# 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..172]--> unknown_A (12) <--[1..6]--> unknown_B (11) <--[1..3]--> unknown_C (13) <--[31..99]--> unknown_E (16) <--[0..1]--> unknown_F (13) <--[0..13]--> unknown_G (22) <--[1..7]--> unknown_H (21) <--[0..11]--> unknown_I (13) <--[0..20]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig1814520180911_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 = 29644, name = Contig18145) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig18145 AUGUSTUS gene 8951 33411 0.01 - . g1 Contig18145 AUGUSTUS transcript 8951 33411 0.01 - . g1.t1 Contig18145 AUGUSTUS tts 8951 8951 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 8951 9078 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS stop_codon 9018 9020 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 9079 13742 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 13804 14065 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 14088 14141 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 14163 17491 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 17516 22022 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 22045 25347 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 25368 27142 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 27179 28268 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 28406 29614 0.18 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 29709 29863 0.76 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS intron 29884 32032 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 9018 9078 0.02 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 13743 13803 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 13743 13803 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 14066 14087 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 14066 14087 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 14142 14162 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 14142 14162 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 17492 17515 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 17492 17515 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 22023 22044 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 22023 22044 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 25348 25367 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 25348 25367 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 27143 27178 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 27143 27178 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 28269 28405 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 28269 28405 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 29615 29708 0.7 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 29615 29708 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 29864 29883 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 29864 29883 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS CDS 32033 32120 0.03 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 32033 32123 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS start_codon 32118 32120 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS exon 33300 33411 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS tss 33411 33411 . - . transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 9063 9078 1.32 - 1 target "unknown_I[8..13]"; target_start 174; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 13743 13765 1.05 - 0 target "unknown_I[1..8]"; target_start 174; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 13784 13803 1.53 - 2 target "unknown_H[15..21]"; target_start 147; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 14066 14087 1.28 - 0 target "unknown_H[8..15]"; target_start 147; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 14142 14162 2.53 - 0 target "unknown_H[1..7]"; target_start 147; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 17495 17515 1.55 - 0 target "unknown_G[16..22]"; target_start 124; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 22023 22044 3.51 - 1 target "unknown_G[8..15]"; target_start 124; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 25348 25367 1.23 - 0 target "unknown_G[2..8]"; target_start 124; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 27143 27145 0.109 - 0 target "unknown_G[1..1]"; target_start 124; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 27152 27178 2.18 - 0 target "unknown_F[5..13]"; target_start 109; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 28269 28280 8.13 - 0 target "unknown_F[1..4]"; target_start 109; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 28284 28331 2.77 - 0 target "unknown_E[1..16]"; target_start 92; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 29649 29687 6.86 - 0 target "unknown_C[1..13]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 29691 29708 12.6 - 0 target "unknown_B[6..11]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 29864 29878 7.36 - 0 target "unknown_B[1..5]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig18145 AUGUSTUS protein_match 32037 32072 4.43 - 0 target "unknown_A[1..12]"; target_start 16; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcagaggttcaagagagggacttttttgaaattgaaggaccaaagccagatgttacatacccaatgaaagttgcat # attgtggagaatgctccatgcctttagagtattgtgaatattacccaaattacgaaaaatgcaagaaatggctcgagaaaaatctacccgatgaattc # agcaaattaatgagtgataaaccagaagacgaaggagatggtgacacagataaaaaacgacagaagcgaggtgggaagggacagataaaaaccaagaa # gaagtcagaacctaaaggcattagactgggcacagccaagaggggcaagaagaagcatataactcatgttcagagactatacctttttgattacaatc # aaaaatttgagtctgtttcattggaatttggattgaaattcactatagaatcgtcagttacagtcagacaaattgttattgtgaaggacgtaagtgat # gttttaaatgtaacgaatccagaaaaaaacccaattgttttggatttcctgtttatgaatgcaaatattttttgagtaatcgaccacagaatgcttta # caattttaccagtattacaataaaattttcattttaa] # protein sequence = [MAEVQERDFFEIEGPKPDVTYPMKVAYCGECSMPLEYCEYYPNYEKCKKWLEKNLPDEFSKLMSDKPEDEGDGDTDKK # RQKRGGKGQIKTKKKSEPKGIRLGTAKRGKKKHITHVQRLYLFDYNQKFESVSLEFGLKFTIESSVTVRQIVIVKDVSDVLNVTNPEKNPIVLDFLFM # NANIFXVIDHRMLYNFTSITIKFSF] # sequence of block unknown_I 174 [FMNANIFXVIDHR] 187 # sequence of block unknown_H 147 [QIVIVKDVSDVLNVTNPEKNP] 168 # sequence of block unknown_G 124 [QKFESVSLEFGLKFTIESSVTV] 146 # sequence of block unknown_F 109 [KHITHVQRLYLFD] 122 # sequence of block unknown_E 92 [KSEPKGIRLGTAKRGK] 108 # sequence of block unknown_C 43 [YEKCKKWLEKNLP] 56 # sequence of block unknown_B 31 [SMPLEYCEYYP] 42 # sequence of block unknown_A 16 [PDVTYPMKVAYC] 28 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937106Y.prfl --predictionStart=7227 --predictionEnd=47370 --species=fly ./tmp/Contig1814520180911_busco_2432604931_.temp