# HG changeset patch # User iuc # Date 1558649825 14400 # Node ID b3f5d0879dab880a36e417aac7b41a445fe7cdc4 # Parent 4de31938431bb44e70dbd2789ad5538bcae55cdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d diff -r 4de31938431b -r b3f5d0879dab augustus.xml --- a/augustus.xml Fri Oct 20 03:48:57 2017 -0400 +++ b/augustus.xml Thu May 23 18:17:05 2019 -0400 @@ -69,6 +69,13 @@ $utr --genemodel=$genemodel + #if $hints.usehints == 'T' + --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg' + #end if + + #if $range.userange == 'T' + --predictionStart=$range.start --predictionEnd=$range.stop + #end if #if $model.augustus_mode == 'history' --species=local @@ -223,7 +230,7 @@ + help="Gene Model to predict, for more information please refer to the help."> @@ -231,6 +238,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -279,6 +316,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chr2R +TTGCAATTTGCACTTTTCAATTGCCCCAAAAGATACGCCAACGAAATGCT +TATTAAAGTATCAAAAACAAATACCAGAAAGCTGTCACCAATCCCGCCCC +ATAGAAAACATGCCCACTTTGCCGCAGAATTTGCATATTTGTCTCCGTCG +GCGGTCGTCATTTTAATAAAAAAAAAATGTTTGTATAATTTCAGGTCGTC +GTGGGATGCGGCGGCTGCTTGCttataaaattaattttaaattaaacaat +tttaattatGATTCAATAATCAACAAACACACTGCAGCTTCGTCAATGTT +GTCGCAGACTTTCAACAATGCAAATATTGGTTTACGGCCATAAAGGCCCA +GCGCGACCAACCAAACCATTAATCCAACTCCGCTCGACTATTGCAAATTG +TTTAATAGCCGCCTTTCTTTCTTTTATGTTTGCAAAAAGAATGTATTTCC +ATAATATTGCCGCTTTATGTTTCATCTGGAACCACTTAACTTTGCCTCTG +CTAATTCAATTAAAAGGAGAATTTAAAAACTTGAATAGCTTGTAAAGTGA +CAAAAAATTCAGTACTTCTTTTATTGAGTTAGTAACTAATATCAATGCTA +ATTCAATTCGCAGATGCCCTTGTTTCCACCAAAAATTTAAATTACTACAT +TGAAAAAAAAAATAATTCTAATAAACTATATTGATTTGCAATAGTATATT +CCCAATGCTCCATAAACTTGCTTCACATGACttaaaaaataaattaaaat +ttataGAAAAAACTTGATTTTTGAATTTGTTCCTTGCTTGAAACTTGCTG +AATTTTTTTATGTGCAGAAATATTTTCGATGGTAATTGAATTAACTCTTA +ATTTGGTATTTTGCCTGTGTGGTCATAAAATTTAAAGAGCACATTAATTG +TCTAATTGAAAAAACGGTTTGGCTGCATAAATTGCTCGACGACTTGCTCA +TTTTTCTCATGATTATTATAGTTATGACAACCATTTGTTTAAGCTAGTTA +CAGTGCCTCTTGGGAAGACTTACTAAGGGAATGCACCTTTAGTCAAATGC +AACAGATATTAATTAAATATTCAGTGCTTAATCACTTGCAACAAGTTAAA +TGTTGATTTTTGCCCAGAGCCCTCTGTGACTTTATTCAATTAGCGTTTGT +TAACTCCCGTTCCCGAACTTCTCCAGATTTTTTGCCAATCTTTTTCGATG +CCGGCGGGCACATCATTACATATGCCACGCCCACCTCGCCATTGCCTGCC +CCAAGCTTTATGCTTGGTGTACGCAAAAATTTATTTACACGCATAATTTA +AAAAACCTTTTGCGCTTTGCTTAATGGCCATTCATTTATTGTAACACACA +CACACACTCGCTGGGTGACACTTGCATTATTGAATCTGCCACGCCCACCA +AAAAGGCGGAGGCACATAATGGGCTGATTTCGTTAGTTGACAGCCACATG +TTTGCGGTACTCGTTAAGCTGAAAACATGCCTTTTCAAGGGGTTTTGGCA +TTTATTTTATAATTTAAGTATCTATGCCCATGAAGCTTTTAATATAAAAC +CACTCAAAACATTTTAAAATACTTTTAAAATATACATTACGTTACATTAA +ATAATCAAATCAATTGATAGTACGAAACTGACATATAAACAATATTATAG +GAATGAACACATTTCACACTTACAAAATGTAGAATTTAATTTAAAGGCTA +TGAAGTATAAACGTATAAAATATATCCAATTATTAAAATATTAAAACAAA +ATATCAAGTTGAGGCCGCCACCTTTGTTTAAATCTATAAATTGGGAAACA +GTTTGTTTATTTGTGCTGGACATTAATTGTCTGTTCGAAGAAAGGTAATT +AAAACAAATCCACATTGTTATCCTGCGCTATCAATATGCCAGCAAATTAA +TTATGATGTGTTAGACAGATCAATGACATTCTTGCTGAGAGCCGAGTTGC +TGCAACTCGCTTGCCAAAGTTAAACGCACTCACTTAACTCGCACCATTCA +GCTTTAGTCACCTGGATTTGATTCGATTTTGTCATCTGCCCGGGCAACAa +cacatacatatatactacacatgcaaacatatacatatatgcccatatct +acatGGCCAACTACTTCGATTCCTGGCCTTTTGTACTGGCCCCTTTCGCC +TGTGGCAATGCTTCCTGTCTGATGTTGCACGAGTAGATGTTGCCgctgtt +gctgttgctgttgctgttgctTGTGTGCCTTGAGTTGGCAGGCCACGTTC +TGGTTTCGGTTGCGGTTTCGGTTTGCTGGCTGCGATGGGCGCCTGTTGAC +GCTTTCGGCTACCCAGACATGGGTATCAGCCAGGTACCGACTTGGCTCTC +CAGTTTATGGCCGTTTACATGCTCACCGCCCGTTTCTCATATCACTTTAT +TTGCCAGCGGAATTCGCACGCAACTCCCTCGGTAATGATGCTCAAGAATT +TTTAATAAAAAACTGCCAGCCAAGCAGGAGGAGCTTTGCTCTTTTATTTT +TGTGCTGCGACTGATGAAGGCAATTGGAAGGACCTTAATGACAGGCAGCC +TTTGTGGGTTAAGCAATATATTAATCAGCATATTAATTATGCAGCAAGGT +AGTTTTGCCCGAGTGCGGGCGGGCATGGCCAGTGTCGAAGGTCAACGAAC +TGCAGCGGCCGCATGCATTGTTGGGGCATATAAATTGTTTAAACAACTTT +ACAGACAACATCCGTTGGGCCAGGCAAAATGGCCCGAAGGCGATGGGAAT +TCGAGTACCAGGCTgccagccagccagccagccagccagccagccagcca +gtcagccaTGTGACAGGCAGTCGGTCATTATTTCGCACTTTTGTTGCCGC +TGCGGAAATTTCACAGCAAGAGGCAGCGGCAAACATGCGACACGTGCAAC +ACCGAAAGTCGAGAGTCTGGGCGATACAGTGTGCCATAACAATAATGCCA +CAACAAAGATAGAGTCCCTGCCAGTAGAGAGCAGGCTGGGCGAAAAATGT +GTGCGGGAGTCAGGTGGAAAAGATGCACAAGTCGGTGGCAGACAAAATGG +AATTTTAATGATATGAGAAGGCGCGCCTTCTGAATATTTTTGCAGGTGAA +ACTGCTTACCAGCCATCCACTTGGCCACCTCCCCCTCCACCAAACAGCAC +CAAACTCTTACCCTTTGAACTCGCGTAGTACAACCGGCACTTGAACTACG +CCGCTTACTACGCTCTTGGCGCTCTTTTCAGTTTGTTTTTGCTGCGTTAT +AGTGCCCGTTTTTTTTCTGTCCTGACTCAGGCGCAGGCGAGTTGGCCCAG +AAGAGCGCAAGAGAACCGCTAAGAGCGCATTTACGATTGGCAAGCCGGTA +AAAATAGAAAAATAAGTAGTTTGAACACAGTTTGTATGAAGGTATGCTGT +TTCGCTTGAAATTTAATGCAGTTTATATTACAGAAATAGAAAACTAACCA +ATTACTTTGTTTATTTTGGTATTAAATGAATGAGCTGCACTTACACTTTT +CAAAATAGTTTATCCAAAGCACTTGACATTTTGGTGGTAGTTATTGCATA +GTTCAGGTGCTTTTTGTAGTTTAAAACATTTTGAAACCCCTTTTAAGATA +TCACAAGCACAAAGCACAAAGGCGCACTCACACAATTGCGAACGGCAAGC +GCCATGTGCGCCTGGCGGTATGCAATAGTTTCTGTTTCTCTTTCGTTTCC +GTAAATGGTAGTGCGCGTATAGTAgtgtgcgtttgcgtatgcgtgtgtgt +gtgtgtgtgtgtgtgcgtTTTAGCCGACAAAGTGCAACACACAGCGCAAT +GACCGACGTACTCGAGCGTTGACTCGTTTCTGCGACAACTTTTCTCGCTC +CTCGCCGATGGGAATAATGATCTCAGCGTAATGACGATTTTTAGCAGCCA +GTAAGCTTGTTGATGCTGTGCCGATGACGTTGCGAACTCGCTCTCTCCGG +GCCGCTCGCTCTCTCTTTCCCACACTCTCTCGGCCATTTTGCGGAAGTTT +CAACTCACCGCAAAACGCTCCAAAATGAGCAGCCAAATTGCGAGTTCCTT +CCTTAATTGCGCACTCGTATCGTTCATTTGTATTTGTATTCCCTCCCATC +AGCATTTTCTCTTCGGCCATATAACAGTTTTCTCTTATACTTTCGCTTCG +GTTTATAGCACGCACATTCCCGGTGACGTCACAAGGCTTTCCCAACGCTT +TTTCCATAGAATCAGTTGTTGTTTGGGCTGCACAAGCCGGCAATGTAAAC +AAAACATAAAATATATGAATGGGTGAGTGAGTTGTGCGGGTGTCTGGGTT +ATTCGACTGCTTCGGCTGAGTGGGTGGCTGTTTTGGGTGGAAATTGGGTG +ACCCCGATGCACTGGTGTTGGTGCAAATTCGGCAATGCGTGTGCGCTGCG +CCTGATGAATGAAAAGTTCGAGTGGCCGCGTGGAAAGCGGGAAAACATCT +GAGCGTCAGCTGCACGGTCATATGTTTGATATTATTCCTGTGAAAGCGGA +AAATGATTTTGAATATTAAAGGAAATCGATGCGGAAAATGTTTTGGAGTA +TTTAATAGCCATTAAATGGATAACGTAGATTTTGTCACAGGTTTATAAAA +TGTAGTTATAGGTAATATATTCACTAAAACAGAAACTGCCTTACACACTT +TTAGTATATTGTTTTATTTACTTAAATTACCTAAGTAAATAAAAGTATTT +TCAAATTGTTACAAAAAGCACACCCTTTTTTCTATTTTTGTTAATATTTG +AATGCCCCACCAATCGATTGAATTTGAAGCCAATTCGTGATTCGGAAAGC +GCAGAGTGTCCTGTATTAAATTCAGCCTTGCAGACAAATGCAAAAACCAT +CGACAGGCCGTGTCAGAAAACACACGAAAATCGAGTGAGCCCCAGAGCAA +TCGCATTTTAATTTGAATTCTTTCTGGTGAGGCCCTTACAAAAGCCCCCA +TGCGATGTGCACGACCAAAAAATGAACTTAAGTTTCGGCCAAGAATCTTG +TTGAAGAATTTCTATTTGAGCATTTGTCATGTCTTCGCCTTAGTCTATAA +AATATACTGTCGGTGGATGGGGACGCGGGGTGTGTGCAAATATGCGAAAG +CTAAATGTCAGAGTCAACCCTTTCGCAGGCCATTCTGCCTGCTTTTTTTT +CAGCCTTTTCTGGCCGGTGTTGCCGCCTTGGCCCCTTTTTTGGGTGGAAA +GGAAAGTTTTTATCTTAAGCTGCGCGCTGACAGGCAGCAAAGCGGCAAGC +GAGGCAACACAAGTACAAGCCGGACAAAGAAGCCAGGGGGAGTGGGGATG +GGCTGGCCGAACGGAAAATGGGAAATGGAAAATGGACGGGCAACGACAAG +GCGGGCAAACGTCAAGTTATAGAAAATGCTAGTGCCTGCACAATAAGAAA +AGTGTCATCCGAATTGCTAATCAATGGAATGATGTTGAGGAGACTCAAAA +GAAATTTAAAGACCTACTAATAAGAAAAAACTGAAAAATCATTAAGTTTT +TAAACTATTCAAACATATTTAAATAATAATTTGTGCAAATTTATTATTGC +TTAAAACAACTAAATAAAAATATATAATGTCATTCAAAGTTTCAAAAAAA +ATTTATTCAATTAAACAAAGGCCATTTTGTATCTTTTCAAAAGTATATGA +CTTAAAAATAGGTTCATTCATTTTGCTTATGCAAGCTAAGGACTCAGCTT +TTTGTCAAAGTGCAGAAAAGGGGAATGAAACTGGTCTTAGAGGGAGAAAA +AATTAAAGGACATGCTGAACGCATTCCTTGGGACACGGGCTGACAGTGAG +TGATTTGACCATACCCTCATTTGCGTGCAGCAAGGACCAAGATCCGAGCT +CTGGGTTCCGGGTTCCGGGGTTCCGACTACCGAGATCCAGGCACACCAAT +GGATTAATGTGCAAGGATGCGACTCGTCAGGCAGGCCAAGAAAATTACGT +CAAGCTACGCAATGGGCCCGTGCCTTTCCCACTGCCCCCCACCACCCCAc +aacctaaccaaatccaacccagcccagcacaacccaaaccaTTATCCTTT +TGGAAATCTGATGATGAGCGCCGACTGCTGCGGGCGGGCGACTCAAAATG +GGAGTGACTCATTTACGCGCTGCACTCGAGTTTCAACCGGCAGCCGGCGA +AGGAAAAGCGGGACTCCGAGAACTTTTCCAAGCTATTTCTGCGCCCAAAT +GACAGCGAAATGTAATAATGAAAAACTTTTTCTTTGTCAACTTGATGAGT +ATGAAATTTTTCACaaaaaaaaaaaaagaaaaaagattaaataaaataaa +agaCGAGCGGCAAAGGAACGGGTTGAGCTTGGGTGGCAGGGCGGTGAGCT +AGAAATATGAAACGTCAGGACTGGTCCTTAGTCTTAGGTTGGCCTTAGTC +TTGGTTGGCCTTCGAGATTAGTTATGGCAAAGGAATTTCCAAGCGAAGGC +GCACGCAAATGATTGCATGCCGCATTACGCATACGCCCGGTTGTGCGTGG +CCGGTTTTAAAATTGAATTTTAATATACAGCAGACACAAAGAGATGTACA +TGACCATATGTATATGTATATAGCTGATCCCTGGCCATGGCTGCTATAAG +CCAGGTTATCCAGCCACCCCGAAAAAACACATGTTCTGCATTTTTACTTT +GTACTGGACCAGGACCCACGGTCCATCATCCCTACCATTTTGCTGCTGCA +CCGCATCGGGGATTGCGGAATTCATAAGCTATGTGCGTTTGCTACAAAAG +TGGAATTTTCGCCACGCCAAAGGATACCCGCTTGCAGGCTCCCAGCTCAC +AGTTCCCACTTCCCGTTTCCTAGATCCTGAGCATGCCATTAACCCACTCG +CAAAAAGCGCAAAATCGCTTAAATTATTGTTACAAGCTGCCAGTGCCAAG +TGGCAGGCACAGCAACAGCAAAAACAAGAACAAGACCAGGGGggcaggtg +gcaggtggcaggtggcaCAGGGCAAACCACCTGAGCTTTTGGCCGCGCTT +TGCTTTGAGTGCCAGTTAGCATAACTCCGCAGGCCGCAGGCGAATATGTc +tgttgttgctgcttttgccgctttgctactctcctgatgttgggtgctgc +tcctgattttgctgttgccgttAGAAGTATTTGTGGCGCGGCAAAGGACA +TCCTCTCGGCAGCCCGTTCTCACCTGCCTGCCAAGCTGCAAGCTCCAGCT +GAAAGTGTCTTTGGTGAGCGCTACCCACCACCTAAATATACAAAGTGTGG +GGGAAAAACAAGAAAAATAACAACCTACAATAGTCTCTTCTTTGTTACCT +AAAAATATAAGAAAAGCACACCTCGCAATTGTGTTGAAAAAAACAAATTG +ATACGAAAAAAAGCGATAGGGATGCCACAACAAAGCGCAATCTTATCAAA +CGTATTAAACATTTTGCTTATCAAAACAGCGAGGTTTGCACAACAATGCG +AAATAGGAGGAGGCAAAATTCTTATCTGCATTTCATCAGTCAAACATTTA +CTGTAATCAAAAATCGCAACTATAAGGAACACAAGTAAAGGCCACAAATG +AGAAGCAAATTATTGTTCGATATCCGTGAATTTGAAGGGGAACGTAATGG +CCGGTTCCATGACGAACATGGTCTTGAATGGACGGCTGGCATCCCGATTG +AACTCCACATGGAAATTGCGAATCAACTTGGCCACTGTGGTCTCCATTTC +CAGATCCACCACCCGTTTGCCAATGCACATGCGGGGTCCAAAGCCAAAGG +GAAGGAACGTGAAGGGGCTGACCTGCATCTTCTTTCCGGTCTCCGGATCC +CTTAACCAGCGCTCCGGCAGAAATTCATCTGGTCGTGGATAATATGTAGC +TTCCTTCATCAGCACATTTGAGCCGAGCAGGACAGTCGTTCCCTTGGGCA +CCCGGTAACCCGAAAGTATCACATCATTTTGGCAGGTTCTCATGGTTCCC +AAGCCATTGGGATAGTATCGCAGTGTCTCCTTGATCACAGCCCTCAAATA +TGGCATATCCTTCATGTTCTCCTCGTTGAGTAGGGAATCCTTTGTGGGCA +TGATGCTCAAGAGCTCCTCCCGCAGTTTGGCCTGCTTATCCGGATGCTTT +GAGAGGCAGAGTAAAACAGCCGACAGAAGCGTGGCTGTGGCATCCACACC +AGCGAATAGGATGTCCAGACTCATAATCACCGCCACCTTGGGATCGATCT +CCATTAATCTCTCCAGCATACTGTTACTATTTATTTTTTCGCCAGCCTGG +CGGCGCTTTTCCAGTGCATCCTGATTTTCCTTCAGCATTTTCTGGGCCAC +ATTCAAACTGTCATTGAGAGTTCGCTTCATTTTCCTGTAGGTGGGCGTCG +ATATGATCTTCCACATGGAGGGCTGAATGTCTAGCTTAAATGTGAGACGG +AAAATATCCCTCGAGGTCTGGAAGAGGGTCAATGCATCGGAATTATCGCG +GTTTTTTCTAATCAGACCCATTTGCCGATCGAAAGCCACCAGGCCGAGTG +ACTCGAAAACAAGCCGGCTTATTTCATCCGTAAAATCTTCGGGGACTTCT +AGAGTTTTTGGATCGCGGATTTCCTTAATGCTGCACAGTAAAATGGAATT +TATTGCTATATATAAATAACAATTCAATAACAAAAATTTCTTACCGCTCT +ATAAACTCATTATTGATATTAGACAATGGTTCATAATACATTCTCAAGCC +CCTGGGTTGCATAAAGATGGGATTAATGGCTGATCGTAGTTTTCCCCATG +CCTCATTTTGTCTGAAATATTCAAATTCAATTGTTTCCTTGCTACTTATT +AGATTTTATACTCACGAAGCCACCAATCCTTGAACCTCACCGTAAACATC +TGGTCGAACGTGTTCGCGGAAATATACAATGGAATCCAGGCCATCACGAC +GTGGCCAGATACCCTCGTTGCGGAATACCATCTCAATGTCCTTTGTGTTG +AAAGTGGTGACCCAATCCTTGCGGCCAAACATTCCGGGCATTACATAGAT +ATCTCCATAGCGCTTTCGCATGGCACTGGTGTATTCCGTAATCGATGCAT +TTTGGAATTCACCACCGGGCATGAAAGCCCTCATAAATTTGAATTTGTTG +GGCCGCGGAATCTCATCGTAGGTCTTGTGCTCCTCCGTTATCTATAATTG +GAAACTAATAACATGATAAATCTATTTCGACTGGATTTTGTGCATACTAA +CACTAGATTTAGCTTGTTCATGTGCCAAAACGGAGGCTGATCTTGAAGAT +CGAACGGGACCCACGTAAATCGCCACAGATCGCGCACTGCTCAATGTATT +CATTCTATTCCTTTTGGTGATCAACTGCAACTAAAAACAGTTCCACTTTC +GAGAACGTTCTTATACCAAAGGCTTATCTCTAAAACGTAGAAAAGAGAGG +AGAGCGAATAACTTGAAATGCTTCAAAATGCAAAAATCTCAAACAAAAAC +AAAAGCCAGCAAACAAAGCATGAGTTTCATTTTCTTATCAGCTGAACGGT +ATAATCGCCGTGAATTGCCTACCTCACTCAACTGAAAAAATAAACAAATG +AACGTGACTGGCTAGAAAAACAAATTGAGAGCGTTGGAACTTACAATAAA +TACACCTCAGAGAATTTGATACTACTATTACGACTATTACATACCCGTTA +CTCATTTAGTGGGATCGCTAGaaaaaaatctaaaatatttaaatattttt +taaaaatttataaGGATTCTAGTTCAACGGTAGACAATTTCAAGATAAAT +AACCAAATTAAAGAAAAATAAAAACAATTCTTAGAGTTGATCCTTGTTCT +CTTTGCATACTGatattttatttattttttattttatttatttaCTGGCG +CCGCTTTTCCACAGAGTCCTCGGTGTCCTTTATCATTTTCTGTGAGAACA +TTAAGATGTCATCGAGAAGACGCATCATCATCCGAAAGTTTGGAGTGGAG diff -r 4de31938431b -r b3f5d0879dab test-data/extrinsic.truncated.cfg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extrinsic.truncated.cfg Thu May 23 18:17:05 2019 -0400 @@ -0,0 +1,183 @@ +==# extrinsic information configuration file for AUGUSTUS +# +# protein hints +# include with --extrinsicCfgFile=filename +# date: 16.10.2007 +# Mario Stanke (mstanke@gwdg.de) + + +# source of extrinsic information: +# M manual anchor (required) +# P protein database hit +# E EST/cDNA database hit +# C combined est/protein database hit +# D Dialign +# R retroposed genes +# T transMapped refSeqs +# W wiggle track coverage info from RNA-Seq + +[SOURCES] +M RM E W + +# +# individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set +# and the whole hint group is disregarded when one hint in it is unsatisfiable. +# 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for +# hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby. +# +[SOURCE-PARAMETERS] + + +# feature bonus malus gradelevelcolumns +# r+/r- +# +# the gradelevel colums have the following format for each source +# sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot +# + +[GENERAL] + start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + ass 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + dss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + exonpart 1 .992 M 1 1e+100 RM 1 1 E 1 1 W 1 1.005 + exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + intron 1 .8 M 1 1e+100 RM 1 1 E 1 1000 W 1 1 + CDSpart 1 1 0.985 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + CDS 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + UTRpart 1 1 .973 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 +nonexonpart 1 1 M 1 1e+100 RM 1 1.01 E 1 1 W 1 1 + genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 + +# +# Explanation: +# +# The gff/gtf file containint the hints must contain somewhere in the last +# column an entry source=?, where ? is one of the source characters listed in +# the line after [SOURCES] above. You can use different sources when you have +# hints of different reliability of the same type, e.g. exon hints from ESTs +# and exon hints from evolutionary conservation information. +# +# In the [GENERAL] section the entries second column specify a bonus for obeying +# a hint and the entry in the third column specify a malus (penalty) for +# predicting a feature that is not supported by any hint. The bonus and the +# malus is a factor that is multiplied to the posterior probability of gene +# structueres. +# Example: +# CDS 1000 0.7 .... +# means that, when AUGUSTUS is searching for the most likely gene structure, +# every gene structure that has a CDS exactly as given in a hint gets +# a bonus factor of 1000. Also, for every CDS that is not supported the +# probability of the gene structure gets a malus of 0.7. Increase the bonus to +# make AUGUSTUS obey more hints, decrease the malus to make AUGUSTUS predict few +# features that are not supported by hints. The malus helps increasing +# specificity, e.g. when the exons predicted by AUGUSTUS are suspicious because +# there is no evidence from ESTs, mRNAs, protein databases, sequence +# conservation, transMapped expressed sequences. +# Setting the malus to 1.0 disables those penalties. Setting the bonus to 1.0 +# disables the boni. +# +# start: translation start (start codon), specifies an interval that contains +# the start codon. The interval can be larger than 3bp, in which case +# every ATG in the interval gets a bonus. The