# 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..88]--> unknown_A (16) <--[0..20]--> unknown_B (52) <--[0..1]--> unknown_C (10) <--[0..2]--> unknown_D (69) <--[0..1]--> unknown_E (34) <--[7..26]--> unknown_G (21) <--[0..36]--> unknown_H (66) <--[2..59]--> unknown_I (35) <--[0..47]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig6268920180911_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 = 34348, name = Contig62689) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig62689 AUGUSTUS gene 5652 21036 0.01 - . g1 Contig62689 AUGUSTUS transcript 5652 21036 0.01 - . g1.t1 Contig62689 AUGUSTUS intron 5652 5806 0.58 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 5970 6301 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 6387 6823 0.95 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 6995 7170 1 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 7206 7300 1 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 7413 7641 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 7832 7966 0.52 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 8035 10562 0.39 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 10684 10976 0.7 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 11112 11451 0.58 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 11590 14398 0.51 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 14433 14527 0.87 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 14640 16737 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 16889 17492 0.06 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 17616 20037 0.07 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 20164 20401 0.1 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 20451 20614 0.1 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS intron 20669 20913 0.11 - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 5807 5969 0.62 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 5807 5969 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 6302 6386 0.94 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 6302 6386 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 6824 6994 1 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 6824 6994 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 7171 7205 1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 7171 7205 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 7301 7412 1 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 7301 7412 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 7642 7831 0.62 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 7642 7831 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 7967 8034 0.39 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 7967 8034 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 10563 10683 0.39 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 10563 10683 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 10977 11111 0.87 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 10977 11111 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 11452 11589 0.53 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 11452 11589 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 14399 14432 0.86 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 14399 14432 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 14528 14639 0.87 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 14528 14639 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 16738 16888 0.07 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 16738 16888 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 17493 17615 0.08 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 17493 17615 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 20038 20163 0.11 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 20038 20163 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 20402 20450 0.1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 20402 20450 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 20615 20668 0.1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 20615 20668 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS CDS 20914 20952 0.04 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS exon 20914 21036 . - . transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS start_codon 20950 20952 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig62689 AUGUSTUS tss 21036 21036 