# 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..292]--> unknown_A (19) <--[1..42]--> unknown_B (30) <--[0..2]--> unknown_C (11) <--[0..1]--> unknown_D (15) <--[0..2]--> unknown_E (19) <--[0..1]--> unknown_F (15) <--[0..54]--> unknown_G (22) <--[0..3]--> unknown_H (34) <--[0..61]--> unknown_I (10) <--[0..3]--> unknown_J (19) <--[1..3]--> unknown_K (39) <--[9..74]--> unknown_L (29) <--[16..81]--> unknown_O (29) <--[0..12]--> unknown_P (21) <--[25..62]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2464220180911_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 = 20806, name = Contig24642) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig24642 AUGUSTUS gene 7316 20792 0.01 + . g1 Contig24642 AUGUSTUS transcript 7316 20792 0.01 + . g1.t1 Contig24642 AUGUSTUS tss 7316 7316 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 7316 7400 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 8074 8231 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS start_codon 8076 8078 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 8232 8348 0.32 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 8411 8550 0.82 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 8662 8818 0.88 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 9012 9271 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 9282 9347 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 9478 9601 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 9669 9876 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 9960 10054 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 10131 16213 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 16282 16418 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 16600 16768 0.62 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 16859 16965 0.74 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 17102 17162 0.25 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 17183 17317 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 17376 17454 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 17479 18623 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 18652 18701 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS intron 18727 18845 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 8076 8231 0.36 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 8349 8410 0.32 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 8349 8410 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 8551 8661 0.82 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 8551 8661 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 8819 9011 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 8819 9011 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 9272 9281 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 9272 9281 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 9348 9477 0.02 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 9348 9477 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 9602 9668 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 9602 9668 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 9877 9959 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 9877 9959 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 10055 10130 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 10055 10130 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 16214 16281 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 16214 16281 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 16419 16599 0.58 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 16419 16599 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 16769 16858 0.61 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 16769 16858 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 16966 17101 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 16966 17101 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 17163 17182 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 17163 17182 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 17318 17375 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 17318 17375 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 17455 17478 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 17455 17478 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 18624 18651 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 18624 18651 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 18702 18726 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 18702 18726 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS CDS 18846 18923 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS exon 18846 20792 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS stop_codon 18921 18923 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS tts 20792 20792 . + . transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8367 8410 3.53 + 0 target "unknown_A[1..15]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8551 8563 2.45 + 1 target "unknown_A[15..19]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8573 8661 3.63 + 0 target "unknown_B[1..30]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8819 8819 1 + 1 target "unknown_B[30..30]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8820 8852 4.63 + 0 target "unknown_C[1..11]"; target_start 110; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8853 8897 6.64 + 0 target "unknown_D[1..15]"; target_start 121; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8904 