highest bonus is given +# to ATGs in the middle of the interval, the bonus fades off towards the ends. +# stop: translation end (stop codon), see 'start' +# tss: transcription start site, see 'start' +# tts: transcription termination site, see 'start' +# ass: acceptor (3') splice site, the last intron position +# dss: donor (5') splice site, the first intron position +# exonpart: part of an exon in the biological sense. The bonus applies only +# to exons that contain the interval from the hint. Just +# overlapping means no bonus at all. The malus applies to every +# base of an exon. Therefore the malus for an exon is exponential +# in the length of an exon: malus=exonpartmalus^length. +# Therefore the malus should be close to 1, e.g. 0.99. +# exon: exon in the biological sense. Only exons that exactly match the +# hint get a bonus. Exception: The exons that contain the start +# codon and stop codon. This malus applies to a complete exon +# independent of its length. +# intronpart: introns both between coding and non-coding exons. The bonus +# applies to every intronic base in the interval of the hint. +# intron: An intron gets the bonus if and only if it is exactly as in the hint. +# CDSpart: part of the coding part of an exon. (CDS = coding sequence) +# CDS: coding part of an exon with exact boundaries. For internal exons +# of a multi exon gene this is identical to the biological +# boundaries of the exon. For the first and the last coding exon +# the boundaries are the boundaries of the coding sequence (start, stop). +# UTR: exact boundaries of a UTR exon or the untranslated part of a +# partially coding exon. +# UTRpart: The hint interval must be included in the UTR part of an exon. +# irpart: The bonus applies to every base of the intergenic region. If UTR +# prediction is turned on (--UTR=on) then UTR is considered +# genic. If you choose against the usual meaning the bonus of +# irparts to be much smaller than 1 in the configuration file you +# can force AUGUSTUS to not predict an intergenic region in the +# specified interval. This is useful if you want to tell AUGUSTUS +# that two distant exons belong to the same gene, when AUGUSTUS +# tends to split that gene into smaller genes. +# nonexonpart: intergenic region or intron. The bonus applies to very non-exon +# base that overlaps with the interval from the hint. It is +# geometric in the length of that overlap, so choose it close to +# 1.0. This is useful as a weak kind of masking, e.g. when it is +# unlikely that a retroposed gene contains a coding region but you +# do not want to completely forbid exons. +# genicpart: everything that is not intergenic region, i.e. intron or exon or UTR if +# applicable. The bonus applies to every genic base that overlaps with the +# interval from the hint. This can be used in particular to make Augustus +# predict one gene between positions a and b if a and b are experimentally +# confirmed to be part of the same gene, e.g. through ESTs from the same clone. +# alias: nonirpart +# +# Any hints of types dss, intron, exon, CDS, UTR that (implicitly) suggest a donor splice +# site allow AUGUSTUS to predict a donor splice site that has a GC instead of the much more common GT. +# AUGUSTUS does not predict a GC donor splice site unless there is a hint for one. +# +# Starting in column number 4 you can tell AUGUSTUS how to modify the bonus +# depending on the source of the hint and the score of the hint. +# The score of the hints is specified in the 6th column of the hint gff/gtf. +# If the score is used at all, the score is not used directly through some +# conversion formula but by distinguishing different classes of scores, e.g. low +# score, medium score, high score. The format is the following: +# First, you specify the source character, then the number of classes (say n), then you +# specify the score boundaries that separate the classes (n-1 thresholds) and then you specify +# for each score class the multiplicative modifier to the bonus (n factors). +# +# Examples: +# +# M 1 1e+100 +# means for the manual hint there is only one score class, the bonus for this +# type of hint is multiplied by 10^100. This practically forces AUGUSTUS to obey +# all manual hints. +# +# T 2 1.5 1 5e29 +# For the transMap hints distinguish 2 classes. Those with a score below 1.5 and +# with a score above 1.5. The bonus if the lower score hints is unchanged and +# the bonus of the higher score hints is multiplied by 5x10^29. +# +# D 8 1.5 2.5 3.5 4.5 5.5 6.5 7.5 0.58 0.4 0.2 2.9 0.87 0.44 0.31 7.3 +# Use 8 score classes for the DIALIGN hints. DIALIGN hints give a score, a strand and +# reading frame information for CDSpart hints. The strand and reading frame are often correct but not +# often enough to rely on them. To account for that I generated hints for all +# 6 combinations of a strand and reading frame and then used 2x2x2=8 different +# score classes: +# {low