# 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..60]--> unknown_A (20) <--[1..12]--> unknown_B (15) <--[0..2]--> unknown_C (8) <--[0..2]--> unknown_D (20) <--[2..33]--> unknown_E (28) <--[0..1]--> unknown_F (50) <--[0..2]--> unknown_G (18) <--[0..68]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3758820180911_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 = 29004, name = Contig37588) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig37588 AUGUSTUS gene 2849 10979 0.01 + . g1 Contig37588 AUGUSTUS transcript 2849 10979 0.01 + . g1.t1 Contig37588 AUGUSTUS exon 2849 2912 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS start_codon 2856 2858 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS intron 2913 3612 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS intron 3689 3829 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS intron 3982 8857 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS intron 9004 9448 0.08 + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS CDS 2856 2912 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS CDS 3613 3688 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS exon 3613 3688 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS CDS 3830 3981 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS exon 3830 3981 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS CDS 8858 9003 0.37 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS exon 8858 9003 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS CDS 9449 9647 0.08 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS exon 9449 10979 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS stop_codon 9645 9647 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS tts 10979 10979 . + . transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 3676 3688 8.67 + 0 target "unknown_A[1..5]"; target_start 40; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 3830 3876 4.9 + 2 target "unknown_A[5..20]"; target_start 40; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 3880 3924 4.34 + 0 target "unknown_B[1..15]"; target_start 61; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 3925 3948 5.49 + 0 target "unknown_C[1..8]"; target_start 76; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 3949 3981 7.99 + 0 target "unknown_D[1..11]"; target_start 84; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 8858 8884 5.13 + 0 target "unknown_D[12..20]"; target_start 84; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 8891 8974 10.5 + 0 target "unknown_E[1..28]"; target_start 106; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 8975 9003 5.09 + 0 target "unknown_F[1..10]"; target_start 134; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 9449 9569 6.89 + 1 target "unknown_F[10..50]"; target_start 134; transcript_id "g1.t1"; gene_id "g1"; Contig37588 AUGUSTUS protein_match 9570 9623 3.57 + 0 target "unknown_G[1..18]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcgccgttgtgcattcaagagaaatttcgaaatgcacgaaataagactccatatgactatcaagtctacttccggtt # atgagaaaatggcattggtaaagcgaccacatggtccaaatattttgataacaggaacacctggcacagggaaatccaccttagcaggagaacttggt # cagaaaacaaacctgaaatatgtcaatataggggagattgcaaaggagggtcagttatacgaaggatgggatgaccagtatcaatgtccaattctgga # tgaagaccgagttatagatgaactagaggaagtaatgtccgccgggggaaatattgtggactatcacggctgcgagttctttcctgagagatggtttg # acattgtgtttgtcctcagaacagataacacagtgctgtacgagagactggagaacaggggctacacaggaaagaaattggaagacaacgtccagtgt # gaaatattccagaccattctagatgaggctagagactcatataaaattgaaattgtgcatgaattacctagcaacaccccggaagaccttgaagataa # tttagaaaagatctccgcatggattcaacaatacatcaccaaccaaggaggggttgtatag] # protein sequence = [MRRCAFKRNFEMHEIRLHMTIKSTSGYEKMALVKRPHGPNILITGTPGTGKSTLAGELGQKTNLKYVNIGEIAKEGQL # YEGWDDQYQCPILDEDRVIDELEEVMSAGGNIVDYHGCEFFPERWFDIVFVLRTDNTVLYERLENRGYTGKKLEDNVQCEIFQTILDEARDSYKIEIV # HELPSNTPEDLEDNLEKISAWIQQYITNQGGVV] # sequence of block unknown_A 40 [ILITGTPGTGKSTLAGELGQ] 60 # sequence of block unknown_B 61 [TNLKYVNIGEIAKEG] 76 # sequence of block unknown_C 76 [QLYEGWDD] 84 # sequence of block unknown_D 84 [QYQCPILDEDRVIDELEEVM] 104 # sequence of block unknown_E 106 [GGNIVDYHGCEFFPERWFDIVFVLRTDN] 134 # sequence of block unknown_F 