# 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..942]--> unknown_A (15) <--[0..4]--> unknown_B (16) <--[1..4]--> unknown_C (12) <--[3..6]--> unknown_D (17) <--[0..2]--> unknown_E (13) <--[1..24]--> unknown_F (21) <--[0..26]--> unknown_G (40) <--[0..1]--> unknown_H (15) <--[0..1]--> unknown_I (27) <--[4..29]--> unknown_J (7) <--[0..62]--> unknown_K (23) <--[18..49]--> unknown_N (17) <--[0..5]--> unknown_O (12) <--[0..306]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4563120180911_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 = 28106, name = Contig45631) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig45631 AUGUSTUS gene 2958 24653 0.01 + . g1 Contig45631 AUGUSTUS transcript 2958 24653 0.01 + . g1.t1 Contig45631 AUGUSTUS tss 2958 2958 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 2958 2985 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 3379 3461 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS start_codon 3380 3382 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 3462 3580 0.05 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 3733 4933 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 5062 6482 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 6531 6577 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 6619 8585 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 8628 10021 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 10072 11217 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 11243 12105 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 12150 13544 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 13630 13677 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 13694 17427 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 17502 17678 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 17696 18038 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 18049 18858 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 18874 21410 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 21623 22388 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS intron 22566 23026 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 3380 3461 0.06 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 3581 3732 0.04 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 3581 3732 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 4934 5061 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 4934 5061 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 6483 6530 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 6483 6530 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 6578 6618 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 6578 6618 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 8586 8627 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 8586 8627 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 10022 10071 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 10022 10071 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 11218 11242 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 11218 11242 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 12106 12149 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 12106 12149 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 13545 13629 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 13545 13629 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 13678 13693 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 13678 13693 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 17428 17501 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 17428 17501 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 17679 17695 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 17679 17695 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 18039 18048 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 18039 18048 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 18859 18873 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 18859 18873 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 21411 21622 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 21411 21622 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 22389 22565 0.17 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 22389 22565 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS CDS 23027 23104 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS exon 23027 24653 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS stop_codon 23102 23104 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS tts 24653 24653 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 6499 6530 1.91 + 0 target "unknown_A[1..11]"; target_start 126; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 6578 6590 0.818 + 1 target "unknown_A[11..15]"; target_start 126; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 6603 6618 1.91 + 0 target "unknown_B[1..6]"; target_start 145; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 8586 8617 1.22 + 2 target "unknown_B[6..16]"; target_start 145; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 8624 8627 2.87 + 0 target "unknown_C[1..2]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 10022 10053 1.58 + 2 target "unknown_C[2..12]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 