789   -224  -3653  -4272    359     6
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10581 -11623   -894  -1115  -1706   -528  -7662  -7592 
-     7   -754    226  -7403  -6789   1674  -6816  -5623  -2827  -6468   2883    216  -6493  -6447  -5695  -6136  -5990  -4931    118  -4847  -4810     7
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -45 -10581  -5324   -894  -1115  -1706   -528  -7662  -7585 
-     8     88   1210    766   1181  -1047   -457  -2298   -336   -507  -2410  -3224   -930  -3733    646   1227    819    751  -3756  -4319   -376     8
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10545 -11587   -894  -1115  -2147   -369  -7662  -7577 
-     9  -5069  -7158   2057   -644  -7304   3222  -4254  -7324  -4736  -7143  -6616   -640  -5376  -3954  -5809   -360  -5187  -6736  -7352  -6172     9
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10545 -11587   -894  -1115  -2147   -369  -7662  -7570 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10545 -11587   -894  -1115  -2147   -369  -7662  -7562 
-    11   3494  -4169  -1659  -6409  -6668  -4439  -5943  -1063  -6514  -6709  -5789  -5102   -864  -5978  -6309   -695  -1441  -5277  -6913  -6800    11
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10545 -11587   -894  -1115   -220  -2824  -7662  -7555 
-    12   1111  -4131  -2767  -2208  -4396  -3834   2278  -4094    454   1077  -3239  -2499  -1530    950   1552    514  -2775   -508  -4342  -3716    12
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10630 -11673   -894  -1115   -701  -1378  -7662  -7547 
-    13     -1  -4206  -1338   -522   -846  -3716   1576   -593   -878   -505   -402   1146   -923   1177   -303   1148   1672  -3827  -4392  -3711    13
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7539 
-    14  -3699     76  -5820  -5029  -3064  -5087    156  -1421  -1080  -1241  -2753  -4548   -954  -4009  -3623  -4227  -3629  -3019   5988  -2984    14
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7531 
-    15    517  -2837  -5338   -744   1993  -4554   1046  -1035  -2393    421  -2039  -4194  -4604  -3927  -4107  -3638  -2949   -195   4379   2003    15
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7524 
-    16  -2740  -4213   1045     79  -1111  -1329   1805  -1523   1184   -723   -216   -650  -3807   1010   1131    881    618  -3835  -4396  -3714    16
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7516 
-    17    -31    263  -2594   -220  -4517   -800    305  -1440  -1959  -4215   -355   1460    392   1478    871   1698    -32  -3820    718  -3709    17
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7508 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7500 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7492 
-    20   1382  -4213    231     70  -4534   -556   -861  -4285   -143  -1350  -3302  -2349   1371   1835    567    298    -27  -2374  -4397  -3714    20
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7484 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -     -9 -10631 -11673   -894  -1115   -701  -1378  -7662  -7476 
-    22  -1161    130    249   -287  -4531   -129    -74  -1803   -692  -1851   -572   1375  -3808    779    966   1719     41  -3833   1605   -555    22
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -10632 -11674   -894  -1115   -701  -1378  -7662  -7469 
-    23  -1255  -3374   -429    118   -950  -1375  -2794   2287  -1099   -218   -410  -2980    930    719    205  -3031    207    366    225  -3286    23
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -10 -10631 -11673   -894  -1115   -701  -1378  -7662  -7459 
-    24  -1596  -4202   1663   -735     74    151  -2376   -912   -144  -4216  -3292   1107   -606   -352    493   -608    127    306   1138   1656    24
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -546 -10631  -1694   -894  -1115   -701  -1378  -7662  -7451 
-    25   1299  -3748    321   -802  -4068   -119  -1912  -3817     54    -42  -2838   1286    236    -78    343   -755   -332    425  -3932    -86    25
-     -   -147   -499    238     41   -387    397    109   -626    207   -471   -714    277    393     41    102    359    113   -359   -304   -243 
-     -  -2203   -768  -2396  -1906   -448  -4065    -89  -7662  -7443 
-    26   -789  -2221   -410  -1199   1769   -983  -2476   1323  -2902   -862    735  -3002   1402  -2670     36    869  -2162    844  -2660  -2291    38
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -11  -9790 -10832   -894  -1115  -3721   -114  -7662  -7435 
-    27  -2061  -3515   1150    682    537   -669   1808    756    283  -3528    665  -1676  -3130    996    257    478   -251   -366  -3703  -3025    39
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13 -10635 -11677   -894  -1115   -701  -1378  -7662  -6931 
-    78   1458   2881  -5341  -1659  -2785  -1742  -3421    859  -4302   1305  -2034  -4193  -4600  -3927  -4105   -302  -1064   1261  -3289   -671    91
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -13 -10635 -11677   -894  -1115   -701  -1378  -7662  -6919 
-    79   -111  -4213   1400  -1198  -4534    574   -184  -4285  -1044  -4229    -17    670   2330    255   1041   -355  -1316  -1597  -4397  -3714    92
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -   -727 -10635  -1369   -894  -1115   -701  -1378  -7662  -6907 
-    80    -24  -3601   1223   1026  -3919  -1082   3325   -562  -1350  -3615  -2691    572  -3203  -1310   1689  -2016   -593  -3221    428  -3105    93
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1090  -9922   -941   -894  -1115  -4366    -72  -7662  -6895 
-    81    -43  -1979  -1832   1422  -2026  -2587   3254    443  -1161    -77  -1146    470  -2668  -1070  -1545  -1552  -1350  -1455  -2334   1889    94
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -8849  -9891   -894  -1115  -4290    -76  -7662  -6883 
-    82  -2065  -2715  -3193  -3344  -4568   2786  -3557  -4341  -3739    627  -3740    816  -3599  -3420  -3926   1665  -2451  -3518  -4814  -4449    95
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -  -1141  -8934   -899   -894  -1115  -1801   -488  -7662  -6870 
-    83   -117   1451   1402  -1913  -1812   1127  -1649   -216    359    103   1502  -1972  -2949  -1595     36  -1879   -149    597  -2219  -1809    96
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -17  -9032 -10075   -894  -1115  -2770   -229  -7662  -6858 
-    84  -1778  -2312  -2256  -1697  -2365    843  -1698   -482    -69  -1042   1180    109   1019   1031  -1942    426  -1717   1891  -2682  -2216    97
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16  -9356 -10398   -894  -1115    -30  -5596  -7662  -6845 
-    85  -1774  -2866  -5047    734   1505  -4506  -3361    499  -2056     94   2285    648  -4558  -3763   1263  -1072  -1378    659   2576  -2969    98
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14 -10635 -11678   -894  -1115   -701  -1378  -7662  -6833 
-    86  -1611  -4222   1900    445  -4543     66    212  -4294   -925  -4238  -3312    267    713  -1920  -1096   1234   1814  -3844  -4406  -3722    99
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14 -10636 -11678   -894  -1115   -701  -1378  -7662  -6820 
-    87  -2742    690   2211   2243  -4535  -1389    258  -4286    767   -756  -3304   -356   -149   -624  -2462   -441  -2681  -3836  -4398   -892   100
-     -   -144   -447    233     42   -388    398     98   -622    213   -468   -721    272    389     49     94    359    117   -370   -302   -247 
-     -   -192  -3113 -11678  -3332   -151   -701  -1378  -7662  -6807 
-    88   1120  -4213   1182   1955  -4534  -1552    736  -4285    152  -4229  -3303  -2349    145   1809  -2461  -1096   -420  -1667    452  -3714   120
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -14 -10636 -11678   -894  -1115   -701  -1378  -7662  -6794 
-    89   1703  -4122    637    504  -1403  -3740  -2403   -562   -196  -4121    730  -2392  -3832    -61   -919   1300   -327   -410  -4331   1124   121
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10637 -11679   -894  -1115   -701  -1378  -7662  -6782 
-    90    823  -2939  -4598  -2104   -595  -1044  -3250    565   1482   1664    402  -3810  -4481   1025   -704  -3471  -1639   -179  -3382  -3017   122
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10636 -11678   -894  -1115   -701  -1378  -7662  -6768 
-    91  -1419  -2874  -4996   -166  -2834  -4498  -3350   2192  -4047    893   2115  -1277  -4552    898   -425  -1951  -2931   1569  -3326  -2975   123
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10636 -11678   -894  -1115   -701  -1378  -7662  -6755 
-    92    -76  -4209   -341   1004   -950   -235   1846  -4278  -1226  -1838   -551   -151  -3808   -565   1304   1164    477     53  -4394   -721   124
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -35 -10636  -6161   -894  -1115   -701  -1378  -7662  -6741 
-    93   1500  -3036  -4100  -3522   -848  -4290  -3083   -269   1297  -1148   1015    344  -4355   -811   1917  -3310    743    248  -3462  -3074   125
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -82 -10616  -4462   -894  -1115  -1200   -824  -7662  -6728 
-    94   -232    623  -5382  -4748   3758  -4590  -3444   -657  -4344    426     -2  -4233  -4630  -3956  -1660  -3676  -2979  -2255  -3285   1780   126
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10549 -11591   -894  -1115  -2164   -364  -7662  -6714 
-    95  -2923  -2753  -5240  -4606   -782  -2061  -3337   1062  -1449   1644   2573  -4104  -4517   -862    878  -1538    150    -96  -3210   1568   127
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -15 -10549 -11592   -894  -1115  -2164   -364  -7662  -6700 
-    96    978  -4137   -106    675  -4458      8    289  -4209    991  -4153   -379   1210  -3731    767   1934   -484  -1280  -3759  -4320  -3637   128
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16 -10551 -11593   -894  -1115  -2164   -364  -7662  -6688 
-    97  -1890  -5006  -7160  -7517  -7033   3792  -6646  -7516  -7403  -7615  -6806  -6070  -6009  -6947  -7027  -4766  -4978  -6286    719  -6963   129
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -37 -10550  -6074   -894  -1115   -576  -1603  -7662  -6672 
-    98  -1954  -5230  -8287  -7756  -3698  -8091  -6961   -272  -7594   3060   1462  -7802  -7231  -6491  -7169  -7468  -5696    303  -5529  -5708   130
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16 -10591 -11633   -894  -1115   -320  -2331  -7662  -6658 
-    99   -977  -4213    252  -2039  -4534  -1329    -71  -4284    999   -787  -3302   2027   -922    385   2239   -660   -231  -3835   1268   -871   131
-     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
-     -    -16 -10637 -11679   -894  -1115   -701  -1378  -7662  -6644 
-   100  -1418  -4205   1277   1300  -1156   -249    666   -936   -491  -2013  -3295   -979   1463     75    844  -2623    643  -1003    406     42   132
-     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
-     -      *      *      *      *      *      *      *  -7662      0 
-//

--- a/commons/pyRepetUnit/profilesDB/tests/profilesDBTestSuite.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-import unittest
-import sys
-import TestProfilesDB2Map
-import TestAcceptanceProfilesDB2Map
-import TestCompleteProfilesDBFromProfilesNameListOrAccNumber
-import TestAcceptanceCompleteProfilDB_script
-import TestProfilesDB4Repet
-import TestAcceptanceProfilesDB4Repet
-import TestInsertProfilesMapFileInDB
-
-def main():
-
-        profilesDBTestSuite = unittest.TestSuite() 
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestProfilesDB2Map.TestProfilesDB2Map,'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceProfilesDB2Map.TestAcceptanceProfilesDB2Map,'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestCompleteProfilesDBFromProfilesNameListOrAccNumber.TestCompleteProfilesDBFromProfilesNameListOrAccNumber, 'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceCompleteProfilDB_script.TestAcceptanceCompleteProfilDB_script, 'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestProfilesDB4Repet.TestProfilesDB4Repet, 'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceProfilesDB4Repet.TestAcceptanceProfilesDB4Repet, 'test'))
-        profilesDBTestSuite.addTest(unittest.makeSuite(TestInsertProfilesMapFileInDB.TestInsertProfilesMapFileInDB, 'test'))
-        
-        runner = unittest.TextTestRunner(sys.stderr, 2, 2)
-        runner.run(profilesDBTestSuite)
-
-
-if __name__ == '__main__':
-    main()

--- a/commons/tools/AlignTEOnGenomeAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,282 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import re
-import os
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
-import subprocess
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.core.coord.PathUtils import PathUtils
-from commons.core.coord.SetUtils import SetUtils
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.coord.Set import Set
-from commons.core.sql.DbFactory import DbFactory
-
-## Align a TE on genome according to annotation
-
-LOG_DEPTH = "repet.tools"
-
-class AlignTEOnGenomeAccordingToAnnotation(object):
-    
-    def __init__(self, pathTableName = "", queryTableName = "", subjectTableName = "", mergeSamePathId = False, outTableName = "", matchPenality=10, mism=8, gapo=16, gape=4, gapl=20, configFileName = "", doClean = False, verbosity = 0):
-        self._pathTableName = pathTableName
-        self._queryTableName = queryTableName
-        self._subjectTableName = subjectTableName
-        self._mergeSamePathId = mergeSamePathId
-        self.setOutTableName(outTableName)
-        self._matchPenality = matchPenality
-        self._mismatch = mism
-        self._gapOpening = gapo
-        self._gapExtend = gape
-        self._gapLength = gapl
-        self._configFileName = configFileName
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._iDb = None
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Align a TE on genome according to annotation."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python AlignTEOnGenomeAccordingToAnnotation.py -p DmelChr4_chr_allTEs_nr_noSSR_join_path -q DmelChr4_chr_seq -s DmelChr4_refTEs_seq -v 0"
-        epilog += "\n"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-p", "--path",       dest = "pathTableName",     action = "store",       type = "string", help = "path table name [compulsory] [format: path]", default = "")
-        parser.add_option("-q", "--query",      dest = "queryTableName",    action = "store",       type = "string", help = "query table name [compulsory] [format: seq]", default = "")
-        parser.add_option("-s", "--subject",    dest = "subjectTableName",  action = "store",       type = "string", help = "subject table name [compulsory] [format: seq]", default = "")
-        parser.add_option("-m", "--merge",      dest = "mergeSamePathId",   action = "store_true",                   help = "merge joined matchs [optional] [default: False]", default = False)
-        parser.add_option("-o", "--out",        dest = "outTableName",      action = "store",       type = "string", help = "output table name [default: <pathTableName>_align]", default = "")
-        #TODO: add options for : matchPenality=10, mism=8, gapo=16, gape=4, gapl=20
-        parser.add_option("-C", "--config",     dest = "configFileName",    action = "store",       type = "string", help = "configuration file name (e.g. TEannot.cfg)", default = "")
-        #NOTE: doClean unused
-#        parser.add_option("-c", "--clean",      dest = "doClean",           action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",         action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setPathTableName(options.pathTableName)
-        self.setQueryTableName(options.queryTableName)
-        self.setSubjectTableName(options.subjectTableName)
-        self.setMergeSamePathId(options.mergeSamePathId)
-        self.setOutTableName(options.outTableName)
-        self.setConfigFileName(options.configFileName)
-#        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def _checkConfig(self):       
-        iConfigRules = ConfigRules()
-        iConfigRules.addRuleSection(section="", mandatory=True)
-        iConfigRules.addRuleOption(section="", option ="fasta_name", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section="", option ="clean", mandatory=True, type="bool")
-        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
-        iConfig = iConfigChecker.getConfig()
-        self._setAttributesFromConfig(iConfig)
-        
-    def _setAttributesFromConfig(self, iConfig):
-        self.setOutTableName(self._outTableName)
-        self.setDoClean(iConfig.get("", "clean"))
-        
-    def setPathTableName(self, pathTableName):
-        self._pathTableName = pathTableName
-        
-    def setQueryTableName(self, queryTableName):
-        self._queryTableName = queryTableName
-        
-    def setSubjectTableName(self, subjectTableName):
-        self._subjectTableName = subjectTableName
-        
-    def setMergeSamePathId(self, mergeSamePathId):
-        self._mergeSamePathId = mergeSamePathId
-        
-    def setOutTableName(self, outTableName):
-        if outTableName == "":
-            self._outTableName = "%s_align" % self._pathTableName
-        else:
-            self._outTableName = outTableName
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def setDbInstance(self, iDb):
-        self._iDb = iDb
-        
-    def _checkOptions(self):
-        if self._pathTableName == "" or not self._iDb.doesTableExist(self._pathTableName):
-            self._logAndRaise("ERROR: Missing path table")
-        if self._queryTableName == "" or not self._iDb.doesTableExist(self._queryTableName):
-            self._logAndRaise("ERROR: Missing query table")
-        if self._subjectTableName == "" or not self._iDb.doesTableExist(self._subjectTableName):
-            self._logAndRaise("ERROR: Missing subject table")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-
-    def alignBioseqWithNWalign(self, iBioseq1, iBioseq2):
-        fastaFileName1 = "seqtoalign1.tmp"
-        iBioseq1.save(fastaFileName1)
-        fastaFileName2 = "seqtoalign2.tmp"
-        iBioseq2.save(fastaFileName2)
-        alignBioseqDBFileName = "aligned.tmp"
-        cmd = "NWalign"
-        cmd += " %s" % fastaFileName1
-        cmd += " %s" % fastaFileName2
-        cmd += " -m %s" % self._matchPenality
-        cmd += " -d %s" % self._mismatch
-        cmd += " -g %s" % self._gapOpening
-        cmd += " -e %s" % self._gapExtend
-        cmd += " -l %s" % self._gapLength
-        cmd += " -D"
-        cmd += " -o %s" % alignBioseqDBFileName
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        iAlignedBioseqDB = AlignedBioseqDB()
-        iAlignedBioseqDB.load(alignBioseqDBFileName)
-        os.remove(fastaFileName1)
-        os.remove(fastaFileName2)
-        os.remove(alignBioseqDBFileName)
-        return iAlignedBioseqDB
-    
-    def alignSeqAccordingToPathAndBuildAlignedSeqTable(self):
-        if self._iDb.doesTableExist(self._outTableName):
-            self._logAndRaise("ERROR: out table %s already exists" % self._outTableName)
-            
-        #TODO: create alignedSeq table in DbMySql...
-        sqlCmd="CREATE TABLE %s (path int unsigned, query_aligned_seq longtext, subject_aligned_seq longtext, score int unsigned, identity float unsigned)" % self._outTableName
-        self._iDb.execute(sqlCmd)
-
-        iQueryTSA = TableSeqAdaptator(self._iDb, self._queryTableName)
-        iSubjectTSA = TableSeqAdaptator(self._iDb, self._subjectTableName)
-        iTPA = TablePathAdaptator(self._iDb, self._pathTableName)
-        
-        if self._mergeSamePathId:
-            lPathId = iTPA.getIdList()
-            pathNb = len(lPathId)
-            count = 0
-            for pathNum in lPathId:
-                self._log.debug(count,"/",pathNb,"=>path",pathNum,"...")
-                lPaths = iTPA.getPathListFromId(pathNum)
-                #TODO: getSetListFromQueries() call getSubjectAsSetOfQuery() => "reverse complement" the query (coordinates are inversed, so getBioseq() will take the reverse-comp.) : is it correct ?
-                lQuerySets = PathUtils.getSetListFromQueries(lPaths)
-                #NOTE: merge sets if overlap
-                lQueryMergedSets = SetUtils.mergeSetsInList(lQuerySets)
-                #TODO: getBioseqFromSetList() build a sequence that does not exist : is it correct ?
-                iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQueryMergedSets)
-                lSubjectSets = PathUtils.getSetListFromSubjects(lPaths)
-                #TODO: no merge for subjects : is it correct ? matcher allow overlap on query and not on subject ?
-                iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets)
-                iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq)
-                self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB)
-        else:
-            lPathId = iTPA.getIdList()
-            pathNb = len(lPathId)
-            count = 0
-            for pathNum in lPathId:
-                self._log.debug(count,"/",pathNb,"=>path",pathNum,"...")
-                lPaths = iTPA.getPathListFromId(pathNum)
-                queryName = lPaths[0].getQueryName()
-                subjectName = lPaths[0].getSubjectName()
-                lQueryStart = []
-                lQueryEnd = []
-                lSubjectStart = []
-                lSubjectEnd = []
-                isReversed = not lPaths[0].isSubjectOnDirectStrand()
-                for iPath in lPaths:
-                    lQueryStart.append(iPath.getQueryStart())
-                    lQueryEnd.append(iPath.getQueryEnd())
-                    lSubjectStart.append(iPath.getSubjectStart())
-                    lSubjectEnd.append(iPath.getSubjectEnd())
-                queryStart = min(lQueryStart)
-                queryEnd = max(lQueryEnd)
-                if isReversed:
-                    subjectStart = max(lSubjectStart)
-                    subjectEnd = min(lSubjectEnd)
-                else:
-                    subjectStart = min(lSubjectStart)
-                    subjectEnd = max(lSubjectEnd)
-                lQuerySets = [Set(pathNum,subjectName, queryName,queryStart,queryEnd)]
-                lSubjectSets = [Set(pathNum,queryName, subjectName,subjectStart,subjectEnd)]
-                
-                iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQuerySets)
-                iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets)
-                iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq)
-                self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB)
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        if self._configFileName:
-            self._checkConfig()
-        self._iDb = DbFactory.createInstance()
-        self._checkOptions()
-        self._log.info("START AlignTEOnGenomeAccordingToAnnotation")
-        self._log.debug("path table name: %s" % self._pathTableName)
-        self._log.debug("query table name: %s" % self._queryTableName)
-        self._log.debug("subject table name: %s" % self._subjectTableName)
-        self.alignSeqAccordingToPathAndBuildAlignedSeqTable()
-        self._iDb.close()
-        self._log.info("END AlignTEOnGenomeAccordingToAnnotation")
-
-    def _insertAlignedBioseqDBWithScoreAndIdentityInTable(self, pathNum, iAlignedBioseqDB):
-        scoreWithEndLine = re.split("Score=", iAlignedBioseqDB.db[0].header)[1]
-        score = int(scoreWithEndLine.split()[0])
-        
-        identity = re.split("Identity=", scoreWithEndLine)[1]
-        if identity == "nan":
-            identity = "0.0"
-        identity = float(identity)*100.0
-        
-        #TODO: create TableAlignedSeqAdaptator (to use insert...)
-        sqlCmd = 'INSERT INTO %s VALUES (%d,"%s","%s", %d,%f);' % (self._outTableName, pathNum, iAlignedBioseqDB.db[0].sequence, iAlignedBioseqDB.db[1].sequence, score, identity)
-        self._iDb.execute(sqlCmd)
-        
-        self._log.debug("header:", iAlignedBioseqDB.db[0].header)
-        self._log.debug("path", pathNum, "Score=", score, "Identity=", identity, "ok")
-        self._log.debug(iAlignedBioseqDB.db[0].sequence[:80])
-        self._log.debug(iAlignedBioseqDB.db[1].sequence[:80])
-
-if __name__ == "__main__":
-    iLaunch = AlignTEOnGenomeAccordingToAnnotation()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/tools/AnnotationStats.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,374 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-##@file
-# Give summary information on a TE annotation table.
-# options:
-#     -h: this help
-#     -t: analysis type (default = 1, 1: per transposable element (TE), 2: per cluster, 3: per classification, 4: with map input file)
-#     -p: name of the table (_path) or file (.path) with the annotated TE copies
-#     -s: name of the table (_seq) or file (.fasta or .fa) with the TE reference sequences
-#     -g: length of the genome (in bp)
-#     -m: name of the file with the group and the corresponding TE names (format = 'map')
-#     -o: name of the output file (default = pathTableName + '_stats.txt')
-#     -C: name of the configuration file to access MySQL (e.g. 'TEannot.cfg')
-#     -c: remove map files and blastclust file (if analysis type is 2 or 3)
-#     -I: identity coverage threshold (default = 0)
-#     -L: length coverage threshold (default=0.8)
-#     -v: verbosity level (default = 0)
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.stat.Stat import Stat
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.tools.getCumulLengthFromTEannot import getCumulLengthFromTEannot
-
-LOG_DEPTH = "repet.tools"
-
-#TODO: use templating engine instead of raw strings for AnnotationStatsWriter
-class AnnotationStats( object ):
-
-    def __init__(self, analysisName="TE", clusterFileName="",seqTableName="", pathTableName="", genomeLength=0, statsFileName="", globalStatsFileName="", verbosity=3):
-        self._analysisName = analysisName
-        self._clusterFileName = clusterFileName
-        self._seqTableName = seqTableName
-        self._pathTableName = pathTableName
-        self._genomeLength = genomeLength
-        self._statsFileName = statsFileName
-        self._globalStatsFileName = globalStatsFileName
-        self._iDb = None
-        self._iTablePathAdaptator = None
-        self._iTableSeqAdaptator = None
-        self._save = False
-        self._clean = False
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-        
-    def setCoverageThreshold( self, lengthThresh ):
-        self._coverageThreshold = float(lengthThresh)
-                
-    def setIdentityThreshold( self, identityThresh ):
-        self._identityThreshold = int(identityThresh) 
-            
-    def setAnalyseType(self, analyseType):
-        self._analyseType = str(analyseType)
-            
-    def setPathTableName(self, pathTableName):
-        self._pathTableName = pathTableName
-        
-    def setDBInstance(self, iDb):
-        self._iDb = iDb
-        
-    def setTablePathAdaptator(self, iTablePathAdaptator):
-        self._iTablePathAdaptator = iTablePathAdaptator
-        
-    def setTableSeqAdaptator(self, iTableSeqAdaptator):
-        self._iTableSeqAdaptator = iTableSeqAdaptator
-    
-    ## Get the coverage of TE copies for a given family (using 'mapOp')
-    #
-    # @param consensus string name of a TE family ('subject_name' in the 'path' table)
-    # @return cumulCoverage integer cumulative coverage
-    #
-    def getCumulCoverage( self, consensus = "" ):
-        gclft = getCumulLengthFromTEannot()
-        gclft.setInputTable( self._pathTableName )
-        gclft.setTErefseq( consensus )
-        gclft.setClean()
-        gclft._db = self._iDb
-        gclft._tpA = self._iTablePathAdaptator
-        mapFileName = gclft.getAllSubjectsAsMapOfQueries()
-        mergeFileName = gclft.mergeRanges( mapFileName )
-        cumulCoverage = gclft.getCumulLength( mergeFileName ) #self._iTablePathAdaptator.getCumulPathLength_from_subject( consensus )
-        return cumulCoverage
-    
-    ## Get the number of full-lengths (95% <= L =< 105%)
-    #
-    # @param consensusLength integer
-    # @param lLengths list of integers
-    # @return fullLengthConsensusNb integer
-    #
-    def getNbFullLengths( self, consensusLength, lLengths ):
-        fullLengthConsensusNb = 0
-        for i in lLengths:
-            if i / float(consensusLength ) >= 0.95 and i / float(consensusLength ) <= 1.05:
-                fullLengthConsensusNb += 1
-        return fullLengthConsensusNb
-    
-    def getStatPerTE(self, consensusName):
-        dConsensusStats = {}
-        lLengthPerFragment = self._iTablePathAdaptator.getPathLengthListFromSubject(consensusName)
-        lLengthPerCopy = self._iTablePathAdaptator.getChainLengthListFromSubject(consensusName)
-        lIdentityPerCopy = self._iTablePathAdaptator.getChainIdentityListFromSubject(consensusName)
-        dConsensusStats["length"] = self._iTableSeqAdaptator.getSeqLengthFromAccession(consensusName)
-        dConsensusStats["cumulCoverage"] = self.getCumulCoverage(consensusName)
-        dConsensusStats["nbFragments"] = len(lLengthPerFragment)
-        dConsensusStats["nbFullLengthFragments"] = self.getNbFullLengths(dConsensusStats["length"], lLengthPerFragment)
-        dConsensusStats["nbCopies"] = len(lLengthPerCopy)
-        dConsensusStats["nbFullLengthCopies"] = self.getNbFullLengths(dConsensusStats["length"], lLengthPerCopy)
-        dConsensusStats["statsIdentityPerChain"] = Stat()
-        dConsensusStats["statsLengthPerChain"] = Stat()
-        dConsensusStats["statsLengthPerChainPerc"] = Stat()
-        self._statsForIdentityAndLength(dConsensusStats, lLengthPerCopy, lIdentityPerCopy)
-        return dConsensusStats
-    
-    def getStatPerCluster(self, lConsensusNames):
-        dConsensusClusterStats = {}
-        lLengthPerFragment = []
-        lLengthPerCopy = []
-        cumulCoverageLength = 0
-        for consensusName in lConsensusNames:
-            cumulCoverageLength += self.getCumulCoverage(consensusName)
-            lLengthPerFragment.extend(self._iTablePathAdaptator.getPathLengthListFromSubject(consensusName))
-            lLengthPerCopy.extend(self._iTablePathAdaptator.getChainLengthListFromSubject(consensusName))
-        dConsensusClusterStats["cumulCoverage"] = cumulCoverageLength
-        dConsensusClusterStats["nbFragments"] = len(lLengthPerFragment)
-        dConsensusClusterStats["nbCopies"] = len(lLengthPerCopy)
-        return dConsensusClusterStats
-        
-    def getClusterListFromFile(self):
-        lClusters = []
-        with open(self._clusterFileName) as fCluster:
-            for line in fCluster:
-                lConsensusNames = line.rstrip().split("\t")
-                lClusters.append(lConsensusNames)
-        return lClusters
-        
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._iDb = DbFactory.createInstance()
-        self._iTablePathAdaptator = TablePathAdaptator(self._iDb, self._pathTableName)
-        self._iTableSeqAdaptator = TableSeqAdaptator(self._iDb, self._seqTableName)
-        
-        iASW = AnnotationStatsWriter()
-        if self._analysisName == "TE":
-            with open(self._statsFileName, "w") as fStats:
-                string = "%s\tlength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tmeanLgth\tmeanLgthPerc\n" % self._analysisName
-                fStats.write(string)
-                
-                lNamesTErefseq = self._iTableSeqAdaptator.getAccessionsList()
-                lDistinctSubjects = self._iTablePathAdaptator.getSubjectList()
-                totalCumulCoverage = self.getCumulCoverage()
-                
-                with open(self._globalStatsFileName, "w") as fG:
-                    fG.write("%s\n" % iASW.printResume(lNamesTErefseq, lDistinctSubjects, totalCumulCoverage, self._genomeLength))
-                    for consensusName in lNamesTErefseq:
-                        self._log.debug("processing '%s'..." % consensusName)
-                        dStatForOneConsensus = self.getStatPerTE(consensusName)
-                        iASW.addCalculsOfOneTE(dStatForOneConsensus)
-                        fStats.write("%s\n" % iASW.getStatAsString(consensusName, dStatForOneConsensus))
-                    fG.write(iASW.printStatsForAllTEs(len(lNamesTErefseq)))
-                    
-        elif self._analysisName == "Cluster":
-            lClusters = self.getClusterListFromFile()
-            lClusters.sort(key=lambda k: len(k), reverse=True)
-            with open(self._statsFileName, "w") as fStats:
-                string = "%s\tcovg\tfrags\tcopies\n" % self._analysisName
-                #TODO: add fullLgthFrags and fullLgthCopies ? Is addition of previous results significant ?
-                fStats.write(string)
-                for index, lConsensus in enumerate(lClusters):
-                    self._log.debug("processing '%s'..." % lConsensus)
-                    dStatForOneCluster = self.getStatPerCluster(lConsensus)
-                    fStats.write("%s\n" % iASW.getStatAsStringForCluster(str(index + 1), dStatForOneCluster))
-        
-        if self._save:
-            outTableName = "%s_statsPer%s" % (self._pathTableName, self._analysisName)
-            self._iDb.createTable(outTableName, "pathstat", self._statsFileName)
-            
-        self._iDb.close()
-        self._log.info("END %s" % type(self).__name__)
-
-    def _statsForIdentityAndLength(self, dStat, lLengthPerCopy, lIdentityPerCopy):
-        for i in lIdentityPerCopy:
-            dStat["statsIdentityPerChain"].add(i)
-        lLengthPercPerCopy = []
-        for i in lLengthPerCopy:
-            dStat["statsLengthPerChain"].add(i)
-            lperc = 100 * i / float(dStat["length"])
-            lLengthPercPerCopy.append(lperc)
-            dStat["statsLengthPerChainPerc"].add(lperc)
-
-class AnnotationStatsWriter(object):
-
-    def __init__(self):
-        self._dAllTErefseqs = { "sumCumulCoverage": 0,
-                         "totalNbFragments": 0,
-                         "totalNbFullLengthFragments": 0,
-                         "totalNbCopies": 0,
-                         "totalNbFullLengthCopies": 0,
-                         "nbFamWithFullLengthFragments": 0,
-                         "nbFamWithOneFullLengthFragment": 0,
-                         "nbFamWithTwoFullLengthFragments": 0,
-                         "nbFamWithThreeFullLengthFragments": 0,
-                         "nbFamWithMoreThanThreeFullLengthFragments": 0,
-                         "nbFamWithFullLengthCopies": 0,
-                         "nbFamWithOneFullLengthCopy": 0,
-                         "nbFamWithTwoFullLengthCopies": 0,
-                         "nbFamWithThreeFullLengthCopies": 0,
-                         "nbFamWithMoreThanThreeFullLengthCopies": 0,
-                         "statsAllCopiesMedIdentity": Stat(),
-                         "statsAllCopiesMedLengthPerc": Stat()
-                         }
-        
-    def getAllTEsRefSeqDict(self):
-        return self._dAllTErefseqs
-        
-    def getStatAsString( self, name, d ):
-        """
-        Return a string with all data properly formatted.
-        """
-        string = ""
-        string += "%s" % name
-        string += "\t%i" % d["length"]
-        string += "\t%i" % d["cumulCoverage"]
-        string += "\t%i" % d["nbFragments"]
-        string += "\t%i" % d["nbFullLengthFragments"]
-        string += "\t%i" % d["nbCopies"]
-        string += "\t%i" % d["nbFullLengthCopies"]
-        
-        if d["statsIdentityPerChain"].getValuesNumber() != 0:
-            string += "\t%.2f" % d["statsIdentityPerChain"].mean()
-        else:
-            string += "\tNA"
-            
-        if d["statsLengthPerChain"].getValuesNumber() != 0:
-            string += "\t%.2f" % d["statsLengthPerChain"].mean()
-        else:
-            string += "\tNA"
-                
-        if d["statsLengthPerChainPerc"].getValuesNumber() != 0:
-            string += "\t%.2f" % d["statsLengthPerChainPerc"].mean()
-        else:
-            string += "\tNA"
-                
-        return string
-    
-    def getStatAsStringForCluster( self, name, d ):
-        """
-        Return a string with all data properly formatted.
-        """
-        string = ""
-        string += "%s" % name
-        string += "\t%i" % d["cumulCoverage"]
-        string += "\t%i" % d["nbFragments"]
-        string += "\t%i" % d["nbCopies"]
-            
-        return string
-    
-    def addCalculsOfOneTE(self, dOneTErefseq):
-        self._dAllTErefseqs[ "sumCumulCoverage" ] += dOneTErefseq[ "cumulCoverage" ]
-        
-        self._dAllTErefseqs[ "totalNbFragments" ] += dOneTErefseq[ "nbFragments" ]
-        self._dAllTErefseqs[ "totalNbFullLengthFragments" ] += dOneTErefseq[ "nbFullLengthFragments" ]
-        if dOneTErefseq[ "nbFullLengthFragments" ] > 0:
-            self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ] += 1
-        if dOneTErefseq[ "nbFullLengthFragments" ] == 1:
-            self._dAllTErefseqs[ "nbFamWithOneFullLengthFragment" ] += 1
-        elif dOneTErefseq[ "nbFullLengthFragments" ] == 2:
-            self._dAllTErefseqs[ "nbFamWithTwoFullLengthFragments" ] += 1
-        elif dOneTErefseq[ "nbFullLengthFragments" ] == 3:
-            self._dAllTErefseqs[ "nbFamWithThreeFullLengthFragments" ] += 1
-        elif dOneTErefseq[ "nbFullLengthFragments" ] > 3:
-            self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthFragments" ] += 1
-        
-        self._dAllTErefseqs[ "totalNbCopies" ] += dOneTErefseq[ "nbCopies" ]
-        self._dAllTErefseqs[ "totalNbFullLengthCopies" ] += dOneTErefseq[ "nbFullLengthCopies" ]
-        if dOneTErefseq[ "nbFullLengthCopies" ] > 0:
-            self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ] += 1
-        if dOneTErefseq[ "nbFullLengthCopies" ] == 1:
-            self._dAllTErefseqs[ "nbFamWithOneFullLengthCopy" ] += 1
-        elif dOneTErefseq[ "nbFullLengthCopies" ] == 2:
-            self._dAllTErefseqs[ "nbFamWithTwoFullLengthCopies" ] += 1
-        elif dOneTErefseq[ "nbFullLengthCopies" ] == 3:
-            self._dAllTErefseqs[ "nbFamWithThreeFullLengthCopies" ] += 1
-        elif dOneTErefseq[ "nbFullLengthCopies" ] > 3:
-            self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthCopies" ] += 1
-        
-        if dOneTErefseq[ "statsIdentityPerChain" ].getValuesNumber() != 0:
-            self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].add( dOneTErefseq[ "statsIdentityPerChain" ].median() )
-        
-        if dOneTErefseq[ "statsLengthPerChainPerc" ].getValuesNumber() != 0:
-            self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].add( dOneTErefseq[ "statsLengthPerChainPerc" ].median() )
-
-    def printStatsForAllTEs(self, TEnb):
-#        statString += "(sum of cumulative coverages: %i bp)" % ( self._dAllTErefseqs[ "sumCumulCoverage" ] )
-        statString = "total nb of TE fragments: %i\n" % ( self._dAllTErefseqs[ "totalNbFragments" ] )
-        
-        if self._dAllTErefseqs[ "totalNbFragments" ] != 0:
-            
-            statString += "total nb full-length fragments: %i (%.2f%%)\n" % \
-            ( self._dAllTErefseqs[ "totalNbFullLengthFragments" ], \
-              100*self._dAllTErefseqs[ "totalNbFullLengthFragments" ] / float(self._dAllTErefseqs[ "totalNbFragments" ]) )
-            
-            statString += "total nb of TE copies: %i\n" % ( self._dAllTErefseqs[ "totalNbCopies" ] )
-            
-            statString += "total nb full-length copies: %i (%.2f%%)\n" % \
-            ( self._dAllTErefseqs[ "totalNbFullLengthCopies" ], \
-              100*self._dAllTErefseqs[ "totalNbFullLengthCopies" ] / float(self._dAllTErefseqs[ "totalNbCopies" ]) )
-            
-            statString += "families with full-length fragments: %i (%.2f%%)\n" % \
-            ( self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ], \
-              100*self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ] / float(TEnb) )
-            statString += " with only one full-length fragment: %i\n" % ( self._dAllTErefseqs[ "nbFamWithOneFullLengthFragment" ] )
-            statString += " with only two full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithTwoFullLengthFragments" ] )
-            statString += " with only three full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithThreeFullLengthFragments" ] )
-            statString += " with more than three full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthFragments" ] )
-            
-            statString += "families with full-length copies: %i (%.2f%%)\n" % \
-            ( self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ], \
-              100*self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ] / float(TEnb) )
-            statString += " with only one full-length copy: %i\n" % ( self._dAllTErefseqs[ "nbFamWithOneFullLengthCopy" ] )
-            statString += " with only two full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithTwoFullLengthCopies" ] )
-            statString += " with only three full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithThreeFullLengthCopies" ] )
-            statString += " with more than three full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthCopies" ] )
-            
-            statString += "mean of median identity of all families: %.2f +- %.2f\n" % \
-            ( self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].mean(), \
-              self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].sd() )
-            
-            statString += "mean of median length percentage of all families: %.2f +- %.2f\n" % \
-            ( self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].mean(), \
-              self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].sd() )
-        return statString
-            
-    def printResume(self, lNamesTErefseq, lDistinctSubjects, totalCumulCoverage, genomeLength):
-        statString = "nb of sequences: %i\n" % len(lNamesTErefseq)
-        statString += "nb of matched sequences: %i\n" % len(lDistinctSubjects)
-        statString += "cumulative coverage: %i bp\n" % totalCumulCoverage
-        statString += "coverage percentage: %.2f%%\n" % ( 100 * totalCumulCoverage / float(genomeLength) )
-#            statString += "processing the %i TE families..." % len(lNamesTErefseq)
-        return statString

--- a/commons/tools/BenchmarkTEconsensus.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,567 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Compare two fasta files of TEs to assess how reference sequences are recovered by de novo consensus.
-
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import os
-import sys
-import getopt
-import shutil
-import glob
-
-
-import pyRepet.launcher.programLauncher
-from commons.core.coord.AlignUtils import AlignUtils
-from commons.core.coord.MatchUtils import MatchUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-class BenchmarkTEconsensus( object ):
-    
-    def __init__( self ):
-        self._qryFile = ""
-        self._sbjFile = ""
-        self._method = 1
-        self._keepConflictSbj = False
-        self._thresholdCoverage = 95
-        self._thresholdIdentity = 80
-        self._thresholdEvalue = 1e-10
-        self._thresholdCoverageMatch = 90
-        self._useCluster = False
-        self._queue = ""
-        self._configFileName = ""
-        self._clean = False
-        self._verbose = 0
-        self._pL = pyRepet.launcher.programLauncher.programLauncher()
-        
-        
-    def help( self ):
-        print
-        print "usage: BenchmarkTEconsensus.py [ options ]"
-        print "options:"
-        print "     -h: this help"
-        print "     -q: name of the query file (de novo consensus, format='fasta')"
-        print "     -s: name of the subject file (reference sequences, format='fasta')"
-        print "     -m: method"
-        print "         1: Blaster + Matcher (default)"
-        print "         2: Blaster + merge + Matcher (not with '-Q')"
-        print "         3: Orienter + Mafft + Matcher"
-        print "         4: Yass + Matcher"
-        print "     -a: keep all conflicting subjects in Matcher"
-        print "     -t: coverage threshold over which the match is 'complete' (in %% of the seq length, default=%i)" % self._thresholdCoverage
-        print "     -I: identity threshold for 'CC' matches (default=%i)" % self._thresholdIdentity
-        print "     -E: E-value threshold for 'CC' matches (default=1e-10)"
-        print "     -T: coverage threshold for match length on query compare to subject length (default=%i)" % self._thresholdCoverageMatch
-        print "     -Q: queue name to run in parallel"
-        print "     -C: name of the configuration file (compulsory with '-Q')"
-        print "     -c: clean"
-        print "     -v: verbosity level (default=0/1/2)"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt( sys.argv[1:], "hq:s:m:at:I:E:T:Q:C:cv:" )
-        except getopt.GetoptError, err:
-            sys.stderr.write( "%s\n" % ( str(err) ) )
-            self.help()
-            sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help();
-                sys.exit(0)
-            elif o == "-q":
-                self._qryFile = a
-            elif o == "-s":
-                self._sbjFile = a
-            elif o == "-m":
-                self._method = int(a)
-            elif o == "-a":
-                self._keepConflictSbj = True
-            elif o == "-t":
-                self._thresholdCoverage = int(a)
-            elif o == "-I":
-                self._thresholdIdentity = int(a)
-            elif o == "-E":
-                self._thresholdEvalue = float(a)
-            elif o == "-T":
-                self._thresholdCoverageMatch = int(a)
-            elif o == "-Q":
-                self._useCluster = True
-                self._queue = a
-            elif o == "-C":
-                self._configFile = a
-            elif o == "-c":
-                self._clean = True
-            elif o == "-v":
-                self._verbose = int(a)
-                
-                
-    def checkAttributes( self ):
-        if self._qryFile == "":
-            msg = "ERROR: missing query file (-q)"
-            sys.stderr.write( "%s\n" % ( msg ) )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._qryFile ):
-            msg = "ERROR: can't find file '%s'" % ( self._qryFile )
-            sys.stderr.write( "%s\n" % ( msg ) )
-            self.help()
-            sys.exit(1)
-        if self._sbjFile == "":
-            msg = "ERROR: missing subject file (-s)"
-            sys.stderr.write( "%s\n" % ( msg ) )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._sbjFile ):
-            msg = "ERROR: can't find file '%s'" % ( self._sbjFile )
-            sys.stderr.write( "%s\n" % ( msg ) )
-            self.help()
-            sys.exit(1)
-        if self._useCluster:
-            if self._configFile == "":
-                msg = "ERROR: missing configuration file (-C)"
-                sys.stderr.write( "%s\n" % ( msg ) )
-                self.help()
-                sys.exit(1)
-            if not os.path.exists( self._configFile ):
-                msg = "ERROR: can't find file '%s'" % ( self._configFile )
-                sys.stderr.write( "%s\n" % ( msg ) )
-                self.help()
-                sys.exit(1)
-            if self._method == 2:
-                msg = "ERROR: can't launch method 2 in parallel"
-                sys.stderr.write( "%s\n" % ( msg ) )
-                self.help()
-                sys.exit(1)
-        nbSeqQry = FastaUtils.dbSize( self._qryFile )
-        if nbSeqQry == 0:
-            print "WARNING: query file is empty"
-            sys.exit(0)
-        nbSeqSbj = FastaUtils.dbSize( self._sbjFile )
-        if nbSeqSbj == 0:
-            print "WARNING: subject file is empty"
-            sys.exit(0)
-            
-            
-    def preprocess( self ):
-        tmpDir = "tmp%s_t%i_m%i_I%i" % ( os.getpid(),
-                                         self._thresholdCoverage,
-                                         self._method,
-                                         self._thresholdIdentity )
-        if os.path.exists( tmpDir ):
-            shutil.rmtree( tmpDir )
-        os.mkdir( tmpDir )
-        os.chdir( tmpDir )
-        
-        os.symlink( "../%s" % self._qryFile, self._qryFile )
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile( self._qryFile )
-        csh.setFormat( "fasta" )
-        csh.setStep( 1 )
-        csh.setPrefix( "query" )
-        csh.setOutputFile( "%s.newH" % ( self._qryFile ) )
-        csh.setVerbosityLevel( self._verbose )
-        csh.run()
-        self._qryFile += ".newH"
-        
-        if not os.path.exists( self._sbjFile ):
-            os.symlink( "../%s" % self._sbjFile, self._sbjFile )
-            
-            
-    def compareFastaViaBlasterMatcher( self, merged=False ):
-        """
-        Blaster (+ merged) +  Matcher
-        """
-        if self._keepConflictSbj:
-            s = "match"
-        else:
-            s = "clean_match"
-        matchFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                             self._sbjFile,
-                                             self._method )
-        pathFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                            self._sbjFile,
-                                            self._method )
-        if merged:
-            matchFile += ".merged"
-            pathFile += ".merged"
-        matchFile += ".%s.tab" % ( s )
-        pathFile += ".%s.path" % ( s )
-        
-        if not self._useCluster:
-            prg = "blaster"
-            cmd = prg
-            cmd += " -q %s" % ( self._qryFile )
-            cmd += " -s %s" % ( self._sbjFile )
-            cmd += " -B %s_vs_%s.m%i" % ( self._qryFile,
-                                          self._sbjFile,
-                                          self._method )
-            cmd += " -v %i" % ( self._verbose )
-            self._pL.launch( prg, cmd )
-            
-            if merged:
-                tmpFile = "%s_vs_%s.m%i.align.merged" % ( self._qryFile,
-                                                          self._sbjFile,
-                                                          self._method )
-                AlignUtils.mergeFile( "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                                               self._sbjFile,
-                                                               self._method ),
-                                                               tmpFile )
-            else:
-                tmpFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                                   self._sbjFile,
-                                                   self._method )
-                
-            prg = "matcher"
-            cmd = prg
-            cmd += " -m %s" % ( tmpFile )
-            cmd += " -q %s" % ( self._qryFile )
-            cmd += " -s %s" % ( self._sbjFile )
-            cmd += " -j"
-            if self._keepConflictSbj:
-                cmd += " -a"
-            cmd += " -v %i" % ( self._verbose )
-            self._pL.launch( prg, cmd )
-            
-        else:
-            os.symlink( "../%s" % self._configFile, self._configFileName )
-            
-            prg = os.environ["REPET_PATH"] + "/bin/launchBlasterMatcherPerQuery.py"
-            cmd = prg
-            cmd += " -q %s" % ( self._qryFile )
-            cmd += " -s %s" % ( self._sbjFile )
-            cmd += " -Q %s" % ( self._queue )
-            cmd += " -C %s" % ( self._configFile )
-            cmd += " -n %i" % ( 10 )
-            if self._keepConflictSbj:
-                cmd += " -M \"%s\"" % ( "-j -a" )
-            else:
-                cmd += " -M \"%s\"" % ( "-j" )
-            cmd += " -Z tab"
-            if self._clean:
-                cmd += " -c"
-            cmd += " -v %i" % ( self._verbose - 1 )
-            self._pL.launch( prg, cmd )
-            
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile( matchFile )
-        csh.setFormat( "tab" )
-        csh.setStep( 2 )
-        csh.setLinkFile( "%slink" % ( self._qryFile ) )
-        csh.setOutputFile( matchFile.replace(".newH","") )
-        csh.run()
-        
-        csh.setInputFile( pathFile )
-        csh.setFormat( "path" )
-        csh.setStep( 2 )
-        csh.setOutputFile( pathFile.replace(".newH","") )
-        csh.run()
-        
-        return matchFile.replace(".newH",""), pathFile.replace(".newH","")
-    
-    
-    def compareFastaViaMafft( self ):
-        """
-        Orienter, Mafft, Matcher
-        """
-        FastaUtils.dbSplit( self._qryFile, 1, False, False, "query" )
-        FastaUtils.dbSplit( self._sbjFile, 1, False, False, "subject" )
-        lQueries = glob.glob( "query_*.fa" )
-        lSubjects = glob.glob( "subject_*.fa" )
-        
-        if self._keepConflictSbj:
-            s = "match"
-        else:
-            s = "clean_match"
-        matchFile = "%s_vs_%s.m%i.align.%s.tab" % ( self._qryFile,
-                                                    self._sbjFile,
-                                                    self._method,
-                                                    s )
-        os.system( "touch %s" %  matchFile )
-        pathFile = "%s_vs_%s.m%i.align.%s.path" % ( self._qryFile,
-                                                    self._sbjFile,
-                                                    self._method,
-                                                    s )
-        os.system( "touch %s" %  pathFile )
-        
-        countQueries = 0
-        for query in lQueries:
-            countQueries += 1
-            queryHeader = FastaUtils.dbHeaders( query )[0]
-            queryLength = FastaUtils.dbLengths( query )[0]
-            countSubjects = 0
-            for subject in lSubjects:
-                countSubjects += 1
-                subjectHeader = FastaUtils.dbHeaders( subject )[0]
-                subjectLength = FastaUtils.dbLengths( subject )[0]
-                if self._verbose > 0:
-                    print "compare '%s' (%i bp, %i/%i) and '%s' (%i bp, %i/%i)" % ( queryHeader, queryLength,
-                                                                                    countQueries, len(lQueries),
-                                                                                    subjectHeader, subjectLength,
-                                                                                    countSubjects, len(lSubjects) )
-                    sys.stdout.flush()
-                qsLengthRatio = 100 * queryLength / float(subjectLength)
-                if qsLengthRatio < self._thresholdCoverage - 2 or qsLengthRatio > 100 + (100-self._thresholdCoverage) + 2:
-                    if self._verbose > 0:
-                        print "skip (q/s=%.2f%%)" % ( qsLengthRatio )
-                    continue
-                
-                tmpFile = "%s_vs_%s" % ( query, subject )
-                FileUtils.catFilesFromList( [ query, subject ],
-                                            tmpFile )
-                prg = "OrientSequences.py"
-                cmd = prg
-                cmd += " -i %s" % ( tmpFile )
-                cmd += " -p mummer"
-                cmd += " -c"
-                cmd += " -v %i" % ( self._verbose - 1 )
-                self._pL.launch( prg, cmd )
-                prg = "MafftProgramLauncher.py"
-                cmd = prg
-                cmd += " -i %s.oriented" % ( tmpFile )
-                cmd += " -c"
-                cmd += " -v %i" % ( self._verbose - 1 )
-                self._pL.launch( prg, cmd )
-                
-                absDB = AlignedBioseqDB( "%s.oriented.fa_aln" % tmpFile )
-                lHeaders = absDB.getHeaderList()
-                lAligns = absDB.getAlignList( lHeaders[0], lHeaders[1] )
-                for i in lAligns:
-                    if "re-oriented" in i.getQueryName():
-                        i.setQueryName( queryHeader )
-                        start = i.getQueryStart()
-                        end = i.getQueryEnd()
-                        i.setQueryStart( queryLength - end + 1 )
-                        i.setQueryEnd( queryLength - start + 1 )
-                    if "re-oriented" in i.getSubjectName():
-                        i.setSubjectName( subjectHeader )
-                        start = i.getSubjectStart()
-                        end = i.getSubjectEnd()
-                        i.setSubjectEnd( subjectLength - end + 1 )
-                        i.setSubjectStart( subjectLength - start + 1 )
-                    if not i.isQueryOnDirectStrand():
-                        i.reverse()
-                AlignUtils.writeListInFile( lAligns,
-                                            "%s.oriented.fa_aln.align" % tmpFile )
-                
-                prg = os.environ["REPET_PATH"] + "/bin/matcher"
-                cmd = prg
-                cmd += " -m %s.oriented.fa_aln.align" % ( tmpFile )
-                cmd += " -q %s" % ( query )
-                cmd += " -s %s" % ( subject )
-                cmd += " -j"
-                if self._keepConflictSbj:
-                    cmd += " -a"
-                cmd += " -v %i" % ( self._verbose - 1 )
-                self._pL.launch( prg, cmd )
-                
-                FileUtils.appendFileContent( "%s.oriented.fa_aln.align.%s.path" % ( tmpFile, s ), pathFile )
-                lMatches = MatchUtils.getMatchListFromFile( "%s.oriented.fa_aln.align.%s.tab" % ( tmpFile, s ) )
-                MatchUtils.writeListInFile( lMatches, matchFile, "a" )
-                
-                for f in [ tmpFile,
-                          "%s.oriented" % ( tmpFile ),
-#                          "%s.oriented.fa_aln" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align.match.fa" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align.match.map" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align.match.param" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align.match.path" % ( tmpFile ),
-                          "%s.oriented.fa_aln.align.match.tab" % ( tmpFile ),
-                          ]:
-                    os.remove( f )
-                    
-        if not FileUtils.isEmpty( matchFile ):
-            csh = ChangeSequenceHeaders()
-            csh.setInputFile( matchFile )
-            csh.setFormat( "tab" )
-            csh.setStep( 2 )
-            csh.setLinkFile( "%slink" % ( self._qryFile ) )
-            csh.setOutputFile( matchFile.replace(".newH","") )
-            csh.run()
-            csh.setInputFile( pathFile )
-            csh.setFormat( "path" )
-            csh.setStep( 2 )
-            csh.setOutputFile( pathFile.replace(".newH","") )
-            csh.run()
-            return matchFile.replace(".newH",""), pathFile.replace(".newH","")
-        else:
-            return "", ""
-        
-        
-    def compareFastaViaYassMatcher( self, merged=False ):
-        """
-        Yass +  Matcher
-        """
-        if self._keepConflictSbj:
-            s = "match"
-        else:
-            s = "clean_match"
-        matchFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                             self._sbjFile,
-                                             self._method )
-        pathFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                            self._sbjFile,
-                                            self._method )
-        if merged:
-            matchFile += ".merged"
-            pathFile += ".merged"
-        matchFile += ".%s.tab" % ( s )
-        pathFile += ".%s.path" % ( s )
-        
-        if not self._useCluster:
-            prg = os.environ["REPET_PATH"] + "/bin/YassProgramLauncher.py"
-            cmd = prg
-            cmd += " -i %s" % ( self._qryFile )
-            cmd += " -s %s" % ( self._sbjFile )
-            cmd += " -c"
-#            cmd += " -p '-i 12'"
-            cmd += " -o %s_vs_%s.m%i.align" % ( self._qryFile,
-                                                self._sbjFile,
-                                                self._method )
-            cmd += " -v %i" % ( self._verbose )
-            self._pL.launch( prg, cmd )
-            
-            if merged:
-                tmpFile = "%s_vs_%s.m%i.align.merged" % ( self._qryFile,
-                                                          self._sbjFile,
-                                                          self._method )
-                AlignUtils.mergeFile( "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                                               self._sbjFile,
-                                                               self._method ),
-                                                               tmpFile )
-            else:
-                tmpFile = "%s_vs_%s.m%i.align" % ( self._qryFile,
-                                                   self._sbjFile,
-                                                   self._method )
-                
-            prg = os.environ["REPET_PATH"] + "/bin/matcher"
-            cmd = prg
-            cmd += " -m %s" % ( tmpFile )
-            cmd += " -q %s" % ( self._qryFile )
-            cmd += " -s %s" % ( self._sbjFile )
-            cmd += " -j"
-            if self._keepConflictSbj:
-                cmd += " -a"
-            cmd += " -v %i" % ( self._verbose )
-            self._pL.launch( prg, cmd )
-            
-        csh = ChangeSequenceHeaders()
-        csh.setInputFile( matchFile )
-        csh.setFormat( "tab" )
-        csh.setStep( 2 )
-        csh.setLinkFile( "%slink" % ( self._qryFile ) )
-        csh.setOutputFile( matchFile.replace(".newH","") )
-        csh.run()
-        
-        csh.setInputFile( pathFile )
-        csh.setFormat( "path" )
-        csh.setStep( 2 )
-        csh.setOutputFile( pathFile.replace(".newH","") )
-        csh.run()
-        
-        return matchFile.replace(".newH",""), pathFile.replace(".newH","")
-    
-    
-    def analyzeMatchFile( self, matchFile, pathFile ):
-        if matchFile != "":
-            if self._verbose > 0:
-                print "analyze the 'tab' file..."
-                sys.stdout.flush()
-            prg = os.environ["REPET_PATH"] + "/bin/tabFileReader.py"
-            cmd = prg
-            cmd += " -m %s" % ( matchFile )
-            cmd += " -q %s" % ( self._qryFile.replace(".newH","") )
-            cmd += " -s %s" % ( self._sbjFile.replace(".newH","") )
-            cmd += " -t %i" % ( self._thresholdCoverage )
-            cmd += " -I %i" % ( self._thresholdIdentity )
-            cmd += " -E %g" % ( self._thresholdEvalue )
-            cmd += " -T %i" % ( self._thresholdCoverageMatch )
-            cmd += " -v %i" % ( self._verbose - 1 )
-            self._pL.launch( prg, cmd )
-            for f in [ matchFile, pathFile,
-                      "%s_tabFileReader.txt" %  matchFile,
-                      "%s_qryCategories.txt" %  matchFile,
-                      "%s_sbjCategories.txt" %  matchFile ]:
-                shutil.copy( f, ".." )
-        os.chdir( ".." )
-        
-        
-    def start( self ):
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START BenchmarkTEconsensus.py"
-            sys.stdout.flush()
-            
-            
-    def end( self ):
-        if self._clean:
-            tmpDir = "tmp%s_t%i_m%i_I%i" % ( os.getpid(),
-                                             self._thresholdCoverage,
-                                             self._method,
-                                             self._thresholdIdentity )
-            shutil.rmtree( tmpDir )
-        if self._verbose > 0:
-            print "END BenchmarkTEconsensus.py"
-            sys.stdout.flush()
-            
-            
-    def run( self ):
-        self.start()
-        
-        self.preprocess()
-        
-        if self._method == 1:
-            matchFile, pathFile = self.compareFastaViaBlasterMatcher()
-        elif self._method == 2:
-            matchFile, pathFile = self.compareFastaViaBlasterMatcher( merged=True )
-        elif self._method == 3:
-            matchFile, pathFile = self.compareFastaViaMafft()
-        elif self._method == 4:
-            matchFile, pathFile = self.compareFastaViaYassMatcher()
-            
-        self.analyzeMatchFile( matchFile, pathFile )
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = BenchmarkTEconsensus()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/CalcCoordCumulLength.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Calculate the cumulative length of coordinates data in the L{Map<commons.coreMap>} format.
-"""
-
-import os
-import sys
-import getopt
-from pyRepet.launcher.programLauncher import programLauncher
-from pyRepet.util.Stat import Stat
-from commons.core.checker.CheckerUtils import CheckerUtils
-
-
-class CalcCoordCumulLength( object ):
-    """
-    Compute the coverage of coordinates data in the L{Map<commons.core.ccommons.core    """
-    
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        self._inFileName = ""
-        self._outFileName = ""
-        self._verbose = 0
-        
-        
-    def help( self ):
-        """
-        Display the help on stdout.
-        """
-        print
-        print "usage:",sys.argv[0]," [ options ]"
-        print "options:"
-        print "     -h: this help"
-        print "     -i: name of the input file (format='map')"
-        print "     -o: name of the output file (default=inFileName+'.coverage')"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        """
-        Set the attributes from the command-line.
-        """
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:o:v:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputFileName( a )
-            elif o == "-o":
-                self._outFileName = a
-            elif o == "-v":
-                self._verbose = int(a)
-                
-                
-    def setInputFileName( self, inFileName ):
-        self._inFileName = inFileName
-        
-    def setVerbose( self, verbose ):
-        self._verbose = int(verbose)
-        
-    def checkAttributes( self ):
-        """
-        Check the attributes are valid before running the algorithm.
-        """
-        if self._inFileName == "":
-            print "ERROR: missing input file"
-            self.help(); sys.exit(1)
-        if not os.path.exists( self._inFileName ):
-            print "ERROR: can't find file '%s'" % ( self._inFileName )
-            self.help(); sys.exit(1)
-        if self._outFileName == "":
-            self._outFileName = "%s.coverage" % ( self._inFileName )
-            
-            
-    def mergeCoordinates( self ):
-        """
-        Merge the coordinates with 'mapOp'.
-        """
-        if self._verbose > 0:
-            print "merge the coordinates with mapOp..."; sys.stdout.flush()
-        if not CheckerUtils.isExecutableInUserPath( "mapOp" ):
-            msg = "ERROR: 'mapOp' is not in your PATH"
-            sys.stderr.write( "%s\n" % msg )
-            sys.exit(1)
-        pL = programLauncher()
-        prg = os.environ["REPET_PATH"] + "/bin/mapOp"
-        cmd = prg
-        cmd += " -q %s" % ( self._inFileName )
-        cmd += " -m"
-        cmd += " > /dev/null"
-        pL.launch( prg, cmd, self._verbose - 1 )
-        if self._verbose > 0:
-            print "coordinates merged !"; sys.stdout.flush()
-        mergeFileName = "%s.merge" % ( self._inFileName )
-        inPath, inName = os.path.split( self._inFileName )
-        if inPath != "":
-            os.system( "mv %s.merge %s" % ( inName, inPath ) )
-        return mergeFileName
-    
-    
-    def getStatsPerChr( self, mergeFileName ):
-        """
-        Return summary statistics on the coordinates, per chromosome.
-        @param mergeFileName: L{Map<commons.core.coord.Macommons.coreype mergeFileName: string
-        @return: dictionary whose keys are the chromosomes of the 'map file and values are L{Stat<pyRepet.util.Stat>} instances
-        """
-        dChr2Stats = {}
-        if self._verbose > 0:
-            print "compute the coverage of the coordinates..."; sys.stdout.flush()
-        mergeF = open( mergeFileName, "r" )
-        line = mergeF.readline()
-        while True:
-            if line == "": break
-            tokens = line[:-1].split("\t")
-            if int(tokens[2]) < int(tokens[3]):
-                matchLength = int(tokens[3]) - int(tokens[2]) + 1
-            elif int(tokens[2]) > int(tokens[3]):
-                matchLength = int(tokens[2]) - int(tokens[3]) + 1
-            if not dChr2Stats.has_key( tokens[1] ):
-                dChr2Stats[ tokens[1] ] = Stat()
-            dChr2Stats[ tokens[1] ].add( matchLength )
-            line = mergeF.readline()
-        mergeF.close()
-        os.remove( mergeFileName )
-        return dChr2Stats
-    
-    
-    def saveCumulLength( self, dChr2Stats ):
-        """
-        Write the stats in the output file.
-        """
-        outF = open( self._outFileName, "w" )
-        totalLength = 0
-        for i in dChr2Stats.keys():
-            totalLength += dChr2Stats[i].sum
-            string = "cumulative length (in bp) on '%s': %i" % ( i, dChr2Stats[i].sum )
-            outF.write( "%s\n" % ( string ) )
-            if self._verbose > 0: print string
-        string = "total cumulative length (in bp): %i" % ( totalLength )
-        outF.write( "%s\n" % ( string ) )
-        if self._verbose > 0: print string
-        outF.close()
-        sys.stdout.flush()
-        
-        
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        if self._verbose > 0:
-            print "beginning of %s" % (sys.argv[0].split("/")[-1]); sys.stdout.flush()
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "input file : '%s'" % ( self._inFileName )
-            sys.stdout.flush()
-            
-            
-    def end( self ):
-        """
-        Useful commands before ending the program.
-        """
-        if self._verbose > 0:
-            print "%s finished successfully" % (sys.argv[0].split("/")[-1]); sys.stdout.flush()
-            
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        mergeFileName = self.mergeCoordinates()
-        dChr2Stats = self.getStatsPerChr( mergeFileName )
-        self.saveCumulLength( dChr2Stats )
-        self.end()
-        
-        
-if __name__ == '__main__':
-    i = CalcCoordCumulLength()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/ChangeSequenceHeaders.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,524 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import os
-import sys
-import getopt
-from commons.core.coord.Align import Align
-from commons.core.coord.Path import Path
-from commons.core.coord.Match import Match
-
-
-
-class ChangeSequenceHeaders( object ):
-    
-    def __init__( self, name="ChangeSequenceHeaders", inFile="", format="", step=0, prefix="seq", outFile="",linkFile="", whichCluster = "", replace_query=True, replace_subject=True, verbosity=0):
-        self._name = name
-        self._inFile = inFile
-        self._format = format
-        self._step = step
-        self._prefix = prefix
-        self._linkFile = linkFile
-        self._whichCluster = whichCluster
-        self._outFile = outFile
-        self.replace_query = replace_query
-        self.replace_subject = replace_subject
-        self._verbose = verbosity
-        
-        
-    def help( self ):
-        print
-        print "usage: %s.py [ options ]" % ( self._name )
-        print "options:"
-        print "     -h: this help"
-        print "     -i: name of the input file"
-        print "     -f: format of the input file (fasta/newick/align/path/tab)"
-        print "     -s: step (1: shorten headers / 2: retrieve initial headers)"
-        print "     -p: prefix of new headers (with '-s 1', default='seq')"
-        print "     -l: name of the 'link' file (with '-s 2', format=map)"
-        print "     -w: header formatting type (A: after LTRharvest, B: for ClusterConsensus, not specified: no change)"
-        print "     -o: name of the output file (default=inFile+'.newH'/'.initH')"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:f:s:p:l:w:o:v:")
-        except getopt.GetoptError, err:
-            sys.stderr.write( "%s\n" % ( str(err) ) )
-            self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputFile( a )
-            elif o == "-f":
-                self.setFormat( a )
-            elif o == "-s":
-                self.setStep( a )
-            elif o == "-p":
-                self.setPrefix( a )
-            elif o == "-l":
-                self.setLinkFile( a )
-            elif o == "-w":
-                self.setWhichcluster( a )
-            elif o == "-o":
-                self.setOutputFile( a )
-            elif o == "-v":
-                self.setVerbosityLevel( a )
-                
-                
-    def setInputFile( self, inFile ):
-        self._inFile = inFile
-        
-    def setFormat( self, format ):
-        self._format = format
-        
-    def setPrefix( self, prefix ):
-        self._prefix = prefix
-        
-    def setStep( self, step ):
-        self._step = int(step)
-        
-    def setLinkFile( self, linkFile ):
-        self._linkFile = linkFile
-        
-    def setWhichcluster( self, whichCluster ):
-        self._whichCluster = whichCluster
-        
-    def setOutputFile( self, outFile ):
-        self._outFile = outFile
-        
-    def setVerbosityLevel( self, verbose ):
-        self._verbose = int(verbose)
-        
-        
-    def checkAttributes( self ):
-        if self._inFile == "":
-            sys.stderr.write( "ERROR: missing input file name (-i)\n" )
-            self.help(); sys.exit(1)
-        if not os.path.exists( self._inFile ):
-            sys.stderr.write( "ERROR: input file doesn't exist (-i)\n" )
-            self.help(); sys.exit(1)
-        if self._format not in ["fasta","newick","align","path","tab","axt","lastz", "psl","chain"]:
-            sys.stderr.write( "ERROR: unrecognized format '%s' (-f)\n" )
-            self.help(); sys.exit(1)
-        if self._step not in [1,2]:
-            sys.stderr.write( "ERROR: missing step (-s)\n" )
-            self.help(); sys.exit(1)
-        if self._step == 1 and self._prefix == "":
-            sys.stderr.write( "ERROR: missing prefix (-p)\n" )
-            self.help(); sys.exit(1)
-        if self._step == 2:
-            if self._linkFile == "":
-                sys.stderr.write( "ERROR: missing link file name (-l)\n" )
-                self.help(); sys.exit(1)
-            if not os.path.exists( self._linkFile ):
-                sys.stderr.write( "ERROR: link file doesn't exist (-l)\n" )
-                self.help(); sys.exit(1)
-            if self._whichCluster not in ["A", "B", ""]:
-                sys.stderr.write( "ERROR: formatting type not available (-w option): %s\n" % self._whichCluster)
-                self.help(); sys.exit(1)
-        if self._outFile == "":
-            if self._step == 1:
-                self._outFile = "%s.newH" % ( self._inFile )
-            elif self._step == 2:
-                self._outFile = "%s.initH" % ( self._inFile )
-                
-                
-    def shortenSequenceHeadersForFastaFile( self ):
-        if self._verbose > 0:
-            print "shorten sequence headers for fasta file..."
-            sys.stdout.flush()
-            if self._verbose > 1:
-                print "save sequences in '%s'"  %( self._outFile )
-        inFileHandler = open( self._inFile, "r" )
-        linkFileHandler = open( self._linkFile, "w" )
-        outFileHandler = open( self._outFile, "w" )
-        countSeq = 0
-        lengthSeq = 0
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            if line[0] == ">":
-                countSeq += 1
-                newHeader = "%s%i" % ( self._prefix, countSeq )
-                if self._verbose > 1:
-                    print "initial '%s' -> new '%s'" % ( line[1:-1], newHeader )
-                outFileHandler.write( ">%s\n" % ( newHeader ) )
-                if lengthSeq != 0:
-                    linkFileHandler.write( "\t%i\t%i\n" % ( 1, lengthSeq ) )
-                    lengthSeq = 0
-                linkFileHandler.write( "%s\t%s" % ( newHeader, line[1:-1] ) )
-            else:
-                lengthSeq += len( line.replace("\n","") )
-                outFileHandler.write( line )
-        linkFileHandler.write( "\t%i\t%i\n" % ( 1, lengthSeq ) )
-        inFileHandler.close()
-        linkFileHandler.close()
-        outFileHandler.close()
-        if self._verbose > 0:
-            print "nb of sequences: %i" % ( countSeq )
-            
-            
-    def getLinksNewToInitialHeaders( self ):
-        if self._verbose > 0:
-            print "retrieve the links new->initial headers"
-            sys.stdout.flush()
-        dNew2Init = {}
-        linkFileHandler = open( self._linkFile,"r" )
-        while True:
-            line = linkFileHandler.readline()
-            if line == "":
-                break
-            tokens = line.split("\t")
-            if len(tokens) == 4:
-                dNew2Init[ tokens[0] ] = tokens[1]
-            elif len(tokens) == 2:
-                dNew2Init[ tokens[0] ] = tokens[1].split("\n")[0]
-            else:
-                sys.stderr.write( "ERROR: link file is badly formatted\n" )
-                sys.exit(1)
-        linkFileHandler.close()
-        if self._verbose > 0: print "nb of links: %i" % ( len(dNew2Init.keys()) ); sys.stdout.flush()
-        return dNew2Init
-    
-    
-    def retrieveInitialSequenceHeadersForFastaFile( self, dNew2Init ):
-        if self._verbose > 0:
-            print "retrieve initial headers for fasta file"
-            sys.stdout.flush()
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        countSeq = 0
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            if line[0] == ">":
-                if self._whichCluster == "":
-                    initHeader = line[1:-1]
-                    newHeader = dNew2Init[initHeader]
-                else:
-                    tokens = line[1:-1].split("_")
-                    initHeader = dNew2Init[tokens[1]]
-                    
-                    pattern = ""
-                    if "BlastclustCluster" in tokens[0]:
-                        pattern = "Blc"
-                    if "MCLCluster" in tokens[0]:
-                        pattern = "MCL"
-                    
-                    if self._whichCluster == "A":
-                        newHeader = "%s_%s" % (tokens[0], initHeader)
-                    elif self._whichCluster == "B":
-                        classif = initHeader.split("_")[0]
-                        consensusName = "_".join(initHeader.split("_")[1:])
-                        clusterId = tokens[0].split("Cluster")[1].split("Mb")[0]
-                        newHeader = "%s_%s%s_%s" % (classif, pattern, clusterId, consensusName)
-                        
-                outFileHandler.write( ">%s\n" % newHeader )
-            else:
-                outFileHandler.write( line )
-        inFileHandler.close()
-        outFileHandler.close()
-        if self._verbose > 0:
-            print "nb of sequences: %i" % ( countSeq )
-    
-            
-    def retrieveInitialSequenceHeadersForNewickFile( self, dNew2Init ):
-        inF = open( self._inFile, "r" )
-        lines = inF.readlines()
-        inF.close()
-        line = "".join(lines)   #.replace(";","").replace("\n","")
-        outF = open( self._outFile, "w" )
-        for newH in dNew2Init.keys():
-            line = line.replace( newH+":", dNew2Init[newH].replace(" ","_").replace("::","-").replace(":","-").replace(",","-")+":" )
-        outF.write( line )
-        outF.close()
-        
-        
-    def retrieveInitialSequenceHeadersForAlignFile( self, dNew2Init ):
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        a = Align()
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            a.setFromTuple( line.split("\t") )
-            nameToBeReplaced = a.range_query.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                a.range_query.seqname = dNew2Init[ nameToBeReplaced ]
-            nameToBeReplaced = a.range_subject.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                a.range_subject.seqname = dNew2Init[ nameToBeReplaced ]
-            a.write( outFileHandler )
-        inFileHandler.close()
-        outFileHandler.close()
-        
-        
-    def retrieveInitialSequenceHeadersForPathFile( self, dNew2Init ):
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        p = Path()
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            p.setFromTuple( line.split("\t") )
-            nameToBeReplaced = p.range_query.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                p.range_query.seqname = dNew2Init[ nameToBeReplaced ]
-            nameToBeReplaced = p.range_subject.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                p.range_subject.seqname = dNew2Init[ nameToBeReplaced ]
-            p.write( outFileHandler )
-        inFileHandler.close()
-        outFileHandler.close()
-        
-        
-    def retrieveInitialSequenceHeadersForMatchFile( self, dNew2Init ):
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        m = Match()
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            if line[0:10] == "query.name":
-                continue
-            m.setFromTuple( line.split("\t") )
-            nameToBeReplaced = m.range_query.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                m.range_query.seqname = dNew2Init[ nameToBeReplaced ]
-            nameToBeReplaced = m.range_subject.seqname
-            if dNew2Init.has_key( nameToBeReplaced ):
-                m.range_subject.seqname = dNew2Init[ nameToBeReplaced ]
-            m.write( outFileHandler )
-        inFileHandler.close()
-        outFileHandler.close()
-        
-    def retrieveInitialSequenceHeadersForAxtFile( self, dNew2Init):
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        while True:
-            try:
-                line = inFileHandler.next()
-            except StopIteration:
-                break
-            
-            if line == "" or not "seq" in line:
-                outFileHandler.write(line)
-            else :
-                elems = line.split(" ")
-                try:
-                    subject_seqname = elems[1] 
-                    if self.replace_subject :
-                        nameToBeReplaced = elems[1]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            subject_seqname = dNew2Init[nameToBeReplaced]
-                            subject_seqname = subject_seqname.strip('\n').strip('\r')
-  
-                    query_seqname = elems[4]
-                    if self.replace_query:
-                        nameToBeReplaced = elems[4]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            query_seqname = dNew2Init[nameToBeReplaced]
-                            query_seqname = query_seqname.strip('\n').strip('\r')
-
-                    modedelems = [ elems[0], subject_seqname, elems[2], elems[3], query_seqname, elems[5], elems[6], elems[7], elems[8]]
-                    newLine = " ".join(modedelems)
-                    outFileHandler.write("%s\n" % newLine)
-                    if self._verbose >0 :
-                        print("query", query_seqname, "subject", subject_seqname)
-                        print("Output axt_line : line %s " % newLine)
-                except: pass
-        inFileHandler.close()
-        outFileHandler.close()
-        
-    def retrieveInitialSequenceHeadersForPslFile( self, dNew2Init):
-        
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        while True:
-            try:
-                line = inFileHandler.next()
-            except StopIteration:
-                break
-            
-            if line == "" or not "seq" in line:
-                outFileHandler.write(line)
-            else :
-                elems = line.split()
-                try:
-                    subject_seqname = elems[13] 
-                    if self.replace_subject :
-                        nameToBeReplaced = elems[13]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            subject_seqname = dNew2Init[nameToBeReplaced]
-                            subject_seqname = subject_seqname.strip('\n').strip('\r')
-  
-                    query_seqname = elems[9]
-                    if self.replace_query:
-                        nameToBeReplaced = elems[9]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            query_seqname = dNew2Init[nameToBeReplaced]
-                            query_seqname = query_seqname.strip('\n').strip('\r')
-                    
-                    modedelems =elems[0:9]+[query_seqname]+elems[10:13]+[subject_seqname]+elems[14:21]
-                    #modedelems = [ elems[0], elems[1], elems[2], elems[3], elems[4], elems[5], elems[6], elems[7], elems[8], query_seqname, ]
-                    #modedelems = [ elems[0], subject_seqname, elems[2], elems[3], query_seqname, elems[5], elems[6], elems[7], elems[8]]
-                    newLine = "\t".join(modedelems)
-                    outFileHandler.write("%s\n" % newLine)
-                    if self._verbose >0 :
-                        print("query", query_seqname, "subject", subject_seqname)
-                        print("Output psl_line : line %s " % newLine)
-                except: pass
-        sys.stdout.flush()
-        inFileHandler.close()
-        outFileHandler.close()
-        
-        
-    def retrieveInitialSequenceHeadersForLastZFile( self, dNew2Init):
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        while True:
-            try:
-                line = inFileHandler.next()
-            except StopIteration:
-                break
-            #score, name1, strand1, size1, zstart1, end1, name2, strand2, size2, zstart2, end2, identity, coverage
-            
-            if line == "" or not "seq" in line:
-                outFileHandler.write(line)
-            else :
-                elems = line.split("\t")
-                try:
-                    subject_seqname = elems[1] 
-                    if self.replace_subject :
-                        nameToBeReplaced = elems[1]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            subject_seqname = dNew2Init[nameToBeReplaced]
-                            subject_seqname = subject_seqname.strip('\n').strip('\r')
-  
-                    query_seqname = elems[6]
-                    if self.replace_query:
-                        nameToBeReplaced = elems[6]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            query_seqname = dNew2Init[nameToBeReplaced]
-                            query_seqname = query_seqname.strip('\n').strip('\r')
-
-                    modedelems = [ elems[0], subject_seqname, elems[2], elems[3], elems[4], elems[5], query_seqname, elems[7], elems[8],elems[9],elems[10], elems[11], elems[12],elems[13],elems[14].strip('\n').strip('\r')]
-                    newLine = "\t".join(modedelems)
-                    outFileHandler.write("%s\n" % newLine)
-                    if self._verbose >0 :
-                        print("query", query_seqname, "subject", subject_seqname)
-                        print("Output lastz_line : line %s " % newLine)
-                except: pass
-        inFileHandler.close()
-        outFileHandler.close()
-        
-    def retrieveInitialSequenceHeadersForChainFile( self, dNew2Init):
-        #format: chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id 
-        inFileHandler = open( self._inFile, "r" )
-        outFileHandler = open( self._outFile, "w" )
-        while True:
-            try:
-                line = inFileHandler.next()
-            except StopIteration:
-                break
-            if line == "" or not "seq" in line:
-                outFileHandler.write(line)
-            else :
-                elems = line.split(" ")
-                try:
-                    subject_seqname = elems[2]
-                    if self.replace_subject :
-                        nameToBeReplaced = elems[2]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            subject_seqname = dNew2Init[nameToBeReplaced]
-                            subject_seqname = subject_seqname.strip('\n').strip('\r')
-                            
-                    query_seqname = elems[7]
-                    if self.replace_query:
-                        nameToBeReplaced = elems[7]
-                        if dNew2Init.has_key( nameToBeReplaced ):
-                            query_seqname = dNew2Init[nameToBeReplaced]
-                            query_seqname = query_seqname.strip('\n').strip('\r')
-                    
-                    modedelems = elems[:]
-                    modedelems[2] = subject_seqname
-                    modedelems[7] = query_seqname
-                    newLine = " ".join(modedelems)
-                    outFileHandler.write("%s\n" % newLine)
-                except: pass
-                
-        inFileHandler.close()
-        outFileHandler.close()   
-                    
-        
-    def run( self ):
-        self.checkAttributes()
-        if self._step == 1:
-            if self._linkFile == "":
-                self._linkFile = "%s.newHlink" % ( self._inFile )
-            if self._format == "fasta":
-                self.shortenSequenceHeadersForFastaFile()
-        if self._step == 2:
-            dNew2Init = self.getLinksNewToInitialHeaders()
-            if self._format == "fasta":
-                self.retrieveInitialSequenceHeadersForFastaFile( dNew2Init )
-            elif self._format == "newick":
-                self.retrieveInitialSequenceHeadersForNewickFile( dNew2Init )
-            elif self._format == "align":
-                self.retrieveInitialSequenceHeadersForAlignFile( dNew2Init )
-            elif self._format == "path":
-                self.retrieveInitialSequenceHeadersForPathFile( dNew2Init )
-            elif self._format == "axt":
-                self.retrieveInitialSequenceHeadersForAxtFile( dNew2Init)
-            elif self._format == "psl":
-                self.retrieveInitialSequenceHeadersForPslFile( dNew2Init)
-            elif self._format == "lastz":
-                self.retrieveInitialSequenceHeadersForLastZFile(dNew2Init)
-            elif self._format == "chain":
-                self.retrieveInitialSequenceHeadersForChainFile(dNew2Init)
-            elif self._format in [ "tab", "match" ]:
-                self.retrieveInitialSequenceHeadersForMatchFile( dNew2Init )
-                
-                
-if __name__ == "__main__":
-    i = ChangeSequenceHeaders()
-    i.setAttributesFromCmdLine()
-    i.run()
\ No newline at end of file