134 [TVLYERLENRGYTGKKLEDNVQCEIFQTILDEARDSYKIEIVHELPSNTP] 184 # sequence of block unknown_G 184 [EDLEDNLEKISAWIQQYI] 202 # end gene g1 ### # start gene g2 Contig37588 AUGUSTUS gene 15644 18845 0.04 - . g2 Contig37588 AUGUSTUS transcript 15644 18845 0.04 - . g2.t1 Contig37588 AUGUSTUS tts 15644 15644 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS exon 15644 16876 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS stop_codon 15773 15775 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS intron 16877 17036 0.97 - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS intron 17834 18109 1 - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS intron 18396 18602 0.97 - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS intron 18692 18752 0.71 - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS CDS 15773 16876 0.37 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS CDS 17037 17833 0.97 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS exon 17037 17833 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS CDS 18110 18395 0.99 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS exon 18110 18395 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS CDS 18603 18691 0.71 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS exon 18603 18691 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS CDS 18753 18804 0.71 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS exon 18753 18845 . - . transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS start_codon 18802 18804 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig37588 AUGUSTUS tss 18845 18845 . - . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggtggagtgtactttatatcacagtcaaaaggaaagatgggaaaatacatggtcggccaaggagagattttcaaacc # tgagcatcagggaaatgtctctcaacatggatggggatggtgactgtccatttgatgcggaggatgtggaaaaattgacagcagaaaacctgggattg # aaggaggaggcaaacaaagctcagaatgaagtggtggatcttcgctctgaggtcatgaaactgaggtatagttcagctgtctcgtccgcagaggagga # gaagagactgaccttgaggaaaaacagggagctcaagttggaggtcaacatgctgcagcatgaaaacgaagatctgaagaaactggtgggaagtctga # aatacgggtcgcaccctgggaattccgagggaggatgtcccaaaagaggtcctgataatcaattgcaagagcaaacaaggtccagtacatccatacat # gatgatgatgatggagaagagagagaaagtagcaatgaaaatctaaaagaactgaaggaagatgtgaatttggatgaccgaactgatggtcacatgtt # ggtcaagaggaaacatgtgagcatcattaatgtcgtgtatcctgcttcagacattcagaacatcaattctggtgatgattcggattttgacattgatt # ctgatgaagaagacgaaaatgacatcgattcttttgttgaagttgaatatgaagaaaatgagaatgtaaaaggtcgggaagatatgcctgatggggtg # ggaaagattgagagggagcgagaattttttccttgcagcagccgggtgaacaatgtagagaagcaaggtgatgtgagcacggaggacagtgaaacaga # aactgaaagtaggcattctgatgaaattgaaagtgttgccaaggtagaggatgtggcagaaaatgatgaggaggcacaaaagtatccgatggaggaag # acgtagaaattctggatgaagatttaggggatgaggtagctgaagatgaggaggtgtctaacacaagcacagagaatatcccatctccagaggatgaa # ccaatcaaagggtcccccgatgatggaaagagggaggagaatgctaagagggagggtggatctagtaagaagacggactggagagagacaatgcacaa # gattctgaacaaaaccaaggcttctgtgtccgatgtaactcagcagattcaagacacctggaaacaggtgaaaaatatatcggaggatctctggaaga # aaaacgagccagtttttactaaatttaaaactaatttggtcctgcatgttggagaagcagctcagaagatctcagcaaaactacaggaggagaccaaa # aactggttccgcaagaaagcacgaaagcatgaagactatccaaagcacaggcaaaatgatgattattatccggagaaagaacaaagaagcaaacacta # ccactggaggaatcacgaagatcattatcccaagcacagacagaacgacgatatgtacaaagagaggagaaacaacagagattccattcatttcaagg # ccagaacgaggcgaaggtcattcaaagaggaaagagaaaatcacaaaccttggaggaaacatcacagaaaggcggagaagtatgagaggaaaagggcc # aaaaaattccagaaaatgaagaggagattcgaaaagatgcatgaatatgagttttgcaagatgaatatgaagaagagacagaagttctttgatatatt # ggaggcttttgatgagaaatttcaggctgataagatgcctgatccagatcagatgtggtacagctgtcagtgggactggtggtggaacgctatttctt # tccacatccactttatgttgatggatccaaagtgccagggggcattacttccatggcaggagggcatcttggctgctggaagatgggaatgcccaggt # ttccctcagaatctgaggcaacaaaatcaacaggttttccagtttcaagaatatggccacgatgaggatgatgacctcgatgaagatgacgaaattga # tgaaaagggttttaaaaatgtgccctatttcgatgaatcagaaatcctgcagaaaagcaactacacagaggagttcaaaggatgtgacccaacgaagg # gaatttgcgatttcaacaaaaacgactcctggtaccttaagaaaatgaagtttcgtcaataccagaggttcgcagatgccaaagagaaaggtaaaact # gagtggatgtttgccagagccaaccatcgacaacacgaaagggagagaactgatgacagtcaagtctttcacagattctatgagtgcaagtag] # protein sequence = [MVECTLYHSQKERWENTWSAKERFSNLSIREMSLNMDGDGDCPFDAEDVEKLTAENLGLKEEANKAQNEVVDLRSEVM # KLRYSSAVSSAEEEKRLTLRKNRELKLEVNMLQHENEDLKKLVGSLKYGSHPGNSEGGCPKRGPDNQLQEQTRSSTSIHDDDDGEERESSNENLKELK # EDVNLDDRTDGHMLVKRKHVSIINVVYPASDIQNINSGDDSDFDIDSDEEDENDIDSFVEVEYEENENVKGREDMPDGVGKIEREREFFPCSSRVNNV # EKQGDVSTEDSETETESRHSDEIESVAKVEDVAENDEEAQKYPMEEDVEILDEDLGDEVAEDEEVSNTSTENIPSPEDEPIKGSPDDGKREENAKREG # GSSKKTDWRETMHKILNKTKASVSDVTQQIQDTWKQVKNISEDLWKKNEPVFTKFKTNLVLHVGEAAQKISAKLQEETKNWFRKKARKHEDYPKHRQN # DDYYPEKEQRSKHYHWRNHEDHYPKHRQNDDMYKERRNNRDSIHFKARTRRRSFKEERENHKPWRKHHRKAEKYERKRAKKFQKMKRRFEKMHEYEFC # KMNMKKRQKFFDILEAFDEKFQADKMPDPDQMWYSCQWDWWWNAISFHIHFMLMDPKCQGALLPWQEGILAAGRWECPGFPQNLRQQNQQVFQFQEYG # HDEDDDLDEDDEIDEKGFKNVPYFDESEILQKSNYTEEFKGCDPTKGICDFNKNDSWYLKKMKFRQYQRFADAKEKGKTEWMFARANHRQHERERTDD # SQVFHRFYECK] # end gene g2 ### # start gene g3 Contig37588 AUGUSTUS gene 18946 20447 0.2 + . g3 Contig37588 AUGUSTUS transcript 18946 20447 0.2 + . g3.t1 Contig37588 AUGUSTUS tss 18946 18946 . + . transcript_id "g3.t1"; gene_id "g3"; Contig37588 AUGUSTUS exon 18946 20447 . + . transcript_id "g3.t1"; gene_id "g3"; Contig37588 AUGUSTUS start_codon 19101 19103 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig37588 AUGUSTUS CDS 19101 19940 0.82 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig37588 AUGUSTUS stop_codon 19938 19940 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig37588 AUGUSTUS tts 20447 20447 . + . transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacatacca # atagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaat # gccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaa # atcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacatacca # atagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaat # gccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaaatcccaacataccaatagcatgaccaatgccaagccccagaa # atcacaacttaccaatagcatgaccaatcccaagccccagagcaacagaaatcactaccaccattacgaagttcaaggtgacattaacacttggattg # ggtcgaaagacgtattgtctgatgaggttgttttcagccatcaggtcactgatgtcaacattggaaaatgtagagaaatcgtcgctatggcgatcgtc # actcctgtcactttcaatgcgatcgtcctgctcgtcttccacttctggagacgactccgtatccggatcatctag] # protein sequence = [MTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQK # SQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQKSQHTNSMTNAKPQK # SQHTNSMTNAKPQKSQLTNSMTNPKPQSNRNHYHHYEVQGDINTWIGSKDVLSDEVVFSHQVTDVNIGKCREIVAMAIVTPVTFNAIVLLVFHFWRRL # RIRII] # end gene g3 ### # start gene g4 Contig37588 AUGUSTUS gene 23020 29004 0.07 - . g4 Contig37588 AUGUSTUS transcript 23020 29004 0.07 - . g4.t1 Contig37588 AUGUSTUS tts 23020 23020 . - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS exon 23020 23837 . - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS stop_codon 23629 23631 . - 0 transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS intron 23838 24205 0.92 - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS intron 24366 27609 0.92 - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS intron 27689 29004 0.22 - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS CDS 23629 23837 0.95 - 2 transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS CDS 24206 24365 0.91 - 0 transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS exon 24206 24365 . - . transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS CDS 27610 27688 0.22 - 1 transcript_id "g4.t1"; gene_id "g4"; Contig37588 AUGUSTUS exon 27610 27688 . - . transcript_id "g4.t1"; gene_id "g4"; # coding sequence = [atccctgataatggctgaaagcagttcaagtagttcgggtggatgggaattcataggcaaagatggaaaaagggcagag # agttttgatgataaccagagtgaaacctcagagagttcaatcgaggttgtttctatggataccactgatcttctctccttggaatccgttcggacacc # agttttaccttcggactcctctggaccgttccttgtgctgagacttaggagtaaagagaaggagtctgtgacagaatctgatgaatctgatgaccatc # aaactaaagaccaggggatcatgaagaggcgcaggaaatcaaagcccagatcactgaggtcacaggagcttacgttgtcttcagatttgtcgactcca # agtgaggaagagagggacttcgtagcaatacctgatccgcaaaaggtgacgccattttcagatttctggtcatag] # protein sequence = [SLIMAESSSSSSGGWEFIGKDGKRAESFDDNQSETSESSIEVVSMDTTDLLSLESVRTPVLPSDSSGPFLVLRLRSKE # KESVTESDESDDHQTKDQGIMKRRRKSKPRSLRSQELTLSSDLSTPSEEERDFVAIPDPQKVTPFSDFWS] # end gene g4 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09371088.prfl --predictionStart=0 --predictionEnd=29004 --species=fly ./tmp/Contig3758820180911_busco_2432604931_.temp