# 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..50]--> unknown_A (11) <--[15..33]--> unknown_D (31) <--[9..33]--> unknown_E (19) <--[0..64]--> unknown_F (28) <--[0..6]--> unknown_G (17) <--[21..59]--> unknown_J (33) <--[0..1]--> unknown_K (23) <--[1..13]--> unknown_L (16) <--[3..8]--> unknown_M (17) <--[9..41]--> unknown_N (25) <--[5..93]--> unknown_O (17) <--[70..162]--> unknown_R (35) <--[0..40]--> unknown_S (18) <--[10..57]--> unknown_U (14) <--[6..870]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig49620180911_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 = 20519, name = Contig496) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig496 AUGUSTUS gene 6078 19075 0.01 - . g1 Contig496 AUGUSTUS transcript 6078 19075 0.01 - . g1.t1 Contig496 AUGUSTUS tts 6078 6078 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 6078 6344 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS stop_codon 6258 6260 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 6345 6865 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 6959 8148 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 8265 8985 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 9077 9174 0.09 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 9652 10692 0.08 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 10773 11096 0.07 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 11247 12887 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 13029 13084 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 13110 17082 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 17174 17970 0.74 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS intron 18173 18845 0.57 - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 6258 6344 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 6866 6958 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 6866 6958 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 8149 8264 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 8149 8264 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 8986 9076 0.02 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 8986 9076 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 9175 9651 0.09 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 9175 9651 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 10693 10772 0.07 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 10693 10772 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 11097 11246 0.02 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 11097 11246 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 12888 13028 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 12888 13028 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 13085 13109 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 13085 13109 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 17083 17173 0.21 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 17083 17173 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 17971 18172 0.58 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 17971 18172 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS CDS 18846 18999 0.5 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS exon 18846 19075 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS start_codon 18997 18999 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS tss 19075 19075 . - . transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 6303 6344 2.35 - 0 target "unknown_U[1..14]"; target_start 540; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 6923 6958 4.05 - 0 target "unknown_S[7..18]"; target_start 503; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 8149 8166 2.83 - 0 target "unknown_S[1..6]"; target_start 503; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 8167 8264 3.88 - 2 target "unknown_R[3..35]"; target_start 468; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 8986 8992 1.49 - 0 target "unknown_R[1..3]"; target_start 468; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 9334 9384 2.24 - 0 target "unknown_O[1..17]"; target_start 370; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 9529 9603 3.44 - 0 target "unknown_N[1..25]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 10699 10749 2.48 - 0 target "unknown_M[1..17]"; target_start 262; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 10765 10772 3.28 - 2 target "unknown_L[14..16]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 11097 11136 3.75 - 0 target "unknown_L[1..14]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 11143 11211 7.11 - 0 target "unknown_K[1..23]"; target_start 216; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 11215 11246 6.27 - 2 target "unknown_J[23..33]"; target_start 182; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 12888 12954 6.09 - 0 target "unknown_J[1..23]"; target_start 182; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 13101 13109 0.772 - 0 target "unknown_G[15..17]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 17083 17124 5.66 - 0 target "unknown_G[1..14]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 17125 17173 6.09 - 1 target "unknown_F[12..28]"; target_start 107; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 17971 18005 3.35 - 0 target "unknown_F[1..12]"; target_start 107; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 18006 18062 4.21 - 0 target "unknown_E[1..19]"; target_start 88; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 18117 18172 5.23 - 2 target "unknown_D[13..31]"; target_start 39; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 18846 18882 3.53 - 0 target "unknown_D[1..13]"; target_start 39; transcript_id "g1.t1"; gene_id "g1"; Contig496 AUGUSTUS protein_match 18937 18969 3.05 - 0 target "unknown_A[1..11]"; target_start 10; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcggcaaggtcggaggaggtcctgctgattgtgaataatgttcggaacaagaagacggacggaactctctacatga # tgggagagagactgggttggatgcagggcagcaagagcacgttttccatcagctacatgtatgcagacattaaagcacaaaagatctcacccgattct # aaagagaaggttcaactccagttggttttacatgatggaggggccaacacatttcacttcatcaaccccaaaggtcgagcaatggcaataactgaccg # ggacagtgtgaaggacctcctacaacagctgattccaaaatttcgacgaaaactcagcagtgaactggaggaaaaaaacaggatgcttcaggaaaatc # ccgagttgtttcagttgtacaaggatttggttgtgacaggtgtaattactgcagaggaattctgggcctcgcggggtgaaaacatgttaaaccttgta # taccttgaaaagaaatatagcgatttgacatatgtcgtcttaattcaggctgatataaaaccacagacagatggatgcaatggattgaaatacaacct # cactgccgacatcatagagtcaatatttcgtacatatcccatggtgaaaaagaagcacgctgagcacgttccccacgacatgacagagagcgaattct # ggacccggttcttccagtcgcactacttccacagggacagaacggtgctgggaaccaaagacgtcttctccgattgtgccaaaagtgatgagaaagac # atgaaagaacagatttcagacaagccagtcgacctgtttttggatctcacaaaaatatccgactctcctttacacgaggattatcgtgggctgacaga # agacacacggattagtaacaatgtgacaaatggaaccatgattcgaagatttaatcatcactcaacaatggtgctgaaagcgtgtaccaaagactcgc # agcaaagtactacaaactcaggtcaggcagacgacgccggacggtcaggtgacactcaaaacagtagtgataacgccaaagtgaatggtgtaagcatg # gaagaaggagggccaagtaccagcaaaggttactgggaaccagcagcaaagaaacagaaactgcaggaaaaaattcatatggatgatttaacagacac # gaacagtaaaaagaatgtgaatttacagctgcataagatggagggttatttacacggtccgacgcctgtgacggtgtctcgctataccaccagtgagg # acctcctacgtgcctccgagtcagtgatgaataacgtccaccactggtcacatgatctttcaaatgtcctgttggggtcccaagcgattgtaattctc # agtgaactgtcaccaggaggggcgttattgaaaggaagcagtcattcacagcttaatcagatagtaccacaagacatgcaggaggaagtgaaagctag # ctacagtgctctgttggaattactgaggcatttctggacctgttttccagtctcatctaaatcacttgaagaaaaggttataagaatgaaatccacat # tggagaggtttcagatggccaaattaatgccactgaaagagagactgcaggactaccactataccgtaaatatgaccagtcatatggaggagcttctg # ttggcagcaaacaggaagtttgatatgtggcagtccagaaagtcagccatcaaaaggtga] # protein sequence = [MAARSEEVLLIVNNVRNKKTDGTLYMMGERLGWMQGSKSTFSISYMYADIKAQKISPDSKEKVQLQLVLHDGGANTFH # FINPKGRAMAITDRDSVKDLLQQLIPKFRRKLSSELEEKNRMLQENPELFQLYKDLVVTGVITAEEFWASRGENMLNLVYLEKKYSDLTYVVLIQADI # KPQTDGCNGLKYNLTADIIESIFRTYPMVKKKHAEHVPHDMTESEFWTRFFQSHYFHRDRTVLGTKDVFSDCAKSDEKDMKEQISDKPVDLFLDLTKI # SDSPLHEDYRGLTEDTRISNNVTNGTMIRRFNHHSTMVLKACTKDSQQSTTNSGQADDAGRSGDTQNSSDNAKVNGVSMEEGGPSTSKGYWEPAAKKQ # KLQEKIHMDDLTDTNSKKNVNLQLHKMEGYLHGPTPVTVSRYTTSEDLLRASESVMNNVHHWSHDLSNVLLGSQAIVILSELSPGGALLKGSSHSQLN # QIVPQDMQEEVKASYSALLELLRHFWTCFPVSSKSLEEKVIRMKSTLERFQMAKLMPLKERLQDYHYTVNMTSHMEELLLAANRKFDMWQSRKSAIKR] # sequence of block unknown_U 540 [MTSHMEELLLAANR] 554 # sequence of block unknown_S 503 [KSLEEKVIRMKSTLERFQ] 521 # sequence of block unknown_R 468 [LNQIVPQDMQEEVKASYSALLELLRHFWTCFPVSS] 503 # sequence of block unknown_O 370 [KQKLQEKIHMDDLTDTN] 387 # sequence of block unknown_N 297 [NGTMIRRFNHHSTMVLKACTKDSQQ] 322 # sequence of block unknown_M 262 [KPVDLFLDLTKISDSPL] 279 # sequence of block unknown_L 241 [KDVFSDCAKSDEKDMK] 257 # sequence of block unknown_K 216 [MTESEFWTRFFQSHYFHRDRTVL] 239 # sequence of block unknown_J 182 [CNGLKYNLTADIIESIFRTYPMVKKKHAEHVPH] 215 # sequence of block unknown_G 135 [VTGVITAEEFWASRGEN] 152 # sequence of block unknown_F 107 [RKLSSELEEKNRMLQENPELFQLYKDLV] 135 # sequence of block unknown_E 88 [ITDRDSVKDLLQQLIPKFR] 107 # sequence of block unknown_D 39 [TFSISYMYADIKAQKISPDSKEKVQLQLVLH] 70 # sequence of block unknown_A 10 [IVNNVRNKKTD] 21 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BK5.prfl --predictionStart=0 --predictionEnd=38185 --species=fly ./tmp/Contig49620180911_busco_2432604931_.temp