# 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..62]--> unknown_A (31) <--[0..13]--> unknown_B (24) <--[5..13]--> unknown_C (31) <--[18..34]--> unknown_F (38) <--[1..4]--> unknown_G (17) <--[0..3]--> unknown_H (21) <--[0..22]--> unknown_I (25) <--[0..2]--> unknown_J (9) <--[0..1]--> unknown_K (29) <--[2..32]--> unknown_L (17) <--[0..2]--> unknown_M (38) <--[0..12]--> unknown_N (37) <--[1..7]--> unknown_O (16) <--[1..3]--> unknown_P (42) <--[0..77]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2937620180911_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 = 38158, name = Contig29376) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig29376 AUGUSTUS gene 1 11005 0.01 - . g1 Contig29376 AUGUSTUS transcript 1 11005 0.01 - . g1.t1 Contig29376 AUGUSTUS intron 1 9175 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS intron 9917 10899 0.06 - . transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS CDS 9176 9916 0.15 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS exon 9176 9916 . - . transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS CDS 10900 10907 0.04 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS exon 10900 11005 . - . transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS start_codon 10905 10907 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig29376 AUGUSTUS tss 11005 11005 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggagatgtatgaagaccttgaacagactacaaagtttgataaccagtaccagtggttctatcagggtggaaatggat # ggtggcagtacgatgacagaactagtcaggaactggaatctaaacataagaatggagaaaaagtgtttgaaattttgatcgcagggtttctgtatata # atcgactatgagaatatggtgcaggtaagacgcaatgaccggtcgaggaaacggaagattaggcgggatcttgtttctatacctggtgtgaagggagt # agctggactgaaatattcaaaatcggcatcgccatccaatggacgacccgtaggagatggaaatgaacagtctagtcacgccagtaaccctgcattaa # ggacttccaattccagtcgactcactcgccgatccctcatctcccacggccagccgtccgtcccccacacccccagtaacaccccccagtctgccaac # accccagtcgacagtccccccagcagtgttcagtcctcccagcaagatctcaccagtcacttacaaaacctgaacctgcaagacgacgattcggactc # aaatgaagctcagatgacgagacacgttcccagcggaagcaatgaggacagtccaccttcacccagcgatcagagttctggcgccgaaatagtccgtc # cagataacccgaccagcagtcgtacaaggaccagacaaagcattcagtacgtcgattccgattccagtgatgatgagattgt] # protein sequence = [MEMYEDLEQTTKFDNQYQWFYQGGNGWWQYDDRTSQELESKHKNGEKVFEILIAGFLYIIDYENMVQVRRNDRSRKRK # IRRDLVSIPGVKGVAGLKYSKSASPSNGRPVGDGNEQSSHASNPALRTSNSSRLTRRSLISHGQPSVPHTPSNTPQSANTPVDSPPSSVQSSQQDLTS # HLQNLNLQDDDSDSNEAQMTRHVPSGSNEDSPPSPSDQSSGAEIVRPDNPTSSRTRTRQSIQYVDSDSSDDEI] # end gene g1 ### # start gene g2 Contig29376 AUGUSTUS gene 11426 32974 0.01 + . g2 Contig29376 AUGUSTUS transcript 11426 32974 0.01 + . g2.t1 Contig29376 AUGUSTUS tss 11426 11426 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 11426 11528 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 11729 11823 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS start_codon 11734 11736 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 11824 12567 0.02 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 12686 13083 0.94 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 13202 13314 0.96 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 13358 13497 0.96 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 13603 13962 0.88 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 14089 15179 0.24 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 15305 15465 0.35 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 15587 16905 0.93 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 17008 18047 0.86 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 18158 18273 1 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 18377 18591 1 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS intron 18724 30959 0.07 + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 11734 11823 0.02 