score, high score} x {DIALIGN strand, opposite strand} x {DIALIGN reading frame, other reading frame} +# This example shows that scores don't have to be monotonous. A higher score +# does not have to mean a higher bonus. They are merely a way of classifying the +# hints into categories as you wish. In particular, you could get the effect of +# having different sources by having just hints of one source and then distinguishing +# more scores classes. +# +# +# Future plans: +# - Add fuzzy intron hints. Introns get a bonus only when they approximately +# have the same boundaries as in the hint. +# - Make the splice site hints fuzzy also. Allow a hint interval that contains a +# likely splice site, as opposed to only an individual position. +# - Write a program that automatically optimizes the boni and mali given an +# annotated test set of genes and hints for that set of sequences. + diff -r 4de31938431b -r b3f5d0879dab test-data/hints.truncated.adjusted.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hints.truncated.adjusted.gff Thu May 23 18:17:05 2019 -0400 @@ -0,0 +1,482 @@ +chr2R b2h ep 8895 9191 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h ep 8895 9191 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h ep 8878 9191 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h ep 8878 9191 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h ep 8880 9191 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h ep 8880 9191 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h ep 9252 9338 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h ep 8559 8630 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h ep 8559 8630 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h ep 8866 9172 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h ep 8866 9172 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h ep 8782 8811 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h ep 8782 8811 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h ep 9252 9360 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h ep 9252 9360 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h ep 9077 9191 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h ep 9077 9191 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h ep 9252 9337 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h ep 9252 9337 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h ep 8489 8630 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h ep 8489 8630 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h ep 9252 9339 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h ep 9252 9339 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h ep 8575 8630 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h ep 8575 8630 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h ep 8563 8630 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h ep 8563 8630 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h ep 8487 8630 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h ep 8487 8630 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h ep 9252 9340 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h ep 8550 8630 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h ep 8550 8630 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h ep 8613 8630 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h ep 8613 8630 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h ep 8551 8630 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h ep 8551 8630 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h ep 8614 8630 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h ep 8614 8630 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h ep 9252 9372 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h ep 8536 8630 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h ep 8536 8630 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h ep 9252 9346 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h ep 9252 9346 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h ep 7756 8449 0 . . grp=gi|15542574;pri=4;src=E +chr2R b2h ep 7756 8449 0 . . grp=gi|15542574;pri=4;src=E +chr2R b2h ep 8705 8811 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h ep 8705 8811 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h ep 9252 9342 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h ep 9252 9342 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h ep 8492 8630 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h ep 8492 8630 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h ep 9252 9359 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h ep 9252 9359 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h ep 8508 8630 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h ep 8508 8630 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h ep 9252 9355 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h ep 9252 9355 