# 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..57]--> unknown_A (32) <--[0..4]--> unknown_B (18) <--[18..26]--> unknown_D (16) <--[8..40]--> unknown_F (12) <--[2..29]--> unknown_G (16) <--[2..23]--> unknown_H (43) <--[2..5]--> unknown_I (16) <--[0..30]--> unknown_J (32) <--[2..27]--> unknown_K (29) <--[1..27]--> unknown_L (19) <--[0..2]--> unknown_M (45) <--[0..14]--> unknown_N (8) <--[2..7]--> unknown_O (12) <--[2..15]--> unknown_P (31) <--[0..93]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig13652720180911_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 = 2782, name = Contig136527) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig136527 AUGUSTUS gene 2 2406 0.01 + . g1 Contig136527 AUGUSTUS transcript 2 2406 0.01 + . g1.t1 Contig136527 AUGUSTUS tss 2 2 . + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS exon 2 525 . + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS start_codon 30 32 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS intron 526 1034 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS intron 1233 1634 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS CDS 30 525 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS CDS 1035 1232 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS exon 1035 1232 . + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS CDS 1635 2221 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS exon 1635 2406 . + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS stop_codon 2219 2221 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS tts 2406 2406 . + . transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 33 128 7 + 0 target "unknown_A[1..32]"; target_start 1; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 129 182 6.68 + 0 target "unknown_B[1..18]"; target_start 33; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 249 296 6.83 + 0 target "unknown_D[1..16]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 333 368 6.16 + 0 target "unknown_F[1..12]"; target_start 101; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 375 422 8.52 + 0 target "unknown_G[1..16]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 429 525 6.01 + 0 target "unknown_H[1..33]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1035 1066 5.24 + 2 target "unknown_H[33..43]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1076 1123 2.55 + 0 target "unknown_I[1..16]"; target_start 179; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1151 1232 4.79 + 0 target "unknown_J[1..28]"; target_start 204; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1635 1648 1.42 + 2 target "unknown_J[28..32]"; target_start 204; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1670 1756 5.79 + 0 target "unknown_K[1..29]"; target_start 243; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1760 1816 4.23 + 0 target "unknown_L[1..19]"; target_start 273; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1817 1951 7.43 + 0 target "unknown_M[1..45]"; target_start 292; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1952 1975 6.34 + 0 target "unknown_N[1..8]"; target_start 337; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 1982 2017 2.68 + 0 target "unknown_O[1..12]"; target_start 347; transcript_id "g1.t1"; gene_id "g1"; Contig136527 AUGUSTUS protein_match 2027 2119 2.87 + 0 target "unknown_P[1..31]"; target_start 362; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggttcaaatattgtttttacacccagacttgggaattggaggtgctgagagggccgttatagatgcagcactggcac # tgaaatcaaaaggccaccaagtgcaattcgtaacatctcatcatgacatttcacactgttttcaggagactaaggatggaacattaaaagtgacaagt # gttggagactggctgccacggaaagtcttagggagatgttatgctctttgtgcttacatccgaatgatatatgcagcgctctatgtcattattagtcc # ctctctcaaatatgacattattttttgtgaccaaatatctgcatgtattccagtgctgttactatcctctgcaagaattttgttttattgccactttc # ctgatatgcttctcaccacaagaagaagtttgttgaagactttgtacagaaaacccattgatagactggaggagtataccactgggctggcccacaaa # gtccttgtcaatagtcattttacagctggtatatttaaggaaactttcaagtcactgggtcatgtgcagcctgcagttttgtatccaattcctgactt # caatggcctgaacaaaccggtggatgaagactttatgaaaagcctacctcaaaagccccctttattcctttctataaacagatatgaaagaaaaaaga # atatatctctggcagtaatggcttttgagctactagtggaaaagcacagagcttcgaatgctcacttaataattgctggtggttatgatgaaagagtg # acggaaaaccgagagtaccataaagagctgaccgacctggtggataaactgggcctcacagaaaatgtcacttttctcaggtcaatctcggatgcaca # gaaacggtccctgctgactagcgccacctgtctactgtacacacccgagaacgaacattttggaattgtaccgattgaggccatgtatttacaatgtc # cagttattgcatccaacagtggaggccccctggaaactattgctgatggtgaaactggttatctttgtgatgctgcacctgataagttttgtgacgct # atgagtagattcgtgacagatgaaaacttacataaaaagctgggatctgcaggaaaacatagagtgatagaaaaattctcattttcacagtttacaca # gcagctttgtggtattgttgaagatctcgcacaagacaaatctcacaacatttctcctctctggatcttgacaattgtatctcttattttcattgtat # tcattgcaatgataccttggttttga] # protein sequence = [MVQILFLHPDLGIGGAERAVIDAALALKSKGHQVQFVTSHHDISHCFQETKDGTLKVTSVGDWLPRKVLGRCYALCAY # IRMIYAALYVIISPSLKYDIIFCDQISACIPVLLLSSARILFYCHFPDMLLTTRRSLLKTLYRKPIDRLEEYTTGLAHKVLVNSHFTAGIFKETFKSL # GHVQPAVLYPIPDFNGLNKPVDEDFMKSLPQKPPLFLSINRYERKKNISLAVMAFELLVEKHRASNAHLIIAGGYDERVTENREYHKELTDLVDKLGL # TENVTFLRSISDAQKRSLLTSATCLLYTPENEHFGIVPIEAMYLQCPVIASNSGGPLETIADGETGYLCDAAPDKFCDAMSRFVTDENLHKKLGSAGK # HRVIEKFSFSQFTQQLCGIVEDLAQDKSHNISPLWILTIVSLIFIVFIAMIPWF] # sequence of block unknown_A 1 [VQILFLHPDLGIGGAERAVIDAALALKSKGHQ] 33 # sequence of block unknown_B 33 [VQFVTSHHDISHCFQETK] 51 # sequence of block unknown_D 73 [ALCAYIRMIYAALYVI] 89 # sequence of block unknown_F 101 [DQISACIPVLLL] 113 # sequence of block unknown_G 115 [ARILFYCHFPDMLLTT] 131 # sequence of block unknown_H 133 [SLLKTLYRKPIDRLEEYTTGLAHKVLVNSHFTAGIFKETFKSL] 176 # sequence of block unknown_I 179 [QPAVLYPIPDFNGLNK] 195 # sequence of block unknown_J 204 [LPQKPPLFLSINRYERKKNISLAVMAFELLVE] 236 # sequence of block unknown_K 243 [HLIIAGGYDERVTENREYHKELTDLVDKL] 272 # sequence of block unknown_L 273 [LTENVTFLRSISDAQKRSL] 292 # sequence of block unknown_M 292 [LTSATCLLYTPENEHFGIVPIEAMYLQCPVIASNSGGPLETIADG] 337 # sequence of block unknown_N 337 [ETGYLCDA] 345 # sequence of block unknown_O 347 [DKFCDAMSRFVT] 359 # sequence of block unknown_P 362 [LHKKLGSAGKHRVIEKFSFSQFTQQLCGIVE] 393 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370LMP.prfl --predictionStart=0 --predictionEnd=22104 --species=fly ./tmp/Contig13652720180911_busco_2432604931_.temp