##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-C00SLm0103M17-dEhWY/AUGUSTUS_tom_ugs/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-C00SLm0103M17-dEhWY/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 = 68643, name = C00SLm0103M17.2) ----- # # Delete group HintGroup SGN-U590668, 38269-46348, mult= 1, priority= 4 8 features # Delete group HintGroup SGN-U590177, 38340-46143, mult= 1, priority= 4 10 features # Delete group HintGroup SGN-U592308, 38354-46129, mult= 1, priority= 4 10 features # Delete group HintGroup SGN-U591763, 40741-46089, mult= 1, priority= 4 9 features # Forced unstranded hint group to the only possible strand for 8 groups. # Deleted 4 groups because some hint was not satisfiable. # Predicted genes for sequence number 1 on both strands # start gene g1 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 155 2975 0.14 - . ID=g1 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 155 2975 0.14 - . ID=g1.t1;Parent=g1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 1 154 0.49 - . Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 394 565 0.76 - . Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 788 2771 0.3 - . Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 155 393 0.49 - 0 ID=g1.t1.cds;Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 566 787 0.77 - 0 ID=g1.t1.cds;Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 2772 2975 0.33 - 0 ID=g1.t1.cds;Parent=g1.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 2973 2975 . - 0 Parent=g1.t1 # protein sequence = [MARGGDEKIPFYKLFAFADRNDIILMLFGILGAIASGVSKPLMSLMFGDLIDSYGTSDQSNILDKVSRVGNFVMHMST # FIGGFVVAFIKEWQLTLVLLATIPAIAISFFCAALVLSKMSGSGQAAYANAGKVVEQTVGGIRTVVSFTGENLSIVDYNSKLENAYKPTVNQALASGI # GLGTILMFSLFSYGLAIWYGAKLIIDKNYSGGDIVTVIFSAMLGG] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/3 # 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: 0 # end gene g1 ### # start gene g2 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 7495 8569 1 + . ID=g2 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 7495 8569 1 + . ID=g2.t1;Parent=g2 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 7495 7497 . + 0 Parent=g2.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 8158 8476 1 + . Parent=g2.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 7495 8157 1 + 0 ID=g2.t1.cds;Parent=g2.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 8477 8569 1 + 0 ID=g2.t1.cds;Parent=g2.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 8567 8569 . + 0 Parent=g2.t1 # protein sequence = [MTGEEDLKHGGNKETDGGDVSYLASQDHQFNDKEGTREKQLEIPHSESSIDNNKSNALEKRSNEVNKVAMVEGGIIQV # ERELKLEDESMRNNINIERVEPAKFPREGGLRRRSSSSGKPSMSEDIVQAATSASDIDNEAFGSSEKENEKRELGVMDEKTRKLNVVADTGLEKRDYK # AVATSNAKPFKAVKDDDKLEISYNVPVVDASVRANNMEGSTHEHQPLVALDRRPVQTTSWKSCCGLFEVFAGSNK] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 66.7 # CDS exons: 2/2 # E: 2 # CDS introns: 0/1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 2 # E: 2 (SGN-U581789,SGN-U594518) # incompatible hint groups: 1 # E: 1 (SGN-U566133) # end gene g2 ### # start gene g3 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 15208 19326 0.51 + . ID=g3 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 15208 19326 0.51 + . ID=g3.t1;Parent=g3 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 15208 15210 . + 0 Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 15244 17011 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 17104 17892 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 18031 18111 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 18169 18247 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 18321 18405 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 18469 19116 1 + . Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 15208 15243 1 + 0 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 17012 17103 1 + 0 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 17893 18030 1 + 1 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 18112 18168 1 + 1 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 18248 18320 1 + 1 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 18406 18468 1 + 0 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 19117 19326 0.51 + 0 ID=g3.t1.cds;Parent=g3.