# 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 # No extrinsic information on sequences given. # Initialising the parameters using config directory /augustus/config/ ... # Using protein profile unknown # --[0..244]--> unknown_A (21) <--[0..7]--> unknown_B (155) <--[0..1]--> unknown_C (9) <--[0..97]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2693720180911_busco_2432604931_.temp is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 41863, name = Contig26937) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig26937 AUGUSTUS gene 12487 31434 0.02 + . g1 Contig26937 AUGUSTUS transcript 12487 31434 0.02 + . g1.t1 Contig26937 AUGUSTUS tss 12487 12487 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 12487 12597 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 14644 15266 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS start_codon 14822 14824 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 15267 20688 0.36 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 20912 21382 0.5 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 21491 22655 0.53 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 22770 23166 0.52 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 23257 23782 0.61 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 23943 24298 0.97 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 24421 24541 0.44 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 24633 24740 0.91 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 24951 25132 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 25294 25378 0.99 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 25506 25637 0.87 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 25707 27181 0.87 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 27257 27453 0.92 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 27559 27826 0.96 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 28109 28230 0.89 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 28372 28569 0.93 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 28603 28698 0.75 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 28864 29449 0.72 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 29538 29659 0.81 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 29823 30207 0.79 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS intron 30425 30643 0.88 + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 14822 15266 0.25 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 20689 20911 0.56 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 20689 20911 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 21383 21490 0.58 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 21383 21490 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 22656 22769 0.59 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 22656 22769 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 23167 23256 0.57 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 23167 23256 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 23783 23942 0.98 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 23783 23942 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 24299 24420 0.98 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 24299 24420 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 24542 24632 0.44 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 24542 24632 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 24741 24950 0.91 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 24741 24950 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 25133 25293 0.95 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 25133 25293 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 25379 25505 0.98 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 25379 25505 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 25638 25706 0.88 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 25638 25706 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 27182 27256 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 27182 27256 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 27454 27558 0.93 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 27454 27558 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 27827 28108 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 27827 28108 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 28231 28371 0.89 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 28231 28371 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 28570 28602 0.94 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 28570 28602 