##gff-version 3 # This output was generated with AUGUSTUS (version 2.0.2). # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de). # Please cite: Mario Stanke and Stephan Waack (2003) "Gene prediction with a hidden Markov model and # a new intron submodel", Bioinformatics, Vol. 19 Suppl. 2, ii215-ii225 # reading in the file /tmp/bac-submission-temp-C12HBa0183M06-QT1Rd/AUGUSTUS_tom_ugs/hints.gff ... # Sources of extrinsic information: M E # Have extrinsic information about 1 sequences (in the specified range). # Initialising the parameters ... # human version. Use default transition matrix. # Looks like /tmp/bac-submission-temp-C12HBa0183M06-QT1Rd/AUGUSTUS_tom_ugs/seq_with_defline_removed is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 101022, name = C12HBa0183M06.1) ----- # # Delete group HintGroup SGN-U315332, 6568-8171, priority= 4 4 features # Set orientation to reverse for hint group HintGroup SGN-U315331, 6568-11095, priority= 4 7 features # Delete group HintGroup SGN-U334113, 36953-100328, priority= 4 5 features # Delete group HintGroup SGN-U316575, 36954-100327, priority= 4 3 features # Set orientation to forward for hint group HintGroup SGN-U325848, 63655-66358, priority= 4 7 features # Set orientation to forward for hint group HintGroup SGN-U327700, 67231-70945, priority= 4 17 features # Delete group HintGroup SGN-U312386, 83054-83406, priority= 4 2 features # Delete group HintGroup SGN-U338921, 83054-83417, priority= 4 2 features # Set orientation to reverse for hint group HintGroup SGN-U328599, 97559-98677, priority= 4 3 features # Forced unstranded hint group to the only possible strand for 4 groups. # Deleted 5 groups because some hint was not satisfiable. # Constraints/Hints: # Predicted genes for sequence number 1 on both strands ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 6771 11010 1 - . ID=g1 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 6771 11010 . - . ID=g1.t1;Parent=g1 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 6771 6773 . - 0 Parent=g1.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 6771 6884 . - 0 ID=g1.t1.cds;Parent=g1.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 7696 7860 . - 0 ID=g1.t1.cds;Parent=g1.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 8686 8829 . - 0 ID=g1.t1.cds;Parent=g1.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 10441 11010 . - 0 ID=g1.t1.cds;Parent=g1.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 11008 11010 . - 0 Parent=g1.t1 # protein sequence = [MQMQYKNLGRSGLKVSQLSYGAWVTFGNQLDVKEAKTLLQCCRDHGVNFFDNAEVYANGRAEEIMGQAIRELGWKRSD # IVVSTKIFWGGSGPNDKGLSRKHIIEGTKASLKRLDMDYVDLIYCHRPDTSTPIEETVRAMNYVIDKGWAFYWGTSEWSAQQITEAWGVAQRLDLVGP # IVEQPEYNLLSRHKVESEYLPLYSNYGIGLTTWSPLASGVLTGKYTSGNIPPDSRFALENYKNLASRSLVDDVLRKVNGLKPIAEELGVPLPQLAIAW # CAANPNVSSVITGATKEYQIQENMKAINVIPMLTPAVMEKIEAIVQSKPKRQDSYR] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 4/4 # E: 4 # CDS introns: 3/3 # E: 3 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 1 # E: 1 (SGN-U315331) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 16453 30654 1 - . ID=g2 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 16453 30654 . - . ID=g2.t1;Parent=g2 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 16453 16455 . - 0 Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 16453 16707 . - 0 ID=g2.t1.cds;Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 24349 24461 . - 2 ID=g2.t1.cds;Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 26206 26529 . - 2 ID=g2.t1.cds;Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 27169 30024 . - 2 ID=g2.t1.cds;Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 30636 30654 . - 0 ID=g2.t1.cds;Parent=g2.