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 12568 12685 0.02 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 12568 12685 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 13084 13201 0.94 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 13084 13201 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 13315 13357 0.97 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 13315 13357 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 13498 13602 0.93 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 13498 13602 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 13963 14088 0.91 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 13963 14088 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 15180 15304 0.32 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 15180 15304 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 15466 15586 0.98 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 15466 15586 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 16906 17007 0.99 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 16906 17007 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 18048 18157 0.92 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 18048 18157 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 18274 18376 1 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 18274 18376 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 18592 18723 1 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 18592 18723 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS CDS 30960 31025 0.07 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS exon 30960 32974 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS stop_codon 31023 31025 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS tts 32974 32974 . + . transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 11734 11823 6.75 + 0 target "unknown_A[1..30]"; target_start 0; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 12568 12570 1.25 + 0 target "unknown_A[31..31]"; target_start 0; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 12577 12648 5.48 + 0 target "unknown_B[1..24]"; target_start 33; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 12676 12685 4.53 + 0 target "unknown_C[1..4]"; target_start 66; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 13084 13166 3.42 + 2 target "unknown_C[4..31]"; target_start 66; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 13498 13602 6.04 + 0 target "unknown_F[1..35]"; target_start 123; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 13963 13971 1.66 + 0 target "unknown_F[36..38]"; target_start 123; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 13981 14031 5.85 + 0 target "unknown_G[1..17]"; target_start 164; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 14032 14088 6.1 + 0 target "unknown_H[1..19]"; target_start 181; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15180 15185 4.47 + 0 target "unknown_H[20..21]"; target_start 181; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15189 15263 9 + 0 target "unknown_I[1..25]"; target_start 203; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15264 15290 7.8 + 0 target "unknown_J[1..9]"; target_start 228; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15294 15304 8.23 + 0 target "unknown_K[1..4]"; target_start 238; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15466 15541 9.14 + 1 target "unknown_K[4..29]"; target_start 238; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 15551 15586 5.67 + 0 target "unknown_L[1..12]"; target_start 270; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 16906 16920 6.23 + 0 target "unknown_L[13..17]"; target_start 270; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 16921 17007 9.33 + 0 target "unknown_M[1..29]"; target_start 287; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18048 18074 8.32 + 0 target "unknown_M[30..38]"; target_start 287; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18075 18157 8.54 + 0 target "unknown_N[1..28]"; target_start 325; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18274 18301 7.03 + 1 target "unknown_N[28..37]"; target_start 325; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18305 18352 9.36 + 0 target "unknown_O[1..16]"; target_start 363; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18356 18376 9.11 + 0 target "unknown_P[1..7]"; target_start 380; transcript_id "g2.t1"; gene_id "g2"; Contig29376 AUGUSTUS protein_match 18592 18696 7.18 + 0 target "unknown_P[8..42]"; target_start 380; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggcggaattcgacttgaccacgcgtatgggccaatacttagatcgacatttagtgtttcctttattagaatttttat # ctgtgaaagagctctatgatgagaaagaaatgttaaaggggaagctagacttgctgagtaacacaaacatggtggactttgccatggatgttcacaaa # aacctctacccagaccaggatgtacccaacagtctgaaaggcaaaagacaagatgttgtggcacaattaaaaagcttacaggcagaaacagaactgat # taccaagatttttgaagatccggaggttgtacggcagatgcaaagctcaagggatggtcgacagttgtttgaatttcttaacaaagaacatggttttg # aggccagtatggtagacacgttgtacacatatgccaagtttcagtacgagtgtggaaactattcaggagcagcagaatatctgtattttgtaagagtg # ttgctcccctcgacagatagccatttcctcgacgcgatgtgggggaagttagcctcagaaatcctcatgcagaattgggagactgcactagatgacct # tcagaagcttaaagacatcatcgatagcaatccatttggttcagctctacagaatctacaacagaggacctggttaattcattggagtttgtttgtct # tcttcaatcatcctaaaggccgagatctaattatagatatgttcatttaccagcctttgtacctgaatgctatccagacgacctgtccccacatcctg # aggtacttgaccactgcggtcattacaaacaagagcagacggcggacggtgatgaaggatctggtcaaggtcattcaacaggagagctacaaatacaa # ggatcccatcaccgagtttgtggaatgtctgtatgtcaacttcgactttgatggagcccagcagaaactcagagaatgtgaagaggttctggtgaatg # atttctttttggtggcgtgcttggacgacttcatcgaaaatgctcgactgctgatttttgaaactttctgtagaattcatgaatgtattagtatcaat # atgctggcagaaaagttgaatatgacagaggaggatgcagagaggtggattgtaaatctgatcaggaacgcccgactggatgccaagatcgactcgaa # actcggccatgtcgtcatgggaacacaggccgtgtcgccgtatcaacaggtcatcgagaaaaccaaaggcttggcattcagatcacagatgcttgcca # tgaatatcgaaaagaaacttggagtccgaactggagataacaccaaacagtgctacaaatggacggaacatcggaaggatctactagacaccaaaacc # aattga] # protein sequence = [MAEFDLTTRMGQYLDRHLVFPLLEFLSVKELYDEKEMLKGKLDLLSNTNMVDFAMDVHKNLYPDQDVPNSLKGKRQDV # VAQLKSLQAETELITKIFEDPEVVRQMQSSRDGRQLFEFLNKEHGFEASMVDTLYTYAKFQYECGNYSGAAEYLYFVRVLLPSTDSHFLDAMWGKLAS # EILMQNWETALDDLQKLKDIIDSNPFGSALQNLQQRTWLIHWSLFVFFNHPKGRDLIIDMFIYQPLYLNAIQTTCPHILRYLTTAVITNKSRRRTVMK # DLVKVIQQESYKYKDPITEFVECLYVNFDFDGAQQKLRECEEVLVNDFFLVACLDDFIENARLLIFETFCRIHECISINMLAEKLNMTEEDAERWIVN # LIRNARLDAKIDSKLGHVVMGTQAVSPYQQVIEKTKGLAFRSQMLAMNIEKKLGVRTGDNTKQCYKWTEHRKDLLDTKTN] # sequence of block unknown_A 0 [MAEFDLTTRMGQYLDRHLVFPLLEFLSVKEL] 31 # sequence of block unknown_B 33 [EKEMLKGKLDLLSNTNMVDFAMDV] 57 # sequence of block unknown_C 66 [VPNSLKGKRQDVVAQLKSLQAETELITKIFE] 97 # sequence of block unknown_F 123 [FEASMVDTLYTYAKFQYECGNYSGAAEYLYFVRVLLPS] 161 # sequence of block unknown_G 164 [HFLDAMWGKLASEILMQ] 181 # sequence of block unknown_H 181 [NWETALDDLQKLKDIIDSNPF] 202 # sequence of block unknown_I 203 [SALQNLQQRTWLIHWSLFVFFNHPK] 228 # sequence of block unknown_J 228 [GRDLIIDMF] 237 # sequence of block unknown_K 238 [YQPLYLNAIQTTCPHILRYLTTAVITNKS] 267 # sequence of block unknown_L 270 [TVMKDLVKVIQQESYKY] 287 # sequence of block unknown_M 287 [KDPITEFVECLYVNFDFDGAQQKLRECEEVLVNDFFLV] 325 # sequence of block unknown_N 325 [ACLDDFIENARLLIFETFCRIHECISINMLAEKLNMT] 362 # sequence of block unknown_O 363 [EDAERWIVNLIRNARL] 379 # sequence of block unknown_P 380 [AKIDSKLGHVVMGTQAVSPYQQVIEKTKGLAFRSQMLAMNIE] 422 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AWB.prfl --predictionStart=0 --predictionEnd=38158 --species=fly ./tmp/Contig2937620180911_busco_2432604931_.temp