# 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..148]--> unknown_A (34) <--[4..22]--> unknown_B (16) <--[0..2]--> unknown_C (35) <--[8..81]--> unknown_E (28) <--[8..54]--> unknown_F (17) <--[9..106]--> unknown_G (46) <--[2..53]--> unknown_H (24) <--[0..3]--> unknown_I (30) <--[17..59]--> unknown_K (19) <--[27..203]--> unknown_M (26) <--[11..551]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5140320180911_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 = 29214, name = Contig51403) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig51403 AUGUSTUS gene 19632 31269 0.01 + . g1 Contig51403 AUGUSTUS transcript 19632 31269 0.01 + . g1.t1 Contig51403 AUGUSTUS tss 19632 19632 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 19632 19765 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS start_codon 19705 19707 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 19766 21783 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 21903 22046 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 22096 22247 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 22344 22671 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 22752 22895 0.13 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 22955 24044 0.05 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 24154 25339 0.13 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 25472 25639 0.9 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 25741 25955 0.22 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 26074 26435 0.19 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 26537 26934 0.29 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 27067 29719 0.6 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 29804 29979 0.52 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS intron 30264 30931 0.89 + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 19705 19765 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 21784 21902 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 21784 21902 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 22047 22095 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 22047 22095 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 22248 22343 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 22248 22343 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 22672 22751 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 22672 22751 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 22896 22954 0.15 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 22896 22954 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 24045 24153 0.05 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 24045 24153 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 25340 25471 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 25340 25471 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 25640 25740 0.88 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 25640 25740 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 25956 26073 0.18 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 25956 26073 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 26436 26536 0.28 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 26436 26536 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 26935 27066 0.87 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 26935 27066 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 29720 29803 0.61 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 29720 29803 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 29980 30263 0.58 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 29980 30263 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS CDS 30932 31179 0.49 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS exon 30932 31269 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS stop_codon 31177 31179 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS tts 31269 31269 . + . transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 21798 21899 3.29 + 0 target "unknown_A[1..34]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 22074 22095 9.59 + 0 target "unknown_B[1..8]"; target_start 69; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 22248 22273 8.2 + 2 target "unknown_B[8..16]"; target_start 69; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 22274 22343 7.78 + 0 target "unknown_C[1..24]"; target_start 85; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 22672 22706 6.26 + 2 target "unknown_C[24..35]"; target_start 85; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 