--- a/commons/tools/CheckMysqlConnect.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import sys
-import os
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.RepetException import RepetException
-from commons.tools.CleanClusterNodesAfterRepet import CleanClusterNodesAfterRepet
-
-REPET_PATH = os.environ.get("REPET_PATH")
-
-def main():
-
-    description = "Check MySQL connection on each node"
-    usage = "CheckMysqlConnect.py [options]"
-    examples = "\nExample 1: check MySQL connection from every node of a SGE cluster using environment variables:\n"
-    examples += "\t$ python CheckMysqlConnect.py"
-    examples += "\n\t"
-    examples += "\nExample 2: check MySQL connection from every node of a SGE cluster using configuration file:\n"
-    examples += "\t$ python CheckMysqlConnect.py -C configFileName"
-    examples += "\n\t"
-    examples += "\nExample 3: check MySQL connection from every node of a SGE cluster using environment variables and using a different python executable than the one in the PATH:\n"
-    examples += "\t$ python CheckMysqlConnect.py -p /path/to/python"
-    examples += "\n\n"
-           
-    parser = RepetOptionParser(description = description, usage = usage, version = "v1.0", epilog = examples)
-    parser.add_option( "-p", "--path", dest = "pythonPath", type = "string", help = "path to python executable ('python' included, without finishing '/')", default = "python")
-    parser.add_option( "-C", "--config", dest = "config", type = "string", help = "path to config file", default = "")
-
-    options, args = parser.parse_args()
-    pythonPath = options.pythonPath
-    configFile =  options.config
-    
-    iCleanClusterNodesAfterRepet = CleanClusterNodesAfterRepet()
-    nodesList = iCleanClusterNodesAfterRepet.getAllNodesList()
-    
-    nbNodes = len(nodesList)
-    nodeCount = 0
-    configOption = ""
-    for node in nodesList:
-        try:
-            nodeCount += 1
-            print "Connect to node '%s' (%i/%i)..." % (node, nodeCount, nbNodes)
-            sys.stdout.flush()
-            cmd = "ssh"
-            cmd += " -q %s " % ( node )
-            if configFile != "":
-                configOption = " -C %s" % configFile
-            cmd += "'%s %s/bin/MysqlConnect.py -n %s %s'" % (pythonPath, REPET_PATH, node, configOption)
-            os.system(cmd)
-        except RepetException, e:
-            print e.getMessage()
-
-    iCleanClusterNodesAfterRepet.clean()
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/tools/CleanClusterNodesAfterRepet.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,177 +0,0 @@
-#!/usr/bin/env python
-
-## @file
-# Clean the cluster nodes after REPET was used.
-#
-# usage: CleanClusterNodesAfterRepet.py [ options ]
-# options:
-#      -h: this help
-#      -n: node to clean (otherwise all nodes will be cleaned)
-#      -t: temporary directory (e.g. '/tmp')
-#      -p: pattern (e.g. 'DmelChr4*')
-#      -v: verbosity level (default=0/1/2)
-
-import os
-import sys
-import getopt
-
-class CleanClusterNodesAfterRepet( object ):
-    """
-    Clean the cluster nodes after REPET was used.
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        self._lNodes = []
-        self._tmpDir = ""
-        self._pattern = ""
-        self._verbose = 0
-        self._lNodesToExcept = ["compute-2-46", "compute-2-47"]
-
-    def help( self ):
-        """
-        Display the help on stdout.
-        """
-        print
-        print "usage: %s.py [ options ]" % ( type(self).__name__ )
-        print "options:"
-        print "     -h: this help"
-        print "     -n: node to clean (otherwise all nodes will be cleaned)"
-        print "     -t: temporary directory (e.g. '/tmp')"
-        print "     -p: pattern (e.g. 'DmelChr4*')"
-        print "     -v: verbosity level (default=0/1/2)"
-        print
-        
-    def setAttributesFromCmdLine( self ):
-        """
-        Set the attributes from the command-line.
-        """
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:n:t:p:v:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-n":
-                self.setLNodes( a.split(" ") )
-            elif o == "-t":
-                self.setTempDirectory( a )
-            elif o == "-p":
-                self.setPattern( a )
-            elif o == "-v":
-                self.setVerbosityLevel( a )
-                
-    def setLNodes( self, a ):
-        self._lNodes = a
-        
-    def setTempDirectory( self, a ):
-        if a[-1] == "/":
-            self._tmpDir = a[:-1]
-        else:
-            self._tmpDir = a
-            
-    def setPattern( self, a ):
-        self._pattern = a
-        
-    def setVerbosityLevel( self, verbose ):
-        self._verbose = int(verbose)
-        
-    def checkAttributes( self ):
-        """
-        Before running, check the required attributes are properly filled.
-        """
-        if self._tmpDir == "":
-            print "ERROR: need a valid temporary directory"
-            self.help(); sys.exit(1)
-            
-    def getAllNodesList( self ):
-        """
-        Return the list of the names of each node.
-        """
-        lNodes = []
-        log = os.system( "qhost > qhost.txt" )
-        if log != 0: print "ERROR with qhost"; sys.exit(1)
-        inF = open( "qhost.txt", "r" )
-        line = inF.readline()
-        line = inF.readline()
-        line = inF.readline()
-        while True:
-            if line == "":
-                break
-            tokens = line.split()
-            if tokens[3] == "-":
-                line = inF.readline()
-                continue
-            lNodes.append( tokens[0] )
-            line = inF.readline()
-        inF.close()
-        #Remove nodes to avoid from the nodes list
-        for node in self._lNodesToExcept:
-            if node in lNodes:
-                lNodes.remove(node)
-        return lNodes
-    
-    def showNodeList( self, lNodes ):
-        print "nb of nodes: %i" % ( len(lNodes) )
-        for i in range(0,len(lNodes)):
-            print " %i: %s" % ( i+1, lNodes[i] )
-            
-    def cleanNodes( self):
-        """
-        Connect to each job and clean the temporary directory.
-        """
-        nbNodes = len(self._lNodes)
-        nodeCount = 0
-        for node in self._lNodes:
-            nodeCount += 1
-            if self._verbose > 0:
-                print "connect to node '%s' (%i/%i)..." % ( node, nodeCount, nbNodes )
-                sys.stdout.flush()
-            cmd = "ssh"
-            cmd += " -q %s " % ( node )
-            cmd += "'find %s" % ( self._tmpDir )
-            cmd += " -user %s" % ( os.environ["USER"] )
-            if self._pattern != "":
-                cmd += " -name '%s'" % ( self._pattern )
-            cmd += " 2> /dev/null -exec rm -rf {} \; ; exit'"
-            if self._verbose > 0: print cmd; sys.stdout.flush()
-            os.system( cmd )  # warning, even if everything goes right, ssh returns an error code, i.e. different than 0
-    
-    def clean( self ):
-        if os.path.exists( "qhost.txt" ):
-            os.remove( "qhost.txt" )
-            
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        if self._verbose > 0:
-            print "START %s" % ( type(self).__name__ ); sys.stdout.flush()
-        self.checkAttributes()        
-        
-    def end( self ):
-        """
-        Useful commands before ending the program.
-        """
-        self.clean()
-        if self._verbose > 0:
-            print "END %s" % ( type(self).__name__ ); sys.stdout.flush()
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        if self._lNodes == []:
-            self._lNodes = self.getAllNodesList()
-        if self._verbose > 0: self.showNodeList( self._lNodes )
-        self.cleanNodes()
-        self.end()
-
-if __name__ == "__main__":
-    i = CleanClusterNodesAfterRepet()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/CorrelateTEageWithGCcontent.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,204 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import os
-import getopt
-import math
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.core.coord.PathUtils import PathUtils
-from commons.core.coord.SetUtils import SetUtils
-from commons.core.seq.BioseqUtils import BioseqUtils
-
-
-class CorrelateTEageWithGCcontent( object ):
-    
-    def __init__( self ):
-        self._inputCoord = ""
-        self._inputGenome = ""
-        self._inputTErefseq = ""
-        self._configFile = ""
-        self._outFile = ""
-        self._verbose = 0
-        self._db = None
-        self._tableCoord = ""
-        self._pathA = TablePathAdaptator()
-        self._tableGenome = ""
-        self._seqA = TableSeqAdaptator()
-        
-        
-    def help( self ):
-        print
-        print "usage: CorrelateTEageWithGCcontent.py [ options ]"
-        print "options:"
-        print "     -h: this help"
-        print "     -i: input TE coordinates (can be file or table)"
-        print "         TEs as subjects in 'path' format"
-        print "     -g: input genome sequences (can be fasta file or table)"
-        print "     -r: input TE reference sequences (can be fasta file or table)"
-        print "     -C: configuration file (if table as input)"
-        print "     -o: output fasta file (default=inputCoord+'.gc')"
-        print "     -v: verbosity level (default=0/1)"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:g:r:C:o:v:")
-        except getopt.GetoptError, err:
-            msg = "%s" % str(err)
-            sys.stderr.write( "%s\n" % msg )
-            self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self._inputCoord = a
-            elif o == "-g":
-                self._inputGenome = a
-            elif o == "-r":
-                self._inputTErefseq = a
-            elif o == "-C":
-                self._configFile = a
-            elif o =="-o":
-                self._outFile = a
-            elif o == "-v":
-                self._verbose = int(a)
-                
-                
-    def checkAttributes( self ):
-        if self._inputCoord == "":
-            msg = "ERROR: missing input TE coordinates (-i)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._inputCoord ):
-            if not os.path.exists( self._configFile ):
-                msg = "ERROR: neither input file '%s' nor configuration file '%s'" % ( self._inputCoord, self._configFile )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-            if not os.path.exists( self._configFile ):
-                msg = "ERROR: can't find configuration file '%s'" % ( self._configFile )
-                sys.stderr.write( "%s\n" % msg )
-                sys.exit(1)
-            self._db = DbMySql( cfgFileName=self._configFile )
-            if not self._db.exist( self._inputCoord ):
-                msg = "ERROR: can't find table '%s'" % ( self._inputCoord )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-            self._tableCoord = self._inputCoord
-        else:
-            self._tableCoord = self._inputCoord.replace(".","_")
-        if self._inputGenome == "":
-            msg = "ERROR: missing input genome sequences (-g)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._inputGenome ):
-            if not self._db.doesTableExist( self._inputGenome ):
-                msg = "ERROR: can't find table '%s'" % ( self._inputGenome )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-            self._tableGenome = self._inputGenome
-        else:
-            self._tableGenome = self._inputGenome.replace(".","_")
-        if self._inputTErefseq == "":
-            msg = "ERROR: missing input TE reference sequences (-r)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._inputTErefseq ):
-            if not self._db.doesTableExist( self._inputTErefseq ):
-                msg = "ERROR: can't find table '%s'" % ( self._inputTErefseq )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-        if self._outFile == "":
-            self._outFile = "%s.gc" % ( self._inputCoord )
-            
-            
-    def getLengthOfTErefseqs( self ):
-        if os.path.exists( self._inputTErefseq ):
-            return BioseqUtils.getLengthPerSeqFromFile( self._inputTErefseq )
-        else:
-            dTErefseq2Length = {}
-            refseqA = TableSeqAdaptator( self._db, self._inputTErefseq )
-            lAccessions = refseqA.getAccessionsList()
-            for acc in lAccessions:
-                dTErefseq2Length[ acc ] = refseqA.getSeqLengthFromAccession( acc )
-            return dTErefseq2Length
-        
-        
-    def start( self ):
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START CorrelateTEageWithGCcontent.py"
-            sys.stdout.flush()
-        if os.path.exists( self._inputCoord ):
-            self._db = DbMySql( cfgFileName=self._configFile )
-            self._db.createTable( self._tableCoord, "path", self._inputCoord, True )
-        self._pathA = TablePathAdaptator( self._db, self._tableCoord )
-        if os.path.exists( self._inputGenome ):
-            self._db.createTable( self._tableGenome, "seq", self._inputGenome, True )
-        self._seqA = TableSeqAdaptator( self._db, self._tableGenome )
-        if self._verbose > 0:
-            print "output fasta file: %s" % self._outFile
-            
-            
-    def end( self ):
-        if os.path.exists( self._inputCoord ):
-            self._db.dropTable( self._tableCoord )
-        if os.path.exists( self._inputGenome ):
-            self._db.dropTable( self._tableGenome )
-        self._db.close()
-        if self._verbose > 0:
-            print "END CorrelateTEageWithGCcontent.py"
-            sys.stdout.flush()
-            
-            
-    def run( self ):
-        self.start()
-        
-        dTErefseq2Length = self.getLengthOfTErefseqs()
-        
-        outFileHandler = open( self._outFile, "w" )
-        outFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" )
-        
-        lIdentifiers = self._pathA.getIdList()
-        nbTEcopies = len(lIdentifiers)
-        if self._verbose > 0:
-            print "nb of TE copies: %i" % ( nbTEcopies )
-            sys.stdout.flush()
-        count = 0
-        power10 = int( math.floor( math.log10( nbTEcopies ) ) ) - 1
-        for id in lIdentifiers:
-            count += 1
-            if self._verbose > 0 and power10 > 0 and count % math.pow(10,power10) == 0:
-                print "%s / %s" % ( str(count).zfill(power10+2), str(nbTEcopies).zfill(power10+2) )
-                sys.stdout.flush()
-            lPaths = self._pathA.getPathListFromId( id )
-            lSets = PathUtils.getSetListFromQueries( lPaths )
-            lMergedSets = SetUtils.mergeSetsInList( lSets )
-            bs = self._seqA.getBioseqFromSetList( lMergedSets )
-            data = "%i" % id
-            data += "\t%s" % ( bs.header.split("::")[0] )
-            data += "\t%s" % ( lPaths[0].getQueryName() )
-            data += "\t%i" % ( bs.getLength() )
-            data += "\t%.2f" % ( PathUtils.getIdentityFromPathList( lPaths ) )
-            data += "\t%.2f" % ( bs.getGCpercentage() )
-            data += "\t%.2f" % ( 100 * bs.getLength() / float( dTErefseq2Length[ bs.header.split("::")[0] ] ) )
-            outFileHandler.write( "%s\n" % data )
-            
-        outFileHandler.close()
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = CorrelateTEageWithGCcontent()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/FilterAlign.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,149 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import getopt
-import os
-
-
-def help():
-    print
-    print "usage: ",sys.argv[0].split("/")[-1],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='align')"
-    print "     -E: maximum E-value (default=100)"
-    print "     -S: minimum score (default=0)"
-    print "     -I: minimum identity (default=0)"
-    print "     -l: minimum length (default=0)"
-    print "     -L: maximum length (default=1000000000)"
-    print "     -o: name of the output file (default=inFileName+'.filtered')"
-    print "     -v: verbose (default=0/1)"
-    print
-    
-    
-def main():
-    """
-    This program filters the output from BLASTER ('align' file recording HSPs).
-    """
-    
-    inFileName = ""
-    outFileName = ""
-    maxEValue = 100
-    minIdentity = 0
-    minLength = 0
-    maxLength = 1000000000
-    minScore = 0
-    verbose = 0
-    
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:E:S:I:l:L:o:v:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit()
-        elif o == "-i":
-            inFileName = a
-        elif o == "-E":
-            maxEValue = float(a)
-        elif o == "-S":
-            minScore = int(float(a))
-        elif o == "-I":
-            minIdentity = int(float(a))
-        elif o == "-l":
-            minLength = int(a)
-        elif o == "-L":
-            maxLength = int(a)
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-            
-    if inFileName == "":
-        print "ERROR: missing input file name"
-        help()
-        sys.exit(1)
-        
-    if outFileName == "":
-        outFileName = "%s.filtered" % ( inFileName )
-        
-    if os.path.exists( os.environ["REPET_PATH"] + "/bin/filterAlign" ):
-        prg = os.environ["REPET_PATH"] + "/bin/filterAlign"
-        cmd = prg
-        cmd += " -i %s" % ( inFileName )
-        cmd += " -E %g" % ( maxEValue )
-        cmd += " -S %i" % ( minScore )
-        cmd += " -I %f" % ( minIdentity )
-        cmd += " -l %i" % ( minLength )
-        cmd += " -L %i" % ( maxLength )
-        cmd += " -o %s" % ( outFileName )
-        cmd += " -v %i" % ( verbose )
-        return os.system( cmd )
-    
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    inFile = open( inFileName, "r" )
-    outFile = open( outFileName, "w" )
-    
-    nbMatches = 0
-    nbFiltered = 0
-    
-    line = inFile.readline()
-    while True:
-        if line == "":
-            break
-        nbMatches += 1
-        data = line.split("\t")
-        qryName = data[0]
-        qryStart = data[1]
-        qryEnd = data[2]
-        sbjName = data[3]
-        sbjStart = data[4]
-        sbjEnd = data[5]
-        Evalue = data[6]
-        score = data[7]
-        identity = data[8]
-        
-        if int(qryStart) < int(qryEnd):
-            matchLength = int(qryEnd) - int(qryStart) + 1
-        elif int(qryStart) > int(qryEnd):
-            matchLength = int(qryStart) - int(qryEnd) + 1
-
-        if float(Evalue) <= maxEValue and matchLength >= minLength and \
-               float(identity) >= minIdentity and matchLength <= maxLength and \
-               int(score) >= minScore:
-            string = qryName + "\t" + qryStart + "\t" + qryEnd + "\t" +\
-                     sbjName + "\t" + sbjStart + "\t" + sbjEnd + "\t" +\
-                     Evalue + "\t" + score + "\t" + identity
-            outFile.write( string )
-        else:
-            nbFiltered += 1
-            string = "qry %s (%s-%s) vs subj %s (%s-%s): Eval=%s identity=%s matchLength=%s score=%s" %\
-            ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Evalue, identity.split("\n")[0], matchLength, score )
-            if verbose > 1:
-                print string; sys.stdout.flush()
-                
-        line = inFile.readline()
-        
-    inFile.close()
-    outFile.close()
-    
-    if verbose > 0:
-        msg = "total number of matches: %i" % ( nbMatches )
-        msg += "\nnumber of filtered matches: %i" % ( nbFiltered )
-        print msg; sys.stdout.flush()
-        
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/GFF3Maker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,498 +0,0 @@
-#!/usr/bin/env python
-
-##@file GFF3Maker.py
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-import sys
-import os
-
-## GFF3Maker exports annotations from a 'path' table into a GFF3 file.
-#
-class GFF3Maker(object):
-
-    def __init__(self, inFastaName = "", tablesFileName = "", classifTableName = "", isChado = False, isGFF3WithoutAnnotation = False, isWithSequence = False, areMatchPartsCompulsory = False, configFileName = "", verbose = 0, doMergeIdenticalMatches = False, doSplit = False):
-        self._inFastaName = inFastaName
-        self._tablesFileName = tablesFileName
-        self._classifTableName = classifTableName
-        self._isChado = isChado
-        self._isGFF3WithoutAnnotation = isGFF3WithoutAnnotation
-        self._isWithSequence = isWithSequence
-        self._areMatchPartsCompulsory = areMatchPartsCompulsory
-        self._configFileName = configFileName
-        self._doMergeIdenticalMatches = doMergeIdenticalMatches
-        self._doSplit = doSplit
-        self._iDB = None
-        self._verbose = verbose
-    
-    def setAttributesFromCmdLine(self):
-        description = "GFF3Maker exports annotations from 'path', 'set' and/or 'classif' tables into a GFF3 file\n"
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-f", "--inseq",              dest = "inFastaName",               action = "store",       type = "string", help = "'seq' table recording the input sequences", default = "")
-        parser.add_option("-t", "--tablesfile",         dest = "tablesFileName",            action = "store",       type = "string", help = "tabulated file of table name to use to create the gff3 files (fields: tier name, format, table name)", default = "")
-        parser.add_option("-w", "--withSequence",       dest = "isWithSequence",            action = "store_true",                   help = "write the sequence at the end of GFF3 file", default = False)
-        parser.add_option("-a", "--withoutAnnotation",  dest = "isGFF3WithoutAnnotation",   action = "store_true",                   help = "write GFF3 files even if no annotation", default = False)
-        parser.add_option("-p", "--matchPart",          dest = "areMatchPartsCompulsory",   action = "store_true",                   help = "always associate a match_part to a match", default = False)
-        parser.add_option("-i", "--classifTable",       dest = "classifTable",              action = "store",       type = "string", help = "name of the TE library classification table [optional]", default = "")
-        parser.add_option("-c", "--chado",              dest = "isChado",                   action = "store_true",                   help = "Chado compliance", default = False)
-        parser.add_option("-m", "--doMergeIdenticalMatches",              dest = "doMergeIdenticalMatches",                   action = "store_true",                   help = "merge identical matches based on query start, query end, score", default = False)
-        parser.add_option("-s", "--doSplit",            dest = "doSplit",                   action = "store_true",                   help = "split each GFF3 per annotation type", default = False)
-        parser.add_option("-C", "--config",             dest = "configFileName",            action = "store",       type = "string", help = "configuration file for database connection", default = "")
-        parser.add_option("-v", "--verbose",            dest = "verbose",                   action = "store",       type = "int",    help = "verbosity level (default=0, else 1 or 2)", default = 0)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    #TODO: write a "setAttributesFromConfig"
-    def _setAttributesFromOptions(self, options):
-        self.setInFastaName(options.inFastaName)
-        self.setTablesFileName(options.tablesFileName)
-        self.setClassifTable(options.classifTable)
-        self.setIsChado(options.isChado)
-        self.setDoMergeIdenticalMatches(options.doMergeIdenticalMatches)
-        self.setIsWithSequence(options.isWithSequence)
-        self.setIsGFF3WithoutAnnotation(options.isGFF3WithoutAnnotation)
-        self.setAreMatchPartCompulsory(options.areMatchPartsCompulsory)
-        self.setDoSplit(options.doSplit)
-        self.setConfigFileName(options.configFileName)
-        self.setVerbose(options.verbose)
-        
-    def setInFastaName(self, inFastaName):
-        self._inFastaName = inFastaName
-        
-    def setTablesFileName(self, tablesFileName):
-        self._tablesFileName = tablesFileName
-        
-    def setIsWithSequence(self, isWithSequence):
-        self._isWithSequence = isWithSequence
-    
-    def setIsGFF3WithoutAnnotation(self, isGFF3WithoutAnnotation):
-        self._isGFF3WithoutAnnotation = isGFF3WithoutAnnotation
-        
-    def setAreMatchPartCompulsory(self, areMatchPartsCompulsory):
-        self._areMatchPartsCompulsory = areMatchPartsCompulsory
-        
-    def setClassifTable(self, classifTable):
-        self._classifTableName = classifTable
-        
-    def setIsChado(self, isChado):
-        self._isChado = isChado
-        
-    def setDoMergeIdenticalMatches(self, doMergeIdenticalMatches):
-        self._doMergeIdenticalMatches = doMergeIdenticalMatches
-        
-    def setDoSplit(self, doSplit):
-        self._doSplit = doSplit
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setVerbose(self, verbose):
-        self._verbose = verbose
-
-    def checkOptions(self):       
-        if self._inFastaName == "":
-            raise Exception("ERROR: options -f required")
-    
-        if self._configFileName != "":
-            if not FileUtils.isRessourceExists(self._configFileName):
-                raise Exception("ERROR: configuration file does not exist!")
-    
-        if self._classifTableName and not self._iDB.doesTableExist(self._classifTableName):
-            raise Exception("ERROR: classification table '%s' does not exist!" % self._classifTableName)
-        
-    ## Retrieve the features to write in the GFF3 file.
-    #
-    # @param pathTable string name of the table recording the annotations (i.e. the features)
-    # @param seqName string name of the sequence (the source feature) on which we want to visualize the matches (the features)
-    # @param source string the program that generated the feature (i.e. REPET)
-    # @param frame string "." by default (or "+", "-")
-    # @return pathString string which will be printed in path file 
-    #
-    def _getPathFeatures(self, pathTable, seqTable, seqName, source, feature, frame):
-        pathString = ""
-        iTPA = TablePathAdaptator(self._iDB, pathTable)
-        lPaths = iTPA.getPathListSortedByQueryCoordAndScoreFromQuery(seqName)
-        # organise them into 'match' and 'match_part'
-        if lPaths:
-            dPathID2Data = self._gatherSamePathFeatures(lPaths)
-            # build the output string
-            for pathID in dPathID2Data:
-                pathString += self._organizeEachPathFeature(pathID, dPathID2Data[pathID], seqName, source, frame, seqTable)
-        return pathString
-    
-    ## Gather matches with the same path ID.
-    #
-    # @param data list of string lists results of a SQL request
-    # @return dPathID2Matchs dict whose keys are path IDs and values are matches data
-    #
-    def _gatherSamePathFeatures(self, lPaths):
-        dPathID2Matchs = {}
-        iPreviousPath = lPaths[0]
-        iPreviousPath.otherTargets = []
-        for iPath in lPaths[1:]:
-            if self._doMergeIdenticalMatches and iPreviousPath.getQueryStart() == iPath.getQueryStart() and iPreviousPath.getQueryEnd() == iPath.getQueryEnd() and iPreviousPath.getScore() == iPath.getScore() and iPreviousPath.getSubjectName() != iPath.getSubjectName():
-                iPreviousPath.otherTargets.append("%s %d %d" % (iPath.getSubjectName(), iPath.getSubjectStart(), iPath.getSubjectEnd()))
-            else:
-                self._addPathToMatchDict(dPathID2Matchs, iPreviousPath)
-                iPreviousPath = iPath
-                iPreviousPath.otherTargets = []
-        self._addPathToMatchDict(dPathID2Matchs, iPreviousPath)
-        return dPathID2Matchs
-    
-    def _getClassifEvidenceBySeqName(self, seqName):
-        lseqName = seqName.split('_')
-        seqNameStructure =  '%s_%%' % lseqName[0]
-        if lseqName[-1] == 'reversed':
-            seqNameStructure +=  '%s_%s' % (lseqName[-2],lseqName[-1])
-        else:
-            seqNameStructure += lseqName[-1]
-        qry = "SELECT evidence FROM %s WHERE seq_name like \"%s\"" % (self._classifTableName, seqNameStructure)
-        self._iDB.execute(qry)
-        result = ""
-        try:
-            result = "".join(self._iDB.fetchall()[0])
-        except: pass
-        return  result
-    
-    def _addPathToMatchDict(self, dPathID2Matchs, iPreviousPath):
-        pathId = iPreviousPath.getIdentifier()
-        subjectStart = iPreviousPath.getSubjectStart()
-        subjectEnd = iPreviousPath.getSubjectEnd()
-        strand = iPreviousPath.getSubjectStrand()
-        if subjectStart > subjectEnd:
-            tmp = subjectStart
-            subjectStart = subjectEnd
-            subjectEnd = tmp
-        queryStart = iPreviousPath.getQueryStart()
-        queryEnd = iPreviousPath.getQueryEnd()
-        subjectName = iPreviousPath.getSubjectName()
-        eValue = iPreviousPath.getEvalue()
-        identity = iPreviousPath.getIdentity()
-        otherTargets = iPreviousPath.otherTargets
-        if dPathID2Matchs.has_key(pathId):
-            dPathID2Matchs[pathId].append([queryStart, queryEnd, strand, subjectName, subjectStart, subjectEnd, eValue, identity, otherTargets])
-        else:
-            dPathID2Matchs[pathId] = [[queryStart, queryEnd, strand, subjectName, subjectStart, subjectEnd, eValue, identity, otherTargets]]
-
-    def _getConsensusLengthByTargetName(self, targetName, seqTableName):
-        iTableSeqAdaptator = TableSeqAdaptator(self._iDB, seqTableName)
-        return  iTableSeqAdaptator.getSeqLengthFromDescription(targetName)
-    
-    ## For a specific path ID, organize match data according to the GFF3 format.
-    #
-    # @param pathID string path ID
-    # @param lMatches match list
-    # @param seqName string name of the source feature
-    # @param source string 'source' field for GFF3 format
-    # @param frame string 'frame' field for GFF3 format
-    # @return lines string to write in the GFF3 file
-    #
-    def _organizeEachPathFeature(self, pathID, lMatches, seqName, source, frame, seqTable = ""):
-        lines = ""
-        minStart = lMatches[0][0]
-        maxEnd = lMatches[0][1]
-        minStartSubject = lMatches[0][4]
-        maxEndSubject = lMatches[0][5]
-        strand = lMatches[0][2]
-    
-        # for each match
-        for i in lMatches:
-            if i[0] < minStart:
-                minStart = i[0]
-            if i[1] > maxEnd:
-                maxEnd = i[1]
-            if i[4] < minStartSubject:
-                minStartSubject = i[4]
-            if i[5] > maxEndSubject:
-                maxEndSubject = i[5]
-    
-        target = lMatches[0][3]
-        
-        targetDescTag = ""
-        if self._classifTableName != "":
-            targetDescTag = self._getClassifEvidenceBySeqName(target)
-            if targetDescTag != "":
-                targetDescTag = ";TargetDescription=%s" % targetDescTag.replace('=', ':').replace(';', '').replace(',', ' |')
-                
-        targetLengthTag = ""
-        if seqTable != "":
-            targetLengthTag = self._getConsensusLengthByTargetName(target, seqTable)
-            targetLengthTag = ";TargetLength=%i" % targetLengthTag
-        
-        attributes = "ID=ms%s_%s_%s" % (pathID, seqName, target)
-        if self._isChado:
-            attributes += ";Target=%s+%s+%s" % (target, minStartSubject, maxEndSubject)
-        else:
-            attributes += ";Target=%s %s %s" % (target, minStartSubject, maxEndSubject)
-            
-        if lMatches[0][8]:
-            otherTargets = ", ".join(lMatches[0][8])
-            attributes += ";OtherTargets=%s" % otherTargets
-        else:
-            attributes += targetLengthTag
-            attributes += targetDescTag
-            if len(lMatches) == 1:
-                attributes += ";Identity=%s" % lMatches[0][7]
-        
-
-        lines += "%s\t%s\tmatch\t%s\t%s\t0.0\t%s\t%s\t%s\n" % (seqName, source, minStart, maxEnd, strand, frame, attributes)
-    
-        if len(lMatches) > 1 or self._areMatchPartsCompulsory:
-            count = 1
-            for i in lMatches:
-                attributes = "ID=mp%s-%i_%s_%s" % (pathID, count, seqName, target)
-                attributes += ";Parent=ms%s%s%s%s%s" % (pathID, "_", seqName, "_", target)
-                if self._isChado:
-                    attributes += ";Target=%s+%s+%s" % (target, i[4], i[5])
-                else:
-                    attributes += ";Target=%s %s %s" % (target, i[4], i[5])
-                    
-                if not i[8]:
-                    attributes += ";Identity=%s" % i[7]
-                lines += "%s\t%s\tmatch_part\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, i[0], i[1], i[6], i[2], frame, attributes)
-                count += 1
-    
-        return lines
-    
-    ## Retrieve the features to write in the GFF3 file.
-    #
-    # @param table string name of the table recording the annotations (i.e. the features)
-    # @param key string name of the sequence (the source feature) on which we want to visualize the matches (the features)
-    # @param source string the program that generated the feature (i.e. REPET)
-    # @param frame string "." by default (or "+", "-")
-    # @return setString string which will be printed in set file 
-    # 
-    def _getSetFeatures(self, table, key, source, feature, frame):
-        setString = ""
-        # retrieve all the data about the matches
-        qry = "SELECT DISTINCT path,name,start,end FROM %s WHERE chr=\"%s\"" % (table, key)
-        self._iDB.execute(qry)
-        data = self._iDB.fetchall()
-        # organise them into 'match' and 'match_part'
-        dPathID2Data = self._gatherSameSetFeatures(data)
-        # build the output string
-        for pathID in dPathID2Data:
-            setString += self._organizeEachSetFeature(pathID, dPathID2Data[pathID], key, source, frame)
-        return setString
-    
-    ## Gather matches with the same path ID.
-    #
-    # @param data list of string lists results of a SQL request
-    # @return dSetID2Matchs dict whose keys are set IDs and values are matches data
-    #
-    def _gatherSameSetFeatures(self, data):
-        dSetID2Matchs = {}
-    
-        for i in data:
-            setID = i[0]
-            name = i[1]
-            start = i[2]
-            end = i[3]
-    
-            matchStart = min(start, end)
-            matchEnd = max(start, end)
-            strand = self._getStrand(start, end)
-    
-            if dSetID2Matchs.has_key(setID):
-                dSetID2Matchs[setID].append([name, matchStart, matchEnd, strand])
-    
-            else:
-                dSetID2Matchs[setID] = [[name, matchStart, matchEnd, strand]]
-    
-        return dSetID2Matchs
-    
-    ## For a specific set ID, organize match data according to the GFF3 format.
-    #
-    # @param setID string path ID
-    # @param lMatches match list
-    # @param seqName string name of the source feature
-    # @param source string 'source' field for GFF3 format
-    # @param frame string 'frame' field for GFF3 format
-    # @return lines string to write in the GFF3 file
-    #
-    def _organizeEachSetFeature(self, setID, lMatches, seqName, source, frame):
-        lines = ""
-        minStart = min(lMatches[0][1], lMatches[0][2])
-        maxEnd = max(lMatches[0][1], lMatches[0][2])
-        strand = lMatches[0][3]
-    
-        # for each match
-        for i in lMatches:
-            start = min(i[1],i[2])
-            if start < minStart:
-                minStart = start
-            end = max(i[1],i[2])
-            if end > maxEnd:
-                maxEnd = end
-    
-        target = lMatches[0][0].replace("(","").replace(")","").replace("#","")
-        
-        attributes = "ID=ms%s_%s_%s" % (setID, seqName, target)
-        if self._isChado:
-            attributes += ";Target=%s+%s+%s" % (target, "1", abs(minStart-maxEnd)+1)
-        else:
-            attributes += ";Target=%s %s %s" % (target, "1", abs(minStart-maxEnd)+1)
-        lines += "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, "match", minStart, maxEnd, "0.0", strand, frame, attributes)
-
-        if len(lMatches) > 1 or self._areMatchPartsCompulsory:    
-            count = 1
-            for i in lMatches:
-                attributes = "ID=mp%s-%i_%s_%s" % (setID, count, seqName, target)
-                attributes += ";Parent=ms%s%s%s%s%s" % (setID, "_", seqName, "_", target)
-                if self._isChado:
-                    attributes += ";Target=%s+%s+%s" % (target, "1", abs(i[1]-i[2])+1)
-                else:
-                    attributes += ";Target=%s %s %s" % (target, "1", abs(i[1]-i[2])+1)
-                lines += "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, "match_part", i[1], i[2], "0.0", i[3], frame, attributes)
-                count += 1
-
-        return lines
-    
-    ## Return the strand ('+' if start < end, '-' otherwise).
-    #
-    # @param start integer start coordinate
-    # @param end integer end coordinate
-    # @return strand string "+" or "-"
-    #
-    def _getStrand(self, start, end):
-        if start < end:
-            return "+"
-        else:
-            return "-"
-        
-    def run(self):
-        #TODO: cat all gff in one gff file in option
-        if self._configFileName == "":
-            self._iDB = DbFactory.createInstance()
-        else:
-            self._iDB = DbFactory.createInstance(self._configFileName)
-        
-        self.checkOptions()
-        if self._verbose > 0:
-            print "START GFF3Maker"
-            sys.stdout.flush()
-
-        tablesFile = open(self._tablesFileName, "r")
-        linesFromAnnotationTablesFile = tablesFile.readlines()
-        tablesFile.close()
-        feature = "region"
-        frame = "."
-        
-        iTSA = TableSeqAdaptator(self._iDB, self._inFastaName)
-        lTuples = iTSA.getAccessionAndLengthList()
-        for seqName, length in lTuples :
-            if not self._doSplit:
-                fileName = "%s.gff3" % seqName
-                outFile = open(fileName, "w")
-                outFile.write("##gff-version 3\n")
-                outFile.write("##sequence-region %s 1 %s\n" % (seqName, length))
-                for line in linesFromAnnotationTablesFile:
-                    if line[0] == "#":
-                        continue
-                    tok = line.split()
-                    if len(tok) == 0:
-                        break
-                    source = tok[0]
-                    format = tok[1]
-                    table = tok[2]
-                    tableseq = ""
-                    if len(tok) == 4:
-                        tableseq = tok[3]
-                    if format == 'path' :
-                        annotations = self._getPathFeatures(table, tableseq, seqName, source, feature, frame)
-                    elif format == 'set' :
-                        annotations = self._getSetFeatures(table, seqName, source, feature, frame)
-                    else:
-                        raise Exception("Wrong format : %s" % format)
-                    outFile.write(annotations)
-                outFile.close()
-                #TODO: check getNbLinesInSingleFile() to handle big files
-                if not self._isGFF3WithoutAnnotation and FileUtils.getNbLinesInSingleFile(fileName) == 2:
-                    os.remove(fileName)
-                elif self._isWithSequence:
-                    outFile = open(fileName, "a")
-                    outFile.write("##FASTA\n")
-                    iBioseq = iTSA.getBioseqFromHeader(seqName)
-                    iBioseq.write(outFile)
-                    outFile.close()
-            else:
-                count = 1
-                for line in linesFromAnnotationTablesFile:
-                    if line[0] == "#":
-                        continue
-                    tok = line.split()
-                    if len(tok) == 0:
-                        break
-                    source = tok[0]
-                    format = tok[1]
-                    table = tok[2]
-                    tableseq = ""
-                    if len(tok) == 4:
-                        tableseq = tok[3]
-                    fileName = "%s_Annot%i.gff3" % (seqName, count)
-                    outFile = open(fileName, "w")
-                    outFile.write("##gff-version 3\n")
-                    outFile.write("##sequence-region %s 1 %s\n" % (seqName, length))
-                    if format == 'path' :
-                        annotations = self._getPathFeatures(table, tableseq, seqName, source, feature, frame)
-                    elif format == 'set' :
-                        annotations = self._getSetFeatures(table, seqName, source, feature, frame)
-                    else:
-                        raise Exception("Wrong format : %s" % format)
-                    outFile.write(annotations)
-                    outFile.close()
-                    #TODO: check getNbLinesInSingleFile() to handle big files
-                    if not self._isGFF3WithoutAnnotation and FileUtils.getNbLinesInSingleFile(fileName) == 2:
-                        os.remove(fileName)
-                    elif self._isWithSequence:
-                        outFile = open(fileName, "a")
-                        outFile.write("##FASTA\n")
-                        iBioseq = iTSA.getBioseqFromHeader(seqName)
-                        iBioseq.write(outFile)
-                        outFile.close()
-                    count += 1
-            
-        self._iDB.close()
-    
-        if self._verbose > 0:
-            print "END GFF3Maker"
-            sys.stdout.flush()
-            
-if __name__ == "__main__":
-    iGFF3Maker = GFF3Maker()
-    iGFF3Maker.setAttributesFromCmdLine()
-    iGFF3Maker.run()
-    
\ No newline at end of file

--- a/commons/tools/GameXmlMaker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,384 +0,0 @@
-#!/usr/bin/env python
-
-##@file GameXmlMaker.py
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import glob
-import sys
-import xml.dom.minidom
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.sql.TableSetAdaptator import TableSetAdaptator
-from commons.core.sql.TableMapAdaptator import TableMapAdaptator
-
-## GameXmlMaker exports .
-#
-class GameXmlMaker(object):
-
-    def __init__(self, inFastaName = "", tablesFileName = "", configFileName = "", verbose = 0):
-        self._inFastaName = inFastaName
-        self._tablesFileName = tablesFileName
-        self._configFileName = configFileName
-        self._verbose = verbose
-        self._gameXMLFileName = ""
-    
-    def setAttributesFromCmdLine(self):
-        description = "GameXmlMaker with -f option <=> step 1 : create gff files (write only the sequence and not the annotation. Only one sequence in each file)\n"
-        description += "GameXmlMaker with -t option <=> step 2 : add annotations in each file\n"
-        parser = RepetOptionParser(description = description)
-        parser.add_option("-f", "--inseq",       dest = "inFastaName",      action = "store",       type = "string", help = "'fasta' file or 'seq' table recording the input sequences (required to generate new '.gamexml' files)", default = "")
-        parser.add_option("-t", "--tablesfile",  dest = "tablesFileName",   action = "store",       type = "string", help = "tabulated file of table name to use to update the GameXML files (fields: tier name, format, table name)", default = "")
-        parser.add_option("-g", "--gameXML",     dest = "gameXML",          action = "store",       type = "string", help = "gameXML file to update (if not specified, update all gameXML files in directory", default = "")
-        parser.add_option("-C", "--config",      dest = "configFileName",   action = "store",       type = "string", help = "configuration file for database connection", default = "")
-        parser.add_option("-v", "--verbose",     dest = "verbose",          action = "store",       type = "int",    help = "verbosity level (default=0, else 1 or 2)", default = 0)
-        (options, args) = parser.parse_args()
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setInFastaName(options.inFastaName)
-        self.setTablesFileName(options.tablesFileName)
-        self.setGameXMLFileName(options.gameXML)
-        self.setConfigFileName(options.configFileName)
-        self.setVerbose(options.verbose)
-        
-    def setInFastaName(self, inFastaName):
-        self._inFastaName = inFastaName
-        
-    def setTablesFileName(self, tablesFileName):
-        self._tablesFileName = tablesFileName
-        
-    def setGameXMLFileName(self, gamexmlFileName):   
-        self._gameXMLFileName = gamexmlFileName
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setVerbose(self, verbose):
-        self._verbose = verbose
-
-    def checkOptions(self):       
-        if self._inFastaName == "" and self._tablesFileName == "":
-            raise Exception("ERROR: options -f or -t required")
-    
-        if self._configFileName != "":
-            if not FileUtils.isRessourceExists(self._configFileName):
-                raise Exception("ERROR: configuration file does not exist!")
-            
-    def run(self):
-        self.checkOptions()
-        if self._verbose > 0:
-            print "START GameXmlMaker"
-            sys.stdout.flush()
-        
-        if self._inFastaName != "":
-            self._createGameXMLFiles()
-        
-        if self._tablesFileName != "":
-            lXMLNewFile = []    
-            if self._gameXMLFileName == "":
-                lXMLNewFile = glob.glob("*.gamexml")
-            else:
-                lXMLNewFile.append(self._gameXMLFileName)  
-                
-            for newGamexmlFile in lXMLNewFile:
-                self._updateGameXMLFileFromlTablesFile(newGamexmlFile)
-            
-        if self._verbose > 0:
-            print "END GFF3Maker"
-            sys.stdout.flush()
-            
-    ## Create as many XML files as sequences given in fasta file.
-    #
-    def _createGameXMLFiles(self):
-        if self._verbose > 0:
-            print "reading file %s" % self._inFastaName
-            sys.stdout.flush()
-            
-        iBioseqDB = BioseqDB(self._inFastaName)
-        
-        if self._verbose > 0:
-            print "nb of sequences = %i" % iBioseqDB.getSize()
-            sys.stdout.flush()
-            
-        for iBioseq in iBioseqDB.db:
-            self._writeGameXMLFileFromBioseq(iBioseq)
-
-    def _writeGameXMLFileFromBioseq(self, iBioseq):
-        """
-        write new '.gamexml' file with <game> and <seq> tags
-        """
-        docXML = xml.dom.minidom.getDOMImplementation().createDocument(None, 'game', None)
-        root = docXML.documentElement
-
-        seq = docXML.createElement('seq')
-        seq.setAttribute('id', iBioseq.getHeader())
-        seq.setAttribute('focus', 'true')
-        root.appendChild(seq)
-        
-        seqNameTag = docXML.createElement('name')
-        seqNameTag.appendChild(docXML.createTextNode(iBioseq.getHeader()))
-        seq.appendChild(seqNameTag)
-        
-        residuesTag = docXML.createElement('residues')
-        residuesTag.appendChild(docXML.createTextNode(iBioseq.getSequence()))
-        seq.appendChild(residuesTag)
-
-        mapPos = docXML.createElement('map_position')
-        root.appendChild(mapPos)
-        
-        arm = docXML.createElement('arm')
-        arm.appendChild(docXML.createTextNode(iBioseq.getHeader()))
-        mapPos.appendChild(arm)
-        
-        span = docXML.createElement('span')
-        mapPos.appendChild(span)
-        
-        start = docXML.createElement('start')
-        start.appendChild(docXML.createTextNode('1'))
-        span.appendChild(start)
-        
-        end = docXML.createElement('end')
-        end.appendChild(docXML.createTextNode(str(iBioseq.getLength())))
-        span.appendChild(end)
-        
-        fileName = "%s.gamexml" % iBioseq.getHeader()
-        docXML.writexml(open(fileName, "w"))
-        
-        if self._verbose > 0:
-            print "file '%s' written" % fileName
-            sys.stdout.flush()
-
-
-    def _parseResultSpanInfo(self, element, type):
-        Qstart = -1
-        Qend = -1
-        Sstart = -1
-        Send = -1
-        query = ""
-        subject = ""
-        identity = 0
-        id = ""
-        
-        if type == "path":
-            Qstart = element.getQueryStart()
-            Qend = element.getQueryEnd()
-            Sstart = element.getSubjectStart()
-            Send = element.getSubjectEnd()
-            query = element.getQueryName()
-            subject = element.getSubjectName()
-            identity = element.getIdentity()
-            id = element.getIdentifier()
-        
-        elif type == "set":
-            Qstart = element.getStart()
-            Qend = element.getEnd()
-            query = element.getName()
-            subject = element.getName()
-            id = element.getId()
-
-        elif type == "map":
-            Qstart = element.getStart()
-            Qend = element.getEnd()
-            query = element.getSeqname()
-            subject = element.getName()
-            id  = "-1"
-            
-        return (Qstart,Qend,Sstart,Send,query,subject,identity,id)
-
-    def _addPathSpan(self, docXML, spanInfo, parent):
-        Qstart,Qend,Sstart,Send,query,subject,identity,id = spanInfo
-        Qstart = str(Qstart)
-        Qend = str(Qend)
-        Sstart = str(Sstart)
-        Send = str(Send)
-        identity = str(identity)
-        id = str(id)
-        
-        resultSpan = docXML.createElement('result_span')
-        parent.appendChild(resultSpan)
-        
-        relship1 = docXML.createElement('seq_relationship')
-        relship1.setAttribute('type', 'query')
-        relship1.setAttribute('seq', query)
-        relship2 = docXML.createElement('seq_relationship')
-        relship2.setAttribute('type', 'subject')
-        relship2.setAttribute('seq', '%s::%s' % (subject, id))
-        score = docXML.createElement('score')
-        resultSpan.appendChild(relship1)
-        resultSpan.appendChild(relship2)
-        score.appendChild(docXML.createTextNode(identity))
-        resultSpan.appendChild(score)
-        sp1 = docXML.createElement('span')
-        sp2 = docXML.createElement('span')
-        start1 = docXML.createElement('start')
-        start1.appendChild(docXML.createTextNode(Qstart))
-        start2 = docXML.createElement('start')
-        start2.appendChild(docXML.createTextNode(Sstart))
-        end1 = docXML.createElement('end')
-        end1.appendChild(docXML.createTextNode(Qend))
-        end2 = docXML.createElement('end')
-        end2.appendChild(docXML.createTextNode(Send))
-        relship1.appendChild(sp1)
-        sp1.appendChild(start1)
-        sp1.appendChild(end1)
-        relship2.appendChild(sp2)
-        sp2.appendChild(start2)
-        sp2.appendChild(end2)
-
-    def _addComputationalAnalysisTags(self, docXML, programName):
-        computationalAnalysis = None
-        
-        lComputationalAnalysis = docXML.getElementsByTagName('computational_analysis')
-        for computationalAnalysisTag in lComputationalAnalysis:
-            if computationalAnalysisTag.getElementsByTagName("program")[0].nodeValue == programName:
-                computationalAnalysis = computationalAnalysisTag
-                break
-            
-        if computationalAnalysis == None :
-            computationalAnalysis = docXML.createElement('computational_analysis')
-            root = docXML.documentElement
-            root.appendChild(computationalAnalysis)
-            
-            program = docXML.createElement('program')
-            program.appendChild(docXML.createTextNode(programName))
-            computationalAnalysis.appendChild(program)
-            
-            db = docXML.createElement('database')
-            db.appendChild(docXML.createTextNode('db'))
-            computationalAnalysis.appendChild(db)
-            
-        return computationalAnalysis
-        
-    def _addResultSetFromPath(self, docXML, iPath, parent):
-        computationalAnalysis = parent
-        resultSet = docXML.createElement('result_set')
-        resultSet.setAttribute('id', str(iPath.getIdentifier())) 
-        computationalAnalysis.appendChild(resultSet)
-        resultSetName = docXML.createElement('name')
-        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iPath.getSubjectName(),str(iPath.getIdentifier()))))
-        resultSet.appendChild(resultSetName)
-        return resultSet
-    
-    def _addResultSetFromSet(self, docXML, iSet, parent):
-        computationalAnalysis = parent
-        resultSet = docXML.createElement('result_set')
-        resultSet.setAttribute('id', str(iSet.getId())) 
-        computationalAnalysis.appendChild(resultSet)
-        resultSetName = docXML.createElement('name')
-        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iSet.getName(),str(iSet.getId()))))
-        resultSet.appendChild(resultSetName)
-        return resultSet
-    
-    def _addResultSetFromMap(self, docXML, iMap, parent):
-        computationalAnalysis = parent
-        resultSet = docXML.createElement('result_set')
-        resultSet.setAttribute('id', "-1") 
-        computationalAnalysis.appendChild(resultSet)
-        resultSetName = docXML.createElement('name')
-        resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iMap.getName(), "-1")))
-        resultSet.appendChild(resultSetName)
-        return resultSet
-
-    def _updateGameXMLFileFromlTablesFile(self, gameXMLFile):
-        docXML = xml.dom.minidom.parse(gameXMLFile) 
-        
-        f = open(self._tablesFileName, "r")
-        line = f.readline()
-            
-        while line: 
-            if not line.startswith("#"):
-                list = line.split()
-                programName = list[0]
-                format = list[1]
-                table = list[2]
-
-                gameXMLFileName = os.path.splitext(gameXMLFile)[0]
-                computationalAnalysis = self._addComputationalAnalysisTags(docXML,programName)
-                if format == "path":    
-                    iDB = DbFactory.createInstance(self._configFileName)
-                    iTpa = TablePathAdaptator(iDB, table)
-                    
-                    lPaths = iTpa.getPathListFromQuery(gameXMLFileName)
-                    dResultSets = {}
-
-                    for iPath in lPaths:
-                        if dResultSets.get(iPath.getIdentifier()) is None:
-                            resultSet = self._addResultSetFromPath(docXML, iPath,computationalAnalysis)
-                            dResultSets[iPath.getIdentifier()] = resultSet
-                        else:
-                            resultSet = dResultSets[iPath.getIdentifier()]
-                        spanInfo = self._parseResultSpanInfo(iPath, "path")
-                        self._addPathSpan(docXML, spanInfo, resultSet)
-                        
-                if format == "set":
-                    iDB = DbFactory.createInstance(self._configFileName)
-                    iTsa = TableSetAdaptator(iDB, table)
-                    lSet = iTsa.getSetListFromSeqName(gameXMLFileName)
-                    
-                    dResultSets = {}
-
-                    for iSet in lSet:
-                        if dResultSets.get(iSet.getId()) is None:
-                            resultSet = self._addResultSetFromSet(docXML, iSet,computationalAnalysis)
-                            dResultSets[iSet.getId()] = resultSet
-                        else:
-                            resultSet = dResultSets[iSet.getId()]
-                            
-                        spanInfo = self._parseResultSpanInfo(iSet, "set")
-                        self._addPathSpan(docXML, spanInfo, resultSet)
-                        
-                if format == "map":
-                    iDB = DbFactory.createInstance(self._configFileName)
-                    iTma = TableMapAdaptator(iDB, table)
-                    lMap = iTma.getMapListFromChr(gameXMLFileName)
-                    dResultSets = {}
-                    for iMap in lMap:
-                        resultSet = self._addResultSetFromMap(docXML, iMap,computationalAnalysis)
-                        spanInfo = self._parseResultSpanInfo(iMap, "map")
-                        self._addPathSpan(docXML, spanInfo, resultSet)
-                        
-            line = f.readline()
-            
-        outputGameXMLFile = open(gameXMLFile, "w")            
-        xmlstr = docXML.toxml()
-        outputGameXMLFile.write(xmlstr)
-        outputGameXMLFile.close()
-            
-if __name__ == "__main__":
-    iGameXmlMaker = GameXmlMaker()
-    iGameXmlMaker.setAttributesFromCmdLine()
-    iGameXmlMaker.run()
-    
\ No newline at end of file

