# 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..16]--> unknown_A (7) <--[1..2]--> unknown_B (27) <--[0..9]--> unknown_C (18) <--[0..3]--> unknown_D (57) <--[0..4]--> unknown_E (18) <--[6..9]--> unknown_G (26) <--[1..5]--> unknown_H (19) <--[7..16]--> unknown_I (8) <--[0..7]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig1876420180911_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 = 26929, name = Contig18764) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig18764 AUGUSTUS gene 246 3009 0.04 + . g1 Contig18764 AUGUSTUS transcript 246 3009 0.04 + . g1.t1 Contig18764 AUGUSTUS tss 246 246 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 246 491 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 849 882 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS start_codon 872 874 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS intron 883 985 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS intron 1130 1330 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS intron 1455 2469 0.66 + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS intron 2587 2644 0.89 + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS CDS 872 882 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS CDS 986 1129 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 986 1129 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS CDS 1331 1454 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 1331 1454 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS CDS 2470 2586 0.87 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 2470 2586 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS CDS 2645 2740 0.94 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS exon 2645 3009 . + . transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS stop_codon 2738 2740 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig18764 AUGUSTUS tts 3009 3009 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgggagggggaaatgaagtgacaaagcttcaagaggagttgtcccaggtgacgatgcattacgacagtcgcagtgaag # attacaagcttctggaggacaaactggagtcgaccaaacgagagtacgacggccacatcaaccaactaatcaagagtaatgagcagctgaatagtctt # gtgaatgaggagattaataaattgaaggatttcatccagaacagaactatggccagtgttccaggcaatgccactattgaagaggaactatatgatgc # tcagctccttcctttcaccacagagcccgtagtccaagcccaactccacaaaatccaacaaagaaagatgaacatcaaagtcgtgactctcacaaacg # gcgttgtcatctggatgttaaagtcctcctctggatcacttacagaacatcatgatctttttagtcctgtcctggagatctacaaacatcagatcttt # ttgtcctctctggatcgctaa] # protein sequence = [MGGGNEVTKLQEELSQVTMHYDSRSEDYKLLEDKLESTKREYDGHINQLIKSNEQLNSLVNEEINKLKDFIQNRTMAS # VPGNATIEEELYDAQLLPFTTEPVVQAQLHKIQQRKMNIKVVTLTNGVVIWMLKSSSGSLTEHHDLFSPVLEIYKHQIFLSSLDR] # end gene g1 ### # start gene g2 Contig18764 AUGUSTUS gene 10696 22390 0.01 + . g2 Contig18764 AUGUSTUS transcript 10696 22390 0.01 + . g2.t1 Contig18764 AUGUSTUS tss 10696 10696 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 10696 11080 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 12172 13213 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS start_codon 13189 13191 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 13214 14999 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 15048 15275 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 15316 15593 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 15646 16137 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 16214 17603 0.09 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 17708 17860 0.85 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 18064 18804 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS intron 18851 19543 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 13189 13213 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 15000 15047 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 15000 15047 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 15276 15315 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 15276 15315 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 15594 15645 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 15594 15645 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 16138 16213 0.07 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 16138 16213 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 17604 17707 0.08 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 17604 17707 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 17861 18063 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 17861 18063 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 18805 18850 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 18805 18850 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS CDS 19544 19576 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 19544 19746 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS stop_codon 19574 19576 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS exon 21785 22390 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS tts 22390 22390 . + . transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 13192 13212 8.24 + 0 target "unknown_A[1..7]"; target_start 1; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 15002 15047 7.39 + 0 target "unknown_B[1..16]"; target_start 9; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 15276 15310 9.52 + 2 target "unknown_B[16..27]"; target_start 9; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 15595 15645 9.94 + 0 target "unknown_C[1..17]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 16138 16140 1.01 + 0 target "unknown_C[18..18]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 16150 16213 6.06 + 0 target "unknown_D[1..22]"; target_start 59; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 17604 17707 7.15 + 1 target "unknown_D[22..57]"; target_start 58; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 17861 17863 10.6 + 0 target "unknown_D[57..57]"; target_start 59; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 17876 17929 8.44 + 0 target "unknown_E[1..18]"; target_start 120; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 17948 18025 3.25 + 0 target "unknown_G[1..26]"; target_start 144; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 18035 18063 2.43 + 0 target "unknown_H[1..10]"; target_start 173; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 18805 18832 3.78 + 1 target "unknown_H[10..19]"; target_start 173; transcript_id "g2.t1"; gene_id "g2"; Contig18764 AUGUSTUS protein_match 19550 19573 7.06 + 0 target "unknown_I[1..8]"; target_start 200; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggtttattatttcactagcaatgttgtatccccagcgtacactatatacatgggtgaagataagcatgaaaacgagg # aacttattagatggggttttcctgaagatgtctggttccatgttgacaagctctcctctgcacatgtgtatcttaggttacatttaaatgaaacattg # gatgatgttccacaatctgtgatagatgactgtgcacagcttgtaaaggcaaacagtatctcaggtaacaaaatgaataacctagaagttgtgtacac # aatgtgggctaaccttaagaaaactcagggcatggatgttgggcaggtcggattcttcaaggataaagaggtcagaaaagtgaaaatagagaaaagaa # taaatgaaatagttaacaggttaaataaaacgaaaacagaagatcaccccgatttccgtaagctaagggaagatcgagatcgggaggaaagagacaat # caaaagaagaagatggcggagcagaggaagcgagagagggaggcagaggaacagaaaaagaaagactcggaaatacgatcatatgcaagtttaatgag # acctgaaaatatgcaatcaaatcaagatgatggcaacgactcggatgattttatgtga] # protein sequence = [MVYYFTSNVVSPAYTIYMGEDKHENEELIRWGFPEDVWFHVDKLSSAHVYLRLHLNETLDDVPQSVIDDCAQLVKANS # ISGNKMNNLEVVYTMWANLKKTQGMDVGQVGFFKDKEVRKVKIEKRINEIVNRLNKTKTEDHPDFRKLREDRDREERDNQKKKMAEQRKREREAEEQK # KKDSEIRSYASLMRPENMQSNQDDGNDSDDFM] # sequence of block unknown_A 1 [VYYFTSN] 8 # sequence of block unknown_B 9 [VSPAYTIYMGEDKHENEELIRWGFPED] 36 # sequence of block unknown_C 38 [FHVDKLSSAHVYLRLHLN] 56 # sequence of block unknown_D 59 [DDVPQSVIDDCAQLVKANSISGNKMNNLEVVYTMWANLKKTQGMDVGQVGFFKDKEV] 116 # sequence of block unknown_E 120 [IEKRINEIVNRLNKTKTE] 138 # sequence of block unknown_G 144 [KLREDRDREERDNQKKKMAEQRKRER] 170 # sequence of block unknown_H 173 [EQKKKDSEIRSYASLMRPE] 192 # sequence of block unknown_I 200 [GNDSDDFM] 208 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370W86.prfl --predictionStart=0 --predictionEnd=37692 --species=fly ./tmp/Contig1876420180911_busco_2432604931_.temp