##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-C03HBa0176B05-TIpyD/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-C03HBa0176B05-TIpyD/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 = 116402, name = C03HBa0176B05.1) ----- # # Delete group HintGroup SGN-E281511, 1553-1791, mult= 1, priority= 4 3 features # Delete group HintGroup SGN-E304478, 67131-69013, mult= 1, priority= 4 7 features # Delete group HintGroup SGN-E295093, 67149-69152, mult= 1, priority= 4 8 features # Delete group HintGroup , 69025-69126, mult= 2, priority= 4 1 features # Delete group HintGroup , 69026-69126, mult= 4, priority= 4 1 features # Delete group HintGroup SGN-E391901, 72247-72451, mult= 1, priority= 4 2 features # Forced unstranded hint group to the only possible strand for 25 groups. # Deleted 6 groups because some hint was not satisfiable. # Predicted genes for sequence number 1 on both strands # start gene g1 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 1544 3767 0.98 + . ID=g1 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 1544 3767 0.98 + . ID=g1.t1;Parent=g1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 1 1543 0.98 + . Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 1605 1719 1 + . Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 1856 1976 1 + . Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 2302 3095 1 + . Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 3225 3315 1 + . Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 1544 1604 1 + 2 ID=g1.t1.cds;Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 1720 1855 1 + 1 ID=g1.t1.cds;Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 1977 2301 1 + 0 ID=g1.t1.cds;Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 3096 3224 1 + 2 ID=g1.t1.cds;Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 3316 3767 1 + 2 ID=g1.t1.cds;Parent=g1.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 3765 3767 . + 0 Parent=g1.t1 # protein sequence = [LLSVDSEDAFESSSNILSYPWAINTKYYNADVSVWMAHLHEDFSIGALPAYDQLVALVMVFDVTDLSSFVALKDFVSR # TDILKFEILLCIGNKVDLLPGHSAHVEYRQLLLKSADSSGSPYSEMDSGISETEGSSLLGDDDSSFDAKRSYLEWCLEHSIEYVEACASNAEFDKCLS # MDGDSQGAERLFGALSAYMWPGMILKSGDKITEPSLPEHQELSDEESDYELEYEILSAGSADPWDDTDVGWVSADATVVTTGTEGSVPNGKTEIRLIR # GEMQPSSSTSQLEGESDRKELPRADADDGDSEDDKGTTYDFENLEQLMSEIGNVRDSLRLMPDFQRREMAANLAMKMAAMFGDSSGDEGGLE] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 90 # CDS exons: 5/5 # E: 5 # CDS introns: 4/5 # E: 4 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 6 # E: 6 (SGN-E202769,SGN-E270413,SGN-E704102,SGN-E270240) # incompatible hint groups: 1 # E: 1 (SGN-E373321) # end gene g1 ### # start gene g2 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 18548 21198 0.67 - . ID=g2 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 18548 21198 0.67 - . ID=g2.t1;Parent=g2 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 18548 18550 . - 0 Parent=g2.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 19203 20443 1 - . Parent=g2.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 18548 19202 1 - 1 ID=g2.t1.cds;Parent=g2.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 20444 21198 0.67 - 0 ID=g2.t1.cds;Parent=g2.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 21196 21198 . - 0 Parent=g2.t1 # protein sequence = [MAMGELKISEMRDLTRIERIGAHSHIRGLGLDSSLEPRLSSEGMVGQIPARKAAGIIVKMVQQGKIAGRALLLAGQPG # TGKTAIAMGMAKSLGQETPFAMLAGSELYSLDMSKTEALMQAFRKAIGVRIKEEAEVIEGEVVEVHIDRPAVAGAASKTGKLTLKTTDMETVYDLGAK # MIEALGKEKVQSGDVIAIDKASGKITKLGRSFSRSRDYDAMGPQTKFVQCPEGELQKRKEIVHCVTLHEIDVINSRTQGFLALFTGDTGEIRAEVREQ # IDTKVAEWREEGKAEIVPGVLFIDEVHMLDIECFSFLNRALENDMAPILVVATNRGITTIRGTNYRSPHGIPIDFLDRLLIISTQPYKEEEIRKILDI # RCQEEDVEMSEDAKVLLTKIGVNTSLRYAIHLITSAALACQKRKGKAVEVEDITRVYNLFYDVKRSTQYLMEYQSQYMFNEVPAGEAEEDETAAMVS] # 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: 2 # E: 2 (SGN-E244255,SGN-E203571) # incompatible hint groups: 2 # E: 2 (SGN-E549815,SGN-E705938) # end gene g2 ### # start gene g3 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 41518 42801 1 + . ID=g3 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 41518 42801 1 + . ID=g3.t1;Parent=g3 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 41518 41520 . + 0 Parent=g3.