--- a/commons/tools/GetMultAlignAndPhylogenyPerTErefSeq.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,547 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies.
-# usage: GetMultAlignAndPhylogenyPerTErefSeq.py [ options ]
-# options:
-#      -h: this help
-#      -S: step (0: all steps [default], 1:file generation, 2:multiple alignements, 3:phylogenies)
-#      -p: table with the annotations (format=path)
-#      -s: table with the TE reference sequences (format=seq)
-#      -g: table with the genome sequence (format=seq)
-#      -r: name or file with TE reference sequence(s) (all by default)
-#      -m: MSA method (default=Refalign/Map)
-#      -l: minimum length of copies (default=100)
-#      -n: number of longest copies to use (default=20)
-#      -y: minimum  copy proportion compare to references (default=0.5)
-#      -R: keep the reference sequence (only with Refalign)
-#      -C: configuration file
-#      -q: queue name
-#      -c: clean
-#      -d: temporary directory
-#      -v: verbosity level (default=0/1)
-
-import os
-import sys
-import glob
-import ConfigParser
-
-import pyRepet.launcher.programLauncher
-
-from commons.core.coord.PathUtils import PathUtils
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.coord.SetUtils import SetUtils
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.tools.OrientSequences import OrientSequences
-from ConfigParser import MissingSectionHeaderError
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.launcher import LaunchMap
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
-from commons.core.launcher.Launcher import Launcher
-from commons.core.utils.FileUtils import FileUtils
-
-
-LOG_DEPTH = "repet.tools"
-
-## For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies.
-#
-class GetMultAlignAndPhylogenyPerTErefSeq(object):
-    
-    def __init__(self, pathTableName="",refSeqTableName="", genomeSeqTableName="", step=0, mSAmethod="RefAlign",keepRefseq=False, configFileName= "", clean = True, verbosity=3):
-        """
-        Constructor.
-        """
-        self.step = step
-        self._pathTable = pathTableName
-        self._refSeqTable = refSeqTableName
-        self._genomeSeqTable = genomeSeqTableName
-        self._TErefseq = ""
-        self._MSAmethod = mSAmethod
-        self._minCopyLength = 100
-        self._nbLongestCopies = 20
-        self._minPropCopy = 0.5
-        self._keepRefseq = keepRefseq
-        self.setConfigFileName(configFileName)
-        self._queue = ""
-        self._tmpDir = ""
-        self._clean = clean
-        self._verbosity = verbosity
-        self._db = None
-        self._tpaAnnot = None
-        self._tsaRef = None
-        self._pL = pyRepet.launcher.programLauncher.programLauncher()
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-              
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def setAttributesFromCmdLine(self):
-        desc = "For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies.\n"
-        #Commented: it's not true, Config File is mandatory!
-#        desc += "Connection to the database parameters are retrieved from the environment"
-        
-        #TODO: format options as other scripts (have a look at LaunchTemplate)
-        parser = RepetOptionParser(description = desc, epilog = "")
-        parser.add_option("-S", "--step",      dest = "step" ,              action = "store", type = "int", help = "step (0: all steps [default], 1:file generation, 2:multiple alignments, 3:phylogenies)", default = 0 )
-        parser.add_option("-p", "--pathTable", dest = "path",               action= "store",  type = "string", help = "(mandatory) table with the annotations (format=path)",  default = "")
-        parser.add_option("-s", "--refSeqTable",dest = "refSeqTable",       action= "store", type = "string", help = "(mandatory) table with the TE reference sequences (format=seq)",  default = "")
-        parser.add_option("-g", "--genomeSeqTable",dest = "genomeSeqTable",action= "store", type = "string", help = "(mandatory) table with the genome sequence (format=seq)",  default = "")
-        parser.add_option("-r", "--TErefseq",dest = "TErefseq",         action= "store", type = "string", help = "name or file with TE reference sequence(s) (all by default)",  default = "")
-        parser.add_option("-m", "--MSAmethod",dest = "MSAmethod",         action= "store", type = "string", help = "MSA method (default=RefAlign/Map)",  default = "RefAlign")
-        parser.add_option("-l", "--minCopyLength",dest = "minCopyLength",         action= "store", type = "int", help = "minimum length of copies (default=100)",  default = 100)
-        parser.add_option("-n", "--nbLongestCopies",dest = "nbLongestCopies",         action= "store", type = "int", help = "number of longest copies to use (default=20)",  default = 20)
-        parser.add_option("-y", "--minPropCopy",dest = "minPropCopy",         action= "store", type = "float", help = "minimum  copy proportion compare to references (default=0.5)",  default = 0.5)
-        parser.add_option("-R", "--keepRefseq",dest = "keepRefseq",         action="store_true", help = "keep the reference sequence (only with Refalign)",  default = False)
-        parser.add_option("-C", "--config",    dest = "configFileName",     action = "store", type = "string", help = "(mandatory) config file name to set database connection", default = "")
-        parser.add_option("-q", "--queue",dest = "queue",         action= "store", type = "string", help = "queue name",  default = "")
-        parser.add_option("-c", "--clean", action="store_false", dest = "clean", help = "don't clean", default = True) 
-        parser.add_option("-d", "--tmpDir",dest = "tmpDir",         action= "store", type = "string", help = "temporary directory",  default = "")
-        parser.add_option("-v", "--verbosity",   dest = "verbosity",             action = "store", type = "int",    help = "verbosity level (default=0)", default = 0)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setConfigFileName(options.configFileName)
-        self.setStep(options.step)
-        self.setPathTable(options.path)
-        self.setRefSeqTable(options.refSeqTable)
-        self.setGenomeSeqTable(options.genomeSeqTable)
-        self.setTErefseq(options.TErefseq)
-        self.setMSAmethod(options.MSAmethod)
-        self.setMinCopyLength(options.minCopyLength)
-        self.setNbLongestCopies(options.nbLongestCopies)
-        self.setMinPropCopy(options.minPropCopy)
-        self.setKeepRefseq(options.keepRefseq)
-        self.setQueue(options.queue)
-        self.setClean(options.clean)
-        self.setTmpDir(options.tmpDir)
-        self.setVerbosity(options.verbosity)
-        
-    def setStep(self, step):
-        self.step = step
-       
-    def setPathTable(self, path):
-        self._pathTable = path
-       
-    def setRefSeqTable(self, refSeqTable):
-        self._refSeqTable = refSeqTable
-       
-    def setGenomeSeqTable(self, genomeSeqTable):
-        self._genomeSeqTable = genomeSeqTable
-       
-    def setTErefseq(self, TErefseq):
-        self._TErefseq = TErefseq
-       
-    def setMSAmethod(self, MSAmethod):
-        self._MSAmethod = MSAmethod
-        
-    def setMinCopyLength(self, minCopyLength):
-        self._minCopyLength = minCopyLength
-        
-    def setNbLongestCopies(self, nbLongestCopies):
-        self._nbLongestCopies = nbLongestCopies
-        
-    def setMinPropCopy(self, minPropCopy):
-        self._minPropCopy = minPropCopy
-        
-    def setKeepRefseq(self, keepRefseq):
-        self._keepRefseq = keepRefseq
-        
-    def setQueue(self, queue):
-        self._queue = queue
-
-    def setClean(self, clean):
-        self._clean = clean
- 
-    def setTmpDir(self, tmpDir):
-        self._tmpDir = tmpDir 
-                
-    def setVerbosity(self, verbosity):        
-        self._verbosity = verbosity     
-               
-    def setup_env(self):
-        configFileHandle = open(self._configFileName)
-        # Use RepetConfigParser?
-        config = ConfigParser.ConfigParser()
-        try :
-            config.readfp(configFileHandle)
-        except MissingSectionHeaderError:
-            self._logAndRaise("Configuration file %s must begin with a section header" % self._configFileName) 
-
-        os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
-        os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
-        os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
-        os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
-        os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
-        os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
-                  
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-                    
-    def checkAttributes( self ):
-        """
-        Check the attributes are valid before running the algorithm.
-        """
-        if self._pathTable == "":
-            self._logAndRaise("PathTable is mandatory")
-        if self._refSeqTable == "":
-            self._logAndRaise("RefSeqTable is mandatory")  
-        if self._genomeSeqTable == "":
-            self._logAndRaise("GenomeSeqTable is mandatory")
-        if self._configFileName == "":
-            self._logAndRaise("Configuration file is mandatory")
-        else:
-            if FileUtils.isRessourceExists(self._configFileName):
-                self.setup_env()
-            else:
-                self._logAndRaise("Configuration file '%s' does not exist!" % self._configFileName)
-            
-        if ( self.step == 2 or self.step == 3 ) and self._MSAmethod not in ["RefAlign","Map"]:
-            if self._MSAmethod == None or self._MSAmethod == "":
-                self._logAndRaise("Missing method option")
-            self._logAndRaise("Method '%s' not yet available" % ( self._MSAmethod ))
-            
-        if self._tmpDir == "":
-            self._tmpDir  = os.getcwd()    
-            
-    def connectSql(self):  
-        self._db =  DbFactory().createInstance(configFileName = self._configFileName, verbosity = 1)
-        self._tpaAnnot = TablePathAdaptator(self._db, self._pathTable)
-        self._tsaRef = TableSeqAdaptator(self._db,self._refSeqTable)
-                
-    def getNamesOfTErefSeq( self ):
-        """
-        Return a list with the names of reference TEs.
-        """
-        lNamesTErefSeq = []
-        if self._TErefseq == "":
-            lNamesTErefSeq = self._tsaRef.getAccessionsList()
-        else:
-            if os.path.isfile( self._TErefseq ):
-                refseqFileHandler = open( self._TErefseq, "r" )
-                while True:
-                    line = refseqFileHandler.readline()
-                    if line == "":
-                        break
-                    lNamesTErefSeq.append( line[:-1].split("\t")[0] )
-                refseqFileHandler.close()
-            else:
-                lNamesTErefSeq = [ self._TErefseq ]
-                for name in lNamesTErefSeq:
-                    if not self._tsaRef.isAccessionInTable( name ):
-                        self._log.warning("'%s' not in table '%s'" % (name, self._refSeqTable))
-                        lNamesTErefSeq.remove( name )
-        lNamesTErefSeq.sort()
-        self._log.info("nb of TE reference sequences: %d" % (len(lNamesTErefSeq)))
-        return lNamesTErefSeq
-    
-    
-    def getTErefSeqInFastaFiles( self, lNamesTErefSeq ):
-        """
-        Save sequences of reference TEs in fasta files.
-        """
-        for name in lNamesTErefSeq:
-            self._log.debug("save sequence of '%s'..." % ( name ))
-            self._tsaRef.saveAccessionsListInFastaFile( [name], name+".fa" )
-            
-    def getCopiesInFastaFilesPerTErefSeq( self, lNamesTErefSeq ):
-        """
-        Save sequences of TE copies in fasta files.
-        """
-        self._log.info("retrieve the copies...")
-        tsaChr = TableSeqAdaptator( self._db, self._genomeSeqTable )
-        totalNbCopies = 0
-        totalNbSavedCopies = 0
-        for name in lNamesTErefSeq:
-            nbCopies = 0
-            if os.path.exists(name+"_copies.fa"):
-                continue
-            outFile = open( name+"_copies.fa", "w" )
-            self._log.debug("Fetching path nums for subject: %s " % name)
-            lPathNums = self._tpaAnnot.getIdListSortedByDecreasingChainLengthFromSubject(name)
-            nbCopies = len(lPathNums)
-            totalNbCopies += nbCopies
-            self._log.debug("refseq '%s': %d copies" % ( name, nbCopies ))
-            i = 0
-            nbSavedCopies = 0
-            nbSavedFragments = 0
-            lengthRefseq = self._tsaRef.getSeqLengthFromAccession( name )
-            while i < len(lPathNums) and nbSavedCopies < self._nbLongestCopies:
-                lPaths = self._tpaAnnot.getPathListFromId( lPathNums[i] )
-                lSets = PathUtils.getSetListFromQueries( lPaths )
-                copyLength = SetUtils.getCumulLength( lSets )
-                if copyLength >= self._minCopyLength \
-                and copyLength >= self._minPropCopy * lengthRefseq:
-                    bs = tsaChr.getBioseqFromSetList( lSets )
-                    bs.write(outFile)
-                    nbSavedCopies += 1
-                    nbSavedFragments += len(lPaths)
-                i += 1
-            
-            self._log.debug(" (saved: %d copies, %d fragments)\n" % ( nbSavedCopies, nbSavedFragments ) )
-            outFile.close()
-            totalNbSavedCopies += nbSavedCopies
-            if nbSavedCopies == 0 and nbCopies != 0:
-                self._log.warning("No copy >= %d" % ( self._minCopyLength ))
-        self._log.info("nb of copies: %d (%d saved)" % ( totalNbCopies, totalNbSavedCopies ))
-            
-    def filter4Alignments( self, lNamesTErefSeq ):
-        """
-        Filter TE copy sequences according to their length.
-        """
-        self._log.info("filtering copies...")
-        if len(lNamesTErefSeq) == 1:
-            if not os.path.exists( "%s_copies.fa" % ( lNamesTErefSeq[0] ) ):
-                self._logAndRaise("first run step 1")
-            lInFiles = [ "%s_copies.fa" % ( lNamesTErefSeq[0] ) ]
-        else:
-            lInFiles = glob.glob( "*_copies.fa" )
-            if len(lInFiles) == 0:
-                self._logAndRaise("no file '*_copies.fa'")
-        count = 0
-        for inFileName in lInFiles:
-            if os.path.exists( "%s.filtered" % ( inFileName ) ):
-                continue
-            count += 1
-            self._log.debug("TE %d --> %s" %(count,inFileName))
-            FastaUtils.dbLengthFilter( self._minCopyLength, inFileName, verbose=self._verbosity )
-            FastaUtils.dbLongestSequences( self._nbLongestCopies, inFileName+".Sup"+str(self._minCopyLength), verbose=self._verbosity )
-            os.rename( inFileName+".Sup"+str(self._minCopyLength)+".best"+str(self._nbLongestCopies), inFileName+".filtered" )
-            os.remove( inFileName+".Sup"+str(self._minCopyLength) )
-            os.remove( inFileName+".Inf"+str(self._minCopyLength) )
-        self._log.info("files filtered: %d" % (count))
-            
-    def buildInFiles4Launcher( self, lNamesTErefSeq ):
-        """
-        Save sequences of TE copies with reference in fasta files for launcher usage.
-        """
-        self._log.info("building input files for launcher...")
-        for name in lNamesTErefSeq:
-            if os.path.exists( "%s_all.fa.oriented" % ( name ) ):
-                continue
-            if FastaUtils.dbSize( "%s_copies.fa.filtered" % ( name ) ) > 0:
-                os.system( "cat "+name+".fa "+ name+"_copies.fa.filtered > " + name+"_all.fa" )
-                ors = OrientSequences(inFileName= "%s_all.fa" %(name), prgToOrient="mummer", clean=True, verbosity =self._verbosity - 1)
-                ors.run()
-                ors.clean()
-        if len( glob.glob("*_all.fa.oriented") ) == 0:
-            self._logAndRaise("no copies")
-        self._log.info("done building input files for launcher...")   
-            
-    def renameFile( self, fromName, toName):
-        lFiles = glob.glob( "*%s" %fromName )
-        for f in lFiles:
-            os.rename( f, f.replace(fromName,toName))
-    
-    def _preparejobs(self, iLauncher, cDir):
-        self._log.info("Preparing Align jobs")
-        lCmdsTuples = []
-        print(self.queriesDir,self.alignFileSuffix)
-        queryFiles = glob.glob("%s/%s" % (self.queriesDir,self.alignFileSuffix))
-        print("queryFiles",queryFiles)
-        for queryFile in queryFiles:#os.listdir(self.queriesDir):
-            lCmds = []
-            lCmdStart = []
-            lCmdFinish = [] #['shutil.move("%s/*" %newDir, "../" )']
-            queryFilePath = os.path.join(self.queriesDir,queryFile)
-            lCmds.append(self._createLaunchAlignCommands(iLauncher, queryFilePath))
-            #lCmdFinish.append("shutil.move(\"%s.%s\", \"%s/%s.%s\")" % (benchName,self.outputformat,self.resultsDir,benchName,self.outputformat))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))   
-        self._log.info("Finished preparing Align jobs")
-        return  lCmdsTuples
-
-    def _preparePhyMljobs(self, iLauncher, cDir):
-        self._log.info("Preparing PhyMl jobs")
-        lCmdsTuples = []
-        queryFiles = glob.glob("%s/%s" % (self.queriesDir,self.phyloFileSuffix))
-        print("queryFiles",queryFiles)
-        for queryFile in queryFiles:#os.listdir(self.queriesDir):
-            lCmds = []
-            lCmdStart = []
-            lCmdFinish = [] #['shutil.move("%s/*" %newDir, "../" )']
-            queryFilePath = os.path.join(self.queriesDir,queryFile)
-            lCmds.append(self._createLaunchPhyMLCommands(iLauncher, queryFilePath))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))   
-        self._log.info("Finished preparing PhyMl jobs")
-        return  lCmdsTuples
-    
-    def _createLaunchAlignCommands(self, iLauncher, query):
-        if self._MSAmethod == "Map":
-            prg = "LaunchMap.py"
-        elif self._MSAmethod == "RefAlign":
-            prg = "LaunchRefAlign.py"
-            
-        lArgs = []
-        lArgs.append("-i %s" % query)
-        lArgs.append(" -o %s.fa_aln" % query)    
-        lArgs.append("-v 1" )
-        
-        if self._MSAmethod == "RefAlign" and self._keepRefseq:
-            lArgs.append("-r " )
-        
-        self._log.debug("Prepared Align commands : %s %s" % (prg, " ".join(lArgs)))
-        
-        
-        return iLauncher.getSystemCommand("%s" % prg, lArgs)
-                 
-    def launchMultAlignments(self, lNamesTErefSeq):
-        """
-            Make multiple alignments via Map for each TE family
-        """
-        self.queriesDir =  os.getcwd()
-        
-        if len(lNamesTErefSeq) == 1:
-            self.alignFileSuffix = "%s_all.fa.oriented" % (lNamesTErefSeq[0])
-        else:
-            self.alignFileSuffix = "*_all.fa.oriented"
-        
-        queue = self._queue
-        cDir = os.getcwd()
-        tmpDir =  self._tmpDir 
-        groupid = "%s_%s" % ( self._refSeqTable, self._MSAmethod )
-        acronym = "Align"
-        iDb = DbFactory.createInstance(configFileName=self._configFileName)
-        iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-        iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid)
-        lCmdsTuples = self._preparejobs(iLauncher, cDir)
-        iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._clean) 
-            
-        self.renameFile("_all.fa.oriented.fa_aln", "_all.fa.oriented_%s.fa_aln" % (self._MSAmethod.lower()) )
-            
-#    def __makeMultAlignments( self, lNamesTErefSeq ):
-#        """
-#        Make multiple alignments via Map or Refalign for each TE family
-#        """
-#        self._pL.reset("")
-#        if self._MSAmethod == "Map":
-#            
-#            prg = os.environ["REPET_PATH"] + "/bin/srptMAP.py"
-#        elif self._MSAmethod == "RefAlign":
-#            prg = os.environ["REPET_PATH"] + "/bin/srptRefalign.py"
-#        cmd = prg
-#        cmd += " -g %s_%s" % ( self._refSeqTable, self._MSAmethod )
-#        cmd += " -q %s" % ( os.getcwd() )
-#        if len(lNamesTErefSeq) == 1:
-#            cmd += " -S %s_all.fa.oriented" % ( lNamesTErefSeq[0] )
-#        else:
-#            cmd += " -S '*_all.fa.oriented'"
-#        cmd += " -Q %s" % ( self._queue )
-#        cmd += " -C %s" % ( self._configFileName )
-#        if self._MSAmethod == "Refalign" and self._keepRefseq:
-#            cmd += " -r"
-#        if not self._clean :
-#            cmd += " -c"
-#        if self._tmpDir != "":
-#            cmd += " -d %s" % ( self._tmpDir )
-#        cmd += " -v %d" % ( self._verbosity )
-#        self._pL.launch( prg, cmd )
-#        lFiles = glob.glob( "*_all.fa.oriented.fa_aln" )
-#        for f in lFiles:
-#            os.rename( f, f.replace("_all.fa.oriented.fa_aln","_all.fa.oriented_%s.fa_aln" % (self._MSAmethod.lower()) ) )
-            
-            
-    def filter4phylogenies( self, verbosity=0 ):
-        """
-        Filter TE copy alignment for better phylogenies.
-        """
-        self._log.info("Filtering MSA")
-        lInFiles = glob.glob( "*_all.fa.oriented_%s.fa_aln" % ( self._MSAmethod.lower() ) )
-        count = 0
-        for inFileName in lInFiles:
-            count += 1    
-            self._log.debug("clean MSA %d --> %s" % (count,inFileName))  
-            alignDB = AlignedBioseqDB()
-            alignDB.load(inFileName)
-            alignDB.cleanMSA()
-            if alignDB.getSize() > 2:                
-                alignDB.save( inFileName + ".clean" )
-                self._log.debug("clean!")
-            else:
-                self._log.debug("skip!")
-        self._log.info("MSA cleaned: %d" % count)
-            
-
-    def _createLaunchPhyMLCommands(self, iLauncher, query):
-#        prg = os.environ["REPET_PATH"] + "/bin/srptPhyML.py"
-#        cmd = prg
-#        cmd += " -g %s_PHY_%s" % ( self._refSeqTable, os.getpid() )
-#        cmd += " -q %s" % ( os.getcwd() )
-#        cmd += " -S '*_all.fa.oriented_%s.fa_aln.clean'" % ( self._MSAmethod.lower() )
-#        cmd += " -Q %s" % ( self._queue )
-#        cmd += " -C %s" % ( self._configFileName )
-
-        prg = "LaunchPhyML.py"
-        lArgs = []
-        lArgs.append("-i %s" % query)
-        lArgs.append("-o %s.fa_phylo" % query)    
-        lArgs.append("-v %d" % (self._verbosity-1))
-        
-        self._log.debug("Prepared Phyml commands : %s %s" % (prg, " ".join(lArgs)))
-        return iLauncher.getSystemCommand("%s" % prg, lArgs)
-   
-    def makePhylogenies( self ):
-        """
-        Launch PhyML on each TE family.
-        """
-        self.phyloFileSuffix = "*_all.fa.oriented_%s.fa_aln.clean" % ( self._MSAmethod.lower() )
-        
-        queue = self._queue
-        cDir = os.getcwd()
-        tmpDir =  self._tmpDir 
-        groupid = "%s_PHY_%s" % ( self._refSeqTable, os.getpid() )
-        acronym = "Phylo"
-        iDb = DbFactory.createInstance(configFileName=self._configFileName)
-        iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-        iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid)
-        lCmdsTuples = self._preparePhyMljobs(iLauncher, cDir)
-        iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._clean) 
-
-        
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        self.checkAttributes()
-        self._log.info("START GetMultAlignAndPhylogenyPerTErefSeq.py STEP %d" % self.step)
-        self.connectSql()
-            
-    def end( self ):
-        """
-        Useful commands before ending the program.
-        """
-        self._db.close()
-        self._log.info("END GetMultAlignAndPhylogenyPerTErefSeq.py STEP %d" % self.step)
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self.start()
-        lNamesTErefSeq = self.getNamesOfTErefSeq()
-        self._log.debug("lNamesTErefSeq: %s" %  " ".join(lNamesTErefSeq))
-        
-        if self.step in [0, 1]:
-            self.getTErefSeqInFastaFiles( lNamesTErefSeq )
-            self.getCopiesInFastaFilesPerTErefSeq( lNamesTErefSeq )
-            
-        if self.step in [0, 2]:
-            self.filter4Alignments(lNamesTErefSeq)
-            self.buildInFiles4Launcher(lNamesTErefSeq)
-            self.launchMultAlignments(lNamesTErefSeq)
-            
-        if self.step in [0, 3]:
-            self.filter4phylogenies(verbosity=self._verbosity)
-            self.makePhylogenies()
-        self.end()
-        
-if __name__ == "__main__":
-    iGetMultAlignAndPhylogenyPerTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq()
-    iGetMultAlignAndPhylogenyPerTErefSeq.setAttributesFromCmdLine()
-    iGetMultAlignAndPhylogenyPerTErefSeq.run()
-    

--- a/commons/tools/GetSpecificTELibAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,178 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import os
-import sys
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.core.LoggerFactory import LoggerFactory
-
-LOG_DEPTH = "repet.tools"  
-LOG_FORMAT = "%(message)s"
-#TODO: use configuration file
-
-## Get 3 annotation files, using output from TEannot:
-#- consensus with one or more full length copy, 
-#- consensus with one or more full length fragment,
-#- consensus without copy
-
-class GetSpecificTELibAccordingToAnnotation(object):
-    
-    def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
-        self._inInfoFileName = inInfoFileName
-        self._tableName = tableName
-        self._verbose = verbose
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose, LOG_FORMAT)
-    
-    def setAttributesFromCmdLine(self):
-        desc = "Splits a GiveInfoTEannot \"statsPerTE.txt\" file in 3 subfiles containing consensus which have at least one copy, one full length fragment or one full length copy. "
-        desc += "A TEs library is built according to each category. Connection to the database parameters are retrieved from the environment"
-        
-        examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
-        examples += "\t$ python GetSpecificTELibAccordingToAnnotation.py -i MyTEannotAnalysis_chr_allTEs_nr_noSSR_join_path_statsPerTE.txt -t MyTEannotAnalysis_refTEs_seq"
-        examples += "\n\t"
-        examples += "\n\n"
-        
-        parser = RepetOptionParser(description = desc, epilog = examples)
-        parser.add_option("-i", "--file",     dest = "inInfoFileName",  action = "store", type = "string", help = "input file (mandatory) = output file from GiveInfoTEannot.py (e.g. <project_name>_chr_allTEs_nr_noSSR_join_path_statsPerTE.txt)",  default = "")
-        parser.add_option("-t", "--table",    dest = "tableName",       action = "store", type = "string", help = "table name of TEs sequences (mandatory, seq format, e.g. <project_name>_refTEs_seq)", default = "")
-        parser.add_option("-v", "--verbose",  dest = "verbose",         action = "store", type = "int",    help = "verbosity level (default=0, else 1)", default = 0)
-        (options, args) = parser.parse_args()
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setInInfoFileName(options.inInfoFileName)
-        self.setTableName(options.tableName)
-        self.setVerbose(options.verbose)
-        
-    def setTableName(self, tableName):
-        self._tableName = tableName
-        
-    def setInInfoFileName(self, inInfoFileName):
-        self._inInfoFileName = inInfoFileName
-        
-    def setVerbose(self, verbose):
-        self._verbose = verbose
-   
-    def checkOptions(self):
-        if self._inInfoFileName != "":
-            if not FileUtils.isRessourceExists(self._inClassifFileName):
-                self._logAndRaise("ERROR: Input GiveInfoTEannot.txt output file does not exist!")
-        else:
-            self._logAndRaise("ERROR: No specified -i option!")
-        
-        if self._tableName != "":
-            iDb = DbMySql()
-            if not iDb.doesTableExist(self._tableName):
-                self._logAndRaise("ERROR: table does not exist!")
-            iDb.close()
-        else:
-            self._logAndRaise("ERROR: No specified -t option!")
-
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-
-    def writeFastaFileFromGiveInfoTEAnnot(self, fileName):
-        fFileHandler = open(fileName,"r")
-        lineHeader = fFileHandler.readline()
-        line = fFileHandler.readline()
-        lConsensusName = []
-        while line:         
-            lConsensusName.append(line.split()[0])
-            line = fFileHandler.readline()
-
-        fFileHandler.close()
-        iDb = DbMySql()
-        iTSA = TableSeqAdaptator(iDb, self._tableName)
-        outPutFileName = "%s.fa" % os.path.splitext(fileName)[0]
-        iTSA.saveAccessionsListInFastaFile(lConsensusName, outPutFileName)
-        iDb.close()
-                      
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbose)
-
-        outInfoFileNameFullCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
-        outInfoFileNameCopy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
-        outInfoFileNameFullFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0]
-        
-        outInfoFileFullCopy = open(outInfoFileNameFullCopy, "w")
-        outInfoFileCopy = open(outInfoFileNameCopy, "w")
-        outInfoFileFullFrag = open(outInfoFileNameFullFrag, "w")
-            
-        self._log.info("START GetSpecificTELibAccordingToAnnotation\n input info file: %s" % self._inInfoFileName)
-        
-        inFileFh = open(self._inInfoFileName, "r")
-        line = inFileFh.readline()
-        lHeaders = line.split()
-        if "fullLgthCopies" not in lHeaders:
-            self._logAndRaise("ERROR: No headers in %s!" % self._inInfoFileName )
-        
-        outInfoFileFullCopy.write(line)
-        outInfoFileCopy.write(line)
-        outInfoFileFullFrag.write(line)
-            
-        line = inFileFh.readline()
-        while line:
-            dTokens = {}
-            for index, token in enumerate(line.split()):
-                dTokens[lHeaders[index]] = token
-                    
-            if int(dTokens["fullLgthCopies"]) > 0:
-                outInfoFileFullCopy.write(line)
-            if int(dTokens["copies"]) > 0:
-                outInfoFileCopy.write(line)
-            if int(dTokens["fullLgthFrags"]) > 0:
-                outInfoFileFullFrag.write(line)
-            line = inFileFh.readline()
-                
-        inFileFh.close()
-        outInfoFileFullCopy.close()
-        outInfoFileCopy.close()
-        outInfoFileFullFrag.close()
-        
-        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullCopy)
-        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameCopy)
-        self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullFrag)
-        
-        self._log.info("END GetSpecificTELibAccordingToAnnotation\n" )
-            
-        return 0
-
-if __name__ == '__main__':
-    iGetTELib = GetSpecificTELibAccordingToAnnotation()
-    iGetTELib.setAttributesFromCmdLine()
-    iGetTELib.run() 
-    
\ No newline at end of file

--- a/commons/tools/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-from commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align import HmmpfamOutput2align
-from commons.pyRepetUnit.align.hmmOutputParsing.HmmscanOutput2align import HmmscanOutput2align
-from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat
-from commons.core.utils.FileUtils import FileUtils
-
-#------------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the command-line parameters.
-    """
-
-    print ""
-    print "usage: ",sys.argv[0],"[ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='hmmpfam Output' or 'hmmscan Output)"
-    print "     -o: name of the output file (default=inFileName+'.align')"
-    print "     -T: name of the consensus File (To launch the transformation of aa positions in nt positions and Filter positive score, default=no transformation)"
-    print "     -v: verbose (default=0/1/2)"
-    print "     -p: name of program (default=hmmpfam, but you can specify hmmscan too)"
-    print "     -c: clean"
-    print ""
-
-#------------------------------------------------------------------------------
-
-def main():
-
-    inFileName = ""
-    outFileName = ""
-    verbose = 0
-    clean = False
-    consensusFileName = ""
-    program = "hmmpfam"
-
-    try:
-        opts,args=getopt.getopt(sys.argv[1:],"hi:o:T:v:p:c")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-T":
-            consensusFileName = a
-        elif o == "-v":
-            verbose = int(a)
-        elif o == "-p":
-            program = a
-        elif o == "-c":
-            clean = True
-            
-    if inFileName == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "beginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    if outFileName == "":
-        outFileName = "%s.align" % ( inFileName )
-    
-    if program == "hmmpfam":
-        hmmpfamOutput2align = HmmpfamOutput2align( )
-        hmmpfamOutput2align.setInputFile( inFileName )
-        if consensusFileName == "":
-            hmmpfamOutput2align.setOutputFile( outFileName )
-        else:
-            hmmpfamOutput2align.setOutputFile( outFileName + ".tmp" )
-        hmmpfamOutput2align.run( )
-    else:
-        if program == "hmmscan":
-            hmmscanOutput2align = HmmscanOutput2align( )
-            hmmscanOutput2align.setInputFile( inFileName )
-            if consensusFileName == "":
-                hmmscanOutput2align.setOutputFile( outFileName )
-            else:
-                hmmscanOutput2align.setOutputFile( outFileName + ".tmp" )
-            hmmscanOutput2align.run( )
-        else:
-            print "\nWarning: You must specify a valid program (-p option). Only hmmpfam or hmmscan are supported !\n"
-    
-    if consensusFileName != "":
-        alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()
-        alignTransformation.setInFileName( outFileName + ".tmp" )
-        alignTransformation.setOutFileName( outFileName )
-        alignTransformation.setConsensusFileName( consensusFileName ) 
-        alignTransformation.setIsFiltered(True)
-        alignTransformation.run()
-        os.remove( outFileName + ".tmp" )
-        
-    
-    if clean == True:
-        os.remove( inFileName )
-
-    if verbose > 0:
-        if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )):
-            print "%s finished successfully" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-        else:
-            print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-
-    return 0
-
-#------------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/tools/LaunchBlaster.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,204 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-import subprocess
-
-LOG_DEPTH = "repet.tools"
-
-##Launch BLASTER
-#
-class LaunchBlaster(object):
-    
-    def __init__(self, queryFileName = "", subjectFileName = "", evalue = 1e-300, identity = 90, length = 100, doAllByall = False, type = "ncbi", nbCPU = 1, program="blastn",extraParams="", doClean = False, verbosity = 0):
-        self._queryFileName = queryFileName
-        self.setSubjectFileName(subjectFileName)
-        self._eValue = evalue
-        self._identity = identity
-        self._length = length
-        self._doAllByall = doAllByall
-        self._blastType = type
-        self._program = program
-        self._extraParams = extraParams
-        self._nbCPU = nbCPU
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch Blaster."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchBlaster.py -q query.fa -v 0"
-        epilog += "\n\t"
-        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
-        epilog += "\t$ python LaunchBlaster.py -q query.fa -s nr.fa -c -v 2"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [compulsory] [format: fasta]",       default = "")
-        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [default: query] [format: fasta]", default = "")
-        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "Blast e-value [default: 1e-300]",                           default = "1e-300")
-        parser.add_option("-d", "--id",         dest = "identity",      action = "store",       type = "int",    help = "Blast identity [default: 90]",                             default = 90)
-        parser.add_option("-l", "--length",     dest = "length",        action = "store",       type = "int",    help = "Minimal hit length [default: 100]",                        default = 100)
-        parser.add_option("-a", "--aba",        dest = "doAllByall",    action = "store_true",                   help = "all-by-all Blast [default: False]",                        default = False)
-        parser.add_option("-t", "--type",       dest = "type",          action = "store",       type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]",         default = "ncbi")
-        parser.add_option("-u", "--program",    dest = "program",       action = "store",       type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]",         default = "blastn")
-        parser.add_option("-x", "--extraParams",dest = "extraParams",   action = "store",       type = "string", help = "Additional blast program parameters[default: '']",         default = "")
-        parser.add_option("-n", "--ncpu",       dest = "cpu",           action = "store",       type = "int",    help = "Number of CPUs to use [default: 1]",                       default = 1)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setQueryFileName(options.query)
-        self.setSubjectFileName(options.subject)
-        self.setEvalue(options.evalue)
-        self.setIdentity(options.identity)
-        self.setLength(options.length)
-        self.setDoAllByall(options.doAllByall)
-        self.setType(options.type)
-        self.setProgram(options.program)
-        self.setExtraParams(options.extraParams)
-        self.setCPU(options.cpu)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-        
-    
-    def setQueryFileName(self, queryFileName):
-        self._queryFileName = queryFileName
-        
-    def setSubjectFileName(self, subjectFileName):
-        if subjectFileName == "":
-            self._subjectFileName = self._queryFileName
-        else:
-            self._subjectFileName = subjectFileName
-        
-    def setEvalue(self, evalue):
-        self._eValue = evalue
-        
-    def setIdentity(self, identity):
-        self._identity = identity
-        
-    def setLength(self, length):
-        self._length = length
-        
-    def setDoAllByall(self, doAllByall):
-        self._doAllByall = doAllByall
-        
-    def setType(self, blastType):
-        self._blastType = blastType
-        
-    def setProgram(self, program):
-        self._program = program
-        
-    def setExtraParams(self, extraParams):
-        self._extraParams = extraParams
-        
-    def setCPU(self, cpu):
-        self._nbCPU = cpu
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._queryFileName == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-        
-        lBlastType = ["ncbi", "wu", "blastplus"]    
-        if self._blastType.lower() not in lBlastType:
-            self._logAndRaise("ERROR: unknown Blast type '%s' - correct values are %s" % (self._blastType, lBlastType))
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-
-    def _getBlasterCmd(self):
-        lArgs = []
-        lArgs.append("-n %s" % self._program)
-        lArgs.append("-q %s" % self._queryFileName)
-        lArgs.append("-s %s" % self._subjectFileName)
-        lArgs.append("-B %s" % self._queryFileName)
-        if self._doAllByall:
-            lArgs.append("-a")
-        lArgs.append("-E %s" % self._eValue)
-        lArgs.append("-L %s" % self._length)
-        lArgs.append("-I %s" % self._identity)
-        if self._blastType == "ncbi": 
-            lArgs.append("-N")
-            lArgs.append("-p '-a %s %s'" % (self._nbCPU, self._extraParams))
-        elif self._blastType == "wu":
-            lArgs.append("-W")
-            lArgs.append("-p '-cpus=%s %s'" % (self._nbCPU, self._extraParams))
-        elif self._blastType == "blastplus":
-            lArgs.append("-X")
-            lArgs.append("-p '-num_threads %s %s'" % (self._nbCPU, self._extraParams))
-# TODO: check the check option at the beginning of step 2 to allow to launch megablast for blast and blast+
-#    elif config.get(sectionName, "blast") == "mega":
-#        lArgs.append("-N")
-#        lArgs.append("-n megablast")
-#    elif config.get(sectionName, "blast") == "megablastplus":
-#        lArgs.append("-X")
-#        lArgs.append("-n megablast")
-        if self._doClean:
-            lArgs.append("-c")
-        lArgs.append("-v %i" % (self._verbosity - 1))
-        return self._getSystemCommand("blaster", lArgs)
-    
-    def _getSystemCommand(self, prg, lArgs):
-        systemCmd = prg 
-        for arg in lArgs:
-            systemCmd += " " + arg
-        return systemCmd
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START LaunchBlaster")
-        self._log.debug("Query file name: %s" % self._queryFileName)
-        self._log.debug("Subject file name: %s" % self._subjectFileName)
-        if self._doClean:
-            self._log.warning("Files will be cleaned")
-        cmd = self._getBlasterCmd()
-        process = subprocess.Popen(cmd, shell = True)
-        self._log.debug("Running : %s" % cmd)
-        process.communicate()
-        if process.returncode != 0:
-            self._logAndRaise("ERROR when launching '%s'" % cmd)
-        self._log.info("END LaunchBlaster")
-
-if __name__ == "__main__":
-    iLaunch = LaunchBlaster()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/tools/LaunchBlasterInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,301 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import shutil
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
-from commons.core.launcher.Launcher import Launcher
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
-from commons.tools.MergeMatchsFiles import MergeMatchsFiles
-
-LOG_DEPTH = "repet.tools"
-
-##Launch BLASTER in parallel
-#
-class LaunchBlasterInParallel(object):
-    
-    def __init__(self, queryDirectory = "", subjectFilePath = "", outFileName = "", configFileName = "", groupId = "", queryPattern = ".*\.fa", \
-                 doAllByall = False, nbCPU = 1, eValue="1e-300", type = "ncbi", program="blastn", extraParams="", verbosity = 0):
-        self._queryDirectory = queryDirectory
-        self._queryPattern = queryPattern
-        self.setSubjectFilePath(subjectFilePath)
-        self._outFileName = outFileName
-        self._configFileName = configFileName
-        self.setGroupId(groupId)
-        self._doAllByall = doAllByall
-        self._blastType = type
-        self._program = program
-        self._extraParams = extraParams
-        self._nbCPU = nbCPU
-        self._jobSectionName = "jobs"
-        self._blasterSectionName = "alignment"
-        self._prepareDataSectionName = "prepare_data"
-        self._eValue = eValue
-        
-        self._doClean = None
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch Blaster in parallel."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -v 0"
-        epilog += "\n\t"
-        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
-        epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -s nr.fa -c -v 2"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta directory absolute path [compulsory]",         default = "")
-        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta absolute path [compulsory] [format: fasta]", default = "")
-        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output align file name [compulsory] [format: align]",      default = "")
-        parser.add_option("-C", "--config",     dest = "configFileName",action = "store",       type = "string", help = "configuration file name [compulsory] [format: cfg]",       default = "")
-        parser.add_option("-g", "--groupId",    dest = "groupId",       action = "store",       type = "string", help = "jobs groupId [default: Blaster_<pid>]",                    default = "")
-        parser.add_option("-p", "--queryPattern",dest = "queryPattern", action = "store",       type = "string", help = "query file pattern [default: .*\.fa]",                     default = ".*\.fa")
-        parser.add_option("-a", "--aba",        dest = "doAllByall",    action = "store_true",                   help = "all-by-all Blast [default: False]",                        default = False)
-        parser.add_option("-e", "--eValue",     dest = "eValue",        action = "store",       type = "string", help = "Blast e-value [default: 1e300]",                           default = "1e-300")
-        parser.add_option("-t", "--type",       dest = "type",          action = "store",       type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]",         default = "ncbi")
-        parser.add_option("-u", "--program",    dest = "program",       action = "store",       type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]",         default = "blastn")
-        parser.add_option("-x", "--extraParams",dest = "extraParams",   action = "store",       type = "string", help = "Additional blast program parameters[default: '']",         default = "")
-        parser.add_option("-n", "--ncpu",       dest = "cpu",           action = "store",       type = "int",    help = "Number of CPUs to use [default: 1]",                       default = 1)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setQueryDirectory(options.query)
-        self.setQueryPattern(options.queryPattern)
-        self.setSubjectFilePath(options.subject)
-        self.setOutFileName(options.outFileName)
-        self.setConfigFileName(options.configFileName)
-        self.setGroupId(options.groupId)
-        self.setDoAllByall(options.doAllByall)
-        self.setEValue(options.eValue)
-        self.setType(options.type)
-        self.setProgram(options.program)
-        self.setExtraParams(options.extraParams)
-        self.setCPU(options.cpu)
-        self.setVerbosity(options.verbosity)
-        
-    def setQueryDirectory(self, queryDirectory):
-        self._queryDirectory = queryDirectory
-        
-    def setQueryPattern(self, queryPattern):
-        self._queryPattern = queryPattern
-        
-    def setSubjectFilePath(self, subjectFilePath):
-        self._subjectFilePath = subjectFilePath
-        self._subjectFileName = os.path.basename(subjectFilePath)
-            
-    def setOutFileName(self, outFileName):
-        self._outFileName = outFileName
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setGroupId(self, groupId):
-        if groupId == "":
-            self._groupId = "Blaster_%s" % os.getpid()
-        else:
-            self._groupId = groupId
-        
-    def setDoAllByall(self, doAllByall):
-        self._doAllByall = doAllByall
-        
-    def setType(self, blastType):
-        self._blastType = blastType
-        
-    def setProgram(self, program):
-        self._program = program
-        
-    def setExtraParams(self, extraParams):
-        self._extraParams = extraParams
-        
-    def setEValue(self, eValue):
-        self._eValue = eValue
-        
-    def setCPU(self, cpu):
-        self._nbCPU = cpu
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._queryPattern == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def _checkConfig(self):       
-        iConfigRules = ConfigRules()
-        iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True)
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool")
-        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="blast", mandatory=True, type="string", set = ("ncbi", "blastplus", "wu"))
-        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="Evalue", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="length", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="identity", mandatory=True, type="string")
-
-        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
-        self._iConfig = iConfigChecker.getConfig()
-        self._setAttributesFromConfig()
-        
-    def _setAttributesFromConfig(self):
-        self._chunkLength = self._iConfig.get(self._prepareDataSectionName, "chunk_length")
-        self._chunkOverlap = self._iConfig.get(self._prepareDataSectionName, "chunk_overlap")
-        self._resources = self._iConfig.get(self._jobSectionName, "resources")
-        self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir")
-        self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy")
-        self._doClean = self._iConfig.get(self._jobSectionName, "clean")
-        self._blastType = self._iConfig.get(self._blasterSectionName, "blast")
-        self._eValue = self._iConfig.get(self._blasterSectionName, "Evalue")
-        self._length = self._iConfig.get(self._blasterSectionName, "length")
-        self._identity = self._iConfig.get(self._blasterSectionName, "identity")
-        
-        if self._isCopyOnNode and not self._tmpDir:
-            self._isCopyOnNode = False
-        self._log.debug("The copy option is: %s." % self._isCopyOnNode)
-
-    def _getLaunchBlasterCmd(self, iLauncher, file):
-        lArgs = []
-        lArgs.append("-u %s" % self._program)
-        lArgs.append("-q %s" % file)
-        lArgs.append("-s %s" % self._subjectFileName)
-        if self._doAllByall:
-            lArgs.append("-a")
-        lArgs.append("-e %s" % self._eValue)
-        lArgs.append("-l %s" % self._length)
-        lArgs.append("-d %s" % self._identity)
-        lArgs.append("-t %s" % self._blastType)
-        lArgs.append("-x '%s'" % self._extraParams)
-        if self._doClean:
-            lArgs.append("-c")
-        lArgs.append("-v %i" % (self._verbosity - 1))
-        return iLauncher.getSystemCommand("LaunchBlaster.py", lArgs)
-    
-    def _getRmvPairAlignInChunkOverlapsCmd(self, iLauncher, inFileName, outFileName):
-        lArgs = []
-        lArgs.append("-i %s" % inFileName)
-        lArgs.append("-l %s" % self._chunkLength)
-        lArgs.append("-o %s" % self._chunkOverlap)
-        lArgs.append("-m 10")
-        lArgs.append("-O %s" % outFileName)
-        lArgs.append("-v %d" % (self._verbosity - 1))
-        return iLauncher.getSystemCommand("RmvPairAlignInChunkOverlaps.py", lArgs)
-
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkConfig()
-        self._checkOptions()
-        self._log.info("START LaunchBlasterInParallel")
-        self._log.debug("Query file name: %s" % self._queryPattern)
-        self._log.debug("Subject file name: %s" % self._subjectFileName)
-        
-        cDir = os.getcwd()
-        if not self._tmpDir:
-            self._tmpDir = cDir
-    
-        acronym = "Blaster"
-        iDb = DbFactory.createInstance()
-        jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-        iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode)
-
-        lCmdsTuples = []
-        fileSize = float(os.path.getsize(self._subjectFilePath) + 5000000) / 1000000000
-        
-        lCmdSize = []
-        lCmdCopy = []
-        if self._isCopyOnNode:
-            lCmdSize.append("fileSize = %f" % fileSize)       
-            lCmdCopy.append("shutil.copy(\"%s\", \".\")" % self._subjectFilePath)
-            
-        lFiles = FileUtils.getFileNamesList(self._queryDirectory, self._queryPattern)
-        for file in lFiles:
-            lCmds = []
-            lCmds.append(self._getLaunchBlasterCmd(iLauncher, file))
-            lCmdStart = []
-            if self._isCopyOnNode:
-                lCmdStart.append("os.symlink(\"../%s\", \"%s\")" % (self._subjectFileName, self._subjectFileName))
-                lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (self._queryDirectory, file))
-            else:
-                lCmdStart.append("os.symlink(\"%s\", \"%s\")" % (self._subjectFilePath, self._subjectFileName))
-                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (self._queryDirectory, file, file))
-            lCmdFinish = []
-            lCmdFinish.append("if os.path.exists(\"%s.align\"):" % file)
-            lCmdFinish.append("\tshutil.move(\"%s.align\", \"%s/.\" )" % (file, cDir))
-            lCmdFinish.append("shutil.move(\"%s.param\", \"%s/.\" )" % (file, cDir))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy))
-        
-        iLauncher.runLauncherForMultipleJobs("Blaster", lCmdsTuples, self._doClean, self._isCopyOnNode)
-
-        tmpFileName = "tmp_%s.align" % os.getpid()
-        iMMF = MergeMatchsFiles("align", "tmp_%s" % os.getpid(), allByAll = self._doAllByall, clean = self._doClean)
-        iMMF.run()
-
-        if self._doAllByall:
-            iDb = DbFactory.createInstance()
-            jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-            iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, "%s_RmvPairAlignInChunkOverlaps" % self._groupId)
-        
-            lCmdsTuples = []
-            lCmds = []
-            lCmds.append(self._getRmvPairAlignInChunkOverlapsCmd(iLauncher, tmpFileName, self._outFileName))
-            lCmdStart = [] 
-            lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, tmpFileName, tmpFileName))
-            lCmdFinish = []
-            lCmdFinish.append("shutil.move(\"%s\", \"%s/.\")" % (self._outFileName, cDir))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
-        
-            iLauncher.runLauncherForMultipleJobs("RmvPairAlignInChunkOverlaps", lCmdsTuples, self._doClean)
-            if self._doClean:
-                os.remove(tmpFileName)
-        else:
-            shutil.move(tmpFileName, self._outFileName)
-            
-        if self._doClean:
-            FileUtils.removeFilesByPattern("*.param")
-        
-        self._log.info("END LaunchBlasterInParallel")
-
-if __name__ == "__main__":
-    iLaunch = LaunchBlasterInParallel()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/tools/LaunchMatcherInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,285 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
-from commons.core.launcher.Launcher import Launcher
-from commons.core.launcher.LauncherUtils import LauncherUtils
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
-from commons.core.coord.AlignUtils import AlignUtils
-import shutil
-import os
-
-LOG_DEPTH = "repet.tools"
-
-
-class LaunchMatcherInParallel(object):
-    def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", alignPattern = ".*\.align", \
-                 config = "", groupId = "", maxFileSize = 1000000, mergeResults=True, workingDir="tmpMatcher", doClean = False, verbosity = 0):
-        self._alignFileName = align
-        self._queryFileName = queryFileName
-        self.setSubjectFileName(subjectFileName)
-        self.setOutPrefix(prefix)
-        self._alignPattern = alignPattern
-        self._doJoin = doJoin
-        self._eValue = evalue
-        self._keepConflict = keepConflict
-        self._configFileName = config
-        self.setGroupId(groupId)
-        self._maxFileSize = maxFileSize
-        self._mergeResults = mergeResults
-        self._doClean = doClean
-        self._workingDir = workingDir
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        self._jobSectionName = "jobs"
-        
-    def setAttributesFromCmdLine(self):
-        description = "Launch Matcher in parallel."
-        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
-        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -v 0"
-        epilog += "\n\t"
-        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
-        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -q query.fa -s subject.fa -o query -c -v 2"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-a", "--align",      dest = "align",         action = "store",       type = "string", help = "input align file name [compulsory] [format: align]",       default = "")
-        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [optional] [format: fasta]",         default = "")
-        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [optional] [format: fasta]",       default = "")
-        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "E-value filter [default: 1e10]",                           default = "1e-10")
-        parser.add_option("-j", "--join",       dest = "doJoin",        action = "store_true",                   help = "join matches [default: False]",                            default = False)
-        parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true",                   help = "keep conflicting subjects [default: False]",               default = False)
-        parser.add_option("-o", "--outPrefix",  dest = "outPrefix",     action = "store",       type = "string", help = "output file prefix [default: align file name]",            default = "")
-        parser.add_option("-p", "--alignPattern",dest = "alignPattern", action = "store",       type = "string", help = "align file pattern [default: .*\.align]",                  default = ".*\.align")
-        parser.add_option("-n", "--maxFileSize",dest = "maxFileSize",   action = "store",       type = "int",    help = "max file size (1 file for 1 job) [default: 100000]",       default = 10000)
-        parser.add_option("-m", "--notMergeResults",dest = "notMergeResults", action = "store_false",            help = "don't merge results files [default: True]",                default = True)
-        parser.add_option("-w", "--workingDir",dest = "workingDir",     action = "store",       type = "string", help = "working directory [default: tmpMatcher]",                  default = "tmpMatcher")
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setAlignFileName(options.align)
-        self.setQueryFileName(options.query)
-        self.setSubjectFileName(options.subject)
-        self.setEvalue(options.evalue)
-        self.setDoJoin(options.doJoin)
-        self.setKeepConflicts(options.keepConflict)
-        self.setOutPrefix(options.outPrefix)
-        self.setAlignPattern(options.alignPattern)
-        self.setMaxFileSize(options.maxFileSize)
-        self.setMergeResults(options.notMergeResults)
-        self.setWorkingDir(options.workingDir)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-        
-    def setAlignFileName(self, alignFileName):
-        self._alignFileName = alignFileName
-        
-    def setQueryFileName(self, queryFileName):
-        self._queryFileName = queryFileName
-        
-    def setSubjectFileName(self, subjectFileName):
-        self._subjectFileName = subjectFileName
-        
-    def setEvalue(self, evalue):
-        self._eValue = evalue
-        
-    def setDoJoin(self, doJoin):
-        self._doJoin = doJoin
-        
-    def setKeepConflicts(self, keepConflict):
-        self._keepConflict = keepConflict
-        
-    def setOutPrefix(self, outPrefix):
-        if outPrefix == "":
-            self._outPrefix = self._alignFileName
-        else:
-            self._outPrefix = outPrefix
-        
-    def setAlignPattern(self, alignPattern):
-        self._alignPattern = alignPattern
-        
-    def setGroupId(self, groupId):
-        if groupId == "":
-            self._groupId = "Matcher_%s" % os.getpid()
-        else:
-            self._groupId = groupId
-            
-    def setMaxFileSize(self, maxFileSize):
-        self._maxFileSize = maxFileSize
-        
-    def setMergeResults(self, mergeResults):
-        self._mergeResults = mergeResults
-    
-    def setWorkingDir(self, workingDir):
-        self._workingDir = workingDir
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if self._alignFileName == "":
-            self._logAndRaise("ERROR: Missing input align file name")
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def _checkConfig(self):       
-        iConfigRules = ConfigRules()
-        iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True)
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool")
-        iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool")
-
-        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
-        self._iConfig = iConfigChecker.getConfig()
-        self._setAttributesFromConfig()
-        
-    def _setAttributesFromConfig(self):
-        self._resources = self._iConfig.get(self._jobSectionName, "resources")
-        self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir")
-        self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy")
-        self._doClean = self._iConfig.get(self._jobSectionName, "clean")
-        
-        if self._isCopyOnNode and not self._tmpDir:
-            self._isCopyOnNode = False
-        self._log.debug("The copy option is: %s." % self._isCopyOnNode)
-
-    def _getLaunchMatcherCmd(self, iLauncher, file):
-        lArgs = []
-        lArgs.append("-a %s" % file)
-        if self._queryFileName:
-            lArgs.append("-q %s" % self._queryFileName)
-        if self._subjectFileName:
-            lArgs.append("-s %s" % self._subjectFileName)
-        lArgs.append("-e %s" % self._eValue)
-        lArgs.append("-o %s" % file)
-        if self._doJoin:
-            lArgs.append("-j")
-        if self._keepConflict:
-            lArgs.append("-k")
-        lArgs.append("-v %i" % (self._verbosity - 1))
-        return iLauncher.getSystemCommand("LaunchMatcher.py", lArgs)
-    
-    def _splitAlignFilePerSeq(self):
-        lAlign = AlignUtils.getAlignListFromFile(self._alignFileName)
-        lAlignList = AlignUtils.splitAlignListByQueryName(lAlign)
-        inputFileNameWithoutExtension = os.path.splitext(os.path.basename(self._alignFileName))[0]
-        AlignUtils.createAlignFiles(lAlignList, inputFileNameWithoutExtension, self._workingDir)
-        
-    def _writeTabHeader(self, outTabFileName):
-        with open(outTabFileName, 'w') as f:
-            f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
-
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkConfig()
-        self._checkOptions()
-        
-        self._log.info("START LaunchMatcherInParallel")
-        self._log.debug("Align file name: %s" % self._alignFileName)
-        self._log.debug("Query file name: %s" % self._queryFileName)
-        self._log.debug("Subject file name: %s" % self._subjectFileName)
-        if not os.path.exists(self._workingDir):
-            os.makedirs(self._workingDir)
-        else:
-            self._doClean = False
-        self._splitAlignFilePerSeq()
-        os.chdir(self._workingDir)
-        os.symlink("../%s" % self._queryFileName, self._queryFileName)
-        if self._queryFileName != self._subjectFileName:
-            os.symlink("../%s" % self._subjectFileName, self._subjectFileName)
-            
-        cDir = os.getcwd()
-        if not self._tmpDir:
-            self._tmpDir = cDir
-        
-        acronym = "Matcher"
-        iDb = DbFactory.createInstance()
-        jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-        iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode)
-
-        lCmdsTuples = []
-        lCmdSize = []
-        lCmdCopy = []
-
-        lFiles = FileUtils.getFileNamesList(".", self._alignPattern)
-        lFileSizeTuples = []
-        for fileName in lFiles:
-            fileSize = os.path.getsize(fileName)
-            lFileSizeTuples.append((fileName, fileSize))
-        lFileSizeList = LauncherUtils.createHomogeneousSizeList(lFileSizeTuples, self._maxFileSize)
-        
-        for lFiles in lFileSizeList:
-            lCmds = []
-            lCmdStart = []
-            lCmdFinish = []
-            if self._queryFileName:
-                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._queryFileName, self._queryFileName))
-            if self._subjectFileName and self._subjectFileName != self._queryFileName:
-                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._subjectFileName, self._subjectFileName))
-            for file in lFiles:
-                lCmds.append(self._getLaunchMatcherCmd(iLauncher, file))
-                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, file, file))
-                lCmdFinish.append("if os.path.exists(\"%s.match.path\"):" % file)
-                lCmdFinish.append("\tshutil.move(\"%s.match.path\", \"%s/.\" )" % (file, cDir))
-                lCmdFinish.append("if os.path.exists(\"%s.match.tab\"):" % file)
-                lCmdFinish.append("\tshutil.move(\"%s.match.tab\", \"%s/.\" )" % (file, cDir))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy))
-        
-        iLauncher.runLauncherForMultipleJobs("Matcher", lCmdsTuples, self._doClean, self._isCopyOnNode)
-
-        if self._mergeResults:
-            FileUtils.catFilesByPattern("*.match.path", "../%s.match.path" % self._outPrefix)
-            if self._queryFileName or self._subjectFileName:
-                outTabFileName = "../%s.match.tab" % self._outPrefix
-                self._writeTabHeader(outTabFileName)
-                FileUtils.catFilesByPattern("*.match.tab", outTabFileName, skipHeaders = True)
-        os.chdir("..")
-        if self._doClean and self._mergeResults:
-            self._log.warning("Working directory will be cleaned")
-            shutil.rmtree(self._workingDir)
-        self._log.info("END LaunchMatchInParallel")
-
-if __name__ == "__main__":
-    iLaunch = LaunchMatcherInParallel()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()

--- a/commons/tools/ListAndDropTables.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# List and drop MySQL tables.
-#
-# usage: ListAndDropTables.py [ options ]
-# options:
-#      -h: this help
-#      -l: tables to list (can be a pattern, '*' for all)
-#      -d: tables to drop (can be a pattern, '*' for all)
-#      -C: configuration file
-#      -v: verbose (default=0/1)
-# it doesn't drop 'info_tables'
-
-
-import sys
-import getopt
-from commons.core.sql.DbMySql import DbMySql
-
-
-class ListAndDropTables( object ):
-    
-    def __init__( self ):
-        self._action = "list"
-        self._tableNames = ""
-        self._configFileName = ""
-        self._verbose = 0
-        self._db = None
-        
-        
-    def help( self ):
-        print
-        print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-        print "options:"
-        print "     -h: this help"
-        print "     -l: tables to list (can be a pattern, '*' for all)"
-        print "     -d: tables to drop (can be a pattern, '*' for all)"
-        print "     -C: configuration file (otherwise, use env variables)"
-        print "     -v: verbose (default=0/1)"
-        print "Note: it doesn't drop 'info_tables'."
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hl:d:C:v:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-l":
-                self._action = "list"
-                self._tableNames = a
-            elif o == "-d":
-                self._action = "drop"
-                self._tableNames = a
-            elif o == "-C":
-                self._configFileName = a
-            elif o == "-v":
-                self._verbose = int(a)
-                
-                
-    def checkAttributes( self ):
-        """
-        Before running, check the required attributes are properly filled.
-        """
-        if self._tableNames == "":
-            print "ERROR: missing input table"
-            self.help()
-            sys.exit(1)
-#        if self._configFileName == "":
-#            print "ERROR: missing configuration file"
-#            self.help()
-#            sys.exit(1)
-            
-            
-    def getlistTables( self ):
-        """
-        Return a list with the table names corresponding to the given pattern.
-        """
-        lTables = []
-        if self._tableNames != "*":
-            sql_cmd = "SHOW TABLES like '%%%s%%'" % ( self._tableNames )
-        else:
-            sql_cmd = "SHOW TABLES"
-        self._db.execute( sql_cmd )
-        res = self._db.fetchall()
-        for i in res:
-            lTables.append( i[0] )
-        return lTables
-    
-    
-    def list( self ):
-        """
-        List the tables corresponding to the pattern.
-        """
-        lTables = i.getlistTables()
-        if len(lTables) == 0:
-            print "no table corresponding to '%s'" % ( self._tableNames )
-        else:
-            print "list of tables:"
-            for t in lTables:
-                print t
-            print "%i tables corresponding to '%s'" % ( len(lTables), self._tableNames )
-        sys.stdout.flush()
-        
-        
-    def drop( self ):
-        """
-        Drop the tables corresponding to the pattern.
-        """
-        lTables = i.getlistTables()
-        if len(lTables) == 0:
-            print "no table corresponding to '%s'" % ( self._tableNames )
-        else:
-            print "deleting %i tables corresponding to '%s'" % ( len(lTables), self._tableNames )
-            for t in lTables:
-                if t != "info_tables":
-                    self._db.dropTable( t )
-        sys.stdout.flush()
-        
-        
-    def start( self ):
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START %s" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-        if self._configFileName != "":
-            self._db = DbMySql( cfgFileName = self._configFileName )
-        else:
-            if self._verbose > 0:
-                print "WARNING: use environment variables to connect to MySQL"
-                sys.stdout.flush()
-            self._db = DbMySql()
-            
-            
-    def end( self ):
-        self._db.close()
-        if self._verbose > 0:
-            print "END %s" % (sys.argv[0].split("/")[-1])
-            sys.stdout.flush()
-            
-            
-    def run( self ):
-        self.start()
-        if i._action == "list":
-            i.list()
-        if i._action == "drop":
-            i.drop()
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = ListAndDropTables()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/MergeMatchsFiles.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.coord.Align import Align
-import shutil
-import os
-import sys
-
-class MergeMatchsFiles(object):
-
-    def __init__(self, fileType, outFileBaseName, allByAll = False, clean = True, verbose = 0):
-        self._fileType = fileType
-        self._outFileBaseName = outFileBaseName
-        self._allByAll = allByAll
-        self._verbose = verbose
-        self._clean = clean
-
-    def _filterRedundantMatches( self, inFile, outFile ):
-        """
-        When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks),
-        one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...'
-        and we discards 'chunk7-11-110-chunk3-1-100-...'.
-        Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards
-        'chunk5-11-110-chunk5-1-100-...'.
-        For this of course the results need to be sorted by query, on plus strand,
-        and in ascending coordinates (always the case with Blaster).
-        """
-        inFileHandler = open( inFile, "r" )
-        outFileHandler = open( outFile, "w" )
-        iAlign = Align()
-        countMatches = 0
-        tick = 100000
-        while True:
-            line = inFileHandler.readline()
-            if line == "":
-                break
-            countMatches += 1
-            iAlign.setFromString( line )
-            if "chunk" not in iAlign.range_query.seqname \
-                   or "chunk" not in iAlign.range_subject.seqname:
-                print "ERROR: 'chunk' not in seqname"
-                sys.exit(1)
-            if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]):
-                iAlign.write( outFileHandler )
-            elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]):
-                if iAlign.range_query.getMin() < iAlign.range_subject.getMin():
-                    iAlign.write( outFileHandler )
-            if countMatches % tick == 0:   # need to free buffer frequently as file can be big
-                outFileHandler.flush()
-                os.fsync( outFileHandler.fileno() )
-        inFileHandler.close()
-        outFileHandler.close()
-
-    def run(self):
-        if self._verbose > 1:
-            print "concatenate the results of each job"
-            sys.stdout.flush()
-            
-        tmpFileName = "%s.%s_tmp" % (self._outFileBaseName, self._fileType)
-        outFileName = "%s.%s" % (self._outFileBaseName, self._fileType)
-        pattern = "*.%s" % self._fileType
-    
-        if os.path.exists(tmpFileName):
-            os.remove(tmpFileName)
-    
-        FileUtils.catFilesByPattern(pattern, tmpFileName)
-        if self._clean:
-            FileUtils.removeFilesByPattern(pattern)
-    
-        if self._fileType == "align":
-            if self._allByAll:
-                self._filterRedundantMatches(tmpFileName, outFileName)
-            else:
-                shutil.move(tmpFileName, outFileName)
-        else:
-            prg = "%s/bin/%snum2id" % (os.environ["REPET_PATH"], self._fileType)
-            cmd = prg
-            cmd += " -i %s" % tmpFileName
-            cmd += " -o %s" % outFileName
-            cmd += " -v %i" % (self._verbose - 1)
-            log = os.system(cmd)
-            if log != 0:
-                print "*** Error: %s returned %i" % (prg, log)
-                sys.exit(1)
-        if self._clean and FileUtils.isRessourceExists(tmpFileName):
-            os.remove(tmpFileName)
\ No newline at end of file

--- a/commons/tools/MysqlConnect.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-
-def main():
-    description = "Check MySQL connection on a node"
-    usage = "MysqlConnect.py -n hostname"
-           
-    parser = RepetOptionParser(description = description, usage = usage, version = "v1.0")
-    parser.add_option( "-n", "--node", dest = "node", type = "string", help = "node name", default = "")
-    parser.add_option( "-C", "--config", dest = "config", type = "string", help = "path to config file", default = "")
-    
-    options, args = parser.parse_args()
-    
-    node = options.node
-    
-    try:
-        if options.config != "":
-            idbMySQL = DbMySql(cfgFileName = options.config)
-        else:
-            idbMySQL = DbMySql()
-        print "SUCCESS to connect to MySQL database from '%s'" % node
-    except SystemExit:
-        print "FAILED to connect to MySQL database from '%s'" % node
-    
-if __name__ == '__main__':
-    main()
\ No newline at end of file