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgctcaatgtcatcttctcaaggatggaggcccaagctgcccaggaagcaaaagaaagggagagaagtgacagtaaga # gttccaaaaaggaggatgcaggaatagatgtggaagaagaaaagcaggagaataagaataatgaagtagatgaagaaacagtggatgctgcagaggag # gatgtgaaagaagagacacctttggaaattgtacaaggagttttagaggacatgatgagtcaggtggctggagaggacacacccaccagagatgcaca # atgtgtagtggatatatacctgaattatgactgtgatttgggtcttgctaacatctttgaaagacttgtaaatgacttgtcaaagattgcacagggaa # gacaggcattggctctaggtgctactcccattcaagaaaagagcattagaattaaaggcctggaatgtctggtgtctgttctgaagtgtatggtggag # tggagcaaggatctgtatgtcaatcnnnnnnnnnnnnnnnnnnnnnnnnncacactctcagtccaacctaggttcaacaaaaaacctaaaagaggcct # gcattacctacaggaacagggcatgctgggaaccagtccagatgatgtagcagagttctttcactcagatgaaagattggacaagactgttattggag # attttctgggagaaatgaaaaattgccagatgcatctcacagctggaacttggccagttgattggcacaggggtcaaaaccaaggtcaaacaaaggtc # atcaccggagagagagatatgcagaatgctgggcatccactagaggcatttgatccagaagtgatagctaggggtggtttggactctaagagattggc # atctcagagaacagatggaggaaacgagttctcaggtgtggtggtggcagtagatcggatatttaccggctctgtgaaactggatggagatgccatag # cctcacaaaaatcgttgagatttcttattacaacatgggccgtatcaggctgcagtggtcaagaatcttgggaggtcatcggtgatcactttaataag # gtcagtatgggacaaaaactatagtgcgttcccaatatttccttatccaagaccaacttgcgtaagctctctatatctcagttcaatcaaggacagga # aaaaatgcctaacaccgagacagacagtgactctgggaagggtacgatgacgagctacggtagtgtgaattcactcaatacgaacgacggctcacagt # cactcggtagtactcccatggataaccccgagcagttcgagtctcagaaacagcagaaagagatcatggagacaggcattgaaatgttcaacaaaaaa # cctaaaagaggcctgcattacctacaggaacagggcatgctgggaaccagtccagatgatgtagcagagttctttcactcagatgaaagattggacaa # gactgttattggagattttctgggagaaaatgaaaagttcaacaaggaggtaatgtattcctatgtggaccagttagacttactggaaatggactttg # tgtcggcacttaggagattcctggaaggattccgattgcctggagaagcccagaagattgatagactgatggaaaagtttgcctcgcgctactgtgtc # tgtaactcaaacactaatctgtttgccagtgctgatacagcctacgtgttggcctactccattataatgttaaccacggacctccacagtcctcaggt # gatacataaaatgaggaaggatcagtatatcaagatgaacagaggcattaatgatagtaaggacctgccagaggagtatttatctcagatctatgatg # agattgctggtaatgaaataaagatgaaggttgtaggtggagtcaagccaaataaatcatctc] # protein sequence = [MLNVIFSRMEAQAAQEAKERERSDSKSSKKEDAGIDVEEEKQENKNNEVDEETVDAAEEDVKEETPLEIVQGVLEDMM # SQVAGEDTPTRDAQCVVDIYLNYDCDLGLANIFERLVNDLSKIAQGRQALALGATPIQEKSIRIKGLECLVSVLKCMVEWSKDLYVNXXXXXXXXXTL # SVQPRFNKKPKRGLHYLQEQGMLGTSPDDVAEFFHSDERLDKTVIGDFLGEMKNCQMHLTAGTWPVDWHRGQNQGQTKVITGERDMQNAGHPLEAFDP # EVIARGGLDSKRLASQRTDGGNEFSGVVVAVDRIFTGSVKLDGDAIASQKSLRFLITTWAVSGCSGQESWEVIGDHFNKVSMGQKLXCVPNISLSKTN # LRKLSISQFNQGQEKMPNTETDSDSGKGTMTSYGSVNSLNTNDGSQSLGSTPMDNPEQFESQKQQKEIMETGIEMFNKKPKRGLHYLQEQGMLGTSPD # DVAEFFHSDERLDKTVIGDFLGENEKFNKEVMYSYVDQLDLLEMDFVSALRRFLEGFRLPGEAQKIDRLMEKFASRYCVCNSNTNLFASADTAYVLAY # SIIMLTTDLHSPQVIHKMRKDQYIKMNRGINDSKDLPEEYLSQIYDEIAGNEIKMKVVGGVKPNKSS] # end gene g1 ### # start gene g2 Contig62689 AUGUSTUS gene 22017 30415 0.01 + . g2 Contig62689 AUGUSTUS transcript 22017 30415 0.01 + . g2.t1 Contig62689 AUGUSTUS tss 22017 22017 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 22017 22059 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 24575 24651 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 24990 25047 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 25392 25555 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS start_codon 25422 25424 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 25556 25647 0.64 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 25883 26423 0.8 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 26553 27475 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 27542 27722 0.29 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 27809 27921 0.65 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 28034 28480 0.02 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS intron 28630 28766 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 25422 25555 0.65 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 25648 25882 0.61 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 25648 25882 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 26424 26552 0.02 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 26424 26552 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 27476 27541 0.29 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 27476 27541 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 27723 27808 0.74 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 27723 27808 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 27922 28033 0.45 