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 28699 28863 0.75 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 28699 28863 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 29450 29537 0.97 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 29450 29537 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 29660 29822 0.81 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 29660 29822 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 30208 30424 0.89 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 30208 30424 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS CDS 30644 30790 0.88 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS exon 30644 31434 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS stop_codon 30788 30790 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26937 AUGUSTUS tts 31434 31434 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgagaaatagcgcaaagtatcgaagcggtatgtgtacgaggactcgatttctcagtgtgccctggaagtttaccgctt # caaagacagacgatgaaagagtgcaggaatcaaatgtaaaacggatccgaggttcccgtagcgccgatgttcggacagacatttaccggagtgaagat # gaagacgggcatccgtttgtgtcagggccccccaaaaccgtggccgtgaaaagcgtcagtctagattacggcacgttactaggagtgcccccaaggga # tgatgtgagcatgaaattacgcagtcaaagcgatagtgacgtcattgacggcgattcgcagacgccaaatgctcgtagcaaaaggaggaaaatctccg # catttcttaaccgagtgaggattggtagccggcggtcaacggtgtcgtgcatgaacagtcgccccacaccatagaactgcaatgcctactgcttactg # gacatttaccatcctatacataggaactcctcattttcacccaaatcatcacccaaatcatccccgaaatcatcacccaagctaaagaagagctcatc # aactgttcctatcatccactgtagcattacagaagaggtgcaccggacaaacactgccaaacacacatcggaacctcagtggaatgaggagtttgaac # tgccagttgaggacttgctgacagatgaaatccatgtattcatttgcaaccaagatcaagagaatggatcagaaaaacatcaccctgacaagcatcac # ttgttgtccaggagattcctgcccagggctgtgattggtggtgggatgttacaagcccttcctccaaagggagcaaactctcgggtggaaaatgtcgg # atcaaacttcatctatcccaccaacagagctctgagactggtagccagcctttctcagtggaagattactaccaggctgcagaacaaatctacaaaca # tgcaattagagtccaagagacatattgtggtcctcttagagtggtcttgtaaccatggtgatatcagcacagtagaccaggcccttcaggcggcatta # caagaactccagatgatctgggcctccaaacagtttgacctgtccagctgttcacagaaaatgcccatcactgatgctgagacaatgatgtacagaaa # tgctgcgagcagttacatttcctcagtgtccactcacttagacaactactccgagctgtttccaccgtaccttgatggcatcaatactctgaaacaaa # agctgagtgtcagtatgctgctgctggagttggacctctgggactccaagtcttctccccacagtcccctgacacagaaaatcctaaagaagcttcag # gatgatacaaaccgttggatcaatgaaaaggttgaacagatctataaacatgacatggtgcaggatccagttattccgaggatgaccgctctggtgga # actgaccaatctggtgtcctatcactgcctccctatgggtgtggtcaataacctctacaatacactgggcattggctacttcaggattatcaccttct # gtgtagaaaaaaagatcagttcagtgatgagagaactttgtcaggagatggatgtttaccagcgtaaatatcaccagtacagtgtaaatatcacctat # agcagccgactggctctccgcctcttcttcgcggccaagaagttctacagtgttgtccgggacaacgtcagtagaagagatgtgttccggctgacaat # tcaccaataccaggactggtttctagatgctttggtattctggttacagacatttagaaccgagtgtttgaaccggatagaaagagctctggaaattg # acaaagacgtcattgtaacacacagcttggtcaaattctccaactcctcagtggacgtcaaagcttgttttgcacagatcacagaagaatggaggcag # attgactataatgatcctgattccagtgtgatgggaattatcaaaatcacagatctaatatgtgatggggccaggttgtacactgacaaaattcacac # catgatggagcgaagtaacttttatgatgatggtgatgagcagtttgacattacagacacgctttgcattactttgaacaacattgagcatgtgcgac # agtacctgaaggaacttcctgttttgcttgattgggaatctgtctgtatgcttctgtccaccaaacacgagaatgacgatattggtactaaatccagc # tctaccctctcccggcttatccactcagcagggcaggagatcctgttaaagtgctccctccttattgcacaaatcgtggagaaaatgaaggtggacat # gtccagattcatggtactgtttactcagaagactcctgaaaaggcttcatccatagaccagctgtttcagtacctgtccactaacttgcgaaccctga # gggagaggctgtttgacagcatgtacccctacatcacagagcagctgtggatgaccatcacagacctcatggaggaacaagttttcataggggaaaga # ccagaatactactctcaaatgaaacagtttttacgagcgttgacttcctactttgccaaagacggtctaaaagatgataatctacagacagaaccgta # caagaagttaaaagctcgactagaactaaactctctcagcactgaagagctcatgctagaatactttcacaatctggccgatgaaattgtaaatgaaa # caccatttgactttctgggaaatcttgccgtgaagttgtcatatatagaggaaacaagaggaaatgttaccatttttgtaaaagtaattcgagcctca # gacttgccaggattggatcactctggtttgagcgacccttacgtagtagtctccctttatccaaagaccatgtttggccacaacaaaccacagaagac # aaaaattatagaccagacattaaacccggtgttcaacactaccttccagttccccaacgtcccacacgaatatttgacagtgaggggagctgttctgt # tgctaagcattttggatcacgacaagatcgggtctgacgattttgctggcgaagtcgcagtgcatctctctaccatcacaccgatggcaatgtctacc # accgtggattccaagcctgccatcatgatacccatcagaagacccacctctcagacaaagggaccttacaaggttctggtggaaaggagtagctggga # caaaacagcgaaattatttatcaccgaccgacgacgctttattgaaaaacagcggaaacgtactgatctcaataccagaatgtctggcttcttttcct # tcttcaggagcaaaaaatcctaa] # protein sequence = [MRNSAKYRSGMCTRTRFLSVPWKFTASKTDDERVQESNVKRIRGSRSADVRTDIYRSEDEDGHPFVSGPPKTVAVKSV # SLDYGTLLGVPPRDDVSMKLRSQSDSDVIDGDSQTPNARSKRRKISAFLNRVRIGSRRSTVSCMNSRPTPXNCNAYCLLDIYHPIHRNSSFSPKSSPK # SSPKSSPKLKKSSSTVPIIHCSITEEVHRTNTAKHTSEPQWNEEFELPVEDLLTDEIHVFICNQDQENGSEKHHPDKHHLLSRRFLPRAVIGGGMLQA # LPPKGANSRVENVGSNFIYPTNRALRLVASLSQWKITTRLQNKSTNMQLESKRHIVVLLEWSCNHGDISTVDQALQAALQELQMIWASKQFDLSSCSQ # KMPITDAETMMYRNAASSYISSVSTHLDNYSELFPPYLDGINTLKQKLSVSMLLLELDLWDSKSSPHSPLTQKILKKLQDDTNRWINEKVEQIYKHDM # VQDPVIPRMTALVELTNLVSYHCLPMGVVNNLYNTLGIGYFRIITFCVEKKISSVMRELCQEMDVYQRKYHQYSVNITYSSRLALRLFFAAKKFYSVV # RDNVSRRDVFRLTIHQYQDWFLDALVFWLQTFRTECLNRIERALEIDKDVIVTHSLVKFSNSSVDVKACFAQITEEWRQIDYNDPDSSVMGIIKITDL # ICDGARLYTDKIHTMMERSNFYDDGDEQFDITDTLCITLNNIEHVRQYLKELPVLLDWESVCMLLSTKHENDDIGTKSSSTLSRLIHSAGQEILLKCS # LLIAQIVEKMKVDMSRFMVLFTQKTPEKASSIDQLFQYLSTNLRTLRERLFDSMYPYITEQLWMTITDLMEEQVFIGERPEYYSQMKQFLRALTSYFA # KDGLKDDNLQTEPYKKLKARLELNSLSTEELMLEYFHNLADEIVNETPFDFLGNLAVKLSYIEETRGNVTIFVKVIRASDLPGLDHSGLSDPYVVVSL # YPKTMFGHNKPQKTKIIDQTLNPVFNTTFQFPNVPHEYLTVRGAVLLLSILDHDKIGSDDFAGEVAVHLSTITPMAMSTTVDSKPAIMIPIRRPTSQT # KGPYKVLVERSSWDKTAKLFITDRRRFIEKQRKRTDLNTRMSGFFSFFRSKKS] # end gene g1 ### # start gene g2 Contig26937 AUGUSTUS gene 31484 44196 0.01 - . g2 Contig26937 AUGUSTUS transcript 31484 44196 0.01 - . g2.t1 Contig26937 AUGUSTUS tts 31484 31484 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 31484 31726 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS stop_codon 31553 31555 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS intron 31727 31884 1 - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS intron 32005 32092 0.5 - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS intron 32219 33337 0.05 - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS intron 33589 42721 0.18 - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS CDS 31553 31726 1 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS CDS 31885 32004 0.63 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 31885 32004 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS CDS 32093 32218 0.08 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 32093 32218 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS CDS 33338 33588 0.22 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 33338 33588 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS CDS 42722 42767 0.28 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 42722 42799 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS start_codon 42765 42767 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS exon 43959 44196 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS tss 44196 44196 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 31622 31648 7.33 - 0 target "unknown_C[1..9]"; target_start 207; transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 31649 31726 7.11 - 0 target "unknown_B[130..155]"; target_start 52; transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 31885 32004 12.4 - 0 target "unknown_B[90..129]"; target_start 52; transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 32093 32218 7.13 - 0 target "unknown_B[48..89]"; target_start 52; transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 33338 33478 6.46 - 0 target "unknown_B[1..47]"; target_start 52; transcript_id "g2.t1"; gene_id "g2"; Contig26937 AUGUSTUS protein_match 33482 33544 2.67 - 0 target "unknown_A[1..21]"; target_start 30; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgagtaccttcagcacctcaagaagtgagctagtgactggagtttccactgtgagaccccctgtggcccctgaacgta # agaaacagcttgaggacttcggtcagtatgtcggacagtgtctatctaagtatgtacagaccgtgcggctgatgtctggggacgagttggagatccta # attcatcctgaggggatcatcccaactctgacttttctcagggatcattacaatgcccagttcaccaacatcgtggacattgcatgtgtagatgtacc # aaccaggaccaacaggtttgagatagtatacaatttgctgtccatacggtataactcacgtattcgagtccttacttacacagatgagctgacaggta # tagacagttcatgcagtgttttcccaggatcaaactggtacgagagagagatttgggatatgtatggagtttacttccacaatcatcccgatttacgg # agaattcttacagattatggatttgaaggtcatccattcaggaaggatttccctttgacaggctacactgagctccgctacgatgaggaagtccagcg # aatcgtaattgagcctgtagaaatggcccaggaattccgcaaatttgagtacagtacaccctgggagagtttccccaacttccgccccaaggaggagg # aagtcccagagacccccgtccctcaggtggagtctggggataaaaagtga] # protein sequence = [MSTFSTSRSELVTGVSTVRPPVAPERKKQLEDFGQYVGQCLSKYVQTVRLMSGDELEILIHPEGIIPTLTFLRDHYNA # QFTNIVDIACVDVPTRTNRFEIVYNLLSIRYNSRIRVLTYTDELTGIDSSCSVFPGSNWYEREIWDMYGVYFHNHPDLRRILTDYGFEGHPFRKDFPL # TGYTELRYDEEVQRIVIEPVEMAQEFRKFEYSTPWESFPNFRPKEEEVPETPVPQVESGDKK] # sequence of block unknown_C 207 [STPWESFPN] 216 # sequence of block unknown_B 52 [GDELEILIHPEGIIPTLTFLRDHYNAQFTNIVDIACVDVPTRTNRFEIVYNLLSIRYNSRIRVLTYTDELTGIDSSCSVFPGSNWYEREIWDMYGVYFHNHPDLRRILTDYGFEGHPFRKDFPLTGYTELRYDEEVQRIVIEPVEMAQEFRKFEY] 207 # sequence of block unknown_A 30 [EDFGQYVGQCLSKYVQTVRLM] 51 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RRJ.prfl --predictionStart=11652 --predictionEnd=53514 --species=fly ./tmp/Contig2693720180911_busco_2432604931_.temp