# 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 # --[5..512]--> unknown_A (18) <--[0..1]--> unknown_B (8) <--[0..1]--> unknown_C (13) <--[0..25]--> unknown_D (77) <--[18..113]--> unknown_E (20) <--[0..6]--> unknown_F (16) <--[2..3]--> unknown_G (16) <--[3..8]--> unknown_H (18) <--[0..27]--> unknown_I (26) <--[3..77]--> unknown_J (18) <--[2..8]--> unknown_K (42) <--[10..13]--> unknown_L (11) <--[0..85]--> unknown_M (12) <--[0..1]--> unknown_N (23) <--[14..79]--> unknown_P (23) <--[1..4]--> unknown_Q (13) <--[5..12]--> unknown_R (20) <--[1..2]--> unknown_S (7) <--[0..7]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2483820180911_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 = 17927, name = Contig24838) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig24838 AUGUSTUS gene 3946 17898 0.01 + . g1 Contig24838 AUGUSTUS transcript 3946 17898 0.01 + . g1.t1 Contig24838 AUGUSTUS tss 3946 3946 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 3946 4289 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS start_codon 4025 4027 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 4290 4386 0.23 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 4583 9909 0.21 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 10043 10652 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 10936 11023 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 11142 11843 0.14 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 12017 12326 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 12614 12936 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 13120 13421 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 13452 13641 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 13672 13738 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 13806 14166 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 14228 14278 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 14311 15209 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 15241 15369 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 15445 15507 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 15525 15580 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 15616 15853 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 15884 16203 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 16221 16640 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 16675 16878 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 16923 17735 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS intron 17751 17796 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 4025 4289 0.35 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 4387 4582 0.23 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 4387 4582 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 9910 10042 0.41 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 9910 10042 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 10653 10935 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 10653 10935 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 11024 11141 0.11 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 11024 11141 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 11844 12016 0.95 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 11844 12016 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 12327 12613 0.03 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 12327 12613 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 12937 13119 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 12937 13119 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 13422 13451 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 13422 13451 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 13642 13671 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 13642 13671 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 13739 13805 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 13739 13805 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 14167 14227 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 14167 14227 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 14279 14310 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 14279 14310 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 15210 15240 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 15210 15240 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 15370 15444 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 15370 15444 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 15508 15524 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 15508 15524 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 15581 15615 