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 19324 19326 . + 0 Parent=g3.t1 # protein sequence = [MPAVSGPVTPGQVSFLLGYIPVLIAWIYAEWLEYKKWLFPFKVHSDNNLDELEISTTKEEDRAVLLEGGLSKSASVKL # SSSSVKTNIIRFLTMEDAFLLENRATLRAISEFGGILFYYYLCDRTNLFADSTKVICIITTIGSPYGIKAYKHFESYNRDLFIFLYILLIIVSAMTSL # KKHNDKSAFSGKSILYLNRHQTEEWKGWMQASFCVSYFPSLIHALF] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 7/7 # E: 7 # CDS introns: 6/6 # E: 6 # 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-U576553) # end gene g3 ### # start gene g4 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 19972 22154 0.24 + . ID=g4 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 19972 22154 0.24 + . ID=g4.t1;Parent=g4 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 19972 19974 . + 0 Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 20168 20723 0.88 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 20840 20929 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 21017 21113 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 21203 21398 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 21462 21650 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 21708 21814 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 21912 21998 1 + . Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 19972 20167 0.25 + 0 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 20724 20839 1 + 2 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 20930 21016 1 + 0 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 21114 21202 1 + 0 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 21399 21461 1 + 1 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 21651 21707 1 + 1 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 21815 21911 1 + 1 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 21999 22154 0.99 + 0 ID=g4.t1.cds;Parent=g4.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 22152 22154 . + 0 Parent=g4.t1 # protein sequence = [MLYYICPMHTLFTLMVYGALGIGHKYNEIKSVMALKFLLCFVVVILVWEIPGVFEFLWGPFTFMLGYTDPAKPDLPRL # HEWHFRSGLDRYIWIIGMIYAYFHPNVEKWMEKLEESEPKRRRTIKSTICAVTLIVGYLWFEYIYKLDKTAYNKLHPYTSWIPITVYICLRNLTQELR # NFSLTLFAWLGKITLETYISQFHIWLRSNMPNGQPKWLLSFIPGYPMLNFMLTTAIYVLLSCRLFELTNTLKSVFVPTRDNQKLLHNFIAGVAISLCL # YIISFILIQIPH] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 86.7 # CDS exons: 7/8 # E: 7 # CDS introns: 6/7 # E: 6 # 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-U566796) # end gene g4 ### # start gene g5 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 26568 29957 0.47 + . ID=g5 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 26568 29957 0.47 + . ID=g5.t1;Parent=g5 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 26568 26570 . + 0 Parent=g5.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 26649 29834 0.71 + . Parent=g5.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 26568 26648 0.47 + 0 ID=g5.t1.cds;Parent=g5.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 29835 29957 0.47 + 0 ID=g5.t1.cds;Parent=g5.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 29955 29957 . + 0 Parent=g5.t1 # protein sequence = [MFLSQFWGKQKKITLWKKFNKSSWISQMKKYVRMKIPTLNQVDQLIVVPTLPSINGGTKLPFLPFLL] # 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-U573552) # end gene g5 ### # start gene g6 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 32715 33065 0.71 + . ID=g6 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 32715 33065 0.71 + . ID=g6.t1;Parent=g6 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 32715 32717 . + 0 Parent=g6.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 32715 33065 0.71 + 0 ID=g6.t1.cds;Parent=g6.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 33063 33065 . + 0 Parent=g6.t1 # protein sequence = [MTIYESLVASLTNLVVIFASGESRNLRQEMNDFLAIFHSWFNWIDFQGVFIVLQCDWHSWCANGTIFSVLFLHEKMSG # VKVISMFLAMWVFLSYMNQHYLDDLENKAEKSLVREVS] # 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 ### # start gene g7 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 33843 34899 0.98 - . ID=g7 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 33843 34899 0.98 - . ID=g7.t1;Parent=g7 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 33843 33845 . - 0 Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 34020 34599 1 - . Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 34660 34785 1 - . Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 33843 34019 0.98 - 0 ID=g7.t1.cds;Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 34600 34659 1 - 0 ID=g7.t1.cds;Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 34786 34899 1 - 0 ID=g7.t1.cds;Parent=g7.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 34897 34899 . - 0 Parent=g7.t1 # protein sequence = [MQIYRSREVGQSYITSVGTTLVAIAHALWLMIKTRPQVILCNGPGTCIPLCVIAFLFKVLGIRWSSIFYVESIARVRK # LSLSGLLLYKLHMADQLFVQWPQLKEKYPRAHYVGRLM] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 3/3 # E: 3 # CDS introns: 2/2 # E: 2 # 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-U573413) # end gene g7 ### # start gene g8 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 34922 36341 0.96 - . ID=g8 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 34922 36341 0.96 - . ID=g8.t1;Parent=g8 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 34922 34924 . - 0 Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 34951 35941 1 - . Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 36077 36163 1 - . Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 34922 34950 1 - 2 ID=g8.t1.cds;Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 35942 36076 1 - 2 ID=g8.t1.cds;Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 36164 36341 0.96 - 0 ID=g8.t1.cds;Parent=g8.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 36339 36341 . - 0 Parent=g8.t1 # protein sequence = [MEKGDFCISTMASSNIAVLLAIGVITLLVIRIIYVINRRRKPLHSKSPRSLSTLIVLGSGGHTAEMLNLLYVLQTERF # KPRYYIAAATDNMSLQKAHVFEDSLLGLPLILGSA] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 3/3 # E: 3 # CDS introns: 2/2 # E: 2 # 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-U573413) # end gene g8 ### # start gene g9 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 38260 45392 0.44 - . ID=g9 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 38260 45392 0.44 - . ID=g9.t1;Parent=g9 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 38260 38262 . - 0 Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 38462 40598 0.95 - . Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 41421 42638 0.62 - . Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 43447 45367 0.77 - . Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 38260 38461 0.95 - 1 ID=g9.t1.cds;Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 40599 41420 0.62 - 1 ID=g9.t1.cds;Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 42639 43446 0.77 - 2 ID=g9.t1.cds;Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 45368 45392 0.77 - 0 ID=g9.t1.cds;Parent=g9.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 45390 45392 . - 0 Parent=g9.t1 # protein sequence = [MVVVMFQFXFIMAASTMALSSSTFAGKAVKLSPSSSEISGNGRITMRKTAAKPKPASSGSPWYGPDRVKYLGPFSGES # PSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWAC # QVVLMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLAEDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHIADPVNNNAWAFATNF # VPGKVSHSTSIMATSTMALSSSTFAGKAVKLSPSSSEITGNGRVTMRKTATKAKPASSGSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLS # ADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVVLMGAVEGYRIAGGPLGE # VVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWAFATNFVPGKVFLLADDPEAFDELKV # KEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADPVNNNVWAFATNFVPGK] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 57.1 # CDS exons: 4/4 # E: 4 # CDS introns: 0/3 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 7 # E: 7 (SGN-U578503,SGN-U578708,SGN-U577305,SGN-U592342,SGN-U581613,SGN-U589989,SGN-U592540) # incompatible hint groups: 19 # E: 19 (SGN-U579181,SGN-U577456,SGN-U590867,SGN-U581203,SGN-U591584,SGN-U579213,SGN-U592301,...) # end gene g9 ### # start gene g10 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 45434 46237 1 + . ID=g10 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 45434 46237 1 + . ID=g10.t1;Parent=g10 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 45434 45436 . + 0 Parent=g10.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 45434 46237 1 + 0 ID=g10.t1.cds;Parent=g10.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 46235 46237 . + 0 Parent=g10.t1 # protein sequence = [MAASTMALSSSTFAGKTVKLAPSSSEISGNGRITMRKTAAKPKPASSGSPWYGPDRVKYLGPFSGESPSYLTGEFPGD # YGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVVLMGAVEGY # RIAGGPLGEVVDPLYPGGSFDPLGLAEDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHIADPVNNNAWAFATNFVPGK] # 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: 2 # E: 2 (SGN-U591638,SGN-U589957) # incompatible hint groups: 18 # E: 18 (SGN-U579181,SGN-U577456,SGN-U590867,SGN-U581203,SGN-U591584,SGN-U579213,SGN-U592301,...) # end gene g10 ### # start gene g11 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 47137 52707 0.37 - . ID=g11 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 47137 52707 0.37 - . ID=g11.t1;Parent=g11 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 47137 47139 . - 0 Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 47431 47964 1 - . Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 48427 49748 1 - . Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 49905 51620 1 - . Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 51889 52411 1 - . Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 47137 47430 1 - 0 ID=g11.t1.cds;Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 47965 48426 1 - 0 ID=g11.t1.cds;Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 49749 49904 1 - 0 ID=g11.t1.cds;Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 51621 51888 1 - 1 ID=g11.t1.cds;Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 52412 52707 0.37 - 0 ID=g11.t1.cds;Parent=g11.