# 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..217]--> unknown_A (12) <--[0..9]--> unknown_B (19) <--[0..1]--> unknown_C (24) <--[0..2]--> unknown_D (64) <--[3..22]--> unknown_E (34) <--[2..7]--> unknown_F (53) <--[0..22]--> unknown_G (26) <--[0..7]--> unknown_H (138) <--[0..76]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5370120180911_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 = 22602, name = Contig53701) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig53701 AUGUSTUS gene 499 4419 0.05 + . g1 Contig53701 AUGUSTUS transcript 499 4419 0.05 + . g1.t1 Contig53701 AUGUSTUS exon 499 768 . + . transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS start_codon 540 542 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS intron 769 2991 0.27 + . transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS intron 3216 3531 0.87 + . transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS CDS 540 768 0.18 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS CDS 2992 3215 0.64 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS exon 2992 3215 . + . transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS CDS 3532 4098 0.88 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS exon 3532 4419 . + . transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS stop_codon 4096 4098 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig53701 AUGUSTUS tts 4419 4419 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaaggggaccattgagttgagccatgtgattatttcggacgaaaacgtcaaagaaatttgtgatgcagccaatggag # aaaaactgaagtcgctttcgttgcgtgattgtgaaatagagggaacgatgtacaacgctattttgaaggctgtcggagcttgcaaatcaattttgcag # ctaagtttatgtgttggcatggttaaaaccaagaaagacgtttcagcactttgtttgaaagatctttccttaagtgcaaatccaggaatttctcagaa # gttctggggaaaatttggtgtttccctggcagccaacagcgatcttagagagctgtatttggattataacaatcttggcgactgtgcagccagctgta # ttgtggtgggcctctctggatctcagaatcttcaggtcctcgatttagaaggcaccaacatcaatgattcgacagctgagttgattcaacatttactg # gaaaattttcccactcaactacgcaaagttgtactcaaagaaaacagaataaacagcagcatcattgagaaaatttcttctagtctggaggaaagtga # tgacatttccgacacgtttagtatagaatcaatgaaacttaagaccaaatcgtctggcaaaacttcaaagtccaagtcctccacacagaagagttcca # ctctaaaaaacagtacgagagatgatgcttcatcgtcagatgatgataaagaaaacaatgatagagagaaagaagaagagagtgacatgaaagacaca # gtgaaaactgatgaagattatcgtgtgctagaaatggccttggaagagggactgagcacaggaaagatcagtgccctgtctggcaccatggaggagga # cgatattgaagaagaactaaccgaagttcctttgacatcatccagtcatgtgataagattcaccgagaacaaaccactgacttactcagccgaggaat # tccctgatgatggagatgaactgacagaagtaccagtgttacaacgggtcacagtttga] # protein sequence = [MKGTIELSHVIISDENVKEICDAANGEKLKSLSLRDCEIEGTMYNAILKAVGACKSILQLSLCVGMVKTKKDVSALCL # KDLSLSANPGISQKFWGKFGVSLAANSDLRELYLDYNNLGDCAASCIVVGLSGSQNLQVLDLEGTNINDSTAELIQHLLENFPTQLRKVVLKENRINS # SIIEKISSSLEESDDISDTFSIESMKLKTKSSGKTSKSKSSTQKSSTLKNSTRDDASSSDDDKENNDREKEEESDMKDTVKTDEDYRVLEMALEEGLS # TGKISALSGTMEEDDIEEELTEVPLTSSSHVIRFTENKPLTYSAEEFPDDGDELTEVPVLQRVTV] # end gene g1 ### # start gene g2 Contig53701 AUGUSTUS gene 4751 16985 0.01 - . g2 Contig53701 AUGUSTUS transcript 4751 16985 0.01 - . g2.t1 Contig53701 AUGUSTUS tts 4751 4751 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 4751 5013 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS stop_codon 4792 4794 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 5014 5729 0.31 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 5871 7617 0.3 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 7792 8971 0.35 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 9186 14195 0.17 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 14379 14681 0.08 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 14802 15028 0.05 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS intron 15138 16598 0.02 - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 4792 5013 0.31 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 5730 5870 0.38 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 5730 5870 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 7618 7791 0.8 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 7618 7791 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 8972 9185 0.12 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 