--- a/commons/tools/OrientSequences.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,375 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Interface to orient sequences before making a multiple alignment.
-Use hashing or suffix tree to get an idea of the appropriate strand.
-Use 'orienter' by default, otherwise use 'mummer'.
-"""
-
-import sys
-import os
-import glob
-import getopt
-
-from commons.core.seq.BioseqDB import BioseqDB
-import pyRepet.seq.fastaDB
-from commons.core.checker.CheckerUtils import CheckerUtils
-
-class OrientSequences( object ):
-    """
-    Interface to orient sequences before making a multiple alignment.
-    Use hashing or suffix tree to get an idea of the appropriate strand.
-    Use 'orienter' by default, otherwise use 'mummer'.
-    """
-    
-    def __init__(self, inFileName="", minMatchLength=10, prgToOrient = "orienter", outFileName="", clean=False, verbosity=1):
-        """
-        Constructor.
-        """
-        self._inFileName = inFileName
-        self._minMatchLength = minMatchLength
-        self._prgToOrient = prgToOrient
-        self._outFileName = outFileName
-        self._clean = clean
-        self._verbose = verbosity
-        
-    def help( self ):
-        """
-        Display the help on stdout.
-        """
-        print
-        print "usage:",sys.argv[0].split("/")[-1],"[options]"
-        print "options:"
-        print "     -h: this help"
-        print "     -i: name of the input file (format='fasta')"
-        print "     -m: minimum match length (default=10)"
-        print "     -p: program to use first (default=orienter/mummer)"
-        print "     -o: name of the output file (default=inFileName+'.oriented')"
-        print "     -c: clean"
-        print "     -v: verbosity level (0/default=1/2)"
-        print
-        
-    def setAttributesFromCmdLine( self ):
-        """
-        Set the attributes from the command-line.
-        """
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:m:p:o:cv:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputFileName( a )
-            elif o == "-m":
-                self.setMinMatchLength( a )
-            elif o == "-p":
-                self.setPrgToOrient( a )
-            elif o == "-o":
-                self.setOutputFileName( a )
-            elif o == "-c":
-                self.setClean()
-            elif o == "-v":
-                self.setVerbosityLevel( a )
-                
-    def setInputFileName( self, inFileName ):
-        self._inFileName = inFileName
-        
-    def setMinMatchLength( self, minMatchLength ):
-        self._minMatchLength = int(minMatchLength)
-        
-    def setPrgToOrient( self, prgToOrient ):
-        self._prgToOrient = prgToOrient
-        
-    def setOutputFileName( self, outFileName ):
-        self._outFileName = outFileName
-        
-    def setClean( self ):
-        self._clean = True
-        
-    def setVerbosityLevel( self, verbose ):
-        self._verbose = int(verbose)
-        
-    def checkAttributes( self ):
-        """
-        Check the attributes are valid before running the algorithm.
-        """
-        if self._inFileName == "":
-            print "ERROR: missing input file name"
-            self.help(); sys.exit(1)
-        if not os.path.exists( self._inFileName ):
-            print "ERROR: input file '%s' doesn't exist" % ( self._inFileName )
-            self.help(); sys.exit(1)
-        if self._prgToOrient not in [ "orienter", "mummer" ]:
-            print "ERROR: unknown program '%s'" % ( self._prgToOrient )
-            self.help(); sys.exit(1)
-        if self._outFileName == "":
-            self._outFileName = "%s.oriented" % ( self._inFileName )
-            
-    def useOrienter( self ):
-        """
-        Use 'orienter'.
-        @return: exit value of 'orienter'
-        """
-        prg = "orienter"
-        cmd = prg
-        cmd += " -k"
-#        cmd += " -l %i" % ( self._minMatchLength )
-        cmd += " -v %i" % ( self._verbose )
-        cmd += " %s" % ( self._inFileName )
-        log = os.system( cmd )
-        if log == 0 and self._outFileName.split(".")[-1] != "oriented":
-            os.rename( self._inFileName + ".oriented", self._outFileName )
-        return log
-    
-    def compareInputSequencesWithMummer( self, nbInSeq ):
-        """
-        Launch MUmmer on two single-sequence fasta files to find all maximal matches regardless of their uniqueness and record stdout.
-        Only N(N-1)/2 comparisons are made.
-        @param nbInSeq: number of input sequences
-        @type nbInSeq: integer
-        """
-        if self._verbose > 0:
-            print "aligning input sequences..."
-            sys.stdout.flush()
-        if not CheckerUtils.isExecutableInUserPath( "mummer" ):
-            msg = "ERROR: 'mummer' is not in your PATH"
-            sys.stderr.write( "%s\n" % ( msg ) )
-            sys.exit(1)
-        lInFiles = glob.glob( "batch_*.fa" )
-        for i in range( 1, nbInSeq+1 ):
-            for j in range( i+1, nbInSeq+1 ):
-                if self._verbose > 1:
-                    print "launch MUmmer on %i versus %i" % ( i, j )
-                    sys.stdout.flush()
-                prg = "mummer"
-                cmd = prg
-                cmd += " -maxmatch"
-                cmd += " -l %i" % ( self._minMatchLength )
-                cmd += " -b"
-                cmd += " -F"
-                cmd += " batch_%s.fa" % ( str(j).zfill( len( str( len(lInFiles) ) ) ) )
-                cmd += " batch_%s.fa" % ( str(i).zfill( len( str( len(lInFiles) ) ) ) )
-                cmd += " > mummer_%i_vs_%i.txt" % ( i, j )
-                if self._verbose < 3:
-                    cmd += " 2> /dev/null"
-                returnStatus = os.system( cmd )
-                if returnStatus != 0:
-                    msg = "ERROR: '%s' returned '%i'" % ( prg, returnStatus )
-                    sys.stderr.write( "%s\n" % ( msg ) )
-                    sys.exit(1)
-                    
-    def parseMummerOutput( self, mummerFileName, nameSeq1, nameSeq2 ):
-        """
-        Parse the output from MUmmer.
-        @param mummerFileName: file with the output from MUmmer
-        @type mummerFileName: string
-        @param nameSeq1: name of the first sequence in the pairwise comparison
-        @type nameSeq1: string
-        @param nameSeq2: name of the first sequence in the pairwise comparison
-        @type nameSeq2: string
-        @return: dictionary whose keys are strands and values the number of maximal matches
-        """
-        if self._verbose > 1:
-            print "parse '%s'" % ( mummerFileName )
-            sys.stdout.flush()
-        dStrand2NbMatches = {}
-        mummerF = open( mummerFileName, "r" )
-        strand = "direct"
-        nbMatches = 0
-        line = mummerF.readline()
-        while True:
-            if line == "":
-                break
-            if line[0] == ">":
-                if nameSeq1 not in line:
-                    print "ERROR"
-                    print nameSeq1
-                    print nameSeq2
-                    sys.exit(1)
-                if "Reverse" in line:
-                    dStrand2NbMatches[ strand ] = nbMatches
-                    strand = "reverse"
-                    nbMatches = 0
-            else:
-                nbMatches += 1
-            line = mummerF.readline()
-        dStrand2NbMatches[ strand ] = nbMatches
-        mummerF.close()
-        if self._verbose > 1:
-            print " direct: %i maximal matches" % ( dStrand2NbMatches["direct"] )
-            print " reverse: %i maximal matches" % ( dStrand2NbMatches["reverse"] )
-            sys.stdout.flush()
-        return dStrand2NbMatches
-    
-    def getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( self, lInHeaders, nbInSeq ):
-        """
-        For each pairwise comparison, retrieve the number of matches on both strand.
-        @param lInHeaders: list of the sequence headers
-        @type lInHeaders: list of strings
-        @param nbInSeq: number of input sequences
-        @type nbInSeq: integer
-        @return: dictionary whose keys are pairwise comparisons and values are number of matches on both strands
-        """
-        dMatrix = {}
-        for i in range( 1, nbInSeq+1 ):
-            for j in range( i+1, nbInSeq+1 ):
-                pairComp = "%i_vs_%i" % ( i, j )
-                dStrand2NbMatches = self.parseMummerOutput( "mummer_%s.txt" % ( pairComp ), lInHeaders[i-1], lInHeaders[j-1] )
-                dMatrix[ pairComp ] = dStrand2NbMatches
-        return dMatrix
-    
-    def showResultsAsOrienter( self, nbInSeq, dMatrix ):
-        """
-        Not used for the moment but can be useful...
-        """
-        for i in range( 1, nbInSeq+1 ):
-            for j in range( i+1, nbInSeq+1 ):
-                pairComp = "%i_vs_%i" % ( i, j )
-                string = "aligning %i with %i" % ( i, j )
-                string += " %i %i" % ( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] )
-                string += " max=%i" % ( max( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] ) )
-                if dMatrix[pairComp]["reverse"] > dMatrix[pairComp]["direct"]:
-                    string += " strand=-"
-                    string += " nb=%i" % ( dMatrix[pairComp]["reverse"] )
-                else:
-                    string += " strand=+"
-                    string += " nb=%i" % ( dMatrix[pairComp]["direct"] )
-                print string; sys.stdout.flush()
-                
-    def getSequencesToReverseFromMatrix( self, dMatrix, lNewHeaders ):
-        """
-        Retrieve the sequences than need to be re-oriented.
-        @param dMatrix: 
-        @type dMatrix: 
-        @param lInHeaders: list of the new sequence headers
-        @type lInHeaders: list of strings
-        @return: list of headers corresponding to sequences than need to be re-oriented
-        """
-        lSeqToOrient = []
-        
-        for i in range( 1, len(lNewHeaders)+1 ):
-            for j in range( i+1, len(lNewHeaders)+1 ):
-                comp = "%i_vs_%i" % ( i, j )
-                nbDirectMatches = dMatrix[ comp ][ "direct" ]
-                nbReverseMatches = dMatrix[ comp ][ "reverse" ]
-                if self._verbose > 1:
-                    print "%s: direct=%i reverse=%i" % ( comp, nbDirectMatches, nbReverseMatches )
-                if nbReverseMatches > nbDirectMatches and lNewHeaders[i-1] not in lSeqToOrient:
-                    if lNewHeaders[ j-1 ] not in lSeqToOrient:
-                        if self._verbose > 2:
-                            "need to reverse '%s'" % ( lNewHeaders[j-1] )
-                        lSeqToOrient.append( lNewHeaders[ j-1 ] )
-        return lSeqToOrient
-    
-    
-    def getSequencesToReverse( self ):
-        """
-        Return a list with the headers of the sequences to reverse. 
-        """
-        lSequenceHeadersToReverse = []
-        
-        if self._prgToOrient == "orienter":
-            exitStatus = self.useOrienter()
-            if exitStatus == 0:
-                self.end()
-                sys.exit(0)
-            if exitStatus != 0:
-                print "\nWARNING: 'orienter' had a problem, switching to 'mummer'"
-                sys.stdout.flush()
-                
-        lInHeaders = pyRepet.seq.fastaDB.dbHeaders( self._inFileName )
-        nbInSeq = len( lInHeaders )
-        if self._verbose > 0:
-            print "nb of input sequences: %i" % ( nbInSeq )
-            sys.stdout.flush()
-            
-        pyRepet.seq.fastaDB.shortenSeqHeaders( self._inFileName, 1 )
-        tmpFileName = "%s.shortH" % ( self._inFileName )
-        lNewHeaders = pyRepet.seq.fastaDB.dbHeaders( tmpFileName )
-        dNew2Init = pyRepet.seq.fastaDB.retrieveLinksNewInitialHeaders( "%slink" % ( tmpFileName ) )
-        
-        pyRepet.seq.fastaDB.dbSplit( tmpFileName, nbSeqPerBatch=1, newDir=True )
-        os.chdir( "batches" )
-        self.compareInputSequencesWithMummer( nbInSeq )
-        dMatrix = self.getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( lNewHeaders, nbInSeq )
-        os.chdir( ".." )
-        
-        lNewHeadersToReverse = self.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
-        for newH in lNewHeadersToReverse:
-            lSequenceHeadersToReverse.append( dNew2Init[ newH ] )
-        if self._verbose > 0:
-            print "nb of sequences to reverse: %i" % ( len(lNewHeadersToReverse) )
-            for initH in lSequenceHeadersToReverse: print " %s" % ( initH )
-            sys.stdout.flush()
-            
-        if self._clean:
-            os.remove( tmpFileName )
-            os.remove( "%slink" % ( tmpFileName ) )
-            
-        return lSequenceHeadersToReverse
-    
-    def orientInputSequences( self, lSequenceHeadersToReverse, tmpFileName="" ):
-        """
-        Save input sequences while re-orienting those needing it.
-        @param lSequenceHeadersToReverse: list of headers corresponding to sequences than need to be re-oriented
-        @type lSequenceHeadersToReverse: list of strings
-        @param tmpFileName: name of a fasta file (inFileName by default)
-        @type tmpFileName: string
-        """
-        if self._verbose > 0:
-            print "saving oriented sequences..."
-            sys.stdout.flush()
-        if tmpFileName == "":
-            tmpFileName = self._inFileName
-        inDB = BioseqDB( tmpFileName )
-        outDB = BioseqDB()
-        for bs in inDB.db:
-            if bs.header in lSequenceHeadersToReverse:
-                bs.reverseComplement()
-                bs.header += " re-oriented"
-            outDB.add( bs )
-        outDB.save( self._outFileName )
-        
-    def clean( self ):
-        if os.path.exists( "batches" ):
-            os.system( "rm -rf batches" )
-        if os.path.exists( "orienter_error.log" ):
-            os.remove( "orienter_error.log" )
-        for f in glob.glob( "core.*" ):
-            os.remove( f )
-            
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START %s" % ( type(self).__name__ )
-            print "input file: %s" % ( self._inFileName )
-            sys.stdout.flush()
-            
-    def end( self ):
-        """
-        Useful commands before ending the program.
-        """
-        if self._clean:
-            self.clean()
-        if self._verbose > 0:
-            print "END %s" % ( type(self).__name__ )
-            sys.stdout.flush()
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        lSequenceHeadersToReverse = self.getSequencesToReverse()
-        self.orientInputSequences( lSequenceHeadersToReverse )
-        self.end()
-        
-if __name__ == "__main__":
-    i = OrientSequences()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/PostAnalyzeTELib.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,301 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.stat.Stat import Stat
-from commons.core.seq.BioseqDB import BioseqDB
-from commons.launcher.LaunchBlastclust import LaunchBlastclust
-from commons.tools.AnnotationStats import AnnotationStats
-import os
-
-CONSENSUS = "TE"
-CLUSTER = "Cluster"
-LOG_DEPTH = "repet.tools"
-LOG_FORMAT = "%(message)s"
-
-class PostAnalyzeTELib(object):
-    
-    def __init__(self, analysis = 1, fastaFileName = "", clusterFileName = "", pathTableName="", seqTableName="", genomeSize=0, configFileName = "", doClean = False, verbosity = 3):
-        self._analysis = analysis
-        self._fastaFileName = fastaFileName
-        self._pathTableName = pathTableName
-        self._seqTableName = seqTableName
-        self._genomeSize = genomeSize
-        if self._analysis == 1:
-            self.setBioseqDB()
-        self._identity = 0
-        self._coverage = 80
-        self._applyCovThresholdOnBothSeq = False
-        self.setClusterFileName(clusterFileName)
-        self.setStatPerClusterFileName()
-        self.setClassifStatPerClusterFileName()
-        self.setAnnotationStatsPerTEFileName()
-        self.setAnnotationStatsPerClusterFileName()
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity, LOG_FORMAT)
-        
-    def setAttributesFromCmdLine(self):
-        description = "Tool to post-analyze a TE library : clusterize, give stats on cluster, on annotation,...\n"
-        epilog = "\nExample 1: clustering (e.g. to detect redundancy)\n"
-        epilog += "\t$ python PostAnalyzeTELib.py -a 1 -i TElib.fa -L 98 -S 95 -b\n"
-        epilog += "Example 2: classification stats per cluster\n"
-        epilog += "\t$ python PostAnalyzeTELib.py -a 2 -t TElib.tab\n"
-        epilog += "Example 3: annotation stats per consensus\n"
-        epilog += "\t$ python PostAnalyzeTELib.py -a 3 -p project_chr_allTEs_nr_noSSR_join_path -s project_refTEs_seq -g 129919500\n"
-        epilog += "Example 4: annotation stats per cluster\n"
-        epilog += "\t$ python PostAnalyzeTELib.py -a 4 -t TElib.tab -p project_chr_allTEs_nr_noSSR_join_path -s project_refTEs_seq -g 129919500\n"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-a", "--analysis",   dest = "analysis",          action = "store",       type = "int",    help = "analysis number [default: 1, 2, 3, 4]", default = 1)
-        parser.add_option("-i", "--fasta",      dest = "fastaFileName",     action = "store",       type = "string", help = "fasta file name [for analysis 1] [format: fasta]", default = "")
-        parser.add_option("-L", "--coverage",   dest = "coverage",          action = "store",       type = "int",    help = "length coverage threshold [for analysis 1] [format: %] [default: 80]", default = 80)
-        parser.add_option("-S", "--identity",   dest = "identity",          action = "store",       type = "int",    help = "identity threshold [for analysis 1 with BlastClust] [format: %] [default: 0 => no threshold]", default = 0)
-        parser.add_option("-b", "--both",       dest = "bothSeq",           action = "store_true",                   help = "require coverage on both neighbours [for analysis 1] [default: False]", default = False)
-        parser.add_option("-t", "--cluster",    dest = "clusterFileName",   action = "store",       type = "string", help = "cluster file name [for analysis 2 and 4] [default: <input>.tab]", default = "")
-        parser.add_option("-p", "--path",       dest = "pathTableName",     action = "store",       type = "string", help = "name of the table (_path) with the annotated TE copies [for analysis 3 and 4]", default = "")
-        parser.add_option("-s", "--seq",        dest = "seqTableName",      action = "store",       type = "string", help = "name of the table (_seq) with the TE reference sequences [for analysis 3 and 4]", default = "")
-        parser.add_option("-g", "--genome",     dest = "genomeSize",        action = "store",       type = "int",    help = "genome size [for analysis 3 and 4]", default = None)
-        parser.add_option("-c", "--clean",      dest = "doClean",           action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",         action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setAnalysis(options.analysis)
-        if self._analysis == 1:
-            self.setFastaFileName(options.fastaFileName)
-            self.setBioseqDB()
-            self.setIdentity(options.identity)
-            self.setCoverage(options.coverage)
-            self.setApplyCovThresholdOnBothSeq(options.bothSeq)
-        self.setClusterFileName(options.clusterFileName)
-        self.setPathTableName(options.pathTableName)
-        self.setSeqTableName(options.seqTableName)
-        self.setStatPerClusterFileName()
-        self.setClassifStatPerClusterFileName()
-        self.setAnnotationStatsPerTEFileName()
-        self.setAnnotationStatsPerClusterFileName()
-        self.setGenomeSize(options.genomeSize)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def setAnalysis(self, analysis):
-        self._analysis = analysis
-        
-    def setFastaFileName(self, fastaFileName):
-        self._fastaFileName = fastaFileName
-    
-    def setBioseqDB(self):
-        self._iBioseqDB = BioseqDB(name = self._fastaFileName)   
-        
-    def setIdentity(self, identity):
-        self._identity = identity
-        
-    def setCoverage(self, coverage):
-        self._coverage = coverage
-        
-    def setApplyCovThresholdOnBothSeq(self, bothSeq):
-        self._applyCovThresholdOnBothSeq = bothSeq
-    
-    def setClusterFileName(self, clusterFileName):
-        if clusterFileName == "":
-            self._clusterFileName = "%s.tab" % os.path.splitext(os.path.basename(self._fastaFileName))[0]
-        else:
-            self._clusterFileName = clusterFileName
-    
-    def setStatPerClusterFileName(self):
-        self._statPerClusterFileName = "%s.statsPerCluster.tab" % os.path.splitext(self._clusterFileName)[0]
-        self._globalStatPerClusterFileName = "%s.globalStatsPerCluster.txt" % os.path.splitext(self._clusterFileName)[0]
-        
-    def setClassifStatPerClusterFileName(self):
-        self._classifStatPerClusterFileName = "%s.classifStatsPerCluster.tab" % os.path.splitext(self._clusterFileName)[0]
-        
-    def setAnnotationStatsPerTEFileName(self):
-        self._annotStatsPerTEFileName = "%s.annotStatsPerTE.tab" % self._pathTableName
-        self._globalAnnotStatsPerTEFileName = "%s.globalAnnotStatsPerTE.txt" % self._pathTableName
-        
-    def setAnnotationStatsPerClusterFileName(self):
-        self._annotStatsPerClusterFileName = "%s.annotStatsPerCluster.tab" % self._pathTableName
-        
-    def setPathTableName(self, pathTableName):
-        self._pathTableName = pathTableName
-    
-    def setSeqTableName(self, seqTableName):
-        self._seqTableName = seqTableName
-        
-    def setGenomeSize(self, genomeSize):
-        self._genomeSize = genomeSize
-                 
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def _checkOptions(self):
-        if (self._fastaFileName == "" or not FileUtils.isRessourceExists(self._fastaFileName)) and self._analysis == 1:
-            self._logAndRaise("ERROR: Missing fasta file"  )
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self._checkOptions()
-        self._log.info("START PostAnalyzeTELib analysis %d" % self._analysis)
-        if self._analysis == 1:
-            #TODO: option to choose clustering program (blastclust, MCL, uclust,...)
-            self._log.debug("TE lib: %s" % self._fastaFileName)
-            self._log.info("Launch blastclust...")
-            iLaunchBlastclust = LaunchBlastclust(clean = self._doClean)
-            iLaunchBlastclust.setTmpFileName(self._clusterFileName)
-            iLaunchBlastclust.setIdentityThreshold(self._identity)
-            iLaunchBlastclust.setCoverageThreshold(self._coverage/100.0)
-            if self._applyCovThresholdOnBothSeq:
-                iLaunchBlastclust.setBothSequences("T")
-            else:
-                iLaunchBlastclust.setBothSequences("F")
-            iLaunchBlastclust.setVerbosityLevel(self._verbosity - 3)
-            iLaunchBlastclust.launchBlastclust(self._fastaFileName)
-            self._log.info("Compute stats...")
-            self._giveStatsOnTEClusters()
-        if self._analysis == 2:
-            #TODO add global stats (e.g.: nb of cluster without PotentialChimeric, nb of clusters with LTR...) ?
-            self._log.debug("Consensus cluster file name: %s" % self._clusterFileName)
-            self._log.info("Compute classification stats...")
-            self._giveStatsOnConsensusClusters()
-        if self._analysis == 3:
-            #TODO: in option, save stats in DB
-            self._log.info("Compute annotation stats per TE...")
-            iAnnotationStats = AnnotationStats(analysisName="TE", seqTableName=self._seqTableName, pathTableName=self._pathTableName,\
-                                            genomeLength=self._genomeSize, statsFileName=self._annotStatsPerTEFileName, globalStatsFileName=self._globalAnnotStatsPerTEFileName, verbosity=self._verbosity-1)
-            iAnnotationStats.run()
-        if self._analysis == 4:
-            self._log.info("Compute annotation stats per cluster...")
-            iAnnotationStats = AnnotationStats(analysisName="Cluster", clusterFileName=self._clusterFileName, seqTableName=self._seqTableName, pathTableName=self._pathTableName,\
-                                            genomeLength=self._genomeSize, statsFileName=self._annotStatsPerClusterFileName, verbosity=self._verbosity-1)
-            iAnnotationStats.run()
-        self._log.info("END PostAnalyzeTELib analysis %d" % self._analysis)
-
-    def _giveStatsOnConsensusClusters(self):
-        with open(self._classifStatPerClusterFileName, "w") as f:
-            f.write("cluster\tnoCat\tPotentialChimeric\tcomp\tincomp\tclassifs (nbTEs)\n")
-            with open(self._clusterFileName) as fCluster:
-                for clusterId, line in enumerate(fCluster):
-                    dClassifNb = {}
-                    nbIncomp =0
-                    nbComp=0
-                    nbChim=0
-                    nbNoCat=0
-                    lConsensus = line.split()
-                    for consensus in lConsensus:
-                        classifInfos = consensus.split("_")[0]
-                        
-                        if "-incomp" in classifInfos:
-                            nbIncomp += 1
-                            classifInfos = classifInfos.replace("-incomp","")
-                        if "-comp" in classifInfos:
-                            nbComp += 1
-                            classifInfos = classifInfos.replace("-comp","")
-                        if "-chim" in classifInfos:
-                            nbChim += 1
-                            classifInfos = classifInfos.replace("-chim","")
-                        if "noCat" in classifInfos:
-                            nbNoCat += 1
-                            classifInfos = classifInfos.replace("noCat","")
-                            
-                        classif = classifInfos.split("-")[-1]
-                        if classif != "":
-                            if dClassifNb.get(classif, None) is None:
-                                dClassifNb[classif] = 0
-                            dClassifNb[classif] +=1
-                            
-                    occurences= []
-                    for classif, occs in dClassifNb.items():
-                        occurences.append("%s (%d)" % (classif, occs))
-                    
-                    f.write("%d\t%d\t%d\t%d\t%d\t%s\n" % (clusterId+1, nbNoCat, nbChim\
-                                        , nbComp, nbIncomp,"\t".join(occurences)))
-                    
-    def _giveStatsOnTEClusters(self):
-        with open(self._clusterFileName) as fCluster:
-            with open(self._statPerClusterFileName, 'w') as fStatPerCluster:
-                fStatPerCluster.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n")
-                line = fCluster.readline()
-                clusterNb = 0
-                clusterSeqList= line.split()          
-                minClusterSize = len(clusterSeqList)
-                maxClusterSize = 0
-                totalSeqNb = 0
-                seqNbInBigClusters = 0
-                dClusterSize2ClusterNb = {1:0, 2:0, 3:0}
-                while line:
-                    clusterSeqList= line.split()  
-                    seqNb = len(clusterSeqList)
-                    totalSeqNb += seqNb
-                    if seqNb > 2:
-                        seqNbInBigClusters += seqNb
-                        dClusterSize2ClusterNb[3] += 1
-                    else:
-                        dClusterSize2ClusterNb[seqNb] += 1
-                    if seqNb > maxClusterSize:
-                        maxClusterSize = seqNb
-                    if seqNb < minClusterSize:
-                        minClusterSize = seqNb
-                    line = fCluster.readline()
-                    clusterNb += 1
-                    clusterSeqLengths = self._iBioseqDB.getSeqLengthByListOfName(clusterSeqList)
-                    iStatSeqLengths = Stat(clusterSeqLengths)
-                    fStatPerCluster.write("%d\t%d\t%d\t%d\t%d\t%d\n" %(clusterNb, seqNb, min(clusterSeqLengths), max(clusterSeqLengths),  iStatSeqLengths.mean(),  iStatSeqLengths.median()))
-        
-        with open(self._globalStatPerClusterFileName, 'w') as fG:
-            fG.write("nb of clusters: %d\n" % clusterNb)
-            fG.write("nb of clusters with 1 sequence: %d\n" % dClusterSize2ClusterNb[1])
-            fG.write("nb of clusters with 2 sequences: %d\n" % dClusterSize2ClusterNb[2])
-            fG.write("nb of clusters with >2 sequences: %d (%d sequences)\n" % (dClusterSize2ClusterNb[3], seqNbInBigClusters))
-            fG.write("nb of sequences: %d\n" % totalSeqNb)
-            fG.write("nb of sequences in the largest cluster: %d\n" % maxClusterSize)
-            fG.write("nb of sequences in the smallest cluster: %d\n" % minClusterSize)
-            lSeqSizes = self._iBioseqDB.getListOfSequencesLength()
-            iStat = Stat(lSeqSizes)
-            fG.write("size of the smallest sequence: %d\n" % min(lSeqSizes))
-            fG.write("size of the largest sequence: %d\n" % max(lSeqSizes))
-            fG.write("average sequences size: %d\n" % iStat.mean())
-            fG.write("median sequences size: %d\n" % iStat.median())
-
-if __name__ == "__main__":
-    iLaunch = PostAnalyzeTELib()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()
\ No newline at end of file

--- a/commons/tools/PrepareBatches.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import sys
-from ConfigParser import NoSectionError, NoOptionError
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.checker.CheckerException import CheckerException
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.seq.FastaUtils import FastaUtils
-
-class PrepareBatches(object):
-    
-    def __init__(self, pipelineName, projectDir, projectName, iConfig, verbose):
-        self._pipelineName = pipelineName
-        self._projectDir = projectDir
-        self._projectName = projectName
-        self._iConfig = iConfig
-        self._verbose = verbose
-        
-    def run(self):
-        if self._verbose > 0:
-            print "beginning of step 1"
-            sys.stdout.flush()
-        if FileUtils.isRessourceExists("%s_db" % self._projectName):
-            print "ERROR: directory '%s_db' already exists" % self._projectName
-            sys.exit(1)
-        
-        os.mkdir("%s_db" % self._projectName)
-        os.chdir("%s_db" % self._projectName)
-        genomeFastaFileName = "%s.fa" % self._projectName
-        os.symlink("../%s" % genomeFastaFileName, genomeFastaFileName)
-        sectionName = "prepare_batches"
-        self._checkConfig(sectionName)  
-        
-        separator = "\n"
-        inGenomeFileHandler = open(genomeFastaFileName, "r")
-        try:
-            CheckerUtils.checkHeaders(inGenomeFileHandler)
-        except CheckerException, e:
-            print "Error in file %s. Wrong headers are :" % genomeFastaFileName
-            print separator.join(e.messages)
-            print "Authorized characters are : a-z A-Z 0-9 - . : _\n"
-            inGenomeFileHandler.close()
-            sys.exit(1)
-        inGenomeFileHandler.close()
-
-        doClean = False
-        if self._iConfig.get(sectionName, "clean") == "yes":
-            doClean = True
-        chunkFilePrefix = "%s_chunks" % self._projectName
-        chunkLength = int(self._iConfig.get(sectionName, "chunk_length"))
-        chunkOverlap = int(self._iConfig.get(sectionName, "chunk_overlap"))
-        FastaUtils.dbChunks(genomeFastaFileName, chunkLength, chunkOverlap, 0, chunkFilePrefix, doClean, self._verbose)
-        
-        nbSeq = int(self._iConfig.get(sectionName, "nb_seq_per_batch"))
-        FastaUtils.splitFastaFileInBatches("%s.fa" % chunkFilePrefix, nbSeq * chunkLength)
-
-        if self._iConfig.get(sectionName, "clean") == "yes":
-            FileUtils.removeFilesByPattern("%s.fa*" % self._projectName)
-            
-        os.chdir( ".." )
-        if self._verbose > 0:
-            print "step 1 finished successfully"
-            sys.stdout.flush()
-
-    def _checkConfig(self, sectionName):
-        try:
-            CheckerUtils.checkSectionInConfigFile(self._iConfig, sectionName)
-        except NoSectionError:
-            print "ERROR: the section %s must be in your configuration file" % sectionName
-            sys.exit(1)
-        try:
-            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_length")
-        except NoOptionError:
-            print "ERROR: the option 'chunk_length' must be defined in %s in your configuration file" % sectionName
-            sys.exit(1)
-        try:
-            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_overlap")
-        except NoOptionError:
-            print "ERROR: the option 'chunk_overlap' must be defined in %s in your configuration file" % sectionName
-            sys.exit(1)
-        try:
-            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "nb_seq_per_batch")
-        except NoOptionError:
-            print "ERROR: the option 'nb_seq_per_batch' must be defined in %s in your configuration file" % sectionName
-            sys.exit(1)
-        try:
-            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "resources")
-        except NoOptionError:
-            print "ERROR: the option 'resources' must be defined in %s in your configuration file" % sectionName
-            sys.exit(1)
-        try:
-            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "tmpDir")
-        except NoOptionError:
-            print "ERROR: the option 'tmpDir' must be defined in %s in your configuration file" % sectionName
-            sys.exit(1)

--- a/commons/tools/RetrieveInitHeaders.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-#! /usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-from optparse import OptionParser
-from commons.core.sql.DbMySql import DbMySql
-
-class RetrieveInitHeaders(object):
-
-    def __init__(self, inTableName = "", linkFileName = "", outTableName = "", isQueryHeaders = True, clean = False, verbose = 0):
-        self._inTableName = inTableName
-        self._linkFileName = linkFileName
-        if outTableName == "":
-            self._outTableName = self._inTableName
-        else:
-            self._outTableName = outTableName
-        self._isQueryHeaders = isQueryHeaders
-        self._clean = clean
-        self._verbose = verbose
-        self._iDb = None
-        self._tmpTableName = "%s_tmp" % self._inTableName
-
-    #TODO: can handle config file
-    #TODO: description, help...
-    def setAttributesFromCmdLine(self):
-        description = ""
-        parser = OptionParser(description = description)
-        parser.add_option("-i", "--input", dest = "inTableName", type = "string", help = "", default = "")
-        parser.add_option("-l", "--link", dest = "linkFileName", type = "string", help = "", default = "")
-        parser.add_option("-o", "--output", dest = "outTableName", type = "string", help = "(default = input table name)", default = "")
-        parser.add_option("-s", "--subject", dest = "isQueryHeaders", action = "store_false", help = "change subject name and not query name", default = True)
-        parser.add_option("-c", "--clean", dest = "clean", action = "store_true", help = "drop input table", default = False)
-        parser.add_option("-v", "--verbose", dest = "verbose", type = "int", help = "0 or 1", default = 0)
-        options, args = parser.parse_args()
-        self.setAttributesFromOptions(options)
-        
-    def setAttributesFromOptions(self, options):
-        self.setInTableName(options.inTableName)
-        self.setLinkFileName(options.linkFileName)
-        self.setOutTableName(options.outTableName)
-        self.setIsQueryHeaders(options.isQueryHeaders)
-        self.setClean(options.clean)
-        self.setVerbose(options.verbose)
-        
-    def setInTableName(self, inTableName):
-        self._inTableName = inTableName
-        self._tmpTableName = "%s_tmp" % self._inTableName
-        
-    def setLinkFileName(self, linkFileName):
-        self._linkFileName = linkFileName
-        
-    def setOutTableName(self, outTableName):
-        if outTableName == "":
-            self._outTableName = self._inTableName
-        else:
-            self._outTableName = outTableName
-        
-    def setIsQueryHeaders(self, isQueryHeaders):
-        self._isQueryHeaders = isQueryHeaders
-        
-    def setClean(self, clean):
-        self._clean = clean
-        
-    def setVerbose(self, verbose):
-        self._verbose = verbose
-        
-    #TODO: checkOptions
-    def checkOptions(self):
-        pass    
-    
-    def run(self):
-        if self._verbose > 0:
-            print "START RetrieveInitHeaders.py"
-        self.checkOptions()
-        
-        if self._verbose > 0:
-            print "copy '%s' table to '%s' table" % (self._inTableName, self._tmpTableName)
-        self._iDb = DbMySql()
-        self._iDb.copyTable(self._inTableName, self._tmpTableName)
-        
-        if self._verbose > 0:
-            print "read '%s' file" % self._linkFileName
-        f = open(self._linkFileName)
-        line = f.readline()
-        count = 0
-        while line:
-            oldHeader = line.split()[0]
-            newHeader = line.split()[1]
-            if self._isQueryHeaders:
-                self._updateQueryName(oldHeader, newHeader)
-            else:
-                self._updateSubjectName(oldHeader, newHeader)
-            count += 1
-            line = f.readline()
-        f.close()
-        
-        if self._verbose > 0:
-            print "nb of relationships: %i" % count
-        if self._clean:
-            self._iDb.dropTable(self._inTableName)
-            if self._verbose > 0:
-                print "drop '%s' table" % self._inTableName
-        if self._verbose > 0:
-            print "rename '%s' table to '%s' table" % (self._tmpTableName, self._outTableName)
-        self._iDb.renameTable(self._tmpTableName, self._outTableName)
-        self._iDb.close()
-        if self._verbose > 0:
-            print "END RetrieveInitHeaders.py"
-        
-    #TODO: methods must be in TablePathAdaptator ?
-    def _updateQueryName(self, oldH, newH):
-        sqlCmd = "UPDATE %s SET query_name = '%s' WHERE query_name = '%s'" % (self._tmpTableName, newH, oldH)
-        self._iDb.execute(sqlCmd)
-        
-    def _updateSubjectName(self, oldH, newH):
-        sqlCmd = "UPDATE %s SET subject_name = '%s' WHERE subject_name = '%s'" % (self._tmpTableName, newH, oldH)
-        self._iDb.execute(sqlCmd)
-    
-if __name__ == "__main__":
-    iRIH = RetrieveInitHeaders()
-    iRIH.setAttributesFromCmdLine()
-    iRIH.run()
\ No newline at end of file

--- a/commons/tools/RmvPairAlignInChunkOverlaps.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,286 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Remove hits due to chunk overlaps.
-"""
-
-import os
-import sys
-import getopt
-import exceptions
-import copy
-from commons.core.coord.Align import *
-
-
-class RmvPairAlignInChunkOverlaps( object ):
-    """
-    Remove hits due to chunk overlaps.
-    """
-    
-    
-    def __init__( self, inFileName="", chunkLength=200000, chunkOverlap=10000, margin=10, outFileName="", verbose=0 ):
-        """
-        Constructor.
-        """
-        self._inFileName = inFileName
-        self._chunkLength = chunkLength
-        self._chunkOverlap = chunkOverlap
-        self._margin = margin
-        self._outFileName = outFileName
-        self._verbose = verbose
-
-    def help( self ):
-        """
-        Display the help.
-        """
-        print
-        print "usage: %s [ options ]" % ( sys.argv[0] )
-        print "options:"
-        print "     -h: this help"
-        print "     -i: name of the input file (format='align')"
-        print "     -l: chunk length (in bp)"
-        print "     -o: chunk overlap (in bp)"
-        print "     -m: margin to remove match included into a chunk overlap (default=10)"
-        print "     -O: name of the output file (default=inFileName+'.not_over')"
-        print "     -v: verbose (default=0/1)"
-        print
-
-    def setAttributesFromCmdLine( self ):
-        """
-        Set attributes from the command-line arguments.
-        """
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"h:i:l:o:m:O:v:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputFileName( a )
-            elif o == "-l":
-                self.setChunkLength( a )
-            elif o == "-o":
-                self.setChunkOverlap( a )
-            elif o == "-m":
-                self.setMargin( a )
-            elif o == "-O":
-                self.setOutputFileName( a )
-            elif o == "-v":
-                self.setVerbosityLevel( a )
-                
-    def setInputFileName( self, inFileName ):
-        self._inFileName = inFileName
-        
-    def setChunkLength( self, chunkLength ):
-        self._chunkLength = int(chunkLength)
-        
-    def setChunkOverlap( self, chunkOverlap ):
-        self._chunkOverlap = int(chunkOverlap)
-        
-    def setMargin( self, margin ):
-        self._margin = int(margin)
-        
-    def setOutputFileName( self, outFileName ):
-        self._outFileName = outFileName
-        
-    def setVerbosityLevel( self, verbose ):
-        self._verbose = int(verbose)
-        
-    def checkAttributes( self ):
-        """
-        Before running, check the required attributes are properly filled.
-        """
-        if self._inFileName == "":
-            print "ERROR: missing input file"; self.help(); sys.exit(1)
-        if not os.path.exists(self._inFileName ):
-            print "ERROR: input file '%s' doesn't exist"  %( self._inFileName )
-        if self._outFileName == "":
-            self._outFileName = "%s.not_over" % ( self._inFileName )
-            
-            
-    def isPairAlignAChunkOverlap( self, a, chunkQuery, chunkSubject ):
-        """
-        Return True if the pairwise alignment exactly corresponds to a 2-chunk overlap, False otherwise.
-        Take into account cases specific to BLASTER or PALS.
-        """
-        
-        if a.range_query.isOnDirectStrand() != a.range_subject.isOnDirectStrand():
-            if self._verbose > 1: print "on different strand"
-            return False
-        
-        if chunkQuery == chunkSubject + 1:
-            if self._verbose > 1: print "query > subject"
-            if a.range_query.start == 1 and a.range_subject.end == self._chunkLength \
-                   and ( a.range_query.getLength() == self._chunkOverlap \
-                         or a.range_query.getLength() == self._chunkOverlap + 1 ) \
-                         and ( a.range_subject.getLength() == self._chunkOverlap \
-                               or a.range_subject.getLength() == self._chunkOverlap + 1 ):
-                if self._verbose > 1: print "chunk overlap"
-                return True
-            
-        elif chunkQuery == chunkSubject - 1:
-            if self._verbose > 1: print "query < subject"
-            if a.range_query.end == self._chunkLength and a.range_subject.start == 1 \
-                   and ( a.range_query.getLength() == self._chunkOverlap \
-                         or a.range_query.getLength() == self._chunkOverlap + 1 ) \
-                         and ( a.range_subject.getLength() == self._chunkOverlap \
-                               or a.range_subject.getLength() == self._chunkOverlap + 1 ):
-                if self._verbose > 1: print "chunk overlap"
-                return True
-            
-        if self._verbose > 1: print "not a chunk overlap"
-        return False
-    
-    
-    def isInInterval( self, coord, midpoint ):
-        """
-        Check if a given coordinate is inside the interval [midpoint-margin;midpoint+margin].
-        """
-        if coord >= midpoint - self._margin and coord <= midpoint + self._margin:
-            return True
-        return False
-    
-    
-    def isPairAlignWithinAndDueToAChunkOverlap( self, a, chunkQuery, chunkSubject ):
-        """
-        Return True if the pairwise alignment lies within an overlap between two contiguous chunks and is due to it, False otherwise.
-        """
-        uniqLength = self._chunkLength - self._chunkOverlap
-        
-        if a.range_query.isOnDirectStrand() != a.range_subject.isOnDirectStrand():
-            if self._verbose > 1: print "on different strand"
-            return False
-        
-        if chunkQuery == chunkSubject + 1:
-            if self._verbose > 1: print "query > subject"
-            if a.range_query.getMin() >= 1 and a.range_query.getMax() <= self._chunkOverlap \
-                   and a.range_subject.getMin() >= self._chunkLength - self._chunkOverlap + 1 \
-                   and a.range_subject.getMax() <= self._chunkLength:
-                if self._verbose > 1: print "included"
-                if self.isInInterval( a.range_query.getMin(), a.range_subject.getMin() - uniqLength ) \
-                       and self.isInInterval( self._chunkOverlap - a.range_query.getMax(), self._chunkLength - a.range_subject.getMax() ):
-                    if self._verbose > 1: print "due to overlap"
-                    return True
-                else:
-                    if self._verbose > 1: print "not due to overlap"
-                    return False
-                
-        elif chunkQuery == chunkSubject - 1:
-            if self._verbose > 1: print "query < subject"
-            if a.range_query.getMin() >= self._chunkLength - self._chunkOverlap + 1 \
-                   and a.range_query.getMax() <= self._chunkLength \
-                   and a.range_subject.getMin() >= 1 \
-                   and a.range_subject.getMax() <= self._chunkOverlap:
-                if self._verbose > 1: print "included"
-                if self.isInInterval( a.range_subject.getMin(), a.range_query.getMin() - uniqLength ) \
-                       and self.isInInterval( self._chunkOverlap - a.range_subject.getMax(), self._chunkLength - a.range_query.getMax() ):
-                    if self._verbose > 1: print "due to overlap"
-                    return True
-                else:
-                    if self._verbose > 1: print "not due to overlap"
-                    return False
-                
-        else:
-            if self._verbose > 1: print "not contiguous chunks"
-            return False
-        
-        if self._verbose > 1: print "not included"
-        return False
-    
-    
-    def removeChunkOverlaps( self ):
-        """
-        Remove pairwise alignments exactly corresponding to chunk overlaps or those included within such overlaps.
-        """
-        totalNbPairAlign = 0
-        nbChunkOverlaps = 0
-        d = {}
-        nbPairAlignWithinChunkOverlaps = 0
-        
-        inF = open( self._inFileName, "r" )
-        outF = open( self._outFileName, "w" )
-        alignInstance = Align()
-        
-        while True:
-            if not alignInstance.read( inF ): break
-            totalNbPairAlign += 1
-            if self._verbose > 1: alignInstance.show()
-            
-            if "chunk" not in alignInstance.range_query.seqname or "chunk" not in alignInstance.range_subject.seqname:
-                print "WARNING: no 'chunk' in query or subject name"; return False
-                
-            chunkQuery = int(alignInstance.range_query.seqname.replace("chunk",""))
-            chunkSubject = int(alignInstance.range_subject.seqname.replace("chunk",""))
-            
-            if abs( chunkSubject - chunkQuery ) > 1:
-                if self._verbose > 1: print "non contiguous chunks -> keep"
-                alignInstance.write( outF )
-                continue
-            
-            if alignInstance.range_query.isOnDirectStrand() != alignInstance.range_subject.isOnDirectStrand():
-                if self._verbose > 1: print "on different strand"
-                alignInstance.write( outF )
-                continue
-            
-            if abs( chunkSubject - chunkQuery ) == 0:
-                if alignInstance.range_query.start == 1 \
-                       and alignInstance.range_query.end == self._chunkLength \
-                       and alignInstance.range_subject.start == 1 \
-                       and alignInstance.range_subject.end == self._chunkLength:
-                    if self._verbose > 1: print "self-alignment on whole chunk -> remove"
-                    continue
-                
-            if self.isPairAlignAChunkOverlap( alignInstance, chunkQuery, chunkSubject ):
-                if self._verbose > 1: print "chunk overlap -> remove"
-                nbChunkOverlaps += 1
-                
-            elif self.isPairAlignWithinAndDueToAChunkOverlap( alignInstance, chunkQuery, chunkSubject ):
-                if self._verbose > 1: print "within chunk overlap -> remove"
-                nbPairAlignWithinChunkOverlaps += 1
-                
-            else:
-                if self._verbose > 1: print "keep"
-                alignInstance.write( outF )
-                
-        inF.close()
-        if self._verbose > 0: print "nb of pairwise alignments in input file: %i" % ( totalNbPairAlign )
-        if self._verbose > 0: print "nb of chunk overlaps: %i" % ( nbChunkOverlaps )
-        if self._verbose > 0: print "nb of pairwise alignments within chunk overlaps: %i" % ( nbPairAlignWithinChunkOverlaps )
-        
-        for names,lAligns in d.items():
-            for alignInstance in lAligns:
-                alignInstance.write( outF )
-        outF.close()
-        
-        
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        if self._verbose > 0:
-            print "START %s" % ( type(self).__name__ ); sys.stdout.flush()
-        self.checkAttributes()
-        
-        
-    def end( self ):
-        """
-        Useful commands before ending the program.
-        """
-        if self._verbose > 0:
-            print "END %s" % ( type(self).__name__ ); sys.stdout.flush()
-            
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        self.removeChunkOverlaps()
-        self.end()
-        
-        
-if __name__ == '__main__':
-    i = RmvPairAlignInChunkOverlaps()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/SpliceTEsFromGenome.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,193 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import os
-import getopt
-
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.coord.MapUtils import MapUtils
-from commons.core.coord.AlignUtils import AlignUtils
-from commons.core.coord.PathUtils import PathUtils
-
-
-class SpliceTEsFromGenome( object ):
-    
-    def __init__( self ):
-        self._inputData = ""
-        self._formatData = ""
-        self._genomeFile = ""
-        self._configFile = ""
-        self._outFile = ""
-        self._verbose = 0
-        self._db = None
-        
-        
-    def help( self ):
-        print
-        print "usage: SpliceTEsFromGenome.py [ options ]"
-        print "options:"
-        print "     -h: this help"
-        print "     -i: input TE coordinates (can be file or table)"
-        print "         TEs as subjects if align or path format"
-        print "     -f: format of the data (map/align/path)"
-        print "     -g: genome file (format=fasta)"
-        print "     -C: configuration file (if table as input)"
-        print "     -o: output fasta file (default=genomeFile+'.splice')"
-        print "     -v: verbosity level (default=0/1)"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:f:g:C:o:v:")
-        except getopt.GetoptError, err:
-            msg = "%s" % str(err)
-            sys.stderr.write( "%s\n" % msg )
-            self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self._inputData = a
-            elif o == "-f":
-                self._formatData = a
-            elif o == "-g":
-                self._genomeFile = a
-            elif o == "-C":
-                self._configFile = a
-            elif o =="-o":
-                self._outFile = a
-            elif o == "-v":
-                self._verbose = int(a)
-                
-                
-    def checkAttributes( self ):
-        if self._inputData == "":
-            msg = "ERROR: missing input data (-i)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._inputData ):
-            if not os.path.exists( self._configFile ):
-                msg = "ERROR: neither input file '%s' nor configuration file '%s'" % ( self._inputData, self._configFile )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-            if not os.path.exists( self._configFile ):
-                msg = "ERROR: can't find config file '%s'" % ( self._configFile )
-                sys.stderr.write( "%s\n" % msg )
-                sys.exit(1)
-            self._db = DbMySql( cfgFileName=self._configFile )
-            if not self._db.doesTableExist( self._inputData ):
-                msg = "ERROR: can't find table '%s'" % ( self._inputData )
-                sys.stderr.write( "%s\n" % msg )
-                self.help()
-                sys.exit(1)
-        if self._formatData == "":
-            msg = "ERROR: need to precise format (-f)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if self._formatData not in [ "map", "align", "path" ]:
-            msg = "ERROR: format '%s' not yet supported" % ( self._formatData )
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if self._genomeFile == "":
-            msg = "ERROR: missing genome file (-g)"
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if not os.path.exists( self._genomeFile ):
-            msg = "ERROR: can't find genome file '%s'" % ( self._genomeFile )
-            sys.stderr.write( "%s\n" % msg )
-            self.help()
-            sys.exit(1)
-        if self._outFile == "":
-            self._outFile = "%s.splice" % ( self._genomeFile )
-            if self._verbose > 0:
-                print "output fasta file: %s" % self._outFile
-                
-                
-    def getCoordsAsMapFile( self ):
-        if self._verbose > 0:
-            print "get TE coordinates as 'Map' file"
-            sys.stdout.flush()
-        if self._db != None:
-            cmd = "srptExportTable.py"
-            cmd += " -i %s" % ( self._inputData )
-            cmd += " -C %s" % ( self._configFile )
-            cmd += " -o %s.%s" % ( self._inputData, self._formatData )
-            returnStatus = os.system( cmd )
-            if returnStatus != 0:
-                msg = "ERROR while exporting data from table"
-                sys.stderr.write( "%s\n" % msg )
-                sys.exit(1)
-            self._inputData += ".%s" % ( self._formatData )
-           
-        if self._formatData == "map":
-            return self._inputData
-        elif self._formatData == "align":
-            mapFile = "%s.map" % ( self._inputData )
-            AlignUtils.convertAlignFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile )
-            return mapFile
-        elif self._formatData == "path":
-            mapFile = "%s.map" % ( self._inputData )
-            PathUtils.convertPathFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile )
-            return mapFile
-        
-        
-    def mergeCoordsInMapFile( self, mapFile ):
-        if self._verbose > 0:
-            print "merge TE coordinates"
-            sys.stdout.flush()
-        mergeFile = "%s.merge" % ( mapFile )
-        MapUtils.mergeCoordsInFile( mapFile, mergeFile )
-        if self._formatData != "map" or self._db != None:
-            os.remove( mapFile )
-        return mergeFile
-    
-    
-    def spliceFastaFromCoords( self, mergeFile ):
-        if self._verbose > 0:
-            print "splice TE copies from the genome"
-            sys.stdout.flush()
-        FastaUtils.spliceFromCoords( self._genomeFile,
-                                     mergeFile,
-                                     self._outFile )
-    
-        os.remove( mergeFile )
-        
-        
-    def start( self ):
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START SpliceTEsFromGenome.py"
-            sys.stdout.flush()
-            
-            
-    def end( self ):
-        if self._db != None:
-            self._db.close()
-        if self._verbose > 0:
-            print "END SpliceTEsFromGenome.py"
-            sys.stdout.flush()
-            
-            
-    def run( self ):
-        self.start()
-        
-        mapFile = self.getCoordsAsMapFile()
-
-        mergeFile = self.mergeCoordsInMapFile( mapFile )
-        
-        self.spliceFastaFromCoords( mergeFile )
-        
-        self.end()
-        
-        
-if __name__ == "__main__":
-    i = SpliceTEsFromGenome()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/SplicerFromAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,218 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import os
-import sys
-import ConfigParser
-
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.parsing.FastaParser import FastaParser
-from ConfigParser import MissingSectionHeaderError
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.LoggerFactory import LoggerFactory
-
-#TODO: use configuration file
-
-LOG_DEPTH = "repet.tools"
-
-## Get 3 annotation files, using output from TEannot:
-#- consensus with one or more full length copy, 
-#- consensus with one or more full length fragment,
-#- consensus without copy
-
-class SplicerFromAnnotation(object):
-    
-    def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
-        self._inInfoFileName = inInfoFileName
-        self._tableName = tableName
-        self._verbosity = verbose
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def setAttributesFromCmdLine(self):
-        desc = "Splice annotations from genome. These annotations are Full Length Copy or Full Length Fragment according to consensus."
-        desc += "A TEs library and annotation are necessary. Connection to the database parameters are retrieved from the environment"
-        
-        examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
-        examples += "\t$ python SplicerFromAnnotation.py -i inputFastaFileName -C configFileName -t MyTEannotAnalysis_refTEs_seq "
-        examples += "\n\t"
-        examples += "\n\n"
-        
-        parser = RepetOptionParser(description = desc, epilog = examples)
-        parser.add_option("-i", "--file",      dest = "inputFastaFileName",  action = "store", type = "string", help = "input file (mandatory) = output file with .splice)")
-        parser.add_option("-C", "--config",    dest = "configFileName",     action = "store", type = "string", help = "config file name to set database connection", default = "")
-        parser.add_option("-t", "--copyType",  dest = "copyType" ,          action = "store", type = "int", help = "type number [default: 1, 2] 1 is Full Length Copy", default = 1 )
-        parser.add_option("-I", "--identity",  dest = "identity",           action= "store",   type = "float",  help = "identity between 0 and 100 [default: 80]", default = 80) 
-        parser.add_option("-o", "--outputFile",dest = "outputFile",         action= "store", type = "string", help = "output fasta file (default=input File + '.splice')",  default = "")
-        parser.add_option("-v", "--verbose",   dest = "verbose",             action = "store", type = "int",    help = "verbosity level (default=0)", default = 0)
-        (options, args) = parser.parse_args()
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setConfigFileName(options.configFileName)
-        self.setInputFileName(options.inputFastaFileName)
-        self.setOutputFileName(options.outputFile)
-        self.setIdentity(options.identity)
-        self.setCopyType(options.copyType)
-        self.setVerbose(options.verbose)
-        
-    def setCopyType(self, copyType):
-        self._copyType = copyType
-        
-    def setIdentity(self,identity):
-        self._identity=identity
-        
-    def setInputFileName(self, inputFastaFileName):
-        self._inputFastaFileName = inputFastaFileName
-        self._projectName= os.path.basename(self._inputFastaFileName)
-        self._projectName = self._projectName.split('.')[0]
-        self._fF=FastaParser(self._inputFastaFileName)
-        self._fF.getInfos()
-        self.genomeSize=self._fF.size
-        self.nbSeqGenome=self._fF.nbSequences
-        
-    def setOutputFileName(self,outputFile):
-        self._outputFileName = outputFile
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        configFileHandle = open(self._configFileName)
-        config = ConfigParser.ConfigParser()
-    
-        try :
-            config.readfp( configFileHandle )
-        except MissingSectionHeaderError:
-            self._logAndRaise("Config file " + self._configFileName + " must begin with a section header ")
-
-        self.setup_env( config )
-        
-    def setVerbose(self, verbose):
-        self._verbosity = verbose
-   
-    def setup_env(self, config):
-        os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
-        os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
-        os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
-        os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
-        os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
-        os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
-
-    def checkOptions(self):
-        if self._inputFastaFileName != "":
-            if not FileUtils.isRessourceExists(self._inputFastaFileName):
-                self._logAndRaise("Input fasta file does not exist!")
-        else:
-            self._logAndRaise("No specified -i option! It is mandatory")
-       
-        if self._outputFileName =="":
-            self._outputFileName = os.path.basename(self._inputFastaFileName)+'.splice'
-        
-        if self._copyType!=1 or self._copyType!=2:
-            self._logAndRaise("Copy type must be only 1 or 2!")
-        if self._configFileName != "":
-            iDb = DbMySql(cfgFileName = self._configFileName)
-            iDb.close()
-        else:
-            self._logAndRaise("No specified config file name!")
-
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        self.checkOptions()
-        
-        msg = "START SplicerFromAnnotation"
-        msg += "\n input info file: %s" % self._inputFastaFileName
-        msg += "\n Copy type is: %s" % self._copyType
-        msg += "\n identity is: %s" % self._identity
-        msg += "\n host is: %s" % os.environ["REPET_HOST"]
-        msg += "\n user is: %s" % os.environ["REPET_USER"]
-        msg += "\n DB is: %s" % os.environ["REPET_DB"] 
-        msg += "\n port is: %s" % os.environ["REPET_PORT"]
-        self._log.debug("%s\n" % msg)
-        
-        cmd="PostAnalyzeTELib.py -a 3 -p %s_chr_allTEs_nr_noSSR_join_path -s %s_refTEs_seq -g %s" % (self._projectName,self._projectName,self.genomeSize)       
-        os.system(cmd)
-        
-        cmd="GetSpecificTELibAccordingToAnnotation.py -i %s_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab -t %s_refTEs_seq -v 2" % (self._projectName,self._projectName)
-        os.system(cmd) 
-
-        if self._copyType == 1 :
-            f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt", "r")
-        else :
-            f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt", "r")
-        
-        lines=f.readlines()[1:]
-        if len(lines)>0:
-            lConsensusHeader_copyType=[i.split('\t',1)[0] for i in lines] 
-            db = DbFactory.createInstance()
-            
-            sql_cmd = "CREATE TABLE %s_annotationIdentitySup%d_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where identity >=%f" % ( self._projectName,int(self._identity),self._projectName,self._identity)
-            db.execute( sql_cmd )
-    
-            iTPA = TablePathAdaptator(db, "%s_annotationIdentitySup%d_path" % (self._projectName, int(self._identity)))
-            lAllDistinctPath=[]
-            for consensusName in lConsensusHeader_copyType:
-                lDistinctPath = iTPA.getIdListFromSubject(consensusName)
-                lAllDistinctPath=lAllDistinctPath+lDistinctPath
-            
-            iTPA = TablePathAdaptator(db,"%s_chr_allTEs_nr_noSSR_join_path" % self._projectName)
-            sql_cmd = "CREATE TABLE  %s_annotationToSplice_path LIKE %s_chr_allTEs_nr_noSSR_join_path" % ( self._projectName, self._projectName )
-            db.execute( sql_cmd )
-
-            for pathId in lAllDistinctPath:
-                sql_cmd = "INSERT INTO %s_annotationToSplice_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where path =%d" % ( self._projectName, self._projectName, pathId )
-                db.execute( sql_cmd )           
-            db.close()
-            
-            cmd="SpliceTEsFromGenome.py -i %s_annotationToSplice_path -f path -g %s -o %s -C %s -v 2" % (self._projectName, self._inputFastaFileName, self._outputFileName, self._configFileName)       
-            os.system(cmd)
-            
-        else : 
-            msg = "There is no consensus in this copy type.\n"
-            self._log.info(msg)
-        f.close()     
-        
-        self._log.info("END SplicerFromAnnotation")
-        return 0
-
-if __name__ == '__main__':
-    iGetTELib = SplicerFromAnnotation()
-    iGetTELib.setAttributesFromCmdLine()
-    iGetTELib.run() 
-    
\ No newline at end of file

--- a/commons/tools/TEclassifierPE.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,193 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import sys
-
-if not "REPET_PATH" in os.environ.keys():
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append(os.environ["REPET_PATH"])
-if not "PYTHONPATH" in os.environ.keys():
-    os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
-else:
-    os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
-    
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.checker.ConfigChecker import ConfigRules
-from commons.core.checker.ConfigChecker import ConfigChecker
-from commons.core.seq.FastaUtils import FastaUtils
-from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif
-from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif
-from denovo_pipe.DetectTEFeatures import DetectTEFeatures
-from denovo_pipe.LaunchPASTEC import LaunchPASTEC
-from PASTEC.StatPastec import StatPastec
-
-LOG_DEPTH = "repet.tools"
-#LOG_FORMAT = "%(message)s"
-
-####TEclassifier PASTEC Edition
-#
-class TEclassifierPE(object):
-    
-    def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0):
-        self._fastaFileName = fastaFileName
-        self._addWickerCode = addWickerCode
-        self._reverseComp = reverseComp
-        self._configFileName = configFileName
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._projectName = ""
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "TE classifier PASTEC Edition.\n"
-        description += "Detect TE features on consensus and classify them. Give some classification statistics.\n"
-        description += "Can rename headers with classification info and Wicker's code at the beginning.\n"
-        description += "Can reverse-complement consensus if they are detected in reverse strand.\n"
-        description += "Warning : it's highly advised to use sequences in upper case.\n"
-        epilog = "\n"
-        epilog += "Example 1: launch and clean temporary files\n"
-        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n"
-        epilog += "\n"
-        epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n"
-        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--fasta",      dest = "fastaFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-C", "--config",     dest = "configFileName",action = "store",       type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "")
-        parser.add_option("-w", "--wicker",     dest = "addWickerCode", action = "store_true",                   help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False)
-        parser.add_option("-r", "--reverse",    dest = "reverseComp",   action = "store_true",                   help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setFastaFileName(options.fastaFileName)
-        self.setAddWickerCode(options.addWickerCode)
-        self.setReverseComp(options.reverseComp)
-        self.setConfigFileName(options.configFileName)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def _checkConfig(self):       
-        iConfigRules = ConfigRules()
-        iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string")
-        sectionName = "classif_consensus"
-        iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool")
-        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
-        iConfig = iConfigChecker.getConfig()
-        self._setAttributesFromConfig(iConfig)
-        
-    def _setAttributesFromConfig(self, iConfig):
-        self.setProjectName(iConfig.get("project", "project_name"))
-        sectionName = "classif_consensus"
-        self.setDoClean(iConfig.get(sectionName, "clean"))
-        
-    def setFastaFileName(self, fastaFileName):
-        self._fastaFileName = fastaFileName
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setAddWickerCode(self, addWickerCode):
-        self._addWickerCode = addWickerCode
-        
-    def setReverseComp(self, reverseComp):
-        self._reverseComp = reverseComp
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def setProjectName(self, projectName):
-        self._projectName = projectName
-        
-    def _checkOptions(self):
-        if self._fastaFileName == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        if self._configFileName:
-            self._checkConfig()
-        self._checkOptions()
-        self._log.info("START TEclassifier PASTEC Edition")
-        self._log.debug("Fasta file name: %s" % self._fastaFileName)
-        nbSeq = FastaUtils.dbSize(self._fastaFileName)
-        self._log.debug("Total number of sequences: %i)" % nbSeq)
-
-        #TODO: add step => avoid to re-launch DetectTEFeatures, if error with PASTEC (e.g. wrong bank format)
-        #step 1
-        iDF = DetectTEFeatures(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity)
-        iDF.run()
-        
-        #step 2
-        iLP = LaunchPASTEC(configFileName = self._configFileName, inputFileName = self._fastaFileName, projectName = self._projectName, verbose = self._verbosity)
-        iLP.run()
-        
-        classifFileName = "%s.classif" % self._projectName
-
-        iSP = StatPastec(classifFileName)
-        iSP.run()
-        
-        if self._reverseComp:
-            self._log.info("Reverse complement...")
-            iRevComplAccording2Classif = ReverseComplementAccordingToClassif()
-            iRevComplAccording2Classif.setFastaFile(self._fastaFileName)
-            iRevComplAccording2Classif.setClassifFile(classifFileName)
-            iRevComplAccording2Classif.run()
-            tmpFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0]
-        else:
-            tmpFastaFileName = self._fastaFileName
-
-        if self._addWickerCode:
-            self._log.info("Rename headers according to Wicker's code...")
-            iRHC = RenameHeaderClassif(classifFileName, tmpFastaFileName, self._projectName)
-            iRHC.setOutputFileName("")
-            iRHC.run()
-            if self._doClean:
-                os.remove(tmpFastaFileName)
-        
-        self._log.info("END TEclassifier PASTEC Edition")
-
-if __name__ == "__main__":
-    iLaunch = TEclassifierPE()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/tools/TEclassifierPE_parallelized.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,261 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import sys
-import shutil
-
-if not "REPET_PATH" in os.environ.keys():
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append(os.environ["REPET_PATH"])
-if not "PYTHONPATH" in os.environ.keys():
-    os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
-else:
-    os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
-    
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.checker.ConfigChecker import ConfigRules
-from commons.core.checker.ConfigChecker import ConfigChecker
-from commons.core.seq.FastaUtils import FastaUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
-from commons.core.launcher.Launcher import Launcher
-from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif
-from denovo_pipe.DetectTEFeatures_parallelized import DetectTEFeatures_parallelized
-from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif
-from denovo_pipe.LaunchPASTEC import LaunchPASTEC
-from PASTEC.StatPastec import StatPastec
-
-LOG_DEPTH = "repet.tools"
-#LOG_FORMAT = "%(message)s"
-
-####TEclassifier PASTEC Edition - parallelized
-#
-class TEclassifierPE_parallelized(object):
-    
-    def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0):
-        self._fastaFileName = fastaFileName
-        self._addWickerCode = addWickerCode
-        self._reverseComp = reverseComp
-        self._configFileName = configFileName
-        self._doClean = doClean
-        self._verbosity = verbosity
-        self._projectName = ""
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
-        
-    def setAttributesFromCmdLine(self):
-        description = "TE classifier PASTEC Edition.\n"
-        description += "Detect TE features on consensus and classify them. Give some classification statistics.\n"
-        description += "Can rename headers with classification info and Wicker's code at the beginning.\n"
-        description += "Can reverse-complement consensus if they are detected in reverse strand.\n"
-        epilog = "\n"
-        epilog += "Example 1: launch and clean temporary files\n"
-        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n"
-        epilog += "\n"
-        epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n"
-        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n"
-        parser = RepetOptionParser(description = description, epilog = epilog)
-        parser.add_option("-i", "--fasta",      dest = "fastaFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
-        parser.add_option("-C", "--config",     dest = "configFileName",action = "store",       type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "")
-        parser.add_option("-w", "--wicker",     dest = "addWickerCode", action = "store_true",                   help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False)
-        parser.add_option("-r", "--reverse",    dest = "reverseComp",   action = "store_true",                   help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False)
-        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3)
-        options = parser.parse_args()[0]
-        self._setAttributesFromOptions(options)
-        
-    def _setAttributesFromOptions(self, options):
-        self.setFastaFileName(options.fastaFileName)
-        self.setAddWickerCode(options.addWickerCode)
-        self.setReverseComp(options.reverseComp)
-        self.setConfigFileName(options.configFileName)
-        self.setDoClean(options.doClean)
-        self.setVerbosity(options.verbosity)
-
-    def _checkConfig(self):       
-        iConfigRules = ConfigRules()
-        iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string")
-        sectionName = "classif_consensus"
-        iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool")
-        iConfigRules.addRuleOption(section=sectionName, option ="limit_job_nb", type="int")
-        iConfigRules.addRuleOption(section=sectionName, option ="resources", type="string")
-        iConfigRules.addRuleOption(section=sectionName, option ="tmpDir", type="string")
-        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
-        iConfig = iConfigChecker.getConfig()
-        self._setAttributesFromConfig(iConfig)
-        
-    def _setAttributesFromConfig(self, iConfig):
-        self.setProjectName(iConfig.get("project", "project_name"))
-        sectionName = "classif_consensus"
-        self.setDoClean(iConfig.get(sectionName, "clean"))
-        self._maxJobNb = iConfig.get(sectionName, "limit_job_nb")
-        self._resources = iConfig.get(sectionName, "resources")
-        self._tmpDir = iConfig.get(sectionName, "tmpDir")
-        
-    def setFastaFileName(self, fastaFileName):
-        self._fastaFileName = fastaFileName
-        
-    def setConfigFileName(self, configFileName):
-        self._configFileName = configFileName
-        
-    def setAddWickerCode(self, addWickerCode):
-        self._addWickerCode = addWickerCode
-        
-    def setReverseComp(self, reverseComp):
-        self._reverseComp = reverseComp
-        
-    def setDoClean(self, doClean):
-        self._doClean = doClean
-        
-    def setVerbosity(self, verbosity):
-        self._verbosity = verbosity
-        
-    def setProjectName(self, projectName):
-        self._projectName = projectName
-        
-    def _checkOptions(self):
-        if self._fastaFileName == "":
-            self._logAndRaise("ERROR: Missing input fasta file name")
-            
-    def _logAndRaise(self, errorMsg):
-        self._log.error(errorMsg)
-        raise Exception(errorMsg)
-    
-#    def setup_env(config):
-#        os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
-#        os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
-#        os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
-#        os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
-#        os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
-#        os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
-#        os.environ["REPET_QUEUE"] = config.get("repet_env", "repet_job_manager")
-#        os.environ["REPET_JOBS"] = "MySQL"
-    
-    def getPASTECcommand(self, iLauncher, fileName):
-        lArgs = []
-        lArgs.append("-C %s" % self._configFileName)
-        lArgs.append("-P %s" % self._projectName)
-        lArgs.append("-S 2")
-        lArgs.append("-i %s" % fileName)
-        lArgs.append("-v %s" % self._verbosity)
-        return iLauncher.getSystemCommand("LaunchPASTEC.py", lArgs)
-                    
-    def run(self):
-        LoggerFactory.setLevel(self._log, self._verbosity)
-        if self._configFileName:
-            self._checkConfig()
-        self._checkOptions()
-        self._log.info("START TEclassifier PASTEC Edition")
-        self._log.debug("Fasta file name: %s" % self._fastaFileName)
-        nbSeq = FastaUtils.dbSize(self._fastaFileName)
-        self._log.debug("Total number of sequences: %i)" % nbSeq)
-
-        self._log.debug("Launch DetectTEFeatures on each batch")
-        iDF = DetectTEFeatures_parallelized(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity)
-        iDF.run()
-        
-        self._log.debug("Insert banks in database")
-        iLP = LaunchPASTEC(self._configFileName, "1", projectName = self._projectName, verbose = self._verbosity)
-        iLP.run()
-        
-        self._log.info("Split fasta file")
-        if self._maxJobNb == 0 or nbSeq / self._maxJobNb <= 1.0:
-            nbSeqPerBatch = nbSeq
-        else:
-            nbSeqPerBatch = nbSeq / self._maxJobNb + 1
-        FastaUtils.dbSplit(self._fastaFileName, nbSeqPerBatch, True, verbose = self._verbosity - 2)
-        
-        self._log.info("Launch PASTEC on each batch")
-        queue = self._resources
-        cDir = os.getcwd()
-        if self._tmpDir != "":
-            tmpDir = self._tmpDir
-        else:
-            tmpDir = cDir
-            
-        #TODO: allow not to parallelize
-        groupid = "%s_PASTEC" % self._projectName
-        acronym = "PASTEC"
-        iDb = DbFactory.createInstance()
-        iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
-        iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid)
-        lCmdsTuples = []
-        lFiles = FileUtils.getFileNamesList("%s/batches" % cDir, "batch_")
-        if len(lFiles) == 0:
-            self._logAndRaise("ERROR: directory 'batches' is empty")
-        classifFileName = "%s.classif" % self._projectName
-        count = 0
-        for file in lFiles:
-            count += 1
-            lCmds = [self.getPASTECcommand(iLauncher, file)]    
-            lCmdStart = []
-            lCmdStart.append("shutil.copy(\"%s/batches/%s\", \".\")" % (cDir, file))
-            lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (cDir, self._configFileName))
-            lCmdFinish = []
-            lCmdFinish.append("shutil.move(\"%s\", \"%s/%s_%i\")" % (classifFileName, cDir, classifFileName, count))
-            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
-        iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._doClean)  
-        
-        FileUtils.catFilesByPattern("%s_*" % classifFileName, classifFileName)
-        if self._doClean:
-            FileUtils.removeFilesByPattern("%s_*" % classifFileName)
-            shutil.rmtree("batches")
-
-        self._log.debug("Compute stats about classification")
-        iSP = StatPastec(classifFileName)
-        iSP.run()
-        
-        if self._reverseComp:
-            self._log.debug("Reverse complement")
-            iRevComplAccording2Classif = ReverseComplementAccordingToClassif()
-            iRevComplAccording2Classif.setFastaFile(self._fastaFileName)
-            iRevComplAccording2Classif.setClassifFile(classifFileName)
-            iRevComplAccording2Classif.run()
-            newFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0]
-        else:
-            newFastaFileName = self._fastaFileName
-
-        if self._addWickerCode:
-            self._log.debug("Rename headers according to Wicker's code")
-            iRHC = RenameHeaderClassif(classifFileName, newFastaFileName, self._projectName)
-            iRHC.setOutputFileName("")
-            iRHC.run()
-        
-        self._log.info("END TEclassifier PASTEC Edition")
-
-if __name__ == "__main__":
-    iLaunch = TEclassifierPE_parallelized()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()        
\ No newline at end of file

--- a/commons/tools/blast2align.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import getopt
-
-
-def help():
-    print
-    print "usage: blast2align.py [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: input file name (format=tabulated BLAST)"
-    print "     -o: output file name (format=align, default=inFileName+'.align')"
-    print
-
-
-def blast2align( inFile, outFile ):
-    inFileHandler = open( inFile, "r" )
-    outFileHandler = open( outFile, "w" )
-    while True:
-        line = inFileHandler.readline()
-        if line == "":
-            break
-        if line[0] != "#":
-            data = line.split("\t")
-            qryName = data[0]
-            sbjName = data[1]
-            percId = data[2]
-            qryStart = data[6]
-            qryEnd = data[7]
-            sbjStart = data[8]
-            sbjEnd = data[9]
-            Eval = data[10]
-            bitScore = data[11][:-1]
-            string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Eval, bitScore, percId )
-            outFileHandler.write( string )
-    inFileHandler.close()
-    outFileHandler.close()
-    
-    
-def main():
-    inFileName = ""
-    outFileName = ""
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
-    except getopt.GetoptError, err:
-        sys.stderr.write( "%s\n" % str(err) )
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-  
-    if  inFileName == "":
-        msg =  "ERROR: missing input file name (-i)"
-        sys.stderr.write( "%s\n" % msg )
-        help()
-        sys.exit(1)
-
-    if outFileName == "":
-        outFileName = inFileName + ".align"
-
-    blast2align( inFileName, outFileName )
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/dbBestLength.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-#!/usr/bin/env python
-
-## @file
-# This program extracts the n longest sequences from the input fasta file.
-# usage: dbBestLength.py [ options ]
-# options:
-#      -h: this help
-#      -i: name of the input fasta file
-#      -n: maximum number of sequences in the output file (default=20)
-#      -o: name of the output fasta file (default=inFileName+'.best20')
-#      -v: verbose (default=0/1/2)
-
-import os
-import sys
-import getopt
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-from pyRepet.seq.fastaDB import * 
-
-
-def help():
-    """
-    Give the list of the command-line options.
-    """
-    print
-    print "usage: dbBestLength.py [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input fasta file"
-    print "     -n: maximum number of sequences in the output file (default=20)"
-    print "     -o: name of the output fasta file (default=inFileName+'.best20')"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-
-def main():
-    """
-    This program extracts the n longest sequences from the input fasta file.
-    """
-
-    inFileName = ""
-    nbSeq = 20
-    outFileName = ""
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:n:o:v:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-n":
-            nbSeq = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if  inFileName == "":
-        print "ERROR: missing input file (-i)"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START dbBestLength.py"
-        sys.stdout.flush()
-
-    if outFileName == "":
-        outFileName = "%s.best%s" % ( inFileName, nbSeq )
-
-    log = dbBestLength( nbSeq, inFileName, outFileName, verbose )
-    if log != 0:
-        print "ERROR: dbBestLength() returned %i" % ( log )
-        sys.exit(1)
-
-    if verbose > 0:
-        print "END dbBestLength.py"
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/dbConsensus.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import os
-import sys
-import getopt
-
-##@file
-# usage: dbConsensus.py [ options ]
-# options:
-#      -h: this help
-#      -i: name of the input file (format=aligned fasta)
-#      -n: minimum number of nucleotides in a column to edit a consensus (default=1)
-#      -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0)
-#      -o: name of the output file (default=inFileName+'.cons')
-#      -v: verbose (default=0/1/2)
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-import commons.core.seq.AlignedBioseqDB
-
-
-def help():
-    """
-    Give the list of the command-line options.
-    """
-    print
-    print "usage:",sys.argv[0]," [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format=aligned fasta)"
-    print "     -n: minimum number of nucleotides in a column to edit a consensus (default=1)"
-    print "     -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0)"
-    print "     -o: name of the output file (default=inFileName+'.cons')"
-    print "     -H: format the header with pyramid and piles informations (SATannot)"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-
-def main():
-
-    inFileName = ""
-    minNbNt = 1
-    minPropNt = 0.0
-    outFileName = ""
-    header_SATannot = False
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:n:p:o:v:H")
-    except getopt.GetoptError, err:
-        print str(err); help(); sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-n":
-            minNbNt = int(a)
-        elif o == "-p":
-            minPropNt = float(a)
-        elif o == "-o":
-            outFileName = a
-        elif o == "-H":
-            header_SATannot = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if inFileName == "":
-        print "ERROR: missing input file name"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    alnDB = commons.core.seq.AlignedBioseqDB.AlignedBioseqDB( inFileName )
-
-    if alnDB.getSize() < minNbNt:
-        print "WARNING: not enough sequences (<%i)" % ( minNbNt )
-
-    else:
-        consensus = alnDB.getConsensus( minNbNt, minPropNt, verbose,  header_SATannot)
-        if consensus != None:
-            consensus.upCase()
-            if outFileName == "":
-                outFileName = "%s.cons" % ( inFileName )
-            outFile = open( outFileName, "w" )
-            consensus.write( outFile )
-            outFile.close()
-
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-if __name__ == "__main__":
-    main ()

--- a/commons/tools/dbShuffle.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-#!/usr/bin/env python
-
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import os
-import sys
-import getopt
-
-from commons.core.seq.FastaUtils import FastaUtils
-
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     INPUT: use '-i' or '-I'"
-    print "        -i: name of the input file (fasta format)"
-    print "        -I: name of the input directory (containing fasta files)"
-    print "     OUTPUT: use '-o' or '-O'"
-    print "         -o: name of the output file (use only with '-i')"
-    print "         -O: name of the output directory (use only with '-I')"
-    print "             output file are: prefix of input fasta file + '_shuffle.fa')"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-
-def main():
-    inData = ""
-    outData = ""
-    verbose = 0
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hi:I:o:O:v:" )
-    except getopt.GetoptError, err:
-        sys.stderr.write( "%s\n" % str(err) )
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inData = a
-        elif o == "-I":
-            inData = a
-        elif o == "-o":
-            outData = a
-        elif o == "-O":
-            outData = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if inData == "" or ( not os.path.isfile( inData ) \
-                         and not os.path.isdir( inData ) ):
-        msg = "ERROR: missing input file or directory (-i or -I)"
-        sys.stderr.write( "%s\n" % msg )
-        help()
-        sys.exit(1)
-
-    if outData == "":
-        print "ERROR: missing name of output file or directory (-o or -O)"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-        
-    FastaUtils.dbShuffle( inData, outData, verbose )
-    
-    if verbose > 0:
-        print "END %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/dbSplit.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,92 +0,0 @@
-#!/usr/bin/env python
-
-
-##@file
-# Split the input fasta file in several output files
-# usage: dbSplit.py [ options ]
-# options:
-#      -h: this help
-#      -i: name of the input file (format='fasta')
-#      -n: number of sequences per output file (default=1)
-#      -d: record the output fasta files in a directory called 'batches'
-#      -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
-#      -p: use a prefix for the output files (default='batch')"
-#      -v: verbose (default=0/1)
-
-
-import sys
-import getopt
-
-from commons.core.seq.FastaUtils import FastaUtils
-
-
-## Give the list of the command-line options
-#
-def help():
-    print
-    print "usage: dbSplit.py [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (format='fasta')"
-    print "     -n: number of sequences per batch file (default=1)"
-    print "     -d: record the output fasta files in a directory called 'batches'"
-    print "     -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
-    print "     -p: use a prefix for the output files (default='batch')"
-    print "     -v: verbosity level (default=0/1/2)"
-    print
-
-
-## Split the input fasta file in several output files
-#
-def main():
-    inFile = ""
-    nbSeqPerBatch = 1
-    newDir = False
-    useSeqHeader = False
-    prefix = "batch"
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hi:n:dsp:v:" )
-    except getopt.GetoptError, err:
-        sys.stderr.write( "%s\n" % ( str(err) ) )
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFile = a
-        elif o == "-n":
-            nbSeqPerBatch = int(a)
-        elif o == "-d":
-            newDir = True
-        elif o == "-s":
-            useSeqHeader = True
-        elif o == "-p":
-            prefix = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if inFile == "":
-        msg = "ERROR: missing input file (-i)"
-        sys.stderr.write( "%s\n" % ( msg ) )
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    FastaUtils.dbSplit( inFile, nbSeqPerBatch, newDir, useSeqHeader, prefix, verbose )
-
-    if verbose > 0:
-        print "END %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/filterOutMatcher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import logging
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-import pyRepet.coord.MatchDB
-import pyRepet.seq.BioseqDB
-
-
-def help():
-    """
-    Give the list of the command-line options.
-    """
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0] )
-    print "options:"
-    print "     -h: this help"
-    print "     -q: fasta filename of the queries"
-    print "     -s: fasta filename of the subjects (same as queries if left blank)"
-    print "     -m: output file from Matcher (format='tab')"
-    print "     -o: name of the output query file (format=fasta, default=qryFileName+'.filtered')"
-    print "     -i: identity threshold (default=0.95)"
-    print "     -l: length threshold (default=0.98)"
-    print "     -L: name of a 'log' file (usually from 'rmvRedundancy.py')"
-    print "     -v: verbose (default=0/1)"
-    print
-
-
-def writeOutQuery( qryDB, outFileName, lQryToKeep ):
-    """
-    Write in a fasta file the queries than haven't been filtered (i.e. they are not included in any subject).
-    """
-    outFile = open( outFileName, "w" )
-    nbRmvSeq = 0
-    for bs in qryDB.db:
-        if bs.header in lQryToKeep:
-            bs.write( outFile )
-        else:
-            nbRmvSeq += 1
-    outFile.close()
-    if verbose > 0:
-        print "%i removed queries out of %i" % ( nbRmvSeq, qryDB.getSize() ); sys.stdout.flush()
-
-
-def main():
-    """
-    This program filters the ouput from Matcher by removing queries 'included' in subjects.
-    """
-    qryFileName = ""
-    sbjFileName = ""
-    tabFileName = ""
-    outFileName = ""
-    thresIdentity = 0.95   # remove the seq if it is identical to 95% of another seq
-    thresLength = 0.98   # and if its length is 98% of that seq
-    logFileName = ""
-    global verbose
-    verbose = 0
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"h:q:s:m:o:i:l:L:v:")
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-q":
-            qryFileName = a 
-        elif o == "-s":
-            sbjFileName = a 
-        elif o == "-m":
-            tabFileName = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-i":
-            thresIdentity = float(a) 
-        elif o == "-l":
-            thresLength = float(a)
-        elif o == "-L":
-            logFileName = a
-        elif o == "-v":
-            verbose = int(a)
-    if qryFileName == "" or tabFileName == "":
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    # prepare the 'log' file
-    handler = logging.FileHandler( logFileName )
-    formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )
-    handler.setFormatter( formatter )
-    logging.getLogger('').addHandler( handler )
-    logging.getLogger('').setLevel( logging.DEBUG )
-    logging.info( "use '%s' on '%s'" % ( sys.argv[0].split("/")[-1], tabFileName ) )
-
-    if sbjFileName == "":
-        sbjFileName = qryFileName
-    if outFileName == "":
-        outFileName = "%s.filtered" % ( qryFileName )
-
-    # load the input fasta file corresponding to the queries
-    qryDB = pyRepet.seq.BioseqDB.BioseqDB( qryFileName )
-    if sbjFileName != qryFileName:
-        string = "nb of input sequences (as query only): %i" % ( qryDB.getSize() ); sys.stdout.flush()
-        logging.info( string )
-        if verbose > 0: print string
-    else:
-        string = "nb of input sequences (as query and subject): %i" % ( qryDB.getSize() ); sys.stdout.flush()
-        logging.info( string )
-        if verbose > 0: print string
-
-    # load the input 'tab' file
-    matchDB = pyRepet.coord.MatchDB.MatchDB()
-    tabFile = open( tabFileName, "r" )
-    matchDB.read( tabFile, thresIdentity, thresLength, verbose )
-    tabFile.close()
-    longString = ""
-    string = "nb of matches (id>=%.2f,qlgth>=%.2f): %i" % ( thresIdentity, thresLength, matchDB.getNbMatchesWithThres( thresIdentity, thresLength ) )
-    longString += "\n%s" % ( string )
-    if verbose > 0: print string
-    string = "nb of distinct queries having matches (id>=%.2f,qlgth>=%.2f): %i" % ( thresIdentity, thresLength, matchDB.getNbDistinctQryWithThres( thresIdentity, thresLength ) )
-    longString += "\n%s" % ( string )
-    if verbose > 0: print string
-    logging.info( longString )
-    sys.stdout.flush()
-
-    lQryToKeep = matchDB.filterDiffQrySbj( qryDB, thresIdentity, thresLength, verbose - 1 )
-
-    # here, possibility to save the information about by which match a specific query has been removed
-
-    string = "%i queries to be kept" % ( len(lQryToKeep) ); sys.stdout.flush()
-    logging.info( string )
-    if verbose > 0: print string
-
-    # write the output fasta file without the included queries
-    writeOutQuery( qryDB, outFileName, lQryToKeep )
-
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main ()