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 27922 28033 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 28481 28629 0.02 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 28481 28629 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS CDS 28767 28854 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS exon 28767 30415 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS stop_codon 28852 28854 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS tts 30415 30415 . + . transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 25428 25475 4.51 + 0 target "unknown_A[1..16]"; target_start 2; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 25485 25555 6.61 + 0 target "unknown_B[1..24]"; target_start 21; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 25648 25732 9.33 + 1 target "unknown_B[24..52]"; target_start 21; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 25736 25765 7.87 + 0 target "unknown_C[1..10]"; target_start 74; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 25766 25882 9.67 + 0 target "unknown_D[1..39]"; target_start 84; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 26424 26513 14.5 + 0 target "unknown_D[40..69]"; target_start 84; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 26517 26552 12.2 + 0 target "unknown_E[1..12]"; target_start 154; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 27476 27541 10.2 + 0 target "unknown_E[13..34]"; target_start 154; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 27744 27806 10.5 + 0 target "unknown_G[1..21]"; target_start 195; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 27807 27808 1 + 0 target "unknown_H[1..1]"; target_start 216; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 27922 28033 7.8 + 0 target "unknown_H[2..39]"; target_start 215; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 28481 28564 5.09 + 0 target "unknown_H[39..66]"; target_start 216; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 28592 28629 4.2 + 0 target "unknown_I[1..13]"; target_start 291; transcript_id "g2.t1"; gene_id "g2"; Contig62689 AUGUSTUS protein_match 28767 28833 6.1 + 1 target "unknown_I[13..35]"; target_start 291; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggactcgaaaaatgctcagaaaacttgggagtttagcaacaacgtagaaaatgtcagcggtgttgacgaaatataca # gatatgacaagaaacaacagcaagatattttgacagctaaaccatgggaaaaggatcctcattattttaagcacataaaagttagtgctttggctctg # ctgaaaatggtaatgcactcaagatcaggtggaaatctggaggtgatgggacttctgcttgggaaggttgatggtaacacaatgattgtcatggacag # ttttgctttaccagtagaaggaacagagacaagagtgaatgcccaagcacaggcatatgagtatatggctgcatacactgaggcagctaagcaagtag # gaagactggagaatgctattggttggtatcacagtcaccctggttatggctgttggttgtcaggaatagacgttagtacacagatgttaaatcagcag # ttccaggaaccatttgttgcaatagtggtagatccagtaagaacaatatctgcaggaaaggttaatataggagcattcagaacttatcccaagggttt # taagcccccagatgagggtccatcagaatatcagtctatacctctgaacaagatagaagattttggagtgcattgtaaacactattacagtttagaaa # tgtcctactttaaatcagtggcagacagaaaactgttagaatctctatggaacaaatattgggtcaatacactcagttcctccagtctgttaacgaat # gcagactacactaccggccagatctttgacttggctgacaaactcgagcagtccgaggtccagctctgtagagggggctttatgctggggatggacac # acatgaaaagaaatcagaggataaacttgccaaagcaactaaagacgggtgtaaaactacaatggaagcaattcatggcctaatgtcgcaagtgataa # aagacagattatttaatcaagtgcatacttcaaaatga] # protein sequence = [MDSKNAQKTWEFSNNVENVSGVDEIYRYDKKQQQDILTAKPWEKDPHYFKHIKVSALALLKMVMHSRSGGNLEVMGLL # LGKVDGNTMIVMDSFALPVEGTETRVNAQAQAYEYMAAYTEAAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAIVVDPVRTISAG # KVNIGAFRTYPKGFKPPDEGPSEYQSIPLNKIEDFGVHCKHYYSLEMSYFKSVADRKLLESLWNKYWVNTLSSSSLLTNADYTTGQIFDLADKLEQSE # VQLCRGGFMLGMDTHEKKSEDKLAKATKDGCKTTMEAIHGLMSQVIKDRLFNQVHTSK] # sequence of block unknown_A 2 [SKNAQKTWEFSNNVEN] 18 # sequence of block unknown_B 21 [VDEIYRYDKKQQQDILTAKPWEKDPHYFKHIKVSALALLKMVMHSRSGGNLE] 73 # sequence of block unknown_C 74 [MGLLLGKVDG] 84 # sequence of block unknown_D 84 [NTMIVMDSFALPVEGTETRVNAQAQAYEYMAAYTEAAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQM] 153 # sequence of block unknown_E 154 [NQQFQEPFVAIVVDPVRTISAGKVNIGAFRTYPK] 188 # sequence of block unknown_G 195 [GPSEYQSIPLNKIEDFGVHCK] 216 # sequence of block unknown_H 216 [HYYSLEMSYFKSVADRKLLESLWNKYWVNTLSSSSLLTNADYTTGQIFDLADKLEQSEVQLCRGGF] 282 # sequence of block unknown_I 291 [KSEDKLAKATKDGCKTTMEAIHGLMSQVIKDRLFN] 326 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GIK.prfl --predictionStart=5652 --predictionEnd=48006 --species=fly ./tmp/Contig6268920180911_busco_2432604931_.temp