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 41518 42801 1 + 0 ID=g3.t1.cds;Parent=g3.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 42799 42801 . + 0 Parent=g3.t1 # protein sequence = [MGFEKDKASSSSHVLQIPREDTPLLSKNHQHLSSPSKTFANVFIAIVGAGVLGLPYTFKRTGWVMGALMLFTVAFLTY # HCMMLLVYSRRKIESHLKISQISSFGDLGFAVCGPIGRSAVDVMIVLSQAGFCISYLIFIANTLAYCFNYSKTNPNPKVFGFPPKAVYIWSCFPFQLG # LNSIPTLTLLAPLSIFADVVELGAMGVVMVKDVMIYVKSSHVLETFGGFSVFFYGLGVAVYAFEGVGMVLPLEAETKDKAKFGKILGFSMALISLLYG # AFGVLGYFAFGEDTKDIITTNLGQGLLSSLVQIGLCINLFFTFPLMMNPVYEVVERRFCEGSYCVWIRWIMVLVVTFVALFVPNFADFLSLVGSSVCI # ILGFVLPALFHLIVFKDELRWHGLACDGAIIVVAAVFSVYGTYSSLLEILFGAKE] # 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: 1 # E: 1 (SGN-E286936) # incompatible hint groups: 4 # E: 4 (SGN-E371935,SGN-E733487,SGN-E371934,SGN-E275013) # end gene g3 ### # start gene g4 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 46118 47011 1 - . ID=g4 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 46118 47011 1 - . ID=g4.t1;Parent=g4 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 46118 46120 . - 0 Parent=g4.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 46118 47011 1 - 0 ID=g4.t1.cds;Parent=g4.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 47009 47011 . - 0 Parent=g4.t1 # protein sequence = [MEGNTCDINHLDSDVLLPPRKRLLVGLKKQNFDDNPCSPSSSTDDVTEFEFDMRLNNLLKFHSDDCNRSIEEIVEASK # VAALKAVELAKAARAVAEEKAVKASEAMAAAKSAMELVATVSGEVTDRDKYSKKKKKKNKYKGTENCTTDEELARMLSRTINSSPRISKNSTSNLRNQ # KHKRLKRSSLSENAKHQNGRTSWEANRPSTSNGIDIAGNKASNGPSKEKELIRIDSSVAKFNKADLRKMENGKGEPMNSKEEFGESPNDICNVDKKKG # RMKQKMLPLSNCSLRDKVNPKRT] # 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: 0 # incompatible hint groups: 2 # E: 2 (SGN-E389872,SGN-E231095) # end gene g4 ### # start gene g5 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 50278 54182 0.72 - . ID=g5 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 50278 54182 0.72 - . ID=g5.t1;Parent=g5 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 50278 50280 . - 0 Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 50892 51104 0.99 - . Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 51280 51509 0.73 - . Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 52980 53587 1 - . Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 53659 54112 1 - . Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 50278 50891 1 - 2 ID=g5.t1.cds;Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 51105 51279 0.99 - 0 ID=g5.t1.cds;Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 51510 52979 0.73 - 0 ID=g5.t1.cds;Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 53588 53658 1 - 2 ID=g5.t1.cds;Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 54113 54182 0.99 - 0 ID=g5.t1.cds;Parent=g5.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 54180 54182 . - 0 Parent=g5.t1 # protein sequence = [MVRLSDLIDVDAGGTMRMSKRHGGLEAPRNRLEKPAESFCDGGDDILCTYHMTNDWPEKKNCYVKEVPMKKLISEELA # KRPNTGQNVPSVVARLMGLDTLSVDEESLREVSSRQTVFDSFDRRSRNSLKFNELKPREHPQEEELQKFKKEFEAYQAAKFKEGSKFVELNTNTVLYA # NSTRKMVTERFIDLKGLAATENIHERGISKIQKDKNEFLAAARNKTIRALNVKSGSAPAKIVILRPVSDRTGKNEESWANSPRISEDGSSMEEFLQEV # KGRLKFELQEKSFRKTIEKPSDAKIIAQCIAKQARESVTRDVGTTHHRSKSMQSDRSEIQRDEASSPEFTKRDTRRILTERLRNVLSDESSHDIDKHD # RVSSTSVAQHREKSKSEEMRYAPNEVCHGDDMKDESDRQCRYSRQELSNDVMLDQKLFHRNLVRSLSAPVSRSSFGKLLLEDQDMLTGAHIRRQHEAI # EEVTVNVKKWRKEKFNLKAKVSSFKHSFVLKGKLFGRKIQSLEESHGNKQMHMKDLQNTQTVASKFYENSTEVPPSPASVCSTSNEEFWRQTDNFSPS # SSSISDVNPLDDTEIPHVFKEISSNLNELRRQLNQLETYDSEETMIVEQPIEKEIVMEIDDPAEAFVRDLLVASGLYDGSCDKYLSKWDPLGKSISNH # VFEEAEESYKRQKINDYDEGSSNDHQSKKLNHKLSCDFLNEVLPSVLGSSSMRRTISPTPRAPRGNKLLECVWEIARISSDMSSQSLETILARDLQCT # RWDRLVDEDVNALGKDVEYQIVGDLIHEMINDMQP] # 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: 0 # end gene g5 ### # start gene g6 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 56167 63113 1 - . ID=g6 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 56167 63113 1 - . ID=g6.t1;Parent=g6 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 56167 56169 . - 0 Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 56283 57711 1 - . Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 57869 58097 1 - . Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 58183 62439 1 - . Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 62531 62874 1 - . Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 62963 63071 1 - . Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 56167 56282 1 - 2 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 57712 57868 1 - 0 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 58098 58182 1 - 1 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 62440 62530 1 - 2 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 62875 62962 1 - 0 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 63072 63113 1 - 0 ID=g6.t1.cds;Parent=g6.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 63111 63113 . - 0 Parent=g6.t1 # protein sequence = [MAAAGKCFLVTGPAGIGKTTLIVRVLETLRNSNPNLKVQGFYTREIREGTERIGFEVVTLDGRTGLLASNKISSAQSL # RWPTVGRYRVDVASFESLALQELQVREDTDLFIIDEIGKMELYSSSFFPAVLKVLQSNIPLLASIPITKVGRDIPGVARMKNHPGARVFTLDANNRDA # MREQICSTLADVLQKP] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 6/6 # E: 6 # CDS introns: 5/5 # E: 5 # 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-E706719) # end gene g6 ### # start gene g7 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 66536 66790 0.8 - . ID=g7 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 66536 66790 0.8 - . ID=g7.t1;Parent=g7 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 66536 66538 . - 0 Parent=g7.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 66536 66790 0.8 - 0 ID=g7.t1.cds;Parent=g7.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 66788 66790 . - 0 Parent=g7.t1 # protein sequence = [MIMQLFRQFVFLFLYLCRAYCLFLLERSLVPTYISTEYAVSGPYVIITSIFGSIFCYYTHLDKVLLLAFKFSLSTFSA # SVENVA] # 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: 0 # incompatible hint groups: 11 # E: 11 (SGN-E352367,SGN-E250568,SGN-E541067,SGN-E541070,SGN-E369215,SGN-E727380,SGN-E747327,...) # end gene g7 ### # start gene g8 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 67205 72341 0.26 - . ID=g8 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 67205 72341 0.26 - . ID=g8.t1;Parent=g8 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 67205 67207 . - 0 Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 67226 67309 1 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 67385 67475 1 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 67557 67637 0.95 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 67643 67827 0.68 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 67890 67984 1 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 68087 68976 1 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 69028 69127 1 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 69239 72324 0.51 - . Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67205 67225 1 - 0 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67310 67384 1 - 0 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67476 67556 0.95 - 0 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67638 67642 0.95 - 2 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67828 67889 0.71 - 1 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 67985 68086 1 - 1 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 68977 69027 1 - 1 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 69128 69238 0.99 - 1 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 72325 72341 0.28 - 0 ID=g8.t1.cds;Parent=g8.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 72339 72341 . - 0 Parent=g8.t1 # protein sequence = [MLGLYGPSPKPLLILSSQHTHNTQFISKGKKYLFVFFSLNPRSFFLIMKGGKSKGKADNKLGVKKSAAQTKKEKNAAK # DPNKPKRPASAFFVFMEDFRKQYKEKHPGNKSVAAVNLEKAPYIAKAEKRKADYEKLMDAYNRKQAGEAEEDEESDKSKSEVDEEDGSDEEEEDDD] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 70.6 # CDS exons: 7/9 # E: 7 # CDS introns: 5/8 # E: 5 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 14 # E: 14 (SGN-E338645,SGN-E718063,SGN-E349200,SGN-E324785,SGN-E688158,SGN-E294799,SGN-E324547,...) # incompatible hint groups: 36 # E: 36 (SGN-E250568,SGN-E541067,SGN-E541070,SGN-E369215,SGN-E727380,SGN-E747327,SGN-E703618,...) # end gene g8 ### # start gene g9 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 78495 79271 0.9 + . ID=g9 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 78495 79271 0.9 + . ID=g9.t1;Parent=g9 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 78495 78497 . + 0 Parent=g9.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 78495 79271 0.9 + 0 ID=g9.t1.cds;Parent=g9.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 79269 79271 . + 0 Parent=g9.t1 # protein sequence = [MLGSGGVSDGYENGSKRPRMMESNPCFAVSSGSSGYHQPYGYGSGRFQPSGFPVVRLRGLPFNCTEIDIHKFFAGLDI # VDVFLVNKDGRFVGEAFVVFAGHMQVDYALQRDRQNMGRRYVEVFSCKKEEYYQAVAAEVKEGGKDNEYRSPPLSRPKRSVNKDDMEYSVILKLRGLP # YSVRKTDIGRFFGEEFNVKPDKVHIAYRSDGKATGEAYVEFASTEEAKKAMCKDNMKIGSRYIELFPSHPDEARRAESRSQH] # 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: 0 # incompatible hint groups: 2 # E: 2 (SGN-E731168,SGN-E578034) # end gene g9 ### # start gene g10 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 85272 90245 1 + . ID=g10 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 85272 90245 1 + . ID=g10.t1;Parent=g10 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 85272 85274 . + 0 Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 85357 86716 1 + . Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 87049 88005 1 + . Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 88142 88225 1 + . Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 88369 88776 1 + . Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 88901 89808 1 + . Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 85272 85356 1 + 0 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 86717 87048 1 + 2 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 88006 88141 1 + 0 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 88226 88368 1 + 2 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 88777 88900 1 + 0 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 89809 90245 1 + 2 ID=g10.t1.cds;Parent=g10.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 90243 90245 . + 0 Parent=g10.t1 # protein sequence = [MGNCFGAKLSNSKSSSTYPSFSARPSTPDTSKSYSTGVGYSATSGSIGCSNFSAAASEDICLNGEILPIPNLKIYSFS # DLKLSTKNFKSDSVLGIGGFGTVYKGWVDEKTLAPTKAGTGMIVAIKKLNSESTQGFEEWQSEVNFLGRLSHPNLVKLLGYCHEDKELLLVYEFMPKG # SLENHLFRRSAAIEPLSWDLRLKIAIGAARGLAFLHTSEKKVIYRDFKASNILLDGNYNAKISDFGLAKLGPSGSNSHVTTRVMGTYGYAAPEYVETG # HLYVKSDVYGFGVVVLELLTGLRALDTKRPNRQEKLVDWVKPMLSNKRKLKSIMDARMEGQYSSKAATLAAQITLKCLEVDPKNRPSMKEVMNVLEQI # EAMKENPKESKSKSEHSSSHRHRQSPRSRQSPRQTNGQGFRSGSGK] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 6/6 # E: 6 # CDS introns: 5/5 # E: 5 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 9 # E: 9 (SGN-E243055,SGN-E248575,SGN-E396965,SGN-E279686) # incompatible