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h exon 8695 8811 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h exon 8866 9191 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|2701440;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2700091;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2701304;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2701309;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|2871896;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|3101873;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4203815;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4245769;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|4245770;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|13769068;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14693753;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14695912;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14699170;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|14700619;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15539951;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15543159;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|15543927;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . grp=gi|38623822;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=SRR023546.8642467/1;pri=4;src=E +chr2R b2h intron 8631 8694 0 . . grp=SRR023546.8642467/1;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . mult=8;pri=4;src=E +chr2R b2h intron 8812 8865 0 . . mult=8;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . mult=3;pri=4;src=E +chr2R b2h intron 9192 9251 0 . . mult=3;pri=4;src=E +chr2R w2h ep 7551 7560 5.300 . . src=W;mult=5; +chr2R w2h ep 7551 7560 5.300 . . src=W;mult=5; +chr2R w2h ep 7561 7570 7.400 . . src=W;mult=7; +chr2R w2h ep 7561 7570 7.400 . . src=W;mult=7; +chr2R w2h ep 7571 7580 9.700 . . src=W;mult=9; +chr2R w2h ep 7571 7580 9.700 . . src=W;mult=9; +chr2R w2h ep 7581 7590 10.200 . . src=W;mult=10; +chr2R w2h ep 7581 7590 10.200 . . src=W;mult=10; +chr2R w2h ep 7591 7600 9.000 . . src=W;mult=9; +chr2R w2h ep 7591 7600 9.000 . . src=W;mult=9; +chr2R w2h ep 7601 7610 9.700 . . src=W;mult=9; +chr2R w2h ep 7601 7610 9.700 . . src=W;mult=9; +chr2R w2h ep 7611 7620 13.000 . . src=W;mult=13; +chr2R w2h ep 7611 7620 13.000 . . src=W;mult=13; +chr2R w2h ep 7621 7630 15.300 . . src=W;mult=15; +chr2R w2h ep 7621 7630 15.300 . . src=W;mult=15; +chr2R w2h ep 7631 7640 13.400 . . src=W;mult=13; +chr2R w2h ep 7631 7640 13.400 . . src=W;mult=13; +chr2R w2h ep 7641 7650 13.700 . . src=W;mult=13; +chr2R w2h ep 7641 7650 13.700 . . src=W;mult=13; +chr2R w2h ep 7651 7660 14.400 . . src=W;mult=14; +chr2R w2h ep 7651 7660 14.400 . . src=W;mult=14; +chr2R w2h ep 7661 7670 14.600 . . src=W;mult=14; +chr2R w2h ep 7661 7670 14.600 . . src=W;mult=14; +chr2R w2h ep 7671 7680 16.800 . . src=W;mult=16; +chr2R w2h ep 7671 7680 16.800 . . src=W;mult=16; +chr2R w2h ep 7681 7690 16.700 . . src=W;mult=16; +chr2R w2h ep 7681 7690 16.700 . . src=W;mult=16; +chr2R w2h ep 7691 7700 17.600 . . src=W;mult=17; +chr2R w2h ep 7691 7700 17.600 . . src=W;mult=17; +chr2R w2h ep 7701 7710 20.300 . . src=W;mult=20; +chr2R w2h ep 7701 7710 20.300 . . src=W;mult=20; +chr2R w2h ep 7711 7720 20.500 . . src=W;mult=20; +chr2R w2h ep 7711 7720 20.500 . . src=W;mult=20; +chr2R w2h ep 7721 7730 18.800 . . src=W;mult=18; +chr2R w2h ep 7721 7730 18.800 . . src=W;mult=18; +chr2R w2h ep 7731 7740 16.700 . . src=W;mult=16; +chr2R w2h ep 7731 7740 16.700 . . src=W;mult=16; +chr2R w2h ep 7741 7750 16.800 . . src=W;mult=16; +chr2R w2h ep 7741 7750 16.800 . . src=W;mult=16; +chr2R w2h ep 7751 7760 15.500 . . src=W;mult=15; +chr2R w2h ep 7751 7760 15.500 . . src=W;mult=15; +chr2R w2h ep 7761 7770 17.400 . . src=W;mult=17; +chr2R w2h ep 7761 7770 17.400 . . src=W;mult=17; +chr2R w2h ep 7771 7780 19.500 . . src=W;mult=19; +chr2R w2h ep 7771 7780 19.500 . . src=W;mult=19; +chr2R w2h ep 7781 7790 19.100 . . src=W;mult=19; +chr2R w2h ep 7781 7790 19.100 . . src=W;mult=19; +chr2R w2h ep 7791 7800 20.100 . . src=W;mult=20; +chr2R w2h ep 7791 7800 20.100 . . src=W;mult=20; +chr2R w2h ep 7801 7810 22.700 . . src=W;mult=22; +chr2R w2h ep 7801 7810 22.700 . . src=W;mult=22; +chr2R w2h ep 7811 7820 24.400 . . src=W;mult=24; +chr2R w2h ep 7811 7820 24.400 . . src=W;mult=24; +chr2R w2h ep 7821 7830 23.600 . . src=W;mult=23; +chr2R w2h ep 7821 7830 23.600 . . src=W;mult=23; +chr2R w2h ep 7831 7840 19.500 . . src=W;mult=19; +chr2R w2h ep 7831 7840 19.500 . . src=W;mult=19; +chr2R w2h ep 7841 7850 16.200 . . src=W;mult=16; +chr2R w2h ep 7841 7850 16.200 . . src=W;mult=16; +chr2R w2h ep 7851 7860 14.800 . . src=W;mult=14; +chr2R w2h ep 7851 7860 14.800 . . src=W;mult=14; +chr2R w2h ep 7861 7870 14.000 . . src=W;mult=14; +chr2R w2h ep 7861 7870 14.000 . . src=W;mult=14; +chr2R w2h ep 7871 7880 14.300 . . src=W;mult=14; +chr2R w2h ep 7871 7880 14.300 . . src=W;mult=14; +chr2R w2h ep 