# HG changeset patch
# User bgruening
# Date 1548839552 18000
# Node ID 5d006d19f70aa1a86768d8108aba657a64acc62b

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

diff -r 000000000000 -r 5d006d19f70a AnnotateRNAz.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AnnotateRNAz.py	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,205 @@
+# AnnotateRnaz.py ---
+#
+# Filename: AnnotateRnaz.py
+# Description:
+# Author: Joerg Fallmann
+# Maintainer:
+# Created: Sat Jan 26 12:45:25 2019 (+0100)
+# Version:
+# Package-Requires: ()
+# Last-Updated: Tue Jan 29 13:52:57 2019 (+0100)
+#           By: Joerg Fallmann
+#     Update #: 188
+# URL:
+# Doc URL:
+# Keywords:
+# Compatibility:
+#
+#
+
+# Commentary:
+# This script is a replacement for rnazAnnotate.pl
+# rnazAnnotate can not handle the output from version 2 adequatly
+# This script uses the bedtools API to fast intersect an annotation Bed
+# with output from RNAz
+
+# Change Log:
+#
+#
+#
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+
+# Code:
+
+#!/usr/bin/env python3
+
+import sys
+import glob
+import argparse
+from io import StringIO
+import gzip
+import traceback as tb
+import pybedtools
+import re
+import tempfile
+
+def parseargs():
+    parser = argparse.ArgumentParser(description='Intersect RNAz output with Annotation from BED')
+    parser.add_argument("-b", "--bed", type=str, help='Annotation BED file')
+    parser.add_argument("-i", "--input", type=str, help='RNAz output')
+    parser.add_argument("-o", "--bedout", type=str, help='Annotation BED output')
+    parser.add_argument("-r", "--rnazout", type=str, help='Annotation rnaz output')
+    return parser.parse_args()
+
+def annotate(bed, input, bedout, rnazout):
+    try:
+
+        pybedtools.set_tempdir('.')  # Make sure we do not write somewhere we are not supposed to
+        anno = pybedtools.BedTool(bed)
+        rnaz=readrnaz(input)
+        tmpbed = pybedtools.BedTool(rnaztobed(rnaz), from_string=True)
+
+        intersection = tmpbed.intersect(anno,wa=True,wb=True,s=True)  # intersect strand specific, keep all info on a and b files
+
+        bedtornaz(intersection, rnaz, bedout, rnazout)
+
+        return 1
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+def readin(file):
+    try:
+        if '.gz' in file:
+            f = gzip.open(file,'rt')
+        else:
+            f = open(file,'rt')
+        return f
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+def readrnaz(rnaz):
+    try:
+        toparse = readin(rnaz)
+        tointersect = {}
+        header = []
+        for line in toparse:
+            if '#' in line[0]:
+                tointersect['header']=line.strip()
+                line = re.sub('^#','',line)
+                cont = line.strip().split('\t')
+                foi = cont.index('seqID') # need to find which column contains seqID
+                sf = cont.index('start') # need to find which column contains start
+                ef = cont.index('end') # need to find which column contains end
+                if 'strand' in cont:# need to find which column contains strand
+                    df = cont.index('strand')
+                else:
+                    df = None
+            else:
+                content = line.strip().split('\t')
+                newid=re.split('\.|\,|\s|\\|\/|\_', content[foi])[1]  # I can only hope that we have species.chromosome.whatever as annotation in aln or maf, if not this is hardly parseable
+                if df:
+                    longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', content[df]])
+                    tointersect[longid] = content
+                else:
+                    longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '+'])
+                    tointersect[longid] = content
+                    longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '-'])
+                    tointersect[longid] = content
+
+        return tointersect
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+
+def rnaztobed(rnaz):
+    try:
+        tmpbed = []
+        for key in rnaz:
+            if key != 'header':
+                tmpbed.append('\t'.join(key.split('_')))
+
+        return '\n'.join(tmpbed)
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+def bedtornaz(bed, rnaz, bedout, rnazout):
+    try:
+        b = open(bedout,'w')
+        r = open(rnazout,'w')
+
+        annotatedbed=[]
+        annotatedrnaz=[]
+        annotatedrnaz.append(str.join('\t',[rnaz['header'],'Annotation']))
+        for line in open(bed.fn):
+            out = line.strip().split("\t")
+            annotatedbed.append(str.join('\t',out[0:3]+out[9:10]+out[4:6]))
+            key = str.join('_',out[0:6])
+            annotatedrnaz.append(str.join('\t',rnaz[key]+out[9:10]))
+
+        print(str.join('\n', annotatedbed),file=b)
+        print(str.join('\n', annotatedrnaz),file=r)
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+
+def closefile(file):
+    try:
+        file.close()
+
+    except Exception as err:
+        exc_type, exc_value, exc_tb = sys.exc_info()
+        tbe = tb.TracebackException(
+            exc_type, exc_value, exc_tb,
+        )
+        print(''.join(tbe.format()),file=sys.stderr)
+
+
+
+
+####################
+####    MAIN    ####
+####################
+if __name__ == '__main__':
+    args=parseargs()
+    annotate(args.bed, args.input, args.bedout, args.rnazout)
+######################################################################
+# AnnotateRnaz.py ends here
diff -r 000000000000 -r 5d006d19f70a rnazRandomizeAln.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazRandomizeAln.xml	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,75 @@
+<tool id="rnaz_randomize_aln" name="RNAz Randomize Aln" version="2.1">
+    <requirements>
+        <requirement type="package" version="2.1">rnaz</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    rnazRandomizeAln.pl
+        --window $window
+        --slide $slide
+        --level $level
+        '$input'
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="text" />
+        <param argument="--window" name="window" type="integer" value="120" label="Window size, default 120" />
+        <param argument="--slide" name="slide" type="integer" value="120" label="Window step size, default 120" />
+        <param argument="--level" name="level" type="integer" value="2" label="Level of coarse graining" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="randomize.aln"/>
+            <output name="output" file="notsorandom.aln"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    Usage:
+    rnazRandomizeAln.pl [options] [file]
+    
+    Options:
+    -w N, --window=N
+    -s N, --slide=N
+    Long alignment blocks should be shuffled locally in order to
+    maintain local characteristics of the alignment. Therefore
+    alignments can be shuffled in windows. You can specify here the
+    size of a window and the offset. Defaults are window=120 and
+    slide=120, i.e. the alignments are shuffled in non-overlapping
+    windows of 120 columns.
+    
+    -l N, --level=N
+    The shuffling algorithm tries to mantain local conservation
+    patterns, i.e. it shuffles only columns of the same degree of
+    conservation. This becomes limiting if you have many sequences
+    in your alignment. Therfore you can choose the level of coarse
+    graining with this option.
+    
+    To decide which columns have the same degree of conservation,
+    the mean pairwise identity (MPI) of each column is calculated
+    and finally only columns of the same value are shuffled. You can
+    adjust the rounding of the MPI and thus the coarse graining
+    level with this option. If you have two columns with say 0.52
+    and 0.48 MPI you get:
+    
+    level 0: 1 and 0
+    
+    level 1: 50 and 50
+    
+    level 2: 52 and 48
+    
+    So on level 0 you only have conserved (MPI > 0.5) and
+    non-conserved (MPI < 0.5) columns while on level 2 you need
+    almost exactly the same MPI to shuffle two columns.
