# 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 # --[6..630]--> unknown_A (44) <--[1..61]--> unknown_B (26) <--[0..1]--> unknown_C (33) <--[4..17]--> unknown_D (24) <--[0..1244]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig36720180911_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 = 26141, name = Contig367) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig367 AUGUSTUS gene 2208 4605 0.01 - . g1 Contig367 AUGUSTUS transcript 2208 4605 0.01 - . g1.t1 Contig367 AUGUSTUS tts 2208 2208 . - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS exon 2208 2602 . - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS stop_codon 2381 2383 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS intron 2603 2798 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS intron 3824 3936 0.85 - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS CDS 2381 2602 0.78 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS CDS 2799 3823 0.87 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS exon 2799 3823 . - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS CDS 3937 4255 0.91 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS exon 3937 4273 . - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS start_codon 4253 4255 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS exon 4552 4605 . - . transcript_id "g1.t1"; gene_id "g1"; Contig367 AUGUSTUS tss 4605 4605 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggccgaccaatctgaacaagggccaacagtggatgatgacaacaagagtaccaaaagtgggccaaaaagtcaaacag # gatcaaagccagtttctagggctgggtctgcacagtccggaaaaagcggtaaaagtgggggaagcaaaaaagctggagatgcccctgttcctccatcc # ccaactggatcggccaaggataatccggcagctgactggaggaccatgaggagaataattgctgaggacccagaatattccctagcaacagtgccaag # actcattgagctatgcatttcacacattgtgtccaattttgagaataattcaacaatcttaaacaatcttctaccaaaacacaagtcgatagttcttg # aaaagatatcaactgacctaccgctgaagatcacagctaatcttgtggaggatgaaggatattggaagcgctgctgcaaagcccgctggcaaatctgt # gatgtagctgcatatggcaacaactggaagcgaatgtactttgaaagaaatctccaacaaatcattgaacactttgtaccagaatcaacagacatgac # agaactaaacgagactcttccattatcggctaattatgtcaagaaattggatattagacagctccttcctccagtgagggaggcccccaaaggtccag # atttcgatgatgcctcagatgctgggagtgaggccggagatgaaccagaatgtgatcattttaactttgggccaattttgaaacagctgccaaatata # gaagaacttcatttaacgtatggagtgaaagactgtggtatgaattttgaatggaacttatttaatttcactgctagagactgtttacttctggctca # atgtgtggctgccacaaaaggactcaaagttttcaggttgcacagaagcaaagtggacgatgataaagtccgagtgctgatcagtcacatactggacc # accctgctttgattgagttagatctgtcccacaatgtgatcagtgaccgcggtgccagggcgataggaaagttcctcaataatcacagccagctagtt # aagctgaacctctgtgataatgatgtgagacacagcggtgcccaggccatagcccatgccctgacgaaaaactcaacgttgaccgatttgaacattcg # actgaatcgtttgggagatgagggaggacaagctgtctgtaaagctttactaaagaacacaactctctgtaatgtaaacatggctagtagtgatctag # gagaaccaacggctgctattttctcccaagttgtcatgcagaacacaaccctcaaggctgtggatctgtcatcaaacagacttggtgcagagggtgga # aagcaaatccaggagggaatggaggacaataccactattacacacatggaccttaggctgaccgactctgggcaagaagctgagtactgtattaacca # gattctgcaccgaaaccaggaaagagagcgggaaagcaagatttctgagcccccaccaccttccaagaaaattcagcctcaagctgcccacaggttta # aaccaacaaaggcctaa] # protein sequence = [MADQSEQGPTVDDDNKSTKSGPKSQTGSKPVSRAGSAQSGKSGKSGGSKKAGDAPVPPSPTGSAKDNPAADWRTMRRI # IAEDPEYSLATVPRLIELCISHIVSNFENNSTILNNLLPKHKSIVLEKISTDLPLKITANLVEDEGYWKRCCKARWQICDVAAYGNNWKRMYFERNLQ # QIIEHFVPESTDMTELNETLPLSANYVKKLDIRQLLPPVREAPKGPDFDDASDAGSEAGDEPECDHFNFGPILKQLPNIEELHLTYGVKDCGMNFEWN # LFNFTARDCLLLAQCVAATKGLKVFRLHRSKVDDDKVRVLISHILDHPALIELDLSHNVISDRGARAIGKFLNNHSQLVKLNLCDNDVRHSGAQAIAH # ALTKNSTLTDLNIRLNRLGDEGGQAVCKALLKNTTLCNVNMASSDLGEPTAAIFSQVVMQNTTLKAVDLSSNRLGAEGGKQIQEGMEDNTTITHMDLR # LTDSGQEAEYCINQILHRNQERERESKISEPPPPSKKIQPQAAHRFKPTKA] # end gene g1 ### # start gene g2 Contig367 AUGUSTUS gene 4786 13601 0.01 + . g2 Contig367 AUGUSTUS transcript 4786 13601 0.01 + . g2.t1 Contig367 AUGUSTUS tss 4786 4786 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS exon 4786 4898 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS start_codon 4856 4858 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS intron 4899 6122 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS intron 6214 12484 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS intron 12588 12731 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS intron 12865 13130 0.04 + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS CDS 4856 4898 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS CDS 6123 6213 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS exon 6123 6213 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS CDS 12485 12587 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS exon 12485 12587 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS CDS 12732 12864 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS exon 12732 12864 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS CDS 13131 13303 0.1 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS exon 13131 13601 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS stop_codon 13301 13303 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS tts 13601 13601 . + . transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 4895 4898 7.78 + 0 target "unknown_A[1..2]"; target_start 13; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 6123 6213 4.67 + 1 target "unknown_A[2..32]"; target_start 12; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 12485 12521 5.9 + 1 target "unknown_A[32..44]"; target_start 13; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 12528 12587 7.54 + 0 target "unknown_B[1..20]"; target_start 59; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 12732 12749 3.88 + 0 target "unknown_B[21..26]"; target_start 59; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 12750 12848 4.07 + 0 target "unknown_C[1..33]"; target_start 85; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 12864 12864 1 + 0 target "unknown_D[1..1]"; target_start 123; transcript_id "g2.t1"; gene_id "g2"; Contig367 AUGUSTUS protein_match 13131 13201 7.9 + 2 target "unknown_D[1..24]"; target_start 123; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgaaagctataattcagagagttacccaagcaagcgttacagttggtgaggaaacagtcagttccattggacaaggat # tatgtgtcttgattgggattgcaagaagtgatacagagaaggaacttgaatacatggcaaggaaaatattaaatattcggctgtttgatggagatgat # ggaaagagatggaacaagagtgttattgataaacagctcgaagtattatgtgtcagccagttcacactctctgcaattctgaaaggaaacaagccaga # cttccatgaagccatgggtcctgaaacttctgaaaaggcataccaggattttctgcagattatgaaaaactcctatagtccagataaaattaaagatg # gtaaatttggggcctacatgcaggtacatatacagaatgatggcccagtaacaatacccatagaatctccagccaatctaccggaacggaaaaagaag # actgcctttgtagcaccatccgtccattcactgtccatagcttcaaaagagggagatgactcaggttcttga] # protein