7881 7890 11.400 . . src=W;mult=11; +chr2R w2h ep 7881 7890 11.400 . . src=W;mult=11; +chr2R w2h ep 7891 7900 12.900 . . src=W;mult=12; +chr2R w2h ep 7891 7900 12.900 . . src=W;mult=12; +chr2R w2h ep 7901 7910 14.000 . . src=W;mult=14; +chr2R w2h ep 7901 7910 14.000 . . src=W;mult=14; +chr2R w2h ep 7911 7920 14.800 . . src=W;mult=14; +chr2R w2h ep 7911 7920 14.800 . . src=W;mult=14; +chr2R w2h ep 7921 7930 14.800 . . src=W;mult=14; +chr2R w2h ep 7921 7930 14.800 . . src=W;mult=14; +chr2R w2h ep 7931 7940 14.200 . . src=W;mult=14; +chr2R w2h ep 7931 7940 14.200 . . src=W;mult=14; +chr2R w2h ep 7941 7950 11.800 . . src=W;mult=11; +chr2R w2h ep 7941 7950 11.800 . . src=W;mult=11; +chr2R w2h ep 7951 7960 13.300 . . src=W;mult=13; +chr2R w2h ep 7951 7960 13.300 . . src=W;mult=13; +chr2R w2h ep 7961 7970 13.700 . . src=W;mult=13; +chr2R w2h ep 7961 7970 13.700 . . src=W;mult=13; +chr2R w2h ep 7971 7980 12.400 . . src=W;mult=12; +chr2R w2h ep 7971 7980 12.400 . . src=W;mult=12; +chr2R w2h ep 7981 7990 17.100 . . src=W;mult=17; +chr2R w2h ep 7981 7990 17.100 . . src=W;mult=17; +chr2R w2h ep 7991 8000 19.900 . . src=W;mult=19; +chr2R w2h ep 7991 8000 19.900 . . src=W;mult=19; +chr2R w2h ep 8001 8010 20.000 . . src=W;mult=20; +chr2R w2h ep 8001 8010 20.000 . . src=W;mult=20; +chr2R w2h ep 8011 8020 22.700 . . src=W;mult=22; +chr2R w2h ep 8011 8020 22.700 . . src=W;mult=22; +chr2R w2h ep 8021 8030 21.900 . . src=W;mult=21; +chr2R w2h ep 8021 8030 21.900 . . src=W;mult=21; +chr2R w2h ep 8031 8040 21.000 . . src=W;mult=21; +chr2R w2h ep 8031 8040 21.000 . . src=W;mult=21; +chr2R w2h ep 8041 8050 25.100 . . src=W;mult=25; +chr2R w2h ep 8041 8050 25.100 . . src=W;mult=25; +chr2R w2h ep 8051 8060 23.500 . . src=W;mult=23; +chr2R w2h ep 8051 8060 23.500 . . src=W;mult=23; +chr2R w2h ep 8061 8070 20.300 . . src=W;mult=20; +chr2R w2h ep 8061 8070 20.300 . . src=W;mult=20; +chr2R w2h ep 8071 8080 19.800 . . src=W;mult=19; +chr2R w2h ep 8071 8080 19.800 . . src=W;mult=19; +chr2R w2h ep 8081 8090 19.100 . . src=W;mult=19; +chr2R w2h ep 8081 8090 19.100 . . src=W;mult=19; +chr2R w2h ep 8091 8100 15.400 . . src=W;mult=15; +chr2R w2h ep 8091 8100 15.400 . . src=W;mult=15; +chr2R w2h ep 8101 8110 15.800 . . src=W;mult=15; +chr2R w2h ep 8101 8110 15.800 . . src=W;mult=15; +chr2R w2h ep 8111 8120 12.500 . . src=W;mult=12; +chr2R w2h ep 8111 8120 12.500 . . src=W;mult=12; +chr2R w2h ep 8121 8130 9.400 . . src=W;mult=9; +chr2R w2h ep 8121 8130 9.400 . . src=W;mult=9; +chr2R w2h ep 8131 8140 5.800 . . src=W;mult=5; +chr2R w2h ep 8131 8140 5.800 . . src=W;mult=5; +chr2R w2h ep 8210 8219 4.200 . . src=W;mult=4; +chr2R w2h ep 8210 8219 4.200 . . src=W;mult=4; +chr2R w2h ep 8220 8229 4.200 . . src=W;mult=4; +chr2R w2h ep 8220 8229 4.200 . . src=W;mult=4; +chr2R w2h ep 8230 8239 4.200 . . src=W;mult=4; +chr2R w2h ep 8230 8239 4.200 . . src=W;mult=4; +chr2R w2h ep 8240 8249 5.000 . . src=W;mult=5; +chr2R w2h ep 8240 8249 5.000 . . src=W;mult=5; +chr2R w2h ep 8260 8269 4.800 . . src=W;mult=4; +chr2R w2h ep 8260 8269 4.800 . . src=W;mult=4; +chr2R w2h ep 8270 8279 8.000 . . src=W;mult=8; +chr2R w2h ep 8270 8279 8.000 . . src=W;mult=8; +chr2R w2h ep 8280 8289 8.000 . . src=W;mult=8; +chr2R w2h ep 8280 8289 8.000 . . src=W;mult=8; +chr2R w2h ep 8290 8299 7.300 . . src=W;mult=7; +chr2R w2h ep 8290 8299 7.300 . . src=W;mult=7; +chr2R w2h ep 8300 8309 7.000 . . src=W;mult=7; +chr2R w2h ep 8300 8309 7.000 . . src=W;mult=7; +chr2R w2h ep 8310 8319 7.300 . . src=W;mult=7; +chr2R w2h ep 8310 8319 7.300 . . src=W;mult=7; +chr2R w2h ep 8320 8329 9.600 . . src=W;mult=9; +chr2R w2h ep 8320 8329 9.600 . . src=W;mult=9; +chr2R w2h ep 8330 8339 11.600 . . src=W;mult=11; +chr2R w2h ep 8330 8339 11.600 . . src=W;mult=11; +chr2R w2h ep 8340 8349 10.800 . . src=W;mult=10; +chr2R w2h ep 8340 8349 10.800 . . src=W;mult=10; +chr2R w2h ep 8350 8359 10.100 . . src=W;mult=10; +chr2R w2h ep 8350 8359 10.100 . . src=W;mult=10; +chr2R w2h ep 8360 8369 11.000 . . src=W;mult=11; +chr2R w2h ep 8360 8369 11.000 . . src=W;mult=11; +chr2R w2h ep 8370 8379 13.400 . . src=W;mult=13; +chr2R w2h ep 8370 8379 13.400 . . src=W;mult=13; +chr2R w2h ep 8380 8389 13.000 . . src=W;mult=13; +chr2R w2h ep 8380 8389 13.000 . . src=W;mult=13; +chr2R w2h ep 8390 8399 11.800 . . src=W;mult=11; +chr2R w2h ep 8390 8399 11.800 . . src=W;mult=11; +chr2R w2h ep 8400 8409 9.000 . . src=W;mult=9; +chr2R w2h ep 8400 8409 9.000 . . src=W;mult=9; +chr2R w2h ep 8410 8419 7.700 . . src=W;mult=7; +chr2R w2h ep 8410 8419 7.700 . . src=W;mult=7; +chr2R w2h ep 8420 8429 8.900 . . src=W;mult=8; +chr2R w2h ep 8420 8429 8.900 . . src=W;mult=8; +chr2R w2h ep 8430 8439 11.500 . . src=W;mult=11; +chr2R w2h ep 8430 8439 11.500 . . src=W;mult=11; +chr2R w2h ep 8440 8449 11.400 . . src=W;mult=11; +chr2R w2h ep 8440 8449 11.400 . . src=W;mult=11; +chr2R w2h ep 8450 8459 9.800 . . src=W;mult=9; +chr2R w2h ep 8450 8459 9.800 . . src=W;mult=9; +chr2R