+    
+    Default value is 2.
+
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1142/9789814295291_0009</citation>
+    </citations>    
+
+</tool>
diff -r 000000000000 -r 5d006d19f70a test-data/Annotation.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Annotation.bed	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,3 @@
+chr1	10	500	WhoKnows	0	+
+chr1	90	900	WhoKnows2	0	-
+chr4	1352400	1352700	tRNAContainer	0	+
diff -r 000000000000 -r 5d006d19f70a test-data/IRE.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IRE.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,17 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65     TAAGGCTTTGGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACAAAA
+393758_SINFRUG00000122977_FUGU_3358_3422/1-65      TAAAAGCATTTCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAGGGGAGGAAAAC
+393758_ENSRNOG00000003872_RAT_9703_9767/1-65       TAAGGCTTTAGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACATAA
+393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 -AAGGTTATTTCTCTCCGACTTCAGCTACAGTGATAGCTAAGTTTGGAGAGGAGAGAAGG
+                                                    **     *  ** *** *************** **************  * **  *   
+
+
+393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65     AGAAG
+393758_SINFRUG00000122977_FUGU_3358_3422/1-65      GGGAG
+393758_ENSRNOG00000003872_RAT_9703_9767/1-65       AGAAG
+393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 GAGA-
+                                                      * 
+
+
+//
diff -r 000000000000 -r 5d006d19f70a test-data/miRNA.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/miRNA.maf	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,15 @@
+##maf version=1
+a score=0
+s hg16.chr11             64433968 110 - 134482954 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s panTro1.chr9           65642342 110 - 136640551 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s baboon.1                 349423 110 -    497844 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s rheMac1.SCAFFOLD120618    41607 110 -     48031 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s marmoset.1               290457 110 -    415896 GCCGAGACCGAGTGCACAAGGCTCTGACCTATGAGTTGACAGCCAGTGCTCTGGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s galago.1                 408904 110 -    511463 GCCAAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCCCCTCTGGCTGCCAATTACATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s rn3.chr1               58923176 110 + 268121971 GTCAAGATGGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTGATCTCGCCTCTGGCTGCCAGTTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s mm6.chr19              54573156 110 +  60626890 GCCAAGATGGCGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTTTTCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCACCTCAATGCCAGC
+s canFam1.chr18           3536304 110 +  66173745 GCTGAGATCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s rfbat.1                  111329 110 -    223543 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTGTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC
+s tenrec.32                   717 110 -      2965 GCCCAGACCGAGTGCACAAGTCTCTGACCTATGAATTGACAGCCAGTGCCTTGGGCTCCCCTCTGGCTGCCAATACCATAGGTCACAGGTATGTTTGCCTCCATGCCAGC
+s danRer2.chr10          14345337 107 +  36600514 GGTTAAGTCTAGGACACAGGGTGATGACCTATGAATTGACAGCCAGTGTTTGCAGT--CCAGCTGCCTGTCAGTTCTGTAGGCCACTGCCCTGTTTATCCTACTAAACA-
+
diff -r 000000000000 -r 5d006d19f70a test-data/notsorandom.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notsorandom.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,13 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1          AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+panTro1.chr1       AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+canFam1.chr9       AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+mm5.chr2           AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+rn3.chr3           AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+galGal2.chr17      AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+fr1.chrUn          AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+danRer1.chr11      AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
+
diff -r 000000000000 -r 5d006d19f70a test-data/randomize.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/randomize.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,12 @@
+CLUSTAL W (1.83) multiple sequence alignment
+
+
+hg17.chr1          AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+panTro1.chr1       AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+canFam1.chr9       AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+mm5.chr2           AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+rn3.chr3           AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+galGal2.chr17      AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+fr1.chrUn          AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+danRer1.chr11      AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+                   ************************************************************
\ No newline at end of file
diff -r 000000000000 -r 5d006d19f70a test-data/snoRNA.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snoRNA.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,36 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+470004_ENSG00000182512_HUMAN_8267_8506/1-243    GTACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC
+470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 GTACCCTAGAGCACACCAGACTTGCAGAGAAAGCAGACAACAGAGGAAGCTGAGGCATGC
+470004_SINFRUG00000145950_FUGU_5916_6140/1-243  --------GGGCACAACAAGGTTGC--AGAAAGCAT-C-CCAAAGGATGAAAAGGCGTGA
+470004_ENSRNOG00000004206_RAT_8331_8570/1-243   -TACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC
+                                                        * ***** **   ****  * ******  *  ** **** *   **** ** 
+
+
+470004_ENSG00000182512_HUMAN_8267_8506/1-243    CTGCTCGAGAGCCAGCTGTTCCATGTGCAATTTTCCTCTGATAGTTTCTGGTCACTGTTG
+470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CTGCTCGAGAGGCAGCAGGCCCATGTGCAATTTTCCTCTGATAGGGCCTGGGTACTGTTG
+470004_SINFRUG00000145950_FUGU_5916_6140/1-243  CTTCCAGAGGTCTGGGAATTCCACGTGCGATGTT-CTTTGA-A---CAAACACCTGCTTT
+470004_ENSRNOG00000004206_RAT_8331_8570/1-243   CTGCTCGAGAGCCAGCGGTTCCATGTGCAATTTTCCTCTGATAAATCCTGGGTACTGTTG
+                                                ** *  ***     *     *** **** ** ** ** *** *              ** 
+
+
+470004_ENSG00000182512_HUMAN_8267_8506/1-243    CCACGGTGATAATGACTGGGCTATGTCATTATCTATCCGCCAACAGTAAGAGAAGCTTTG
+470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CCACGGTGATAATGGCTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTGG
+470004_SINFRUG00000145950_FUGU_5916_6140/1-243  CCACGGTGGCGATGGCCTTGTTCTGTAGCCATCGCATTTCTTGAGGCAGGTAGAAAAAAA
+470004_ENSRNOG00000004206_RAT_8331_8570/1-243   CCACGGTGATAATGACTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTTG
+                                                ********   *** *   *   ***     **      *     *   *   *      
+
+
+470004_ENSG00000182512_HUMAN_8267_8506/1-243    CAGTCGAGATATTGTTT--AGCAGATGGAGTGTTTTCTGTTGAACACTAAGTACTGCCAC
+470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTACTGCCAC
+470004_SINFRUG00000145950_FUGU_5916_6140/1-243  CAG-CATGATATTGTTTGAAGCGGGGAGAGCTGTTCCCGTCAGACACTGTCCGCTGTCAC
+470004_ENSRNOG00000004206_RAT_8331_8570/1-243   CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTGCTGCTAC
+                                                *** *  **********  *** *   ***   ** * **   *****     ***  **
+
+
+470004_ENSG00000182512_HUMAN_8267_8506/1-243    AA-
+470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 AAA
+470004_SINFRUG00000145950_FUGU_5916_6140/1-243  AGC
+470004_ENSRNOG00000004206_RAT_8331_8570/1-243   AAG
+                                                *  
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,14 @@
+CLUSTAL W (1.83) multiple sequence alignment
+
+
+sacCer1         GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+sacBay          GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+sacKlu          GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC
+sacCas          GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC
+                ** *   * ** ** **** ** ****  * *** *****  ****    * ****** *
+
+sacCer1         CCCCTACAGGGCT
+sacBay          CCCCTACAGGGCT
+sacKlu          CCCCTACAGGGCT
+sacCas          CTCCCCTGGAGCA
+                * **    * ** 
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.aln.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.aln.window	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,30 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+sacCer1/0-73      GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+sacBay/0-73       GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+sacKlu/0-73       GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC
+sacCas/0-73       GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC
+
+
+sacCer1/0-73      CCCCTACAGGGCT
+sacBay/0-73       CCCCTACAGGGCT
+sacKlu/0-73       CCCCTACAGGGCT
+sacCas/0-73       CTCCCCTGGAGCA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+sacCer1_rev/0-73      AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT
+sacBay_rev/0-73       AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT
+sacKlu_rev/0-73       AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATT
+sacCas_rev/0-73       TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACT
+
+
+sacCer1_rev/0-73      GCGCCAACAAGGC
+sacBay_rev/0-73       GCGCCAACAAGGC
+sacKlu_rev/0-73       GCGCCAACAAGGC
+sacCas_rev/0-73       GAGCTACTGAAGC
+
+
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.maf	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,6 @@
+##maf version=1
+a score=119673.000000
+s sacCer1.chr4      1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT 
+s sacBay.contig_465   14962 73 -   57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT
+s sacKlu.Contig1694     137 73 +    4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT 
+s sacCas.Contig128      258 73 +     663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.maf.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.maf.window	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,12 @@
+a score=0
+s sacCer1.chr4 1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT
+s sacBay.contig_465 14962 73 - 57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT
+s sacKlu.Contig1694 137 73 + 4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT
+s sacCas.Contig128 258 73 + 663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA
+
+a score=0
+s sacCer1.chr4 1352453 73 + 1531914 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC
+s sacBay.contig_465 14962 73 + 57401 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC
+s sacKlu.Contig1694 137 73 - 4878 AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC
+s sacCas.Contig128 258 73 - 663 TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACTGAGCTACTGAAGC
+
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,156 @@
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 4
+ Columns: 73
+ Reading direction: forward
+ Mean pairwise identity:  80.82
+ Shannon entropy: 0.31118
+ G+C content: 0.54795
+ Mean single sequence MFE: -27.20
+ Consensus MFE: -26.50
+ Energy contribution: -23.63
+ Covariance contribution:  -2.87
+ Combinations/Pair:   1.43
+ Mean z-score:  -1.82
+ Structure conservation index:   0.97
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:   2.15
+ SVM RNA-class probability: 0.984068
+ Prediction: RNA
+
+######################################################################
+
+>sacCer1.chr4 1352453 73 - 1531914
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
+>sacBay.contig_465 14962 73 - 57401
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
+>sacKlu.Contig1694 137 73 + 4878
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score =  -1.34, R)
+>sacCas.Contig128 258 73 + 663
+GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
+(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score =  -1.22, R)
+>consensus
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 +  -2.87) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 4
+ Columns: 73
+ Reading direction: reverse
+ Mean pairwise identity:  80.82
+ Shannon entropy: 0.31118
+ G+C content: 0.54795
+ Mean single sequence MFE: -24.15
+ Consensus MFE: -26.66
+ Energy contribution: -23.35
+ Covariance contribution:  -3.31
+ Combinations/Pair:   1.48
+ Mean z-score:  -1.79
+ Structure conservation index:   1.10
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:   2.58
+ SVM RNA-class probability: 0.992927
+ Prediction: RNA
+
+######################################################################
+
+>sacCer1.chr4 1352453 73 + 1531914
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
+>sacBay.contig_465 14962 73 + 57401
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
+>sacKlu.Contig1694 137 73 - 4878
+AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score =  -1.87, R)
+>sacCas.Contig128 258 73 - 663
+UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
+.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score =  -0.83, R)
+>consensus
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 +  -3.31) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 4
+ Columns: 73
+ Reading direction: forward
+ Mean pairwise identity:  80.82
+ Shannon entropy: 0.31118
+ G+C content: 0.54795
+ Mean single sequence MFE: -24.15
+ Consensus MFE: -26.66
+ Energy contribution: -23.35
+ Covariance contribution:  -3.31
+ Combinations/Pair:   1.48
+ Mean z-score:  -1.79
+ Structure conservation index:   1.10
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:   2.58
+ SVM RNA-class probability: 0.992927
+ Prediction: RNA
+
+######################################################################
+
+>sacCer1.chr4 1352453 73 + 1531914
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
+>sacBay.contig_465 14962 73 + 57401
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
+>sacKlu.Contig1694 137 73 - 4878
+AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score =  -1.87, R)
+>sacCas.Contig128 258 73 - 663
+UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
+.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score =  -0.83, R)
+>consensus
+AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
+.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 +  -3.31) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 4
+ Columns: 73
+ Reading direction: reverse
+ Mean pairwise identity:  80.82
+ Shannon entropy: 0.31118
+ G+C content: 0.54795
+ Mean single sequence MFE: -27.20
+ Consensus MFE: -26.50
+ Energy contribution: -23.63
+ Covariance contribution:  -2.87
+ Combinations/Pair:   1.43
+ Mean z-score:  -1.82
+ Structure conservation index:   0.97
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:   2.15
+ SVM RNA-class probability: 0.984068
+ Prediction: RNA
+
+######################################################################
+
+>sacCer1.chr4 1352453 73 - 1531914
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
+>sacBay.contig_465 14962 73 - 57401
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
+>sacKlu.Contig1694 137 73 + 4878
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score =  -1.34, R)
+>sacCas.Contig128 258 73 + 663
+GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
+(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score =  -1.22, R)
+>consensus
+GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 +  -2.87) 
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.rnaz.clustered
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz.clustered	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,2 @@
+# locusID	seqID	start	end	maxN	maxIdentity	maxP	minZ
+locus1	sacCer1.chr4	1352453	1352526	4	80.82	0.992927	-1.82
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.rnaz.clustered.annotated.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz.clustered.annotated.bed	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,1 @@
+chr4	1352453	1352526	tRNAContainer	0	+
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA.rnaz.clustered.annotated.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz.clustered.annotated.rnaz	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,2 @@
+# locusID	seqID	start	end	maxN	maxIdentity	maxP	minZ	Annotation
+locus1	sacCer1.chr4	1352453	1352526	4	80.82	0.992927	-1.82	tRNAContainer