sequence = [MKAIIQRVTQASVTVGEETVSSIGQGLCVLIGIARSDTEKELEYMARKILNIRLFDGDDGKRWNKSVIDKQLEVLCVS # QFTLSAILKGNKPDFHEAMGPETSEKAYQDFLQIMKNSYSPDKIKDGKFGAYMQVHIQNDGPVTIPIESPANLPERKKKTAFVAPSVHSLSIASKEGD # DSGS] # sequence of block unknown_A 13 [TVGEETVSSIGQGLCVLIGIARSDTEKELEYMARKILNIRLFDG] 57 # sequence of block unknown_B 59 [GKRWNKSVIDKQLEVLCVSQFTLSAI] 85 # sequence of block unknown_C 85 [LKGNKPDFHEAMGPETSEKAYQDFLQIMKNSYS] 118 # sequence of block unknown_D 123 [DGKFGAYMQVHIQNDGPVTIPIES] 147 # end gene g2 ### # start gene g3 Contig367 AUGUSTUS gene 15466 19715 0.02 - . g3 Contig367 AUGUSTUS transcript 15466 19715 0.02 - . g3.t1 Contig367 AUGUSTUS tts 15466 15466 . - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS exon 15466 17439 . - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS stop_codon 17337 17339 . - 0 transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS intron 17440 17752 0.96 - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS intron 17847 18745 0.31 - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS CDS 17337 17439 0.91 - 1 transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS CDS 17753 17846 0.94 - 2 transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS exon 17753 17846 . - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS CDS 18746 19625 0.33 - 0 transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS exon 18746 19715 . - . transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS start_codon 19623 19625 . - 0 transcript_id "g3.t1"; gene_id "g3"; Contig367 AUGUSTUS tss 19715 19715 . - . transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgaaacaagacattaactgcttcatcatgaagaaattacgaatgatgcgtcagaataatattctatgtgatttggaag # tgttatctggcgacggaacaaaacgtcgcgtccatagctgtgtctgggttgcagcgtttgaagacaatcgaactcttcaatcaaatgaatacaaagga # tgtggaaatgaaacctcagaaataaaactgaacaacattagtggagatgtactgtcaacaattgtagatttcatatacggtgaggaaataaagataat # tccagtaggactagatgatgcattgaaacgactaggatttcatggattgacatactatctcgacaatggtctgtctaatctatcatgcagtcaagcaa # gttcactgacagttacacaacattcagatgagacagatattgagatcccaaaacgacaattgaactccaacgacacccaggcaaagtctgaccagagc # attaatgaagtgaaagttaaatctgaaaggatagaagaagataattcatctgtatcccttgatactggaaatcatgaaaaagaagatttatctaaaat # ccatacaaccccggtcaatgtcaagcttgaacctgttgagatgtcagattctttaagtttcaatacagatgatgaaaatgatgatggaatgaataata # tcaaaatatattcaaaacaagatggagatgatcaaacagtcacagtttgtgtggaatatgactgttcagagaatgatgagagcgagattgtgcaaatg # gatgaaacgaactcaatccaactttcacatgctcccgatgatataactcctgaaaatgacaaacatgaaaaagataaatgggcaactcaacttctgca # gcaagacagtgctgtagtctggtcaattcataccattatcttcaatgacaacaccagtgacctcagtatcacaatcaagtggtttaaagactgtggtc # ccgtcaaaaccaggttcttgaagcgtaagaaacctgtagatatggttgctgaactttacaagaattctggtggagggacaacaaggagtacatcaaac # gactctatgaaatcttga] # protein sequence = [MKQDINCFIMKKLRMMRQNNILCDLEVLSGDGTKRRVHSCVWVAAFEDNRTLQSNEYKGCGNETSEIKLNNISGDVLS # TIVDFIYGEEIKIIPVGLDDALKRLGFHGLTYYLDNGLSNLSCSQASSLTVTQHSDETDIEIPKRQLNSNDTQAKSDQSINEVKVKSERIEEDNSSVS # LDTGNHEKEDLSKIHTTPVNVKLEPVEMSDSLSFNTDDENDDGMNNIKIYSKQDGDDQTVTVCVEYDCSENDESEIVQMDETNSIQLSHAPDDITPEN # DKHEKDKWATQLLQQDSAVVWSIHTIIFNDNTSDLSITIKWFKDCGPVKTRFLKRKKPVDMVAELYKNSGGGTTRSTSNDSMKS] # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09371330.prfl --predictionStart=0 --predictionEnd=32863 --species=fly ./tmp/Contig36720180911_busco_2432604931_.temp