# 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 # --[1..188]--> unknown_A (19) <--[0..3]--> unknown_B (10) <--[2..3]--> unknown_C (7) <--[0..4]--> unknown_D (9) <--[9..24]--> unknown_E (27) <--[16..102]--> unknown_G (11) <--[10..15]--> unknown_I (27) <--[0..3]--> unknown_J (23) <--[0..2]--> unknown_K (38) <--[4..132]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5249320180911_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 = 23428, name = Contig52493) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig52493 AUGUSTUS gene 2616 8899 0.01 + . g1 Contig52493 AUGUSTUS transcript 2616 8899 0.01 + . g1.t1 Contig52493 AUGUSTUS tss 2616 2616 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 2616 2633 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 3196 3254 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 4207 4274 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS start_codon 4240 4242 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS intron 4275 5927 0.39 + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS intron 6076 6787 0.5 + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS intron 6924 7571 0.51 + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS CDS 4240 4274 0.26 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS CDS 5928 6075 0.38 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 5928 6075 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS CDS 6788 6923 0.55 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 6788 6923 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS CDS 7572 7906 0.52 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS exon 7572 8899 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS stop_codon 7904 7906 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52493 AUGUSTUS tts 8899 8899 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcatatcgttgcgataggtaatctcggcctcagacacccgtccaatttgatgctggacaggacaagtgggaaagtga # tccacattgattttggcgactgttttgaggtcgccatggtgagggaaaagtttcctgagaagatacctttccgtctgactcgcatgctgatcaatgcc # atggaggtgacaggtattgatgggaactacaagatgacgtgtgagagtgttatggatgtcctgagagaacacaaggacagtctgatggccgtcctgga # agccttcgtgtacgaccccctactcaactggaggctcatggacacgacagccaagggaaaaacaaaaaccaaagagtcgtactccgggggaagtcagg # aacagacagacatgctggaaaacgtggacctcagtcaggccacacataaacgctccgccccagaagctgttaattccatcaatggcgaaaactttcag # tcggaggtcatcaacaagaaggccctgtctattattaaccgcgtccgggacaaactgaccggccgggacttctccttgggggatcccatcgatgtccc # tacccaggtggaactcctcatcaaacaggccacctcccacgaaaatctgtgtcagtgttacattggctggtgtcctttctggtga] # protein sequence = [MHIVAIGNLGLRHPSNLMLDRTSGKVIHIDFGDCFEVAMVREKFPEKIPFRLTRMLINAMEVTGIDGNYKMTCESVMD # VLREHKDSLMAVLEAFVYDPLLNWRLMDTTAKGKTKTKESYSGGSQEQTDMLENVDLSQATHKRSAPEAVNSINGENFQSEVINKKALSIINRVRDKL # TGRDFSLGDPIDVPTQVELLIKQATSHENLCQCYIGWCPFW] # end gene g1 ### # start gene g2 Contig52493 AUGUSTUS gene 9980 20205 0.01 - . g2 Contig52493 AUGUSTUS transcript 9980 20205 0.01 - . g2.t1 Contig52493 AUGUSTUS tts 9980 9980 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 9980 12253 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS stop_codon 11844 11846 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 12254 13176 0.2 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 13297 13425 0.11 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 13487 14601 0.15 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 14719 14889 0.56 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 14986 15968 0.15 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 16078 16476 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 16598 16915 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 16938 17807 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS intron 17889 19871 0.05 - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 11844 12253 0.63 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 13177 13296 0.22 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 13177 13296 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 13426 13486 0.15 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 13426 13486 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 14602 14718 0.75 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 14602 14718 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 14890 14985 0.54 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 14890 14985 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 15969 16077 0.12 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 15969 16077 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 16477 16597 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 16477 16597 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 16916 16937 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 16916 16937 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 17808 17888 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 17808 17888 