diff -r 000000000000 -r 5d006d19f70a test-data/tRNA_selected.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_selected.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,9 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+sacCer1      GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+
+
+sacCer1      CCCCTACAGGGCT
+
+
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.aln	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,72 @@
+CLUSTAL W (1.83) multiple sequence alignment
+
+
+hg17.chr1          TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT
+panTro1.chr1       TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTTGT
+canFam1.chr9       TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT
+mm5.chr2           TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT
+rn3.chr3           AACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTCGT
+galGal2.chr17      AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT
+fr1.chrUn          AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT
+danRer1.chr11      TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT
+                    ** ** ***** ***** ** **  **** ** *  ** ** ** ** ** ***** **
+
+hg17.chr1          GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+panTro1.chr1       GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+canFam1.chr9       GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+mm5.chr2           GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+rn3.chr3           GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+galGal2.chr17      ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT
+fr1.chrUn          GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT
+danRer1.chr11      GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT
+                    ** ** ** ***** ** ** ** ** ** ** ** ** ** ** ** ** ** ** **
+
+hg17.chr1          CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT
+panTro1.chr1       CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT
+canFam1.chr9       TGAAGTTGTGGCTACTAATGGAGATACTCACCTGGGTGGAGAAGACTTTGACCAACGTGT
+mm5.chr2           TGAAGTGGTGGCCACTAATGGAGATACTCACCTGGGTGGGGAAGACTTTGATCAGCGGGT
+rn3.chr3           TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT
+galGal2.chr17      TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT
+fr1.chrUn          TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT
+danRer1.chr11      TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT
+                     **** ****  ** ** ** ** **  * ** ** **  ******* ** ** *  **
+
+hg17.chr1          CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA
+panTro1.chr1       CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA
+canFam1.chr9       CATGGAACACTTCATCAAACTCTACAAAAAGAAGACTGGCAAAGATGTTAGGAAAGACAA
+mm5.chr2           CATGGAACACTTCATCAAGTTGTACAAAAAGAAAACTGGTAAAGATGTTAGGAAAGACAA
+rn3.chr3           CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA
+galGal2.chr17      TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA
+fr1.chrUn          CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA
+danRer1.chr11      CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA
+                    ***** ***********  * ***** ***** ** ** ***** **  * ** ** **
+
+hg17.chr1          TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA
+panTro1.chr1       TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA
+canFam1.chr9       CAGAGCTGTGCAGAAACTCCGGCGGGAGGTAGAAAAAGCCAAACGGGCCCTGTCTTCTCA
+mm5.chr2           CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCTAAGAGAGCCTTGTCTTCTCA
+rn3.chr3           CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCCAAGAGAGCCCTGTCTTCTCA
+galGal2.chr17      CAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCA
+fr1.chrUn          CCGTGCTGTCCAGAAGCTGCGTCGTGAGGTTGAGAAGGCAAAGAGGGCCCTGTCTGCCCA
+danRer1.chr11      CCGCGCCGTGCAGAAGCTGCGCAGAGAGGTGGAGAAGGCTAAGAGAGCCCTGTCTGCCCA
+                     * ** ** ***** **  *  *  * ** ** ** ** **  * *** ****  * **
+
+hg17.chr1          ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA
+panTro1.chr1       ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA
+canFam1.chr9       ACATCAAGCAAG----AATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTCTCTGAGA
+mm5.chr2           GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA
+rn3.chr3           GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA
+galGal2.chr17      GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA
+fr1.chrUn          GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA
+danRer1.chr11      GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA
+                    ** ** **  *     ** ** ** ** ** ** *  ** ***** ** ** ** ****
+
+hg17.chr1          CCCTGACTCAGGCCAAATTTGAAGAGCTCAA
+panTro1.chr1       CCCTGACTCAGGCCAAATTTGAAGAGCTCAA
+canFam1.chr9       CTCTGACTCGGGCCAAATTTGAAGAGCTAAA
+mm5.chr2           CCCTTACTCGGGCCAAATTTGAAGAGCTGAA
+rn3.chr3           CCCTTACTCGGGCCAAATTTGAAGAGCTGAA
+galGal2.chr17      CGCTTACTCGTGCCAAATTTGAAGAACTGAA
+fr1.chrUn          CACTGACCCGTGCCAAATTTGAAGAGCTTAA
+danRer1.chr11      CTCTCACCAGAGCCAAGTTTGAAGAGCTCAA
+                   * ** **    ***** ******** ** **
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.aln.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.aln.window	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,152 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1/0-120          TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT
+canFam1.chr9/0-120       TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT
+mm5.chr2/0-120           TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT
+galGal2.chr17/0-120      AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT
+fr1.chrUn/0-120          AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT
+danRer1.chr11/0-120      TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT
+
+
+hg17.chr1/0-120          GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+canFam1.chr9/0-120       GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+mm5.chr2/0-120           GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT
+galGal2.chr17/0-120      ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT
+fr1.chrUn/0-120          GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT
+danRer1.chr11/0-120      GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1_rev/0-120          AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAGGTTCCACCACCCAGGTCAAAC
+canFam1.chr9_rev/0-120       AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAAGTTCCACCACCCAGGTCAAAC
+mm5.chr2_rev/0-120           AAGACACCATTGTCAATGGTGAGAAGAGACACATCGAAGGTGCCGCCACCCAGGTCAAAC
+galGal2.chr17_rev/0-120      AAGACTCCGTTGTCAATTGTCAGGAGGGAGACATCAAAAGTTCCACCACCCAGGTCAAAT
+fr1.chrUn_rev/0-120          AACACACCGTTGTCAATGGTGAGCAGAGACACGTCGAAGGTGCCGCCACCGAGATCGAAC
+danRer1.chr11_rev/0-120      AACACGCCGTTATCGATGGTCAGCAGAGACACGTCAAAGGTGCCACCACCCAGATCGAAC
+
+
+hg17.chr1_rev/0-120          ACCAGGATGTTCTTCTCCCCCTCCCTCTTATCCAGGCCATAAGCAATAGCAGCTGCTGTA
+canFam1.chr9_rev/0-120       ACCAGGATATTCTTCTCCCCTTCCCTCTTATCCAAGCCGTAAGCAATAGCAGCTGCTGTA
+mm5.chr2_rev/0-120           ACAAGGATGTTCTTCTCTCCCTCTCTCTTATCCAGGCCATATGCAATAGCAGCTGCTGTA
+galGal2.chr17_rev/0-120      ACAAGGATGTTCTTTTCACCCTCTCTCTTGTCCAATCCGTATGCAATTGCAGCAGCAGTT
+fr1.chrUn_rev/0-120          ACGAGGATGTTCTTCTCGCCGTCCTTTTTGTCCAGACCATAAGCAATGGCAGCAGCGGTT
+danRer1.chr11_rev/0-120      ACCAGGATGTTTTTCTCTCCGTCCCTCTTGTCCAGACCGTATGCAATGGCAGCCGCCGTA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1/120-240          CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT
+panTro1.chr1/120-240       CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT
+rn3.chr3/120-240           TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT
+galGal2.chr17/120-240      TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT
+fr1.chrUn/120-240          TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT
+danRer1.chr11/120-240      TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT
+
+
+hg17.chr1/120-240          CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA
+panTro1.chr1/120-240       CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA
+rn3.chr3/120-240           CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA
+galGal2.chr17/120-240      TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA
+fr1.chrUn/120-240          CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA
+danRer1.chr11/120-240      CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1_rev/120-240          TTGTCTTTCCTGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG
+panTro1.chr1_rev/120-240       TTGTCTTTCCCGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG
+rn3.chr3_rev/120-240           TTGTCCTTTCTGACATCTTTCCCAGTCTTCTTTTTGTACAGCTTGATGAAGTGCTCCATG
+galGal2.chr17_rev/120-240      TTATCCTTCCTGACATCTTTTCCTGTTTTCTTCTTGTAGAGTTTGATGAAGTGCTCCATA
+fr1.chrUn_rev/120-240          TTGTCTTTGCGCACGTCTTTGCCAGTCTTCTTCTTGTATAGCTTGATGAAGTGTTCCATG
+danRer1.chr11_rev/120-240      TTGTCTTTGCGCACATCTTTGCCCGTCTTCTTCTTGTACAGCTTGATGAAGTGCTCCATG
+
+
+hg17.chr1_rev/120-240          ACACGCTGGTCAAAGTCTTCTCCACCCAGATAAGTATCTCCATTAGTGGCCACAACTTTG
+panTro1.chr1_rev/120-240       ACATGCTGGTCAAAGTCTTTTCCACCCAGATGAGTATCTCCATTAGTGACCACAACTTTG
+rn3.chr3_rev/120-240           ACCCGCTGATCAAAGTCTTCCCCACCCAGATGAGTGTCTCCATTAGTGGCCACCACTTCA
+galGal2.chr17_rev/120-240      ACACGCTGGTCAAAGTCTTCTCCACCCAGGTGTGTGTCACCATTTGTAGCCACAACTTCA
+fr1.chrUn_rev/120-240          ACGCGCTGATCAAAGTCTTCACCTCCAAGGTGAGTGTCACCATTGGTGGCCACCACTTCA
+danRer1.chr11_rev/120-240      ACGCGCTGGTCGAAGTCTTCTCCGCCCAGGTGAGTGTCTCCGTTTGTGGCCACCACTTCA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1/240-360          TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA
+mm5.chr2/240-360           CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCTAAGAGAGCCTTGTCTTCTCA
+rn3.chr3/240-360           CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCCAAGAGAGCCCTGTCTTCTCA
+galGal2.chr17/240-360      CAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCA
+fr1.chrUn/240-360          CCGTGCTGTCCAGAAGCTGCGTCGTGAGGTTGAGAAGGCAAAGAGGGCCCTGTCTGCCCA
+danRer1.chr11/240-360      CCGCGCCGTGCAGAAGCTGCGCAGAGAGGTGGAGAAGGCTAAGAGAGCCCTGTCTGCCCA
+
+
+hg17.chr1/240-360          ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA
+mm5.chr2/240-360           GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA
+rn3.chr3/240-360           GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA
+galGal2.chr17/240-360      GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA
+fr1.chrUn/240-360          GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA
+danRer1.chr11/240-360      GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1_rev/240-360          TCTCAGAAAAGTCTTCTCCTTCATAGAAGGACTCAATTTCAATTACTGCTTGCTTGATGT
+mm5.chr2_rev/240-360           TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTTGCTTGATGC
+rn3.chr3_rev/240-360           TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTCGCTTGATGC
+galGal2.chr17_rev/240-360      TCTCAGAGAAATCCTCTCCTTCAAAAAAGGATTCTATTTCAATT----CTAGCTTGGTGC
+fr1.chrUn_rev/240-360          TCTCGGAGAAATCTTCTCCCTCAAAGAAAGACTCGATCTCAATG----CGGGCCTGGTGC
+danRer1.chr11_rev/240-360      TCTCAGAGAAATCTTCTCCCTCAAAGAAGGACTCGATCTCGATG----CGGGCCTGATGC
+
+
+hg17.chr1_rev/240-360          TGAGAAGACAGGGCCCGTTTGGCCTTTTCTACCTTGCGCCAGAGTTTCTGCACAGCTCTA
+mm5.chr2_rev/240-360           TGAGAAGACAAGGCTCTCTTAGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG
+rn3.chr3_rev/240-360           TGAGAAGACAGGGCTCTCTTGGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG
+galGal2.chr17_rev/240-360      TGGGATGACAGGGCCCGCTTCGCTTTCTCTACTTCCCGTCTTAGTTTCTGTACAGCTCTG
+fr1.chrUn_rev/240-360          TGGGCAGACAGGGCCCTCTTTGCCTTCTCAACCTCACGACGCAGCTTCTGGACAGCACGG
+danRer1.chr11_rev/240-360      TGGGCAGACAGGGCTCTCTTAGCCTTCTCCACCTCTCTGCGCAGCTTCTGCACGGCGCGG
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1/271-391          GAAAAGGCCAAACGGGCCCTGTCTTCTCAACATCAAGCAAGCAGTAATTGAAATTGAGTC
+mm5.chr2/271-391           GAAAAGGCTAAGAGAGCCTTGTCTTCTCAGCATCAAGCAAG----GATTGAAATTGAGTC
+rn3.chr3/271-391           GAAAAGGCCAAGAGAGCCCTGTCTTCTCAGCATCAAGCGAG----GATTGAAATTGAGTC
+galGal2.chr17/271-391      GAGAAAGCGAAGCGGGCCCTGTCATCCCAGCACCAAGCTAG----AATTGAAATAGAATC
+fr1.chrUn/271-391          GAGAAGGCAAAGAGGGCCCTGTCTGCCCAGCACCAGGCCCG----CATTGAGATCGAGTC
+danRer1.chr11/271-391      GAGAAGGCTAAGAGAGCCCTGTCTGCCCAGCATCAGGCCCG----CATCGAGATCGAGTC
+
+
+hg17.chr1/271-391          CTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGACTCAGGCCAAATTTGAAGAGCTCAA
+mm5.chr2/271-391           CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA
+rn3.chr3/271-391           CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA
+galGal2.chr17/271-391      CTTTTTTGAAGGAGAGGATTTCTCTGAGACGCTTACTCGTGCCAAATTTGAAGAACTGAA
+fr1.chrUn/271-391          TTTCTTTGAGGGAGAAGATTTCTCCGAGACACTGACCCGTGCCAAATTTGAAGAGCTTAA
+danRer1.chr11/271-391      CTTCTTTGAGGGAGAAGATTTCTCTGAGACTCTCACCAGAGCCAAGTTTGAAGAGCTCAA
+
+
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+hg17.chr1_rev/271-391          TTGAGCTCTTCAAATTTGGCCTGAGTCAGGGTCTCAGAAAAGTCTTCTCCTTCATAGAAG
+mm5.chr2_rev/271-391           TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG
+rn3.chr3_rev/271-391           TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG
+galGal2.chr17_rev/271-391      TTCAGTTCTTCAAATTTGGCACGAGTAAGCGTCTCAGAGAAATCCTCTCCTTCAAAAAAG
+fr1.chrUn_rev/271-391          TTAAGCTCTTCAAATTTGGCACGGGTCAGTGTCTCGGAGAAATCTTCTCCCTCAAAGAAA
+danRer1.chr11_rev/271-391      TTGAGCTCTTCAAACTTGGCTCTGGTGAGAGTCTCAGAGAAATCTTCTCCCTCAAAGAAG
+
+
+hg17.chr1_rev/271-391          GACTCAATTTCAATTACTGCTTGCTTGATGTTGAGAAGACAGGGCCCGTTTGGCCTTTTC
+mm5.chr2_rev/271-391           GACTCAATTTCAATC----CTTGCTTGATGCTGAGAAGACAAGGCTCTCTTAGCCTTTTC
+rn3.chr3_rev/271-391           GACTCAATTTCAATC----CTCGCTTGATGCTGAGAAGACAGGGCTCTCTTGGCCTTTTC
+galGal2.chr17_rev/271-391      GATTCTATTTCAATT----CTAGCTTGGTGCTGGGATGACAGGGCCCGCTTCGCTTTCTC
+fr1.chrUn_rev/271-391          GACTCGATCTCAATG----CGGGCCTGGTGCTGGGCAGACAGGGCCCTCTTTGCCTTCTC
+danRer1.chr11_rev/271-391      GACTCGATCTCGATG----CGGGCCTGATGCTGGGCAGACAGGGCTCTCTTAGCCTTCTC
+
+
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,720 @@
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  83.72
+ Shannon entropy: 0.30516
+ G+C content: 0.50000
+ Mean single sequence MFE: -36.97
+ Consensus MFE: -15.85
+ Energy contribution: -15.72
+ Covariance contribution:  -0.13
+ Combinations/Pair:   1.35
+ Mean z-score:  -0.44
+ Structure conservation index:   0.43
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.76
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/0-120
+UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score =  -0.87, R)
+>canFam1.chr9/0-120
+UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score =  -0.16, R)
+>mm5.chr2/0-120
+UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score =   0.44, R)
+>galGal2.chr17/0-120
+AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU
+.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score =  -0.79, R)
+>fr1.chrUn/0-120
+AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU
+.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score =  -0.61, R)
+>danRer1.chr11/0-120
+UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU
+((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score =  -0.64, R)
+>consensus
+UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU
+....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 +  -0.13) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  83.72
+ Shannon entropy: 0.30516
+ G+C content: 0.50000
+ Mean single sequence MFE: -30.48
+ Consensus MFE: -16.68
+ Energy contribution: -16.27
+ Covariance contribution:  -0.41
+ Combinations/Pair:   1.38
+ Mean z-score:  -0.85
+ Structure conservation index:   0.55
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -2.64
+ SVM RNA-class probability: 0.005929
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA
+..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score =  -1.08, R)
+>canFam1.chr9/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA
+..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score =  -1.16, R)
+>mm5.chr2/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA
+..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score =   0.11, R)
+>galGal2.chr17/0-120
+AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU
+..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score =  -1.92, R)
