# 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..83]--> unknown_A (20) <--[2..16]--> unknown_B (13) <--[0..1]--> unknown_C (33) <--[0..7]--> unknown_D (13) <--[12..27]--> unknown_E (12) <--[12..49]--> unknown_G (25) <--[1..15]--> unknown_H (8) <--[4..21]--> unknown_I (17) <--[1..37]--> unknown_J (26) <--[14..30]--> unknown_M (22) <--[13..58]--> unknown_N (27) <--[0..44]--> unknown_O (16) <--[5..45]--> unknown_P (18) <--[10..169]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig9474320180911_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 = 15081, name = Contig94743) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig94743 AUGUSTUS gene 1 15024 0.01 + . g1 Contig94743 AUGUSTUS transcript 1 15024 0.01 + . g1.t1 Contig94743 AUGUSTUS start_codon 1 3 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 8 6974 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 7041 7865 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 7942 9701 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 9732 10957 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 10974 11028 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 11062 11229 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 11269 11369 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 11512 11939 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 12094 12439 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 12545 12850 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 12958 13321 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 13345 13463 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 13478 13716 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 13828 13941 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 13959 14019 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14033 14265 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14277 14349 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14362 14501 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14553 14688 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14734 14803 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS intron 14833 14883 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 1 7 0.05 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 1 7 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 6975 7040 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 6975 7040 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 7866 7941 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 7866 7941 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 9702 9731 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 9702 9731 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 10958 10973 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 10958 10973 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 11029 11061 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 11029 11061 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 11230 11268 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 11230 11268 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 11370 11511 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 11370 11511 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 11940 12093 0.02 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 11940 12093 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 12440 12544 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 12440 12544 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 12851 12957 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 12851 12957 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 13322 13344 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 13322 13344 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 13464 13477 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 13464 13477 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 13717 13827 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 13717 13827 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 13942 13958 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 13942 13958 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14020 14032 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14020 14032 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14266 14276 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14266 14276 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14350 14361 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14350 14361 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14502 14552 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14502 14552 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14689 14733 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14689 14733 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14804 14832 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14804 14832 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS CDS 14884 14967 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS exon 14884 15024 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS stop_codon 14965 14967 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS tts 15024 15024 . + . transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 6992 7040 3.65 + 0 target "unknown_A[1..17]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 7866 7876 2.77 + 2 target "unknown_A[17..20]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 7901 7939 5.96 + 0 target "unknown_B[1..13]"; target_start 36; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 9703 9731 3.12 + 0 target "unknown_C[1..10]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 