# 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..234]--> unknown_A (43) <--[0..1]--> unknown_B (18) <--[0..3]--> unknown_C (8) <--[2..11]--> unknown_D (25) <--[0..8]--> unknown_E (33) <--[3..13]--> unknown_F (19) <--[0..65]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig4572520180911_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 = 34541, name = Contig45725) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig45725 AUGUSTUS gene 4686 5213 0.98 + . g1 Contig45725 AUGUSTUS transcript 4686 5213 0.98 + . g1.t1 Contig45725 AUGUSTUS intron 4686 5060 0.98 + . transcript_id "g1.t1"; gene_id "g1"; Contig45725 AUGUSTUS CDS 5061 5213 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45725 AUGUSTUS stop_codon 5211 5213 . + 0 transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [acaatgggcattgcaagtagtaaagacagggatttgctgaaaaagaaaatcaaagagattaaaacgggaatggagaagg # agaaaaagattcaggaaaaggagaggaaagctaaagagaaagaacagaaaaaacagcttcagaagaaaaaatga] # protein sequence = [TMGIASSKDRDLLKKKIKEIKTGMEKEKKIQEKERKAKEKEQKKQLQKKK] # end gene g1 ### # start gene g2 Contig45725 AUGUSTUS gene 9031 9282 0.49 - . g2 Contig45725 AUGUSTUS transcript 9031 9282 0.49 - . g2.t1 Contig45725 AUGUSTUS stop_codon 9031 9033 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45725 AUGUSTUS CDS 9031 9282 0.49 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45725 AUGUSTUS start_codon 9280 9282 . - 0 transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgggagcgacccattctctcacacagaatggacgggagggagtgacccatgctcccacagaatggatggatgggagcg # acccattctctcacacagaatggacgggagggagtgacccatgctcccacagaatggatggatgggagcgacccattctcccacagaatggatgtgtg # ggagagacccagtctcccacagaatggatgggtgggagtgacccattctcccacataatggatggatgggagtga] # protein sequence = [MGATHSLTQNGREGVTHAPTEWMDGSDPFSHTEWTGGSDPCSHRMDGWERPILPQNGCVGETQSPTEWMGGSDPFSHI # MDGWE] # end gene g2 ### # start gene g3 Contig45725 AUGUSTUS gene 9622 10182 0.5 + . g3 Contig45725 AUGUSTUS transcript 9622 10182 0.5 + . g3.t1 Contig45725 AUGUSTUS start_codon 9622 9624 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig45725 AUGUSTUS CDS 9622 10182 0.5 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig45725 AUGUSTUS stop_codon 10180 10182 . + 0 transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgggtcacatctcatcccataccgtgagagaatgggtcactcccacccatccattctgtgtgagaatgggtcactccc # acccatccattccgtgggagatgggtctctcccatccatccattctgtgtgagatggtcactcacacccgtccattccgtgggagaatgggtccactc # ccataccatcctattcgtgggagaatgggtcactcccacactttcaattccgtgggagaatgggtgtcactcccactaccattccgtgggagaatggg # tcactcccatccattctgtggggagaatgggtcactcccaccccgtcattctgtgggagaatgggtcactcccaccgtctattctgtggagaatgggt # cactccctccatccattctgtgggagaaatgggtcactcctccctccattctgtgggagaatgggtcctccctccgcgtccattctgtgggagaatgg # gtcactcctcccgtccattgtgggagaatgggtcactccctcccgtccattccgtgggagatgggtcactcccacccatccatcgtgtga] # protein sequence = [MGHISSHTVREWVTPTHPFCVRMGHSHPSIPWEMGLSHPSILCEMVTHTRPFRGRMGPLPYHPIRGRMGHSHTFNSVG # EWVSLPLPFRGRMGHSHPFCGENGSLPPRHSVGEWVTPTVYSVENGSLPPSILWEKWVTPPSILWENGSSLRVHSVGEWVTPPVHCGRMGHSLPSIPW # EMGHSHPSIV] # end gene g3 ### # start gene g4 Contig45725 AUGUSTUS gene 10287 10805 0.92 - . g4 Contig45725 AUGUSTUS transcript 10287 10805 0.92 - . g4.t1 Contig45725 AUGUSTUS stop_codon 10287 10289 . - 0 transcript_id "g4.t1"; gene_id "g4"; Contig45725 AUGUSTUS CDS 10287 10805 0.92 - 0 transcript_id "g4.t1"; gene_id "g4"; Contig45725 AUGUSTUS start_codon 10803 10805 . - 0 transcript_id "g4.t1"; gene_id "g4"; # coding sequence = [atggatgagagtgaccattctcacacggaatggatgagagtgacccattctcacacgaatggatgggtgggagtgacca # ttctcacacagagatggatgggtgggagtgacccattctcttccggtatggatgagatggacccattcgcaccggaatggatgagagtgacccattct # cacacggaatggatgggtggaatgacccatctcacacagaatggatgggtgggagtgacccattctctcacggtatggatgagagtgacccatttgca # cacggaatggatgagtgacccattctcaccacgggaatggatgagagtgacccattctcacacggaatggatgggtgggagtgacccattctctcacg # gaatggatgagagtgacccatttctcacaggaatggatgggtggagtgatggacccattctctcacggaatggatggagtgacccgtctacagaatgg # atgggagggagtgacccattctctcacatagaatggacggtggagtga] # protein sequence = [MDESDHSHTEWMRVTHSHTNGWVGVTILTQRWMGGSDPFSSGMDEMDPFAPEWMRVTHSHTEWMGGMTHLTQNGWVGV # THSLTVWMRVTHLHTEWMSDPFSPREWMRVTHSHTEWMGGSDPFSHGMDESDPFLTGMDGWSDGPILSRNGWSDPSTEWMGGSDPFSHIEWTVE] # end gene g4 ### # start gene g5 Contig45725 AUGUSTUS gene 11708 25899 0.01 + . g5 Contig45725 AUGUSTUS transcript 11708 25899 0.01 + . g5.t1 Contig45725 AUGUSTUS start_codon 11708 11710 . + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 11743 13014 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 13106 14338 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 14363 14757 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 14773 14968 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 14979 15369 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 15386 16575 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 16596 18053 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 18067 19724 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 19741 21766 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 21780 23251 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 23280 23926 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 23968 