+>fr1.chrUn/0-120
+AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU
+.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score =  -0.90, R)
+>danRer1.chr11/0-120
+AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA
+.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score =  -0.16, R)
+>consensus
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA
+....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 +  -0.41) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  83.72
+ Shannon entropy: 0.30516
+ G+C content: 0.50000
+ Mean single sequence MFE: -30.48
+ Consensus MFE: -16.68
+ Energy contribution: -16.27
+ Covariance contribution:  -0.41
+ Combinations/Pair:   1.38
+ Mean z-score:  -0.85
+ Structure conservation index:   0.55
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -2.64
+ SVM RNA-class probability: 0.005929
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA
+..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score =  -1.08, R)
+>canFam1.chr9_rev/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA
+..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score =  -1.16, R)
+>mm5.chr2_rev/0-120
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA
+..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score =   0.11, R)
+>galGal2.chr17_rev/0-120
+AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU
+..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score =  -1.92, R)
+>fr1.chrUn_rev/0-120
+AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU
+.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score =  -0.90, R)
+>danRer1.chr11_rev/0-120
+AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA
+.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score =  -0.16, R)
+>consensus
+AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA
+....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 +  -0.41) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  83.72
+ Shannon entropy: 0.30516
+ G+C content: 0.50000
+ Mean single sequence MFE: -36.97
+ Consensus MFE: -15.85
+ Energy contribution: -15.72
+ Covariance contribution:  -0.13
+ Combinations/Pair:   1.35
+ Mean z-score:  -0.44
+ Structure conservation index:   0.43
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.76
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/0-120
+UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score =  -0.87, R)
+>canFam1.chr9_rev/0-120
+UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score =  -0.16, R)
+>mm5.chr2_rev/0-120
+UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU
+.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score =   0.44, R)
+>galGal2.chr17_rev/0-120
+AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU
+.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score =  -0.79, R)
+>fr1.chrUn_rev/0-120
+AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU
+.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score =  -0.61, R)
+>danRer1.chr11_rev/0-120
+UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU
+((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score =  -0.64, R)
+>consensus
+UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU
+....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 +  -0.13) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  85.83
+ Shannon entropy: 0.26644
+ G+C content: 0.46111
+ Mean single sequence MFE: -29.08
+ Consensus MFE: -17.18
+ Energy contribution: -17.27
+ Covariance contribution:   0.09
+ Combinations/Pair:   1.38
+ Mean z-score:  -0.03
+ Structure conservation index:   0.59
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.58
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/120-240
+CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA
+(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score =  -0.65, R)
+>panTro1.chr1/120-240
+CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA
+(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score =  -0.03, R)
+>rn3.chr3/120-240
+UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA
+(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score =   0.92, R)
+>galGal2.chr17/120-240
+UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA
+((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score =   0.87, R)
+>fr1.chrUn/120-240
+UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA
+.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score =  -1.77, R)
+>danRer1.chr11/120-240
+UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA
+....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score =   0.50, R)
+>consensus
+UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA
+((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 +   0.09) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  85.83
+ Shannon entropy: 0.26644
+ G+C content: 0.46111
+ Mean single sequence MFE: -23.40
+ Consensus MFE:  -9.31
+ Energy contribution:  -9.48
+ Covariance contribution:   0.17
+ Combinations/Pair:   1.36
+ Mean z-score:   0.40
+ Structure conservation index:   0.40
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -7.30
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/120-240
+UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG
+.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score =  -0.12, R)
+>panTro1.chr1/120-240
+UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG
+.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score =   1.10, R)
+>rn3.chr3/120-240
+UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA
+.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score =   0.66, R)
+>galGal2.chr17/120-240
+UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA
+..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score =   0.35, R)
+>fr1.chrUn/120-240
+UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA
+..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score =  -0.65, R)
+>danRer1.chr11/120-240
+UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA
+..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score =   1.03, R)
+>consensus
+UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA
+.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 =  -9.48 +   0.17) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  85.83
+ Shannon entropy: 0.26644
+ G+C content: 0.46111
+ Mean single sequence MFE: -23.40
+ Consensus MFE:  -9.31
+ Energy contribution:  -9.48
+ Covariance contribution:   0.17
+ Combinations/Pair:   1.36
+ Mean z-score:   0.40
+ Structure conservation index:   0.40
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -7.30
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/120-240
+UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG
+.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score =  -0.12, R)
+>panTro1.chr1_rev/120-240
+UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG
+.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score =   1.10, R)
+>rn3.chr3_rev/120-240
+UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA
+.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score =   0.66, R)
+>galGal2.chr17_rev/120-240
+UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA
+..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score =   0.35, R)
+>fr1.chrUn_rev/120-240
+UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA
+..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score =  -0.65, R)
+>danRer1.chr11_rev/120-240
+UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA
+..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score =   1.03, R)
+>consensus
+UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA
+.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 =  -9.48 +   0.17) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  85.83
+ Shannon entropy: 0.26644
+ G+C content: 0.46111
+ Mean single sequence MFE: -29.08
+ Consensus MFE: -17.18
+ Energy contribution: -17.27
+ Covariance contribution:   0.09
+ Combinations/Pair:   1.38
+ Mean z-score:  -0.03
+ Structure conservation index:   0.59
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.58
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/120-240
+CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA
+(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score =  -0.65, R)