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 30652 30654 . - 0 Parent=g2.t1 # protein sequence = [MLQKSREGLNAEGMYLLELKKSLKDESNNLGNWNPSDETPCRWKGVNCTFDYNPVVQSLDLSLMNLSGTLSSSIGGLV # SLTVLDLSFNRFTGNIPKEIGNCSKLQSLQLHDNEFYGQIPDELYNLSHLKDLNLFNNMISGSILEEFGRLSSLVSFVAYTNNLTGSLPRSLGKLKKL # ETFRVGQNPLSGTLPPEIGDCKSLQVLGLAQNNVGGNIPKEIGMLKRLKQLVLWDNKLSGYIPKELGNCTKLELLALYQNNLVGEIPAAIGKLKSLKR # LYLYRNGLNGTIPRVIGNLSSAIEIDFSENYLIGDIPNEFSQIKGLKLLYLFNNQLNGVIPRELSSLRKLERLDLSINYLYGSIPFSFQYLTELVQLQ # LFQNSLSGTIPQGLGNYSRLWVVDFSYNYLTGGIPPNICRDSNLIWLNLGSNNLHGVIPSGVIKCDSLVQLRLDGNWLQGNFPYGLCKLSNLSALELG # QNTFSGLIPPEIGNCRKLQRLDLSGNYFTHELPREIGNLETLVTFNVSSNLLSGQVPLEILKCKELQRLDLSRNSFSGTIPDEIGKLAQLERLLVSDN # KFSGKIPVSLGRLSRLNELQMGGNSFSGEMPSELGDLTGLQIAMNLSDNNLSGSIPPKLGNLILLESLYLNNNHLSGEIPITFRNLTSLMSCNFSYNN # LTGPLPNLPLFQNMDVSSFIGNNGLCGGRLGGCKESPPFNSDPPTKNAGGPREKIVIVVVAVGSGVFLVLIMVILYVMKRKPVDQMVASVKDKDMSFP # ASDIYFPPEEEFTFQDLVEATNNFQDSYVVGRGAVGTVYKAVMQSGRKIAVKKLASNREGNNIEKSFRAEISTLGKIRHRNIVKLYGFCYHQGSNLLL # YEYMEKGSLGELLHGASCGLDWPQRFMIALGAAEGLSYLHHDCKPQIIHRDIKSNNILLDEKLEAHVGDFGLAKVIDMPQTKSMSAIAGSYGYIAPEY # AYTMKVTEKCDIYSYGVVLLELLTGRTPVQPLDQGGDLVTYVRHFIRDNSLTPGVLDIRLDLTDKTAVSHMLTVLKIGLVCTCLSPADRPSMREVVSM # LMESDEQEESRDIDDDVLHRIGVYGRRVGLRHSKSCVTKRYHQNLKSTTTNTSGTANTAANPFEPGTTKTATDSTNTTGGTTNAANGTAKYWQHPTYS # TNSGTTTYATICYKIFVVIKSSNFAWCWRIST] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/5 # CDS introns: 0/4 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 3 # E: 3 (SGN-U316067,SGN-U316068,SGN-U332690) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 36832 37407 1 - . ID=g3 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 36832 37407 . - . ID=g3.t1;Parent=g3 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 36832 36834 . - 0 Parent=g3.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 36832 37407 . - 0 ID=g3.t1.cds;Parent=g3.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 37405 37407 . - 0 Parent=g3.t1 # protein sequence = [MGWFNEYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX # XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLKSSSLFFFFFFLFFFFFLNFCXXXXXXXXXXXXXXXXXXX # XXXXXXXXXXXXXXL] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 1/1 # E: 1 # CDS introns: 0/0 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 37 # E: 37 (SGN-U323846,SGN-U341720,SGN-U325876,SGN-U340043,SGN-U338835,SGN-U313051,SGN-U331105,...) # incompatible hint groups: 1 # E: 1 (SGN-U322600) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 39008 42865 1 + . ID=g4 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 39008 42865 . + . ID=g4.t1;Parent=g4 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 39008 39010 . + 0 Parent=g4.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 39008 39057 . + 0 ID=g4.t1.cds;Parent=g4.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 42547 42865 . + 1 ID=g4.t1.cds;Parent=g4.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 42863 42865 . + 0 Parent=g4.t1 # protein sequence = [MSFILCLARYCCIKVFGFRSVTDKEAKAEAEFRELKEEANEVYAKFIENQDALERATREIERLKQGYEEFDNWIQQKI # ERMRYESLEDKGRLGEGFLLILRYMFQQHKNQKNDDGAGSSGAA] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/2 # CDS introns: 0/1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 2 # E: 2 (SGN-U322600,SGN-U340078) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 57635 71709 1 + . ID=g5 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 57635 71709 . + . ID=g5.t1;Parent=g5 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 57635 57637 . + 0 Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 57635 57731 . + 0 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 63735 63759 . + 2 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 63963 64002 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 65744 66116 . + 0 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 66220 66369 . + 2 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 66960 67042 . + 2 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 67151 67359 . + 0 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 68136 68204 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 68483 68601 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 69081 69156 . + 2 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 69227 69268 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 69693 69801 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 70240 70337 . + 0 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 70424 70517 . + 1 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 70605 70665 . + 0 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 71489 71709 . + 2 ID=g5.t1.cds;Parent=g5.