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS CDS 19872 20144 0.15 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS exon 19872 20205 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS start_codon 20142 20144 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS tss 20205 20205 . - . transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 12096 12209 3.97 - 0 target "unknown_K[1..38]"; target_start 348; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 12216 12253 5.12 - 2 target "unknown_J[11..23]"; target_start 323; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 13177 13207 4.11 - 0 target "unknown_J[1..11]"; target_start 323; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 13217 13296 3.63 - 2 target "unknown_I[1..27]"; target_start 293; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 13426 13426 1 - 0 target "unknown_I[1..1]"; target_start 293; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 13460 13486 7.44 - 0 target "unknown_G[3..11]"; target_start 271; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 14602 14607 2.81 - 0 target "unknown_G[1..2]"; target_start 271; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16029 16077 2.08 - 1 target "unknown_E[11..27]"; target_start 155; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16477 16508 2.3 - 0 target "unknown_E[1..11]"; target_start 155; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16551 16577 2.99 - 0 target "unknown_D[1..9]"; target_start 132; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16590 16597 0.941 - 2 target "unknown_C[5..7]"; target_start 121; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16916 16928 0.817 - 0 target "unknown_C[1..5]"; target_start 121; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 16935 16937 1.37 - 0 target "unknown_B[10..10]"; target_start 109; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 17808 17834 2.78 - 0 target "unknown_B[1..9]"; target_start 109; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 17835 17888 4.33 - 0 target "unknown_A[2..19]"; target_start 90; transcript_id "g2.t1"; gene_id "g2"; Contig52493 AUGUSTUS protein_match 19872 19874 3.69 - 0 target "unknown_A[1..1]"; target_start 90; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgccgcgtgtccgtcccaaatacgagttgtgtgtggggtttgatgaggaggaggtcagcgaggaggaagctggcgggg # aggagtgtggtcaggaaacggaagctccaagggaggaggagtttaacattcggcgggtatggcatgagctgaaaaaagaagaagcggacagattgcgg # gaaaaagaggacaagaaacgagcaggggctatacgacataacaacgaacaggccaaacagcgcagctcctttctcgcctggaaaaataagattcagga # taatgaaaaacccacaaaggaagaatatgccatcgctaaacatcttcgatttaaatgcccggtcaaagaggcgaagtttgagacgtacaatcattaca # cagtcctgtttaaattaacaggaaatcaggccattgacactttgatggattcaaaatgggcaaaatcctccaagagtgaaattcagtttacagacagg # aaatcgtgtgtttatttcttggaaaggttaatggtgaaaggactatttcatcgagccacgaaaatagaaagaggcaaaaaggacaaagataaattgcg # gaagaaaaagagagaagaagaaccggaggaggataaggagaagaaaagcaaaaaagagaaaaaaaagataaaggataaagatgctaaggattcagacg # cagacaaacctgcagacactcctgaggacaagaaggtggaagagaaagataagaagaaagatgaaccaaagaaggaggaagaaaagaaaaagaaagag # aagaaactaagattagacatggcggacgaacagcgtttcattgatggggaggagatatatgtgtggatatatgacccagtgccaatgtctacatttct # catcggactcttgatggtactgggggcggccctgctctgtgtgtttcccctgtggccggactggttgagggtggccgtatactacatcagtttagtgg # gagccagttttgttggcttcatcttgttcttggctgtcattcgtggcattctgttttgtgttctatgggctttgactctgggcaaagtgcatctatgg # attctaccaaatctaacagaagatgtgggattctttgactcatttaagccattatatacatacaaagtgatgaacaaggaagagcaggaaaaagagaa # aaagaagaaagaagaaaagagaaaaaagaaaaagaaacgagaggaagaggggggtgactcggagagtgagataaatgataagaatgaggaccaaggtg # aggttcaggaccgtggggaggaagaggctcaaaacggggaccaggaatttgaaatggtgcagagggaggagcttgaagatgaggatcaggaagaggag # gggtcagaggaaggggagggaactgaggcagaggaggaggacaaaaagactaagtga] # protein sequence = [MPRVRPKYELCVGFDEEEVSEEEAGGEECGQETEAPREEEFNIRRVWHELKKEEADRLREKEDKKRAGAIRHNNEQAK # QRSSFLAWKNKIQDNEKPTKEEYAIAKHLRFKCPVKEAKFETYNHYTVLFKLTGNQAIDTLMDSKWAKSSKSEIQFTDRKSCVYFLERLMVKGLFHRA # TKIERGKKDKDKLRKKKREEEPEEDKEKKSKKEKKKIKDKDAKDSDADKPADTPEDKKVEEKDKKKDEPKKEEEKKKKEKKLRLDMADEQRFIDGEEI # YVWIYDPVPMSTFLIGLLMVLGAALLCVFPLWPDWLRVAVYYISLVGASFVGFILFLAVIRGILFCVLWALTLGKVHLWILPNLTEDVGFFDSFKPLY # TYKVMNKEEQEKEKKKKEEKRKKKKKREEEGGDSESEINDKNEDQGEVQDRGEEEAQNGDQEFEMVQREELEDEDQEEEGSEEGEGTEAEEEDKKTK] # sequence of block unknown_K 348 [KVHLWILPNLTEDVGFFDSFKPLYTYKVMNKEEQEKEK] 386 # sequence of block unknown_J 323 [FVGFILFLAVIRGILFCVLWALT] 346 # sequence of block unknown_I 293 [VLGAALLCVFPLWPDWLRVAVYYISLV] 320 # sequence of block unknown_G 271 [EEIYVWIYDPV] 282 # sequence of block unknown_E 155 [DRKSCVYFLERLMVKGLFHRATKIERG] 182 # sequence of block unknown_D 132 [NQAIDTLMD] 141 # sequence of block unknown_C 121 [NHYTVLF] 128 # sequence of block unknown_B 109 [KCPVKEAKFE] 119 # sequence of block unknown_A 90 [QDNEKPTKEEYAIAKHLRF] 109 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QCX.prfl --predictionStart=0 --predictionEnd=32212 --species=fly ./tmp/Contig5249320180911_busco_2432604931_.temp