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 52705 52707 . - 0 Parent=g11.t1 # protein sequence = [MLSYLVAVEDVNVSVSSVAANLQQLSVKDAAGLPSDGDSPSVVIPDHLQVQTADCSHLSFGSFGGVSFSGSLASAPVK # TSLEDASRDADSSSVGHLGTRATEYYGDGTLRNEADSNLFHRNNANAGNYELPAASQPESLKAEASDGHYSYPSSAAGYSYESAQQLNAAFSQPQTSS # HMQNLASFSNETVYTNSLQSDMLTANVHPGRESELSYSPFSTTQAMPTKYGNSISSISGSAMPEAMKTVGFSSAQPTQQMLSGNSVATGPGVPQHLTV # HQYSQQAVPIAPYGNMISYPFVPQNYSYIPSAFQQAYPGNSSYHQSLAAMLPQYKNTVSASSLPQSATIPSGYGAFGNTTSIPGNFPINPPAAPSGTN # LSYDDVLSAQFKDTNHLMSLQQNENSALWLHGHGSRTMPTVPANTYYGFQGQNQQTGGFRQGQQPSQSYGSLGGYPHFYNSQAGISLDQQQQENLRDG # SLSGSQGQPKQSQQQLWQNGY] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 5/5 # E: 5 # CDS introns: 4/4 # E: 4 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 1 # E: 1 (SGN-U589503) # incompatible hint groups: 1 # E: 1 (SGN-U565379) # end gene g11 ### # start gene g12 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 53679 59075 0.2 - . ID=g12 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 53679 59075 0.2 - . ID=g12.t1;Parent=g12 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 53679 53681 . - 0 Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 54328 54703 1 - . Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 54819 54922 1 - . Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 55023 55285 0.75 - . Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 55330 58882 0.61 - . Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 53679 54327 0.37 - 1 ID=g12.t1.cds;Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 54704 54818 1 - 2 ID=g12.t1.cds;Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 54923 55022 0.86 - 0 ID=g12.t1.cds;Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 55286 55329 0.75 - 2 ID=g12.t1.cds;Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 58883 59075 0.99 - 0 ID=g12.t1.cds;Parent=g12.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 59073 59075 . - 0 Parent=g12.t1 # protein sequence = [MTSRGGGKNSNNGGGIGVQSIPPGSRKMVQSLKEIVNCPEAEIYAMLKECNMDPNEAVNRLLTQDPFHEVKSKREKRK # EIKDPTESRSWITSSTPSRGSRAGGDRYVGRGGSESTKPAPAYRKESGSQTNNFSSTPLIAGGNTDRRPTAISDAAGNDSKRLAPAAVDGHSAASQPS # SGYQPTWGGVPGQVSMADIVKMGRPQSKVPSVPNISDSTAGVNQNHDQAPPPYGASHGNMQFSDDQSTVPEVHQEPRDNSSQNLSANDEWPSIEQPSA # ASQPAVSEPPTNSVPHPDPSNMSFDRVDHQTQIDESQEADESANENLDCSLSSRKLQEDNADGTSLYDNDPYRYQHQNHTFDHPQGEYVWKS] # 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: 2 # E: 2 (SGN-U604102,SGN-U568367) # end gene g12 ### # start gene g13 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 61690 64483 0.81 + . ID=g13 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 61690 64483 0.81 + . ID=g13.t1;Parent=g13 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 61690 61692 . + 0 Parent=g13.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 61705 64204 0.81 + . Parent=g13.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 61690 61704 0.81 + 0 ID=g13.t1.cds;Parent=g13.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 64205 64483 0.98 + 0 ID=g13.t1.cds;Parent=g13.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 64481 64483 . + 0 Parent=g13.t1 # protein sequence = [MVLGWMDWQGQKLVEQLMQILLVSFGVVAFLTGYMLGSFQTMLLTYAGGVVFTALLTIPNWPVYNRNPLNWLDPSVVE # KYPKPLPATTGSKKKSTKK] # 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: 0 # incompatible hint groups: 3 # E: 3 (SGN-U577169,SGN-U592488,SGN-U575381) # end gene g13 ### # start gene g14 C00SLm0103M17.2 AUGUSTUS_tom_ugs gene 66966 68092 0.72 + . ID=g14 C00SLm0103M17.2 AUGUSTUS_tom_ugs transcript 66966 68092 0.72 + . ID=g14.t1;Parent=g14 C00SLm0103M17.2 AUGUSTUS_tom_ugs start_codon 66966 66968 . + 0 Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 67017 67416 1 + . Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 67552 67636 1 + . Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs intron 67808 68062 0.72 + . Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 66966 67016 1 + 0 ID=g14.t1.cds;Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 67417 67551 1 + 0 ID=g14.t1.cds;Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 67637 67807 1 + 0 ID=g14.t1.cds;Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs CDS 68063 68092 0.72 + 0 ID=g14.t1.cds;Parent=g14.t1 C00SLm0103M17.2 AUGUSTUS_tom_ugs stop_codon 68090 68092 . + 0 Parent=g14.t1 # protein sequence = [MAASSAIASSSTTFINKKDVGLSAFSSQASFSVQTARKRISKRIVSVMTPQQTERKPATTGSVKTGMTMTEKILAKAS # DKPDVSPGDNVWVNVDVLMTHDVCGPGSIGIFKKEFGQNAKCKFDLALST] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 71.4 # CDS exons: 3/4 # E: 3 # CDS introns: 2/3 # E: 2 # 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-U576270) # end gene g14 ### # command line: # /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C00SLm0103M17-dEhWY/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00SLm0103M17-dEhWY/AUGUSTUS_tom_ugs/seq_with_defline_removed