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 15581 15615 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 15854 15883 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 15854 15883 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 16204 16220 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 16204 16220 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 16641 16674 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 16641 16674 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 16879 16922 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 16879 16922 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 17736 17750 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 17736 17750 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS CDS 17797 17827 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS exon 17797 17898 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS stop_codon 17825 17827 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS tts 17898 17898 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 10755 10808 3.51 + 0 target "unknown_A[1..18]"; target_start 232; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 10809 10832 3.78 + 0 target "unknown_B[1..8]"; target_start 250; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 10833 10871 4.52 + 0 target "unknown_C[1..13]"; target_start 258; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 10872 10935 3.73 + 0 target "unknown_D[1..22]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 11024 11141 5.26 + 1 target "unknown_D[22..61]"; target_start 270; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 11844 11892 4.74 + 1 target "unknown_D[61..77]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 11965 12016 6.5 + 0 target "unknown_E[1..18]"; target_start 372; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12327 12334 0.743 + 2 target "unknown_E[18..20]"; target_start 372; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12341 12388 5.18 + 0 target "unknown_F[1..16]"; target_start 394; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12398 12445 4.41 + 0 target "unknown_G[1..16]"; target_start 413; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12458 12511 5.06 + 0 target "unknown_H[1..18]"; target_start 433; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12512 12589 4.94 + 0 target "unknown_I[1..26]"; target_start 451; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 12943 12996 4.56 + 0 target "unknown_J[1..18]"; target_start 487; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 13003 13119 3.77 + 0 target "unknown_K[1..39]"; target_start 507; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 13422 13430 1.42 + 0 target "unknown_K[40..42]"; target_start 507; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 13654 13671 1.11 + 0 target "unknown_L[1..6]"; target_start 560; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 13739 13753 1.49 + 0 target "unknown_L[7..11]"; target_start 560; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 14199 14227 1.03 + 0 target "unknown_M[1..10]"; target_start 599; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 14279 14285 0.273 + 1 target "unknown_M[10..12]"; target_start 599; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 14286 14310 1.04 + 0 target "unknown_N[1..9]"; target_start 611; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15210 15240 1.38 + 1 target "unknown_N[9..19]"; target_start 610; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15370 15382 0.712 + 1 target "unknown_N[19..23]"; target_start 611; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15431 15444 0.722 + 0 target "unknown_P[1..5]"; target_start 650; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15508 15524 0.918 + 0 target "unknown_P[6..11]"; target_start 649; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15581 15615 1.41 + 1 target "unknown_P[11..23]"; target_start 649; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15854 15856 1.07 + 0 target "unknown_P[23..23]"; target_start 650; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 15869 15883 0.87 + 0 target "unknown_Q[1..5]"; target_start 677; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 16204 16220 1.54 + 2 target "unknown_Q[6..11]"; target_start 676; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 16641 16647 0.174 + 1 target "unknown_Q[11..13]"; target_start 677; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 16663 16674 1.15 + 0 target "unknown_R[1..4]"; target_start 695; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 16879 16922 1.14 + 2 target "unknown_R[5..19]"; target_start 694; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 