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 71707 71709 . + 0 Parent=g5.t1 # protein sequence = [MFRMCFRVDDSCWFVGCLLFFAWLVIAVLRCLEETPLLLLSMNGSRRNPIISFKVLSWNSLYSGSNKSRVYHPILCLK # RSGNDNSGSCSPSCYIEQMYRNRMFSQPIRRCRKIFIDKQSLLVIQNGLAFIPRKFKSSLRKTLKHSELCKSIVPEIFVRSCIGLMLVMAVNAAVVKA # PSFALTEENLLFLEAWRTIDRAYIDKTFNGQSWFRYREDALRNEPMNTRQETYAAIKKMLATLNDPFTRFLEPEKFKSLRSGTQNALTGVGLSIGYPL # GKNESASGLVVISASPGGPANRAGISSGDIILQIDNTSTENMGIYDAAERLQGPEGSGVELTVLHGSERRQLPLIREKVSLNPVKSRICKLPTGGDDA # PLIGYIKLSTFNQNASGAVREAIETLRKNNVKAFVLDLRDNSGGLFPEGVEIAKIWLDKGVIVYICDSRGVRDIYDTDGSNVVAASEPLAVLVNKGTA # SASEILAGALKDNKRAQLFGEPTYGKGKIQSVFQLSDGSGVAVTVARYETPAHNDIDKVGVTPDHPLPASFPKDDESFSREEEEESTMKPMVVDYLAD # MEEQGSTMAMDVDDVDTIDMFGEGPLGGGEHLRLADSDFFNLFQDDFDDSDIN] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 71 # CDS exons: 11/16 # E: 11 # CDS introns: 11/15 # E: 11 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 12 # E: 12 (SGN-U322600,SGN-U340078,SGN-U326037,SGN-U320306,SGN-U315060,SGN-U313979,SGN-U319112,...) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 77614 88356 1 - . ID=g6 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 77614 88356 . - . ID=g6.t1;Parent=g6 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 77614 77616 . - 0 Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 77614 77628 . - 0 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 77943 78466 . - 2 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 78629 79376 . - 0 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 83381 83437 . - 0 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 87760 87938 . - 2 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 88041 88154 . - 2 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 88296 88356 . - 0 ID=g6.t1.cds;Parent=g6.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 88354 88356 . - 0 Parent=g6.t1 # protein sequence = [MASLGKERQDLLSTIDALKEEKKLLQEKLRKTSDSGKSLDVSRSMPSKKDVSTSTEDLREEKIVNTTLDGPNLGARSS # EGPTFSYLSENDQLSLESLSTTVPPDQIRMIQSINTLISEKFLKKNPKKKNKKKKKQRALEEFRKKKAEKAKKSTSNNQPHGSGGGFDNQPSDSEHTR # ITDSRGAGTSDALDGAVSELSRVDVTHDFKNPDLAQKSGFASSYEANASPTHSLHNNDNDASATSTISGNNHGFTSSISTPSHFRDKVLKGDEKPKSS # EQFSDSYNPPEKTENDGALGSIGFGFNTSHSTPNFLSSFPSYSKFSGLFSHDGVAKSEIEGKKTKDLSVMNSSTSHAFPANVSPENSRGPHLQEKPGF # MDRWASGFTSSSYEDHMRPTTSSTKFSLEDGQRDGTVEANSSIISDIGYGQFNNSGFYMNNNSSSWASDSKHEDISSEARSSSSNSKLSTATVGRKSR # PSFLDSINISKVPVVSPSPTESVSADRFDPKGHPTDTLESSNSRNMMTSSTFSASGSDQLNHHAEKDTGNMDNRYQSFAQKQNEDFAALEQNFEV] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 7.69 # CDS exons: 1/7 # E: 1 # CDS introns: 0/6 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 12 # E: 12 (SGN-U345106,SGN-U329874,SGN-U317581,SGN-U344216,SGN-U329864,SGN-U327713,SGN-U315914,...) # incompatible hint groups: 2 # E: 2 (SGN-U322600,SGN-U322601) ### ### C12HBa0183M06.1 AUGUSTUS_tom_ugs gene 97528 98465 1 - . ID=g7 C12HBa0183M06.1 AUGUSTUS_tom_ugs transcript 97528 98465 . - . ID=g7.t1;Parent=g7 C12HBa0183M06.1 AUGUSTUS_tom_ugs stop_codon 97528 97530 . - 0 Parent=g7.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 97528 97884 . - 0 ID=g7.t1.cds;Parent=g7.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs CDS 98355 98465 . - 0 ID=g7.t1.cds;Parent=g7.t1 C12HBa0183M06.1 AUGUSTUS_tom_ugs start_codon 98463 98465 . - 0 Parent=g7.t1 # protein sequence = [MVIVEYINETWKLNPLLSTDSYERATSRFWAKYIEEKSHSSWNVFCYTGEKQQNAIKESLEMFKTIEENALGENNILF # GGENIGFVDIAFGGYSLWMEIIEEIVGIKLLNPHNFPRINNWIKKFKEVQTIKDNLPNRDEMFVYMKNARGRMLASP] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 2/2 # E: 2 # CDS introns: 1/1 # E: 1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 1 # E: 1 (SGN-U328599) ### # command line: # /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C12HBa0183M06-QT1Rd/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C12HBa0183M06-QT1Rd/AUGUSTUS_tom_ugs/seq_with_defline_removed