+>panTro1.chr1_rev/120-240
+CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA
+(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score =  -0.03, R)
+>rn3.chr3_rev/120-240
+UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA
+(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score =   0.92, R)
+>galGal2.chr17_rev/120-240
+UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA
+((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score =   0.87, R)
+>fr1.chrUn_rev/120-240
+UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA
+.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score =  -1.77, R)
+>danRer1.chr11_rev/120-240
+UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA
+....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score =   0.50, R)
+>consensus
+UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA
+((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 +   0.09) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  80.00
+ Shannon entropy: 0.37687
+ G+C content: 0.50603
+ Mean single sequence MFE: -34.52
+ Consensus MFE: -15.70
+ Energy contribution: -14.52
+ Covariance contribution:  -1.19
+ Combinations/Pair:   1.43
+ Mean z-score:   0.11
+ Structure conservation index:   0.45
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.92
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/240-360
+UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA
+..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score =  -1.05, R)
+>mm5.chr2/240-360
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA
+.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score =  -0.73, R)
+>rn3.chr3/240-360
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA
+.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score =   0.75, R)
+>galGal2.chr17/240-360
+CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA
+(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score =   0.14, R)
+>fr1.chrUn/240-360
+CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA
+..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score =   1.69, R)
+>danRer1.chr11/240-360
+CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA
+.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score =  -0.14, R)
+>consensus
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA
+....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 +  -1.19) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  80.00
+ Shannon entropy: 0.37687
+ G+C content: 0.50603
+ Mean single sequence MFE: -31.38
+ Consensus MFE: -17.15
+ Energy contribution: -16.27
+ Covariance contribution:  -0.88
+ Combinations/Pair:   1.50
+ Mean z-score:   0.17
+ Structure conservation index:   0.55
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.07
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/240-360
+UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA
+....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score =  -1.00, R)
+>mm5.chr2/240-360
+UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score =  -1.12, R)
+>rn3.chr3/240-360
+UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score =   0.19, R)
+>galGal2.chr17/240-360
+UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG
+.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score =   0.63, R)
+>fr1.chrUn/240-360
+UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG
+....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score =   1.62, R)
+>danRer1.chr11/240-360
+UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG
+.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score =   0.69, R)
+>consensus
+UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 +  -0.88) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  80.00
+ Shannon entropy: 0.37687
+ G+C content: 0.50603
+ Mean single sequence MFE: -31.38
+ Consensus MFE: -17.15
+ Energy contribution: -16.27
+ Covariance contribution:  -0.88
+ Combinations/Pair:   1.50
+ Mean z-score:   0.17
+ Structure conservation index:   0.55
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.07
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/240-360
+UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA
+....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score =  -1.00, R)
+>mm5.chr2_rev/240-360
+UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score =  -1.12, R)
+>rn3.chr3_rev/240-360
+UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score =   0.19, R)
+>galGal2.chr17_rev/240-360
+UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG
+.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score =   0.63, R)
+>fr1.chrUn_rev/240-360
+UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG
+....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score =   1.62, R)
+>danRer1.chr11_rev/240-360
+UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG
+.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score =   0.69, R)
+>consensus
+UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG
+.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 +  -0.88) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  80.00
+ Shannon entropy: 0.37687
+ G+C content: 0.50603
+ Mean single sequence MFE: -34.52
+ Consensus MFE: -15.70
+ Energy contribution: -14.52
+ Covariance contribution:  -1.19
+ Combinations/Pair:   1.43
+ Mean z-score:   0.11
+ Structure conservation index:   0.45
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -4.92
+ SVM RNA-class probability: 0.000000
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/240-360
+UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA
+..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score =  -1.05, R)
+>mm5.chr2_rev/240-360
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA
+.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score =  -0.73, R)
+>rn3.chr3_rev/240-360
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA
+.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score =   0.75, R)
+>galGal2.chr17_rev/240-360
+CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA
+(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score =   0.14, R)
+>fr1.chrUn_rev/240-360
+CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA
+..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score =   1.69, R)
+>danRer1.chr11_rev/240-360
+CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA
+.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score =  -0.14, R)
+>consensus
+CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA
+....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 +  -1.19) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  82.22
+ Shannon entropy: 0.33146
+ G+C content: 0.47735
+ Mean single sequence MFE: -32.55
+ Consensus MFE: -18.57
+ Energy contribution: -18.10
+ Covariance contribution:  -0.47
+ Combinations/Pair:   1.42
+ Mean z-score:  -0.11
+ Structure conservation index:   0.57
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -3.82
+ SVM RNA-class probability: 0.000001
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/271-391
+GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA
+(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score =  -0.31, R)
+>mm5.chr2/271-391
+GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score =  -0.98, R)
+>rn3.chr3/271-391
+GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score =  -0.51, R)
+>galGal2.chr17/271-391
+GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA
+(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score =   0.10, R)
+>fr1.chrUn/271-391
+GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA
+.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score =  -0.02, R)
+>danRer1.chr11/271-391
+GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA
+((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score =   1.06, R)
+>consensus
+GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 +  -0.47) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  82.22
+ Shannon entropy: 0.33146
+ G+C content: 0.47735
+ Mean single sequence MFE: -33.18
+ Consensus MFE: -22.01
+ Energy contribution: -20.72
+ Covariance contribution:  -1.30
+ Combinations/Pair:   1.48
+ Mean z-score:   0.17
+ Structure conservation index:   0.66
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -3.58
