# 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..473]--> unknown_A (23) <--[22..56]--> unknown_B (68) <--[0..15]--> unknown_C (32) <--[0..1]--> unknown_D (77) <--[0..5]--> unknown_E (57) <--[0..1]--> unknown_F (8) <--[3..22]--> unknown_G (25) <--[12..30]--> unknown_H (11) <--[4..12]--> unknown_I (12) <--[5..15]--> unknown_J (13) <--[2..6]--> unknown_K (14) <--[3..34]--> unknown_L (12) <--[2..7]--> unknown_M (16) <--[1..12]--> unknown_N (22) <--[4..28]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4295120180911_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 = 21288, name = Contig42951) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig42951 AUGUSTUS gene 677 19545 0.01 - . g1 Contig42951 AUGUSTUS transcript 677 19545 0.01 - . g1.t1 Contig42951 AUGUSTUS exon 677 746 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS stop_codon 693 695 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 747 3612 0.1 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 3799 5755 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 5955 6196 0.97 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 6334 6729 0.97 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 6838 6977 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 7086 7533 0.8 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 7624 9334 0.76 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 9485 9812 0.63 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 10128 13233 0.75 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 13351 14764 0.12 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 14844 15911 0.11 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 16081 16730 0.97 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 16861 18639 1 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS intron 18819 19034 0.98 - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 693 746 0.09 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 3613 3798 0.98 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 3613 3798 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 5756 5954 0.96 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 5756 5954 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 6197 6333 1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 6197 6333 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 6730 6837 0.97 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 6730 6837 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 6978 7085 0.95 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 6978 7085 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 7534 7623 0.84 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 7534 7623 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 9335 9484 0.91 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 9335 9484 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 9813 10127 0.65 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 9813 10127 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 13234 13350 0.96 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 13234 13350 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 14765 14843 0.11 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 14765 14843 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 15912 16080 0.53 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 15912 16080 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 16731 16860 1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 16731 16860 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 18640 18818 0.98 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 18640 18818 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS CDS 19035 19248 0.36 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 19035 19343 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS start_codon 19246 19248 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS exon 19505 19545 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS tss 19545 19545 . - . transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 735 746 1.24 - 0 target "unknown_N[19..22]"; target_start 709; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 3613 3666 5.85 - 0 target "unknown_N[1..18]"; target_start 709; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 3676 3723 4.25 - 0 target "unknown_M[1..16]"; target_start 690; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 3733 3768 4 - 0 target "unknown_L[1..12]"; target_start 675; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 5756 5797 5.08 - 0 target "unknown_K[1..14]"; target_start 651; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 5807 5845 5.11 - 0 