10958 10973 1.07 + 0 target "unknown_C[11..16]"; target_start 49; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11029 11061 1.42 + 2 target "unknown_C[16..27]"; target_start 49; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11230 11250 1.45 + 0 target "unknown_C[27..33]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11266 11268 0.931 + 0 target "unknown_D[1..1]"; target_start 88; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11370 11405 3.27 + 0 target "unknown_D[2..13]"; target_start 88; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11469 11504 4.39 + 0 target "unknown_E[1..12]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 11990 12064 5.94 + 0 target "unknown_G[1..25]"; target_start 153; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12071 12093 6.12 + 0 target "unknown_H[1..8]"; target_start 180; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12440 12440 1 + 1 target "unknown_H[8..8]"; target_start 180; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12471 12521 6.75 + 0 target "unknown_I[1..17]"; target_start 198; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12525 12544 5.26 + 0 target "unknown_J[1..7]"; target_start 216; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12851 12908 3.73 + 1 target "unknown_J[7..26]"; target_start 216; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 12951 12957 0.583 + 0 target "unknown_M[1..3]"; target_start 256; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 13322 13344 1.14 + 1 target "unknown_M[3..11]"; target_start 255; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 13464 13477 1.39 + 2 target "unknown_M[11..15]"; target_start 255; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 13717 13738 0.928 + 1 target "unknown_M[15..22]"; target_start 256; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 13808 13827 0.914 + 0 target "unknown_N[1..7]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 13942 13958 1.24 + 0 target "unknown_N[8..13]"; target_start 300; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14020 14032 1.06 + 1 target "unknown_N[13..17]"; target_start 300; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14266 14276 1.13 + 0 target "unknown_N[18..21]"; target_start 300; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14350 14361 1.09 + 1 target "unknown_N[21..25]"; target_start 300; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14502 14509 0.225 + 2 target "unknown_N[25..27]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14516 14552 1.27 + 0 target "unknown_O[1..13]"; target_start 330; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14689 14699 0.711 + 2 target "unknown_O[13..16]"; target_start 330; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14815 14832 1.14 + 0 target "unknown_P[1..6]"; target_start 361; transcript_id "g1.t1"; gene_id "g1"; Contig94743 AUGUSTUS protein_match 14884 14919 1.37 + 0 target "unknown_P[7..18]"; target_start 361; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcagagtttagcaaaaaataaatatgaactatacaaatgctcagcaaatgaatccattcacttcaaacttgtcagaa # aagaggaagacttggaagacgatgcctcaacatttcttccagagatgactcatcaagtgtttggagaaaatgaaagcatttttggatacagacttagg # tgtatagaaatcactcgggtccatggttctcttgtttcatttgcatccagacgtttcagtaagaaggatacatcgctagttgttataaaccctgatga # tgtcgttggacagttacgagaggtccttcctccgggattcctcaccagtagagacgccttcattagctcaataccagacgatgccgatttcaaaccat # tcgggaaacttgttcactcatttagtgtacgaaaagaagggagggagcggcagtttgagatctacaagacggggatcgagagcccaggatttcgggcg # taccacgaacgactgcaaaccttcattttgttctatattgatgccgcgtccttcattgatgtggacgatgaaagatggagattctttttattgtttga # aaaatacaagtgcaatggaaacccgatgtatgcagtggcgggttacatgacagtttacaattactacgcctaccccacaaaagtgcgacccagagtca # gtcaagttttagtcctgccgtcgttccagaagatgggcctttgcgctgagatgttacaaactttctacaatgacacgtacaaaaggaaagaggtgcta # gacatcacagtttcgacacagtcatttaagtgtttgtatgaccacatttccatatacatgtgctatactttggctttattcttatggtttattctatt # cacttttctatggatatttttatcatgcttatgtactttattgagctcactttgccaatgttacatgtgtcaacggttgtgctatatatgcctattaa # ttgccttgatatttgttgttctttacccacaaagttatggctcagttttaaaacaatatgtggagaccaatgaaaaaaagaaagaaagatgggaatcg # tttaaaaactacatggaggatccgtcagagaatttccagagatcggaaaaactcctgaaaggtttctcggaggaaatggcaaaggaggctagtgaaaa # attcaaactaaacaaggtaaatttttaa] # protein sequence = [MQSLAKNKYELYKCSANESIHFKLVRKEEDLEDDASTFLPEMTHQVFGENESIFGYRLRCIEITRVHGSLVSFASRRF # SKKDTSLVVINPDDVVGQLREVLPPGFLTSRDAFISSIPDDADFKPFGKLVHSFSVRKEGRERQFEIYKTGIESPGFRAYHERLQTFILFYIDAASFI # DVDDERWRFFLLFEKYKCNGNPMYAVAGYMTVYNYYAYPTKVRPRVSQVLVLPSFQKMGLCAEMLQTFYNDTYKRKEVLDITVSTQSFKCLYDHISIY # MCYTLALFLWFILFTFLWIFLSCLCTLLSSLCQCYMCQRLCYICLLIALIFVVLYPQSYGSVLKQYVETNEKKKERWESFKNYMEDPSENFQRSEKLL # KGFSEEMAKEASEKFKLNKVNF] # sequence of block unknown_A 8 [YELYKCSANESIHFKLVRKE] 28 # sequence of block unknown_B 36 [TFLPEMTHQVFGE] 49 # sequence of block unknown_C 50 [ESIFGYRLRCIEITRVHGSLVSFASRRFSKKDT] 83 # sequence of block unknown_D 88 [NPDDVVGQLREVL] 101 # sequence of block unknown_E 122 [KPFGKLVHSFSV] 134 # sequence of block unknown_G 153 [GFRAYHERLQTFILFYIDAASFIDV] 178 # sequence of block unknown_H 180 [ERWRFFLL] 188 # sequence of block unknown_I 198 [MYAVAGYMTVYNYYAYP] 215 # sequence of block unknown_J 216 [KVRPRVSQVLVLPSFQKMGLCAEMLQ] 242 # sequence of block unknown_M 256 [ITVSTQSFKCLYDHISIYMCYT] 278 # sequence of block unknown_N 301 [LSSLCQCYMCQRLCYICLLIALIFVVL] 328 # sequence of block unknown_O 330 [QSYGSVLKQYVETNEK] 346 # sequence of block unknown_P 361 [SENFQRSEKLLKGFSEEM] 379 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E36.prfl --predictionStart=0 --predictionEnd=32094 --species=fly ./tmp/Contig9474320180911_busco_2432604931_.temp