--- a/commons/tools/getCumulLengthFromTEannot.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,201 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# usage: getCumulLengthFromTEannot.py [ options ]
-# options:
-#      -h: this help
-#      -i: table with the annotations (format=path)
-#      -r: name of a TE reference sequence (if empty, all subjects are considered)
-#      -g: length of the genome (in bp)
-#      -C: configuration file
-#      -c: clean
-#      -v: verbosity level (default=0/1)
-
-
-import sys
-import os
-import getopt
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-
-
-class getCumulLengthFromTEannot( object ):
-    """
-    Give the cumulative length of TE annotations (subjects mapped on queries).
-    """
-    
-    def __init__( self ):
-        """
-        Constructor.
-        """
-        self._tableName = ""
-        self._TErefseq = ""
-        self._genomeLength = 0
-        self._configFileName = ""
-        self._clean = False
-        self._verbose = 0
-        self._db = None
-        self._tpA = None
-        
-        
-    def help( self ):
-        """
-        Display the help on stdout.
-        """
-        print
-        print "usage: getCumulLengthFromTEannot.py [ options ]"
-        print "options:"
-        print "     -h: this help"
-        print "     -i: table with the annotations (format=path)"
-        print "     -r: name of a TE reference sequence (if empty, all subjects are considered)"
-        print "     -g: length of the genome (in bp)"
-        print "     -C: configuration file"
-        print "     -c: clean"
-        print "     -v: verbosity level (default=0/1)"
-        print
-        
-        
-    def setAttributesFromCmdLine( self ):
-        """
-        Set the attributes from the command-line.
-        """
-        try:
-            opts, args = getopt.getopt(sys.argv[1:],"hi:r:g:C:cv:")
-        except getopt.GetoptError, err:
-            print str(err); self.help(); sys.exit(1)
-        for o,a in opts:
-            if o == "-h":
-                self.help(); sys.exit(0)
-            elif o == "-i":
-                self.setInputTable( a )
-            elif o == "-r":
-                self.setTErefseq( a )
-            elif o == "-g":
-                self.setGenomeLength( a )
-            elif o == "-C":
-                self.setConfigFileName( a )
-            elif o == "-c":
-                self.setClean()
-            elif o == "-v":
-                self.setVerbosityLevel( a )
-                
-                
-    def setInputTable( self, inTable ):
-        self._tableName = inTable
-        
-    def setTErefseq( self, a ):
-        self._TErefseq = a
-        
-    def setGenomeLength( self, genomeLength ):
-        self._genomeLength = int(genomeLength)
-        
-    def setConfigFileName( self, configFileName ):
-        self._configFileName = configFileName
-        
-    def setClean( self ):
-        self._clean = True
-        
-    def setVerbosityLevel( self, verbose ):
-        self._verbose = int(verbose)
-        
-    def checkAttributes( self ):
-        """
-        Check the attributes are valid before running the algorithm.
-        """
-        if self._tableName == "":
-            print "ERROR: missing input table"; self.help(); sys.exit(1)
-            
-            
-    def setAdaptatorToTable( self ):
-        self._db = DbMySql( cfgFileName=self._configFileName )
-        self._tpA = TablePathAdaptator( self._db, self._tableName )
-        
-        
-    def getAllSubjectsAsMapOfQueries( self ):
-        mapFileName = "%s.map" % self._tableName
-        mapFile = open( mapFileName, "w" )
-        if self._TErefseq != "":
-            lPathnums = self._tpA.getIdListFromSubject( self._TErefseq )
-        else:
-            lPathnums = self._tpA.getIdList()
-        if self._verbose > 0:
-            print "nb of paths: %i" % ( len(lPathnums) )
-        for pathnum in lPathnums:
-            lPaths = self._tpA.getPathListFromId( pathnum )
-            for path in lPaths:
-                map = path.getSubjectAsMapOfQuery()
-                map.write( mapFile )
-        mapFile.close()
-        return mapFileName
-    
-    
-    def mergeRanges( self, mapFileName ):
-        mergeFileName = "%s.merge" % mapFileName
-        prg = os.environ["REPET_PATH"] + "/bin/mapOp"
-        cmd = prg
-        cmd += " -q %s" % ( mapFileName )
-        cmd += " -m"
-        cmd += " 2>&1 > /dev/null"
-        log = os.system( cmd )
-        if log != 0:
-            print "*** Error: %s returned %i" % ( prg, log )
-            sys.exit(1)
-        if self._clean:
-            os.remove( mapFileName )
-        return mergeFileName
-    
-    
-    def getCumulLength( self, mergeFileName ):
-        mergeFile = open( mergeFileName, "r" )
-        total = 0
-        while True:
-            line = mergeFile.readline()
-            if line == "":
-                break
-            tok = line.split("\t")
-            total += abs( int(tok[3]) - int(tok[2]) ) + 1
-        mergeFile.close()
-        if self._clean:
-            os.remove( mergeFileName )
-        return total
-    
-    
-    def start( self ):
-        """
-        Useful commands before running the program.
-        """
-        self.checkAttributes()
-        if self._verbose > 0:
-            print "START %s" % ( type(self).__name__ ); sys.stdout.flush()
-        self.setAdaptatorToTable()
-        
-        
-    def end( self, mapFileName, mergeFileName ):
-        """
-        Useful commands before ending the program.
-        """
-        self._db.close()
-        if self._verbose > 0:
-            print "END %s" % ( type(self).__name__ ); sys.stdout.flush()
-            
-            
-    def run( self ):
-        """
-        Run the program.
-        """
-        self.start()
-        
-        mapFileName = self.getAllSubjectsAsMapOfQueries()
-        mergeFileName = self.mergeRanges( mapFileName )
-        total = self.getCumulLength( mergeFileName )
-        print "cumulative length: %i bp" % total
-        if self._genomeLength > 0:
-            print "TE content: %.2f%%" % ( 100 * total / float(self._genomeLength) )
-            
-        self.end( mapFileName, mergeFileName )
-        
-        
-if __name__ == "__main__":
-    i = getCumulLengthFromTEannot()
-    i.setAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/pathnum2id.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-
-def setup_env():
-    if "REPET_PATH" in os.environ.keys():
-        sys.path.append( os.environ["REPET_PATH"] )
-    else:
-        print "*** Error: no environment variable REPET_PATH ***"
-        sys.exit(1)
-setup_env()
-
-from commons.core.parsing.PathNum2Id import PathNum2Id
-
-#-----------------------------------------------------------------------------
-
-def help():
-
-    print ""
-    print "usage:",sys.argv[0]," [ options ]"
-    print "option:"
-    print "    -h: this help"
-    print "    -i: input file name (path format)"
-    print "    -o: output file name (path format, default=inFileName+'.path')"
-    print ""
-
-#-----------------------------------------------------------------------------
-
-def main():
-
-    inFileName = ""
-    outFileName = ""
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-o":
-            outFileName = a
-
-    if inFileName == "":
-        print "*** Error: missing input file name"
-        help()
-        sys.exit(1)
-
-    if outFileName == "":
-        outFileName = inFileName + ".path"
-        
-    pathNum2Id = PathNum2Id()
-    pathNum2Id.setInFileName( inFileName )
-    pathNum2Id.setOutFileName( outFileName )
-    pathNum2Id.run()
-
-    return 0
-
-#-----------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/tools/refalign2fasta.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,408 +0,0 @@
-#!/usr/bin/env python
-
-##@file
-# Convert the output from Refalign (MSA program) into the 'fasta' format.
-# Usually used before subsequent analysis such as the estimation of deletion rate.
-#
-# usage: refalign2fasta.py [ options ]
-# options:
-#      -h: this help
-#      -i: name of the input file (output from refalign)
-#      -r: name of the reference sequence (discard if not provided)
-#      -g: for the gaps, keep only deletions ('d'), only insertions ('i') or both (default='id')
-#      -o: name of the output file (default=inFileName'.fa_aln',format='fasta')
-
-import os
-import sys
-import getopt
-import exceptions
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "ERROR: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-import pyRepet.seq.Bioseq
-
-
-def help():
-    """
-    Give the list of the command-line options.
-    """
-    print
-    print "usage:",sys.argv[0]," [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the input file (output from refalign)"
-    print "     -r: name of the reference sequence (discard if not provided)"
-    print "     -g: for the gaps, keep only deletions ('d'), only insertions ('i') or both (default='id')"
-    print "     -o: name of the output file (default=inFileName'.fa_aln',format='fasta')"
-    print
-
-
-def getAlignments( inFileName ):
-    """
-    Retrieve the alignments from the input file.
-
-    @param inFileName: name of the input file
-    @type: string
-
-    @return: list of alignments ( refseq, seq, header of seq )
-    @rtype: list of 3d-tuples
-    """
-
-    lAlign = []
-
-    inFile = open( inFileName, "r" )
-    line = inFile.readline()
-    while True:
-        if line == "":
-            break
-        refseq, seq, label = line[:-1].split("\t")[:3]
-        lAlign.append( ( refseq, seq, label ) )
-        line = inFile.readline()
-    inFile.close()
-
-    return lAlign
-
-
-def getGaps( seq ):
-    """
-    Get the gaps on a sequence, start coordinate and length. The start
-    coordinate of a gap is the # of the nucleotide after which it starts.
-
-    @param seq: sequence to analyse
-    @type seq: string
-
-    @return: list of gaps ( start coordinate, length )
-    @rtype: list of 2d-tuples
-    """
-
-    prev = "N"
-    lGapsOnSeq = []
-    i = 0
-    lengthGap = 0
-    for c in seq:
-        if c == "-" and prev != "-":
-            startGap = i
-        if c != "-" and prev == "-":
-            lGapsOnSeq.append( ( startGap, lengthGap ) )
-            lengthGap = 0
-        if c != "-":
-            i += 1
-        else:
-            lengthGap += 1
-        prev = c
-
-     # case with a gap at the end of the sequence
-    if seq[ len(seq) - 1 ] == "-":
-        lGapsOnSeq.append( ( startGap, lengthGap ) )
-
-    return lGapsOnSeq
-
-
-def getGapsOnRefSeq( lAlign ):
-    """
-    Retrieve the gaps on the ref seq in all the alignments.
-
-    @param lAlign: list of alignments ( refseq, seq, header of seq )
-    @type lAlign: list of 3d-tuples
-
-    @return: list of gaps per alignment
-    @rtype: list of lists of 2d-tuples
-    """
-
-    lGapsOnRef = []
-
-    for align in lAlign:
-        refseq = align[0]
-        lGapsOnRef.append( getGaps( refseq ) )
-
-    return lGapsOnRef
-
-
-def insertGap( seq, startGap, lengthGap ):
-    """
-    Get a new seq by inserting a gap in the give seq.
-
-    @param seq: sequence
-    @type seq: string
-
-    @param startGap:
-    @type: startGap: integer
-
-    @param lengthGap: length of the gap
-    @type lengthGap: integer
-
-    @return: new seq made from the give seq by inserting the gap
-    @rtype: string
-    """
-
-    new_seq = seq[:startGap] + (lengthGap*'-') + seq[startGap:] 
-    return new_seq
-
-
-def insertListGaps( inSeq, lGaps ):
-    """
-    Insert all the gaps from the list into the sequence.
-
-    @param inSeq: sequence
-    @type inSeq: string
-
-    @param lGaps: list of gaps ( start coordinate, length )
-    @type: list of 2d-tuples
-
-    @return: sequence with the gaps
-    @rtype: string
-    """
-
-    # insert gaps from the right to the left
-    lGaps.sort()
-    lGaps.reverse()
-
-    prevPos = 0
-    outSeq = inSeq
-
-    for startGap, lengthGap in lGaps:
-        if startGap != prevPos:
-            outSeq = insertGap( outSeq, startGap, lengthGap )
-            prevPos = startGap
-
-    return outSeq
-
-
-def insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName ):
-    """
-    Get the ref seq with all its gaps inserted.
-
-    @param lAlign: list of alignments ( refseq, seq, header of seq )
-    @type lAlign: list of 3d-tuples
-
-    @param lGapsOnRefSeqPerAlign: list of list of gaps on the seq ref per alignment
-    @type lGapsOnRefSeqPerAlign: list of list of 2d-tuples
-
-    @param refseqName: name of the reference sequence
-    @type refseqName: string
-
-    @return: ref seq with all its gaps inserted
-    @rtype: string
-    """
-
-    # retrieve the initial ref seq, ie without any gap
-    initRefSeq = lAlign[0][0].replace("-","")
-
-    # convert the list of lists of gaps into a list of gaps
-    flat_lGaps = []
-    for gaps in lGapsOnRefSeqPerAlign:
-        flat_lGaps.extend( gaps )
-
-    # insert the gaps in the sequence of ref seq
-    finalRefSeq = insertListGaps( initRefSeq, flat_lGaps )
-
-    Align_refseq = ( refseqName, finalRefSeq )
-
-    return Align_refseq
-
-
-def insertgap_seq( lAlign, lGapsOnRefSeqPerAlign ):
-    """
-    Insert in the sequences all the gaps found on the ref seq.
-
-    @param lAlign: list of alignments ( refseq, seq, header of seq )
-    @type lAlign: list of 3d-tuples
-
-    @param lGapsOnRefSeqPerAlign: list of list of gaps on the seq ref per alignment
-    @type lGapsOnRefSeqPerAlign: list of list of 2d-tuples
-
-    @return: list of lists (sequence with gaps, header)
-    @rtype: list of 2d-tuples
-
-    insert dans les seq les gaps donnes par la liste de liste de gap
-    retourne une liste des nouvelles seq apres insertion des gaps
-    """
-
-    # for each gap, add the nb of the alignment in which it has been found
-    newlistgap_seq =[]
-    alignID = 0
-    for lGaps in lGapsOnRefSeqPerAlign:
-        for startGap,lengthGap in lGaps:
-            newlistgap_seq.append( ( startGap, lengthGap, alignID ) )
-        alignID += 1
-    newlistgap_seq.sort()
-
-    Align_seq = []
-
-    # for each alignment
-    for j in xrange(0,len(lAlign)):
-
-        #create a new list = list of gaps to be inserted in a given seq
-        newlist = []
-        offset = 0
-        longmax = 0
-        longself = 0
-        posprec = 0
-        for startGap, lengthGap, alignID in newlistgap_seq:
-            # when 2 gaps have the same start, we keep the longer one
-            if startGap != posprec:
-                if longmax > longself:
-                    newlist.append( (posprec + offset, longmax - longself) )
-                offset += longself
-                longmax=0
-                longself=0
-            #lorsque le numero de la seq du tuple a la meme valeur que j
-            #on stocke la valeur de lengthGap
-            if j == alignID:
-                longself = lengthGap
-            #sinon on prend comme valeur de longmax la valeur maximale de longmax et lengthGap
-            else:
-                longmax = max(longmax, lengthGap)
-            posprec = startGap
-        if longmax > longself:
-            newlist.append((posprec + offset, longmax - longself))
-
-        newSeq = insertListGaps( (lAlign[j][1]), newlist )
-        header = lAlign[j][2]
-        Align_seq.append( ( header, newSeq ) )
-
-    return Align_seq
-
-
-def getSeqWithDeletions( lAlign ):
-    """
-    Get the sequences by putting gaps only when they correspond to a deletion compare to ref seq.
-    Used for instance when we want to estimate the deletion rate.
-
-    @param lAlign: list of alignments ( refseq, seq, header of seq )
-    @type lAlign: list of 3d-tuples
-
-    @return: list of lists ( header, sequence with gaps )
-    @rtype: list of 2d-tuples
-    """
-
-    Align_seq = []
-
-    for align in lAlign:
-        refseq = align[0]
-        seq = align[1]
-        header = align[2]
-        newSeq = ""
-        for i in xrange(0,len(refseq)):
-            if refseq[i] != "-":
-                newSeq += seq[i]
-        Align_seq.append( ( header, newSeq ) )
-
-    return Align_seq
-
-
-def saveMSA( outFileName, Align_seq, Align_seqref=None ):
-    """
-    Save the results as a multiple sequence alignment (MSA) in the 'fasta' format.
-
-    @param outFileName: name of the output file
-    @type outFileName: string
-
-    @param Align_seqref: sequence of ref seq
-    @type Align_seqref: string
-    """
-
-    outFile = open( outFileName, "w" )
-    bs = pyRepet.seq.Bioseq.Bioseq()
-
-    # if provided, save the ref seq
-    if Align_seqref != None:
-        bs.header = Align_seqref[0]
-        bs.sequence = Align_seqref[1]
-        bs.write( outFile )
-
-    # save the other sequences
-    for i in Align_seq:
-        bs.header = i[0]
-        bs.sequence = i[1]
-        bs.write( outFile )
-
-    outFile.close()
-    
-    
-def saveOnlyWithDeletions( lAlign, refseqName, outFileName ):
-    Align_seq = getSeqWithDeletions( lAlign )
-    if refseqName != "":
-        Align_seqref = ( refseqName, lAlign[0][0].replace("-","") )
-        saveMSA( outFileName, Align_seq, Align_seqref )
-    else:
-        saveMSA( outFileName, Align_seq )
-        
-        
-def main():
-    
-    inFileName = ""
-    refseqName = ""
-    keepGap = "id"
-    outFileName = ""
-    global verbose
-    verbose = 0
-    
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:r:g:o:v:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inFileName = a
-        elif o == "-r":
-            refseqName = a
-        elif o == "-g":
-            keepGap = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if inFileName == "":
-        print "ERROR: missing input file name"
-        help()
-        sys.exit(1)
-        
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    lAlign = getAlignments( inFileName )
-    if verbose > 0:
-        print "nb of alignments: %i" % ( len(lAlign) )
-        sys.stdout.flush()
-        
-    if outFileName == "":
-        outFileName = "%s.fa_aln" % ( inFileName )
-    if verbose > 0:
-        print "output file: '%s'" % ( outFileName )
-        
-    if keepGap == "id":
-        lGapsOnRefSeqPerAlign = getGapsOnRefSeq( lAlign )
-        Align_seq = insertgap_seq( lAlign, lGapsOnRefSeqPerAlign )
-        if refseqName != "":
-            Align_seqref = insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName )
-            saveMSA( outFileName, Align_seq, Align_seqref )
-        else:
-            saveMSA( outFileName, Align_seq )
-            
-    elif keepGap == "d":
-        saveOnlyWithDeletions( lAlign, refseqName, outFileName )
-        
-    elif keepGap == "i":
-        print "ERROR: '-g i' not yet available"
-        sys.exit(1)
-        
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    return 0
-
-
-if __name__ == "__main__" :
-    main ()

--- a/commons/tools/removeDescriptionInFastaHeaderProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#!/usr/bin/env python
-
-import re
-from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
-
-class removeDescriptionInFastaHeaderProgramLauncher(AbstractProgramLauncher):
-
-    def __init__( self ):
-        AbstractProgramLauncher.__init__( self )
-        self._formatInFile = "fasta"
-                
-    def run( self ):
-        self.checkInput()
-        fastaHandler = open(self.getInputFile(), "r")
-        lines = fastaHandler.readlines()
-        fastaHandler.close()
-        newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"])
-        
-        self._writePreprocessedFastaFile(lines, newFastaName)
-        
-    def _writePreprocessedFastaFile(self, lines, newFastaName):
-        newFastaHandler = open(newFastaName, "w")
-        for line in lines:
-            if re.match(">", line):
-                newLine = line.split(" ",1)[0] + "\n"
-                newFastaHandler.write(newLine)
-            else:
-                newFastaHandler.write(line)
-        newFastaHandler.close()
-
-        
-        
-        
-if __name__ == "__main__":
-    i = removeDescriptionInFastaHeaderProgramLauncher()
-    i.checkAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#!/usr/bin/env python
-
-import re
-from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
-
-class replaceGreaterThanSymbolInFastaHeaderProgramLauncher(AbstractProgramLauncher):
-
-    def __init__( self ):
-        AbstractProgramLauncher.__init__( self )
-        self._formatInFile = "fasta"
-                
-    def run( self ):
-        self.checkInput()
-        fastaHandler = open(self.getInputFile(), "r")
-        lines = fastaHandler.readlines()
-        fastaHandler.close()
-        newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"])
-        
-        self._writePreprocessedFastaFile(lines, newFastaName)
-        
-    def _writePreprocessedFastaFile(self, lines, newFastaName):
-        newFastaHandler = open(newFastaName, "w")
-        for line in lines:
-            if re.match(">", line):
-                newLine = re.sub("-->|->", " to ", line)
-                newFastaHandler.write(newLine)
-            else:
-                newFastaHandler.write(line)
-        newFastaHandler.close()
-
-        
-        
-        
-if __name__ == "__main__":
-    i = replaceGreaterThanSymbolInFastaHeaderProgramLauncher()
-    i.checkAttributesFromCmdLine()
-    i.run()

--- a/commons/tools/setnum2id.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import exceptions
-
-#-----------------------------------------------------------------------------
-
-def help():
-
-        print "\nusage:",sys.argv[0]," [ options ]"
-        print "option:"
-        print "    -h: this help"
-        print "    -i: input set file"
-        print "output on stdout\n"
-
-#-----------------------------------------------------------------------------
-
-def main():
-
-    inFileName = ""
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:")
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        if o == "-i":
-            inFileName = a
-
-    if inFileName == "":
-        print "*** Error: missing input file name"
-        help()
-        sys.exit(1)
-
-    inFile = open( inFileName, "r" )
-    line = inFile.readline()
-
-    dID2count = {}
-    count = 1
-
-    while 1:
-
-        if line == "":
-            break
-
-        line = line.split()
-
-        path = line[0]
-        sbjName = line[1]
-        qryName = line[2]
-        qryStart = line[3]
-        qryEnd = line[4]
-
-        key_id = path + "-" + qryName + "-" + sbjName
-        if key_id not in dID2count.keys():
-	    newPath = count
-	    count += 1
-	    dID2count[ key_id ] = newPath
-	else:
-	    newPath = dID2count[ key_id ]
-
-        data = str(newPath) + "\t" + sbjName + "\t" + qryName + "\t"
-        data += qryStart + "\t" + qryEnd
-
-        print data
-        sys.stdout.flush()
-
-        line = inFile.readline()
-
-    inFile.close()
-
-    return 0
-
-#-----------------------------------------------------------------------------
-
-if __name__ == '__main__':
-	main()

--- a/commons/tools/srptBlasterMatcher.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,448 +0,0 @@
-#!/usr/bin/env python
-
-"""
-This program takes a query directory as input,
-then launches Blaster and/or Matcher on each file in it,
-finally results are optionally gathered in a single file.
-"""
-
-import os
-import sys
-import getopt
-import logging
-import glob
-import ConfigParser
-
-from pyRepet.launcher.programLauncher import programLauncher
-from pyRepet.launcher import Launcher
-from pyRepet.sql.RepetJobMySQL import RepetJob
-from commons.core.coord.Align import Align
-
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     -g: name of the group identifier (same for all the jobs)"
-    print "     -q: name of the query directory"
-    print "     -S: suffix in the query directory (default='*.fa' for Blaster, '*.align' for Matcher)"
-    print "     -s: absolute path to the subject databank"
-    print "     -Q: resources needed on the cluster)"
-    print "     -d: absolute path to the temporary directory"
-    print "     -m: mix of Blaster and/or Matcher"
-    print "         1: launch Blaster only"
-    print "         2: launch Matcher only (on '*.align' query files)"
-    print "         3: launch Blaster+Matcher in the same job"
-    print "     -B: parameters for Blaster (e.g. \"-a -n tblastx\")"
-    print "     -M: parameters for Matcher (e.g. \"-j\")"
-    print "     -Z: collect all the results into a single file"
-    print "         align (after Blaster)"
-    print "         path/tab (after Matcher)"
-    print "     -C: configuration file from TEdenovo or TEannot pipeline"
-    print "     -t: name of the table recording the jobs (default=jobs)"
-    print "     -p: absolute path to project directory (if jobs management via files)"
-    print "     -c: clean (remove job launch files and job stdout)"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-
-def filterRedundantMatches( inFile, outFile ):
-    """
-    When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks),
-    one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...'
-    and we discards 'chunk7-11-110-chunk3-1-100-...'.
-    Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards
-    'chunk5-11-110-chunk5-1-100-...'.
-    For this of course the results need to be sorted by query, on plus strand,
-    and in ascending coordinates (always the case with Blaster).
-    """
-    inFileHandler = open( inFile, "r" )
-    outFileHandler = open( outFile, "w" )
-    iAlign = Align()
-    countMatches = 0
-    tick = 100000
-    while True:
-        line = inFileHandler.readline()
-        if line == "":
-            break
-        countMatches += 1
-        iAlign.setFromString( line )
-        if "chunk" not in iAlign.range_query.seqname \
-               or "chunk" not in iAlign.range_subject.seqname:
-            print "ERROR: 'chunk' not in seqname"
-            sys.exit(1)
-        if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]):
-            iAlign.write( outFileHandler )
-        elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]):
-            if iAlign.range_query.getMin() < iAlign.range_subject.getMin():
-                iAlign.write( outFileHandler )
-        if countMatches % tick == 0:   # need to free buffer frequently as file can be big
-            outFileHandler.flush()
-            os.fsync( outFileHandler.fileno() )
-    inFileHandler.close()
-    outFileHandler.close()
-
-
-def runCollect( groupid, collect, allByAll ):
-    """
-    Gather the results of each job in a single job and adapt path ID if necessary.
-    """
-    if verbose > 0:
-        print "concatenate the results of each job"; sys.stdout.flush()
-
-    # retrieve the list of the files
-    lFiles = glob.glob( "*.%s" % ( collect ) )
-    lFiles.sort()
-
-    # concatenate all the individual files
-    if os.path.exists( "%s.%s_tmp" % ( groupid, collect ) ):
-        os.remove( "%s.%s_tmp" % ( groupid, collect ) )
-    for resFile in lFiles:
-        prg = "cat"
-        cmd = prg
-        cmd += " %s >> %s.%s_tmp" % ( resFile, groupid, collect )
-        pL.launch( prg, cmd )
-        if clean == True:
-            prg = "rm"
-            cmd = prg
-            cmd += " -f %s" % ( resFile )
-            pL.launch( prg, cmd )
-
-    if os.path.exists( "%s.%s" % ( groupid, collect ) ):
-        os.remove( "%s.%s" % ( groupid, collect ) )
-
-    if collect == "align":
-        if not allByAll:
-            os.system( "mv %s.%s_tmp %s.%s" % ( groupid, collect, groupid, collect ) )
-        else:
-            filterRedundantMatches( "%s.%s_tmp" % ( groupid, collect ),
-                                    "%s.%s" % ( groupid, collect ) )
-
-    # adapt the path IDs if necessary
-    elif collect == "path":
-        prg = os.environ["REPET_PATH"] + "/bin/"
-        if os.path.exists( prg + "pathnum2id" ):
-            prg += "pathnum2id"
-            cmd = prg
-            cmd += " -i %s.path_tmp" % ( groupid )
-            cmd += " -o %s.path" % ( groupid )
-            cmd += " -v %i" % ( verbose - 1 )
-            pL.launch( prg, cmd )
-        else:
-            prg += "pathnum2id.py"
-            cmd = prg
-            cmd += " -i %s.path_tmp" % ( groupid )
-            cmd += " -o %s.path" % ( groupid )
-            pL.launch( prg, cmd )
-
-    elif collect == "tab":
-        prg = os.environ["REPET_PATH"] + "/bin/"
-        if os.path.exists( prg + "tabnum2id" ):
-            prg += "tabnum2id"
-            cmd = prg
-            cmd += " -i %s.tab_tmp" % ( groupid )
-            cmd += " -o %s.tab" % ( groupid )
-            cmd += " -v %i" % ( verbose - 1 )
-            pL.launch( prg, cmd )
-        else:
-            prg += "tabnum2id.py"
-            cmd = prg
-            cmd += " -i %s.tab_tmp" % ( groupid )
-            cmd += " -o %s.tab" % ( groupid )
-            pL.launch( prg, cmd )
-
-    if clean == True:
-        os.remove( "%s.%s_tmp" % ( groupid, collect ) )
-
-
-def main():
-    """
-    This program takes a query directory as input,
-    then launches Blaster and/or Matcher on each file in it,
-    finally results are optionally gathered in a single file.
-    """
-
-    groupid = ""
-    queryDir = ""
-    patternSuffix = ""
-    subjectBank = ""
-    queue = ""
-    tmpDir = ""
-    mix = ""
-    paramBlaster = ""
-    paramMatcher = ""
-    collect = ""
-    configFileName = ""
-    jobTable = "jobs"
-    projectDir = ""
-    global clean
-    clean = False
-    global verbose
-    verbose = 0
-    allByAll = False
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:s:Q:d:m:B:M:Z:C:t:p:cv:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-g":
-            groupid = a
-        elif o == "-q":
-            queryDir = a
-            if queryDir[-1] == "/":
-                queryDir = queryDir[:-1]
-        elif o == "-S":
-            patternSuffix = a
-        elif o == "-s":
-            subjectBank = a
-        elif o == "-Q":
-            queue = a
-        elif o == "-d":
-            tmpDir = a
-            if tmpDir[-1] == "/":
-                tmpDir = tmpDir[:-1]
-        elif o == "-m":
-            mix = a
-        elif o == "-B":
-            paramBlaster = a
-        elif o == "-M":
-            paramMatcher = a
-        elif o == "-C":
-            configFileName = a
-        elif o == "-Z":
-            collect = a
-        elif o == "-t":
-            jobTable = a
-        elif o == "-p":
-            projectDir = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if groupid == "":
-        print "ERROR: missing group identifier (-g)"
-        help()
-        sys.exit(1)
-
-    if queryDir == "":
-        print "ERROR: missing query directory (-q)"
-        help()
-        sys.exit(1)
-
-    if mix in [ "1", "3" ] and subjectBank == "":
-        print "ERROR: missing subject bank for Blaster"
-        sys.exit(1)
-
-    if os.environ["REPET_JOBS"] == "files" and projectDir == "":
-        print "ERROR: missing compulsory options for jobs management via files"
-        help()
-        sys.exit(1)
-
-    if not os.path.exists( queryDir ):
-        print "ERROR: can't find query directory '%s'" % ( queryDir )
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-
-    logFileName = "%s_pid%s.log" % ( groupid, os.getpid() )
-    handler = logging.FileHandler( logFileName )
-    formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )
-    handler.setFormatter( formatter )
-    logging.getLogger('').addHandler( handler )
-    logging.getLogger('').setLevel( logging.DEBUG )
-    logging.info( "started" )
-
-
-    if configFileName != "":
-        if not os.path.exists( configFileName ):
-            print "ERROR: configuration file '%s' doesn't exist" % ( configFileName )
-            sys.exit(1)
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-    else:
-        host = os.environ["REPET_HOST"]
-        user = os.environ["REPET_USER"]
-        passwd = os.environ["REPET_PW"]
-        dbname = os.environ["REPET_DB"]
-
-    if os.environ["REPET_JOBS"] == "files":
-        jobdb = RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] )
-    elif os.environ["REPET_JOBS"] == "MySQL":
-        jobdb = RepetJob( user, host, passwd, dbname )
-    else:
-        print "ERROR: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] )
-        sys.exit(1)
-
-
-    currentDir = os.getcwd()
-    if tmpDir == "":
-        tmpDir = currentDir
-
-    global pL
-    pL = programLauncher()
-
-    if "-a" in paramBlaster:
-        allByAll = True
-
-
-    # if Blaster will be launched, prepare the subject data if necessary
-    if mix != "2" and not os.path.exists( "%s_cut" % ( subjectBank ) ):
-        if verbose > 0:
-            print "prepare subject bank '%s'..." % ( subjectBank.split("/")[-1] )
-            sys.stdout.flush()
-        prg = "blaster"
-        cmd = prg
-        cmd += " -q %s" % ( subjectBank )
-        cmd += " %s" % ( paramBlaster )
-        cmd += " -P"
-        pL.launch( prg, cmd )
-
-
-    # launch Blaster only (on '*.fa' in queryDir)
-    if mix == "1":
-        launcher = Launcher.BlasterLauncher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "Blaster" )
-        if patternSuffix == "":
-            patternSuffix = "*.fa"
-        launcher.run( patternSuffix, verbose )
-        if clean == True:
-            launcher.clean()
-
-    # launch Matcher only (on '*.align' in queryDir; don't use '-q' or '-s', only '-m')
-    elif mix == "2":
-        launcher = Launcher.MatcherLauncher( jobdb, queryDir, subjectBank, paramMatcher, currentDir, tmpDir, jobTable, queue, groupid, "Matcher" )
-        if patternSuffix == "":
-            patternSuffix = "*.align"
-        launcher.run( patternSuffix, verbose  )
-        if clean == True:
-            launcher.clean()
-
-    # launch Blaster+Matcher (on '*.fa' in queryDir)
-    elif mix == "3":
-        launcher = Launcher.Launcher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "BlasterMatcher" )
-        launcher.beginRun()
-        if patternSuffix == "":
-            patternSuffix = "*.fa"
-        lFaFiles = glob.glob( queryDir + "/" + patternSuffix )
-        if len(lFaFiles) == 0:
-            print "ERROR: query directory '%s' is empty of suffix '%s'" % ( queryDir, patternSuffix )
-            sys.exit(1)
-        count = 0
-        for inFaName in lFaFiles:
-            count += 1
-            launcher.acronyme = "BlasterMatcher_%i" % ( count )
-            launcher.job.jobname = launcher.acronyme
-            prefix = os.path.basename( inFaName )
-            cmd_start = ""
-            cmd_start += "if not os.path.exists( \"" + prefix + "\" ):\n"
-            cmd_start += "\tos.system( \"cp " + inFaName + " .\" )\n"
-            launchB = ""
-            launchB += "blaster"
-            launchB += " -q %s" % ( prefix )
-            launchB += " -s %s" % ( subjectBank )
-            launchB += " -B %s" % ( prefix )
-            if paramBlaster != "":
-                launchB += " %s" % ( paramBlaster )
-            cleanB = ""
-            cleanB += "if not os.path.exists( \"%s/%s.param\" ):\n" % ( currentDir, prefix )
-            cleanB += "\tos.system( \"mv %s.param %s\" )\n" % ( prefix, currentDir )
-            cleanB += "if os.path.exists( \"" + prefix + ".Nstretch.map\" ):\n"
-            cleanB += "\tos.remove( \"" + prefix + ".Nstretch.map\" )\n"
-            cleanB += "if os.path.exists( \"" + prefix + "_cut\" ):\n"
-            cleanB += "\tos.system( \"rm -f " + prefix + "_cut*\" )\n"
-            cleanB += "if os.path.exists( \"" + prefix + ".raw\" ):\n"
-            cleanB += "\tos.remove( \"" + prefix + ".raw\" )\n"
-            cleanB += "if os.path.exists( \"" + prefix + ".seq_treated\" ):\n"
-            cleanB += "\tos.remove( \"" + prefix + ".seq_treated\" )\n"
-            launchM = ""
-            launchM += os.environ["REPET_PATH"] + "/bin/matcher"
-            launchM += " -m %s.align" % ( prefix )
-            launchM += " -q %s" % ( prefix )
-            launchM += " -s %s" % ( subjectBank )
-            if paramMatcher != "":
-                launchM += " %s" % ( paramMatcher )
-            cleanM = ""
-            s = ""
-            if "-a" in paramMatcher:
-                s = "match"
-            else:
-                s = "clean_match"
-            if collect == "path":
-                cleanM += "if not os.path.exists( \"%s/%s.align.%s.path\" ):\n" % ( currentDir, prefix, s )
-                cleanM += "\tos.system( \"mv %s.align.%s.path %s\" )\n" % ( prefix, s, currentDir )
-                cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".tab\" ):\n"
-                cleanM += "\tos.remove( \"" + prefix + ".align."+s+".tab\" )\n"
-            elif collect == "tab":
-                cleanM += "if not os.path.exists( \"%s/%s.align.%s.tab\" ):\n" % ( currentDir, prefix, s )
-                cleanM += "\tos.system( \"mv %s.align.%s.tab %s\" )\n" % ( prefix, s, currentDir )
-                cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".path\" ):\n"
-                cleanM += "\tos.remove( \"" + prefix + ".align."+s+".path\" )\n"
-            cleanM += "if not os.path.exists( \"%s/%s.align.%s.param\" ):\n" % ( currentDir, prefix, s )
-            cleanM += "\tos.system( \"mv %s.align.%s.param %s\" )\n" % ( prefix, s, currentDir )
-            if tmpDir != currentDir:
-                cleanM += "if os.path.exists( \"%s\" ):\n" % ( prefix )
-                cleanM += "\tos.remove( \"%s\" )\n" % ( prefix )
-            if clean == True:
-                cleanM += "if os.path.exists( \"" + prefix + ".align\" ):\n"
-                cleanM += "\tos.remove( \"" + prefix + ".align\" )\n"
-            else:
-                cleanM += "if not os.path.exists( \"%s/%s.align\" ):\n" % ( currentDir, prefix )
-                cleanM += "\tos.system( \"mv %s.align %s\" )\n" % ( prefix, currentDir )
-            cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".fa\" ):\n"
-            cleanM += "\tos.remove( \"" + prefix + ".align."+s+".fa\" )\n"
-            cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".map\" ):\n"
-            cleanM += "\tos.remove( \"" + prefix + ".align."+s+".map\" )\n"
-            cmd_start += "print \"" + launchB + "\"; sys.stdout.flush()\n"
-            cmd_start += "log = os.system( \"" + launchB + "\" )\n"
-            cmd_start += "if log != 0:\n"
-            cmd_start += launcher.cmd_test( launcher.job, "error", loop=1 )
-            cmd_start += "\tsys.exit(1)\n"
-            cmd_start += cleanB
-            cmd_start += "print \"" + launchM + "\"; sys.stdout.flush()\n"
-            cmd_start += "log = os.system( \"" + launchM + "\" )\n"
-            cmd_start += cleanM
-            launcher.runSingleJob( cmd_start )
-        launcher.acronyme = "BlasterMatcher"
-        launcher._nbJobs = count
-        launcher.endRun()
-        if clean == True:
-            launcher.clean( "BlasterMatcher_*" )
-
-    else:
-        print "ERROR: option '-m %s' not recognized" % ( mix )
-        sys.exit(1)
-
-
-    if collect != "":
-        if collect in [ "align", "path", "tab" ]:
-            runCollect( groupid, collect, allByAll )
-        else:
-            print "ERROR: collect '%s' not implemented" % ( collect )
-            sys.exit(1)
-
-
-    logging.info( "finished" )
-
-    if verbose > 0:
-        print "END %s" % ( sys.argv[0].split("/")[-1] )
-        sys.stdout.flush()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/srptCreateTable.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import ConfigParser
-
-from commons.core.sql.DbMySql import DbMySql
-
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     -f: name of the input file"
-    print "     -n: name of the MySQL table"
-    print "     -t: table type (fasta|align|path|set|match|map|TEclassif|cluster)"
-    print "     -o: overwrite (default=False)"
-    print "     -c: configuration file from TEdenovo or TEannot pipeline"
-    print "     -H: MySQL host (if no configuration file)"
-    print "     -U: MySQL user (if no configuration file)"
-    print "     -P: MySQL password (if no configuration file)"
-    print "     -D: MySQL database (if no configuration file)"
-    print "     -T: MySQL port (if no configuration file, default=3306)"
-    print "     -v: verbose (default=0/1)"
-    print
-
-
-def main():
-    """
-    This program loads data from a file into a MySQL table.
-    """
-    filename = ""
-    tablename = ""
-    filetype = ""
-    overwrite = False
-    configFileName = ""
-    host = ""
-    user = ""
-    passwd = ""
-    dbname = ""
-    port = 0
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hf:t:n:oc:H:U:P:D:T:v:" )
-    except getopt.GetoptError, err:
-        sys.stderr.write( "%s\n" % str(err) )
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-f":
-            filename = a
-        elif o == "-n":
-            tablename = a
-        elif o == "-t":
-            filetype = a
-        elif o == "-o":
-            overwrite = True
-        elif o == "-c":
-            configFileName = a
-        elif o == "-H":
-            host = a
-        elif o == "-U":
-            user = a 
-        elif o == "-P":
-            passwd = a
-        elif o == "-D":
-            dbname = a
-        elif o == "-T":
-            port = int(a)
-        elif o == "-v":
-            verbose = int(a)
-
-    if  filename == "" or tablename == "" or filetype == "":
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if configFileName != "":
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-        port = config.get("repet_env","repet_port")
-
-    if host == "" and os.environ.get( "REPET_HOST" ) != "":
-        host = os.environ.get( "REPET_HOST" )
-    if user == "" and os.environ.get( "REPET_USER" ) != "":
-        user = os.environ.get( "REPET_USER" )
-    if passwd == "" and os.environ.get( "REPET_PW" ) != "":
-        passwd = os.environ.get( "REPET_PW" )
-    if dbname == "" and os.environ.get( "REPET_DB" ) != "":
-        dbname = os.environ.get( "REPET_DB" )
-    if port == 0 and os.environ.get( "REPET_PORT" ) != "":
-        port = int( os.environ.get( "REPET_PORT" ) )
-        
-    if host == "":
-        print "ERROR: missing host"
-        sys.exit(1)
-    if user == "":
-        print "ERROR: missing user"
-        sys.exit(1)
-    if passwd == "":
-        print "ERROR: missing password"
-        sys.exit(1)
-    if dbname == "":
-        print "ERROR: missing db name"
-        sys.exit(1)
-    if port == 0:
-        print "ERROR: missing port"
-        sys.exit(1)
-
-    db = DbMySql(user, host, passwd, dbname, port )
-
-    if not os.path.exists( filename ):
-        print "ERROR: input file '%s' doesn't exist" % ( filename )
-        sys.exit(1)
-
-    db.createTable( tablename, filetype, filename, overwrite)
-
-    db.close()
-
-    return 0
-
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/srptExportTable.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-#!/usr/bin/env python
-
-import user, os, sys, getopt, exceptions, ConfigParser
-
-#-----------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the list of the command-line options.
-    """
-
-    print
-    print "usage:",sys.argv[0]," [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -i: name of the table to export"
-    print "     -o: name of the output file (default=inTable)"
-    print "     -p: extra parameters to add to the SQL query (e.g. 'ORDER BY path')"
-    print "     -k: keep the first line"
-    print "     -C: configuration file from TEdenovo or TEannot pipeline"
-    print "     -H: MySQL host (if no configuration file)"
-    print "     -U: MySQL user (if no configuration file)"
-    print "     -P: MySQL password (if no configuration file)"
-    print "     -D: MySQL database (if no configuration file)"
-    print "     -v: verbose (default=0/1)"
-    print
-
-#-----------------------------------------------------------------------------
-
-def main():
-
-    """
-    This program exports all the data contained in a MySQL table into a flat file in the current directory.
-    """
-
-    inTable = ""
-    outFileName = ""
-    param = ""
-    keepFirstLine = False
-    configFileName = ""
-    host = ""
-    user = ""
-    passwd = ""
-    dbname = ""
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hi:o:p:kC:H:U:P:D:v:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-i":
-            inTable = a
-        elif o == "-o":
-            outFileName = a
-        elif o == "-p":
-            param = a
-        elif o == "-k":
-            keepFirstLine = True
-        elif o == "-C":
-            configFileName = a
-        elif o == "-H":
-            host = a
-        elif o == "-U":
-            user = a 
-        elif o == "-P":
-            passwd = a
-        elif o == "-D":
-            dbname = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if inTable == "":
-        print "*** Error: missing input table name"
-        help()
-        sys.exit(1)
-
-    if configFileName != "":
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-    if host == "" or user == "" or passwd == "" or dbname == "":
-        if os.environ.get( "REPET_HOST" ) not in [ "", None ]:
-            host = os.environ.get( "REPET_HOST" )
-        if os.environ.get( "REPET_USER" ) not in [ "", None ]:
-            user = os.environ.get( "REPET_USER" )
-        if os.environ.get( "REPET_PW" ) not in [ "", None ]:
-            passwd = os.environ.get( "REPET_PW" )
-        if os.environ.get( "REPET_DB" ) not in [ "", None ]:
-            dbname = os.environ.get( "REPET_DB" )
-    if host == "" or user == "" or passwd == "" or dbname == "":
-        print "*** Error: missing information about MySQL connection"
-        sys.exit(1)
-
-    if outFileName == "":
-        outFileName = inTable
-
-    prg = "mysql"
-    cmd = prg
-    cmd += " -h %s" % ( host )
-    cmd += " -u %s" % ( user )
-    cmd += " -p\"%s\"" % ( passwd )
-    cmd += " --database=%s" % ( dbname )
-    cmd += " -e\"SELECT * FROM %s" % ( inTable )
-    if param != "":
-        cmd += " %s" % ( param )
-    cmd += ";\""
-    cmd += " > "
-    if keepFirstLine == False:
-        cmd += "%s.tmp" % ( outFileName )
-    else:
-        cmd += "%s" % ( outFileName )
-    if verbose > 0: print cmd; sys.stdout.flush()
-    log = os.system( cmd )
-    if log != 0:
-        print "*** Error: %s returned %i" % ( prg, log )
-        sys.exit(1)
-
-    if keepFirstLine == False:
-        tmpFileName = "%s.tmp" % ( outFileName )
-        tmpFile = open( tmpFileName, "r" )
-        outFile = open( outFileName, "w" )
-        i = 0
-        for line in tmpFile:
-            if i > 0:
-                outFile.write( line )
-            i += 1
-        tmpFile.close()
-        outFile.close()
-        os.remove( tmpFileName )
-
-    return 0
-
-#----------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/tools/srptGameXmlMaker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,283 +0,0 @@
-#!/usr/bin/env python
-
-import user, os, sys, getopt, ConfigParser
-from os import listdir
-
-def setup_env():
-    if "REPET_PATH" in os.environ.keys():
-        sys.path.append( os.environ["REPET_PATH"] )
-    else:
-        print "*** Error: no environment variable REPET_PATH ***"
-        sys.exit(1)
-setup_env()
-
-from pyRepet.sql.RepetDBMySQL import *
-from pyRepet.gamexml.Xml_writer import *
-from pyRepet.gamexml.computational import *
-
-#------------------------------------------------------------------------------
-
-def help():
-
-    print ""
-    print "usage:",sys.argv[0],"[options]"
-    print "options:"
-    print "     -h: this help"
-    print "     -f: fasta file (required to generate new '.gamexml' files)"
-    print "     -n: annotation tier_name"
-    print "     -g: gamexml file (for Apollo). If it's not mentionned, all '.gamexml' files will be updated with the result file"
-    print "     -l: light gameXML file (without sequence)"
-    print "     -r: result files (require -n)"
-    print "     -R: reverse the query and subject of Blaster results"
-    print "     -s: tier_name of an annotation to remove from a gameXML file"
-    print "     -t: file of table name to use to create the gamexml files (tier name 'tab' format 'tab' table name)"
-    print "     -c: configuration file from TEdenovo or TEannot pipeline"
-    print "     -H: MySQL host (if no configuration file)"
-    print "     -U: MySQL user (if no configuration file)"
-    print "     -P: MySQL password (if no configuration file)"
-    print "     -D: MySQL database (if no configuration file)"
-    print "     -v: verbose (default=0/1/2)"
-    print ""
-
-#------------------------------------------------------------------------------
-
-def automatisation( result_file, tier_name, reverse, comput ):
-
-    if verbose > 1:
-        print "Auto update"; sys.stdout.flush()
-    writer = Xml_writer()
-    file_liste = []
-    liste_comp = []
-    liste_comp = listdir('./')
-
-    if result_file != "":
-        for j in liste_comp:
-            if writer.file_in_keys( j, comput ):
-                file_liste = file_liste + [j]
-
-        for i in file_liste:
-            writer.update_gamexml( i, result_file, tier_name, comput )
-
-    else:
-        for j in liste_comp:
-            if j.find( "gamexml" ) != -1:
-                writer.parse_gamexml( j )
-                writer.verif_name_prog( tier_name )
-                writer.write( j )
-                if verbose > 1:
-                    print tier_name + " program from " +j +" removed"
-
-#------------------------------------------------------------------------------
-
-def main():
-
-    f_result = ""
-    f_gamexml = ""
-    f_fasta = ""
-    f_table = ""
-    tier_name = ""
-    substract_name = ""
-    no_seq = 0
-    configFileName = ""
-    host = ""
-    user = ""
-    passwd = ""
-    dbname = ""
-    verbose = 0
-
-    try:
-        options,arguments=getopt.getopt(sys.argv[1:],"hn:f:g:r:s:lRt:c:H:U:P:D:v:",["help","tier_name=","fasta","gamexml","result","substract_program","light","reverse_result","table"])
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    if options == []:
-        help()
-        sys.exit(1)
-    for o,a in options:
-        if o == "-h" or o == "--help":
-            help()
-            sys.exit(0)
-        elif o == "-f" or o == "--fasta":
-            f_fasta = a
-        elif o == "-g" or o == "--gamexml":
-            f_gamexml = a 
-        elif o == "-n" or o == "--tier_name":
-            tier_name = a
-        elif o == "-r" or o == "--result":
-            f_result = a
-        elif o == "-s" or o == "--subtract_program":
-            substract_name = a
-        elif o == "-l" or o == "--light":
-            no_seq = 1
-        elif o == "-R" or o == "--reverse_result":
-            writer.set_reverse()
-        elif o == "-t" or o == "--table":
-            f_table = a
-        elif o == "-c":
-            configFileName = a
-        elif o == "-H":
-            host = a
-        elif o == "-U":
-            user = a 
-        elif o == "-P":
-            passwd = a
-        elif o == "-D":
-            dbname = a
-        elif o == "-v":
-            verbose = int(a)
-
-    if tier_name == "" and substract_name == "" and f_result != "":
-        print "*** Error: option -n required"
-        help()
-        sys.exit(1)
-
-    if f_fasta == "" and f_gamexml == "":
-        print "*** Error: options -g or -f required"
-        help()
-        sys.exit(1)
-    
-    if substract_name!="" and f_result!="" :
-        print "Error: option -s and -r together"
-        help()
-        sys.exit(1)
-
-
-    if verbose > 0:
-        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    if configFileName != "":
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-
-    if host == "" and os.environ.get( "REPET_HOST" ) != None:
-        host = os.environ.get( "REPET_HOST" )
-    if user == "" and os.environ.get( "REPET_USER" ) != None:
-        user = os.environ.get( "REPET_USER" )
-    if passwd == "" and os.environ.get( "REPET_PW" ) != None:
-        passwd = os.environ.get( "REPET_PW" )
-    if dbname == "" and os.environ.get( "REPET_DB" ) != None:
-        dbname = os.environ.get( "REPET_DB" )
-
-    writer = Xml_writer()
-
-    # create the dico
-    comput = computational()
-
-    # create all the ".gamexml" files (option '-f')
-    if f_fasta != "":
-        writer.create_gamexml( f_fasta, f_result, tier_name, comput, no_seq )
-
-    # 
-    if f_result != "":
-       if f_gamexml != "":
-           key = ".".join( f_gamexml.split(".")[:-1] )
-       else:
-           key = ""
-       format = writer.find_type_file( f_result )
-       resFile = open( f_result )
-       if format == "path":
-	       comput.load_dico_path_from_file( key, f_result )
-
-    if f_table != "":
-            if verbose > 1:
-                print "parsing file %s... " % ( f_gamexml ); sys.stdout.flush()
-	    writer.parse_gamexml( f_gamexml )
-
-	    if f_gamexml != "":
-##                key=".".join(f_gamexml.split(".")[:-1])
-                key = f_gamexml.split(".")[0]
-	    else:
-                key = ""
-
-	    tfile = open( f_table )
-	    lines = tfile.readlines()
-	    for l in lines:
-                if l[0] == "#":
-                    continue
-                tok = l.split()
-                #print tok
-                if len(tok) == 0:
-                    break
-                tier_name = tok[0]
-                format = tok[1]
-                table = tok[2]
-                alias = ""
-                if verbose > 1:
-                    print "table: " + table + " (format=" + format + ")"
-                if len(tok) > 3:
-                    alias = tok[3]
-                    if verbose > 1:
-                        print " alias=" + alias
-
-                if host == "" or user == "" or passwd == "" or dbname == "":
-                    print "*** Error: missing information about MySQL connection"
-                    sys.exit(1)
-                db = RepetDB( user, host, passwd, dbname )
-
-                if format == "path":
-                    comput.load_dico_path_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "rpath":
-                    comput.load_dico_rpath_from_table( db, key, table, alias )
-                elif format == "ipath":
-                    comput.load_dico_ipath_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "align":
-                    comput.load_dico_align_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "map":
-                    comput.load_dico_map_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "rmap":
-                    comput.load_dico_rmap_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "set":
-                    comput.load_dico_set_from_table( db, key, table, alias )
-                    writer.update_gamexml_comput( tier_name, comput )
-                elif format == "annot":
-                    comput.load_dico_annot_from_table( db, key, table, alias )
-                    writer.update_gamexml_annot( table, comput )
-                elif format == "annot_set":
-                    comput.load_dico_annotset_from_table( db, key, table, alias )
-                    writer.update_gamexml_annot( table, comput )
-                else:
-                    print "*** Error: unknown format '%s'" % ( format )
-                    sys.exit(1)
-            writer.write(f_gamexml)
-
-            db.close()
-
-    # 
-    if f_gamexml == "" and f_result != "" and f_fasta == "":
-        automatisation( f_result, tier_name, writer.get_reverse(), comput )
-
-    # update a ".gamexml" file (options '-g' and '-t')
-    if f_gamexml != "" and f_result != "":
-        writer.update_gamexml( f_gamexml, f_result, tier_name, comput )
-
-    # remove a comput
-    if substract_name != "" and tier_name == "":
-        if f_gamexml != "":
-            writer.parse_gamexml( f_gamexml )
-            writer.verif_name_prog( substract_name )
-            writer.write( f_gamexml )
-            if verbose > 1:
-                print substract_name + " program from " + f_gamexml +" removed"
-        else:
-            automatisation( "", substract_name, 0, None )
-
-    if verbose > 0:
-        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-#------------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/tools/srptPhyML.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,165 +0,0 @@
-#!/usr/bin/env python
-
-import user, os, sys, getopt, exceptions, logging, ConfigParser
-
-if not os.environ.has_key( "REPET_PATH" ):
-    print "*** Error: no environment variable REPET_PATH"
-    sys.exit(1)
-sys.path.append( os.environ["REPET_PATH"] )
-
-import pyRepet.sql.RepetJobMySQL
-import pyRepet.launcher.Launcher
-
-#-----------------------------------------------------------------------------
-
-def help():
-
-    """
-    Give the list of the command-line options.
-    """
-
-    print
-    print "usage:",sys.argv[0]," [ options ]"
-    print "options:"
-    print "     -h: this help"
-    print "     -g: name of the group identifier (same for all the jobs)"
-    print "     -q: name of the query directory"
-    print "     -S: suffix in the query directory  (default='*.fa')"
-    print "     -Q: name of the queue (on the cluster)"
-    print "     -d: absolute path to the temporary directory"
-    print "     -C: configuration file from TEdenovo or TEannot pipeline"
-    print "     -t: job table name (default=jobs)"
-    print "     -p: absolute path to project directory (if jobs management via files)"
-    print "     -c: clean (remove job launch files and job stdout)"
-    print "     -v: verbose (default=0/1/2)"
-    print
-
-#-----------------------------------------------------------------------------
-
-def main():
-
-    """
-    This program takes a directory as input and launches MAP on each file in it.
-    """
-
-    groupid = ""
-    queryDir = ""
-    patternSuffix = "*.fa"
-    queue = ""
-    tmpDir = ""
-    configFileName = ""
-    jobTable = "jobs"
-    projectDir = ""
-    clean = False
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:Q:d:C:t:p:cv:")
-    except getopt.GetoptError, err:
-        print str(err)
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-g":
-            groupid = a
-        elif o == "-q":
-            queryDir = a
-        elif o == "-S":
-            patternSuffix = a
-        elif o == "-Q":
-            queue = a
-        elif o == "-d":
-            tmpDir = a
-        elif o == "-C":
-            configFileName = a
-        elif o == "-t":
-            jobTable = a
-        elif o == "-p":
-            projectDir = a
-        elif o == "-c":
-            clean = True
-        elif o == "-v":
-            verbose = int(a)
-
-    if  groupid == "" or queryDir == "":
-        print "*** Error: missing compulsory options"
-        help()
-        sys.exit(1)
-
-    if os.environ["REPET_JOBS"] == "files" and projectDir == "":
-        print "*** Error: missing compulsory options for jobs management via files"
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    #--------------------------------------------------------------------------
-
-    # create the 'log' file
-
-    logFileName = "%s_pid%s.log" % ( groupid, os.getpid() )
-    handler = logging.FileHandler( logFileName )
-    formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )
-    handler.setFormatter( formatter )
-    logging.getLogger('').addHandler( handler )
-    logging.getLogger('').setLevel( logging.DEBUG )
-    logging.info( "started" )
-
-
-    # open a connection to the MySQL table
-
-    if configFileName != "":
-        if not os.path.exists( configFileName ):
-            print "*** Error: configuration file '%s' doesn't exist" % ( configFileName )
-            sys.exit(1)
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-    else:
-        host = os.environ["REPET_HOST"]
-        user = os.environ["REPET_USER"]
-        passwd = os.environ["REPET_PW"]
-        dbname = os.environ["REPET_DB"]
-
-    if os.environ["REPET_JOBS"] == "files":
-        jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] )
-    elif os.environ["REPET_JOBS"] == "MySQL":
-        jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( user, host, passwd, dbname )
-    else:
-        print "*** Error: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] )
-        sys.exit(1)
-
-
-    currentDir = os.getcwd()
-    if tmpDir == "":
-        tmpDir = currentDir
-
-    # launch PhyML on each fasta file in queryDir
-    cL = pyRepet.launcher.Launcher.PhyMlLauncher( jobdb=jobdb, query=queryDir, cdir=currentDir, tmpdir=tmpDir, job_table=jobTable, queue=queue, groupid=groupid, acro="PhyML" )
-    cL.run( patternSuffix )
-
-    # clean
-    if clean == True:
-        cL.clean()
-
-
-    logging.info( "finished" )
-
-    if verbose > 0:
-        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    return 0
-
-#----------------------------------------------------------------------------
-
-if __name__ == '__main__':
-    main()

--- a/commons/tools/srptTableOverlap.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,319 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import getopt
-import logging
-import string
-import ConfigParser
-
-from pyRepet.sql.TableAdaptator import *
-import pyRepet.sql.RepetDBMySQL
-import pyRepet.coord.Map
-import pyRepet.coord.Path
-import pyRepet.coord.Set
-
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     -q: query table"
-    print "     -s: subject table"
-    print "     -p: by path"
-    print "     -t: table type comparison: qtype/stype where qtype=[map,set,path] and stype=[path,set,map]"
-    print "     -c: configuration file from TEdenovo or TEannot pipeline"
-    print "     -H: MySQL host (if no configuration file)"
-    print "     -U: MySQL user (if no configuration file)"
-    print "     -P: MySQL password (if no configuration file)"
-    print "     -D: MySQL database (if no configuration file)"
-    print
-    
-    
-def pathOverlapByPath( qtable, qtype, stable, stype, db, fout, verbose=0 ):
-    
-    if qtype == "path":
-        db.create_path_index( qtable )
-        qtablePathAdaptator = TablePathAdaptator( db, qtable )
-        path_num_list = qtablePathAdaptator.getPath_num()
-    elif qtype == "set":
-        db.create_set_index( qtable )
-        qtableSetAdaptator = TableSetAdaptator( db, qtable )
-        path_num_list = qtableSetAdaptator.getSet_num()
-    else:
-        string = "unknown query table type: %s" % ( qtype )
-        if verbose > 0:
-            print string
-        logging.error( string )
-        sys.exit(1)
-    string = "nb of paths in query table: %i" % (len(path_num_list) )
-    if verbose > 0:
-        print string
-    logging.info( string )
-    
-    if stype == "path":
-        stablePathAdaptator = TableBinPathAdaptator( db, stable )
-#        stablePathAdaptator=TablePathAdaptator(db,stable)
-    elif stype == "set":
-        stableSetAdaptator = TableBinSetAdaptator( db, stable )
-#        stableSetAdaptator=TableSetAdaptator(db,stable)
-    else:
-        string = "unknown subject table type: %s" % ( stype )
-        if verbose > 0:
-            print string
-        logging.error( string )
-        sys.exit(1)
-        
-    count = 0
-    for path_num in path_num_list:
-        if qtype == "path":
-            qlist = qtablePathAdaptator.getPathList_from_num( path_num )
-            qlist = pyRepet.coord.Path.path_list_rangeQ2Set( qlist )
-        elif qtype == "set":
-            qlist = qtableSetAdaptator.getSetList_from_num( path_num )
-            
-        qlist.sort()
-        qmin, qmax = pyRepet.coord.Set.set_list_boundaries( qlist )
-        
-        qmin = qmin - 1
-        qmax = qmax + 1
-        if stype == "path":
-            slist = stablePathAdaptator.getPathList_from_qcoord(qlist[0].seqname.split()[0],qmin,qmax)
-            slist = pyRepet.coord.Path.path_list_rangeQ2Set( slist )
-        elif stype == "set":
-            slist = stableSetAdaptator.getSetList_from_qcoord(qlist[0].seqname.split()[0],qmin,qmax)
-            
-        if len(slist) > 0:
-            print "----------------------------------------"
-            print "query:"
-            pyRepet.coord.Set.set_list_show( qlist )
-            qlist=pyRepet.coord.Set.set_list_merge( qlist )
-            qsize=pyRepet.coord.Set.set_list_size( qlist )
-            print "query size=",qsize
-            
-            slist_dict = pyRepet.coord.Set.set_list_split( slist )
-            subj_names = ""
-            for i,l in slist_dict.items():
-                if subj_names != "":
-                    subj_names += "|"
-                subj_names += "%d:%s" % (i,l[0].name)
-            subj_count = len(slist_dict.keys())
-            
-            print "subject:"
-            pyRepet.coord.Set.set_list_show( slist )
-            slist = pyRepet.coord.Set.set_list_merge( slist )
-            ssize = pyRepet.coord.Set.set_list_size( slist )
-            osize = pyRepet.coord.Set.set_list_overlap_size( qlist, slist )
-            
-            print "subject size=",ssize
-            print "overlap size=",osize
-            
-            fout.write("%d\t%s\t%d\t%s\t%d\t%d\t%d\t%f\t%f\n"\
-                       %(path_num,qlist[0].name,\
-                         qsize,\
-                         subj_names,\
-                         subj_count,\
-                         ssize,\
-                         osize,\
-                         float(osize)/qsize,\
-                         float(osize)/ssize))
-        else:
-            print "----------------------------------------"
-            print "query:"
-            pyRepet.coord.Set.set_list_show( qlist )
-            qlist = pyRepet.coord.Set.set_list_merge( qlist )
-            qsize = pyRepet.coord.Set.set_list_size( qlist )
-            print "query size=",qsize
-            print "No match!"
-            fout.write("%d\t%s\t%d\t-\t0\t0\t0\t0.0\t0.0\n"\
-                       %(path_num,qlist[0].name,qsize))
-            
-            
-def getOverlapAllPaths( qtable, qtype, stable, stype, db, verbose=0 ):
-    """
-    For each query in qtable, compute the overlap between its matches and the matches in stable.
-    """
-    if qtype =="map":
-        qtableAdaptator = pyRepet.sql.TableAdaptator.TableMapAdaptator( db, qtable )
-    elif qtype == "path":
-        qtableAdaptator = pyRepet.sql.TableAdaptator.TablePathAdaptator( db, qtable )
-    elif qtype == "set":
-        qtableAdaptator = pyRepet.sql.TableAdaptator.TableSetAdaptator( db, qtable )
-    else:
-        string = "unknown query table type: %s" % ( qtype )
-        if verbose > 0:
-            print string
-        logging.error( string )
-        sys.exit(1)
-        
-    string = "fetching query table data..."
-    contigs = qtableAdaptator.getContig_name()
-    string += " %i contig(s)" % ( len(contigs) )
-    if verbose > 0:
-        print string; sys.stdout.flush()
-    logging.info( string )
-    
-    if stype == "map":
-        stableAdaptator = pyRepet.sql.TableAdaptator.TableMapAdaptator( db, stable )
-    elif stype == "path":
-        stableAdaptator = pyRepet.sql.TableAdaptator.TablePathAdaptator( db, stable )
-    elif stype == "set":
-        stableAdaptator = pyRepet.sql.TableAdaptator.TableSetAdaptator( db, stable )
-    else:
-        string = "unknown subject table type: %s" % ( stype )
-        if verbose > 0:
-            print string
-        logging.error( string )
-        sys.exit(1)
-        
-    string = "looking for overlaps with subject data..."
-    if verbose > 0:
-        print string; sys.stdout.flush()
-    logging.info( string )
-    sum_qsize = 0
-    sum_osize = 0
-    sum_non_osize = 0
-    for c in contigs:
-        string = "contig '%s': "%(c)
-        qlist = qtableAdaptator.getSetList_from_contig( c )
-        qlist = pyRepet.coord.Set.set_list_merge( qlist )
-        slist = stableAdaptator.getSetList_from_contig( c )
-        slist = pyRepet.coord.Set.set_list_merge( slist )
-        qsize = pyRepet.coord.Set.set_list_size( qlist )
-        osize = pyRepet.coord.Set.set_list_overlap_size( qlist, slist )
-        sum_osize += osize
-        sum_qsize += qsize
-        sum_non_osize += qsize - osize
-        string += "qsize=%d osize=%d" % ( qsize, osize )
-        logging.debug( string )
-        if verbose > 0:
-            print string; sys.stdout.flush()
-            
-    string = "summary:"
-    string += "\ncumulative coverage of the query table: %i nt" % ( sum_qsize )
-    string += "\nsize of overlaps with the subject table: %i nt" % ( sum_osize )
-    string += "\n proportion of query: %.3f" % ( float(sum_osize)/sum_qsize )
-    string += "\nsize of non-overlaps with the subject table: %i nt" % ( sum_non_osize )
-    string += "\n proportion of query: %.3f" % ( float(sum_non_osize)/sum_qsize )
-    if verbose > 0:
-        print string; sys.stdout.flush()
-    logging.info( string )
-    
-    return sum_osize, sum_non_osize, sum_qsize
-
-
-def main ():
-    """
-    This program computes the overlaps between two tables recording spatial coordinates.
-    """
-    qtable = ""
-    stable = ""
-    type = ""
-    by_path = False
-    configFileName = ""
-    host = ""
-    user = ""
-    passwd = ""
-    db = ""
-    verbose = 0
-    try:
-        opts, args = getopt.getopt( sys.argv[1:], "hq:s:t:pc:H:U:P:D:v:" )
-    except getopt.GetoptError:
-        help()
-        sys.exit(1)
-    if len(args) != 0:
-        help()
-        sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-q":
-            qtable = a
-        elif o == "-s":
-            stable = a
-        elif o == "-t":
-            type = a
-        elif o == "-p":
-            by_path = True
-        elif o == "-c":
-            configFileName = a
-        elif o == "-H":
-            host = a
-        elif o == "-U":
-            user = a 
-        elif o == "-P":
-            passwd = a
-        elif o == "-D":
-            db = a
-        elif o == "-v":
-            verbose = int(a)
-    if qtable=="" or stable=="" or \
-    (configFileName== "" and (host=="" or \
-                              user=="" or passwd=="" or db=="")):
-        print "ERROR: missing compulsory options"
-        help()
-        sys.exit(1)
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    if configFileName != "":
-        config = ConfigParser.ConfigParser()
-        config.readfp( open(configFileName) )
-        host = config.get("repet_env","repet_host")
-        user = config.get("repet_env","repet_user")
-        passwd = config.get("repet_env","repet_pw")
-        dbname = config.get("repet_env","repet_db")
-        
-    logfilename = qtable + "-" + stable + "-" + str(os.getpid()) + ".log"
-    handler = logging.FileHandler( logfilename )
-    formatter = logging.Formatter("%(asctime)s %(levelname)s: %(message)s")
-    handler.setFormatter( formatter )
-    logging.getLogger('').addHandler(handler)
-    logging.getLogger('').setLevel(logging.DEBUG)
-    logging.info("started")
-    
-    db = pyRepet.sql.RepetDBMySQL.RepetDB( user, host, passwd, dbname )
-    
-    qtype, stype = type.split("/")
-    
-    if not db.exist( qtable ):
-        if not os.path.exists( qtable ):
-            msg = "ERROR: neither table nor file '%s'" % ( qtable )
-            sys.stderr.write( "%s\n" % msg )
-            sys.exit(1)
-        tmp = qtable.replace(".","_")
-        db.create_table( db, tmp, qtable, qtype )
-        qtable = tmp
-    if not db.exist( stable ):
-        if not os.path.exists( stable ):
-            msg = "ERROR: neither table nor file '%s'" % ( stable )
-            sys.stderr.write( "%s\n" % msg )
-            sys.exit(1)
-        tmp = stable.replace(".","_")
-        db.create_table( db, tmp, stable, qtype )
-        stable = tmp
-        
-    string = "input tables:"
-    string += "\nquery table: %s ('%s' format)" % ( qtable, qtype )
-    string += "\nsubject table: %s ('%s' format)" % ( stable, stype )
-    logging.info( string )
-    
-    if by_path:
-        fout = open(qtable+"_vs_"+stable+".dat","w")
-        pathOverlapByPath( qtable, qtype, stable, stype, db, fout, verbose )
-        fout.close()
-    else:
-        getOverlapAllPaths( qtable, qtype, stable, stype, db, verbose )
-        
-    logging.info("finished")
-    
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-        
-if __name__ == "__main__":
-    main()