10066 10071 0.877 + 0 target "unknown_D[1..2]"; target_start 179; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 11218 11242 1.99 + 2 target "unknown_D[3..11]"; target_start 178; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 12106 12125 1.1 + 2 target "unknown_D[11..17]"; target_start 179; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 12132 12149 1.1 + 0 target "unknown_E[1..6]"; target_start 198; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 13545 13565 1.2 + 0 target "unknown_E[7..13]"; target_start 198; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 13596 13629 1.49 + 0 target "unknown_F[1..12]"; target_start 221; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 13678 13693 0.986 + 1 target "unknown_F[12..17]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 17428 17440 1.25 + 1 target "unknown_F[17..21]"; target_start 221; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 17471 17501 1.17 + 0 target "unknown_G[1..11]"; target_start 252; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 17679 17695 1.08 + 1 target "unknown_G[11..17]"; target_start 251; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 18039 18048 1.33 + 2 target "unknown_G[17..20]"; target_start 251; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 18859 18873 4.94 + 1 target "unknown_G[20..25]"; target_start 251; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 21411 21457 5.26 + 2 target "unknown_G[25..40]"; target_start 252; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 21461 21505 7.24 + 0 target "unknown_H[1..15]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 21506 21586 4.5 + 0 target "unknown_I[1..27]"; target_start 308; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 21620 21622 11.7 + 0 target "unknown_J[1..1]"; target_start 346; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 22389 22406 5.29 + 0 target "unknown_J[2..7]"; target_start 346; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 22407 22475 7.68 + 0 target "unknown_K[1..23]"; target_start 353; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 22542 22565 3.81 + 0 target "unknown_N[1..8]"; target_start 398; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 23027 23053 6.46 + 0 target "unknown_N[9..17]"; target_start 398; transcript_id "g1.t1"; gene_id "g1"; Contig45631 AUGUSTUS protein_match 23054 23089 5.03 + 0 target "unknown_O[1..12]"; target_start 415; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgagtaaagtggacattcagagattaaaaaataggctcaataaaataggaaatgctgatactggcacatttgaaataa # aagatcctaaggaatggattgaattaattgaaagtagagggaacaaacctaaagactggctggattttatgcggtacatgacggcaaactcacatttt # tctgatgagttccagcaccataactacttgtcagatctttatgagacagcatttgataaaacttttatacgacctaaaatgttttatttatttcttga # acatctgcttcagaaaattcccagagaggaaaacaagcgaaacattttttacggttccctgtttgtggagtttgcacgaatgaaaagctcctctcaaa # gttttgaagatagggtctatgtaaatcatttgaagatccgggttgcacaagtgcaaaaccggcttattggtgaatggcgatcagtgaagggcttctca # gttaaaattatttctggaggagttgagttaacattgaaaatgttcaccctcgaaaaaccattgtcaactgatgggaatgtaaaaaatgaattaacttt # gagggaaaaattgtataaatatgcctccaccatatgcagtttgtattctcatcattatcaggttcccaccatggagaccatgtatatcaatagaaagc # tgtaccaggtattacgatgtattggtcatgttctcaggggtttcaagatcaagaagcacagagggacaatgaaatcactgctaacgatcgtatgcagt # atactaatgattagacctatctatcggattattcttagatcctttcatactcttcacaaggaaggaattattcactcggatctgaagccatctaattt # cctccttcgccatggtaacttgaagttgattgactttggaatctctaaagccattcaacaggacaaaaccagcatcatcacagacacacaggtgggga # ccctgaactacatgtcacccgagagcatcagagagcattgtgggtatgcagaagaggatgcacacaaacctgtgtttaagataagtgtgaagtcggac # gtttggtcgctggggtgtattctgtactgtatggtgtacggccacacccctttccagaaggtggtgaaacaatatgccaagctccttgccatcatcaa # cccagaatatgaaatcaagtttcccgagatccaagataagaagttgatggatgttatgaagaggtgtctcaatcgtgaccccaagcagaggccgagca # tagacgaactgttacagcacgagtatctacactcagtgtga] # protein sequence = [MSKVDIQRLKNRLNKIGNADTGTFEIKDPKEWIELIESRGNKPKDWLDFMRYMTANSHFSDEFQHHNYLSDLYETAFD # KTFIRPKMFYLFLEHLLQKIPREENKRNIFYGSLFVEFARMKSSSQSFEDRVYVNHLKIRVAQVQNRLIGEWRSVKGFSVKIISGGVELTLKMFTLEK # PLSTDGNVKNELTLREKLYKYASTICSLYSHHYQVPTMETMYINRKLYQVLRCIGHVLRGFKIKKHRGTMKSLLTIVCSILMIRPIYRIILRSFHTLH # KEGIIHSDLKPSNFLLRHGNLKLIDFGISKAIQQDKTSIITDTQVGTLNYMSPESIREHCGYAEEDAHKPVFKISVKSDVWSLGCILYCMVYGHTPFQ # KVVKQYAKLLAIINPEYEIKFPEIQDKKLMDVMKRCLNRDPKQRPSIDELLQHEYLHSV] # sequence of block unknown_A 126 [EDRVYVNHLKIRVAQ] 141 # sequence of block unknown_B 145 [LIGEWRSVKGFSVKII] 161 # sequence of block unknown_C 163 [GVELTLKMFTLE] 175 # sequence of block unknown_D 179 [TDGNVKNELTLREKLYK] 196 # sequence of block unknown_E 198 [STICSLYSHHYQV] 211 # sequence of block unknown_F 221 [KLYQVLRCIGHVLRGFKIKKH] 242 # sequence of block unknown_G 252 [VCSILMIRPIYRIILRSFHTLHKEGIIHSDLKPSNFLLRH] 292 # sequence of block unknown_H 293 [NLKLIDFGISKAIQQ] 308 # sequence of block unknown_I 308 [DKTSIITDTQVGTLNYMSPESIREHCG] 335 # sequence of block unknown_J 346 [KISVKSD] 353 # sequence of block unknown_K 353 [VWSLGCILYCMVYGHTPFQKVVK] 376 # sequence of block unknown_N 398 [KKLMDVMKRCLNRDPKQ] 415 # sequence of block unknown_O 415 [RPSIDELLQHEY] 427 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GHM.prfl --predictionStart=1413 --predictionEnd=42505 --species=fly ./tmp/Contig4563120180911_busco_2432604931_.temp