# 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..691]--> unknown_A (20) <--[0..4]--> unknown_B (35) <--[9..56]--> unknown_D (47) <--[0..1]--> unknown_E (77) <--[6..55]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig346920180911_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 = 18404, name = Contig3469) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig3469 AUGUSTUS gene 366 18205 0.01 + . g1 Contig3469 AUGUSTUS transcript 366 18205 0.01 + . g1.t1 Contig3469 AUGUSTUS start_codon 366 368 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 449 590 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 636 814 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 838 1339 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 1358 2087 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 2099 2813 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 2842 3555 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 3699 15321 0.09 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 15448 15544 0.98 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 15627 16659 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 16678 17237 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 17251 17400 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 17417 17612 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 17624 17868 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS intron 17879 18172 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 366 448 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 591 635 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 815 837 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 1340 1357 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 2088 2098 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 2814 2841 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 3556 3698 0.06 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 15322 15447 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 15545 15626 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 16660 16677 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 17238 17250 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 17401 17416 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 17613 17623 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 17869 17878 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS CDS 18173 18205 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS stop_codon 18203 18205 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 417 448 1.28 + 0 target "unknown_A[1..11]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 591 618 1.53 + 1 target "unknown_A[11..20]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 619 635 0.932 + 0 target "unknown_B[1..6]"; target_start 37; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 815 837 1.1 + 0 target "unknown_B[7..14]"; target_start 36; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 1340 1357 1.53 + 1 target "unknown_B[14..20]"; target_start 36; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 2088 2098 2.39 + 1 target "unknown_B[20..24]"; target_start 36; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 2814 2841 1.22 + 2 target "unknown_B[24..33]"; target_start 36; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 3556 3563 1.27 + 2 target "unknown_B[33..35]"; target_start 37; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 3609 3698 4.65 + 0 target "unknown_D[1..30]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 15322 15372 7.11 + 0 target "unknown_D[31..47]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 15373 15447 7.17 + 0 target "unknown_E[1..25]"; target_start 134; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 15545 15626 2.98 + 2 target "unknown_E[26..53]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 16660 16677 0.968 + 1 target "unknown_E[53..59]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 17238 17250 1.67 + 1 target "unknown_E[59..63]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 17401 17416 1.3 + 0 target "unknown_E[64..69]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 17613 17623 1.39 + 2 target "unknown_E[69..72]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 17869 17878 1.41 + 0 target "unknown_E[73..76]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig3469 AUGUSTUS protein_match 18173 18178 0.402 + 0 target "unknown_E[76..77]"; target_start 134; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcccactacatcagcaacacactattgaggacagtggtaaatgtgtcaactagacattcccctgctccctggaact # gtttaaaccagactccggctgggtggaccggctgcgttattctgcggccaatgtcatttaccgtgactcaataaagcattttcagaatcccttgttct # ctctactccttaggtgtgatagcacaaaaccgaaggggaggtaaggccatccagctcggcagtgagaaggtggagagtatgaaaccccaggaccgagt # catcaccgtcaaatttaatgcggatttgtctgctcagatgcaatggcagttcagaccccaacagagagaaatacaggttcgagttggggaaactgcct # tggcattttacactgcaaagaatcccacagaaaaacccatcatagggatttccacgtacaccatagttccgtttcaagctggatactatttcaacaaa # attcagtgtttctgctttgaggaacagaggttaaacccaggcgaagaggtaaatttacttacagtaatttacgtacaggaccatttagagaatgatgt # gattgtgggggcatgtgattcagtttattatggttattccaaattttgtgctctacgtgcaattgcccttaagaacttaaagaccaagtaa] # protein sequence = [MAHYISNTLLRTVVNVSTRHSPAPWNCLNQTPAGWTGCVILRPMSFTVTQXSIFRIPCSLYSLGVIAQNRRGGKAIQL # GSEKVESMKPQDRVITVKFNADLSAQMQWQFRPQQREIQVRVGETALAFYTAKNPTEKPIIGISTYTIVPFQAGYYFNKIQCFCFEEQRLNPGEEVNL # LTVIYVQDHLENDVIVGACDSVYYGYSKFCALRAIALKNLKTK] # sequence of block unknown_A 17 [TRHSPAPWNCLNQTPAGWTG] 37 # sequence of block unknown_B 37 [CVILRPMSFTVTQXSIFRIPCSLYSLGVIAQNRRG] 72 # sequence of block unknown_D 87 [PQDRVITVKFNADLSAQMQWQFRPQQREIQVRVGETALAFYTAKNPT] 134 # sequence of block unknown_E 134 [EKPIIGISTYTIVPFQAGYYFNKIQCFCFEEQRLNPGEEVNLLTVIYVQDHLENDVIVGACDSVYYGYSKFCALRAI] 211 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UEC.prfl --predictionStart=0 --predictionEnd=35625 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig346920180911_busco_2432604931_.temp