w2h ep 8460 8469 10.200 . . src=W;mult=10; +chr2R w2h ep 8460 8469 10.200 . . src=W;mult=10; +chr2R w2h ep 8470 8479 10.800 . . src=W;mult=10; +chr2R w2h ep 8470 8479 10.800 . . src=W;mult=10; +chr2R w2h ep 8480 8489 10.000 . . src=W;mult=10; +chr2R w2h ep 8480 8489 10.000 . . src=W;mult=10; +chr2R w2h ep 8490 8499 8.200 . . src=W;mult=8; +chr2R w2h ep 8490 8499 8.200 . . src=W;mult=8; +chr2R w2h ep 8500 8509 7.100 . . src=W;mult=7; +chr2R w2h ep 8500 8509 7.100 . . src=W;mult=7; +chr2R w2h ep 8510 8519 4.200 . . src=W;mult=4; +chr2R w2h ep 8510 8519 4.200 . . src=W;mult=4; +chr2R w2h ep 8520 8529 4.700 . . src=W;mult=4; +chr2R w2h ep 8520 8529 4.700 . . src=W;mult=4; +chr2R w2h ep 8739 8748 4.300 . . src=W;mult=4; +chr2R w2h ep 8739 8748 4.300 . . src=W;mult=4; +chr2R w2h ep 8749 8758 5.700 . . src=W;mult=5; +chr2R w2h ep 8749 8758 5.700 . . src=W;mult=5; +chr2R w2h ep 8759 8768 8.000 . . src=W;mult=8; +chr2R w2h ep 8759 8768 8.000 . . src=W;mult=8; +chr2R w2h ep 8769 8778 8.000 . . src=W;mult=8; +chr2R w2h ep 8769 8778 8.000 . . src=W;mult=8; +chr2R w2h ep 8779 8788 8.600 . . src=W;mult=8; +chr2R w2h ep 8779 8788 8.600 . . src=W;mult=8; +chr2R w2h ep 8789 8798 8.700 . . src=W;mult=8; +chr2R w2h ep 8789 8798 8.700 . . src=W;mult=8; +chr2R w2h ep 8880 8889 12.700 . . src=W;mult=12; +chr2R w2h ep 8880 8889 12.700 . . src=W;mult=12; +chr2R w2h ep 8890 8899 15.300 . . src=W;mult=15; +chr2R w2h ep 8890 8899 15.300 . . src=W;mult=15; +chr2R w2h ep 8900 8909 17.600 . . src=W;mult=17; +chr2R w2h ep 8900 8909 17.600 . . src=W;mult=17; +chr2R w2h ep 8910 8919 17.900 . . src=W;mult=17; +chr2R w2h ep 8910 8919 17.900 . . src=W;mult=17; +chr2R w2h ep 8920 8929 17.200 . . src=W;mult=17; +chr2R w2h ep 8920 8929 17.200 . . src=W;mult=17; +chr2R w2h ep 8930 8939 18.400 . . src=W;mult=18; +chr2R w2h ep 8930 8939 18.400 . . src=W;mult=18; +chr2R w2h ep 8940 8949 19.900 . . src=W;mult=19; +chr2R w2h ep 8940 8949 19.900 . . src=W;mult=19; +chr2R w2h ep 8950 8959 19.100 . . src=W;mult=19; +chr2R w2h ep 8950 8959 19.100 . . src=W;mult=19; +chr2R w2h ep 8960 8969 15.200 . . src=W;mult=15; +chr2R w2h ep 8960 8969 15.200 . . src=W;mult=15; +chr2R w2h ep 8970 8979 13.000 . . src=W;mult=13; +chr2R w2h ep 8970 8979 13.000 . . src=W;mult=13; +chr2R w2h ep 8980 8989 14.700 . . src=W;mult=14; +chr2R w2h ep 8980 8989 14.700 . . src=W;mult=14; +chr2R w2h ep 8990 8999 14.500 . . src=W;mult=14; +chr2R w2h ep 8990 8999 14.500 . . src=W;mult=14; +chr2R w2h ep 9000 9009 14.500 . . src=W;mult=14; +chr2R w2h ep 9000 9009 14.500 . . src=W;mult=14; +chr2R w2h ep 9010 9019 12.500 . . src=W;mult=12; +chr2R w2h ep 9010 9019 12.500 . . src=W;mult=12; +chr2R w2h ep 9020 9029 11.900 . . src=W;mult=11; +chr2R w2h ep 9020 9029 11.900 . . src=W;mult=11; +chr2R w2h ep 9030 9039 12.100 . . src=W;mult=12; +chr2R w2h ep 9030 9039 12.100 . . src=W;mult=12; +chr2R w2h ep 9040 9049 10.000 . . src=W;mult=10; +chr2R w2h ep 9040 9049 10.000 . . src=W;mult=10; +chr2R w2h ep 9050 9059 9.700 . . src=W;mult=9; +chr2R w2h ep 9050 9059 9.700 . . src=W;mult=9; +chr2R w2h ep 9060 9069 10.600 . . src=W;mult=10; +chr2R w2h ep 9060 9069 10.600 . . src=W;mult=10; +chr2R w2h ep 9070 9079 12.300 . . src=W;mult=12; +chr2R w2h ep 9070 9079 12.300 . . src=W;mult=12; +chr2R w2h ep 9080 9089 13.100 . . src=W;mult=13; +chr2R w2h ep 9080 9089 13.100 . . src=W;mult=13; +chr2R w2h ep 9090 9099 13.400 . . src=W;mult=13; +chr2R w2h ep 9090 9099 13.400 . . src=W;mult=13; +chr2R w2h ep 9100 9109 12.000 . . src=W;mult=12; +chr2R w2h ep 9100 9109 12.000 . . src=W;mult=12; +chr2R w2h ep 9110 9119 10.700 . . src=W;mult=10; +chr2R w2h ep 9110 9119 10.700 . . src=W;mult=10; +chr2R w2h ep 9120 9129 11.000 . . src=W;mult=11; +chr2R w2h ep 9120 9129 11.000 . . src=W;mult=11; +chr2R w2h ep 9130 9139 10.900 . . src=W;mult=10; +chr2R w2h ep 9130 9139 10.900 . . src=W;mult=10; +chr2R w2h ep 9140 9149 7.900 . . src=W;mult=7; +chr2R w2h ep 9140 9149 7.900 . . src=W;mult=7; +chr2R w2h ep 9150 9159 4.900 . . src=W;mult=4; +chr2R w2h ep 9150 9159 4.900 . . src=W;mult=4; +chr2R w2h ep 9160 9169 4.400 . . src=W;mult=4; +chr2R w2h ep 9160 9169 4.400 . . src=W;mult=4; +chr2R w2h ep 9265 9274 11.400 . . src=W;mult=11; +chr2R w2h ep 9265 9274 11.400 . . src=W;mult=11; +chr2R w2h ep 9275 9284 12.800 . . src=W;mult=12; +chr2R w2h ep 9275 9284 12.800 . . src=W;mult=12; +chr2R w2h ep 9285 9294 13.100 . . src=W;mult=13; +chr2R w2h ep 9285 9294 13.100 . . src=W;mult=13; +chr2R w2h ep 9295 9304 13.600 . . src=W;mult=13; +chr2R w2h ep 9295 9304 13.600 . . src=W;mult=13; +chr2R w2h ep 9305 9314 13.000 . . src=W;mult=13; +chr2R w2h ep 9305 9314 13.000 . . src=W;mult=13; +chr2R w2h ep 9315 9324 12.400 . . src=W;mult=12; +chr2R w2h ep 9315 9324 12.400 . . src=W;mult=12; +chr2R w2h ep 9325 9334 9.000 . . src=W;mult=9; +chr2R w2h ep 9325 9334 9.000 . . src=W;mult=9; +chr2R w2h ep 9335 9344 5.200 . . src=W;mult=5; +chr2R w2h ep 9335 9344 5.200 . . src=W;mult=5;