8960 4 + 0 target "unknown_E[1..19]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 8961 9005 3.83 + 0 target "unknown_F[1..15]"; target_start 157; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 9609 9668 6.01 + 0 target "unknown_G[1..20]"; target_start 223; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 9877 9882 0.41 + 0 target "unknown_G[21..22]"; target_start 223; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 9892 9959 6.2 + 0 target "unknown_H[1..23]"; target_start 248; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 10055 10088 13 + 1 target "unknown_H[23..34]"; target_start 248; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 10095 10124 4.73 + 0 target "unknown_I[1..10]"; target_start 284; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 10125 10130 5.11 + 0 target "unknown_J[1..2]"; target_start 294; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 16214 16264 11.5 + 0 target "unknown_J[3..19]"; target_start 294; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 16268 16281 6.14 + 0 target "unknown_K[1..5]"; target_start 314; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 16419 16521 8.97 + 1 target "unknown_K[5..39]"; target_start 314; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 16576 16599 4.22 + 0 target "unknown_L[1..8]"; target_start 371; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 16769 16831 5.68 + 0 target "unknown_L[9..29]"; target_start 371; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 17080 17101 1.1 + 0 target "unknown_O[1..8]"; target_start 447; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 17163 17182 0.982 + 1 target "unknown_O[8..15]"; target_start 446; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 17318 17362 1.23 + 0 target "unknown_O[15..29]"; target_start 447; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 17463 17478 2.44 + 0 target "unknown_P[1..6]"; target_start 483; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 18624 18651 1.25 + 1 target "unknown_P[6..15]"; target_start 482; transcript_id "g1.t1"; gene_id "g1"; Contig24642 AUGUSTUS protein_match 18702 18720 1.12 + 1 target "unknown_P[15..21]"; target_start 483; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgagtgaacaaacagagaaacactcaaacctaacagcagagaaggtcaatgaagagactaaaccaaagaacccagaca # ttggtgcgttttccagagaaggttcagtagcatccaatgcgtcaacttcaagtggcgagaaaattgtttccaaggagttcttctcaggaaatccaatg # gtggaaaggacatgtgggatcttgcacctgtacaaagacaacaagaagacatcactgaaggaagaggtccctagaagtgaattgatttgtatgttggc # tgtgccagcagcctacactattcatgatttggttaaattcactgccccagtggtagaaggtatagagtacatgaggatcatcagggacaccactccta # accagtacatggtcctcgtcaagttccgcaatcagaggctggcagacgagtttttcaacacatacaacaatgtgtcctttaactccatagaacccgac # atctgtcagctgatttatgtggcaaaggtggaggtcatgaaggattcagagctatgtcgaaatatctcggagtttgttctcagtcccatcaagtttga # gataacaaggttcaactactcacaagaacataatctttgcaacaaggcatccacatttaatttacataaaaataacaatttcacaccagaaaaggggc # ttgttttacctgtgactggtctgacagaactgcccaactgcccagtgtgtctagacagaatgtctgtagatggtacaccagtgttgacaattttgtgc # aatcacacttttcatgtcaactgtttggcaaaatggggtgatacaagctgtccagtgtgtcgatactgtcagacccccgaggaaacagctgaccagag # atgcatgacttgtggctctcaggaaagtttatggatttgcttggtatgtggtaacattggatgtggcagatatgtagaacttcacgcatacaagcatt # ttcaagaaacacagcacacgtatgccatgcagttaggtaacagtcgagtttgggattacgttggcgataattttgtccatcgtttggttcagagtaaa # ggtgatggtaaactggtagctgtggaggaccagcaaagctcagaaatggatggaaaagttgatgctttatcactagagtacacatatctattgacaag # tcagcttgaacagcaacggaaatattttgaacagaagatgactcaagttgaaaaaagtgcacaagaaagggctgatatattggacgtgaaatataaaa # ccactatagatgacttagagaaagtgaaaataacgctaatgtgcgatgccttaccatcggaatgtagacaagcacatctgctggaaacagatcatggt # ttgcgagcacacagggcacagactgaactcctaaaaattaaacagaaatacctcatgtacacactaaaaaatagacagaagatacttggaaacatgga # acaggaaaatacttcactaaaaaacatggacagaaatacttcaacatacttgcaacaggaaatacttttgtacaacactaaaaacataaaacagaaat # acttgttacaacataaaaacatgacagaaatacctgtacaacactaa] # protein sequence = [MSEQTEKHSNLTAEKVNEETKPKNPDIGAFSREGSVASNASTSSGEKIVSKEFFSGNPMVERTCGILHLYKDNKKTSL # KEEVPRSELICMLAVPAAYTIHDLVKFTAPVVEGIEYMRIIRDTTPNQYMVLVKFRNQRLADEFFNTYNNVSFNSIEPDICQLIYVAKVEVMKDSELC # RNISEFVLSPIKFEITRFNYSQEHNLCNKASTFNLHKNNNFTPEKGLVLPVTGLTELPNCPVCLDRMSVDGTPVLTILCNHTFHVNCLAKWGDTSCPV # CRYCQTPEETADQRCMTCGSQESLWICLVCGNIGCGRYVELHAYKHFQETQHTYAMQLGNSRVWDYVGDNFVHRLVQSKGDGKLVAVEDQQSSEMDGK # VDALSLEYTYLLTSQLEQQRKYFEQKMTQVEKSAQERADILDVKYKTTIDDLEKVKITLMCDALPSECRQAHLLETDHGLRAHRAQTELLKIKQKYLM # YTLKNRQKILGNMEQENTSLKNMDRNTSTYLQQEILLYNTKNIKQKYLLQHKNMTEIPVQH] # sequence of block unknown_A 58 [MVERTCGILHLYKDNKKTS] 77 # sequence of block unknown_B 80 [EVPRSELICMLAVPAAYTIHDLVKFTAPVV] 110 # sequence of block unknown_C 110 [EGIEYMRIIRD] 121 # sequence of block unknown_D 121 [TTPNQYMVLVKFRNQ] 136 # sequence of block unknown_E 138 [ADEFFNTYNNVSFNSIEPD] 157 # sequence of block unknown_F 157 [ICQLIYVAKVEVMKD] 172 # sequence of block unknown_G 223 [VLPVTGLTELPNCPVCLDRMSV] 245 # sequence of block unknown_H 248 [PVLTILCNHTFHVNCLAKWGDTSCPVCRYCQTPE] 282 # sequence of block unknown_I 284 [ADQRCMTCGS] 294 # sequence of block unknown_J 294 [QESLWICLVCGNIGCGRYV] 313 # sequence of block unknown_K 314 [LHAYKHFQETQHTYAMQLGNSRVWDYVGDNFVHRLVQSK] 353 # sequence of block unknown_L 371 [KVDALSLEYTYLLTSQLEQQRKYFEQKMT] 400 # sequence of block unknown_O 447 [TDHGLRAHRAQTELLKIKQKYLMYTLKNR] 476 # sequence of block unknown_P 483 [EQENTSLKNMDRNTSTYLQQE] 504 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093709HP.prfl --predictionStart=0 --predictionEnd=36617 --species=fly ./tmp/Contig2464220180911_busco_2432604931_.temp