hint groups: 5 # E: 5 (SGN-E722343,SGN-E698012,SGN-E718005,SGN-E698727,SGN-E396964) # end gene g10 ### # start gene g11 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 91221 100935 0.83 - . ID=g11 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 91221 100935 0.83 - . ID=g11.t1;Parent=g11 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 91221 91223 . - 0 Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 91370 91463 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 91551 92067 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 92097 92325 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 92385 92947 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 93062 93183 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 93396 94233 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 94993 100670 1 - . Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 91221 91369 1 - 2 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 91464 91550 1 - 2 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 92068 92096 1 - 1 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 92326 92384 1 - 0 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 92948 93061 1 - 0 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 93184 93395 1 - 2 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 94234 94992 1 - 2 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 100671 100935 0.83 - 0 ID=g11.t1.cds;Parent=g11.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 100933 100935 . - 0 Parent=g11.t1 # protein sequence = [MSMGGGDASVPAGDSGDSNKVSNTGAGGGVTINIRCSSGSKFSVQVSLDSTVGSFKSILAQQANIPAEQQRLIYKGRI # LKDEQTLESYGLEADHTVHLVRGSAPAPSANPACAPNVGGPNTAQNAPRSAASDAGGPFPGSGLGASMFPGLGSGGGGGLFGAGLPDFEQVQQQLTQN # PDMMRDMMNMPLVQNLMNNPETIRNLIMNNPQMREIMDRNPELAHVLNDPATLRQTMEAARNPELMREMMRNTDRAMSNIESSPEGFNMLRRMYENVQ # EPFLNASTLSGDTRNDAGSNPFAALLGAQGGLGRQQANNPPTAGSETTDNLPAPNTNPLPNPWASAGTGAAQANTAARSNTAGDTRGAPLGLGGLGSP # GLEQMLGGMPDTTSLNQMMQNPAISQMMQSLLSNPQYMNQVLGMNPQLRSMLDSNPQLREMMQNPEFIRQLTSPETVQQLMTFQQGLASQLGRQQTNQ # QPGQNAGGAALDNSGMEMLMNMFGGLGTGGLGVPNRSNVPPEELYATQLTQLQEMGFFDTQENIRALTASGGNVHAAVERLLGNLGQ] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 8/8 # E: 8 # CDS introns: 7/7 # E: 7 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 11 # E: 11 (SGN-E261984,SGN-E726057,SGN-E263539,SGN-E322785) # incompatible hint groups: 14 # E: 14 (SGN-E691099,SGN-E303167,SGN-E732992,SGN-E374276,SGN-E374275,SGN-E733299,SGN-E540571,...) # end gene g11 ### # start gene g12 C03HBa0176B05.1 AUGUSTUS_tom_cdna gene 110868 112705 0.14 + . ID=g12 C03HBa0176B05.1 AUGUSTUS_tom_cdna transcript 110868 112705 0.14 + . ID=g12.t1;Parent=g12 C03HBa0176B05.1 AUGUSTUS_tom_cdna start_codon 110868 110870 . + 0 Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 111051 112407 0.93 + . Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna intron 112545 112680 0.16 + . Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 110868 111050 0.89 + 0 ID=g12.t1.cds;Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 112408 112544 0.94 + 0 ID=g12.t1.cds;Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna CDS 112681 112705 0.16 + 1 ID=g12.t1.cds;Parent=g12.t1 C03HBa0176B05.1 AUGUSTUS_tom_cdna stop_codon 112703 112705 . + 0 Parent=g12.t1 # protein sequence = [MICDGCDSGQIDFSKWRKLDSRNFGISRSMIPPSPQVVLKILHGEGDNFFVVFDHSGLATRVSSFDTVAKHAEKEEAP # LVPEIPKGCPEKDFILWNNSMHRDFTINSVSSTSCG] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/3 # CDS introns: 0/2 # 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 g12 ### # command line: # /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C03HBa0176B05-TIpyD/AUGUSTUS_tom_cdna/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C03HBa0176B05-TIpyD/AUGUSTUS_tom_cdna/seq_with_defline_removed