# 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 # --[10..340]--> unknown_A (29) <--[10..34]--> unknown_C (8) <--[9..17]--> unknown_E (31) <--[3..39]--> unknown_F (12) <--[0..1]--> unknown_G (31) <--[1..32]--> unknown_H (19) <--[2..61]--> unknown_I (27) <--[0..103]--> unknown_J (20) <--[9..72]--> unknown_K (21) <--[0..3]--> unknown_L (8) <--[0..38]--> unknown_M (31) <--[0..172]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig3127820180911_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 = 23088, name = Contig31278) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig31278 AUGUSTUS gene 2797 5661 0.2 + . g1 Contig31278 AUGUSTUS transcript 2797 5661 0.2 + . g1.t1 Contig31278 AUGUSTUS start_codon 2797 2799 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS intron 2824 3509 0.42 + . transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS intron 3559 3701 0.72 + . transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS intron 3804 3931 0.98 + . transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS intron 3993 5570 0.41 + . transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS CDS 2797 2823 0.56 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS CDS 3510 3558 0.71 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS CDS 3702 3803 0.98 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS CDS 3932 3992 0.78 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS CDS 5571 5661 0.47 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig31278 AUGUSTUS stop_codon 5659 5661 . + 0 transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggatgggtgggtgatgggttttgaggtcaggagtgatgttaaagttaagacctatatttttggtcaggatggatccc # agctactggagctacatcgtggtcaagggatggacatttactggagggacgctgttgtctgtcccacagaggaagagtacaaggcaatggtcatcaaa # aaaactgggggactctttggattagcggtgggacttatgcaactctttagcgactgtaaaaagatatttgagctgatagaagaacatggcggtaatcc # tatactaactgcattaattaacgaactcaagaaagtgtaccaaggatctcaatga] # protein sequence = [MDGWVMGFEVRSDVKVKTYIFGQDGSQLLELHRGQGMDIYWRDAVVCPTEEEYKAMVIKKTGGLFGLAVGLMQLFSDC # KKIFELIEEHGGNPILTALINELKKVYQGSQ] # end gene g1 ### # start gene g2 Contig31278 AUGUSTUS gene 5978 22799 0.01 - . g2 Contig31278 AUGUSTUS transcript 5978 22799 0.01 - . g2.t1 Contig31278 AUGUSTUS stop_codon 5978 5980 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 6071 6460 0.91 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 6524 7441 0.95 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 7541 7823 0.94 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 7911 10978 0.04 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 11032 11104 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 11123 11955 0.06 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 12015 13094 0.03 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 13187 13565 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 13601 13865 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 13884 14031 0.77 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 14060 14217 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 14236 14715 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 14727 14833 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 14878 15066 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 15077 15154 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 15170 15236 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 15256 15749 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 15853 16348 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 16368 17294 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 17313 17939 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 17950 18674 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 18692 18844 0.06 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 18864 19249 0.03 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 19304 19514 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 19572 19791 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 19809 21218 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 21245 21462 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 21538 22644 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS intron 22673 22774 0.04 - . transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 5978 6070 0.94 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 6461 6523 0.97 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 7442 7540 0.97 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 7824 7910 0.07 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 10979 11031 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 11105 11122 0.05 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 11956 12014 0.41 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 13095 13186 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 13566 13600 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 13866 13883 0.41 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 14032 14059 0.43 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 14218 14235 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 14716 14726 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 14834 14877 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 15067 15076 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 15155 15169 0.34 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 15237 15255 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 15750 15852 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 16349 16367 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 17295 17312 0.21 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 17940 17949 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 18675 18691 0.1 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 18845 18863 0.02 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 19250 19303 0.02 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 19515 19571 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 19792 19808 0.02 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 21219 21244 0.05 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 21463 21537 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 22645 22672 0.06 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS CDS 22775 22799 0.22 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS start_codon 