8972 9185 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 14196 14378 0.13 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 14196 14378 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 14682 14801 0.05 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 14682 14801 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 15029 15137 0.1 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 15029 15137 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS CDS 16599 16740 0.03 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS exon 16599 16985 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS start_codon 16738 16740 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS tss 16985 16985 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 4870 5013 5.18 - 0 target "unknown_H[91..138]"; target_start 271; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 5730 5870 8.4 - 0 target "unknown_H[44..90]"; target_start 271; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 7618 7746 7.97 - 0 target "unknown_H[1..43]"; target_start 271; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 7747 7791 10.4 - 0 target "unknown_G[12..26]"; target_start 245; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 8972 9004 15.3 - 0 target "unknown_G[1..11]"; target_start 245; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 9014 9172 7.67 - 0 target "unknown_F[1..53]"; target_start 189; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 14198 14299 6.33 - 0 target "unknown_E[1..34]"; target_start 150; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 14309 14378 12.4 - 1 target "unknown_D[41..64]"; target_start 83; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 14682 14801 9.2 - 1 target "unknown_D[1..41]"; target_start 83; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 15029 15030 1 - 0 target "unknown_D[1..1]"; target_start 83; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 15037 15108 5.81 - 0 target "unknown_C[1..24]"; target_start 57; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 15109 15137 5.49 - 2 target "unknown_B[10..19]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 16599 16626 6.96 - 0 target "unknown_B[1..10]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig53701 AUGUSTUS protein_match 16639 16674 5.02 - 0 target "unknown_A[1..12]"; target_start 22; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtcagaacctacggaaggaattggagatatgtcgattaaagacgaagagaagcaagaggcaggtgatgaggacgacg # ttgtgaacccatgggaagtggcaacacattcagctactggtgttgattatgacaagttgataaaaaggtttggaagtaccaaaatagatgatgccttg # atacagaggatagagaaagtcacaggaaaacctgtacaccatctactaaggagaggaaaattcttctctcagagagatatgcacatgattctggacat # gtatgaacaaaagaagccattttatttatacacaggaagaggaccatcgtctgatgccatgcatatggggcatcttattccattcattttcaccaaat # ggttacaggacacatttgatgtaccgctagtcatacagctgaccgatgatgagaaattcttgtggaaggaccttactctagaacaagccaatcatatg # gctttcgaaaacacaaaggatatcattgcctgtggattcgatattgagaagacattcattttcagtgatctgaactttatatcgaatagtgcagcttt # ttataggaacatgtgcagagtccagaaactggtgacctacaatcaggtgaaggggatttttggttttggagacagtgactgcattggaaaaatcagtt # tcccagccatccaggcttctcctagttttagttcctctttcccagagattttcaatggacgatccgacattccttgtcttatcccatgtgcaatagat # caggacccctacttcagaatgaccagagatgtggccccaagaatgaatcatctgaagccggctttgattcactccacattcttcccagctcttcaggg # agcccagaccaagatgagtgcaagtgaccccaactcatccatctttgtgacagattctgacaagcagatcaaggataaaatcaacaagtttgcctttt # ctggaggtggagccacagttgaggaacacaaggaaaagggaggtaactgtgatgtagacgtggcgtatcagtatctgacgttcttcatggaagatgat # gaaagattggaggaaatcaggaagacttacacaagtggagagctgttgacaggattcctgaagaaggagttgattgaaatcctacagaagttggtcgg # agagcatcggcagaggagagctaccatcacagacgaagaggtgaagcaattcatgactccaaggaaactgaaatttgactaccccccaccagctcctc # cgtcagagggaaagaagaaaaagaagcaaaagagtgctaaagcactttaa] # protein sequence = [MSEPTEGIGDMSIKDEEKQEAGDEDDVVNPWEVATHSATGVDYDKLIKRFGSTKIDDALIQRIEKVTGKPVHHLLRRG # KFFSQRDMHMILDMYEQKKPFYLYTGRGPSSDAMHMGHLIPFIFTKWLQDTFDVPLVIQLTDDEKFLWKDLTLEQANHMAFENTKDIIACGFDIEKTF # IFSDLNFISNSAAFYRNMCRVQKLVTYNQVKGIFGFGDSDCIGKISFPAIQASPSFSSSFPEIFNGRSDIPCLIPCAIDQDPYFRMTRDVAPRMNHLK # PALIHSTFFPALQGAQTKMSASDPNSSIFVTDSDKQIKDKINKFAFSGGGATVEEHKEKGGNCDVDVAYQYLTFFMEDDERLEEIRKTYTSGELLTGF # LKKELIEILQKLVGEHRQRRATITDEEVKQFMTPRKLKFDYPPPAPPSEGKKKKKQKSAKAL] # sequence of block unknown_H 271 [HLKPALIHSTFFPALQGAQTKMSASDPNSSIFVTDSDKQIKDKINKFAFSGGGATVEEHKEKGGNCDVDVAYQYLTFFMEDDERLEEIRKTYTSGELLTGFLKKELIEILQKLVGEHRQRRATITDEEVKQFMTPRKL] 409 # sequence of block unknown_G 245 [IPCLIPCAIDQDPYFRMTRDVAPRMN] 271 # sequence of block unknown_F 189 [FYRNMCRVQKLVTYNQVKGIFGFGDSDCIGKISFPAIQASPSFSSSFPEIFNG] 242 # sequence of block unknown_E 150 [LEQANHMAFENTKDIIACGFDIEKTFIFSDLNFI] 184 # sequence of block unknown_D 83 [RDMHMILDMYEQKKPFYLYTGRGPSSDAMHMGHLIPFIFTKWLQDTFDVPLVIQLTDDEKFLWK] 147 # sequence of block unknown_C 57 [ALIQRIEKVTGKPVHHLLRRGKFF] 81 # sequence of block unknown_B 38 [TGVDYDKLIKRFGSTKIDD] 57 # sequence of block unknown_A 22 [DEDDVVNPWEVA] 34 # end gene g2 ### # start gene g3 Contig53701 AUGUSTUS gene 18326 21508 0.01 + . g3 Contig53701 AUGUSTUS transcript 18326 21508 0.01 + . g3.t1 Contig53701 AUGUSTUS tss 18326 18326 . + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS exon 18326 19277 . + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS start_codon 18392 18394 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS intron 19278 19918 0.25 + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS intron 20089 20746 0.21 + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS intron 20885 21096 0.2 + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS CDS 18392 19277 0.58 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS CDS 19919 20088 0.25 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS exon 19919 20088 . + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS CDS 20747 20884 0.23 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS exon 20747 20884 . + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS CDS 21097 21222 0.2 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS exon 21097 21508 . + . transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS stop_codon 21220 21222 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig53701 AUGUSTUS tts 21508 21508 . + . transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atggatcttctgaaaagctactatgaagaaagccaaagtgaaacagacaatgaagatgttggagaagggagtgatgaag # aaatttctaaagacataagcaccaagagcaggattgtgtcaaacagcgctggacagtcagctggggcagacttctttggtttgaatgatgattctgat # gaggaaactgaagagcccccagcaaagaaaaaaatgcaatgtttgatcaggttaaaggattcagatagcgaggtggaagtcccggacagtgatttctg # gagaggttttactcctcaaaataatctggatcatcatgaggtcttagaggaaaagaatgaacaggttacacagcagggtcggaaacagggagggcacc # gaaataaacgtcacactgatcctaatcattcttgctcttctaaaacagacagctggcacagtaaggatacaagaggaagtgaacgtgatttcaaccgt # aaactttccagggaatctttcaacagttcttaccagtcccaacagaacataagctctagcagagaatcacaagcacagcgacagctcttctacgtaca # ttcaaagatagcaccacatatgaccaaatgtaacgttcacaatagacatccgtgccgggtggagagagaactaggagatcatacacagacggttaaca # gggtgatgtggaataagtccccatactgccatctgtttctgtcggccgctatggatggaactgtcaggatctggaatatctggactcagctttcaccc # tgtgttaagcttctcagaatccatagcagagctgtaaaagatgctgtatggagtcatgacgggacacatgttctaagctgtagttacgacaagactgc # gaagtggatagatgtagaaaaaggtttagcattatccacctttaaacactcctcatatgtaacgagctgtaaagttcacccaaatgacccccatctca # gcattacgggatcttggaacagtattcactgctgggacactagggtcagcatttctccctgtaaaacatacacacacaaggactcgtatggtcaggtt # caggatcttctgttcaacagagatggagacacatttttctctgcaggagatgagatcagccaagactctgcagacagaaatatcatggcctgggattt # caagtccactagcgtcttatccaaccagatatatcaggataaagaattcatacaagatgataaagtaaattgtcaaggtcaaagccatttaattgatg # aaggtgaaggtcattcatcaaggttaaatttgccacagttgaatatgttcacgggtataccgtag] # protein sequence = [MDLLKSYYEESQSETDNEDVGEGSDEEISKDISTKSRIVSNSAGQSAGADFFGLNDDSDEETEEPPAKKKMQCLIRLK # DSDSEVEVPDSDFWRGFTPQNNLDHHEVLEEKNEQVTQQGRKQGGHRNKRHTDPNHSCSSKTDSWHSKDTRGSERDFNRKLSRESFNSSYQSQQNISS # SRESQAQRQLFYVHSKIAPHMTKCNVHNRHPCRVERELGDHTQTVNRVMWNKSPYCHLFLSAAMDGTVRIWNIWTQLSPCVKLLRIHSRAVKDAVWSH # DGTHVLSCSYDKTAKWIDVEKGLALSTFKHSSYVTSCKVHPNDPHLSITGSWNSIHCWDTRVSISPCKTYTHKDSYGQVQDLLFNRDGDTFFSAGDEI # SQDSADRNIMAWDFKSTSVLSNQIYQDKEFIQDDKVNCQGQSHLIDEGEGHSSRLNLPQLNMFTGIP] # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E0Y.prfl --predictionStart=0 --predictionEnd=34803 --species=fly ./tmp/Contig5370120180911_busco_2432604931_.temp