24686 0.86 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 24874 25317 0.01 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS intron 25345 25790 0.37 + . transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 11708 11742 0.01 + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 13015 13105 0.01 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 14339 14362 0.01 + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 14758 14772 0.01 + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 14969 14978 0.01 + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 15370 15385 0.01 + 2 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 16576 16595 0.01 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 18054 18066 0.01 + 2 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 19725 19740 0.01 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 21767 21779 0.01 + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 23252 23279 0.01 + 2 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 23927 23967 0.01 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 24687 24873 0.12 + 2 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 25318 25344 0.01 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS CDS 25791 25899 0.42 + 1 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS stop_codon 25897 25899 . + 0 transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 13055 13105 1.39 + 0 target "unknown_A[1..17]"; target_start 25; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 14339 14362 1.04 + 2 target "unknown_A[18..26]"; target_start 24; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 14758 14772 1.34 + 2 target "unknown_A[26..31]"; target_start 24; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 14969 14978 1.48 + 2 target "unknown_A[31..34]"; target_start 24; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 15370 15385 1.05 + 1 target "unknown_A[34..39]"; target_start 24; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 16576 16588 4.27 + 1 target "unknown_A[39..43]"; target_start 25; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 16589 16595 0.757 + 0 target "unknown_B[1..3]"; target_start 68; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 18054 18066 2.13 + 1 target "unknown_B[3..7]"; target_start 67; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 19725 19740 1.56 + 0 target "unknown_B[8..13]"; target_start 67; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 21767 21779 2.28 + 2 target "unknown_B[13..17]"; target_start 67; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 23252 23256 0.122 + 2 target "unknown_B[17..18]"; target_start 68; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 23263 23279 1.68 + 0 target "unknown_C[1..6]"; target_start 88; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 23927 23933 0.343 + 1 target "unknown_C[6..8]"; target_start 88; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 23949 23967 1.11 + 0 target "unknown_D[1..7]"; target_start 101; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 24687 24742 6.03 + 2 target "unknown_D[7..25]"; target_start 101; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 24743 24841 7.51 + 0 target "unknown_E[1..33]"; target_start 126; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 24872 24873 1 + 0 target "unknown_F[1..1]"; target_start 169; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 25318 25344 6.41 + 0 target "unknown_F[2..10]"; target_start 168; transcript_id "g5.t1"; gene_id "g5"; Contig45725 AUGUSTUS protein_match 25791 25818 3.36 + 1 target "unknown_F[10..19]"; target_start 169; transcript_id "g5.t1"; gene_id "g5"; # coding sequence = [atgaatgcagactggcagcatctcagaagtcaatgctgcgttagtgggttacaatttccttttctgcaatatttgctgt # cttcatcgcccaataaaccaacaaagaaagatatttctttcgaccagtattttagagcaatgagctgtggtacttgtaaacgggagcatgctatgcgc # acgcaatcagaaacttgttacgttaacgacatgacaattgtgttcttgggtttcaacagtcacagtaatcacatgttgtttcttgaaggtatagtgag # gagggtgataaggggtttgcaaaagaatgacttgaaggtgggtcgagtgtgccacgcagaacttaatgccgttctgaataaaaactcggcggatgtga # agaagtgcagtatttacgtggctctgttcccctgtaatgagtgcgcgaaggtcgtgatccagtctggaattaaggaggtgatctattactccgacaaa # taccacaataagccagagtttgtggcgtccagaaggatgttagacatggctggagtcaaatacagacagcacattccaaagaagcagcagattacgat # cgattttacagccattgaagtaatgacaggaaacagcgtagaggaggttctaaatggtgaccacacccacaagtaa] # protein sequence = [MNADWQHLRSQCCVSGLQFPFLQYLLSSSPNKPTKKDISFDQYFRAMSCGTCKREHAMRTQSETCYVNDMTIVFLGFN # SHSNHMLFLEGIVRRVIRGLQKNDLKVGRVCHAELNAVLNKNSADVKKCSIYVALFPCNECAKVVIQSGIKEVIYYSDKYHNKPEFVASRRMLDMAGV # KYRQHIPKKQQITIDFTAIEVMTGNSVEEVLNGDHTHK] # sequence of block unknown_A 25 [LSSSPNKPTKKDISFDQYFRAMSCGTCKREHAMRTQSETCYVN] 68 # sequence of block unknown_B 68 [DMTIVFLGFNSHSNHMLF] 86 # sequence of block unknown_C 88 [GIVRRVIR] 96 # sequence of block unknown_D 101 [DLKVGRVCHAELNAVLNKNSADVKK] 126 # sequence of block unknown_E 126 [CSIYVALFPCNECAKVVIQSGIKEVIYYSDKYH] 159 # sequence of block unknown_F 169 [MLDMAGVKYRQHIPKKQQI] 188 # end gene g5 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KGV.prfl --predictionStart=4686 --predictionEnd=44892 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4572520180911_busco_2432604931_.temp