22797 22799 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 5987 6070 3.21 - 0 target "unknown_M[4..31]"; target_start 376; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 6461 6469 4.48 - 0 target "unknown_M[1..3]"; target_start 376; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 6479 6502 3.48 - 0 target "unknown_L[1..8]"; target_start 365; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 6503 6523 6.64 - 0 target "unknown_K[15..21]"; target_start 344; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 7442 7483 4.59 - 0 target "unknown_K[1..14]"; target_start 344; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 7511 7540 5.13 - 0 target "unknown_J[11..20]"; target_start 315; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 7824 7853 3.56 - 0 target "unknown_J[1..10]"; target_start 315; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 11000 11031 1.18 - 2 target "unknown_I[17..27]"; target_start 262; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 11105 11122 1.11 - 2 target "unknown_I[11..17]"; target_start 262; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 11956 11986 1.3 - 0 target "unknown_I[1..11]"; target_start 262; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 13172 13186 3.13 - 0 target "unknown_H[15..19]"; target_start 208; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 13566 13600 1.49 - 2 target "unknown_H[3..14]"; target_start 208; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 13866 13872 0.635 - 0 target "unknown_H[1..3]"; target_start 208; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 14048 14059 0.912 - 0 target "unknown_G[28..31]"; target_start 168; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 14218 14235 1.43 - 0 target "unknown_G[22..27]"; target_start 168; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 14716 14726 0.508 - 2 target "unknown_G[18..21]"; target_start 168; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 14834 14877 1.57 - 1 target "unknown_G[3..18]"; target_start 168; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 15067 15074 1.93 - 0 target "unknown_G[1..3]"; target_start 168; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 15156 15169 1.11 - 2 target "unknown_F[8..12]"; target_start 155; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 15237 15255 2.48 - 0 target "unknown_F[2..8]"; target_start 155; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 15750 15752 0.694 - 0 target "unknown_F[1..1]"; target_start 155; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 15828 15852 1.29 - 1 target "unknown_E[23..31]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 16349 16367 1.12 - 2 target "unknown_E[17..23]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 17295 17312 1.13 - 2 target "unknown_E[11..17]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 17940 17949 2.31 - 0 target "unknown_E[8..11]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 18675 18691 2.9 - 2 target "unknown_E[2..7]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 18845 18848 3.1 - 0 target "unknown_E[1..2]"; target_start 99; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 19265 19288 2.31 - 0 target "unknown_C[1..8]"; target_start 81; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 19554 19571 1.06 - 0 target "unknown_A[24..29]"; target_start 34; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 19792 19808 1.77 - 2 target "unknown_A[18..23]"; target_start 34; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 21219 21244 1.35 - 1 target "unknown_A[9..18]"; target_start 34; transcript_id "g2.t1"; gene_id "g2"; Contig31278 AUGUSTUS protein_match 21463 21488 1.13 - 0 target "unknown_A[1..9]"; target_start 34; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtcacacagtggccgggtctcaggtaatgtcatacagcggctgggtcacagtccaatacatgaaccaagagcatcca # gaagggctggaagcctggtgttgttttatcagaatacccagagcgtccaatacccagagtgtccagtaggattttaatacccagagtgtccaataccc # agaccgttccaggagattttgtttgttttatatcagataccaaggtgtccaataccagagagtccagttaggatttgtttgtttatcagatacccaga # gcgtccaataccaagagtgctgtccaatacccaggaccgtccatttaggttttatacccagacccatccagatacaaagatgcgcttccaataccaag # agacagtccacgtaggattttgttctgttttatcagcaatcccaagacatccagtaggacttttgtttttttatcagcatacccagagtgtccagaac # gtccagctaggattttataccagagtgtccataggactttgatgtccagcaggattttatttgttttcatatgattataaagagtttacccagaccat # ccaagaccggtccaaaccaggggggataccccagacccgtccagatacccagcaccgatccaaacgttccgaggattttgtttgtttattaatccaga # taccagagtgtccagtaggatttgtttggttttcagataccaagagtttgtccaagtggattttgtttgttttaatcagtaccagactccaaacccag # acgcgtccagtagggattttgttgttttatccagatatcagagacgttccagataccaagcaccgttccaattttgtttatcagtacccagacccgtc # cagtgatttgttggttatgatacgagtaatgtcgcactgcggccgggtcacaggtaaatctgtcagacaatcgatagctgagaagtccctaaaaccac # tgattggatctcagattatcatgtacaaaaatggcacgtcgcagggactagcatatgaggacatcttcgagggtgtgtactatcccgcagcatcgctg # tacaagaacgccaaggtgaccttgaatttcggaccagaatttaagtgtcctccgcagggcctcaaggacttcagaccgatgtcggatgctgcctccca # aacaatggtggaatatgctcttgcagacatcatataccatgtagagaatgaaggaaaactaccagaattttga] # protein sequence = [MSHSGRVSGNVIQRLGHSPIHEPRASRRAGSLVLFYQNTQSVQYPECPVGFXYPECPIPRPFQEILFVLYQIPRCPIP # ESPVRICLFIRYPERPIPRVLSNTQDRPFRFYTQTHPDTKMRFQYQETVHVGFCSVLSAIPRHPVGLLFFYQHTQSVQNVQLGFYTRVSIGLXCPAGF # YLFSYDYKEFTQTIQDRSKPGGIPQTRPDTQHRSKRSEDFVCLLIQIPECPVGFVWFSDTKSLSKWILFVLISTRLQTQTRPVGILLFYPDIRDVPDT # KHRSNFVYQYPDPSSDLLVMIRVMSHCGRVTGKSVRQSIAEKSLKPLIGSQIIMYKNGTSQGLAYEDIFEGVYYPAASLYKNAKVTLNFGPEFKCPPQ # GLKDFRPMSDAASQTMVEYALADIIYHVENEGKLPEF] # sequence of block unknown_M 376 [FRPMSDAASQTMVEYALADIIYHVENEGKLP] 407 # sequence of block unknown_L 365 [EFKCPPQG] 373 # sequence of block unknown_K 344 [GVYYPAASLYKNAKVTLNFGP] 365 # sequence of block unknown_J 315 [KSLKPLIGSQIIMYKNGTSQ] 335 # sequence of block unknown_I 262 [LFYPDIRDVPDTKHRSNFVYQYPDPSS] 289 # sequence of block unknown_H 208 [RSKRSEDFVCLLIQIPECP] 227 # sequence of block unknown_G 168 [GLXCPAGFYLFSYDYKEFTQTIQDRSKPGGI] 199 # sequence of block unknown_F 155 [QNVQLGFYTRVS] 167 # sequence of block unknown_E 99 [SNTQDRPFRFYTQTHPDTKMRFQYQETVHVG] 130 # sequence of block unknown_C 81 [VRICLFIR] 89 # sequence of block unknown_A 34 [FYQNTQSVQYPECPVGFXYPECPIPRPFQ] 63 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BYX.prfl --predictionStart=0 --predictionEnd=27540 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3127820180911_busco_2432604931_.temp