Mercurial > repos > bgruening > rnaz_window
changeset 0:2436fa5c7d53 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
| author | bgruening |
|---|---|
| date | Wed, 30 Jan 2019 03:57:47 -0500 |
| parents | |
| children | |
| files | AnnotateRNAz.py rnazWindow.xml test-data/Annotation.bed test-data/IRE.aln test-data/miRNA.maf test-data/notsorandom.aln test-data/randomize.aln test-data/snoRNA.aln test-data/tRNA.aln test-data/tRNA.aln.window test-data/tRNA.maf test-data/tRNA.maf.window test-data/tRNA.rnaz test-data/tRNA.rnaz.clustered test-data/tRNA.rnaz.clustered.annotated.bed test-data/tRNA.rnaz.clustered.annotated.rnaz test-data/tRNA_selected.aln test-data/unknown.aln test-data/unknown.aln.window test-data/unknown.rnaz test-data/unknown.rnaz.clustered test-data/unknown.rnaz.clustered.annotated.bed test-data/unknown.rnaz.clustered.annotated.rnaz |
| diffstat | 23 files changed, 1665 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotateRNAz.py Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnazWindow.xml Wed Jan 30 03:57:47 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Annotation.bed Wed Jan 30 03:57:47 2019 -0500 @@ -0,0 +1,3 @@ +chr1 10 500 WhoKnows 0 + +chr1 90 900 WhoKnows2 0 - +chr4 1352400 1352700 tRNAContainer 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/IRE.aln Wed Jan 30 03:57:47 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- + * + + +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miRNA.maf Wed Jan 30 03:57:47 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- +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/notsorandom.aln Wed Jan 30 03:57:47 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 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/randomize.aln Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snoRNA.aln Wed Jan 30 03:57:47 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 + *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln Wed Jan 30 03:57:47 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 + * ** * **
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln.window Wed Jan 30 03:57:47 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 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf.window Wed Jan 30 03:57:47 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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz Wed Jan 30 03:57:47 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.bed Wed Jan 30 03:57:47 2019 -0500 @@ -0,0 +1,1 @@ +chr4 1352453 1352526 tRNAContainer 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.rnaz Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_selected.aln Wed Jan 30 03:57:47 2019 -0500 @@ -0,0 +1,9 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC + + +sacCer1 CCCCTACAGGGCT + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln Wed Jan 30 03:57:47 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 + * ** ** ***** ******** ** **
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln.window Wed Jan 30 03:57:47 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 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz Wed Jan 30 03:57:47 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered Wed Jan 30 03:57:47 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.bed Wed Jan 30 03:57:47 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 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.rnaz Wed Jan 30 03:57:47 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