# HG changeset patch
# User bgruening
# Date 1548839578 18000
# Node ID fdfe3dcf8fc491551ebd647ae8acd82f333e1979

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

diff -r 000000000000 -r fdfe3dcf8fc4 AnnotateRNAz.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AnnotateRNAz.py	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 rnazWindow.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazWindow.xml	Wed Jan 30 04:12:58 2019 -0500
@@ -0,0 +1,154 @@
+<tool id="rnaz_window" name="RNAz windows" version="2.1">
+    <requirements>
+        <requirement type="package" version="2.1">rnaz</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    rnazWindow.pl
+        --window $window
+        --slide $slide
+        --max-length $maxlength
+        --max-gap $maxgap
+        --max-masked $maxmask
+        --min-id $minid
+        --min-seqs $minseqs
+        --max-seqs $maxseqs
+        --num-samples $numsamples
+        --min-length $minlength
+        --opt-id $optid
+        --$forward_or_reverse
+        #if $noref:
+            $noref
+        #end ifx
+        '$input'
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param format="txt" name="input" type="data" label="Input Alignment File" />
+        <param argument="--window" name="window" type="integer" value="120" min="80" label="Window size, default 120" />
+        <param argument="--slide" name="slide" type="integer" value="120" min="1" label="Window step size, default 120" />
+        <param argument="--max-length" name="maxlength" type="integer" value="120" label="Min size of block before slicing, default is window size 120" />
+        <param argument="--max-gap" name="maxgap" type="float" value="0.25" label="Maximum fraction of gaps, default 0.25" />
+        <param argument="--max-masked" name="maxmask" type="float" value="0.1" label="Maximum fraction of masked letters in sequence, default 0.1" />
+        <param argument="--min-id" name="minid" type="integer" value="50"
+            label="Discard alignment windows with an overall mean pairwise identity smaller than X%. (Default: 50)" />
+        <param argument="--min-seqs" name="minseqs" type="integer" value="2"
+            label="Minimum number of sequences in an alignment. Discard any windows with less than N sequences (Default:2)" />
+        <param argument="--max-seqs" name="maxseqs" type="integer" value="6"
+            label="Maximum number of sequences in an alignment. Discard any windows with less than N sequences (Default:6)" />
+        <param argument="--num-samples" name="numsamples" type="integer" value="1"
+            label="Number of different subsets of sequences that is sampled if there are more sequences in the alignment than --max-seqs (Default: 1)" />
+        <param argument="--min-length" name="minlength" type="integer" value="0"
+            label="Minimum number of columns of an alignment slice. After removing sequences from the alignment, all-gap columns are removed. If the resulting alignment has fewer than N columns, the complete alignment is discarded." />
+        <param argument="--opt-id" name="optid" type="integer" value="80"
+            label="If the number of sequences has to be reduced (see --max-seqs) a subset of sequences is chosen which is optimized for this value of mean pairwise identity. (In percent, default: 80)" />
+        <param name="forward_or_reverse" type="select" label="Scored strand">
+            <option value="forward">Score forward strand (-f)</option>
+            <option value="reverse">Score reverse strand (-r)</option>
+            <option value="both-strands" selected="true">Score both strands (-b)</option>
+        </param>
+        <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
+            label="By default the first sequence is interpreted as reference sequence. This means, for example, that if the reference sequence is removed during filtering steps the complete alignment is discarded. Also, if there are too many sequences in the alignment, the reference sequence is never removed when choosing an appropriate subset. Having a reference sequence is crucial if you are doing screens of genomic regions. For some other applications it might not be necessary and in such cases you can change the default behaviour by setting this option." />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="unknown.aln"/>
+            <output name="output" file="unknown.aln.window"/>
+        </test>
+        <test>
+            <param name="input" value="tRNA.maf"/>
+            <output name="output" file="tRNA.maf.window"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+
+RNAz cannot score alignments longer than 400
+columns. In practice, it is generally advisable that you score
+long alignments, say more than 200 columns, in shorter, overlapping
+windows.  For general purpose screens we recommend a window
+size of 120.  This window size appears large enough to detect
+local secondary structures within long ncRNAs and, on the
+other hand, small enough to find short secondary structures
+without loosing the signal in a much too long window
+
+Usage: rnazWindow.pl [options] [file]
+Options:
+-w, --window=N Size of the window (Default: 120)
+
+-s, --slide=N Step size (Default: 120)
+
+-m, --max-length Slice only alignments longer than N columns. This
+means blocks longer than the window size given by --window but shorter
+than N are kept intact and not sliced. Per default this length is set
+to the window size given by --window (or 120 by default).