--- a/commons/tools/tabFileReader.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,600 +0,0 @@
-#!/usr/bin/env python
-
-###@file
-# Read a file recording matches in the 'tab' format (output from Matcher) and return the number of matches between queries and subjects being CC, CI, IC and II.
-# A match is said to be CC (for complete-complete) when both query and subject match over x% of their entire respective length. By default, x=95.
-#
-# usage: tabFileReader.py [ options ]
-# options:
-#      -h: this help
-#      -m: name of the file recording the matches (format='tab', output from Matcher)
-#      -q: name of the fasta file recording the queries
-#      -s: name of the fasta file recording the subjects
-#      -t: threshold over which the match is 'complete', in % of the seq length (default=95)
-#      -i: identity below which matches are ignored (default=0)
-#      -l: length below which matches are ignored (default=0)
-#      -o: overlap on query and subject below which matches are ignored (default=0)
-#      -v: verbose (default=0/1)
-
-import sys
-import getopt
-from string import *
-
-import pyRepet.seq.BioseqDB
-import pyRepet.util.Stat
-
-#TODO: remove case changes in headers (4 lower() method calls in this script) 
-
-#----------------------------------------------------------------------------
-
-def help():
-    print
-    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
-    print "options:"
-    print "     -h: this help"
-    print "     -m: name of the file recording the matches (format='tab', output from Matcher)"
-    print "     -q: name of the fasta file recording the queries"
-    print "     -s: name of the fasta file recording the subjects"
-    print "     -t: coverage threshold over which the match is 'complete' (in %% of the seq length, default=95)"
-    print "     -i: identity below which matches are ignored (default=0)"
-    print "     -l: length below which matches are ignored (default=0)"
-    print "     -o: overlap on query and subject below which matches are ignored (default=0)"
-    print "     -I: identity threshold for 'CC' matches (default=90)"
-    print "     -E: E-value threshold for 'CC' matches (default=1e-10)"
-    print "     -T: coverage threshold for match length on query compare to subject length (default=90)"
-    print "     -v: verbose (default=0/1)"
-    print
-
-#----------------------------------------------------------------------------
-
-#here are the fields of a '.tab' file:
-#[0]: query sequence name
-#[1]: whole match start coordinate on the query sequence
-#[2]: whole match end coordinate on the query sequence
-#[3]: length on the query sequence
-#[4]: length in percentage of the query sequence
-#[5]: length on the query relative to the subject length in percentage
-#[6]: subject sequence name
-#[7]: whole match start coordinate on the subject sequence
-#[8]: whole match end coordinate on the subject sequence
-#[9]: length on the subject sequence
-#[10]: length in percentage of the subject sequence
-#[11]: BLAST E-value
-#[12]: BLAST score
-#[13]: identity percentage
-#[14]: path
-
-class tabFileReader( object ):
-
-    def __init__( self, line ):
-
-        columns = line.split("\t")
-
-        self.name_sbj = (columns[6])
-        self.length_sbj = int(round(int(columns[9])/float(columns[10]),0))  #length of the subject
-        self.prct_sbj = float(columns[10]) * 100  #prct_sbj = length of the match on the subject divided by the length of the subject * 100
-        if int(columns[7]) < int(columns[8]):
-            self.start_sbj = int(columns[7])                        #start of the match on the subject
-            self.end_sbj = int(columns[8])                          #end of the match on the subject
-        else:
-            self.start_sbj = int(columns[8])
-            self.end_sbj = int(columns[7])
-        self.sbj_dist_ends = int(columns[9])                    #length on the subject that matches with the query
-
-        self.name_qry = columns[0]
-        self.length_qry = int(round(int(columns[3])/float(columns[4]),0))  #length of the query
-        self.prct_qry = float(columns[4]) * 100   #prct_qry = length of the match on the query divided by the length of the query * 100
-        if int(columns[1]) < int(columns[2]):
-            self.start_qry = int(columns[1])                        #start of the match on the query
-            self.end_qry = int(columns[2])                          #end of the match on the query
-        else:
-            self.start_qry = int(columns[2])
-            self.end_qry = int(columns[1])
-        self.qry_dist_ends = int(columns[3])                    #length on the query that matches with the subject
-
-        self.length_match = int(columns[3])
-        self.prct_matchQryOverSbj = float(columns[5]) * 100   #length on the query relative to the subject length in percentage
-        self.identity = float(columns[13])
-        self.score = int(columns[12])
-        self.evalue = float(columns[11])
-
-        self.sbj2qry = [self.length_sbj,self.prct_sbj,self.start_sbj,self.end_sbj,self.name_qry,self.length_sbj,self.prct_qry,self.start_qry,self.end_qry,self.identity,self.score]
-        
-        self.qry2sbj = [self.length_qry,self.prct_qry,self.start_qry,self.end_qry,self.name_sbj,self.length_sbj,self.prct_sbj,self.start_sbj,self.end_sbj,self.identity,self.score]
-
-#----------------------------------------------------------------------------
-
-def make_dico( lMatches ):
-    """
-    Record the matches in two dictionaries which keys are the queries or the subjects.
-    """
-
-    Sbj2Qry = {}
-    Qry2Sbj = {}
-
-    for match in lMatches:
-        if Sbj2Qry.has_key( match.name_sbj ):
-            Sbj2Qry[match.name_sbj].append( match )
-        else:
-            Sbj2Qry[match.name_sbj] = [ match ]
-        if Qry2Sbj.has_key( match.name_qry ):
-            Qry2Sbj[match.name_qry].append( match )
-        else:
-            Qry2Sbj[match.name_qry] = [ match ]
-
-    return [ Sbj2Qry, Qry2Sbj ]
-
-#----------------------------------------------------------------------------
-
-def find_UniqRedun( list_matchs ):
-
-    list_total_sbj = [];list_total_qry = []
-    list_uniq_sbj = [];list_redun_sbj = []
-    list_uniq_qry = [];list_redun_qry = []
-
-    for match in list_matchs:
-        list_total_sbj.append(match.name_sbj)
-        list_total_qry.append(match.name_qry)
-
-    for name_sbj in list_total_sbj:
-        if list_total_sbj.count(name_sbj) == 1:
-            list_uniq_sbj.append(name_sbj)
-        else:
-            if name_sbj not in list_redun_sbj:
-                list_redun_sbj.append(name_sbj)
-
-    for name_qry in list_total_qry:
-        if list_total_qry.count(name_qry) == 1:
-            list_uniq_qry.append(name_qry)
-        else:
-            if name_qry not in list_redun_qry:
-                list_redun_qry.append(name_qry)
-
-    return [ list_uniq_sbj, list_redun_sbj, list_uniq_qry, list_redun_qry ]
-
-#----------------------------------------------------------------------------
-
-def remove( all, sup_sbjqry, sup_sbj, sup_qry, inf_sbjqry ):
-
-    for name_sbj in all.keys():
-
-        if sup_sbjqry.has_key( name_sbj ) and sup_sbj.has_key( name_sbj ):
-            del sup_sbj[ name_sbj ]
-
-        if sup_sbjqry.has_key( name_sbj ) and sup_qry.has_key( name_sbj ):
-            del sup_qry[ name_sbj ]
-
-        if sup_sbjqry.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ):
-            del inf_sbjqry[ name_sbj ]
-
-        if sup_sbj.has_key( name_sbj ) and sup_qry.has_key( name_sbj ):
-            del sup_qry[ name_sbj ]
-
-        if sup_sbj.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ):
-            del inf_sbjqry[ name_sbj ]
-
-        if sup_qry.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ):
-            del inf_sbjqry[ name_sbj ]
-
-    return [ sup_sbj, sup_qry, inf_sbjqry ]
-
-#----------------------------------------------------------------------------
-
-def write_output( outFile, match_type, Sbj2Qry, dSbj2Cat, Qry2Sbj, dQry2Cat ):
-    """
-    Save the results (subjects in each category and its matches) in a human-readable way.
-    """
-
-    if match_type == 'CC':
-        msg = "Matches with L >= %i%% for subject and query (CC)" % ( thresholdCoverage )
-    elif match_type == 'CI':
-        msg = "Matches with L >= %i%% for subject and L < %i%% for query (CI)" % ( thresholdCoverage, thresholdCoverage )
-    elif match_type == 'IC':
-        msg = "Matches with L < %i%% for subject and L >= %i%% for query (IC)" % ( thresholdCoverage, thresholdCoverage )
-    elif match_type == 'II':
-        msg ="Matches with L < %i%% for subject and query (II)" % ( thresholdCoverage )
-    if verbose > 1:
-        print "%s: %i subjects" % ( msg, len(Sbj2Qry.keys()) )
-    outFile.write("\n%s\n" % ( msg ) )
-
-    for name_sbj in Sbj2Qry.keys():
-        matchs = Sbj2Qry[name_sbj]
-        if len(matchs) == 1:
-            outFile.write("-> subject %s (%s: %s,%s) matches with query %s (%s: %s,%s): prct_sbj %.3f & prct_qry %.3f (id=%.3f,Eval=%g)\n" % (name_sbj,matchs[0].length_sbj,matchs[0].start_sbj,matchs[0].end_sbj,matchs[0].name_qry,matchs[0].length_qry,matchs[0].start_qry,matchs[0].end_qry,matchs[0].prct_sbj,matchs[0].prct_qry,matchs[0].identity,matchs[0].evalue))
-        else:
-            outFile.write("-> subject %s (%s: %s,%s) matches with %s queries:\n" % (name_sbj,matchs[0].length_sbj,matchs[0].start_sbj,matchs[0].end_sbj,len(matchs)))
-            for match in matchs:
-                outFile.write("%s versus %s (%s: %s,%s): prct_sbj %.3f & prct_qry %.3f (id=%.3f,Eval=%g)\n"%(name_sbj,match.name_qry,match.length_qry,match.start_qry,match.end_qry,match.prct_sbj,match.prct_qry,match.identity,match.evalue))
-
-    tmpList = []
-    for name_sbj in Sbj2Qry.keys():
-        tmpList.append( name_sbj.split(" ")[0].lower() )
-    tmpList.sort()
-    for name_sbj in tmpList:
-        outFile.write( name_sbj+"\n" )
-        dSbj2Cat[ name_sbj ] = match_type
-
-    tmpList = []
-    for name_qry in Qry2Sbj.keys():
-        tmpList.append( name_qry.split(" ")[0].lower() )
-    tmpList.sort()
-    for name_qry in tmpList:
-        outFile.write( name_qry+"\n" )
-        dQry2Cat[ name_qry ] = match_type
-
-#----------------------------------------------------------------------------
-
-def writeSubjectCategory( dSbj2Cat ):
-    """
-    Save the category (CC/CI/IC/II/NA) in which each subject has been found.
-
-    @param dSbj2Cat: dictionary which keys are subject names and values the category of that subject
-    @type dSbj2Cat: dictionary
-    """
-
-    # sort the subject names in alphabetical order
-    lSbjSorted = dSbj2Cat.keys()
-    lSbjSorted.sort()
-
-    catFile = open( tabFileName + "_sbjCategories.txt", "w" )
-    for sbj in lSbjSorted:
-        string = "%s\t%s\n" % ( sbj, dSbj2Cat[ sbj ] )
-        catFile.write( string )
-    catFile.close()
-
-#----------------------------------------------------------------------------
-
-def writeQueryCategory( dQry2Cat ):
-    """
-    Save the category (CC/CI/IC/II/NA) in which each query has been found.
-
-    @param dQry2Cat: dictionary which keys are query names and values the category of that query
-    @type dQry2Cat: dictionary
-    """
-
-    # sort the query names in alphabetical order
-    lQrySorted = dQry2Cat.keys()
-    lQrySorted.sort()
-
-    catFile = open( tabFileName + "_qryCategories.txt", "w" )
-    for qry in lQrySorted:
-        string = "%s\t%s\n" % ( qry, dQry2Cat[ qry ] )
-        catFile.write( string )
-    catFile.close()
-    
-#----------------------------------------------------------------------------
-
-def main():
-
-    global tabFileName
-    tabFileName = ""
-    qryFileName = ""
-    sbjFileName = ""
-    global thresholdCoverage
-    thresholdCoverage = 95
-    minIdentity = 0
-    minLength = 0
-    minOverlap = 0
-    global thresholdIdentity
-    thresholdIdentity = 90
-    global thresholdEvalue
-    thresholdEvalue = 1e-10
-    global thresholdCoverageMatch
-    thresholdCoverageMatch = 90
-    global verbose
-    verbose = 0
-
-    try:
-        opts, args = getopt.getopt(sys.argv[1:],"hm:q:s:t:i:l:I:E:T:o:v:")
-    except getopt.GetoptError, err:
-        print str(err); help(); sys.exit(1)
-    for o,a in opts:
-        if o == "-h":
-            help()
-            sys.exit(0)
-        elif o == "-m":
-            tabFileName = a
-        elif o == "-q":
-            qryFileName = a
-        elif o == "-s":
-            sbjFileName = a
-        elif o == "-t":
-            thresholdCoverage = int(a)
-        elif o == "-i":
-            minIdentity = float(a)
-        elif o == "-l":
-            minLength = int(a)
-        elif o == "-o":
-            minOverlap = float(a)
-        elif o == "-I":
-            thresholdIdentity = int(a)
-        elif o == "-E":
-            thresholdEvalue = float(a)
-        elif o == "-T":
-            thresholdCoverageMatch = int(a)
-        elif o == "-v":
-            verbose = int(a)
-
-    if tabFileName == "":
-        msg = "ERROR: missing 'tab' file (-m)"
-        sys.stderr.write( "%s\n" % msg )
-        help()
-        sys.exit(1)
-    if qryFileName == "" or sbjFileName == "":
-        msg = "ERROR: missing 'fasta' files (-q or -s)"
-        sys.stderr.write( "%s\n" % msg )
-        help()
-        sys.exit(1)
-
-    if verbose > 0:
-        print "START %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-
-    # 4 categories of matchs:
-    # type 1 (CC): the length of the match on the subject is >= 95% of the total length of the subject, idem for the query
-    # type 2 (CI): sbj >= 95% & qry < 95%
-    # type 3 (IC): sbj < 95% & qry >= 95%
-    # type 4 (II): sbj & qry < 95%
-    ListMatches_all = []
-    ListMatches_sup_sbjqry = []
-    ListMatches_sup_sbj = []
-    ListMatches_sup_qry = []
-    ListMatches_inf_sbjqry = []
-
-    qryDB = pyRepet.seq.BioseqDB.BioseqDB( qryFileName )
-    nbQry = qryDB.getSize()
-    if verbose > 0:
-        print "nb of queries in '%s': %i" % ( qryFileName, nbQry )
-    dQry2Cat = {}
-    for bs in qryDB.db:
-        dQry2Cat[ bs.header.split(" ")[0].lower() ] = "NA"
-
-    sbjDB = pyRepet.seq.BioseqDB.BioseqDB( sbjFileName )
-    nbSbj = sbjDB.getSize()
-    if verbose > 0:
-        print "nb of subjects in '%s': %i" % ( sbjFileName, nbSbj )
-    dSbj2Cat = {}
-    for bs in sbjDB.db:
-        dSbj2Cat[ bs.header.split(" ")[0].lower() ] = "NA"
-
-    tabFile = open( tabFileName )
-    nbMatchesInTab = 0
-    dSubject2DistinctQueries = {}
-    dQuery2DistinctSubjects = {}
-
-    # For each match, create a 'tabFileReader' object and record it in a list according to the type of the match
-    if verbose > 0:
-        print "parse the 'tab' file..."; sys.stdout.flush()
-    while True:
-        line = tabFile.readline()
-        if line == "":
-            break
-        if line[0:10] == "query.name":
-            continue
-        nbMatchesInTab += 1
-
-        match = tabFileReader( line )
-        if match.identity < minIdentity:
-            line = tabFile.readline()
-            continue
-        if match.length_match < minLength:
-            line = tabFile.readline()
-            continue
-        if match.prct_qry < minOverlap or match.prct_sbj < minOverlap:
-            line = tabFile.readline()
-            continue
-        ListMatches_all.append( match )
-
-        # type 1: sbj C & qry C
-        if match.prct_sbj >= thresholdCoverage and match.prct_qry >= thresholdCoverage:
-            qsLengthRatio = 100 * match.length_qry / float(match.length_sbj)
-            if match.identity >= thresholdIdentity \
-            and match.evalue <= thresholdEvalue \
-            and qsLengthRatio >= thresholdCoverage - 2 \
-            and qsLengthRatio <= 100 + (100-thresholdCoverage) + 2 \
-            and match.prct_matchQryOverSbj >= thresholdCoverageMatch:
-                ListMatches_sup_sbjqry.append( match )
-            else:
-                ListMatches_inf_sbjqry.append( match )
-
-        # type 2: sbj C & qry I
-        elif match.prct_sbj >= thresholdCoverage and match.prct_qry < thresholdCoverage:
-            ListMatches_sup_sbj.append( match )
-
-        # type 3: sbj I & qry C
-        elif match.prct_qry >= thresholdCoverage and match.prct_sbj < thresholdCoverage:
-            ListMatches_sup_qry.append( match )
-
-        # type 4: sbj I & qry I
-        elif match.prct_qry < thresholdCoverage and match.prct_sbj < thresholdCoverage:
-            ListMatches_inf_sbjqry.append( match )
-
-        if not dSubject2DistinctQueries.has_key( match.name_sbj ):
-            dSubject2DistinctQueries[ match.name_sbj ] = []
-        if not match.name_qry in dSubject2DistinctQueries[ match.name_sbj ]:
-            dSubject2DistinctQueries[ match.name_sbj ].append( match.name_qry )
-        if not dQuery2DistinctSubjects.has_key( match.name_qry ):
-            dQuery2DistinctSubjects[ match.name_qry ] = []
-        if not match.name_sbj in dQuery2DistinctSubjects[ match.name_qry ]:
-            dQuery2DistinctSubjects[ match.name_qry ].append( match.name_sbj )
-
-    if verbose > 0:
-        print "parsing done !"; sys.stdout.flush()
-        print "nb matches in '%s': %i" % ( tabFileName, nbMatchesInTab )
-        print "nb matches 'CC': %i" % ( len(ListMatches_sup_sbjqry) )
-        if verbose > 1:
-            for match in ListMatches_sup_sbjqry:
-                print "\t%s (%.2f%%) - %s (%.2f%%) id=%.2f" % ( match.name_sbj, match.prct_sbj, match.name_qry, match.prct_qry, match.identity )
-        print "nb matches 'CI': %i" % ( len(ListMatches_sup_sbj) )
-        if verbose > 1:
-            for match in ListMatches_sup_sbj:
-                print "\t%s (%.2f%%) - %s (%.2f%%) id=%.2f" % ( match.name_sbj, match.prct_sbj, match.name_qry, match.prct_qry, match.identity )
-        print "nb matches 'IC': %i" % ( len(ListMatches_sup_qry) )
-        print "nb matches 'II': %i" % ( len(ListMatches_inf_sbjqry) )
-
-    if nbMatchesInTab == 0:
-        print "nothing to do"
-        sys.exit(0)
-
-    # For each type of matchs, record them in 2 dictionaries: Sbj2Qry and Qry2Sbj
-    D_all = make_dico( ListMatches_all )
-    Sbj2Qry_all = D_all[0]
-    Qry2Sbj_all = D_all[1]
-
-    D_sup_sbjqry = make_dico(ListMatches_sup_sbjqry)
-    Sbj2Qry_sup_sbjqry = D_sup_sbjqry[0]
-    Qry2Sbj_sup_sbjqry = D_sup_sbjqry[1]
-
-    D_sup_sbj = make_dico(ListMatches_sup_sbj)
-    Sbj2Qry_sup_sbj = D_sup_sbj[0]
-    Qry2Sbj_sup_sbj = D_sup_sbj[1]
-
-    D_sup_qry = make_dico(ListMatches_sup_qry)
-    Sbj2Qry_sup_qry = D_sup_qry[0]
-    Qry2Sbj_sup_qry = D_sup_qry[1]
-
-    D_inf_sbjqry = make_dico(ListMatches_inf_sbjqry)
-    Sbj2Qry_inf_sbjqry = D_inf_sbjqry[0]
-    Qry2Sbj_inf_sbjqry = D_inf_sbjqry[1]
-
-
-    # For each type of matches, find the subjects/queries that are involve in one or several match
-    list_all = find_UniqRedun(ListMatches_all)
-    UniqSbj_all = list_all[0]
-    RedunSbj_all = list_all[1]
-    UniqQry_all = list_all[2]
-    RedunQry_all = list_all[3]
-
-    list1 = find_UniqRedun(ListMatches_sup_sbjqry)
-    UniqSbj_sup_sbjqry = list1[0]
-    RedunSbj_sup_sbjqry = list1[1]
-    UniqQry_sup_sbjqry = list1[2]
-    RedunQry_sup_sbjqry = list1[3]
-
-    list2 = find_UniqRedun(ListMatches_sup_sbj)
-    UniqSbj_sup_sbj = list2[0]
-    RedunSbj_sup_sbj = list2[1]
-    UniqQry_sup_sbj = list2[2]
-    RedunQry_sup_sbj = list2[3]
-    
-    list3 = find_UniqRedun(ListMatches_sup_qry)
-    UniqSbj_sup_qry = list3[0]
-    RedunSbj_sup_qry = list3[1]
-    UniqQry_sup_qry = list3[2]
-    RedunQry_sup_qry = list3[3]
-    
-    list4 = find_UniqRedun(ListMatches_inf_sbjqry)
-    UniqSbj_inf_sbjqry = list4[0]
-    RedunSbj_inf_sbjqry = list4[1]
-    UniqQry_inf_sbjqry = list4[2]
-    RedunQry_inf_sbjqry = list4[3]
-    
-    iStatSbj = pyRepet.util.Stat.Stat()
-    for subject in dSubject2DistinctQueries.keys():
-        iStatSbj.add( len( dSubject2DistinctQueries[ subject ] ) )
-    iStatQry = pyRepet.util.Stat.Stat()
-    for query in dQuery2DistinctSubjects.keys():
-        iStatQry.add( len( dQuery2DistinctSubjects[ query ] ) )
-
-
-    # Write the review of the '.tab' file
-    outFile = open( tabFileName + "_tabFileReader.txt", "w" )
-    outFile.write( "Input: %s\n" % ( tabFileName ) )
-
-    outFile.write( "\n# Number of subjects in '%s': %i\n" % ( sbjFileName, nbSbj ) )
-    outFile.write( "# Number of queries in '%s': %i\n" % ( qryFileName, nbQry ) )
-
-    outFile.write( "\nNumber of matches: %s\n" % (len(ListMatches_all)))
-    outFile.write( "    # Number of different subjects that match: %s (Sn*=%.2f%%)\n" % ( len(Sbj2Qry_all.keys()), 100 * len(Sbj2Qry_all.keys()) / float(nbSbj) ) )
-    outFile.write( "        Among them, number of different subjects having exactly one match: %s (%.2f%%)\n" % ( len(UniqSbj_all), 100 * len(UniqSbj_all) / float(len(Sbj2Qry_all.keys())) ) )
-    outFile.write( "        Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_all)))
-    outFile.write( "        Different queries per subject: mean=%.2f sd=%.2f min=%.2f q25=%.2f med=%.2f q75=%.2f max=%.2f\n" % ( iStatSbj.mean(), iStatSbj.sd(), iStatSbj.min, iStatSbj.quantile(0.25), iStatSbj.median(), iStatSbj.quantile(0.75), iStatSbj.max ) )
-    outFile.write( "    # Number of different queries that match: %s (Sp*=%.2f%%)\n" % ( len(Qry2Sbj_all.keys()), 100 * len(Qry2Sbj_all.keys()) / float(nbQry) ) )
-    outFile.write( "        Among them, number of different queries having exactly one match: %s (%.2f%%)\n" % ( len(UniqQry_all), 100 * len(UniqQry_all) / float(len(Qry2Sbj_all.keys())) ) )
-    outFile.write( "        Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_all)) )
-    outFile.write( "        Different subjects per query: mean=%.2f sd=%.2f min=%.2f q25=%.2f med=%.2f q75=%.2f max=%.2f\n" % ( iStatQry.mean(), iStatQry.sd(), iStatQry.min, iStatQry.quantile(0.25), iStatQry.median(), iStatQry.quantile(0.75), iStatQry.max ) )
-
-    outFile.write( "\nNumber of matches with L >= %i%% for subject & query: %i\n" % ( thresholdCoverage, len(ListMatches_sup_sbjqry) ) )
-    outFile.write( "    # Number of different subjects in the 'CC' case: %s (%.2f%%)\n" % ( len(Sbj2Qry_sup_sbjqry), 100 *  len(Sbj2Qry_sup_sbjqry) / float(nbSbj) ) )
-    outFile.write( "        Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_sbjqry)))
-    outFile.write( "        Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_sbjqry)))
-    outFile.write( "    # Number of different queries in the 'CC' case: %s (%.2f%%)\n" % ( len(Qry2Sbj_sup_sbjqry), 100 * len(Qry2Sbj_sup_sbjqry) / float(nbQry) ) )
-    outFile.write( "        Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_sbjqry)))
-    outFile.write( "        Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_sbjqry)))
-
-    outFile.write( "\nNumber of matches with L >= %i%% for subject and L < %i%% for query: %i\n" % ( thresholdCoverage, thresholdCoverage, len(ListMatches_sup_sbj) ) )
-    outFile.write( "    Number of different subjects in that case: %s\n" % (len(Sbj2Qry_sup_sbj)))
-    outFile.write( "        Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_sbj)))
-    outFile.write( "        Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_sbj)))
-    outFile.write( "    Number of different queries in that case: %s\n" % (len(Qry2Sbj_sup_sbj)))
-    outFile.write( "        Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_sbj)))
-    outFile.write( "        Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_sbj)))
-
-    outFile.write( "\nNumber of matches with L < %i%% for subject and L >= %i%% for query: %i\n" % ( thresholdCoverage, thresholdCoverage, len(ListMatches_sup_qry) ) )
-    outFile.write( "    Number of different subjects in that case: %s\n" % (len(Sbj2Qry_sup_qry)))
-    outFile.write( "        Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_qry)))
-    outFile.write( "        Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_qry)))
-    outFile.write( "    Number of different queries in that case: %s\n" % (len(Qry2Sbj_sup_qry)))
-    outFile.write( "        Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_qry)))
-    outFile.write( "        Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_qry)))
-
-    outFile.write( "\nNumber of matches with L < %i%% for subject & query: %i\n" % ( thresholdCoverage, len(ListMatches_inf_sbjqry) ) )
-    outFile.write( "    Number of different subjects in that case: %s\n" % (len(Sbj2Qry_inf_sbjqry)))
-    outFile.write( "        Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_inf_sbjqry)))
-    outFile.write( "        Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_inf_sbjqry)))
-    outFile.write( "    Number of different queries in that case: %s\n" % (len(Qry2Sbj_inf_sbjqry)))
-    outFile.write( "        Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_inf_sbjqry)))
-    outFile.write( "        Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_inf_sbjqry)))
-    
-    
-    # For the elements already counted in the matches with L >= 95% for subject & query, remove them from the other dictionnaries
-    rmv_Sbj2Qry = remove( Sbj2Qry_all, Sbj2Qry_sup_sbjqry, Sbj2Qry_sup_sbj, Sbj2Qry_sup_qry, Sbj2Qry_inf_sbjqry )
-    rmv_Qry2Sbj = remove( Qry2Sbj_all, Qry2Sbj_sup_sbjqry, Qry2Sbj_sup_sbj, Qry2Sbj_sup_qry, Qry2Sbj_inf_sbjqry )
-    
-    outFile.write("\n\nAfter removal of the subjects/queries already counted in the matches with L >= %i%% for them:\n" % ( thresholdCoverage ) )
-    
-    outFile.write( "\nMatches with L >= %i%% for subject and L < %i%% for query:\n" % ( thresholdCoverage, thresholdCoverage ) )
-    outFile.write( "    # Number of different subjects in the 'CI' case: %s (%.2f%%)\n" % ( len(rmv_Sbj2Qry[0]), 100*len(rmv_Sbj2Qry[0])/float(nbSbj) ) )
-    outFile.write( "    # Number of different queries in the 'CI' case: %s (%.2f%%)\n" % ( len(rmv_Qry2Sbj[0]), 100*len(rmv_Qry2Sbj[0])/float(nbQry) ) )
-    
-    outFile.write( "\nMatches with L < %i%% for subject and L >= %i%% for query:\n" % ( thresholdCoverage, thresholdCoverage ) )
-    outFile.write( "    # Number of different subjects in the 'IC' case: %s (%.2f%%)\n" % (len(rmv_Sbj2Qry[1]), 100*len(rmv_Sbj2Qry[1])/float(nbSbj) ) )
-    outFile.write( "    # Number of different queries in the 'IC' case: %s (%.2f%%)\n" % (len(rmv_Qry2Sbj[1]), 100*len(rmv_Qry2Sbj[1])/float(nbQry) ) )
-    
-    outFile.write( "\nMatches with L < %i%% for subject & query:\n" % ( thresholdCoverage ) )
-    outFile.write( "    # Number of different subjects in the 'II' case: %s (%.2f%%)\n" % (len(rmv_Sbj2Qry[2]), 100*len(rmv_Sbj2Qry[2])/float(nbSbj) ) )
-    outFile.write( "    # Number of different queries in the 'II' case: %s (%.2f%%)\n" % (len(rmv_Qry2Sbj[2]), 100*len(rmv_Qry2Sbj[2])/float(nbQry) ) )
-    
-    outFile.write("\n==========================================================================\n")
-    
-    write_output( outFile, 'CC', Sbj2Qry_sup_sbjqry, dSbj2Cat, Qry2Sbj_sup_sbjqry, dQry2Cat )
-    
-    outFile.write("\n==========================================================================\n")
-    
-    write_output( outFile, 'CI', rmv_Sbj2Qry[0], dSbj2Cat, rmv_Qry2Sbj[0], dQry2Cat )
-    
-    outFile.write("\n==========================================================================\n")
-    
-    write_output( outFile, 'IC', rmv_Sbj2Qry[1], dSbj2Cat, rmv_Qry2Sbj[1], dQry2Cat )
-    
-    outFile.write("\n==========================================================================\n")
-    
-    write_output( outFile, 'II', rmv_Sbj2Qry[2], dSbj2Cat, rmv_Qry2Sbj[2], dQry2Cat )
-    
-    outFile.write("\n==========================================================================\n")
-    
-    outFile.close()
-    
-    writeSubjectCategory( dSbj2Cat )
-    writeQueryCategory( dQry2Cat )
-    
-    if verbose > 0:
-        print "END %s" % (sys.argv[0].split("/")[-1])
-        sys.stdout.flush()
-        
-    return 0
-
-#-----------------------------------------------------------------------------------------------------
-
-if __name__ == "__main__":
-    main()

--- a/commons/tools/tests/MockFastaForReplaceGreaterThanSymbolInFastaHeader.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-class MockFastaForReplaceGreaterThanSymbolInFastaHeader(object):
-	def write(self, inFileName):
-		f = open(inFileName, 'w')
-		f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1-->2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n")
-		f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n")
-		f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n")
-		f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n")
-		f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n")
-		f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n")
-		f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n")
-		f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n")
-		f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n")
-		f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n")
-		f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n")
-		f.write(">sp|Q694C1|ABC3G_GORGO DNA dC->dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n")
-		f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n")
-		f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n")
-		f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n")
-		f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n")
-		f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n")
-		f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n")
-		f.write("WDGLEEHSQALSGRLQAILQNQGN\n")
-		f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n")
-		f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n")
-		f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n")
-		f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n")
-		f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n")
-		f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n")
-		f.close()
-		
-class MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan(object):
-	def write(self, inFileName):
-		f = open(inFileName, 'w')
-		f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1 to 2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n")
-		f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n")
-		f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n")
-		f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n")
-		f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n")
-		f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n")
-		f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n")
-		f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n")
-		f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n")
-		f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n")
-		f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n")
-		f.write(">sp|Q694C1|ABC3G_GORGO DNA dC to dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n")
-		f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n")
-		f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n")
-		f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n")
-		f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n")
-		f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n")
-		f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n")
-		f.write("WDGLEEHSQALSGRLQAILQNQGN\n")
-		f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n")
-		f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n")
-		f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n")
-		f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n")
-		f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n")
-		f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n")
-		f.close()

--- a/commons/tools/tests/Test_AlignTEOnGenomeAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,304 +0,0 @@
-from commons.core.seq.Bioseq import Bioseq
-from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.coord.Path import Path
-import os
-import unittest
-from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation
-
-class Test_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase):
-
-    def test_alignBioseqWithNWalign(self):
-        iBioseq1 = Bioseq("dmel_chr4", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAGTAGAAGAAA")
-        iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTTCTTCTACCTATTACATACTTTTCAACAAATCTAGCATACCCTTTTACTCTACGAGTA")
-        iAlignedBioseq1 = Bioseq("dmel_chr4 Score=58 Identity=0.7", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTT-TAGA-AGTACGTTACTAGTAGAAGAAA----------------------------")
-        iAlignedBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat Score=58 Identity=0.7", "----------------------------TTTCTTCTACCTATTACAT-ACTTTTC-AACAAATCTAGCATACCCTTTTACTCTACGAGTA")
-        expiAlignedBioseqDB = AlignedBioseqDB()
-        expiAlignedBioseqDB.add(iAlignedBioseq1)
-        expiAlignedBioseqDB.add(iAlignedBioseq2)
-        
-        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation()
-        obsiAlignedBioseqDB = iATEOGATA.alignBioseqWithNWalign(iBioseq1, iBioseq2)
-        
-        self.assertEquals(expiAlignedBioseqDB, obsiAlignedBioseqDB)
-    
-    def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_one_path(self):
-        iBioseq1 = Bioseq("dmel_chr4", "TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA")
-        iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC")
-        iPath = Path()
-        iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67))
-
-        seqTable1 = "seqTable1_seq"
-        seqTable2 = "seqTable2_seq"
-        pathTable = "pathTable_path"
-        
-        iDb = DbFactory.createInstance()
-        iDb.createTable(seqTable1, "seq", overwrite = True)
-        iDb.createTable(seqTable2, "seq", overwrite = True)
-        iDb.createTable(pathTable, "path", overwrite = True)
-        
-        iTSA1 = TableSeqAdaptator(iDb, seqTable1)
-        iTSA2 = TableSeqAdaptator(iDb, seqTable2)
-        iTPA = TablePathAdaptator(iDb, pathTable)
-        iTSA1.insert(iBioseq1)
-        iTSA2.insert(iBioseq2)
-        iTPA.insert(iPath)
-        
-        expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),)
-        
-        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTable, seqTable1, seqTable2)
-        iATEOGATA.setMergeSamePathId(True)
-        iATEOGATA.setDbInstance(iDb)
-        iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable()
-        
-        #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator
-        sqlCmd = "SELECT * FROM %s_align" % pathTable
-        iDb.execute(sqlCmd)
-        obsTTuples = iDb.fetchall()
-        
-        iDb.dropTable(seqTable1)
-        iDb.dropTable(seqTable2)
-        iDb.dropTable(pathTable)
-        iDb.dropTable("%s_align" % pathTable)
-        iDb.close()
-        
-        self.assertEquals(expTTuples, obsTTuples)
-        
-    def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_n_paths(self):
-        queryTableName = "query_seq"
-        subjectTableName = "subject_seq"
-        pathTableName = "table_path"
-        
-        iDb = DbFactory.createInstance()
-        queryFileName = "dummyDmelChr4.fa"
-        self._writeDummyDmelChr4(queryFileName)
-        iDb.createTable(queryTableName, "seq", queryFileName, True)
-        os.remove(queryFileName)
-        iDb.createTable(subjectTableName, "seq", overwrite = True)
-        iDb.createTable(pathTableName, "path", overwrite = True)
-        
-        iTSA = TableSeqAdaptator(iDb, subjectTableName)
-        iTPA = TablePathAdaptator(iDb, pathTableName)
-        iBioseq1 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC")
-        iBioseq2 = Bioseq("DmelChr4-B-R4-Map5_NoCat", "CCAAAATTGCCCTCTTTCCGCTCGCTCACGCTGAGAGCATAAGAAATCTAAAAATAGAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGTGTGCGTGTTGTGCTAGAAGACTATTTTCGGGCCGAAATCAATTCTGATCGAAAAAACGAATTTACATTGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAATAAAATAATTTTTAAAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTAAAATTTGTTTGTTAAAATCGCCGATCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTTGAAACACTTTTAATGTTAAAAATGACTTAATAAATATACTAAATAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAAAATATGATAACTGTTTATTGCAAAAGTCATATCAAAGACACTAGAATTATTCTAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAAAGTCAAAGAACTTCTAAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACAGTTGTCTGCTATCACTTTATGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTCCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCGAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGGTA")
-        iBioseq3 = Bioseq("DmelChr4-B-G9-Map3_NoCat", "ACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAATATGATAACTGTTTATTGCAAAAGTAATATCAAAGACACTAGAATAATTCTAATGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCGCACTTCGTGC")
-        iTSA.insert(iBioseq1)
-        iTSA.insert(iBioseq2)
-        iTSA.insert(iBioseq3)
-        iPath = Path()
-        iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67))
-        iTPA.insert(iPath)
-        iPath.setFromTuple((28, "dmel_chr4", 280, 1380, "DmelChr4-B-G9-Map3_NoCat", 3, 1100, 0, 7456, 94.400000))#28 => seems to be a join from "long join"
-        iTPA.insert(iPath)
-        iPath.setFromTuple((28, "dmel_chr4", 8971, 9459, "DmelChr4-B-G9-Map3_NoCat", 1102, 1590, 0, 758, 96.707800))
-        iTPA.insert(iPath)
-        iPath.setFromTuple((30, "dmel_chr4", 9815, 9826, "DmelChr4-B-G9-Map3_NoCat", 574, 563, 0, 4, 78.162700))#30 => seems to be a join from "matcher"
-        iTPA.insert(iPath)
-        iPath.setFromTuple((30, "dmel_chr4", 9957, 10047, "DmelChr4-B-G9-Map3_NoCat", 429, 337, 0, 33, 78.162700))
-        iTPA.insert(iPath)
-        iPath.setFromTuple((30, "dmel_chr4", 10094, 10127, "DmelChr4-B-G9-Map3_NoCat", 290, 256, 0, 13, 78.162700))
-        iTPA.insert(iPath)
-        
-        expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),\
-                      (28, "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGCGCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAAT-----------TT-------GTT---------------ATGTTTAATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAA-CACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAATTAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA--AATATGATA---ACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCAAA-CAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGAACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACACATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTACGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATAAGGCAATGATTGTTG----CTTGTGTCCGTCCGCACTTCGTGC", "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCT------CT--CATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAA-----------------TATGATAACT---GT--TT------ATTGCA-AAAGTAATATCAAAGACACTAGAATAATTCTAATG------CTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCG----CACTTCGTGC", 13732, 96.1763),\
-                      (30, "------------------------------------ACATTTACAT-TTTTTGAATTTGTGGG-------CGTGGCA-GAACGGGCAATAT-GTATGCATA---ATATGTATGCATAATCTCTACCTTCTTGCTTTTATAGTTCCTGAGACCTCGACGTTCATACGGACAGACGAAATATGCGAAA", "ACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGC--TACCGTTTACACATTTATATTTATGTTTAAT-TCTAATTTGTCAATATCAAAGAC-------------------------------------------", 158, 64.835200000000004))
-
-        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName)
-        iATEOGATA.setMergeSamePathId(True)
-        iATEOGATA.setDbInstance(iDb)
-        iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable()
-        
-        #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator
-        sqlCmd = "SELECT * FROM %s_align" % pathTableName
-        iDb.execute(sqlCmd)
-        obsTTuples = iDb.fetchall()
-        
-        iDb.dropTable(queryTableName)
-        iDb.dropTable(subjectTableName)
-        iDb.dropTable(pathTableName)
-        iDb.dropTable("%s_align" % pathTableName)
-        iDb.close()
-        
-        self.assertEquals(expTTuples, obsTTuples)
-        
-    def _writeDummyDmelChr4(self, fileName):
-        with open(fileName, "w") as f:
-            f.write(">dmel_chr4\n")
-            f.write("TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA\n")
-            f.write("TGTTGGTATTAATGGTCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAG\n")
-            f.write("AATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAG\n")
-            f.write("AAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTAC\n")
-            f.write("TTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGCAAAGACACTAGAATAACAAG\n")
-            f.write("ATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAA\n")
-            f.write("ATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCT\n")
-            f.write("TGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAA\n")
-            f.write("GACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTA\n")
-            f.write("GGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGC\n")
-            f.write("GCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAATTTGTTATGTTTA\n")
-            f.write("ATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTA\n")
-            f.write("AACACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAAT\n")
-            f.write("TAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA\n")
-            f.write("AATATGATAACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGT\n")
-            f.write("GCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAAT\n")
-            f.write("ACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATAT\n")
-            f.write("GTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCA\n")
-            f.write("AACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGA\n")
-            f.write("ACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACA\n")
-            f.write("CATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTC\n")
-            f.write("GCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCC\n")
-            f.write("AAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTG\n")
-            f.write("GTAAAATGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAAAAGAAAGCGTTTTCGA\n")
-            f.write("CCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGC\n")
-            f.write("CATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCA\n")
-            f.write("CAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTG\n")
-            f.write("TCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCA\n")
-            f.write("TCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGT\n")
-            f.write("TCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGC\n")
-            f.write("TTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTA\n")
-            f.write("TAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTA\n")
-            f.write("CGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTAT\n")
-            f.write("TGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATT\n")
-            f.write("TTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCT\n")
-            f.write("TTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTA\n")
-            f.write("TTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTT\n")
-            f.write("GGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTC\n")
-            f.write("CTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGT\n")
-            f.write("TTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTA\n")
-            f.write("ACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACC\n")
-            f.write("GTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCA\n")
-            f.write("TAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAA\n")
-            f.write("ACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAA\n")
-            f.write("AAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCA\n")
-            f.write("TCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATA\n")
-            f.write("TCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAA\n")
-            f.write("AATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATA\n")
-            f.write("ACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCA\n")
-            f.write("TCGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACT\n")
-            f.write("CTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATT\n")
-            f.write("AATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGT\n")
-            f.write("ATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTAT\n")
-            f.write("TCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTA\n")
-            f.write("ATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGAT\n")
-            f.write("AGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCC\n")
-            f.write("GTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTA\n")
-            f.write("TTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGA\n")
-            f.write("TCGACTCGCATATTGATGCTGATCAAGAATATTTATATTTTACATGATCGGAAACGCTTC\n")
-            f.write("ATTGCTCTACGAGTAATGGGTACAATAATTTAAAACAAACATATTAAAAGTATAGCAAAA\n")
-            f.write("CCCTATCTGAAGGACTAAAATTTTATCGCATTTTAAAATTTGTTGCATTAAAATCTTTGA\n")
-            f.write("TAACCTTTCGTTGAATTAGGTGCTTCGACTTTTTTTACCCTAAGAACAATTTCGATTTGG\n")
-            f.write("CATACATTGAAAACGTAGAAACTCAACCCTGCATTCATTCATAGAACTTATAAAGAGCTA\n")
-            f.write("CATCTTCGAAAATAAAAAAAAGGTTTGTTTTTAAGACTTAATGCGTACAATGTCGCTTTC\n")
-            f.write("GACATTAGGGTATTGCTAGAATTAATATTCGCTTTGTTGTTTACTTTTCCAAACAAACAT\n")
-            f.write("AATGGGTAAACCAAAAAAATGGGAAACGTCAGTATTAAGTGCTATCGAAAACGTTTAGAA\n")
-            f.write("TATGGAGAATCTAGTTGTTATTACCAAAACGCATAAATACTAAGCATATACTAAAACAAA\n")
-            f.write("ATAGAAAAAGATAATGTTTATTTTAGACTCACCTTAGCAAACAGCAACTTATTCGACGGC\n")
-            f.write("GAATCTTTTCCAAGTCTGTGCTCTGATGTTAAACAAGCGTCCATAAATGTTTGTGCAATG\n")
-            f.write("ACACTTAAACAGGAATCAACGCTGTATGTTTTATTTACATCAAATATAAAATCCGGATTT\n")
-            f.write("TTTATAAAATTAACCCAGAATCGAAGGGGCAAACAATTTGACTTCCAAGCGTGCACAATA\n")
-            f.write("TCAGTATCAGCAATATCATGGCGTCGCGCAGCTTCATCAAGTAAGTCAAAGAGCCATTTA\n")
-            f.write("ACGGCAGGTGGCAACTCCTCATTAACAGTTAAAATAATTGAGAAAAAATCATCAACAAAT\n")
-            f.write("TTTTGTATAGTTCCTTTTGTGGCCAGAAGACGCGTAAGGTAAACTTCTGGTATTGTTTTG\n")
-            f.write("TTCACCCTGTCATTACAATTATTAACGACATGCGATTGAAATGCTGGTGATCCTCCGGAT\n")
-            f.write("AACACGGAATTTTTAATGTTCATATAATGATCAGGTATATTGGGCTTAACAAGATGGTAA\n")
-            f.write("ACCCGGGGCTGCTGCAAACCTGATTCGATATCATTATTAATTATAATATGACTTTGCGAA\n")
-            f.write("TTGTTTATAAAATAAACTGCAAAAAGGCAAAACAATTAATTAAAAAATTTTTAGATATTG\n")
-            f.write("GGCTTAGTACTTACAATTGTGGTATGGTGCCGAATTTTGGTTTTTACTGTATGGTATATG\n")
-            f.write("ATAATTATCATTTTGACGTGCAATTAGTGACATTACTGCAGATTCTTTGACTCCATAATG\n")
-            f.write("AGCTAATGTGTTAAGGCGCTTCCATCCGTTAACGGTTTTGGTTGTCAAGTCTTCATCTTG\n")
-            f.write("TAATGTAAGATGACCTCCTCGGCCGTGCCTCCATTCTAAGTCTACTTCGTTTACAGATGG\n")
-            f.write("CCTCATAGAGAAAGGAGTGTTTTTAAAAATTGCGTCGAGGATTTTAAGCTTAACTTGAGA\n")
-            f.write("AATGGTATCCCAATCGTTAACGCGACATTGGACTTTTTCATCAAGATCATCTTGTAAAAT\n")
-            f.write("ATGCTATATTACAACAGAATGGGTAACTTGTTCATGCAGAAGACGTTCTTCTGAAAGGGA\n")
-            f.write("GTAACGGGCATCGTTGGTTATTGCGTCCACTAAACCCTTTTCAATTTGATGCTTTATTGC\n")
-            f.write("TTTGAAGAGCAAAAATAAATTTGATCCGGCGTACTCTTTCAGGTAATCGTACATACAAAT\n")
-            f.write("TGCTAGGTAGTTGGTCAACATTTTTTCAACAACGCTTTCAGTACGCCTTAGCATCAGCTG\n")
-            f.write("AGGATGTTTGCTGGCAAGTGATTTATCTATCAAACGTAATAAAAGGGACTTCAAAATTTC\n")
-            f.write("CGTGGCATATTCCATCTTGTTCATTAAAACAACCATTATTAATGAGGCAACGTTAACTCG\n")
-            f.write("GTCTCTAATAGAAAATGATGAACGTTGAGCTTCTAATGTTTCTATGAACATTAATAAAAA\n")
-            f.write("ATATTTATTGCCAATCAGTTGTTCAAATTGTACCATAGCTGCGTCATAGTTAGTCTGTGG\n")
-            f.write("GCTACCTTCACGAAATTTTGGAGAATTTAAAATAGGATGATCTGATACACCAGGGAAAAA\n")
-            f.write("CACCTTCATAATATAGTTGACGTGATCTAAAGTTGGTATGCCTGTGCTCTCCAAATCTGC\n")
-            f.write("TGTTAGGTCGGTCATGTCCGTTTGGAGCTCAGCGAATGCCTGTTTACACTCAGAACGTAC\n")
-            f.write("GTTGCTTTCTAATGTAATCATCTGTATCTGAATACGTTTATACTCGCGTTCTGCTTGTGT\n")
-            f.write("TGATTTCCTTCTGAATATTATAAGTACAATTACAAAAACAACGACCAGAAGTGCTACCGT\n")
-            f.write("TAATATGCCGACTAACAAGGCATGTGAGAAAACATAGGGTTTATTTAAATCATACTTAAG\n")
-            f.write("ATATCCTATTACAAAACGAAGATTTCGACCTACTTTAACGACAACAAGAGGTAAATCAGT\n")
-            f.write("TGATTGATCCACACCATTTTCATCAGTTGGAAGTGGTTGTTGCTCCGGCGGAATGCATAA\n")
-            f.write("AAGTTGGTTAAGTGCCAGGCTGGTAATATTGCATTGGGAAGTTCCAATAGTTACATTTAC\n")
-            f.write("ATCGTACTCATCAGCTGCCAAGTTTAATAGCTCGCCTTCTATGACCAAGCTGTCACCCTT\n")
-            f.write("GTAGAGTTTAACGCCGTCGTTGGGAAATGGCAAATATTTTGGGTCTGCTAAATAGACAAT\n")
-            f.write("AGTGCTCCTTATGTCATGAAAATATTTATTCAAGTTTCGAACTAGTTGTACATTGTCCAT\n")
-            f.write("TACAAAACTTAGTTGTAAGTTAAATTGAGTTTCATGAACCTTAACGAATGTGGTGACGTC\n")
-            f.write("CATATTATTGTTAACAAAATAGTTGGCTGAAGATCCTGCATTTGTGTATAAGCGAAAAGT\n")
-            f.write("GTCTCCAAAGTCGGCTCGCCGCTTTTTTCTATCATATTCATTTTTATACCTGGTTTCAGT\n")
-            f.write("TTGAAACGAAGAATTTTGTAAGTGCAATTCAGTATCCATCTTTCTGTTCGTCTTTTTAAA\n")
-            f.write("AGTCTCAAATTTTTAATTTACCGGAGGAGATGGACATTCCATTTGATTAGAGTTGATCAC\n")
-            f.write("CACACAAGATGTTTTATTTACTCTTTCATTGTCATAAAACACTTCTAGTTCAGGTTTTTG\n")
-            f.write("GTTTTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGTTCAGTGTTTGTT\n")
-            f.write("GGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATT\n")
-            f.write("TCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAAC\n")
-            f.write("TTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGT\n")
-            f.write("TAGTCTTAATAATACCCGTACTTGTAGAGTAAAAGGGTATGCTAGATTTGTAGAAAAGTA\n")
-            f.write("TGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGG\n")
-            f.write("ATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAG\n")
-            f.write("AGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCG\n")
-            f.write("ATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACT\n")
-            f.write("TTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAAT\n")
-            f.write("ATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGG\n")
-            f.write("GAAACTCAACCATAACATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAA\n")
-            f.write("GAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTAT\n")
-            f.write("ATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCA\n")
-            f.write("ACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAAT\n")
-            f.write("GGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGT\n")
-            f.write("TATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTA\n")
-            f.write("AGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGT\n")
-            f.write("CAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCC\n")
-            f.write("TTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAG\n")
-            f.write("TCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGG\n")
-            f.write("CTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAG\n")
-            f.write("ATATAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATAT\n")
-            f.write("TTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTCTCTTA\n")
-            f.write("CATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAA\n")
-            f.write("ATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTAAAAAATCATATTG\n")
-            f.write("ATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCG\n")
-            f.write("TGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACA\n")
-            f.write("AAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGA\n")
-            f.write("TCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCT\n")
-            f.write("TCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGT\n")
-            f.write("GGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCC\n")
-            f.write("TGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACT\n")
-            f.write("TATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAAT\n")
-            f.write("ATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATT\n")
-            f.write("TGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATA\n")
-            f.write("GGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACA\n")
-            f.write("GAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATT\n")
-            f.write("TTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTA\n")
-            f.write("TATTTTCATACGGACGGACATGGCCAGATCAAAGACACTAGAATAACAAGATGCGTAACG\n")
-            f.write("CCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCT\n")
-            f.write("CTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTA\n")
-            f.write("CGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATT\n")
-            f.write("TGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGAT\n")
-            f.write("CAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAA\n")
-            f.write("AATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATG\n")
-            f.write("ACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATA\n")
-            f.write("AGGCAATGATTGTTGCTTGTGTCCGTCCGCACTTCGTGCCTCAAGATATGACCAAAACAA\n")
-            f.write("AGACACTAGAATAATTCTAGTGTCTTTGATGTGACTTTTGCAATAAACAGTTTTCATATT\n")
-            f.write("TTTATTTATTTTACAAATTTTTATTTTCTACTTCGTATTATTTTTATGAAATATTTATTT\n")
-            f.write("CTCGATGTAATGTATTCCTTTTGTTATAAGTAGTTATAATAATTTATATTTTACTTCCTT\n")
-            f.write("CAATATCACAAAATAAATTTCAAGTATGGCTTTATATTAGAATAATTGTCATTAAATTAT\n")
-            f.write("TCAGCTTGGGACGTGGGAAAAATTAGAGTAGACATGTCTAGTAGACATCGATTCTTAGGT\n")
-            f.write("GCTTCTGACCGCACGTCGTGCCTCAAGAAATCAATTTCGCATATTTATACCCATTATTTC\n")
-            f.write("TAGAGTAAAAGGGTATACTACATTCGTTGAAAAGTATGTAACAGGCAGAAGAAAGCGTTT\n")
-            f.write("CCGACTATATAATGTATAAAGATCAGGATCAACAGCCGAGTCGATCTGGCCATGTCCGTC\n")
-            f.write("TGTCCGTATGAACGTCGAGGTCTCAGGAACTATAAAAGCAAGAAGGTAGAGATTATGCAT\n")
-            f.write("ACATATTATGCATACATATTGCCCGTTGACCCATGTTGTCACGCCCACTCTAACGTCCAC\n")
-            f.write("AAACCGCACAAAACTGCCACGCCCACAAATTCAAAAAATGTAAATGTAATTGACCAAATT\n")
-            f.write("TAACAAAACTCTAAAAATGTAACTTTGTTTCTTAGATCAAAATTTAGACCAGAAAATCGT\n")
-            f.write("CTTCATCTTCTAATGTTTTTACTCACACAAGAAAGCAAATTCTATTTTTAGATTTTAAAG\n")
-            f.write("TACTCCATTTTACGCGAGCGGAGAGAGAGAGCAATTTTGGCCGTCACCAAAAAAGTGTCT\n")
-
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_CalcCoordCumulLength.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-import unittest
-import os
-import time
-from commons.tools.CalcCoordCumulLength import CalcCoordCumulLength
-from commons.core.utils.FileUtils import FileUtils
-from pyRepet.util.Stat import Stat
-
-
-class Test_CalcCoordCumulLength( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = CalcCoordCumulLength()
-        self._uniqId = time.strftime("%Y%m%d%H%M%S")
-        
-        
-    def tearDown( self ):
-        self._i = None
-        self._uniqId = None
-        
-        
-    def test_mergeCoordinates( self ):
-        inFileName = "dummyInFile_%s"  %( self._uniqId )
-        inF = open( inFileName, "w" )
-        inF.write( "TE1\tchr1\t101\t200\n" )
-        inF.write( "TE2\tchr1\t401\t600\n" )
-        inF.write( "TE2\tchr1\t451\t500\n" )
-        inF.close()
-        expFileName = "dummyExpFile_%s"  %( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write( "TE1\tchr1\t101\t200\n" )
-        expF.write( "TE2\tchr1\t401\t600\n" )
-        expF.close()
-        self._i.setInputFileName( inFileName )
-        obsFileName = self._i.mergeCoordinates()
-        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ inFileName, expFileName, obsFileName ]: os.remove( f )
-        
-        
-    def test_getStatsPerChr( self ):
-        inFileName = "dummyInFile_%s"  %( self._uniqId )
-        inF = open( inFileName, "w" )
-        inF.write( "TE1\tchr1\t101\t200\n" )
-        inF.write( "TE2\tchr1\t401\t600\n" )
-        inF.write( "TE1\tchr2\t1301\t1600\n" )
-        inF.close()
-        dExp = { "chr1": Stat(), "chr2": Stat() }
-        dExp["chr1"].add( 200-101+1 )
-        dExp["chr1"].add( 600-401+1 )
-        dExp["chr2"].add( 1600-1301+1 )
-        dObs = self._i.getStatsPerChr( inFileName )
-        self.assertEqual( dObs, dExp )
-        
-        
-    def test_zRunAsScript( self ):
-        cDir = os.getcwd()
-        inFileName = "dummyInFile_%s"  %( self._uniqId )
-        inF = open( inFileName, "w" )
-        inF.write( "TE1\tchr1\t101\t200\n" )
-        inF.write( "TE2\tchr1\t401\t600\n" )
-        inF.write( "TE2\tchr1\t451\t500\n" )
-        inF.close()
-        outFileName = "dummyOutFile_%s"  %( self._uniqId )
-        cmd = "CalcCoordCumulLength.py"
-        cmd += " -i %s" % ( inFileName )
-        cmd += " -o %s" % ( outFileName )
-        cmd += " -v 0"
-        log = os.system( cmd )
-        self.assertTrue( log == 0 )
-        
-        for f in [ inFileName, outFileName ]: os.remove( f )
-        os.chdir( cDir )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_ChangeSequenceHeaders.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,428 +0,0 @@
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-import unittest
-import os
-import time
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
-
-
-class Test_ChangeSequenceHeaders( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = ChangeSequenceHeaders()
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-        
-        
-    def tearDown( self ):
-        self._i = None
-        self._uniqId = None
-        
-        
-    def test_script_no_input_file( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 1"
-        cmd += " -p TE"
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertFalse( exitStatus == 0 )
-        
-        os.chdir( cDir )
-        
-        
-    def test_shortenSequenceHeadersForFastaFile_fasta_script( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" )
-        inF.write( ">consensus524\nGTGCGGATGGAACAGT\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">TE1\nATGTACGATGACGATCAG\n" )
-        expF.write( ">TE2\nGTGCGGATGGAACAGT\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 1"
-        cmd += " -p TE"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-        
-    def test_retrieveInitialSequenceHeaders_fasta_script( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">seq2\nATGTACGATGACGATCAG\n" )
-        inF.write( ">seq1\nGTGCGGATGGAACAGT\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tconsensus524\t1\t18\n" )
-        linkF.write( "seq2\tDmelChr4-B-G387-MAP16\t1\t16\n" )
-        linkF.write( "seq3\treference2\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" )
-        expF.write( ">consensus524\nGTGCGGATGGAACAGT\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-    def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_Blastclust( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
-        inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" )
-        linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" )
-        linkF.write( "seq3\treference2\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">BlastclustCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" )
-        expF.write( ">BlastclustCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        whichCluster = "A"
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -w %s" % ( whichCluster )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-    def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_Blastclust( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
-        inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" )
-        linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" )
-        linkF.write( "seq3\treference2\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">DHX-incomp_Blc8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" )
-        expF.write( ">RLX-incomp_Blc1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        whichCluster = "B"
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -w %s" % ( whichCluster )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-    def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_MCL( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
-        inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" )
-        linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" )
-        linkF.write( "seq3\treference2\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">MCLCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" )
-        expF.write( ">MCLCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        whichCluster = "A"
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -w %s" % ( whichCluster )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-    def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_MCL( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFaFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
-        inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" )
-        linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" )
-        linkF.write( "seq3\treference2\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( ">DHX-incomp_MCL8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" )
-        expF.write( ">RLX-incomp_MCL1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        whichCluster = "B"
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f fasta"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -w %s" % ( whichCluster )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-    def test_retrieveInitialSequenceHeaders_newick_script( self ):
-        cDir = os.getcwd()
-        
-        inFile = "dummyInFile_%s" % ( self._uniqId )
-        inF = open( inFile, "w" )
-        inF.write( "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))" )
-        inF.close()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\t1360\n" )
-        linkF.write( "seq2\tDmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies\n" )
-        linkF.write( "seq3\tDmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies\n" )
-        linkF.write( "seq4\tDmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies\n" )
-        linkF.close()
-        
-        expFile = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFile, "w" )
-        expF.write( "(DmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies:0.012511,(DmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies:0.005340,DmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies:0.002201))" )
-        expF.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f newick"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-        
-    def test_retrieveInitialSequenceHeadersForAlignFile( self ):
-        cDir = os.getcwd()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" )
-        linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" )
-        linkF.close()
-        
-        inFile = "dummyAlignFile_%s" % ( self._uniqId )
-        inFileHandler = open( inFile, "w" )
-        inFileHandler.write( "seq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" )
-        inFileHandler.write( "seq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" )
-        inFileHandler.close()
-        
-        expFile = "dummyExpAlignFile_%s" % ( self._uniqId )
-        expFileHandler = open( expFile, "w" )
-        expFileHandler.write( "name=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" )
-        expFileHandler.write( "name=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" )
-        expFileHandler.close()
-        
-        obsFile = "dummyObsAlignFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f align"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-        
-    def test_retrieveInitialSequenceHeadersForPathFile( self ):
-        cDir = os.getcwd()
-        
-        linkFile = "dummyLinkFile_%s" % ( self._uniqId )
-        linkF = open( linkFile, "w" )
-        linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" )
-        linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" )
-        linkF.close()
-        
-        inFile = "dummyAlignFile_%s" % ( self._uniqId )
-        inFileHandler = open( inFile, "w" )
-        inFileHandler.write( "11\tseq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" )
-        inFileHandler.write( "2\tseq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" )
-        inFileHandler.close()
-        
-        expFile = "dummyExpAlignFile_%s" % ( self._uniqId )
-        expFileHandler = open( expFile, "w" )
-        expFileHandler.write( "11\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" )
-        expFileHandler.write( "2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" )
-        expFileHandler.close()
-        
-        obsFile = "dummyObsAlignFile_%s" % ( self._uniqId )
-        
-        cmd = "python ../ChangeSequenceHeaders.py"
-        cmd += " -i %s" % ( inFile )
-        cmd += " -f path"
-        cmd += " -s 2"
-        cmd += " -l %s" % ( linkFile )
-        cmd += " -o %s" % ( obsFile )
-        exitStatus = os.system( cmd )
-        
-        self.assertTrue( exitStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ inFile, linkFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-        
-if __name__ == "__main__":
-        unittest.main()

--- a/commons/tools/tests/Test_CorrelateTEageWithGCcontent.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_CorrelateTEageWithGCcontent( unittest.TestCase ):
-    
-    def test_zLaunchAsScript( self ):
-        cDir = os.getcwd()
-        
-        coordFile = "dummyPathFile"
-        coordFileHandler = open( coordFile, "w" )
-        coordFileHandler.write( "1\tchr1\t1\t5\tTE1\t1\t5\t0.0\t100\t98.7\n" )
-        coordFileHandler.write( "1\tchr1\t11\t20\tTE1\t6\t15\t0.0\t100\t98.7\n" )
-        coordFileHandler.write( "2\tchr1\t26\t30\tTE1\t1\t5\t0.0\t100\t96.7\n" )
-        coordFileHandler.write( "3\tchr2\t1\t10\tTE2\t1\t10\t0.0\t100\t98.7\n" )
-        coordFileHandler.close()
-        
-        genomeFile = "dummyGenomeFile"
-        genomeFileHandler = open( genomeFile, "w" )
-        genomeFileHandler.write( ">chr1\n" )
-        genomeFileHandler.write( "AGCTGTTTTTAGCAGACGCATTTTTGGAGGTTTT\n" )
-        genomeFileHandler.write( ">chr2\n" )
-        genomeFileHandler.write( "ATATATATGGTTTTTTTTTT\n" )
-        genomeFileHandler.close()
-        
-        refseqFile = "dummyRefseqFile"
-        refseqFileHandler = open( refseqFile, "w" )
-        refseqFileHandler.write( ">TE1\nAGCAGCGACGACGACGACGACTTTT\n" )
-        refseqFileHandler.write( ">TE2\nAGCAGCGACGACGACGACGACTTTT\n" )
-        refseqFileHandler.write( ">TE3\nAGCAGCGACGACGACGACGACTTTT\n" )
-        refseqFileHandler.close()
-        
-        expFile = "dummyExpFile"
-        expFileHandler = open( expFile, "w" )
-        expFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" )
-        expFileHandler.write( "1\tTE1\tchr1\t15\t98.70\t%.2f\t%.2f\n" % ( 100 * 9 / 15.0, 100 * 15 / 25.0 ) )
-        expFileHandler.write( "2\tTE1\tchr1\t5\t96.70\t%.2f\t%.2f\n" % ( 100 * 4 / 5.0, 100 * 5 / 25.0 ) )
-        expFileHandler.write( "3\tTE2\tchr2\t10\t98.70\t%.2f\t%.2f\n" % ( 100 * 2 / 10.0, 100 * 10 / 25.0 ) )
-        expFileHandler.close()
-        
-        obsFile = "dummyObsFile"
-        
-        cmd = "CorrelateTEageWithGCcontent.py"
-        cmd += " -i %s" % ( coordFile )
-        cmd += " -g %s" % ( genomeFile )
-        cmd += " -r %s" % ( refseqFile )
-        cmd += " -o %s" % ( obsFile )
-        cmd += " -v %i" % ( 0 )
-        returnStatus = os.system( cmd )
-        
-        self.assertTrue( returnStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ coordFile, genomeFile, refseqFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_AlignTEOnGenomeAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-from commons.core.sql.DbFactory import DbFactory
-from commons.core.utils.FileUtils import FileUtils
-import subprocess
-import os
-import unittest
-from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation
-
-class Test_F_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase):
-
-    def test_run_merge_same_paths(self):
-        pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
-        queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
-        subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
-        pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
-        queryTableName = "testDmelChr4_chr_seq"
-        subjectTableName = "testDmelChr4_refTEs_seq"
-        iDb = DbFactory.createInstance()
-        iDb.createTable(queryTableName, "seq", queryFileName, True)
-        iDb.createTable(subjectTableName, "seq", subjectFileName, True)
-        iDb.createTable(pathTableName, "path", pathFileName, True)
-        expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
-        
-        iATOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName, True)
-        iATOGATA.run()
-        obsFileName = "obs%s_merge.alignedSeq" % pathTableName
-        iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        iDb.dropTable(queryTableName)
-        iDb.dropTable(subjectTableName)
-        iDb.dropTable(pathTableName)
-        iDb.dropTable("%s_align" % pathTableName)
-        iDb.close()
-
-    def test_run_as_script_merge_same_paths(self):
-        pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
-        queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
-        subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
-        pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
-        queryTableName = "testDmelChr4_chr_seq"
-        subjectTableName = "testDmelChr4_refTEs_seq"
-        iDb = DbFactory.createInstance()
-        iDb.createTable(queryTableName, "seq", queryFileName, True)
-        iDb.createTable(subjectTableName, "seq", subjectFileName, True)
-        iDb.createTable(pathTableName, "path", pathFileName, True)
-        expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
-        
-        cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s -m " % (pathTableName, queryTableName, subjectTableName)
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        obsFileName = "obs%s_merge.alignedSeq" % pathTableName
-        iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        iDb.dropTable(queryTableName)
-        iDb.dropTable(subjectTableName)
-        iDb.dropTable(pathTableName)
-        iDb.dropTable("%s_align" % pathTableName)
-        iDb.close()
-
-    def test_run_as_script_without_merge(self):
-        pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
-        queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
-        subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
-        pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
-        queryTableName = "testDmelChr4_chr_seq"
-        subjectTableName = "testDmelChr4_refTEs_seq"
-        iDb = DbFactory.createInstance()
-        iDb.createTable(queryTableName, "seq", queryFileName, True)
-        iDb.createTable(subjectTableName, "seq", subjectFileName, True)
-        iDb.createTable(pathTableName, "path", pathFileName, True)
-        expFileName = "%s/Tools/exp%s.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
-        
-        cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName)
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        obsFileName = "obs%s.alignedSeq" % pathTableName
-        iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(obsFileName)
-        iDb.dropTable(queryTableName)
-        iDb.dropTable(subjectTableName)
-        iDb.dropTable(pathTableName)
-        iDb.dropTable("%s_align" % pathTableName)
-        iDb.close()
-        
-#    def test_run_as_script_merge_same_paths_old(self):
-#        pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
-#        queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
-#        subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
-#        pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
-#        queryTableName = "testDmelChr4_chr_seq"
-#        subjectTableName = "testDmelChr4_refTEs_seq"
-#        iDb = DbFactory.createInstance()
-#        iDb.createTable(queryTableName, "seq", queryFileName, True)
-#        iDb.createTable(subjectTableName, "seq", subjectFileName, True)
-#        iDb.createTable(pathTableName, "path", pathFileName, True)
-#        expFileName = "%s/Tools/exp%s_merge_old.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
-#        
-#        cmd = "srptAlignPath.py -m %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName)
-#        process = subprocess.Popen(cmd, shell = True)
-#        process.communicate()
-#        obsFileName = "obs%s.alignedSeq" % pathTableName
-#        iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
-#        
-#        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-#        
-#        os.remove(obsFileName)
-#        iDb.dropTable(queryTableName)
-#        iDb.dropTable(subjectTableName)
-#        iDb.dropTable(pathTableName)
-#        iDb.dropTable("%s_align" % pathTableName)
-#        iDb.close()
-#        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_CheckMysqlConnect.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-import unittest
-import os
-import socket
-
-class Test_F_CheckMysqlConnect(unittest.TestCase):
-    
-    HOST_NAME = "compute-2-46.local"
-    
-    def setUp(self):
-        self._host = socket.gethostname()
-        self._cmd = ""
-
-    def tearDown(self):
-        os.remove("testOutputCheckMysqlConnect.txt")
-    
-    def test_CheckMysqlConnect_as_script_True(self):
-        if self.HOST_NAME in self._host:
-            self._cmd = "CheckMysqlConnect.py -p /share/apps/bin/python > testOutputCheckMysqlConnect.txt"
-        else:
-            self._cmd = "CheckMysqlConnect.py > testOutputCheckMysqlConnect.txt"
-        os.system(self._cmd)
-        
-        self.assertFalse(self._isFailedInOutputFile())
-        
-    def test_CheckMysqlConnect_as_script_False(self):
-        configFile = "%s/repet_tools/tests/config.cfg" % os.environ.get("REPET_PATH")
-        host = "unknownServer"
-        self._writeConfig(configFile, host)
-        
-        if self.HOST_NAME in self._host:
-            self._cmd = "CheckMysqlConnect.py -p /share/apps/bin/python -C %s > testOutputCheckMysqlConnect.txt" % configFile
-        else:
-            self._cmd = "CheckMysqlConnect.py -C %s > testOutputCheckMysqlConnect.txt " % configFile
-        os.system(self._cmd)
-        os.remove(configFile)
-        
-        self.assertTrue(self._isFailedInOutputFile())
-        
-    def _isFailedInOutputFile(self):
-        f = open("testOutputCheckMysqlConnect.txt", "r")
-        line = f.readline()
-        
-        while line:
-            if "FAILED" in line:
-                f.close()
-                return True
-            line = f.readline()
-
-        f.close()
-        return False
-    
-    def _writeConfig(self, configFileName, repetHost = os.environ.get("REPET_HOST")):
-        f = open( configFileName, "w" )
-        f.write("[repet_env]\n")
-        f.write("repet_host: %s\n" % repetHost)
-        f.write("repet_user: %s\n" % os.environ.get("REPET_USER"))
-        f.write("repet_pw: %s\n" % os.environ.get("REPET_PW"))
-        f.write("repet_db: %s\n" % os.environ.get("REPET_DB"))
-        f.write("repet_port: %s\n" % os.environ.get("REPET_PORT"))
-        f.close()
-    
-if __name__ == "__main__":
-    unittest.main()
-    
\ No newline at end of file