+ SVM RNA-class probability: 0.000003
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1/271-391
+UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC
+((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score =  -0.30, R)
+>mm5.chr2/271-391
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC
+....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score =  -0.81, R)
+>rn3.chr3/271-391
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC
+((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score =   0.10, R)
+>galGal2.chr17/271-391
+UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC
+....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score =   0.33, R)
+>fr1.chrUn/271-391
+UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC
+.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score =   0.29, R)
+>danRer1.chr11/271-391
+UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC
+..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score =   1.40, R)
+>consensus
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC
+...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 +  -1.30) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: forward
+ Mean pairwise identity:  82.22
+ Shannon entropy: 0.33146
+ G+C content: 0.47735
+ Mean single sequence MFE: -33.18
+ Consensus MFE: -22.01
+ Energy contribution: -20.72
+ Covariance contribution:  -1.30
+ Combinations/Pair:   1.48
+ Mean z-score:   0.17
+ Structure conservation index:   0.66
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -3.58
+ SVM RNA-class probability: 0.000003
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/271-391
+UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC
+((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score =  -0.30, R)
+>mm5.chr2_rev/271-391
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC
+....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score =  -0.81, R)
+>rn3.chr3_rev/271-391
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC
+((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score =   0.10, R)
+>galGal2.chr17_rev/271-391
+UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC
+....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score =   0.33, R)
+>fr1.chrUn_rev/271-391
+UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC
+.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score =   0.29, R)
+>danRer1.chr11_rev/271-391
+UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC
+..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score =   1.40, R)
+>consensus
+UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC
+...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 +  -1.30) 
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 6
+ Columns: 120
+ Reading direction: reverse
+ Mean pairwise identity:  82.22
+ Shannon entropy: 0.33146
+ G+C content: 0.47735
+ Mean single sequence MFE: -32.55
+ Consensus MFE: -18.57
+ Energy contribution: -18.10
+ Covariance contribution:  -0.47
+ Combinations/Pair:   1.42
+ Mean z-score:  -0.11
+ Structure conservation index:   0.57
+ Background model: dinucleotide
+ Decision model: sequence based alignment quality
+ SVM decision value:  -3.82
+ SVM RNA-class probability: 0.000001
+ Prediction: OTHER
+
+######################################################################
+
+>hg17.chr1_rev/271-391
+GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA
+(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score =  -0.31, R)
+>mm5.chr2_rev/271-391
+GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score =  -0.98, R)
+>rn3.chr3_rev/271-391
+GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score =  -0.51, R)
+>galGal2.chr17_rev/271-391
+GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA
+(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score =   0.10, R)
+>fr1.chrUn_rev/271-391
+GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA
+.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score =  -0.02, R)
+>danRer1.chr11_rev/271-391
+GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA
+((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score =   1.06, R)
+>consensus
+GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA
+.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 +  -0.47) 
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.rnaz.clustered
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz.clustered	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,17 @@
+# windowID	clusterID	seqID	start	end	strand	N	columns	identity	meanMFE	consensusMFE	energyTerm	covarianceTerm	combPerPair	z	SCI	decValue	P
+GCwindow1	locus1	>hg17.chr1	0	120	+	6	120	83.72	-36.97	-15.85	-15.72	-0.13	1.35	-0.44	0.43	-4.76	0.000000	0.50000
+window2	locus1	>hg17.chr1	0	120	-	6	120	83.72	-30.48	-16.68	-16.27	-0.41	1.38	-0.85	0.55	-2.64	0.005929	0.50000
+window3	locus2	>hg17.chr1_rev	0	120	+	6	120	83.72	-30.48	-16.68	-16.27	-0.41	1.38	-0.85	0.55	-2.64	0.005929	0.50000
+window4	locus2	>hg17.chr1_rev	0	120	-	6	120	83.72	-36.97	-15.85	-15.72	-0.13	1.35	-0.44	0.43	-4.76	0.000000	0.50000
+window5	locus3	>hg17.chr1	120	240	+	6	120	85.83	-29.08	-17.18	-17.27	0.09	1.38	-0.03	0.59	-4.58	0.000000	0.46111
+window6	locus3	>hg17.chr1	120	240	-	6	120	85.83	-23.40	-9.31	-9.48	0.17	1.36	0.40	0.40	-7.30	0.000000	0.46111
+window7	locus4	>hg17.chr1_rev	120	240	+	6	120	85.83	-23.40	-9.31	-9.48	0.17	1.36	0.40	0.40	-7.30	0.000000	0.46111
+window8	locus4	>hg17.chr1_rev	120	240	-	6	120	85.83	-29.08	-17.18	-17.27	0.09	1.38	-0.03	0.59	-4.58	0.000000	0.46111
+window9	locus5	>hg17.chr1	240	360	+	6	120	80.00	-34.52	-15.70	-14.52	-1.19	1.43	0.11	0.45	-4.92	0.000000	0.50603
+window10	locus5	>hg17.chr1	240	360	-	6	120	80.00	-31.38	-17.15	-16.27	-0.88	1.50	0.17	0.55	-4.07	0.000000	0.50603
+window11	locus6	>hg17.chr1_rev	240	360	+	6	120	80.00	-31.38	-17.15	-16.27	-0.88	1.50	0.17	0.55	-4.07	0.000000	0.50603
+window12	locus6	>hg17.chr1_rev	240	360	-	6	120	80.00	-34.52	-15.70	-14.52	-1.19	1.43	0.11	0.45	-4.92	0.000000	0.50603
+window13	locus7	>hg17.chr1	271	391	+	6	120	82.22	-32.55	-18.57	-18.10	-0.47	1.42	-0.11	0.57	-3.82	0.000001	0.47735
+window14	locus7	>hg17.chr1	271	391	-	6	120	82.22	-33.18	-22.01	-20.72	-1.30	1.48	0.17	0.66	-3.58	0.000003	0.47735
+window15	locus8	>hg17.chr1_rev	271	391	+	6	120	82.22	-33.18	-22.01	-20.72	-1.30	1.48	0.17	0.66	-3.58	0.000003	0.47735
+window16	locus8	>hg17.chr1_rev	271	391	-	6	120	82.22	-32.55	-18.57	-18.10	-0.47	1.42	-0.11	0.57	-3.82	0.000001	0.47735
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.rnaz.clustered.annotated.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz.clustered.annotated.bed	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,8 @@
+chr1	0	120	WhoKnows	0	+
+chr1	0	120	WhoKnows2	0	-
+chr1	120	240	WhoKnows	0	+
+chr1	120	240	WhoKnows2	0	-
+chr1	240	360	WhoKnows	0	+
+chr1	240	360	WhoKnows2	0	-
+chr1	271	391	WhoKnows	0	+
+chr1	271	391	WhoKnows2	0	-
diff -r 000000000000 -r 5d006d19f70a test-data/unknown.rnaz.clustered.annotated.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz.clustered.annotated.rnaz	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,9 @@
+# windowID	clusterID	seqID	start	end	strand	N	columns	identity	meanMFE	consensusMFE	energyTerm	covarianceTerm	combPerPair	z	SCI	decValue	P	Annotation
+window3	locus2	>hg17.chr1_rev	0	120	+	6	120	83.72	-30.48	-16.68	-16.27	-0.41	1.38	-0.85	0.55	-2.64	0.005929	0.50000	WhoKnows
+window4	locus2	>hg17.chr1_rev	0	120	-	6	120	83.72	-36.97	-15.85	-15.72	-0.13	1.35	-0.44	0.43	-4.76	0.000000	0.50000	WhoKnows2
+window7	locus4	>hg17.chr1_rev	120	240	+	6	120	85.83	-23.40	-9.31	-9.48	0.17	1.36	0.40	0.40	-7.30	0.000000	0.46111	WhoKnows
+window8	locus4	>hg17.chr1_rev	120	240	-	6	120	85.83	-29.08	-17.18	-17.27	0.09	1.38	-0.03	0.59	-4.58	0.000000	0.46111	WhoKnows2
+window11	locus6	>hg17.chr1_rev	240	360	+	6	120	80.00	-31.38	-17.15	-16.27	-0.88	1.50	0.17	0.55	-4.07	0.000000	0.50603	WhoKnows
+window12	locus6	>hg17.chr1_rev	240	360	-	6	120	80.00	-34.52	-15.70	-14.52	-1.19	1.43	0.11	0.45	-4.92	0.000000	0.50603	WhoKnows2
+window15	locus8	>hg17.chr1_rev	271	391	+	6	120	82.22	-33.18	-22.01	-20.72	-1.30	1.48	0.17	0.66	-3.58	0.000003	0.47735	WhoKnows
+window16	locus8	>hg17.chr1_rev	271	391	-	6	120	82.22	-32.55	-18.57	-18.10	-0.47	1.42	-0.11	0.57	-3.82	0.000001	0.47735	WhoKnows2