17736 17739 0.138 + 1 target "unknown_R[19..20]"; target_start 695; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 17743 17750 0.192 + 0 target "unknown_S[1..3]"; target_start 716; transcript_id "g1.t1"; gene_id "g1"; Contig24838 AUGUSTUS protein_match 17797 17809 1.25 + 1 target "unknown_S[3..7]"; target_start 716; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggtccaaagtccaacagccatctggcagcactattgtcatggtcccaaagtccaacagcatcactgtcatttgtcca # gaagtcgcaacagcatcactgtcaatggttcaaagcccagcatactgcacaatctttgtcatagtccaaagtccaacagcaatactgtcatggtccaa # aagcccaacagcatcatgtccatggtcgcaagccaacacggcatcaactgtcatggtccaaagcccaacacatcaattgtccagtcattgtctgtatg # gtccaaagcccaacagcatcatgtccatggtccaaatcccaacaacatacgtgtcatcgtcgcaaagccaacagcatcatctgtcatggtccaaagcc # cacaacaatcactgtgcatggtcccagaaagcccacagcaatcatttgtcatggctccaaagtctccagagcagcaattactgtcacttgatgatatt # gggattttggagagagtgtctggcatggcagtgacctccattgtacatgaaaggataaagaaccacattgaaaacacatgtaaaggcaactttgagac # ctcatacctaaagagtctagaggagtggctggacaggaaagtcttaggctggctcagattggttttctccgaaaactgcaaaaacacacacacagaat # gtatagagggatttaaagggagactactgcactttatgtttgaaacctttgctagaactcacattgatcagctgtttaacatcattattgagttccct # gagtcggagcctgctattctggacttgaagatctgcctagagaagacagacctaagggggacccttgtctcatctcttaagactgccctggagacccg # ccttttgcatccaggtgtgaatacatccgacattttgacagcttacatagctgctatccgtgcactccggatattggatccagttggagttatactag # agcttgtgtgtgatccagttagaaagtatttaaggtcaagggacgacactgttagacagattgtatccaatctgacggatgatggcagtaatgagttg # ctggatgagcttcagaagggtcatcctctgctggatgacggctgtagtagtgatgatgaactggatgactgggagagttggatgccagatcctgtgga # tgcggatccacgaagcacctcaaaaagccgaagggcctcagatatcatcagtatgttggtcaacatttatggaagcaaggaactttttgtacaagaat # atcgaacactgctagcagatcgaattttgacacagtttaactatgaaattgtgaaagaaatccgctatcttgagctcttgaaattaagatttggagaa # tctcagcttcattattgtgaggttatgttaaaggatgtggctgattccaaaagactgaactcgaggattatggatgtgaggaaaaaatcggcagagag # agaggagattgaagtaaatgcaatggtcctctcagcccagttttggcccgccttcagagaagagaagataaagttaccagatgtcatgcagaaattgt # tggaggaatacaccaagaagtttgaaaccctgaaagggaacagaacactcaattggaagcctcatttaggtaaagtaaaaggaaaaatgaaactaggg # catagatttttcagaaaattgactgaacttatgcatttgtgtgtctgttttgcatttgaaacttatacttttcaatttgtcttggacctaaccaaggt # agtaaaaatcaaggtcactgtacctcaacttacaaagtcgtaccttaattacactcactctacaagtcgtgaccttctaattcgtgacctttctaatg # tcacctcactacaaaaaatacttgcatattatgtgaacatgatcacagtgtttcgtcccctatcgtctctgtacacagaggttgtggaggatcattca # gtgtgtcataaccctgaaccaaggaaaaaaaatattataaatgtacagactgtcatcaacatgctgcaacaattttcacaaggttattatatgatatt # taaggaattcatgagaattgttagacataatctgcgtaaaacgcgtagtcgttatcatctttcaaaattcctcagaatttcagaaaaatctcttaaaa # tattccgggccctagcgctttacagcgtagatattcaaaagccgttttga] # protein sequence = [MVQSPTAIWQHYCHGPKVQQHHCHLSRSRNSITVNGSKPSILHNLCHSPKSNSNTVMVQKPNSIMSMVASQHGINCHG # PKPNTSIVQSLSVWSKAQQHHVHGPNPNNIRVIVAKPTASSVMVQSPQQSLCMVPESPQQSFVMAPKSPEQQLLSLDDIGILERVSGMAVTSIVHERI # KNHIENTCKGNFETSYLKSLEEWLDRKVLGWLRLVFSENCKNTHTECIEGFKGRLLHFMFETFARTHIDQLFNIIIEFPESEPAILDLKICLEKTDLR # GTLVSSLKTALETRLLHPGVNTSDILTAYIAAIRALRILDPVGVILELVCDPVRKYLRSRDDTVRQIVSNLTDDGSNELLDELQKGHPLLDDGCSSDD # ELDDWESWMPDPVDADPRSTSKSRRASDIISMLVNIYGSKELFVQEYRTLLADRILTQFNYEIVKEIRYLELLKLRFGESQLHYCEVMLKDVADSKRL # NSRIMDVRKKSAEREEIEVNAMVLSAQFWPAFREEKIKLPDVMQKLLEEYTKKFETLKGNRTLNWKPHLGKVKGKMKLGHRFFRKLTELMHLCVCFAF # ETYTFQFVLDLTKVVKIKVTVPQLTKSYLNYTHSTSRDLLIRDLSNVTSLQKILAYYVNMITVFRPLSSLYTEVVEDHSVCHNPEPRKKNIINVQTVI # NMLQQFSQGYYMIFKEFMRIVRHNLRKTRSRYHLSKFLRISEKSLKIFRALALYSVDIQKPF] # sequence of block unknown_A 232 [HFMFETFARTHIDQLFNI] 250 # sequence of block unknown_B 250 [IIEFPESE] 258 # sequence of block unknown_C 258 [PAILDLKICLEKT] 271 # sequence of block unknown_D 271 [DLRGTLVSSLKTALETRLLHPGVNTSDILTAYIAAIRALRILDPVGVILELVCDPVRKYLRSRDDTVRQIVSNLTDD] 348 # sequence of block unknown_E 372 [ELDDWESWMPDPVDADPRST] 392 # sequence of block unknown_F 394 [SRRASDIISMLVNIYG] 410 # sequence of block unknown_G 413 [LFVQEYRTLLADRILT] 429 # sequence of block unknown_H 433 [EIVKEIRYLELLKLRFGE] 451 # sequence of block unknown_I 451 [SQLHYCEVMLKDVADSKRLNSRIMDV] 477 # sequence of block unknown_J 487 [EVNAMVLSAQFWPAFREE] 505 # sequence of block unknown_K 507 [KLPDVMQKLLEEYTKKFETLKGNRTLNWKPHLGKVKGKMKLG] 549 # sequence of block unknown_L 560 [HLCVCFAFETY] 571 # sequence of block unknown_M 599 [THSTSRDLLIRD] 611 # sequence of block unknown_N 611 [LSNVTSLQKILAYYVNMITVFRP] 634 # sequence of block unknown_P 650 [NPEPRKKNIINVQTVINMLQQFS] 673 # sequence of block unknown_Q 677 [MIFKEFMRIVRHN] 690 # sequence of block unknown_R 695 [SRYHLSKFLRISEKSLKIFR] 715 # sequence of block unknown_S 716 [LALYSVD] 723 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370EL3.prfl --predictionStart=0 --predictionEnd=32580 --species=fly ./tmp/Contig2483820180911_busco_2432604931_.temp