--- a/commons/tools/tests/Test_F_FilterAlign.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import unittest
-import os
-
-class Test_F_FilterAlign(unittest.TestCase):
-
-    def test_as_script(self):
-        alignFileName = "batch.fa.align"
-        self._writeAlignFile(alignFileName)
-        expFileName = "exp.filtered"
-        self._writeExpFile(expFileName)
-        obsFileName = "batch.fa.align.filtered"
-        cmd = "FilterAlign.py"
-        cmd += " -i %s" % alignFileName
-        cmd += " -S 100"
-        cmd += " -v 1"
-        os.system(cmd)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(alignFileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        
-    def _writeExpFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t0\t249\t77.5463\n")
-        f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t0\t571\t78.0453\n")
-        f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n")
-        f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t0\t343\t78.3912\n")
-        f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t0\t154\t83.0601\n")
-        f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n")
-        f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t0\t132\t79.0323\n")
-        f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t0\t218\t71.4668\n")
-        f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n")
-        f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t0\t347\t80.0539\n")
-        f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t0\t278\t78.5942\n")
-        f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t0\t417\t77.8644\n")
-        f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t0\t584\t73.8655\n")
-        f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t0\t493\t95.7386\n")
-        f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t0\t260\t77.1289\n")
-        f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n")
-        f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n")
-        f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n")
-        f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t0\t414\t84.7418\n")
-        f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t0\t384\t82.6087\n")
-        f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t0\t240\t78.5377\n")
-        f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n")
-        f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n")
-        f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t0\t522\t98.0282\n")
-        f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t0\t411\t95.8763\n")
-        f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.2039e-45\t161\t81.1881\n")
-        f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t0\t431\t92.1127\n")
-        f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n")
-        f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t0\t257\t77.4193\n")
-        f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t0\t188\t80.0948\n")
-        f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t0\t711\t72.3792\n")
-        f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n")
-        f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n")
-        f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n")
-        f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n")
-        f.close()
-        
-    def _writeAlignFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("chunk09914\t5038\t5133\trefTE_745\t288\t389\t1.3e-15\t38\t86.747\n")
-        f.write("chunk09914\t6415\t6574\trefTE_745\t605\t761\t1.3e-15\t76\t78.9116\n")
-        f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t3.8e-165\t249\t77.5463\n")
-        f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t3.8e-165\t571\t78.0453\n")
-        f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n")
-        f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t3.4e-133\t343\t78.3912\n")
-        f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t3.4e-133\t154\t83.0601\n")
-        f.write("chunk09914\t4640\t4702\trefTE_764\t1676\t1738\t3.4e-133\t39\t86.2069\n")
-        f.write("chunk09914\t1436\t1549\trefTE_779\t749\t628\t3.9e-33\t38\t75.7009\n")
-        f.write("chunk09914\t3992\t4156\trefTE_779\t958\t743\t2.6e-34\t42\t85.4305\n")
-        f.write("chunk09914\t4050\t4229\trefTE_779\t782\t602\t6.5e-39\t57\t82.6923\n")
-        f.write("chunk09914\t4430\t4499\trefTE_779\t1029\t952\t1.2e-33\t39\t83.3333\n")
-        f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n")
-        f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t4e-86\t132\t79.0323\n")
-        f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t4e-86\t218\t71.4668\n")
-        f.write("chunk09914\t4689\t4718\trefTE_812\t828\t855\t1.6e-32\t37\t92.8571\n")
-        f.write("chunk09914\t6178\t6204\trefTE_812\t1111\t1138\t1.6e-32\t36\t92.5926\n")
-        f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n")
-        f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t2e-97\t347\t80.0539\n")
-        f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t1.1e-73\t278\t78.5942\n")
-        f.write("chunk09914\t3315\t3420\trefTE_818\t423\t318\t2e-97\t41\t74\n")
-        f.write("chunk09914\t3339\t3429\trefTE_818\t153\t49\t1.7e-96\t38\t82.5581\n")
-        f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t1.6e-281\t417\t77.8644\n")
-        f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t1.6e-281\t584\t73.8655\n")
-        f.write("chunk09914\t2593\t2700\trefTE_831\t905\t798\t1.2e-15\t85\t75\n")
-        f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t2.6e-138\t493\t95.7386\n")
-        f.write("chunk09914\t5276\t5639\trefTE_842\t725\t1094\t1.7e-16\t47\t71.8563\n")
-        f.write("chunk09914\t6223\t6594\trefTE_842\t1689\t2058\t1.7e-16\t70\t73.8602\n")
-        f.write("chunk09914\t6180\t6594\trefTE_844\t3220\t2788\t3e-19\t97\t71.5013\n")
-        f.write("chunk09914\t6415\t6593\trefTE_847\t3137\t2959\t2e-15\t85\t74.4186\n")
-        f.write("chunk09914\t4691\t4762\trefTE_852\t2829\t2755\t1.9e-21\t36\t82.0895\n")
-        f.write("chunk09914\t6172\t6594\trefTE_852\t1201\t770\t1.9e-21\t97\t71.2121\n")
-        f.write("chunk09914\t2441\t2723\trefTE_861\t995\t1282\t3.9e-54\t78\t75.3906\n")
-        f.write("chunk09914\t3323\t3437\trefTE_861\t1683\t1811\t3.9e-54\t36\t81.3084\n")
-        f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t3.9e-54\t260\t77.1289\n")
-        f.write("chunk09914\t4602\t4701\trefTE_861\t3281\t3372\t3.9e-54\t39\t85.7143\n")
-        f.write("chunk09914\t360\t470\trefTE_864\t2853\t2962\t6.3e-17\t38\t77.2277\n")
-        f.write("chunk09914\t4200\t4472\trefTE_864\t3062\t3320\t6.3e-17\t81\t75.2066\n")
-        f.write("chunk09914\t2594\t2736\trefTE_865\t3\t145\t1.3e-26\t62\t71.7391\n")
-        f.write("chunk09914\t3531\t3622\trefTE_865\t727\t810\t1.3e-26\t38\t80\n")
-        f.write("chunk09914\t4025\t4484\trefTE_865\t2086\t2534\t1.3e-26\t79\t78.7179\n")
-        f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n")
-        f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n")
-        f.write("chunk09914\t646\t733\trefTE_870\t3379\t3466\t6.1e-19\t96\t79.5455\n")
-        f.write("chunk09914\t6272\t6716\trefTE_875\t2153\t1701\t3.7e-13\t77\t73.7624\n")
-        f.write("chunk09914\t646\t737\trefTE_877\t3412\t3502\t2.2e-18\t94\t82.2222\n")
-        f.write("chunk09914\t3596\t3756\trefTE_880\t2230\t2079\t7.8e-35\t53\t79.2857\n")
-        f.write("chunk09914\t4090\t4521\trefTE_880\t1702\t1261\t4.1e-24\t90\t81.3699\n")
-        f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n")
-        f.write("chunk09914\t2569\t2725\trefTE_885\t789\t935\t6.6e-18\t73\t76.9231\n")
-        f.write("chunk09914\t2583\t2699\trefTE_885\t118\t1\t4.4e-17\t90\t81.25\n")
-        f.write("chunk09914\t3507\t3758\trefTE_885\t1631\t1887\t6.6e-18\t49\t77.6786\n")
-        f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t3e-117\t414\t84.7418\n")
-        f.write("chunk09914\t3841\t3924\trefTE_904\t1044\t1130\t3.1e-11\t60\t82.2785\n")
-        f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t3.9e-108\t384\t82.6087\n")
-        f.write("chunk09914\t4660\t4708\trefTE_904\t1763\t1813\t3e-117\t40\t79.5918\n")
-        f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t3.9e-62\t240\t78.5377\n")
-        f.write("chunk09914\t4689\t4718\trefTE_914\t3130\t3103\t8.6e-30\t37\t92.8571\n")
-        f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n")
-        f.write("chunk09914\t4691\t4755\trefTE_930\t2120\t2187\t2.3e-14\t39\t86.6667\n")
-        f.write("chunk09914\t6172\t6506\trefTE_930\t3738\t4087\t2.3e-14\t71\t72.293\n")
-        f.write("chunk09914\t3755\t3945\trefTE_931\t4127\t3947\t0\t45\t79.3939\n")
-        f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n")
-        f.write("chunk09914\t4692\t4772\trefTE_962\t2382\t2453\t1.5e-16\t39\t85.0746\n")
-        f.write("chunk09914\t6178\t6560\trefTE_962\t3929\t4309\t1.5e-16\t79\t70.5882\n")
-        f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t4e-147\t522\t98.0282\n")
-        f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t1.5e-115\t411\t95.8763\n")
-        f.write("chunk09914\t1139\t1203\trefTE_966\t4770\t4681\t1.5e-115\t38\t87.5\n")
-        f.write("chunk09914\t646\t734\trefTE_967\t4583\t4671\t4.8e-16\t87\t76.4045\n")
-        f.write("chunk09914\t3565\t3698\trefTE_969\t1106\t990\t4.3e-45\t53\t79.646\n")
-        f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.3e-45\t161\t81.1881\n")
-        f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t6.8e-120\t431\t92.1127\n")
-        f.write("chunk09914\t4691\t4762\trefTE_986\t3059\t3133\t3.3e-21\t36\t82.0895\n")
-        f.write("chunk09914\t6172\t6594\trefTE_986\t4689\t5120\t3.3e-21\t97\t71.2121\n")
-        f.write("chunk09914\t149\t280\trefTE_987\t3872\t3721\t2.8e-18\t38\t79.2\n")
-        f.write("chunk09914\t4689\t4769\trefTE_987\t3186\t3102\t2.8e-18\t37\t83.5616\n")
-        f.write("chunk09914\t6178\t6594\trefTE_987\t1600\t1188\t2.8e-18\t77\t72.0317\n")
-        f.write("chunk09914\t4108\t4241\trefTE_991\t2079\t2237\t1.2e-12\t62\t82.1705\n")
-        f.write("chunk09914\t4602\t4701\trefTE_991\t2535\t2634\t1.2e-12\t43\t78.022\n")
-        f.write("chunk09914\t3596\t3757\trefTE_999\t6434\t6307\t3.6e-39\t52\t85.124\n")
-        f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n")
-        f.write("chunk09914\t4348\t4702\trefTE_999\t5619\t5295\t5.9e-13\t54\t79.7251\n")
-        f.write("chunk09914\t4541\t4805\trefTE_1002\t3207\t2973\t6.8e-27\t57\t85.5769\n")
-        f.write("chunk09914\t6178\t6723\trefTE_1002\t1494\t946\t6.8e-27\t96\t75.7764\n")
-        f.write("chunk09914\t4085\t4179\trefTE_1004\t3933\t4033\t1.5e-17\t47\t80\n")
-        f.write("chunk09914\t4690\t4718\trefTE_1004\t4126\t4153\t1.5e-17\t38\t92.8571\n")
-        f.write("chunk09914\t6262\t6594\trefTE_1004\t5242\t5574\t1.5e-17\t65\t70.2265\n")
-        f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t2.5e-134\t257\t77.4193\n")
-        f.write("chunk09914\t3134\t3382\trefTE_1006\t1450\t1199\t2.9e-118\t45\t75.7991\n")
-        f.write("chunk09914\t3331\t3661\trefTE_1006\t1468\t1146\t2.5e-134\t98\t78.2313\n")
-        f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t2.5e-134\t188\t80.0948\n")
-        f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t3.8e-204\t711\t72.3792\n")
-        f.write("chunk09914\t2670\t2723\trefTE_1009\t6642\t6591\t7.1e-18\t39\t86\n")
-        f.write("chunk09914\t3328\t3647\trefTE_1009\t5826\t5508\t7.1e-18\t84\t75\n")
-        f.write("chunk09914\t6\t130\trefTE_1011\t3884\t3994\t1.6e-11\t38\t76.6355\n")
-        f.write("chunk09914\t4690\t4741\trefTE_1011\t4997\t5046\t1.6e-11\t37\t91.1111\n")
-        f.write("chunk09914\t6180\t6716\trefTE_1011\t6676\t7235\t1.6e-11\t55\t71.2274\n")
-        f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n")
-        f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n")
-        f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n")
-        f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_GFF3Maker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,707 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.GFF3Maker import GFF3Maker
-
-class Test_F_GFF3Maker(unittest.TestCase):
-
-    def setUp(self):
-        self._projectName = "projectName"
-        self._iDb = DbMySql()
-        self._tablesFileName = "annotation_tables.txt"
-        self._fastaFileName = "%s_chr.fa" % self._projectName
-        self._fastaTableName = "%s_chr_seq" % self._projectName
-        self._writeFastaFile(self._fastaFileName)
-        self._iDb.createTable(self._fastaTableName, "seq", self._fastaFileName, True)
-        self._inputFileName = "%s_chr_allTEs_nr_noSSR_join.pathOrSet" % self._projectName
-        self._expGFFFileName = "explm_SuperContig_29_v2.gff3"
-        self._obsGFFFileName = "lm_SuperContig_29_v2.gff3"
-        self._obsGFFEmptyFileName = "lm_SuperContig_30_v2.gff3"
-        
-    def tearDown(self):
-        self._iDb.dropTable(self._fastaTableName)
-        self._iDb.dropTable(self._inputTableName)
-        self._iDb.close()
-        os.remove(self._obsGFFFileName)
-        os.remove(self._expGFFFileName)
-        os.remove(self._fastaFileName)
-        os.remove(self._tablesFileName)
-        os.remove(self._inputFileName)
-        
-    def test_run_as_script_path_with_seq_withAllFiles(self):
-        self._writeTablesFile("path")
-        self._writePathFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        self._writeExpPathGFFFile(self._expGFFFileName)
-        expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3"
-        self._writeExpEmptyPathGFFFileWithSeq(expGFFEmptyFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -w -a -p"% (self._tablesFileName, self._fastaTableName) 
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName))
-        
-        os.remove(expGFFEmptyFileName)
-        os.remove(self._obsGFFEmptyFileName)
-       
-    def test_run_as_script_path_without_seq_withAllFiles(self):
-        self._writeTablesFile("path")
-        self._writePathFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        self._writeExpPathGFFFile_without_seq(self._expGFFFileName)
-        expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3"
-        self._writeExpEmptyPathGFFFile(expGFFEmptyFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -a -p" % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName))
-        
-        os.remove(expGFFEmptyFileName)
-        os.remove(self._obsGFFEmptyFileName)
-   
-    def test_run_without_seq(self):
-        self._writeTablesFile("path")
-        self._writePathFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        self._writeExpPathGFFFile_without_seq(self._expGFFFileName)
-        
-        iGFF3Maker = GFF3Maker()
-        iGFF3Maker.setTablesFileName(self._tablesFileName)
-        iGFF3Maker.setInFastaName(self._fastaTableName)
-        iGFF3Maker.setAreMatchPartCompulsory(True)
-        iGFF3Maker.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
-   
-    def test_run_without_seq_and_match_part_not_compulsory(self):
-        self._writeTablesFile("path")
-        self._writePathFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        self._writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self._expGFFFileName)
-        
-        iGFF3Maker = GFF3Maker()
-        iGFF3Maker.setTablesFileName(self._tablesFileName)
-        iGFF3Maker.setInFastaName(self._fastaTableName)
-        iGFF3Maker.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
-
-    def test_run_as_script_pathReversed(self):
-        self._writeTablesFile("path")
-        self._writePathFileReverse(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        self._writeExpPathGFFFileReversed(self._expGFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -w -p" % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
-      
-    def test_run_as_script_set(self):
-        self._writeTablesFile("set")
-        self._writeSetFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName
-        self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True)
-        self._writeExpSetGFFFile(self._expGFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
-        
-    def test_run_as_script_setReversed(self):
-        self._writeTablesFile("set")
-        self._writeSetFileReverse(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName
-        self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True)
-        self._writeExpSetGFFFileReversed(self._expGFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
-       
-    def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8(self):
-        self._writeTablesFile("path")
-        self._writePathFile_withClassif(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        
-        self._writeClassifFile("input.classif")
-        inputClassifTableName = "%s_classif" % self._projectName
-        self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
-        
-        self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
-        self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
-        self._writeExpPathGFFFile_without_seq_withClassif(self._expGFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -i %s -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        
-        os.remove("input.classif")
-        os.remove("lm_SuperContig_29_v2.gff3")
-        self._iDb.dropTable(inputClassifTableName)
-
-    def test_run_as_script_path_without_seq_withAllFilesWithTargetLength(self):
-        fastaFileName = "genome.fa"
-        self._writeFastaFileExtended(fastaFileName)
-        self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True)
-        os.remove(fastaFileName)
-        
-        self._writeTablesFile_withTESeqTables("path")
-        
-        self._writePathFile(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        
-        inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName
-        self._writePathFile2(inFileName2)
-        bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName
-        self._iDb.createTable(bankPathTableName, "path", inFileName2, True)
-        os.remove(inFileName2)
-        
-        refTEsFastaFileName = "%s_refTEs.fa" % self._projectName
-        self._writeRefTEsSeqFile(refTEsFastaFileName)
-        refTESeqTableName = "%s_refTEs_seq" % self._projectName
-        self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True) 
-        os.remove(refTEsFastaFileName)     
-          
-        bankBLRtxFastaFileName = "dummyRepbase.fa"
-        self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName)
-        bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName
-        self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True)
-        os.remove(bankBLRtxFastaFileName)
-        
-        self._expGFFFileName = "explm_SuperContig_29_v2.gff3"
-        expSeq2GFFFileName = "expChr1.gff3"
-        self._obsGFFFileName = "lm_SuperContig_29_v2.gff3"
-        obsSeq2GFFFileName = "chr1.gff3"
-        self._writeExpPathGFFFile_without_seq_withTargetLength_seq1(self._expGFFFileName)
-        self._writeExpPathGFFFile_without_seq_withTargetLength_seq2(expSeq2GFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -p" % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expSeq2GFFFileName, obsSeq2GFFFileName))
-        
-        os.remove(expSeq2GFFFileName)
-        os.remove(obsSeq2GFFFileName)
-        self._iDb.dropTable(refTESeqTableName)
-        self._iDb.dropTable(bankBLRtxTableName)
-        self._iDb.dropTable(bankPathTableName)
-        
-    def test_run_as_script_split_file_by_annotation_method(self):
-        fastaFileName = "dummyDmelChr4.fa"
-        self._writeFastaFile_DmelChr4(fastaFileName)
-        self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True)
-        os.remove(fastaFileName)
-        
-        self._writeTablesFile_withTESeqTables("path")
-        
-        self._writePathFile_refTEs_annotation(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        
-        inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName
-        self._writePathFile_bankBLRtx_annotation(inFileName2)
-        bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName
-        self._iDb.createTable(bankPathTableName, "path", inFileName2, True)
-        os.remove(inFileName2)
-        
-        refTEsFastaFileName = "%s_refTEs.fa" % self._projectName
-        self._writeRefTEsSeqFile(refTEsFastaFileName)
-        refTESeqTableName = "%s_refTEs_seq" % self._projectName
-        self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True) 
-        os.remove(refTEsFastaFileName)     
-          
-        bankBLRtxFastaFileName = "dummyRepbase.fa"
-        self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName)
-        bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName
-        self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True)
-        os.remove(bankBLRtxFastaFileName)
-        
-        self._expGFFFileName = "expdmel_chr4_Annot1.gff3"
-        expGFFFileName2 = "expdmel_chr1_Annot1.gff3"
-        expGFFFileName3 = "expdmel_chr4_Annot2.gff3"
-        self._obsGFFFileName = "dmel_chr4_Annot1.gff3"
-        obsGFFFileName2 = "dmel_chr1_Annot1.gff3"
-        obsGFFFileName3 = "dmel_chr4_Annot2.gff3"
-        self._writeExpPathGFFFile_split_file1(self._expGFFFileName)
-        self._writeExpPathGFFFile_split_file2(expGFFFileName2)
-        self._writeExpPathGFFFile_split_file3(expGFFFileName3)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -s -p" % (self._tablesFileName, self._fastaTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName2, obsGFFFileName2))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName3, obsGFFFileName3))
-        
-        os.remove(expGFFFileName2)
-        os.remove(expGFFFileName3)
-        os.remove(obsGFFFileName2)
-        os.remove(obsGFFFileName3)
-        self._iDb.dropTable(refTESeqTableName)
-        self._iDb.dropTable(bankBLRtxTableName)
-        self._iDb.dropTable(bankPathTableName)
-        
-    def test_run_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self):
-        self._writeTablesFile("path")
-        self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        
-        self._writeClassifFile("input.classif")
-        inputClassifTableName = "%s_classif" % self._projectName
-        self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
-        
-        self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
-        self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
-        self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName)
-        
-        iGFF3Maker = GFF3Maker()
-        iGFF3Maker.setTablesFileName(self._tablesFileName)
-        iGFF3Maker.setInFastaName(self._fastaTableName)
-        iGFF3Maker.setClassifTable(inputClassifTableName)
-        iGFF3Maker.setDoMergeIdenticalMatches(True)
-        iGFF3Maker.setAreMatchPartCompulsory(True)
-        iGFF3Maker.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        
-        os.remove("input.classif")
-        os.remove("lm_SuperContig_29_v2.gff3")
-        self._iDb.dropTable(inputClassifTableName) 
-        
-    def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self):
-        self._writeTablesFile("path")
-        self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName)
-        self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
-        self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
-        
-        self._writeClassifFile("input.classif")
-        inputClassifTableName = "%s_classif" % self._projectName
-        self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
-        
-        self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
-        self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
-        self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName)
-        
-        cmd = "GFF3Maker.py -t %s -f %s -i %s -m -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
-        
-        os.remove("input.classif")
-        os.remove("lm_SuperContig_29_v2.gff3")
-        self._iDb.dropTable(inputClassifTableName)
-        
-    def _writeRefTEsSeqFile(self, inFileName):
-        with open(inFileName, "w") as f:
-            f.write(">DTX-incomp_DmelChr4-L-B1-Map3\n")
-            f.write("ATCGATCGTT\n")
-            f.write(">DTX-incomp_DmelChr4-B-P0.0-Map3\n")
-            f.write("GCTAGCTA\n")
-        
-    def _writeBankBLRtxSeqFile(self, inFileName):
-        with open(inFileName, "w") as f:
-            f.write(">PROTOP_B:classII:TIR\n")
-            f.write("ATCGATCGTT\n")
-            f.write(">DMRT1C:classI:?\n")
-            f.write("GCTAGCTA\n")
-            f.write(">BATUMI_I:classI:LTR_retrotransposon\n")
-            f.write("GCTAATGGCATA\n")
-            
-    def _writeExpPathGFFFile_without_seq_withTargetLength_seq1(self, inFileName):
-        with open(inFileName, "w") as f:
-            f.write("##gff-version 3\n")
-            f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;TargetLength=10;Identity=30.56\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;TargetLength=10;Identity=23.99\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;TargetLength=8\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-            f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        
-    def _writeExpPathGFFFile_without_seq_withTargetLength_seq2(self, inFileName):
-        with open(inFileName, "w") as f:
-            f.write("##gff-version 3\n")
-            f.write("##sequence-region chr1 1 18\n")
-            f.write("chr1\tprojectName_REPET_TEs\tmatch\t1\t100\t0.0\t-\t.\tID=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;TargetLength=10;Identity=30.56\n")
-            f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t1\t100\t1e-20\t-\t.\tID=mp1-1_chr1_PROTOP_B:classII:TIR;Parent=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;Identity=30.56\n")
-            f.write("chr1\tprojectName_REPET_TEs\tmatch\t100\t1000\t0.0\t-\t.\tID=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;TargetLength=8;Identity=30.56\n")
-            f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t100\t1000\t1e-30\t-\t.\tID=mp2-1_chr1_DMRT1C:classI:?;Parent=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;Identity=30.56\n")
-        
-    def _writeExpPathGFFFile_split_file1(self, inFileName):
-        with open(inFileName, 'w') as f:
-            f.write("##gff-version 3\n")
-            f.write("##sequence-region dmel_chr4 1 18\n")
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4630\t4889\t0.0\t+\t.\tID=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 512;TargetLength=8\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4630\t4704\t0.0\t+\t.\tID=mp21-1_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 312;Identity=84.4417\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4837\t4889\t0.0\t+\t.\tID=mp21-2_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 456 512;Identity=84.4417\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp6-1_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName)
-
-    def _writeExpPathGFFFile_split_file2(self, inFileName):
-        with open(inFileName, 'w') as f:
-            f.write("##gff-version 3\n")
-            f.write("##sequence-region dmel_chr1 1 25\n")
-            f.write("dmel_chr1\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName)
-            f.write("dmel_chr1\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp35-1_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName)
-
-    def _writeExpPathGFFFile_split_file3(self, inFileName):
-        with open(inFileName, 'w') as f:
-            f.write("##gff-version 3\n")
-            f.write("##sequence-region dmel_chr4 1 18\n")
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t3143\t4364\t0.0\t-\t.\tID=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 2206;TargetLength=8\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3143\t3361\t0.0\t-\t.\tID=mp66-1_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1988 2206;Identity=89.7202\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3345\t3410\t0.0\t-\t.\tID=mp66-2_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1654 1719;Identity=54.55\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3448\t3572\t0.0\t-\t.\tID=mp66-3_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1495 1619;Identity=77.3433\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3564\t3693\t0.0\t-\t.\tID=mp66-4_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1380 1509;Identity=83.7306\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3705\t3857\t0.0\t-\t.\tID=mp66-5_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 539 691;Identity=84.5762\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3861\t3992\t0.0\t-\t.\tID=mp66-6_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 403 534;Identity=67.1422\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3985\t4106\t0.0\t-\t.\tID=mp66-7_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 290 411;Identity=76.612\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4102\t4248\t0.0\t-\t.\tID=mp66-8_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 139 285;Identity=75.3027\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4236\t4364\t0.0\t-\t.\tID=mp66-9_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 152;Identity=66.6657\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4412\t4889\t0.0\t-\t.\tID=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 1082;TargetLength=10\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4412\t4501\t5e-108\t-\t.\tID=mp27-1_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 993 1082;Identity=91.3066\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4483\t4652\t9e-146\t-\t.\tID=mp27-2_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 821 990;Identity=86.5572\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4672\t4775\t9e-146\t-\t.\tID=mp27-3_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 684 787;Identity=88.8013\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4782\t4889\t9e-141\t-\t.\tID=mp27-4_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 661;Identity=53.7067\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4917\t5195\t0.0\t+\t.\tID=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7303;TargetLength=12\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4917\t5007\t2e-144\t+\t.\tID=mp141-1_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7120;Identity=94.1756\n" % self._projectName)
-            f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4976\t5195\t2e-144\t+\t.\tID=mp141-2_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7087 7303;Identity=82.2343\n" % self._projectName)
-        
-    def _writeClassifFile(self, inputFileName):
-        f = open(inputFileName, "w")
-        f.write("PotentialHostGene-chim_fTest05105818-B-G11-Map20\t1240\t+\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 95.65%); other=(TE_BLRtx: PROTOP:classII:TIR: 12.03%, PROTOP_A:classII:TIR: 49.14%; TermRepeats: termTIR: 49; SSRCoverage=0.25<0.75)\n")
-        f.write("DTX-comp-chim_fTest05105818-B-G7-Map3_reversed\t1944\t-\tPotentialChimeric\tII\tTIR\tcomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 12.77%, PROTOP_A:classII:TIR: 25.16%, PROTOP_A:classII:TIR: 100.00%); struct=(TElength: <700bps; TermRepeats: termTIR: 844); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 29.48%; SSRCoverage=0.24<0.75)\n")
-        f.write("DTX-incomp_fTest05105818-B-G9-Map3_reversed\t1590\t-\tok\tII\tTIR\tincomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 10.92%, PROTOP:classII:TIR: 11.03%, PROTOP_A:classII:TIR: 55.20%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60%; SSRCoverage=0.21<0.75)\n")
-        f.write("DTX-incomp_fTest05105818-B-P0.0-Map3\t1042\t.\tok\tII\tTIR\tincomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 17.39%, PROTOP_A:classII:TIR: 22.17%); struct=(TElength: >700bps; TermRepeats: termTIR: 50); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 47.22%; SSRCoverage=0.25<0.75)\n")
-        f.write("DTX-comp_fTest05105818-B-P1.0-Map9_reversed\t1137\t-\tok\tII\tTIR\tcomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 6.70%, PROTOP_A:classII:TIR: 66.43%, PROTOP_B:classII:TIR: 6.42%); struct=(TElength: >700bps; TermRepeats: termTIR: 52); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 51.19%; SSRCoverage=0.22<0.75)\n")
-        f.write("RLX-incomp_fTest05105818-B-R12-Map3_reversed\t2284\t-\tok\tI\tLTR\tincomplete\tCI=28; coding=(TE_BLRtx: ROOA_I:classI:LTR_retrotransposon: 27.57%, ROOA_LTR:classI:LTR_retrotransposon: 94.56%; TE_BLRx: BEL11_AGp:classI:LTR_retrotransposon: 19.47%, BEL2-I_Dmoj_1p:classI:LTR_retrotransposon: 11.49%); struct=(TElength: >700bps); other=(SSRCoverage=0.07<0.75)\n")
-        f.write("DTX-incomp_fTest05105818-B-R19-Map4\t705\t+\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1-2_DM:classII:TIR: 42.70%; TE_BLRx: TC1-2_DMp:classII:TIR: 41.18%); struct=(TElength: >700bps); other=(SSRCoverage=0.14<0.75)\n")
-        f.write("DHX-incomp_fTest05105818-B-R1-Map4\t2367\t.\tok\tII\tHelitron\tincomplete\tCI=20; coding=(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00%, DNAREP1_DYak:classII:Helitron: 9.08%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52%; SSRCoverage=0.18<0.75)\n")
-        f.write("noCat_fTest05105818-B-R2-Map6\t4638\t.\tok\tnoCat\tnoCat\tNA\tCI=NA; coding=(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%); struct=(SSRCoverage=0.05<0.75)\n")
-        f.write("PotentialHostGene-chim_fTest05105818-B-R4-Map5_reversed\t1067\t-\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%); other=(TE_BLRtx: PROTOP:classII:TIR: 13.06%, PROTOP_A:classII:TIR: 37.47%; SSRCoverage=0.27<0.75)\n")
-        f.write("DTX-incomp_fTest05105818-B-R9-Map3_reversed\t714\t-\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1_DM:classII:TIR: 40.88%; TE_BLRx: Tc1-1_TCa_1p:classII:TIR: 30.18%, Tc1-3_FR_1p:classII:TIR: 9.97%); struct=(TElength: >700bps); other=(SSRCoverage=0.08<0.75)\n")        
-        f.close()
-        
-    def _writePathFile_withClassif(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n')
-        f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n')
-        f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
-        f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
-        f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n')
-        f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n')
-        f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n')
-        f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n')
-        f.close() 
-        
-    def _writeExpPathGFFFile_without_seq_withClassif(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;TargetDescription=CI:NA coding:(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%) struct:(SSRCoverage:0.05<0.75);Identity=34.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp7-1_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Parent=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;Identity=34.89\n")
-       
-        f.close()
-
-    def _writePathFile_withClassif_withIdenticalMatches(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n')
-        f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n')
-        f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
-        f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
-        f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n')
-        f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n')
-        f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n')
-
-        f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n')
-        f.write('8\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t100\t190\t3e-26\t101\t39.89\n')
-        f.write('9\tlm_SuperContig_30_v2\t288031\t288080\tRLX-incomp_fTest05105818-B-R12-Map3_reversed\t1100\t1290\t3e-26\t101\t40.89\n')
-        f.write('10\tlm_SuperContig_30_v2\t288031\t288080\tPotentialHostGene-chim_fTest05105818-B-G11-Map20\t990\t1890\t3e-26\t101\t38.09\n')
-
-        f.write('11\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-G1-Map3\t990\t1890\t3e-26\t301\t38.09\n')
-        
-        f.write('12\tlm_SuperContig_30_v2\t388031\t388080\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
-        f.write('12\tlm_SuperContig_30_v2\t388081\t388380\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
-        
-        f.write('13\tlm_SuperContig_30_v2\t388031\t388080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t119\t309\t3e-21\t101\t30.89\n')
-        f.write('13\tlm_SuperContig_30_v2\t388081\t388380\tDTX-incomp_fTest05105818-B-P0.0-Map3\t250\t450\t3e-22\t101\t35.89\n')
-        f.close() 
-
-    def _writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
-       
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n")
-        
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890;OtherTargets=RLX-incomp_fTest05105818-B-R12-Map3_reversed 1100 1290, DTX-incomp_fTest05105818-B-P0.0-Map3 100 190, noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp10-1_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Parent=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890\n")
-
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp11-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n")
-
-        #TODO:
-        #Should this case really occur : If merging multiple match-parts, the current behaviour needs to be fixed to get correct subject start/end coordinates 
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t388031\t388380\t0.0\t+\t.\tID=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;OtherTargets=DTX-incomp_fTest05105818-B-P0.0-Map3 119 309\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388031\t388080\t3e-21\t+\t.\tID=mp12-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209\n")
-        f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388081\t388380\t3e-22\t+\t.\tID=mp12-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350\n")
-        f.close()
-
-    def _writeTablesFile_withTESeqTables(self, tableType):
-        tableFile = open( self._tablesFileName, "w" )
-        string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\t%s_refTEs_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName)
-        tableFile.write(string)
-        string = "%s_REPET_TEs\t%s\t%s_chr_bankBLRtx_%s\t%s_bankBLRtx_nt_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName)
-        tableFile.write(string)
-        tableFile.close()
-        
-    def _writeTablesFile(self, tableType):
-        tableFile = open( self._tablesFileName, "w" )
-        string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\n" % (self._projectName, tableType, self._projectName, tableType)
-        tableFile.write(string)
-        tableFile.close()
-        
-    def _writePathFile(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tlm_SuperContig_29_v2\t193781\t194212\tDTX-incomp_DmelChr4-L-B1-Map3\t228\t85\t1e-40\t84\t30.56\n')
-        f.write('2\tlm_SuperContig_29_v2\t192832\t193704\tDTX-incomp_DmelChr4-L-B1-Map3\t522\t229\t1e-40\t106\t23.99\n')
-        f.write('3\tlm_SuperContig_29_v2\t78031\t78080\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n')
-        f.write('3\tlm_SuperContig_29_v2\t78081\t78588\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n')
-        f.close() 
-        
-    def _writePathFile2(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tchr1\t1\t100\tPROTOP_B:classII:TIR\t228\t85\t1e-20\t84\t30.56\n')
-        f.write('2\tchr1\t100\t1000\tDMRT1C:classI:?\t228\t85\t1e-30\t84\t30.56\n')
-        f.close() 
-        
-    def _writePathFile_refTEs_annotation(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('6\tdmel_chr4\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n')
-        f.write('21\tdmel_chr4\t4630\t4704\tDTX-incomp_DmelChr4-B-P0.0-Map3\t232\t312\t0\t65\t84.4417\n')
-        f.write('21\tdmel_chr4\t4837\t4889\tDTX-incomp_DmelChr4-B-P0.0-Map3\t456\t512\t0\t46\t84.4417\n')
-        f.write('35\tdmel_chr1\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n')
-        f.close()
-        
-    def _writePathFile_bankBLRtx_annotation(self,inFileName):
-        f = open(inFileName, 'w')
-        f.write('27\tdmel_chr4\t4412\t4501\tPROTOP_B:classII:TIR\t1082\t993\t5e-108\t702\t91.3066\n')
-        f.write('27\tdmel_chr4\t4483\t4652\tPROTOP_B:classII:TIR\t990\t821\t9e-146\t707\t86.5572\n')
-        f.write('27\tdmel_chr4\t4672\t4775\tPROTOP_B:classII:TIR\t787\t684\t9e-146\t707\t88.8013\n')
-        f.write('27\tdmel_chr4\t4782\t4889\tPROTOP_B:classII:TIR\t661\t553\t9e-141\t356\t53.7067\n')
-        f.write('66\tdmel_chr4\t3143\t3361\tDMRT1C:classI:?\t2206\t1988\t0\t1878\t89.7202\n')
-        f.write('66\tdmel_chr4\t3345\t3410\tDMRT1C:classI:?\t1719\t1654\t0\t313\t54.55\n')
-        f.write('66\tdmel_chr4\t3448\t3572\tDMRT1C:classI:?\t1619\t1495\t0\t1252\t77.3433\n')
-        f.write('66\tdmel_chr4\t3564\t3693\tDMRT1C:classI:?\t1509\t1380\t0\t1565\t83.7306\n')
-        f.write('66\tdmel_chr4\t3705\t3857\tDMRT1C:classI:?\t691\t539\t0\t1252\t84.5762\n')
-        f.write('66\tdmel_chr4\t3861\t3992\tDMRT1C:classI:?\t534\t403\t0\t1565\t67.1422\n')
-        f.write('66\tdmel_chr4\t3985\t4106\tDMRT1C:classI:?\t411\t290\t0\t1252\t76.612\n')
-        f.write('66\tdmel_chr4\t4102\t4248\tDMRT1C:classI:?\t285\t139\t0\t1565\t75.3027\n')
-        f.write('66\tdmel_chr4\t4236\t4364\tDMRT1C:classI:?\t152\t24\t0\t1565\t66.6657\n')
-        f.write('141\tdmel_chr4\t4917\t5007\tBATUMI_I:classI:LTR_retrotransposon\t7030\t7120\t2e-144\t984\t94.1756\n')
-        f.write('141\tdmel_chr4\t4976\t5195\tBATUMI_I:classI:LTR_retrotransposon\t7087\t7303\t2e-144\t2098\t82.2343\n')
-        f.close() 
-        
-    def _writePathFileReverse(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t228\t85\t1e-40\t84\t30.56\n')
-        f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t522\t229\t1e-40\t106\t23.99\n')
-        f.write('3\tlm_SuperContig_29_v2\t78080\t78031\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n')
-        f.write('3\tlm_SuperContig_29_v2\t78588\t78081\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n')
-        f.close() 
-        
-    def _writeSetFile(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n')
-        f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n')
-        f.write('3\tset3\tlm_SuperContig_29_v2\t78031\t78080\n')
-        f.write('3\tset3\tlm_SuperContig_29_v2\t78081\t78588\n')
-        f.close() 
-        
-    def _writeSetFileReverse(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n')
-        f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n')
-        f.write('3\tset3\tlm_SuperContig_29_v2\t78080\t78031\n')
-        f.write('3\tset3\tlm_SuperContig_29_v2\t78588\t78081\n')
-        f.close() 
-    
-    def _writeExpEmptyPathGFFFile(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
-        f.close()
-    
-    def _writeExpPathGFFFile(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.write("##FASTA\n")
-        self._writeSeq1(f)
-        f.close()
-    
-    def _writeExpEmptyPathGFFFileWithSeq(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
-        f.write("##FASTA\n")
-        self._writeSeq2(f)
-        f.close()
-    
-    def _writeExpPathGFFFile_without_seq(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.close()
-    
-    def _writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
-        f.close()
-        
-    def _writeExpPathGFFFileReversed(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n")
-        f.write("##FASTA\n")
-        self._writeSeq1(f)
-        f.close()
-        
-    def _writeExpSetGFFFile(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n")
-        f.write("##FASTA\n")
-        self._writeSeq1(f)
-        f.close()
-        
-    def _writeExpSetGFFFileReversed(self, inFileName):
-        f = open(inFileName, 'w')
-        f.write("##gff-version 3\n")
-        f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n")
-        f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n")
-        f.write("##FASTA\n")
-        self._writeSeq1(f)
-        f.close()
-    
-    def _writeFastaFile(self, inFileName):
-        f = open(inFileName,'w')
-        self._writeSeq2(f)
-        self._writeSeq1(f)
-        f.close()
-        
-    def _writeFastaFileExtended(self, inFileName):
-        f = open(inFileName,'w')
-        self._writeSeq2(f)
-        self._writeSeq1(f)
-        f.write(">chr1\n")
-        f.write("CTAAGCTGCGCTATGTAG\n")
-        f.close()
-    
-    def _writeSeq1(self, f):
-        f.write('>lm_SuperContig_29_v2\n')
-        f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n')
-        f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n')
-
-    def _writeSeq2(self, f):
-        f.write('>lm_SuperContig_30_v2\n')
-        f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
-        
-    def _writeFastaFile_DmelChr4(self, inFileName):
-        f = open(inFileName,'w')
-        f.write(">dmel_chr4\n")
-        f.write("CTAAGCTGCGCTATGTAG\n")
-        f.write(">dmel_chr1\n")
-        f.write("CGTAACGCTAGCGCTTATAGTGAGC\n")
-        f.close()
-
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_GameXmlMaker.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,281 +0,0 @@
-import unittest
-import os
-import glob
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.tools.GameXmlMaker import GameXmlMaker
-
-
-class Test_F_GameXmlMaker(unittest.TestCase):
-
-    def setUp(self):
-        pass
-
-
-    def tearDown(self):
-        FileUtils.removeFilesByPattern("*gamexml")
-
-
-    def test_run_as_script_step1(self):
-        fastaFileName = "input.fa"
-        self._writeFastaFile(fastaFileName)
-        
-        cmd = "GameXmlMaker.py -f %s " % fastaFileName 
-        os.system(cmd)
-       
-        lObsGameXmlNew = glob.glob("*.gamexml")
-        self._writeStep1ExpectedXmls()
-        self.assertTrue(len(lObsGameXmlNew) > 0)
-        for obsGameXmlNew in lObsGameXmlNew:
-            expGameXmlNew = "exp_%s" % obsGameXmlNew
-            self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
-        
-        os.remove(fastaFileName)
-    
-    def test_run_as_script_step2(self):
-        self._tableFileName = "annotation_tables.txt"
-        
-        self._writeStep2InputTableFile()
-        self._writeStep2InputXmls()
-        self._writeStep2InputPathFile()
-        self._writeStep2InputSetFile()
-        self._writeStep2InputMapFile()
-        self._createStep2Tables()
-        
-        lObsGameXmlNew = glob.glob("*.gamexml")
-        
-        cmd = "GameXmlMaker.py -t %s " % self._tableFileName
-        os.system(cmd)
-        
-        self._writeStep2ExpXmls()
-        
-        self.assertTrue(len(lObsGameXmlNew) > 0)
-        for obsGameXmlNew in lObsGameXmlNew:
-            expGameXmlNew = "exp_%s" % obsGameXmlNew
-            self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
-            
-        os.remove("Test_F_GameXmlMaker_path.path")
-        os.remove("Test_F_GameXmlMaker_set.set")
-        os.remove("Test_F_GameXmlMaker_chk_map.map")
-            
-        os.remove(self._tableFileName)
-        os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
-            
-    def test_run_step2(self):
-        self._tableFileName = "annotation_tables.txt"
-        
-        self._writeStep2InputTableFile()
-        self._writeStep2InputXmls()
-        self._writeStep2InputPathFile()
-        self._writeStep2InputSetFile()
-        self._writeStep2InputMapFile()
-        self._createStep2Tables()
-        
-        lObsGameXmlNew = glob.glob("*.gamexml")
-        
-        iGameXmlMaker = GameXmlMaker(tablesFileName = self._tableFileName)
-        iGameXmlMaker.run()
-        self._writeStep2ExpXmls()
-        self.assertTrue(len(lObsGameXmlNew) > 0)
-        for obsGameXmlNew in lObsGameXmlNew:
-            expGameXmlNew = "exp_%s" % obsGameXmlNew
-            self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
-            
-        os.remove("Test_F_GameXmlMaker_path.path")
-        os.remove("Test_F_GameXmlMaker_set.set")
-        os.remove("Test_F_GameXmlMaker_chk_map.map")
-        
-        os.remove(self._tableFileName)
-        os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
-        
-    def _writeFastaFile(self, inFileName):
-        f = open(inFileName,'w')
-        f.write('>seq1\n')
-        f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA\n')
-        f.write('>seq2\n')
-        f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
-        f.write('>seq3\n')
-        f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n')
-        f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n')
-        f.write('>seq4\n')
-        f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
-        f.write('CAGGAATCATGAAGGGTACGACTGTTCG\n')
-        f.close()
-        
-    def _writeStep1ExpectedXmls(self):
-        f = open("exp_seq1.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
-        f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
-        f.close()
-        f = open("exp_seq2.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
-        f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
-        f.close()
-        f = open("exp_seq3.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
-        f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
-        f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
-        f.close()
-        f = open("exp_seq4.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
-        f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
-        f.close()
-      
-    def _createStep2Tables(self):
-        iDb = DbFactory.createInstance()
-        iDb.createTable("Test_F_GameXmlMaker_set", "set", "Test_F_GameXmlMaker_set.set", True)
-        iDb.createTable("Test_F_GameXmlMaker_chk_map", "map", "Test_F_GameXmlMaker_chk_map.map", True)
-        iDb.createTable("Test_F_GameXmlMaker_path", "path", "Test_F_GameXmlMaker_path.path", True)
-        iDb.close()
-    
-    def _writeStep2InputXmls(self):
-        f = open("seq1.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
-        f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
-        f.close()
-        f = open("seq2.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
-        f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
-        f.close()
-        f = open("seq3.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
-        f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
-        f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
-        f.close()
-        f = open("seq4.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
-        f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
-        f.close()
-        
-    def _writeStep2InputPathFile(self):
-        f = open("Test_F_GameXmlMaker_path.path", 'w')
-        f.write("1\tseq1\t1\t10\tTE1\t1\t10\t0\t550\t80.7\n")
-        f.write("2\tseq1\t15\t50\tTE1\t12\t47\t0\t770\t90.8\n")
-        f.write("2\tseq1\t55\t70\tTE1\t50\t65\t0\t5410\t97.7\n")
-        f.write("3\tseq1\t75\t80\tTE2\t10\t15\t0\t8710\t60.0\n")
-        f.write("4\tseq2\t1\t10\tTE2\t20\t30\t0\t5410\t75.7\n")
-        f.write("5\tseq3\t1\t120\tTE2\t450\t550\t0\t5410\t75.7\n")
-        f.close()
-        
-    def _writeStep2InputSetFile(self):
-        f = open("Test_F_GameXmlMaker_set.set", 'w')
-        f.write("1\tseq1\tseq1\t1\t10\n")
-        f.write("2\tseq1\tseq1\t15\t50\n")
-        f.write("3\tseq1\tseq1\t75\t80\n")
-        f.write("4\tseq2\tseq2\t1\t10\n")
-        f.write("5\tseq3\tseq3\t1\t120\n")
-        f.close()
-        
-    def _writeStep2InputMapFile(self):
-        f = open("Test_F_GameXmlMaker_chk_map.map", 'w')        
-        f.write("chunk1\tseq1\t1\t200000\n")
-        f.write("chunk2\tseq1\t190001\t390000\n")
-        f.write("chunk3\tseq3\t380001\t580000\n")
-        f.write("chunk4\tseq4\t570001\t770000\n")
-        f.write("chunk5\tseq5\t760001\t960000\n")
-        f.write("chunk6\tseq6\t950001\t1150000\n")
-        f.write("chunk7\tseq7\t1140001\t1281640\n")
-        f.close()
-        
-    def _writeStep2ExpXmls(self):
-        f = open("exp_seq1.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
-        f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="1"><name>TE1::1</name>')
-        f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship><seq_relationship seq="TE1::1" type="subject"><span>')
-        f.write('<start>1</start><end>10</end></span></seq_relationship><score>80.7</score></result_span></result_set><result_set id="2"><name>TE1::2</name><result_span>')
-        f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship><seq_relationship seq="TE1::2" type="subject"><span><start>12</start>')
-        f.write('<end>47</end></span></seq_relationship><score>90.8</score></result_span><result_span><seq_relationship seq="seq1" type="query"><span><start>55</start><end>70</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="TE1::2" type="subject"><span><start>50</start><end>65</end></span></seq_relationship><score>97.7</score></result_span></result_set><result_set id="3"><name>TE2::3</name>')
-        f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship><seq_relationship seq="TE2::3" type="subject"><span><start>10</start><end>15</end></span></seq_relationship>')
-        f.write('<score>60.0</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database>')
-        f.write('<result_set id="1"><name>seq1::1</name><result_span>')
-        f.write('<seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="seq1::1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set>')
-        f.write('<result_set id="2"><name>seq1::2</name><result_span>')
-        f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="seq1::2" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set>')
-        f.write('<result_set id="3"><name>seq1::3</name><result_span>')
-        f.write('<seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="seq1::3" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
-        f.write('<result_set id="-1"><name>chunk1::-1</name>')
-        f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>200000</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="chunk1::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set>')
-        f.write('<result_set id="-1"><name>chunk2::-1</name>')
-        f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>190001</start><end>390000</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="chunk2::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship><score>0</score></result_span></result_set></computational_analysis></game>')
-        f.close()
-        
-        f = open("exp_seq2.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
-        f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="4"><name>TE2::4</name>')
-        f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span>')
-        f.write('</seq_relationship><seq_relationship seq="TE2::4" type="subject"><span><start>20</start><end>30</end></span></seq_relationship>')
-        f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="4"><name>seq2::4</name>')
-        f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="seq2::4" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database></computational_analysis></game>')
-        f.close()
-        
-        f = open("exp_seq3.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
-        f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
-        f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="5"><name>TE2::5</name>')
-        f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span>')
-        f.write('</seq_relationship><seq_relationship seq="TE2::5" type="subject"><span><start>450</start><end>550</end></span></seq_relationship>')
-        f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="5"><name>seq3::5</name>')
-        f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="seq3::5" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
-        f.write('<result_set id="-1"><name>chunk3::-1</name>')
-        f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>380001</start><end>580000</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="chunk3::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
-        f.close()
-        
-        f = open("exp_seq4.gamexml", 'w')
-        f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
-        f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
-        f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database></computational_analysis>')
-        f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
-        f.write('<result_set id="-1"><name>chunk4::-1</name>')
-        f.write('<result_span><seq_relationship seq="seq4" type="query"><span><start>570001</start><end>770000</end></span></seq_relationship>')
-        f.write('<seq_relationship seq="chunk4::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
-        f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
-        f.close()
-                
-    def _writeStep2InputTableFile(self):
-        f = open(self._tableFileName,'w')
-        f.write("Test_F_GameXmlMaker_path\tpath\tTest_F_GameXmlMaker_path\n")
-        f.write("Test_F_GameXmlMaker_set\tset\tTest_F_GameXmlMaker_set\n")
-        f.write("Test_F_GameXmlMaker_chk_map\tmap\tTest_F_GameXmlMaker_chk_map")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-import subprocess
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
-from shutil import rmtree
-from glob import glob
-
-class Test_F_GetMultAlignAndPhylogenyPerTErefSeq(unittest.TestCase):
-    
-    def setUp(self):
-        self._verbosity = 3
-        
-        self._testPrefix = 'Test_GMAAPperTErefSeq_'
-        self._configFileName = "%sConfig.cfg" % self._testPrefix
-        self._iDb = DbMySql()
-
-        self.inPathTableName = "%sDmelChr4_chr_allTEs_nr_noSSR_join_path" % (self._testPrefix)
-        self.inPathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
-        self._iDb.createTable(self.inPathTableName, "path", self.inPathFileName, True)
-        
-        self.RefTETableName = "%sDmelChr4_refTEs" % (self._testPrefix)
-        self.RefTEFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
-        self._iDb.createTable(self.RefTETableName, "seq", self.RefTEFileName, True)
-        
-        self.genomeTableName = "%sDmelChr4_chr" % (self._testPrefix)
-        self.genomeFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
-        self._iDb.createTable(self.genomeTableName, "seq", self.genomeFileName, True)
-
-        try:
-            os.makedirs(self._testPrefix)
-        except:pass
-        os.chdir(self._testPrefix)
-        self._writeConfigFile()
-        
-#        self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"]
-#        self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"]
-#        self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"]
-#        self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"]
-#        self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"]
-#        self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"]
-
-        
-#        inputFastaFileName = "input_TEannot_refTEs.fa"
-#        os.symlink(self._expFastaFileName_Copy, inputFastaFileName)
-        
-#        self._tableName = "Dummy_Atha_refTEs_seq"
-#        self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True)
-#        os.remove(inputFastaFileName)      
-#        
-#        self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-#        self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-#        self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-#        self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0]
-#        self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0]
-#        self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0]
-        
-    def tearDown(self):
-#        self._iDb.dropTable(self.inPathTableName)
-#        self._iDb.dropTable(self.RefTETableName)
-#        self._iDb.dropTable(self.genomeTableName)
-#        self._iDb.close()
-        
-        os.chdir("..")
-#        try:
-#            rmtree(self._testPrefix)
-#        except:pass
-        
-
-#    def test_run_step1(self):
-#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, configFileName=self._configFileName, step=1, verbosity=self._verbosity)
-#        iGMAAPperTErefSeq.run()
-#        
-#        copiesFiles = glob("*_copies.fa")
-#        self.assertTrue(len(copiesFiles) > 0)
-#        self.assertTrue(os.stat("DmelChr4-B-R9-Map3_NoCat_copies.fa")[6] != 0)#check if file is empty
-#    
-#    def test_run_step1Step2Map(self):
-#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
-#        iGMAAPperTErefSeq.run()
-#        iGMAAPperTErefSeq.step = 2
-#        iGMAAPperTErefSeq.run()
-#
-#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
-#
-#    def test_run_step1Step2RefAlign(self):
-#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="RefAlign", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
-#        iGMAAPperTErefSeq.run()
-#        iGMAAPperTErefSeq.step = 2
-#        iGMAAPperTErefSeq.run()
-#
-#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_refalign.fa_aln")[6] != 0)
-
-    def test_run_step1Step2Step3Map(self):
-        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
-        iGMAAPperTErefSeq.run()
-        iGMAAPperTErefSeq.step = 2
-        iGMAAPperTErefSeq.run()
-        iGMAAPperTErefSeq.step = 3
-        iGMAAPperTErefSeq.run()
-
-        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
-    
-    def _writeConfigFile(self):
-        f = open(self._configFileName, "w")
-        f.write("[repet_env]\n")
-        f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
-        f.write("repet_user: %s\n" % os.environ["REPET_USER"])
-        f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
-        f.write("repet_db: %s\n" % os.environ["REPET_DB"])
-        f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
-        f.write("repet_job_manager: SGE\n")
-        f.close()
-    
-                    
-#    def test_run_as_script_step1Step2Map(self):
-#        #cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -m 'Map' -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
-#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
-#        subprocess.call(cmd, shell = True)
-#        
-#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 2 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
-#        subprocess.call(cmd, shell = True)
-#        
-#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
-        
-        
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
-
-#    def test_run_as_script_step2(self):
-#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
-#        print cmd
-#        subprocess.call(cmd, shell = True)
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
-#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
-    
-if __name__ == "__main__":
-    unittest.main()