22953 22954 1 + 0 target "unknown_E[1..1]"; target_start 154; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 24045 24126 4.84 + 1 target "unknown_E[1..28]"; target_start 154; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 24151 24153 1.38 + 0 target "unknown_F[1..1]"; target_start 190; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 25340 25387 2.77 + 0 target "unknown_F[2..17]"; target_start 190; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 25427 25471 3.94 + 0 target "unknown_G[1..15]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 25640 25732 6.8 + 0 target "unknown_G[16..46]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 25963 26034 3.34 + 0 target "unknown_H[1..24]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 26041 26073 4.09 + 0 target "unknown_I[1..11]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 26436 26492 7.54 + 0 target "unknown_I[12..30]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 26978 27034 3.18 + 0 target "unknown_K[1..19]"; target_start 356; transcript_id "g1.t1"; gene_id "g1"; Contig51403 AUGUSTUS protein_match 29990 30067 3.91 + 0 target "unknown_M[1..26]"; target_start 417; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgatgtgcaaccattattgtgttagctcagctgcatgttctaaagaatttcctaagggaaacctgtgttcggtgacca # tgccttttctcctcctgtctgatgtgtttgaccttattccactgagtcagtgtgagattgtgttctatgtagtggaggaaaaactacctgtttggaaa # ttggcattattttatgatgcagggaaaaacttcctattaagaatgtgcaatgatctgctgagaaggttaagtaaatcccagaacacagttttctgtgg # ccgaattcagttgtttctctcgagactgttcccactttcagaaaaatcagccctgaatctcatgagtcagttcaaccttgaaaatgtcaccatttact # ccacgaagtcagatgaaatgaagcttaaaatgcgtgaagtcgctgatgatgtcatggaggttgaggaaggagaaatggaggatttatcggggtcaact # cctatagattacaacttgtacaggaggttctgggcactgcaggattactttagaaaaccatctcagtgctacgaaaaagttccatggaaagcatttca # gcagaatgctgatgtggtgctgaatgcatttgccagttctaaattagatgacatgaaatcttcacgaaggaaactcgatctacctcgcccagccgata # cgaaagccttctttgccaagtatttgacaagtgaaaagttgatggacttgcaactgaatgatagtaactttaggagatatgtgcttgttcagttcctc # attattttccagtatttgagttcacaagttaaattcaagagtcccagtcaaactctcacagaggaccaaaatcagtgggtcaaaacaacccaggataa # agtataccagcttatcagagaaactcctcctgatggagaaaagttctgtaaaacagttcagcacatcctaggacgagaggaacattggaataaatgga # aaaatgagggatgccccgacttcgctagaaaaccagaaggagatgaaaaaaaagccaagtccagagctaagcgacggtgggtaggagatgacctacaa # gctcaaggaggaaaaattatcaaaatgggcagcgcagaactcactcgattatggaacttgaatcctgataacctagaggcctgcaaagccgagaaaag # ggtatttctaccttctctcgaggactttttctcagaagccatggaacaagcagatcctgaggcccaatttgaagagcaatacaaaatggtaaataatc # ccgtgttccagtggaagtctctccgacttctggccagacgaagtccgcatttctttggtcacaacaacaccccagccatgccacttcctcagtacttg # gagcttatgctgaacaaagtagcacaagagctaccgtccaccgggactaacggagaagtaacgcaggaaacaagcaacgaggagatgaggacagagct # tggtgaggatgaggcgataaaagaggcgcaggatggcgacgaggaggaactcaaagagcaggcagaggagcaaggtcgagaagatatgccagaagata # ttctttccaaggaacagatagaccttattgctgagaaagtgggtggggagtggaaaaagctggccacagagctaaactttcccgaggaagatatgact # tattttgagagtgaaaacagtgaagaaactgcatgtgctaaaaagatgttgacaatttggcaggtaggagactgcaagtacattgtaattcacgaagt # cttattccatgtcctttatgtattgtag] # protein sequence = [MMCNHYCVSSAACSKEFPKGNLCSVTMPFLLLSDVFDLIPLSQCEIVFYVVEEKLPVWKLALFYDAGKNFLLRMCNDL # LRRLSKSQNTVFCGRIQLFLSRLFPLSEKSALNLMSQFNLENVTIYSTKSDEMKLKMREVADDVMEVEEGEMEDLSGSTPIDYNLYRRFWALQDYFRK # PSQCYEKVPWKAFQQNADVVLNAFASSKLDDMKSSRRKLDLPRPADTKAFFAKYLTSEKLMDLQLNDSNFRRYVLVQFLIIFQYLSSQVKFKSPSQTL # TEDQNQWVKTTQDKVYQLIRETPPDGEKFCKTVQHILGREEHWNKWKNEGCPDFARKPEGDEKKAKSRAKRRWVGDDLQAQGGKIIKMGSAELTRLWN # LNPDNLEACKAEKRVFLPSLEDFFSEAMEQADPEAQFEEQYKMVNNPVFQWKSLRLLARRSPHFFGHNNTPAMPLPQYLELMLNKVAQELPSTGTNGE # VTQETSNEEMRTELGEDEAIKEAQDGDEEELKEQAEEQGREDMPEDILSKEQIDLIAEKVGGEWKKLATELNFPEEDMTYFESENSEETACAKKMLTI # WQVGDCKYIVIHEVLFHVLYVL] # sequence of block unknown_A 25 [TMPFLLLSDVFDLIPLSQCEIVFYVVEEKLPVWK] 59 # sequence of block unknown_B 69 [FLLRMCNDLLRRLSKS] 85 # sequence of block unknown_C 85 [QNTVFCGRIQLFLSRLFPLSEKSALNLMSQFNLEN] 120 # sequence of block unknown_E 154 [GSTPIDYNLYRRFWALQDYFRKPSQCYE] 182 # sequence of block unknown_F 190 [QNADVVLNAFASSKLDD] 207 # sequence of block unknown_G 220 [ADTKAFFAKYLTSEKLMDLQLNDSNFRRYVLVQFLIIFQYLSSQVK] 266 # sequence of block unknown_H 271 [QTLTEDQNQWVKTTQDKVYQLIRE] 295 # sequence of block unknown_I 297 [PDGEKFCKTVQHILGREEHWNKWKNEGCPD] 327 # sequence of block unknown_K 356 [GKIIKMGSAELTRLWNLNP] 375 # sequence of block unknown_M 417 [NPVFQWKSLRLLARRSPHFFGHNNTP] 443 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BGO.prfl --predictionStart=2247 --predictionEnd=42351 --species=fly ./tmp/Contig5140320180911_busco_2432604931_.temp