##gff-version 3 # This output was generated with AUGUSTUS (version 2.3). # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de) # and Oliver Keller (keller@cs.uni-goettingen.de). # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # reading in the file /tmp/bac-submission-temp-C00HBa0080C09-Z7MX7/AUGUSTUS_tom_cdna/hints.gff ... # Setting 1group1gene for E. # Sources of extrinsic information: M E # Have extrinsic information about 1 sequences (in the specified range). # Initialising the parameters ... # tomato version. Use default transition matrix. # Looks like /tmp/bac-submission-temp-C00HBa0080C09-Z7MX7/AUGUSTUS_tom_cdna/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 = 115143, name = C00HBa0080C09.1) ----- # # Delete group HintGroup SGN-E295752, 80217-83609, mult= 1, priority= 4 4 features # Forced unstranded hint group to the only possible strand for 9 groups. # Deleted 1 groups because some hint was not satisfiable. # Predicted genes for sequence number 1 on both strands # start gene g1 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 18014 31094 0.5 - . ID=g1 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 18014 31094 0.5 - . ID=g1.t1;Parent=g1 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 18014 18016 . - 0 Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 18525 18599 0.83 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 18645 19370 0.74 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 19424 19517 0.85 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 19635 22817 0.99 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 22913 24234 0.75 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 24305 24489 0.87 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 24588 25472 0.82 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 25567 27585 1 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 27677 27772 1 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 27866 27956 1 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 28283 30776 0.95 - . Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 18014 18524 0.95 - 1 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 18600 18644 0.85 - 1 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 19371 19423 0.85 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 19518 19634 0.99 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 22818 22912 0.95 - 2 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 24235 24304 0.74 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 24490 24587 0.82 - 2 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 25473 25566 0.96 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 27586 27676 1 - 1 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 27773 27865 1 - 1 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 27957 28282 0.95 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 30777 31094 0.97 - 0 ID=g1.t1.cds;Parent=g1.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 31092 31094 . - 0 Parent=g1.t1 # protein sequence = [MGGLCSRRANADSTTDHGIPHGNGHLSYGAGTVYQSRGLPIQLSSDPMPPAGESQQLTEPTLSYPEMNDISLGIPMDD # VDDGIPILSRVLSNKSISARSKQVAIAKVSEMSSLLGRAGTAGLGKAVNVLDTLGSSMTNLNLSSGFVSNMATKGNKISILAFEVANTIVKAANLIHS # LSEENVKHLKEVVLLSEGVQLLITKDMDELLRIAAADKRDELKIFSGEVVRFGNRCKDPQWHNLERYFEKLESELTPHEHLKEEAEALMVQLMISVQY # TAELYHEFHALDRFEQDYRRKVQEEDTSSATQRGDTIAILRADLKSQRKHVKNLKKKSLWSKILEEVTEKLVDIVHYLHLEIHAAFGSADGEISMKNN # NQRLGSAGLALHYANIITQIDTIVARPGSVPPNTRDALYHGLPPSIKSALRFKLMSFSLKEEVIELYSFPCAVDSATNQRAHHGFGWVGEWANTGSEM # NRKSSSQVDLLRIETLYHADKEKTEAYILELVVWLHYLVSQSKRANAGVRSPVKSPICSPNQKTIELSNHQSSSPSSPLSVEDQEMLRDVSKRKLTPG # ISKSQEFAKTGLSKYNRLSKSNSHSPINETRKNPFPIKRPSSVPVFDFDTDRLKALDVIDRVDTVRGA] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 26.1 # CDS exons: 3/12 # E: 3 # CDS introns: 3/11 # 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-E208112) # end gene g1 ### # start gene g2 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 36301 36522 0.87 + . ID=g2 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 36301 36522 0.87 + . ID=g2.t1;Parent=g2 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 36301 36303 . + 0 Parent=g2.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 36301 36522 0.87 + 0 ID=g2.t1.cds;Parent=g2.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 36520 36522 . + 0 Parent=g2.t1 # protein sequence = [MSFLLLLRTSAYILSMIFLTFYWGWAFGISVRFGFFFGFFGFGFCKLRTEYXXXXXXXXXXXXXXXXXXISVF] # 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: 4 # E: 4 (SGN-E258761,SGN-E391663,SGN-E746293,SGN-E396524) # incompatible hint groups: 0 # end gene g2 ### # start gene g3 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 72668 83664 0.6 - . ID=g3 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 72668 83664 0.6 - . ID=g3.t1;Parent=g3 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 72668 72670 . - 0 Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 72691 73563 0.62 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 73652 73960 0.65 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 74103 74191 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 74341 78078 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 78211 79946 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 80082 80207 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 80291 80378 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 80476 83316 1 - . Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 72668 72690 1 - 2 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 73564 73651 0.6 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 73961 74102 1 - 1 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 74192 74340 1 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 78079 78210 1 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 79947 80081 1 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 80208 80290 1 - 2 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 80379 80475 1 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 83317 83664 1 - 0 ID=g3.t1.cds;Parent=g3.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 83662 83664 . - 0 Parent=g3.t1 # protein sequence = [MISLAGQQHTREPKRKKKRTKKVETTGSAVSVRSRSRRSAMAAAGNPLSSAVTFTEPPPVAPGTANKSLDFSADSVLQ # RIVLSPDQRSHCLEALKAFKQKRCHSPDKIASEFSTLQENRLKASEMKSRCLVALDSTNISKNRYTDVIPFDNNRVVLDPCKDYRPSAKGYINASFIE # ISEGVSRFVATQGPLAHTFEDFWEMIIQQRCPVIVMLTRLVDNYKMVKCGDYFQAEDGPRTFGNICIVTKYMTSDASLVLRTLEVNYIESEEPPLCVL # HIQYPEWPDHGVPRDTLAVREILKRTYNLPLGLGPIVVHCSAGIGRTGTYCTIHNTIQRILGGDMSALDIVNTVAIFRSQRIGMVQTMVKLKLYALRR # LDGALVQLPRDQDMCLSLRGSIPFLL] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 82.4 # CDS exons: 8/9 # E: 8 # CDS introns: 6/8 # E: 6 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 21 # E: 21 (SGN-E216430,SGN-E232826,SGN-E262568,SGN-E237775,SGN-E241030,SGN-E238112,SGN-E239616,...) # incompatible hint groups: 17 # E: 17 (SGN-E395232,SGN-E374450,SGN-E260187,SGN-E257885,SGN-E252184,SGN-E369150,SGN-E233446,...) # end gene g3 ### # start gene g4 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 85904 88147 0.73 + . ID=g4 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 85904 88147 0.73 + . ID=g4.t1;Parent=g4 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 85904 85906 . + 0 Parent=g4.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 86049 87974 0.73 + . Parent=g4.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 85904 86048 0.97 + 0 ID=g4.t1.cds;Parent=g4.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 87975 88147 0.73 + 2 ID=g4.t1.cds;Parent=g4.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 88145 88147 . + 0 Parent=g4.t1 # protein sequence = [MFIESINASSLVKTEEKLCELLDRYVERVGEQNVVQTVSDNGSNFVLAGLRVYVPPPSPLSLKPLTSVPGAFPSHAEA # RKPLSFMTFIKKVIWNDPSSNMPKPMF] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 33.3 # CDS exons: 1/2 # E: 1 # CDS introns: 0/1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 3 # E: 3 (SGN-E352821,SGN-E577710,SGN-E353226) # incompatible hint groups: 0 # end gene g4 ### # start gene g5 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 88149 93723 0.39 - . ID=g5 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 88149 93723 0.39 - . ID=g5.t1;Parent=g5 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 88149 88151 . - 0 Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 88401 89086 0.98 - . Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 89194 89270 0.99 - . Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna intron 89474 93697 0.4 - . Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 88149 88400 0.99 - 0 ID=g5.t1.cds;Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 89087 89193 0.98 - 2 ID=g5.t1.cds;Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 89271 89473 0.57 - 1 ID=g5.t1.cds;Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 93698 93723 0.41 - 0 ID=g5.t1.cds;Parent=g5.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 93721 93723 . - 0 Parent=g5.t1 # protein sequence = [MSCPWTCECFIHLLSSPSTWDSFMRTDDAKTRVQIHLELRVRALPFDKTSVSLFLRSDKPPSSIHTASVIPKFNPNYL # QLHGDDVYFTLDNCSQDGAQQREGVSGTSTVLSKVQSKSSFGVGSRYSESESDTMSQRLKLDDLPETWYNQFFEKYKSSKSYRLQFGDSETEKRTPEQ # MFFIVKLLRIIRDGVQLLK] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/4 # CDS introns: 0/3 # 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-E321056) # end gene g5 ### # start gene g6 C00HBa0080C09.1 AUGUSTUS_tom_cdna gene 93784 94095 0.98 + . ID=g6 C00HBa0080C09.1 AUGUSTUS_tom_cdna transcript 93784 94095 0.98 + . ID=g6.t1;Parent=g6 C00HBa0080C09.1 AUGUSTUS_tom_cdna start_codon 93784 93786 . + 0 Parent=g6.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna CDS 93784 94095 0.98 + 0 ID=g6.t1.cds;Parent=g6.t1 C00HBa0080C09.1 AUGUSTUS_tom_cdna stop_codon 94093 94095 . + 0 Parent=g6.t1 # protein sequence = [MHSSTSKCNNNPFPNHENREVNIITLDEEYGGPDCPDIDEPNVMTSSVQPVITVQLREPMTVQTYFPRIVVTTIARMG # KYDTKAVPWDYQTGVKGKMIHTVVA] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/1 # CDS introns: 0/0 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 0 # end gene g6 ### # command line: # /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C00HBa0080C09-Z7MX7/AUGUSTUS_tom_cdna/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00HBa0080C09-Z7MX7/AUGUSTUS_tom_cdna/seq_with_defline_removed