--- a/commons/tools/tests/Test_F_GetSpecificTELibAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-import subprocess
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation
-
-class Test_F_GetSpecificTELibAccordingToAnnotation(unittest.TestCase):
-    
-    def setUp(self):
-        self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"]
-        self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"]
-        self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"]
-        self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"]
-        self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"]
-        self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"]
-        
-        self._inFileName = "%s/Tools/GiveInfoTeAnnotFile.txt" % os.environ["REPET_DATA"]
-        inputFastaFileName = "input_TEannot_refTEs.fa"
-        os.symlink(self._expFastaFileName_Copy, inputFastaFileName)
-        self._iDb = DbMySql()
-        self._tableName = "Dummy_Atha_refTEs_seq"
-        self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True)
-        os.remove(inputFastaFileName)      
-        
-        self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-        self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-        self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
-        self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0]
-        self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0]
-        self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0]
-        
-    def tearDown(self):
-        self._iDb.dropTable(self._tableName)
-        self._iDb.close()
-        os.remove(self._obsFileName_FullLengthCopy)
-        os.remove(self._obsFileName_Copy)
-        os.remove(self._obsFileName_FullLengthFrag)
-        os.remove(self._obsFastaFileName_FullLengthCopy)
-        os.remove(self._obsFastaFileName_Copy)
-        os.remove(self._obsFastaFileName_FullLengthFrag)
-
-    def test_run(self):
-        iGetTELib = GetSpecificTELibAccordingToAnnotation(self._inFileName)
-        iGetTELib.setTableName(self._tableName)
-        iGetTELib.run()
-
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
-
-    def test_run_as_script(self):
-        cmd = "GetSpecificTELibAccordingToAnnotation.py -i %s -t %s -v 4" % (self._inFileName, self._tableName)
-        subprocess.call(cmd, shell = True)
-
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-
-CURRENT_DIR = os.getcwd()
-
-class Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script(unittest.TestCase):
-    
-    def setUp(self):
-        self._inputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output"
-        self._outputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmpfam_output.align"
-        self._prg = "HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
-        self._inputFile2 = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest"
-        self._consensusFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/ConsensusTestFile_nt.fsa"
-        self._inputFileScan =  os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput"
-        self._outputFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscan_output.align"
-        self._expectedFile =  os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align"
-        os.chdir(CURRENT_DIR)
-        
-    def testHmmpfamOuput2align(self):
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile )
-        cmd += " -o %s" % ( self._outputFile )
-        os.system( cmd )              
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))  
-        self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile))
-        self._clean()
-        
-    def testHmmpfamOuput2align_clean_option(self):
-        os.system( "cp " + self._inputFile + " " + self._inputFile + "bis" )
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile + "bis" )
-        cmd += " -o %s" % ( self._outputFile )
-        cmd += " -c"
-        os.system( cmd )        
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))  
-        self.assertTrue( FileUtils.are2FilesIdentical( self._inputFile + ".align", self._outputFile) )
-        self.assertFalse( FileUtils.isRessourceExists( self._inputFile + "bis" ) )
-        self._clean()
-        
-    def testHmmpfamOutput2alignAndTransformCoordInNtAndFilterScores(self):
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFile2 )
-        cmd += " -o %s" % ( self._outputFile )
-        cmd += " -T %s" % ( self._consensusFile )
-        os.system( cmd )
-        self._expectedFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/PostPostProcessTestFiltered.align"
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))              
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile))
-        self._clean()    
-        
-    def testHmmscanOuput2align(self):
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFileScan )
-        cmd += " -o %s" % ( self._outputFileScan )
-        cmd += " -p hmmscan"
-        os.system( cmd )             
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFileScan))   
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFileScan))
-        self._cleanScan()
-        
-    def testHmmscanOuput2align_clean_option(self):
-        os.system( "cp " + self._inputFileScan + " " + self._inputFileScan + "bis" )
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFileScan + "bis" )
-        cmd += " -o %s" % ( self._outputFileScan )
-        cmd += " -c -p hmmscan"
-        os.system( cmd )        
-        self.assertTrue( FileUtils.are2FilesIdentical( self._expectedFile, self._outputFileScan) )
-        self.assertFalse( FileUtils.isRessourceExists( self._inputFileScan + "bis" ) )
-        self._cleanScan()
-        
-    def testHmmscanOutput2alignAndTransformCoordInNtAndFilterScores(self):
-        self._inputFileScan2 = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput"
-        self._consensusFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/repetHmmscan.fa"
-        self._expectedFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscanTransformedExpected.align"
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFileScan2 )
-        cmd += " -o %s" % ( self._outputFileScan )
-        cmd += " -T %s" % ( self._consensusFileScan )
-        cmd += " -p hmmscan"
-        os.system( cmd )       
-        self.assertTrue(FileUtils.isRessourceExists(self._outputFileScan))         
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFileScan, self._outputFileScan))
-        self._cleanScan()    
-        
-    def _clean(self):
-        os.system( "rm " + self._outputFile )
-        
-    def _cleanScan(self):
-        os.system( "rm " + self._outputFileScan )
-        
-            
-if __name__ == "__main__":                 
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_LaunchBlaster.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import unittest
-import os
-import glob
-from commons.tools.LaunchBlaster import LaunchBlaster
-
-class Test_F_LaunchBlaster(unittest.TestCase):
-
-    def setUp(self):
-        self._inFileName = "DmelChr4.fa"
-        inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
-        try:
-            os.remove(self._inFileName)
-        except:
-            pass
-        os.symlink(inFilePath, self._inFileName)
-        self._iLaunchBlaster = LaunchBlaster(self._inFileName)
-        self._iLaunchBlaster.setDoAllByall(True)
-        self._iLaunchBlaster.setVerbosity(4)
-
-    def tearDown(self):
-        try:
-            FileUtils.removeFilesByPattern("%s*" % self._inFileName)
-            os.remove("formatdb.log")
-        except:
-            pass
-
-    def test_run_as_class_1_file(self):
-        expFileName = "%s/Tools/DmelChr4.align" % os.environ["REPET_DATA"]
-        obsFileName = "%s.align" % self._inFileName
-        
-        self._iLaunchBlaster.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-    def test_run_as_class_1_file_changed_params(self):
-        expFileName = "DmelChr4.align"
-        with open(expFileName, "w") as fh:
-            fh.write("dmel_chr4\t691910\t692326\tdmel_chr4\t700019\t700435\t0\t827\t100\n")
-        obsFileName = "%s.align" % self._inFileName
-        
-        self._iLaunchBlaster.setIdentity(100)
-        self._iLaunchBlaster.setCPU(4)
-        self._iLaunchBlaster.setDoClean(True)
-        self._iLaunchBlaster.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        self.assertTrue(glob.glob("*fa_cut*") == [])
-        self.assertTrue(glob.glob("*Nstretch*") == [])
-        self.assertTrue(glob.glob("*seq_treated*") == [])
-        self.assertTrue(glob.glob("*.log") == [])
-        
-    def test_run_as_script_1bank_1file(self):
-        inputFileName = "chunks.fa"
-        with open(inputFileName, "w") as f:
-            f.write(">chunk1\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-        expFileName = "exp.align"
-        with open(expFileName, "w") as f:
-            f.write("chunk1\t1\t120\tdmel_chr4\t1\t120\t2e-64\t238\t100\n")
-        obsFileName = "%s.align" % inputFileName
-        
-        cmd = "LaunchBlaster.py -q %s -s %s -e 0.1 -a" % (inputFileName, self._inFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        FileUtils.removeFilesByPattern("%s*" % inputFileName)
-        os.remove(expFileName)
-        
-    def test_run_as_script_1bank_1file_withoutABA(self):
-        queryFileName = "chunks.fa"
-        with open(queryFileName, "w") as f:
-            f.write(">chunk1\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-        subjectFileName = "genome.fa"
-        with open(subjectFileName, "w") as f:
-            f.write(">chunk1\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-            f.write(">chunk2\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-        expFileName = "exp.align"
-        with open(expFileName, "w") as f:
-            f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
-            f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
-        obsFileName = "%s.align" % queryFileName
-        
-        cmd = "LaunchBlaster.py -q %s -s %s -e 0.1" % (queryFileName, subjectFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        FileUtils.removeFilesByPattern("%s*" % queryFileName)
-        FileUtils.removeFilesByPattern("%s*" % subjectFileName)
-        os.remove(expFileName)
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_LaunchBlasterInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import unittest
-import os
-import shutil
-from commons.tools.LaunchBlasterInParallel import LaunchBlasterInParallel
-
-class Test_F_LaunchBlasterInParallel(unittest.TestCase):
-
-    CLUSTER_HOST = "compute-2-46.local"
-
-    def setUp(self):
-        self._inFilePath = "%s/Tools/DmelChr4_chunks.fa" % os.environ["REPET_DATA"]
-        self._configFileName = "TE.cfg"
-        self._outputFileName = "out.align.not_over"
-
-    def tearDown(self):
-        try:
-            os.remove(self._outputFileName)
-            os.remove(self._configFileName)
-        except:
-            pass
-
-    def test_run_as_script_1bank_1file_withoutABA(self):
-        self._outputFileName = "out.align"
-        os.mkdir("tmp")
-        os.chdir("tmp")
-        queryFileName = "chunks.fa"
-        with open(queryFileName, "w") as f:
-            f.write(">chunk1\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-        os.chdir("..")
-        subjectFileName = "genome.fa"
-        with open(subjectFileName, "w") as f:
-            f.write(">chunk1\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-            f.write(">chunk2\n")
-            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
-            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
-        expFileName = "expected"
-        with open(expFileName, "w") as f:
-            f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
-            f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
-        self._writeConfig(0.1)
-        
-        cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s/%s -C %s -o %s" % (os.getcwd(), os.getcwd(), subjectFileName, self._configFileName, self._outputFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        FileUtils.removeFilesByPattern("*.param")
-        shutil.rmtree("tmp")
-        os.remove(subjectFileName)
-        os.remove(expFileName)
-        
-    def test_run_as_script_1bank_2_batches(self):
-        os.mkdir("tmp")
-        os.chdir("tmp")
-        os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
-        os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
-        os.chdir("..")
-        
-        expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
-        self._writeConfig()
-        
-        cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s -a -o %s -C %s" % (os.getcwd(), self._inFilePath, self._outputFileName, self._configFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        FileUtils.removeFilesByPattern("*.param")
-        shutil.rmtree("tmp")
-        
-    def test_run_1bank_1bank_2_batches(self):
-        os.mkdir("tmp")
-        os.chdir("tmp")
-        os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
-        os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
-        os.chdir("..")
-        
-        expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
-        self._writeConfig()
-        
-        iLaunchBlaster = LaunchBlasterInParallel(configFileName = self._configFileName, outFileName = self._outputFileName)
-        iLaunchBlaster.setDoAllByall(True)
-        iLaunchBlaster.setVerbosity(4)
-        iLaunchBlaster.setQueryDirectory("%s/tmp" % os.getcwd())
-        iLaunchBlaster.setSubjectFilePath(self._inFilePath)
-        iLaunchBlaster.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
-        FileUtils.removeFilesByPattern("*.param")
-        shutil.rmtree("tmp")
-        
-    def _writeConfig(self, eValue = 1e-300):
-        with open(self._configFileName, "w") as fh:
-            fh.write("[jobs]\n")
-            if os.getenv("HOSTNAME") == self.CLUSTER_HOST:
-                fh.write("resources: test\n")
-            else:
-                fh.write("resources:\n")
-            fh.write("tmpDir:\n")
-            fh.write("copy: no\n") 
-            fh.write("clean: yes\n")
-            fh.write("\n")
-            fh.write("[prepare_data]\n")
-            fh.write("chunk_length: 200000\n")
-            fh.write("chunk_overlap: 10000\n")
-            fh.write("\n")
-            fh.write("[alignment]\n")
-            fh.write("blast: ncbi\n")
-            fh.write("Evalue: %s\n" % eValue)
-            fh.write("length: 100\n")
-            fh.write("identity: 90\n")
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_LaunchMatcherInParallel.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-import shutil
-import unittest
-import os
-from commons.tools.LaunchMatcherInParallel import LaunchMatcherInParallel
-
-class Test_F_LaunchMatcherInParallel(unittest.TestCase):
-
-    CLUSTER_HOST = "compute-2-46.local"
-
-    def setUp(self):
-        self._configFileName = "TE.cfg"
-        self._writeConfig()
-
-    def tearDown(self):
-        FileUtils.removeFilesByPattern("DmelChr4*")
-        os.remove(self._configFileName)
-
-    def test_run_as_class_1_seq(self):
-        inFileName = "DmelChr4.align"
-        fastaFileName = "DmelChr4.fa"
-        inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
-        inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
-        os.symlink(inFilePath, inFileName)
-        os.symlink(inFastaPath, fastaFileName)
-        expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
-        expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
-        
-        obsPathFileName = "%s.match.path" % inFileName
-        obsTabFileName = "%s.match.tab" % inFileName
-        
-        iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName)
-        iLaunchMatcherInParallel.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
-
-    def test_run_as_class_n_seq_less_jobs_than_n(self):
-        inFileName = "DmelChr4_dummy.align"
-        fastaFileName = "DmelChr4.fa"
-        inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
-        inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
-        os.symlink(inFilePath, inFileName)
-        os.symlink(inFastaPath, fastaFileName)
-        expPathFileName = "%s/Tools/DmelChr4_dummy.align.match.path" % os.environ["REPET_DATA"]
-        expTabFileName = "%s/Tools/DmelChr4_dummy.align.match.tab" % os.environ["REPET_DATA"]
-        
-        obsPathFileName = "%s.match.path" % inFileName
-        obsTabFileName = "%s.match.tab" % inFileName
-        
-        iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, doClean=True)
-        iLaunchMatcherInParallel.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
-        
-    def test_run_as_class_n_seq_less_jobs_than_n_not_merged_results(self):
-        inFileName = "DmelChr4_dummy.align"
-        fastaFileName = "DmelChr4.fa"
-        inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName)
-        inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName)
-        os.symlink(inFilePath, inFileName)
-        os.symlink(inFastaPath, fastaFileName)
-        
-        iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, maxFileSize=100, mergeResults=False)
-        iLaunchMatcherInParallel.run()
-        
-        baseFileName = os.path.splitext(inFileName)[0]
-        lExpMatchFileNames = ["%s_1.align.match.path" % baseFileName, "%s_2.align.match.path" % baseFileName, "%s_3.align.match.path" % baseFileName]
-        lExpTabFileNames = ["%s_1.align.match.tab" % baseFileName, "%s_2.align.match.tab" % baseFileName, "%s_3.align.match.tab" % baseFileName]
-        for i in range(0,3):
-            self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpMatchFileNames[i]))
-            self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpTabFileNames[i]))
-        shutil.rmtree("tmpMatcher")
-
-    def _writeConfig(self):
-        with open(self._configFileName, "w") as fh:
-            fh.write("[jobs]\n")
-            if os.getenv("HOSTNAME") == self.CLUSTER_HOST:
-                fh.write("resources: test\n")
-            else:
-                fh.write("resources:\n")
-            fh.write("tmpDir:\n")
-            fh.write("copy: no\n") 
-            fh.write("clean: yes\n")
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_MergeMatchsFiles.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,302 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.MergeMatchsFiles import MergeMatchsFiles
-
-
-class Test_F_MergeMatchsFiles(unittest.TestCase):
-
-    def test_run_set(self):
-        inFileName1 = "test1.set"
-        inFileName2 = "test2.set"
-        self._writeSetFiles(inFileName1, inFileName2)
-        iMMF = MergeMatchsFiles("set", "out")
-        iMMF.run()
-        obsFileName = "out.set"
-        expFileName = "exp.set"
-        self._writeExpSetFile(expFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        os.remove(obsFileName)
-
-    def test_run_align(self):
-        inFileName1 = "test1.align"
-        inFileName2 = "test2.align"
-        self._writeAlignFiles(inFileName1, inFileName2)
-        iMMF = MergeMatchsFiles("align", "out")
-        iMMF.run()
-        obsFileName = "out.align"
-        expFileName = "exp.align"
-        self._writeExpAlignFile(expFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        os.remove(obsFileName)
-
-    def test_run_align_allByAll(self):
-        inFileName1 = "test1.align"
-        inFileName2 = "test2.align"
-        self._writeAlignFiles(inFileName1, inFileName2)
-        iMMF = MergeMatchsFiles("align", "out", True)
-        iMMF.run()
-        obsFileName = "out.align"
-        expFileName = "exp.align"
-        self._writeExpAlignFile_allByAll(expFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        os.remove(obsFileName)
-
-    def test_run_path(self):
-        inFileName1 = "test1.path"
-        inFileName2 = "test2.path"
-        self._writePathFiles(inFileName1, inFileName2)
-        iMMF = MergeMatchsFiles("path", "out")
-        iMMF.run()
-        obsFileName = "out.path"
-        expFileName = "exp.path"
-        self._writeExpPathFile(expFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        os.remove(obsFileName)
-
-    def test_run_tab(self):
-        inFileName1 = "test1.tab"
-        inFileName2 = "test2.tab"
-        self._writeTabFiles(inFileName1, inFileName2)
-        iMMF = MergeMatchsFiles("tab", "out")
-        iMMF.run()
-        obsFileName = "out.tab"
-        expFileName = "exp.tab"
-        self._writeExpTabFile(expFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        
-    def _writeSetFiles(self, fileName1, fileName2):
-        f = open(fileName1, "w")
-        f.write("1\t(TCTAT)3\tchunk006\t295\t309\n")
-        f.write("2\t(A)33\tchunk006\t679\t711\n")
-        f.write("3\t(G)16\tchunk006\t731\t746\n")
-        f.write("4\t(GAG)9\tchunk006\t903\t929\n")
-        f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n")
-        f.close()
-        f = open(fileName2, "w")
-        f.write("1\t(CCACT)3\tchunk011\t101\t116\n")
-        f.write("2\t(TATATA)7\tchunk011\t316\t357\n")
-        f.write("3\t(AT)22\tchunk011\t323\t366\n")
-        f.close()
-        
-    def _writeExpSetFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("1\t(TCTAT)3\tchunk006\t295\t309\n")
-        f.write("2\t(A)33\tchunk006\t679\t711\n")
-        f.write("3\t(G)16\tchunk006\t731\t746\n")
-        f.write("4\t(GAG)9\tchunk006\t903\t929\n")
-        f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n")
-        f.write("6\t(CCACT)3\tchunk011\t101\t116\n")
-        f.write("7\t(TATATA)7\tchunk011\t316\t357\n")
-        f.write("8\t(AT)22\tchunk011\t323\t366\n")
-        f.close()
-
-    def _writeAlignFiles(self, fileName1, fileName2):
-        f = open(fileName1, "w")
-        f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n")
-        f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n")
-        f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n")
-        f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n")
-        f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n")
-        f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n")
-        f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n")
-        f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n")
-        f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n")
-        f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n")
-        f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n")
-        f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n")
-        f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n")
-        f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n")
-        f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n")
-        f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n")
-        f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n")
-        f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n")
-        f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n")
-        f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n")
-        f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n")
-        f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n")
-        f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n")
-        f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n")
-        f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n")
-        f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n")
-        f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n")
-        f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n")
-        f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n")
-        f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n")
-        f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n")
-        f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n")
-        f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n")
-        f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n")
-        f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n")
-        f.close()
-        f = open(fileName2, "w")
-        f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n")
-        f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n")
-        f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n")
-        f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n")
-        f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n")
-        f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n")
-        f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n")
-        f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n")
-        f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n")
-        f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n")
-        f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n")
-        f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n")
-        f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n")
-        f.close()
-        
-    def _writeExpAlignFile_allByAll(self, fileName):
-        f = open(fileName, "w")
-        f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.360000\n")
-        f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.160000\n")
-        f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.290000\n")
-        f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.630000\n")
-        f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.560000\n")
-        f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.180000\n")
-        f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.590000\n")
-        f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.360000\n")
-        f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.110000\n")
-        f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.620000\n")
-        f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.520000\n")
-        f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.630000\n")
-        f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.740000\n")
-        f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.140000\n")
-        f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.800000\n")
-        f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.510000\n")
-        f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.280000\n")
-        f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.270000\n")
-        f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.080000\n")
-        f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.480000\n")
-        f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.950000\n")
-        f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.420000\n")
-        f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.770000\n")
-        f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.190000\n")
-        f.close()
-        
-    def _writeExpAlignFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n")
-        f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n")
-        f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n")
-        f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n")
-        f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n")
-        f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n")
-        f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n")
-        f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n")
-        f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n")
-        f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n")
-        f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n")
-        f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n")
-        f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n")
-        f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n")
-        f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n")
-        f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n")
-        f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n")
-        f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n")
-        f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n")
-        f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n")
-        f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n")
-        f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n")
-        f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n")
-        f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n")
-        f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n")
-        f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n")
-        f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n")
-        f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n")
-        f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n")
-        f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n")
-        f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n")
-        f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n")
-        f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n")
-        f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n")
-        f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n")
-        f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n")
-        f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n")
-        f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n")
-        f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n")
-        f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n")
-        f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n")
-        f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n")
-        f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n")
-        f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n")
-        f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n")
-        f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n")
-        f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n")
-        f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n")
-        f.close()
-
-    def _writePathFiles(self, fileName1, fileName2):
-        f = open(fileName1, "w")
-        f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n")
-        f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n")
-        f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n")
-        f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n")
-        f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n")
-        f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n")
-        f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n")
-        f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n")
-        f.close()
-        f = open(fileName2, "w")
-        f.write("1\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n")
-        f.write("2\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n")
-        f.write("3\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n")
-        f.write("4\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n")
-        f.write("5\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n")
-        f.write("6\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n")
-        f.close()
-        
-    def _writeExpPathFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n")
-        f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n")
-        f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n")
-        f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n")
-        f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n")
-        f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n")
-        f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n")
-        f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n")
-        f.write("9\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n")
-        f.write("10\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n")
-        f.write("11\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n")
-        f.write("12\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n")
-        f.write("13\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n")
-        f.write("14\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n")
-        f.close()
-        
-    def _writeTabFiles(self, fileName1, fileName2):
-        f = open(fileName1, "w")
-        f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n")
-        f.close()
-        f = open(fileName2, "w")
-        f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t1\n")
-        f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t2\n")
-        f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t3\n")
-        f.close()
-        
-    def _writeExpTabFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n")
-        f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t6\n")
-        f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t7\n")
-        f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t8\n")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_PostAnalyzeTELib.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,294 +0,0 @@
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-from commons.tools.PostAnalyzeTELib import PostAnalyzeTELib
-import subprocess
-import unittest
-import os
-
-
-class Test_F_PostAnalyzeTELib(unittest.TestCase):
-    
-    def setUp(self):
-        self._expStatFileName = "expStats.tab"
-        self._obsStatFileName = ""
-        self._genomeSize = 1281640
-        self._pathTableName = "dummyDmelChr4_chr_allTEs_nr_noSSR_join_path"
-        self._seqTableName = "dummyDmelChr4_denovoLibTEs_seq"
-        
-    def tearDown(self):
-        try:
-            os.remove(self._expStatFileName)
-        except: pass
-        try:
-            os.remove(self._obsStatFileName)
-        except: pass
-
-    def test_run_analysis1(self):
-        libFileName = "TElib.fa"
-        self._writeInputFasta_analysis1(libFileName)
-        expClusterFileName = "expClusters.tab"
-        self._writeExpClusterFile_analysis1(expClusterFileName)
-        expGlobalStatFileName = "expGlobalStats.txt"
-        self._writeExpGlobalStats_analysis1(expGlobalStatFileName)
-        self._writeExpStatsFile_analysis1(self._expStatFileName)
-        obsClusterFileName = "TElib.tab"
-        obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt"
-        self._obsStatFileName = "TElib.statsPerCluster.tab"
-        
-        iPATEL = PostAnalyzeTELib(analysis=1, fastaFileName=libFileName, doClean=True)
-        iPATEL.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
-        
-        os.remove(libFileName)
-        os.remove(expClusterFileName)
-        os.remove(expGlobalStatFileName)
-        os.remove(obsClusterFileName)
-        os.remove(obsGlobalStatFileName)
-
-    def test_run_as_script_analysis1(self):
-        libFileName = "TElib.fa"
-        with open(libFileName, "w") as f:
-            f.write(">transib2\n")
-            f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
-            f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
-            f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTC\n")
-            f.write(">transib3\n")
-            f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
-            f.write("TGAAACTCGTCAGCGTCGTTTCCAAGTCCT\n")
-            f.write(">transib4\n")
-            f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
-            f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
-            f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCAT\n")
-            f.write("AAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
-        expClusterFileName = "expClusters.tab"
-        with open(expClusterFileName, "w") as f:
-            f.write("transib4 \n")
-            f.write("transib2 \n")
-            f.write("transib3 \n")
-        with open(self._expStatFileName, "w") as f:
-            f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n")
-            f.write("1\t1\t238\t238\t238\t238\n")
-            f.write("2\t1\t178\t178\t178\t178\n")
-            f.write("3\t1\t90\t90\t90\t90\n")
-        expGlobalStatFileName = "expGlobalStats.txt"
-        with open(expGlobalStatFileName, "w") as f:
-            f.write("nb of clusters: 3\n")
-            f.write("nb of clusters with 1 sequence: 3\n")
-            f.write("nb of clusters with 2 sequences: 0\n")
-            f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n")
-            f.write("nb of sequences: 3\n")
-            f.write("nb of sequences in the largest cluster: 1\n")
-            f.write("nb of sequences in the smallest cluster: 1\n")
-            f.write("size of the smallest sequence: 90\n")
-            f.write("size of the largest sequence: 238\n")
-            f.write("average sequences size: 168\n")
-            f.write("median sequences size: 178\n")
-        obsClusterFileName = "TElib.tab"
-        obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt"
-        self._obsStatFileName = "TElib.statsPerCluster.tab"
-        
-        cmd = "PostAnalyzeTELib.py -i %s -L 98 -S 95 -b -c -v 3" % libFileName
-        process = subprocess.Popen(cmd, shell = True)
-        process.communicate()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
-        
-        os.remove(libFileName)
-        os.remove(expClusterFileName)
-        os.remove(expGlobalStatFileName)
-        os.remove(obsClusterFileName)
-        os.remove(obsGlobalStatFileName)
-
-    def test_run_analysis2(self):
-        clusterFileName = "ConsensusClusters.tab"
-        self._writeClusterFile_analysis2(clusterFileName)
-        self._writeExpStatsFile_analysis2(self._expStatFileName)
-        self._obsStatFileName = "ConsensusClusters.classifStatsPerCluster.tab"
-        
-        iPATEL = PostAnalyzeTELib(analysis=2, clusterFileName=clusterFileName, verbosity=3)
-        iPATEL.run()
-        print "exp: %s, obs: %s" % (self._expStatFileName, self._obsStatFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
-        
-        os.remove(clusterFileName)
-
-    def test_run_analysis3(self):
-        iDb = DbFactory.createInstance()
-        iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True)
-        iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True)
-       
-        expGlobalStatFileName = "expGlobalStats.txt"
-        self._writeExpGlobalStats_analysis3(expGlobalStatFileName)
-        self._writeExpStatsFile_analysis3(self._expStatFileName)
-        obsGlobalStatFileName = "%s.globalAnnotStatsPerTE.txt" % self._pathTableName
-        self._obsStatFileName = "%s.annotStatsPerTE.tab" % self._pathTableName
-
-        iPATEL = PostAnalyzeTELib(analysis=3, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize)
-        iPATEL.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
-        
-        iDb.dropTable(self._pathTableName)
-        iDb.dropTable(self._seqTableName)
-        iDb.close()
-        os.remove(expGlobalStatFileName)
-        os.remove(obsGlobalStatFileName)
-
-    def test_run_analysis4(self):
-        iDb = DbFactory.createInstance()
-        iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True)
-        iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True)
-        
-        clusterFileName = "clusters.tab"
-        self._writeClusterFile_analysis4(clusterFileName)
-        self._writeExpStatsFile_analysis4(self._expStatFileName)
-        self._obsStatFileName = "%s.annotStatsPerCluster.tab" % self._pathTableName
-        
-        iPATEL = PostAnalyzeTELib(analysis=4, clusterFileName=clusterFileName, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize)
-        iPATEL.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
-        
-        iDb.dropTable(self._pathTableName)
-        iDb.dropTable(self._seqTableName)
-        iDb.close()
-        os.remove(clusterFileName)
-    
-    def _writeInputFasta_analysis1(self, fileName):
-        with open(fileName, "w") as f:
-            f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
-            f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-            f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-            f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-            f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-            f.write(">DTX-incomp_DmelChr4-B-R10-Map3\n")
-            f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
-            f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
-            f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
-            f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
-            f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
-            f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
-            f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
-            f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
-        
-    def _writeExpClusterFile_analysis1(self, fileName):
-        with open(fileName, "w") as f:
-            f.write("DTX-incomp_DmelChr4-B-R10-Map3 DTX-incomp_DmelChr4-B-R9-Map3_reversed \n")
-            f.write("PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed \n")
-        
-    def _writeExpStatsFile_analysis1(self, fileName):
-        #TODO: header in option ?
-        with open(fileName, "w") as f:
-            f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n")
-            f.write("1\t2\t240\t240\t240\t240\n")
-            f.write("2\t1\t180\t180\t180\t180\n")
-        
-    def _writeExpGlobalStats_analysis1(self, fileName):
-        #TODO: file or STDOUT ?
-        with open(fileName, "w") as f:
-            f.write("nb of clusters: 2\n")
-            f.write("nb of clusters with 1 sequence: 1\n")
-            f.write("nb of clusters with 2 sequences: 1\n")
-            f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n")
-            f.write("nb of sequences: 3\n")
-            f.write("nb of sequences in the largest cluster: 2\n")
-            f.write("nb of sequences in the smallest cluster: 1\n")
-            f.write("size of the smallest sequence: 180\n")
-            f.write("size of the largest sequence: 240\n")
-            f.write("average sequences size: 220\n")
-            f.write("median sequences size: 240\n")
-        
-    def _writeClusterFile_analysis2(self, fileName):
-        with open(fileName, "w") as f:
-            f.write("DTX-incomp_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tPotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
-            f.write("DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_Blc1_DmelChr4-B-R10-Map3\n")
-            f.write("DXX-comp_DmelChr4-B-R9-Map3\tDTX-comp_DmelChr4-B-R10-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tnoCat_DmelChr4-B-G1-Map3\tnoCat_DmelChr4-B-R1-Map4\n")
-            f.write("RXX-MITE_DmelChr4-B-G7-Map3\tRXX-MITE_DmelChr4-B-G5-Map3\tRXX-MITE_DmelChr4-B-G2-Map3\tRXX-MITE_DmelChr4-B-G23-Map3\tRXX-MITE_DmelChr4-B-G6-Map3\n")
-        
-    def _writeExpStatsFile_analysis2(self, fileName):
-        #TODO: header in option ?
-        with open(fileName, "w") as f:
-            f.write("cluster\tnoCat\tPotentialChimeric\tcomp\tincomp\tclassifs (nbTEs)\n")
-            f.write("1\t0\t1\t0\t2\tDTX (2)\tPotentialHostGene (1)\n")
-            f.write("2\t0\t0\t0\t2\tDTX (2)\n")
-            f.write("3\t2\t0\t2\t1\tDTX (2)\tDXX (1)\n")
-            f.write("4\t0\t0\t0\t0\tMITE (5)\n")
-
-    def _writeExpStatsFile_analysis3(self, fileName):
-        #TODO: header in option ?
-        with open(fileName, "w") as f:
-            f.write("TE\tlength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tmeanLgth\tmeanLgthPerc\n")
-            f.write("DmelChr4-B-G1-Map3_NoCat\t542\t3701\t12\t4\t10\t4\t95.72\t370.10\t68.28\n")
-            f.write("DmelChr4-B-G11-Map20_classII-TIR-incomp\t1240\t8216\t27\t0\t22\t0\t88.80\t375.00\t30.24\n")
-            f.write("DmelChr4-B-G7-Map3_classII-TIR-incomp\t1944\t15212\t49\t1\t42\t1\t89.44\t382.36\t19.67\n")
-            f.write("DmelChr4-B-G9-Map3_NoCat\t1590\t11564\t24\t0\t21\t1\t92.03\t550.67\t34.63\n")
-            f.write("DmelChr4-B-P0.0-Map3_classII-TIR-incomp\t1042\t4001\t13\t3\t11\t3\t85.11\t366.36\t35.16\n")
-            f.write("DmelChr4-B-R1-Map4_NoCat\t2367\t66031\t484\t0\t361\t0\t77.84\t182.91\t7.73\n")
-            f.write("DmelChr4-B-R12-Map3_NoCat\t2284\t4938\t3\t2\t3\t2\t99.26\t1646.00\t72.07\n")
-            f.write("DmelChr4-B-R19-Map4_NoCat\t705\t3328\t10\t3\t10\t3\t88.51\t332.80\t47.21\n")
-            f.write("DmelChr4-B-R2-Map6_NoCat\t4638\t20539\t34\t2\t29\t3\t80.93\t708.24\t15.27\n")
-            f.write("DmelChr4-B-R4-Map5_NoCat\t1067\t7292\t35\t1\t28\t1\t86.50\t260.54\t24.42\n")
-            f.write("DmelChr4-B-R9-Map3_NoCat\t714\t5453\t19\t2\t16\t2\t81.18\t340.81\t47.73\n")
-        
-    def _writeExpGlobalStats_analysis3(self, fileName):
-        with open(fileName, "w") as f:
-            f.write("nb of sequences: 11\n")
-            f.write("nb of matched sequences: 11\n")
-            f.write("cumulative coverage: 150275 bp\n")
-            f.write("coverage percentage: 11.73%\n")
-            f.write("\n")
-            f.write("total nb of TE fragments: 710\n")
-            f.write("total nb full-length fragments: 18 (2.54%)\n")
-            f.write("total nb of TE copies: 553\n")
-            f.write("total nb full-length copies: 20 (3.62%)\n")
-            f.write("families with full-length fragments: 8 (72.73%)\n")
-            f.write(" with only one full-length fragment: 2\n")
-            f.write(" with only two full-length fragments: 3\n")
-            f.write(" with only three full-length fragments: 2\n")
-            f.write(" with more than three full-length fragments: 1\n")
-            f.write("families with full-length copies: 9 (81.82%)\n")
-            f.write(" with only one full-length copy: 3\n")
-            f.write(" with only two full-length copies: 2\n")
-            f.write(" with only three full-length copies: 3\n")
-            f.write(" with more than three full-length copies: 1\n")
-            f.write("mean of median identity of all families: 88.30 +- 8.33\n")
-            f.write("mean of median length percentage of all families: 30.83 +- 32.30\n")
-            
-    def _writeClusterFile_analysis4(self, fileName):
-        with open(fileName, "w") as f:
-            f.write("1\tDmelChr4-B-R1-Map4_NoCat\tDmelChr4-B-R2-Map6_NoCat\tDmelChr4-B-R4-Map5_NoCat\n")
-            f.write("2\tDmelChr4-B-G7-Map3_classII-TIR-incomp\tDmelChr4-B-P0.0-Map3_classII-TIR-incomp\n")
-
-    def _writeExpStatsFile_analysis4(self, fileName):
-        with open(fileName, "w") as f:
-            f.write("Cluster\tcovg\tfrags\tcopies\n")
-            f.write("1\t93862\t553\t418\n")
-            f.write("2\t19213\t62\t53\n")
-            
-    def _writeConfigFile(self, configFileName):
-        with open(configFileName, "w") as fHandle:
-            fHandle.write("[repet_env]\n")
-            fHandle.write("repet_host: %s\n" % os.environ["REPET_HOST"])
-            fHandle.write("repet_user: %s\n" % os.environ["REPET_USER"])
-            fHandle.write("repet_pw: %s\n" % os.environ["REPET_PW"])
-            fHandle.write("repet_db: %s\n" % os.environ["REPET_DB"])
-            fHandle.write("repet_port: 3306\n")
-            fHandle.write("[analysis1]\n")
-            fHandle.write("fasta_name: %s\n" % self._expStatFileName)
-            
-            fHandle.write("[analysis2]\n")
-            fHandle.write("clusterFileName: %s\n" % self._expStatFileName)
-            
-            fHandle.write("[analysis3]\n")
-            fHandle.write("pathTableName: %s\n" % self._pathTableName)
-            fHandle.write("seqTableName: %s\n" % self._seqTableName)
-            fHandle.write("genomeSize: %s\n" % self._genomeSize)
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.tests.MockFastaForReplaceGreaterThanSymbolInFastaHeader import MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan,\
-    MockFastaForReplaceGreaterThanSymbolInFastaHeader
-from commons.tools.replaceGreaterThanSymbolInFastaHeaderProgramLauncher import replaceGreaterThanSymbolInFastaHeaderProgramLauncher
-
-class Test_F_ReplaceGreaterThanSymbolInHeader(unittest.TestCase):
-
-
-    def test_run(self):
-        inputFileName = "dummy_fasta.fsa"
-        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
-        mockInput.write(inputFileName)
-        
-        expFileName = "exp_dummy_fasta.preprocessed.fsa"
-        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
-        mockInput.write(expFileName)
-        
-        obsFileName = "dummy_fasta.preprocessed.fasta"
-        rgtspl = replaceGreaterThanSymbolInFastaHeaderProgramLauncher()
-        rgtspl.setInputFile(inputFileName)
-        rgtspl.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(inputFileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-
-    def test_run_as_script(self):
-        inputFileName = "dummy_fasta.fsa"
-        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
-        mockInput.write(inputFileName)
-        
-        expFileName = "exp_dummy_fasta.preprocessed.fsa"
-        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
-        mockInput.write(expFileName)
-        
-        obsFileName = "dummy_fasta.preprocessed.fasta"
-
-        cmd2Launch = "replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py -i " + inputFileName
-        os.system(cmd2Launch)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(inputFileName)       
-        os.remove(expFileName)
-        os.remove(obsFileName)    
-
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_RetrieveInitHeaders.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.sql.TablePathAdaptator import TablePathAdaptator
-from commons.core.coord.PathUtils import PathUtils
-from commons.core.utils.FileUtils import FileUtils
-import os
-import unittest
-
-class Test_F_RetrieveInitHeaders(unittest.TestCase):
-    
-    def setUp(self):
-        self._iDb = DbMySql()
-        
-    def tearDown(self):
-        self._iDb.close()
-
-    def test_run_as_script_rename_subject_and_clean_table(self):
-        shortHLinkFileName = "dummy.shortHlink"
-        self._writeShortHLinkFile(shortHLinkFileName)
-        pathTableName = "dummyInput_path"
-        self._createPathTable(pathTableName)
-        expFileName = "exp.path"
-        self._writeExpFile(expFileName)
-        obsTableName = "dummyOutput_path"
-        
-        cmd = "RetrieveInitHeaders.py -i %s -l %s -o %s -s -c -v 1" % (pathTableName, shortHLinkFileName, obsTableName)
-        os.system(cmd)
-
-        self.assertTrue(self._iDb.doesTableExist(obsTableName))        
-        self.assertFalse(self._iDb.doesTableExist(pathTableName))
-        obsFileName = "obs.path"
-        iTPA = TablePathAdaptator(self._iDb, obsTableName)
-        lPaths = iTPA.getListOfAllPaths()
-        PathUtils.writeListInFile(lPaths, obsFileName)
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        os.remove(shortHLinkFileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        self._iDb.dropTable(obsTableName)
-    
-    def _writeShortHLinkFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("refTE_1\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t1\t5388\n")
-        f.write("refTE_2\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t1\t6385\n")
-        f.write("refTE_3\tPaphi_v2-B-R8543-Map9_classI-LTR-comp\t1\t7148\n")
-        f.write("refTE_4\tPaphi_v2-B-R33384-Map4_classI-LTR-incomp\t1\t262\n")
-        f.write("refTE_5\tPaphi_v2-B-P73.1298-Map3_classI-LTR-incomp\t1\t389\n")
-        f.write("refTE_6\tPaphi_v2-B-R36143-Map3_classI-LTR-incomp\t1\t393\n")
-        f.write("refTE_7\tPaphi_v2-B-R35261-Map5_classI-LTR-incomp\t1\t408\n")
-        f.write("refTE_8\tPaphi_v2-B-R12434-Map4_classI-LTR-incomp\t1\t420\n")
-        f.write("refTE_9\tPaphi_v2-B-R20580-Map4_classI-LTR-incomp\t1\t426\n")
-        f.write("refTE_10\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t1\t441\n")
-        f.close()
-        
-    def _createPathTable(self, tableName):
-        fileName = "dummy.path"
-        f = open(fileName, "w")
-        f.write("7615\tchunk0030\t188432\t188611\trefTE_1\t5386\t5208\t0\t174\t97.23\n")
-        f.write("86375\tchunk0372\t155816\t157157\trefTE_1\t2213\t3575\t0\t843\t62.89\n")
-        f.write("88018\tchunk0381\t52141\t53500\trefTE_1\t2191\t3575\t0\t860\t63.3\n")
-        f.write("110377\tchunk0473\t117281\t117518\trefTE_1\t3966\t3716\t0\t230\t97.05\n")
-        f.write("39621\tchunk0169\t123563\t124003\trefTE_10\t1\t441\t0\t439\t99.55\n")
-        f.write("544710\tchunk2778\t62387\t62625\trefTE_10\t100\t327\t0\t165\t69.09\n")
-        f.write("601761\tchunk4780\t441\t559\trefTE_10\t5\t123\t0\t119\t100\n")
-        f.write("17589\tchunk0071\t58591\t59763\trefTE_2\t5139\t6384\t0\t1150\t98.12\n")
-        f.write("21050\tchunk0087\t186576\t186812\trefTE_2\t3636\t3891\t0\t232\t98.31\n")
-        f.close()
-        self._iDb.createTable(tableName, "path", fileName, True)
-        os.remove(fileName)
-        
-    def _writeExpFile(self, fileName):
-        f = open(fileName, "w")
-        f.write("7615\tchunk0030\t188432\t188611\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t5386\t5208\t0\t174\t97.230000\n")
-        f.write("86375\tchunk0372\t155816\t157157\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t2213\t3575\t0\t843\t62.890000\n")
-        f.write("88018\tchunk0381\t52141\t53500\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t2191\t3575\t0\t860\t63.300000\n")
-        f.write("110377\tchunk0473\t117281\t117518\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t3966\t3716\t0\t230\t97.050000\n")
-        f.write("39621\tchunk0169\t123563\t124003\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t1\t441\t0\t439\t99.550000\n")
-        f.write("544710\tchunk2778\t62387\t62625\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t100\t327\t0\t165\t69.090000\n")
-        f.write("601761\tchunk4780\t441\t559\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t5\t123\t0\t119\t100.000000\n")
-        f.write("17589\tchunk0071\t58591\t59763\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t5139\t6384\t0\t1150\t98.120000\n")
-        f.write("21050\tchunk0087\t186576\t186812\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t3636\t3891\t0\t232\t98.310000\n")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_SplicerFromAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,131 +0,0 @@
-import unittest
-import os
-from commons.core.sql.DbMySql import DbMySql
-from commons.core.utils.FileUtils import FileUtils
-#from commons.tools.SplicerFromAnnotation import SplicerFromAnnotation
-
-class Test_F_SplicerFromAnnotation(unittest.TestCase):
-
-    def setUp(self):
-        self._inFastaFileName = "%s/Tools/Splicer_inputFile.fa" % os.environ["REPET_DATA"]
-        self._outFastaFileName = "%s/Tools/Splicer_outputSplicedFile.fa.splice" % os.environ["REPET_DATA"]
-        self._refTEseqFileName = "%s/Tools/Splicer_refTEs_seq.fa" % os.environ["REPET_DATA"]
-        self.configFileName = "TEdenovo.cfg"
-        self._writeConfigFile()
-        self.pathFileName = "annotations_path"
-        self._writePathFile()
-        self._iDb = DbMySql(cfgFileName = self.configFileName)
-        self._tableName = "Splicer_inputFile_chr_allTEs_nr_noSSR_join_path"
-        self._iDb.createTable(self._tableName, "path", self.pathFileName, True)
-        self._tableName_refTEseq = "Splicer_inputFile_refTEs_seq"
-        self._iDb.createTable(self._tableName_refTEseq, "seq", self._refTEseqFileName, True)
-   
-    def tearDown(self):
-        self._iDb.dropTable(self._tableName)
-        self._iDb.dropTable(self._tableName_refTEseq)
-        self._iDb.dropTable("Splicer_inputFile_annotationIdentitySup80_path")
-        self._iDb.dropTable("Splicer_inputFile_annotationToSplice_path")
-        self._iDb.close()
-        os.remove("annotations_path")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.globalAnnotStatsPerTE.txt")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.fa")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.fa")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_OneCopyAndMore.txt")
-        os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_OneCopyAndMore.fa")
-        os.remove("Splicer_inputFile_annotationToSplice_path.path")
-        os.remove(self.configFileName)
-#        os.remove(self.obsOutSplicedFastaFileName)
-        
-    def test_run_as_script_FLC(self):
-        expOutSplicedFastaFileName = "%s/Tools/Splicer_outputSplicedFile_FLC.fa.splice" % os.environ["REPET_DATA"]
-        self.obsOutSplicedFastaFileName = "Splicer_inputFile_FLC.fa.splice"
-        self._writeConfigFile()
-        self._writePathFile()
-        cmd = 'SplicerFromAnnotation.py -i %s -C %s -o %s -v 2' % (self._inFastaFileName,self.configFileName, self.obsOutSplicedFastaFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutSplicedFastaFileName, self.obsOutSplicedFastaFileName))
-        
-    def test_run_as_script_FLF(self):
-        expOutSplicedFastaFileName = "%s/Tools/Splicer_outputSplicedFile_FLF.fa.splice" % os.environ["REPET_DATA"]
-        self.obsOutSplicedFastaFileName = "Splicer_inputFile_FLF.fa.splice"
-        self._writeConfigFile()
-        self._writePathFile()
-        cmd = 'SplicerFromAnnotation.py -i %s -t 3 -C %s -o %s -v 2' % (self._inFastaFileName,self.configFileName, self.obsOutSplicedFastaFileName)
-        os.system(cmd)
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expOutSplicedFastaFileName, self.obsOutSplicedFastaFileName))
-
-    def _writeConfigFile(self):
-        f = open(self.configFileName, "w")
-        f.write("[repet_env]\n")
-        f.write("repet_version: 2.0\n")
-        f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
-        f.write("repet_user: %s\n" % os.environ["REPET_USER"])
-        f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
-        f.write("repet_db: %s\n" % os.environ["REPET_DB"])
-        f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
-        f.write("repet_job_manager: %s\n" % os.environ["REPET_JOB_MANAGER"])
-        f.close()
-
-    def _writePathFile(self):      
-        f = open(self.pathFileName, "w")
-        f.write("1\tA_contig00012\t2853\t3530\tRLX-comp_3b_Itr1_v2-L-B1064-Map1_reversed\t8127\t8803\t0\t648\t95.7227\n")
-        f.write("3\tA_contig00012\t3531\t6064\tRLX-incomp_3b_Itr1_v2-L-B450-Map1\t3207\t709\t0\t2166\t85.4973\n")
-        f.write("4\tA_contig00012\t1\t1542\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t673\t2218\t0\t1460\t94.7437\n")
-        f.write("4\tA_contig00012\t1523\t2849\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t2385\t3693\t0\t1086\t81.9079\n")
-        f.write("23\tA_contig00033\t10551\t10668\tRLX-comp_3b_Itr1_v2-L-B2275-Map1\t668\t784\t1.3e-11\t97\t82.8571\n")
-        f.write("24\tA_contig00033\t7649\t7753\tRLX-comp_3b_Itr1_v2-L-B1105-Map1\t5349\t5453\t1.4e-13\t82\t78.5714\n")
-        f.write("25\tA_contig00033\t2998\t3243\tRLX-comp_3b_Itr1_v2-L-B757-Map1\t4422\t4659\t1.2e-12\t201\t81.8182\n")
-        f.write("26\tA_contig00033\t30462\t30502\tRLX-comp_3b_Itr1_v2-L-B389-Map1_reversed\t1548\t1509\t0\t38\t95.12\n")
-        f.write("26\tA_contig00033\t30462\t30504\tRLX-comp_3b_Itr1_v2-L-B389-Map1_reversed\t1548\t1505\t0\t41\t94.8026\n")
-        f.write("28\tA_contig00033\t6826\t7046\tRLX-comp_3b_Itr1_v2-L-B381-Map1\t5655\t5443\t0\t170\t77.3196\n")
-        f.write("30\tA_contig00033\t11712\t11818\tRLX-comp_3b_Itr1_v2-L-B108-Map1_reversed\t7782\t7682\t0\t80\t75\n")
-        f.write("31\tA_contig00033\t17122\t17221\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t9987\t9889\t0\t75\t75.2187\n")
-        f.write("32\tA_contig00033\t19069\t19131\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t8261\t8325\t2.8e-14\t45\t71.345\n")
-        f.write("33\tA_contig00033\t19343\t19375\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t8229\t8197\t0\t29\t86.6953\n")
-        f.write("34\tA_contig00033\t20411\t20783\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t7558\t7186\t0\t314\t84.4327\n")
-        f.write("35\tA_contig00033\t6346\t6541\tRLX-incomp-chim_3b_Itr1_v2-L-B359-Map1_reversed\t10604\t10416\t1.9e-24\t163\t83.2536\n")
-        f.write("36\tA_contig00033\t16757\t17121\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t8290\t7930\t0\t282\t77.5216\n")
-        f.write("37\tA_contig00033\t17222\t18658\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t7243\t5796\t0\t1094\t76.1977\n")
-        f.write("38\tA_contig00033\t19132\t19342\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5780\t5567\t0\t191\t90.9524\n")
-        f.write("39\tA_contig00033\t19409\t19455\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5558\t5512\t0\t38\t82.9787\n")
-        f.write("39\tA_contig00033\t19416\t19441\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5551\t5526\t0\t24\t96.15\n")
-        f.write("40\tA_contig00033\t19641\t20410\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5533\t4749\t0\t651\t84.55\n")
-        f.write("41\tA_contig00033\t19475\t19640\tDTX-incomp-chim_3b_Itr1_v2-L-B151-Map1_reversed\t9514\t9708\t0\t127\t76.7025\n")
-        f.write("42\tA_contig00033\t3244\t3364\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t2536\t2405\t6.8e-23\t95\t78.8462\n")
-        f.write("43\tA_contig00033\t19376\t19408\tRLX-comp_3b_Itr1_v2-L-B1517-Map1\t705\t733\t1.1e-11\t27\t80.4348\n")
-        f.write("43\tA_contig00033\t19456\t19474\tRLX-comp_3b_Itr1_v2-L-B1517-Map1\t775\t790\t1.1e-11\t15\t80.4348\n")
-        f.write("44\tA_contig00033\t5494\t5583\tRIX-incomp-chim_3b_Itr1_v2-L-B121-Map1\t7419\t7507\t4.9e-11\t68\t76.1905\n")
-        f.write("45\tA_contig00033\t10810\t11031\tRLX-comp_3b_Itr1_v2-L-B2073-Map1\t3079\t3297\t1e-17\t171\t77.2021\n")
-        f.write("46\tA_contig00033\t11253\t11406\tRLX-comp_3b_Itr1_v2-L-B1616-Map1\t1726\t1569\t0\t120\t78.2609\n")
-        f.write("47\tA_contig00033\t11407\t11508\tRLX-comp_3b_Itr1_v2-L-B351-Map1_reversed\t10133\t10039\t0\t79\t77.8689\n")
-        f.write("48\tA_contig00033\t3673\t3719\tRLX-comp_3b_Itr1_v2-L-B228-Map1_reversed\t13011\t12966\t0\t37\t78.629\n")
-        f.write("49\tA_contig00033\t3959\t4055\tRLX-comp_3b_Itr1_v2-L-B134-Map1_reversed\t1917\t2010\t5.5e-24\t74\t77.2727\n")
-        f.write("50\tA_contig00033\t30505\t37270\tRLX-comp_3b_Itr1_v2-L-B124-Map1\t14149\t7383\t0\t6365\t94.0818\n")
-        f.write("51\tA_contig00033\t8859\t9079\tRLX-incomp_3b_Itr1_v2-L-B2010-Map1_reversed\t390\t603\t1.9e-11\t171\t77.6596\n")
-        f.write("52\tA_contig00033\t9080\t9140\tRLX-incomp_3b_Itr1_v2-L-B1720-Map1_reversed\t1393\t1460\t0\t49\t80.8333\n")
-        f.write("53\tA_contig00033\t12386\t12435\tRLX-incomp_3b_Itr1_v2-L-B1706-Map1\t2678\t2725\t1.3e-25\t40\t81.1765\n")
-        f.write("54\tA_contig00033\t5052\t5096\tRLX-incomp_3b_Itr1_v2-L-B77-Map2_reversed\t5445\t5402\t6.1e-13\t37\t84.507\n")
-        f.write("55\tA_contig00033\t14485\t16756\tRLX-incomp_3b_Itr1_v2-L-B965-Map1\t4566\t6848\t0\t1881\t82.8154\n")
-        f.write("57\tA_contig00033\t10229\t10370\tRLX-incomp_3b_Itr1_v2-L-B502-Map1_reversed\t8598\t8438\t0\t109\t77.2727\n")
-        f.write("59\tA_contig00033\t2457\t2617\tRLX-incomp_3b_Itr1_v2-L-B405-Map1\t4742\t4910\t0\t129\t80.2721\n")
-        f.write("60\tA_contig00033\t8071\t8183\tRLX-incomp_3b_Itr1_v2-L-B109-Map1\t4413\t4529\t0\t97\t86.5979\n")
-        f.write("61\tA_contig00033\t12867\t14362\tRXX-LARD-chim_3b_Itr1_v2-L-B1998-Map1_reversed\t1465\t3000\t0\t1283\t85.8025\n")
-        f.write("62\tA_contig00033\t90\t256\tRXX-LARD-chim_3b_Itr1_v2-L-B1928-Map1\t905\t717\t2.5e-38\t128\t76.875\n")
-        f.write("63\tA_contig00033\t5097\t5249\tRXX-LARD-chim_3b_Itr1_v2-L-B1928-Map1\t4158\t4017\t4e-36\t127\t83.3333\n")
-        f.write("64\tA_contig00033\t8689\t8796\tRXX-LARD-chim_3b_Itr1_v2-L-B1905-Map1\t5584\t5469\t5.04467e-44\t85\t79.2079\n")
-        f.write("65\tA_contig00033\t6800\t6825\tRXX-LARD-chim_3b_Itr1_v2-L-B1790-Map1_reversed\t3426\t3399\t0\t21\t79.1667\n")
-        f.write("66\tA_contig00033\t10193\t10228\tRLX-comp-chim_3b_Itr1_v2-L-B1760-Map1_reversed\t1470\t1504\t8.7e-23\t29\t80.5195\n")
-        f.write("67\tA_contig00033\t6542\t6603\tRXX-LARD-chim_3b_Itr1_v2-L-B1741-Map1_reversed\t5509\t5567\t0\t48\t77.9412\n")
-        f.write("69\tA_contig00033\t12769\t12816\tRLX-comp-chim_3b_Itr1_v2-L-B1518-Map1\t2026\t1979\t0\t39\t81.25\n")
-        f.write("70\tA_contig00033\t28383\t29146\tRLX-comp-chim_3b_Itr1_v2-L-B1494-Map1_reversed\t999\t1761\t0\t672\t88.0282\n")
-        f.write("71\tA_contig00033\t21712\t28382\tRLX-incomp-chim_3b_Itr1_v2-L-B1485-Map1\t1132\t7813\t0\t6011\t90.1124\n")
-        f.write("71\tA_contig00033\t20784\t21728\tRLX-incomp-chim_3b_Itr1_v2-L-B1485-Map1\t159\t1113\t0\t833\t88.172 \n")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_F_TEclassifierPE.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-import os
-import unittest
-from commons.tools.TEclassifierPE import TEclassifierPE
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbFactory import DbFactory
-
-class Test_F_TEclassifierPE(unittest.TestCase):
-
-    def test_run(self):
-        projectName = "dummy"
-        configFileName = "dummy.cfg"
-        self.writeConfigFile(configFileName, projectName)
-        inputFileName = "dummy.fa"
-        with open(inputFileName, "w") as f:
-            f.write(">dummySSR\n")
-            f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
-            f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
-        expFileName = "exp.classif"
-        with open(expFileName, "w") as f:
-            f.write("dummySSR\t120\t.\tok\tNA\tSSR\tNA\tCI=100; struct=(TElength: <150bps; SSRCoverage=0.00)\n")
-        obsFileName = "%s.classif" % projectName
-        statsFileName = "%s.classif_stats.txt" % projectName
-        analysisFileName = "%s.SSR.set" % inputFileName
-            
-        iTEclassifierPE = TEclassifierPE(inputFileName, configFileName, doClean = True)
-        iTEclassifierPE.run()
-        
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        
-        iDb = DbFactory.createInstance()
-        iDb.dropTable("%s_TR_set" % projectName)
-        iDb.dropTable("%s_polyA_set" % projectName)
-        iDb.dropTable("%s_ORF_map" % projectName)
-        iDb.dropTable("%s_SSR_set" % projectName)
-        iDb.close()
-        os.remove(configFileName)
-        os.remove(inputFileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        os.remove(statsFileName)
-        os.remove(analysisFileName)
-        
-    def writeConfigFile(self, fileName, projectName):
-        with open(fileName, "w") as f:
-            f.write("[repet_env]\n")
-            f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
-            f.write("repet_user: %s\n" % os.environ["REPET_USER"])
-            f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
-            f.write("repet_db: %s\n" % os.environ["REPET_DB"])
-            f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
-            f.write("\n")
-            f.write("[project]\n")
-            f.write("project_name: %s\n" % projectName)
-            f.write("project_dir: %s\n" % os.getcwd())
-            f.write("\n")
-            f.write("[detect_features]\n")
-            f.write("clean: yes\n")
-            f.write("blast: ncbi\n")
-            f.write("term_rep: no\n")
-            f.write("polyA: no\n")
-            f.write("tand_rep: yes\n")
-            f.write("orf: no\n")
-            f.write("TE_HMMER: no\n")
-            f.write("TE_BLRtx: no\n")
-            f.write("TE_BLRn: no\n")
-            f.write("TE_BLRx: no\n")
-            f.write("HG_BLRn: no\n")
-            f.write("rDNA_BLRn: no\n") 
-            f.write("tRNA_scan: no\n")
-            f.write("TRFmaxPeriod: 15\n")
-            f.write("\n")
-            f.write("[classif_consensus]\n")
-            f.write("max_profiles_evalue: 1e-3\n")
-            f.write("min_TE_profiles_coverage: 20\n")
-            f.write("min_HG_profiles_coverage: 75\n")
-            f.write("max_helitron_extremities_evalue: 1e-3\n")
-            f.write("min_TE_bank_coverage: 5\n")
-            f.write("min_HG_bank_coverage: 95\n")
-            f.write("min_rDNA_bank_coverage: 95\n")
-            f.write("min_HG_bank_identity: 90\n")
-            f.write("min_rDNA_bank_identity: 90\n")
-            f.write("min_SSR_coverage: 0.75\n")
-            f.write("max_SSR_size: 150\n")
-            f.write("clean: yes\n")
-            
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-import unittest
-import os
-import time
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ):
-    
-    def setUp( self ):
-        self.fileUtils = FileUtils()
-        self._inputTEFile = "dummyTE"
-        self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq()
-        self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
-        self._configFileName = "dummyConfig_%s" % self._uniqId
-        configFile = open( self._configFileName, "w" )
-        configFile.write("[repet_env]\n")
-        configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
-        configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
-        configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
-        configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
-        configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
-        configFile.close()
-        
-    def tearDown( self ):
-        os.remove( self._configFileName )
-        os.remove( self._inputTEFile )
-    
-        
-    def test_getNamesOfTErefSeq_fromFile_ok(self):
-        expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed",
-                    "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"]
-        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
-        self.writeInputTEFile()
-        obsTEList = self._iGMAP.getNamesOfTErefSeq()
-        self.assertEqual(obsTEList, expTEList)
-    
-    def test_getNamesOfTErefSeq_from_empty_file(self):
-        expTEList =[]
-        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
-        with open(self._inputTEFile,"w") as TEFile:
-            TEFile.write("")
-        obsTEList = self._iGMAP.getNamesOfTErefSeq()
-        self.assertEqual(obsTEList, expTEList)
-        
-    def writeInputTEFile(self):
-        with open(self._inputTEFile,"w") as TEFile:
-            TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed
-RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse
-DT-comp_DmelChr4-B-P0.0-Map3\t""")
-            
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-import os
-import unittest
-from commons.core.utils.FileUtils import FileUtils
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation
-
-class Test_GetSpecificTELibAccordingToAnnotation(unittest.TestCase):
-    
-    def test_writeFastaFileFromGiveInfoTEAnnot(self):
-        self._iDb = DbMySql()
-        fileName = "GiveInfoTEannot.txt"
-        self._writeGiveInfoTEannotOutput(fileName)
-        tableName = "projectName_refTEs_chr_seq"
-        self._createConsensusTable(tableName)
-        expFileName = "consensusExp.fa"
-        self._writeExpConsensusFile(expFileName)
-        obsFileName = "%s.fa" % os.path.splitext(fileName)[0]
-        iGetTElib = GetSpecificTELibAccordingToAnnotation()
-        iGetTElib.setTableName(tableName)
-        iGetTElib.writeFastaFileFromGiveInfoTEAnnot(fileName)
-        self._iDb.dropTable(tableName)
-        self._iDb.close()
-        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
-        os.remove(fileName)
-        os.remove(expFileName)
-        os.remove(obsFileName)
-        
-    def _writeGiveInfoTEannotOutput(self, fileName):
-        f = open(fileName, "w")
-        f.write("TE\tmaxLength\tmeanLength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tsdId\tminId\tq25Id\tmedId\tq75Id\tmaxId\tmeanLgth\tsdLgth\tminLgth\tq25Lgth\tmedLgth\tq75Lgth\tmaxLgth\tmeanLgthPerc\tsdLgthPerc\tminLgthPerc\tq25LgthPerc\tmedLgthPerc\tq75LgthPerc\tmaxLgthPerc\n")
-        f.write("Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\t2150\t2150\t195657\t158\t49\t152\t52\t84.88\t8.75\t74.29\t77.16\t80.08\t96.40\t97.83\t1287.32\t776.47\t21\t570.00\t1320.50\t2077.00\t2272\t59.88\t36.11\t0.98\t26.51\t61.42\t96.60\t105.67\n")
-        f.write("Atha_benchs-B-R1047-Map6_classI-LINE-comp\t1653\t1653\t25423\t57\t4\t56\t4\t79.09\t8.21\t64.32\t73.63\t79.21\t83.65\t96.65\t453.98\t488.66\t29\t98.00\t244.00\t634.00\t1650\t27.46\t29.56\t1.75\t5.93\t14.76\t38.35\t99.82\n")
-        f.write("Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\t1293\t1293\t24416\t48\t4\t47\t4\t80.31\t5.74\t75.14\t77.00\t78.25\t80.89\t99.46\t519.60\t419.01\t37\t171.00\t334.00\t838.00\t1296\t40.19\t32.41\t2.86\t13.23\t25.83\t64.81\t100.23\n")
-        f.close()
-        
-    def _createConsensusTable(self, tableName):
-        fileName = "consensus.fa"
-        f = open(fileName, "w")
-        f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n")
-        f.write("ATGCTAGCTAGCT\n")
-        f.write(">Atha_benchs-B-R12-Map5_classII-Helitron-comp\n")
-        f.write("ATGCTAGCTAGCTATGCTAGCTAGCATGCTAGCTAGCTT\n")
-        f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n")
-        f.write("ATGCTAGCTAGCT\n")
-        f.write(">Atha_benchs-B-G56-Map5_classII-Helitron-comp\n")
-        f.write("ATGCTAGCTAGCTATGCTAGCTAGCT\n")
-        f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n")
-        f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n")
-        f.close()
-        self._iDb.createTable(tableName, "seq", fileName, True)
-        os.remove(fileName)
-    
-    def _writeExpConsensusFile(self, fileName):
-        f = open(fileName, "w")
-        f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n")
-        f.write("ATGCTAGCTAGCT\n")
-        f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n")
-        f.write("ATGCTAGCTAGCT\n")
-        f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n")
-        f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n")
-        f.close()
-        
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_OrientSequences.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-import unittest
-import time
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.OrientSequences import OrientSequences
-
-
-class Test_OrientSequences( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = OrientSequences ()
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
-        
-        
-    def tearDown( self ):
-        self._i = None
-        self._uniqId = None
-        
-        
-    def test_parseMummerOutput( self ):
-        inFileName = "dummyInFile_%s" % ( self._uniqId )
-        inF = open( inFileName, "w" )
-        inF.write( "> seq1\n" )
-        inF.write( "  seq2      20        1        20\n" )
-        inF.write( "> seq1 Reverse\n" )
-        inF.write( "  seq2      100        1        100\n" )
-        inF.write( "  seq2      450      400        50\n" )
-        inF.close()
-        dExp = { "direct": 1, "reverse": 2 }
-        self._i._verbose = 0
-        dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" )
-        self.assertEqual( dObs, dExp )
-        os.remove( inFileName )
-        
-        
-    def test_getSequencesToReverseFromMatrix_2seq( self ):
-        lNewHeaders = [ "seq1", "seq2" ]
-        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } }
-        lExp = [ "seq2" ]
-        self._i._verbose = 0
-        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lObs, lExp )
-        
-        
-    def test_getSequencesToReverseFromMatrix_3seq( self ):
-        lNewHeaders = [ "seq1", "seq2", "seq3" ]
-        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 },
-                   "1_vs_3": { "direct": 10, "reverse": 1 },
-                   "2_vs_3": { "direct": 1, "reverse": 10 } }
-        lExp = [ "seq2" ]
-        self._i._verbose = 0
-        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_getSequencesToReverseFromMatrix_4seq( self ):
-        lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ]
-        dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 },
-                   "1_vs_3": { "direct": 1, "reverse": 10 },
-                   "1_vs_4": { "direct": 1, "reverse": 10 },
-                   "2_vs_3": { "direct": 1, "reverse": 10 },
-                   "2_vs_4": { "direct": 1, "reverse": 10 },
-                   "3_vs_4": { "direct": 1, "reverse": 2 } }
-        lExp = [ "seq3", "seq4" ]
-        self._i._verbose = 0
-        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
-        lExp.sort()
-        lObs.sort()
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_orientInputSequences( self ):
-        lSeqToOrient = [ "seq1" ]
-        tmpFileName = "dummyInFile_%s" % ( self._uniqId )
-        tmpF = open( tmpFileName, "w" )
-        tmpF.write( ">seq1\n" )
-        tmpF.write( "ATGCGGTGCATG\n" )
-        tmpF.write( ">seq2\n" )
-        tmpF.write( "GGCGAAGTGAAA\n" )
-        tmpF.close()
-        expFileName = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write( ">seq1 re-oriented\n" )
-        expF.write( "CATGCACCGCAT\n" )
-        expF.write( ">seq2\n" )
-        expF.write( "GGCGAAGTGAAA\n" )
-        expF.close()
-        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
-        self._i._verbose = 0
-        self._i._outFileName = obsFileName
-        self._i.orientInputSequences( lSeqToOrient, tmpFileName )
-        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ tmpFileName, expFileName, obsFileName ]:
-            os.remove( f )
-            
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_RmvPairAlignInChunkOverlaps.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
-import unittest
-import os
-import time
-from commons.core.coord.Align import Align
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.RmvPairAlignInChunkOverlaps import RmvPairAlignInChunkOverlaps
-
-
-class Test_RmvPairAlignInChunkOverlaps( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = RmvPairAlignInChunkOverlaps()
-        self._uniqId = "%s" % ( time.strftime("%Y%m%d%H%M%S") )
-
-
-    def tearDown( self ):
-        self._i = None
-        self._uniqId = None
-        
-        
-    def test_isPairAlignAChunkOverlap( self ):
-        a = Align()
-        a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) )
-        self._i.setChunkLength( 500 )
-        self._i.setChunkOverlap( 100 )
-        obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
-        self.assertTrue( obs )
-        a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) )  # reverse subject
-        obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
-        self.assertTrue( obs )
-        a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) )   # chunk subject not contiguous
-        obs = self._i.isPairAlignAChunkOverlap( a, 1, 3 )
-        self.assertFalse( obs )
-        a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) )   # hit longer than chunk overlap
-        obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
-        self.assertFalse( obs )
-        a.setFromTuple( ( "chunk2", "1", "101", "chunk1", "401", "500", "0.0", "500", "100.0" ) )   # chunk overlap returned by PALS (+1), query > subject
-        obs = self._i.isPairAlignAChunkOverlap( a, 2, 1 )
-        self.assertTrue( obs )
-        a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "101", "0.0", "500", "100.0" ) )   # chunk overlap returned by PALS (+1), query < subject
-        obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
-        self.assertTrue( obs )
-        
-        
-    def test_isPairAlignWithinAndDueToAChunkOverlap( self ):
-        a = Align()
-        a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "11", "50", "0.0", "73", "97.6" ) )  # included, due to overlap
-        self._i.setChunkLength( 500 )
-        self._i.setChunkOverlap( 100 )
-        self._i._verbose = 0
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
-        self.assertTrue( obs )
-        a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "50", "11", "0.0", "73", "97.6" ) )  # reverse subject
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
-        self.assertFalse( obs )
-        a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) )   # chunk subject not contiguous
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 3 )
-        self.assertFalse( obs )
-        a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) )   # hit longer than chunk overlap
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
-        self.assertFalse( obs )
-        a.setFromTuple( ( "chunk1", "411", "430", "chunk2", "16", "35", "0.0", "73", "97.6" ) )   # repeat within overlap...
-        self._i._margin = 2   # ... but not due to it
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
-        self.assertFalse( obs )
-        self._i._margin = 10   # ... and due to it
-        obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
-        self.assertTrue( obs )
-        
-        
-    def test_removeChunkOverlaps( self ):
-        inFileName = "dummyInFile_%s" % ( self._uniqId )
-        inF = open( inFileName, "w" )
-        a = Align()
-        a.setFromTuple( ( "chunk1", "411", "490", "chunk2", "11", "90", "0.0", "73", "97.6" ) )
-        a.write( inF )
-        a.setFromTuple( ( "chunk1", "1", "500", "chunk1", "1", "500", "0.0", "500", "100.0" ) )
-        a.write( inF )
-        inF.close()
-        self._i.setInputFileName( inFileName )
-        self._i.setChunkLength( 500 )
-        self._i.setChunkOverlap( 100 )
-        obsFileName = "dummyObsFile_%s"  %( self._uniqId )
-        self._i.setOutputFileName( obsFileName )
-        d = self._i.removeChunkOverlaps()
-        expFileName = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write( "" )
-        expF.close()
-        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ inFileName, obsFileName, expFileName ]: os.remove( f )
-        
-        
-    def test_zRunAsScript( self ):
-        cDir = os.getcwd()
-        
-        alignFileName = "dummyInFile_%s" % ( self._uniqId )
-        aF = open( alignFileName, "w" )
-        aF.write( "chunk1\t401\t500\tchunk2\t1\t100\t0.0\t131\t100.0\n" )  # remove
-        aF.write( "chunk2\t1\t100\tchunk1\t401\t500\t0.0\t132\t100.0\n" )  # remove
-        aF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0.0\t132\t100.0\n" )  # keep because non-contiguous chunks
-        aF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0.0\t132\t100.0\n" )  # keep because non-contiguous chunks
-        aF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0.0\t132\t100.0\n" )  # keep because within overlap but reverse
-        aF.write( "chunk1\t431\t490\tchunk2\t31\t90\t0.0\t132\t100.0\n" )  # remove because within and due to overlap
-        aF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0.0\t132\t100.0\n" )  # keep because within but not due to overlap
-        aF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0.0\t132\t100.0\n" )  # keep because longer HSP on query
-        aF.close()
-        
-        expFileName = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0\t132\t100.000000\n" )
-        expF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0\t132\t100.000000\n" )
-        expF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0\t132\t100.000000\n" )
-        expF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0\t132\t100.000000\n" )
-        expF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0\t132\t100.000000\n" )
-        expF.close()
-        
-        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
-        cmd = "RmvPairAlignInChunkOverlaps.py"
-        cmd += " -i %s" % ( alignFileName )
-        cmd += " -l 500"
-        cmd += " -o 100"
-        cmd += " -O %s" % ( obsFileName )
-        cmd += " -v 0"
-        os.system( cmd )
-        
-        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f )
-        os.chdir( cDir )
-        
-    def test_zRunAsScript_bug_to_fix(self):
-        cDir = os.getcwd()
-        
-        alignFileName = "dummyInFile_%s" % ( self._uniqId )
-        aF = open( alignFileName, "w" )
-        aF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n")
-        aF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n")
-        aF.write("chunk4\t63217\t63680\tchunk6\t5316\t4837\t0\t676\t92.71\n")
-        aF.close()
-        
-        expFileName = "dummyExpFile_%s" % ( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n")
-        expF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n")
-        expF.close()
-        
-        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
-        cmd = "RmvPairAlignInChunkOverlaps.py"
-        cmd += " -i %s" % ( alignFileName )
-        cmd += " -l 200000"
-        cmd += " -o 10000"
-        cmd += " -O %s" % ( obsFileName )
-        cmd += " -v 0"
-        os.system( cmd )
-        
-        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f )
-        os.chdir( cDir )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_SpliceTEsFromGenome.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools.SpliceTEsFromGenome import SpliceTEsFromGenome
-
-
-class Test_SpliceTEsFromGenome( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._i = SpliceTEsFromGenome()
-        
-        
-    def test_zLaunchAsScript( self ):
-        cDir = os.getcwd()
-        
-        coordFile = "dummyCoordFile"
-        coordFileHandler = open( coordFile, "w" )
-        coordFileHandler.write( "TE1\tchr1\t2\t5\n" )
-        coordFileHandler.write( "TE2\tchr1\t11\t15\n" )
-        coordFileHandler.write( "TE3\tchr1\t12\t14\n" )
-        coordFileHandler.close()
-        
-        genomeFile = "dummyGenomeFile"
-        genomeFileHandler = open( genomeFile, "w" )
-        genomeFileHandler.write( ">chr1\n" )
-        genomeFileHandler.write( "AGGGGAAAAACCCCCAAAAA\n" )
-        genomeFileHandler.write( ">chr2\n" )
-        genomeFileHandler.write( "TTTTTTTTTT\n" )
-        genomeFileHandler.close()
-        
-        expFile = "dummyExpFile"
-        expFileHandler = open( expFile, "w" )
-        expFileHandler.write( ">chr1\n" )
-        expFileHandler.write( "AAAAAAAAAAA\n" )
-        expFileHandler.write( ">chr2\n" )
-        expFileHandler.write( "TTTTTTTTTT\n" )
-        expFileHandler.close()
-        
-        obsFile = "dummyObsFile"
-        
-        cmd = "SpliceTEsFromGenome.py"
-        cmd += " -i %s" % ( coordFile )
-        cmd += " -f %s" % ( "map" )
-        cmd += " -g %s" % ( genomeFile )
-        cmd += " -o %s" % ( obsFile )
-        cmd += " -v %i" % ( 0 )
-        returnStatus = os.system( cmd )
-        
-        self.assertTrue( returnStatus == 0 )
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ coordFile, genomeFile, expFile, obsFile ]:
-            os.remove( f )
-        os.chdir( cDir )
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_getCumulLengthFromTEannot.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-import unittest
-import os
-import time
-from commons.core.sql.DbMySql import DbMySql
-from commons.tools.getCumulLengthFromTEannot import getCumulLengthFromTEannot
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_getCumulLengthFromTEannot( unittest.TestCase ):
-    
-    def setUp( self ):
-        self.fileUtils = FileUtils()
-        self._getCumulLengthFromTEannot = None
-        self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
-        self._configFileName = "dummyConfig_%s" % self._uniqId
-        configFile = open( self._configFileName, "w" )
-        configFile.write("[repet_env]\n")
-        configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
-        configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
-        configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
-        configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
-        configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
-        configFile.close()
-        
-        
-    def tearDown( self ):
-        os.remove( self._configFileName )
-        
-        
-    def test_getAllSubjectsAsMapOfQueries( self ):
-        inFileName = "dummyInFile_%s" % self._uniqId
-        expFileName = "dummyExp_%s" % self._uniqId
-        for f in [inFileName,expFileName]:
-            if os.path.exists(f): os.remove(f)
-        inFile = open( inFileName, "w" )
-        inFile.write( "1\tchr1\t1501\t2500\tTE1\t1\t500\t0.0\t880\t95.7\n" )
-        inFile.write( "2\tchr1\t3401\t4000\tTE3\t101\t700\t0.0\t950\t97.2\n" )
-        inFile.close()
-        inTable = "dummyPathTable_%s" % self._uniqId
-        db = DbMySql(cfgFileName=self._configFileName)
-        db.createTable(inTable, "path", inFileName)
-        expFile = open( expFileName, "w" )
-        expFile.write( "TE1\tchr1\t1501\t2500\n" )
-        expFile.write( "TE3\tchr1\t3401\t4000\n" )
-        expFile.close()
-        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
-        self._getCumulLengthFromTEannot._tableName = inTable
-        self._getCumulLengthFromTEannot._configFileName = self._configFileName
-        self._getCumulLengthFromTEannot.setAdaptatorToTable()
-        obsFileName = self._getCumulLengthFromTEannot.getAllSubjectsAsMapOfQueries()
-        self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [inFileName,inTable+".map",expFileName]:
-            if os.path.exists(f): os.remove(f)
-        db.dropTable(inTable)
-        db.close()
-        
-        
-    def test_getCumulLength( self ):
-        mergeFileName = "dummyInFile_%s" % self._uniqId
-        mergeFile = open( mergeFileName, "w" )
-        mergeFile.write( "TE1\tchr1\t1501\t2500\n" )
-        mergeFile.write( "TE3\tchr1\t4000\t3401\n" )
-        mergeFile.close()
-        exp = 1000+600
-        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
-        obs = self._getCumulLengthFromTEannot.getCumulLength( mergeFileName )
-        self.assertEqual( obs, exp )
-        os.remove( mergeFileName )
-
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_pathnum2id.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_pathnum2id( unittest.TestCase ):
-    
-    def setUp( self ):
-        self._inputFileName = "dummyInputPathFile"
-        self._outputFileName = "dummyOutputPathFile"
-        self._expectedFileName = "dummyExpectedPathFile"
-        self._prg = "pathnum2id.py"
-        
-        
-    def test_runWhithoutReturnAtEndOfFile( self ):
-        cDir = os.getcwd()
-        
-        self._createAndFillInputFileWhithoutReturnAtTheEnd()
-        self._createExpectedFile()
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFileName )
-        cmd += " -o %s" % ( self._outputFileName )
-        os.system( cmd )        
-        self.assertTrue( FileUtils.are2FilesIdentical( self._outputFileName, self._expectedFileName ) )
-        
-        os.remove( self._inputFileName )
-        os.remove( self._expectedFileName )
-        if os.path.exists( self._outputFileName ):
-            os.remove( self._outputFileName )
-        os.chdir( cDir )
-        
-        
-    def test_runWhithReturnAtEndOfFile( self ):
-        cDir = os.getcwd()
-        
-        self._createAndFillInputFileWhithReturnAtTheEnd()
-        self._createExpectedFile()
-        cmd = self._prg
-        cmd += " -i %s" % ( self._inputFileName )
-        cmd += " -o %s" % ( self._outputFileName )
-        os.system( cmd )        
-        self.assertTrue( FileUtils.are2FilesIdentical( self._outputFileName, self._expectedFileName ) )
-        
-        os.remove( self._inputFileName )
-        os.remove( self._expectedFileName )
-        if os.path.exists( self._outputFileName ):
-            os.remove( self._outputFileName )
-        os.chdir( cDir )
-        
-        
-    def _createExpectedFile( self ):
-        f = open(self._expectedFileName, "w")
-        f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("4\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n")
-        f.write("5\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("6\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        
-        
-    def _createAndFillInputFileWhithoutReturnAtTheEnd( self ):
-        f = open(self._inputFileName, "w")
-        f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("1\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n")
-        f.write("2\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("3\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0")
-        f.close()
-        
-        
-    def _createAndFillInputFileWhithReturnAtTheEnd( self ):
-        f = open(self._inputFileName, "w")
-        f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n")
-        f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n")
-        f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n")
-        f.write("1\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n")
-        f.write("2\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n")
-        f.write("3\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n")
-        f.close()
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_refalign2fasta.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-import unittest
-import time
-from commons.tools.refalign2fasta import *
-from commons.core.utils.FileUtils import FileUtils
-
-
-class Test_refalign2fasta( unittest.TestCase ):
-    
-    
-    def setUp( self ):
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-        
-        
-    def tearDown( self ):
-        self._uniqId = None
-        
-        
-    def test_getAlignments( self ):
-        inFile = "dummyInFile_%s" % ( self._uniqId )
-        inFileHandler = open( inFile, "w" )
-        inFileHandler.write( "AAAACTTTT-T\tAAAA-TTTGGT\trefseq::1 chr3 1..10\n" )  # 1 insertion and 1 deletion in the copy + 1 mismatch
-        inFileHandler.close()
-        lExp = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lObs = getAlignments( inFile )
-        self.assertEqual( lExp, lObs )
-        os.remove( inFile )
-        
-        
-    def test_getGaps_OneGap( self ):
-        sequence = "AAAACTTTT-T"
-        lExp = [ ( 9, 1 ) ]
-        lObs = getGaps( sequence )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_getGaps_TwoGaps( self ):
-        sequence = "AAAA--CTTT-TT"
-        lExp = [ ( 4, 2 ), ( 8, 1 ) ]
-        lObs = getGaps( sequence )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_getGapsOnRefSeq_OneSeq( self ):
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lExp = [ [ ( 9, 1 ) ] ]
-        lObs = getGapsOnRefSeq( lAlign )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_getGapsOnRefSeq_TwoSeq( self ):
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
-        lExp = [ [ ( 9, 1 ) ] ]
-        lExp.append( [ ( 4, 2 ), ( 8, 1 ) ] )
-        lObs = getGapsOnRefSeq( lAlign )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_insertGap( self ):
-        sequence = "GGGGAAAGTTG"
-        start = 5
-        length = 3
-        exp = "GGGGA---AAGTTG"
-        obs = insertGap( sequence, start, length )
-        self.assertEqual( exp, obs )
-        
-        
-    def test_insertListGaps( self ):
-        sequence = "GGGGAAAGTTG"
-        lGaps =[ ( 5, 3 ), ( 9, 1 ) ]
-        exp = "GGGGA---AAGT-TG"
-        obs = insertListGaps( sequence, lGaps )
-        self.assertEqual( exp, obs )
-        
-        
-    def test_insertGapsInRefSeq( self ):
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
-        lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ]
-        lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] )
-        refseqName = "reference_sequence"
-        lExp = ( refseqName, "AAAA--CTTT-T-T" )
-        lObs = insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_insertgap_seq( self ):
-        # AAAACTTTT-T (refseq)
-        # AAAA-TTTGGT ( copy 1)
-        #
-        # AAAA--CTTT-TT (refseq)
-        # AAAAGGCTTTGTT (copy 2)
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
-        lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ]
-        lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] )
-        lExp = [ ( "refseq::1 chr3 1..10", "AAAA---TTT-GGT" ) ]
-        lExp.append( ( "refseq::2 chr5 1..10", "AAAAGGCTTTGT-T" ) )
-        lObs = insertgap_seq( lAlign, lGapsOnRefSeqPerAlign )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_getSeqWithDeletions( self ):
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
-        lExp = [ ( "refseq::1 chr3 1..10", "AAAA-TTTGT" ) ]
-        lObs = getSeqWithDeletions( lAlign )
-        self.assertEqual( lExp, lObs )
-        
-        
-    def test_saveOnlyWithDeletions( self ):
-        refseqName = "Dm-B-G54-Map3"
-        lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "Dm-B-G54-Map3::1 chr3 1..10" ) ]
-        lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "Dm-B-G54-Map3::2 chr5 1..10" ) )
-        
-        expFile = "dummyExpFile_%s"  %( self._uniqId )
-        expFileHandler = open( expFile, "w" )
-        expFileHandler.write( ">Dm-B-G54-Map3\n" )
-        expFileHandler.write( "AAAACTTTTT\n" )
-        expFileHandler.write( ">Dm-B-G54-Map3::1 chr3 1..10\n" )
-        expFileHandler.write( "AAAA-TTTGT\n" )
-        expFileHandler.write( ">Dm-B-G54-Map3::2 chr5 1..10\n" )
-        expFileHandler.write( "AAAACTTTTT\n" )
-        expFileHandler.close()
-        
-        obsFile = "dummyObsFile_%s" % ( self._uniqId )
-        
-        saveOnlyWithDeletions( lAlign, refseqName, obsFile )
-        
-        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
-        
-        for f in [ expFile, obsFile ]:
-            os.remove( f )
-            
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file

--- a/commons/tools/tests/Test_srptTableOverlap.py	Mon Apr 29 03:23:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-import unittest
-import os
-import time
-import pyRepet.sql.RepetDBMySQL
-from commons.core.utils.FileUtils import FileUtils
-from commons.tools import srptTableOverlap
-
-
-class Test_srptTableOverlap( unittest.TestCase ):
-    
-    def setUp(self):
-        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
-        self._db = pyRepet.sql.RepetDBMySQL.RepetDB( os.environ["REPET_USER"],
-                                                     os.environ["REPET_HOST"],
-                                                     os.environ["REPET_PW"],
-                                                     os.environ["REPET_DB"] )
-        
-        
-    def test_getOverlapAllPaths(self):
-        qryFileName = "dummyQryFile_%s" % ( self._uniqId )
-        qryF = open( qryFileName, "w" )
-        qryF.write("1\tchr1\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
-        qryF.close()
-        qryTable = "dummyQryTable_%s" % ( self._uniqId )
-        self._db.create_table( self._db, qryTable, qryFileName, "path" )
-        sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
-        sbjF = open( sbjFileName, "w" )
-        sbjF.write("1\tchr1\t1001\t1500\tTE1\t11\t17\t1e-20\t30\t90.2\n")   # 200-bp overlap: 1301-1500
-        sbjF.write("2\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n")   # 300-bp overlap: 1501-1800
-        sbjF.write("3\tchr1\t2001\t2100\tTE2\t11\t17\t1e-20\t30\t90.2\n")
-        sbjF.write("4\tchr2\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n")   # different query
-        sbjF.close()
-        sbjTable = "dummySbjTable_%s" % ( self._uniqId )
-        self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
-        exp_sum_osize, exp_sum_non_osize, exp_sum_qsize = 500, 200, 700
-        obs_sum_osize, obs_sum_non_osize, obs_sum_qsize = srptTableOverlap.getOverlapAllPaths( qryTable, "path", sbjTable, "path", self._db )
-        self.assertEqual( obs_sum_osize, exp_sum_osize )
-        self.assertEqual( obs_sum_non_osize, exp_sum_non_osize )
-        self.assertEqual( obs_sum_qsize, exp_sum_qsize )
-        os.remove( qryFileName )
-        os.remove( sbjFileName )
-        self._db.remove_if_exist( qryTable )
-        self._db.remove_if_exist( sbjTable )
-        
-        
-    def test_pathOverlapByPath(self):
-        qryFileName = "dummyQryFile_%s" % ( self._uniqId )
-        qryF = open( qryFileName, "w" )
-        qryF.write("1\tchr1\t1301\t2000\tTE2\t1\t700\t1e-80\t850\t90.2\n")
-        qryF.write("1\tchr1\t2301\t3000\tTE2\t801\t1500\t1e-90\t930\t90.2\n")
-        qryF.close()
-        qryTable = "dummyQryTable_%s" % ( self._uniqId )
-        self._db.create_table( self._db, qryTable, qryFileName, "path" )
-        sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
-        sbjF = open( sbjFileName, "w" )
-        sbjF.write("1\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n")
-        sbjF.write("1\tchr1\t2101\t250000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
-        sbjF.write("2\tchr1\t3501\t4000\tTE3\t11\t17\t1e-20\t30\t90.2\n")
-        sbjF.close()
-        sbjTable = "dummySbjTable_%s" % ( self._uniqId )
-        self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
-        expFileName = "dummyOutFileExp_%s" % ( self._uniqId )
-        expF = open( expFileName, "w" )
-        expF.write("1\tTE2\t1400\t1:TE2\t1\t248300\t1100\t0.785714\t0.004430\n")
-        expF.close()
-        obsFileName = "dummyOutFileObs_%s" % ( self._uniqId )
-        obsF = open( obsFileName, "w" )
-        srptTableOverlap.pathOverlapByPath( qryTable, "path", sbjTable, "path", self._db, obsF )
-        obsF.close()
-        self.assertTrue(  FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
-        for f in [ qryFileName, sbjFileName, expFileName, obsFileName ]:
-            os.remove( f )
-        self._db.remove_if_exist( qryTable )
-        self._db.remove_if_exist( sbjTable )
-        self._db.remove_if_exist( sbjTable+"_bin" )
-        
-        
-if __name__ == "__main__":
-        unittest.main()
\ No newline at end of file