+
+--max-gap=X Maximum fraction of gaps. If a reference sequence is used
+(i.e.  "--no-reference" is not set), each sequence is compared to the
+reference sequence and if in the pairwise comparison the fraction of
+columns with gaps is higher than X the sequence is discarded. If no
+reference sequence is used, all sequences with a fraction of gaps
+higher than X are discarded. (Default: 0.25)
+
+--max-masked=X Maximum fraction of masked (=lowercase letters) in a
+sequence.  All sequences with a fraction of more than X lowercase
+letters are discarded. This is usually used for excluding repeat
+sequences marked by RepeatMasker but any other information can be
+encoded by using lowercase letters. (Default: 0.1)
+
+--min-id=X Discard alignment windows with an overall mean pairwise
+identity smaller than X%. (Default: 50)
+
+--min-seqs=N Minimum number of sequences in an alignment. Discard any
+windows with less than N sequences (Default:2).
+
+--max-seqs=N Maximum number of sequences in an alignment. If the
+number of sequences in a window is higher than N, a subset of
+sequences is used with exactly N sequences. The greedy algorithm of
+the program "rnazSelectSeqs.pl" is used which optimizes for a user
+specified mean pairwise identity (see "--opt-id"). (Default: 6)
+
+--num-samples=N Number of different subsets of sequences that is
+sampled if there are more sequences in the alignment than
+"--max-seqs".  (Default: 1)
+
+--min-length=N Minimum number of columns of an alignment slice. After
+removing sequences from the alignment, all-gap columns are
+removed. If the resulting alignment has fewer than N columns, the
+complete alignment is discarded.
+
+--opt-id=X If the number of sequences has to be reduced (see
+"--max-seqs") a subset of sequences is chosen which is optimized for
+this value of mean pairwise identity. (In percent, default: 80)
+
+--max-id=X One sequence from pairs with pairwise identity higher than
+X % this is removed (default: 99, i.e. only almost identical sequences
+are removed) NOT IMPLEMENTED
+
+--forward --reverse --both-strands Output forward, reverse complement
+or both of the sequences in the windows. Please note: "RNAz" has the
+same options, so if you use "rnazWindow.pl" for an RNAz screen, we
+recommend to set the option directly in "RNAz" and leave the default
+here. (Default: ---forward)
+
+--no-reference By default the first sequence is interpreted as
+reference sequence. This means, for example, that if the reference
+sequence is removed during filtering steps the complete alignment is
+discarded. Also, if there are too many sequences in the alignment, the
+reference sequence is never removed when choosing an appropriate
+subset. Having a reference sequence is crucial if you are doing
+screens of genomic regions. For some other applications it might not
+be necessary and in such cases you can change the default behaviour by
+setting this option.
+
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1142/9789814295291_0009</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r fdfe3dcf8fc4 test-data/Annotation.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Annotation.bed	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/IRE.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IRE.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/miRNA.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/miRNA.maf	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/notsorandom.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notsorandom.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/randomize.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/randomize.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/snoRNA.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snoRNA.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.aln.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.aln.window	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.maf	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.maf.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.maf.window	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA.rnaz.clustered
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz.clustered	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 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 04:12:58 2019 -0500
@@ -0,0 +1,1 @@
+chr4	1352453	1352526	tRNAContainer	0	+
diff -r 000000000000 -r fdfe3dcf8fc4 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 04:12:58 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 fdfe3dcf8fc4 test-data/tRNA_selected.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_selected.aln	Wed Jan 30 04:12:58 2019 -0500
@@ -0,0 +1,9 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+
+sacCer1      GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
+
+
+sacCer1      CCCCTACAGGGCT
+
+
diff -r 000000000000 -r fdfe3dcf8fc4 test-data/unknown.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.aln	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/unknown.aln.window
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.aln.window	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/unknown.rnaz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 test-data/unknown.rnaz.clustered
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unknown.rnaz.clustered	Wed Jan 30 04:12:58 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 fdfe3dcf8fc4 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 04:12:58 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 fdfe3dcf8fc4 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 04:12:58 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