target "unknown_J[1..13]"; target_start 635; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 5879 5914 6.63 - 0 target "unknown_I[1..12]"; target_start 612; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 5927 5954 5.15 - 1 target "unknown_H[2..11]"; target_start 597; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 6197 6201 3.1 - 0 target "unknown_H[1..2]"; target_start 597; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 6253 6327 3.7 - 0 target "unknown_G[1..25]"; target_start 555; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 6739 6762 4.99 - 0 target "unknown_F[1..8]"; target_start 542; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 6763 6837 10.2 - 0 target "unknown_E[33..57]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 6978 7073 11.5 - 0 target "unknown_E[1..32]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 7537 7623 7.47 - 0 target "unknown_D[49..77]"; target_start 403; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 9335 9478 10.4 - 0 target "unknown_D[1..48]"; target_start 403; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 9482 9484 9.12 - 0 target "unknown_C[32..32]"; target_start 370; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 9813 9905 8.33 - 0 target "unknown_C[1..31]"; target_start 370; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 9906 10109 8.29 - 0 target "unknown_B[1..68]"; target_start 302; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 13330 13350 1.66 - 0 target "unknown_A[17..23]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; Contig42951 AUGUSTUS protein_match 14765 14812 3.92 - 0 target "unknown_A[1..16]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgccactgaacattccaggacaaggtaccatgcctcagcaaccagccagtatgccagcacaagtccccatgcaggcag # ctccagtaatgcctacacaagtcggggtgcctccacaggtcaccatgacaacaccaatggtaccacctggtaccatggtaacaccccaaaggccagtt # ggtcccggaatgatgatgcctacagggggtcagcaaggtctgcttccacccgggactcagacggtaccccaaggcacacagattcctgtcactcatcc # tcccatgcaccaggggccccctccaccgggtactcagcctgtgtctgcccagccacagcctcaagagcggcctccaaattctgccccagtagaaatgg # agaaaatgtcttcatcacaggctgaatctgcatcatcaaaggaaataaaattgccacaggccttggagaaggtgttagctttcaaagatgtcagggca # caagaagtgggtgttacacacgaggaaatagaacagatgaacacaccaatggaacgtgatattgacgaggaagatgccagtgaggatgtaggatacgg # tacatatgacatggaggaggaggaggaggaagccaccaaagtgggcgcagttaaagaggtaatgcttaatgatgatactattacatgtcttctagatt # gtgtgaatttggaggtgctaaagaggtatattcaggaacaacttgagcttgatccaactgacccaaattatttcatcttttcaaagatctttgaagcc # ttcaagatttcggaggaaaagagagaagaaaagtcagacaagaaagatgacatgaagaaagagactattcctctgaaaaaggaggaagaggacaagga # tgaggacagtgatgatgacgccccgattaagaaagaggaagatgacggccagaaactgtccaagaaaaagttaaagaagatgacacgactcagcgtag # ctcagctaaaacaactggtcagtcggccagacgtggtagaaatgcatgatgtcactgcccaggacccccgcctactggtacatctaaaagccaccagg # aacactgtccctgttccacgacactggtgtttcaagagaaaatacctccaaggaaagagggggatagagaaacctccatttgaattgcccgattacat # caaagccactggaatcatggagatgagagaggctcttgctgaaaaggaagatcaaaagaatttgaaggccaagatgagggagaaagtgcgaccaaaga # tggggaaaattgacattgattaccagaaactccacgatgctttctttaggtggcaaaccaagcctaaaatgacaattcatggggatctgtattatgag # ggaaaagaatttgaaaccagactgaaggagaaaaagccagggaatctctccgacgagttgaaaactgccctaggaatgcctctaggacacaattccga # gaagtttcctccaccttggttaatcgccatgcagcgatatggaccacccccctcttatccgaacctgaagatcccaggactgagtgctcccattccgg # agagttgttcatttggctaccatgcgggtggatggggaaagccaccagtcgatgaaaatggtaaaccactgtatggtgatgtgtttggtacgcaaagt # tcagaattccagactcctatacctgaggaggatgtagataagtctctctggggagaaatggatgaagaatcttcctcagaagaggaatccgaggaaga # agaggaggaggaggaggatgcctcgggacttgtcactcctggtccggagggtctggtgacacctagtggaataacttctgtaccaatgggaatggaga # ccccagacatgatagaattgaggaagaagaggattgaggatgccatggatcaaggaggagaaacaccagctctctacacaatcttacccgagaaaaag # tcctctgtgggaggggctatgatgggatccgcccacgtgtacgacacgacagctgtaatagcaggtaaaaaagacaaaccaggcacagaaggtattga # agtggcacttaatcctgaagagttagatctcgatacagcagccatgcaagccaaatacgaccagacaatgagggaacagcagtcccagctggagaagg # aagacctcagtgacatggtggctgagcacgctgccaaacaaaaggagaatcataaggtcaccaggtgggagattttactacacatacgattcgcttag] # protein sequence = [MPLNIPGQGTMPQQPASMPAQVPMQAAPVMPTQVGVPPQVTMTTPMVPPGTMVTPQRPVGPGMMMPTGGQQGLLPPGT # QTVPQGTQIPVTHPPMHQGPPPPGTQPVSAQPQPQERPPNSAPVEMEKMSSSQAESASSKEIKLPQALEKVLAFKDVRAQEVGVTHEEIEQMNTPMER # DIDEEDASEDVGYGTYDMEEEEEEATKVGAVKEVMLNDDTITCLLDCVNLEVLKRYIQEQLELDPTDPNYFIFSKIFEAFKISEEKREEKSDKKDDMK # KETIPLKKEEEDKDEDSDDDAPIKKEEDDGQKLSKKKLKKMTRLSVAQLKQLVSRPDVVEMHDVTAQDPRLLVHLKATRNTVPVPRHWCFKRKYLQGK # RGIEKPPFELPDYIKATGIMEMREALAEKEDQKNLKAKMREKVRPKMGKIDIDYQKLHDAFFRWQTKPKMTIHGDLYYEGKEFETRLKEKKPGNLSDE # LKTALGMPLGHNSEKFPPPWLIAMQRYGPPPSYPNLKIPGLSAPIPESCSFGYHAGGWGKPPVDENGKPLYGDVFGTQSSEFQTPIPEEDVDKSLWGE # MDEESSSEEESEEEEEEEEDASGLVTPGPEGLVTPSGITSVPMGMETPDMIELRKKRIEDAMDQGGETPALYTILPEKKSSVGGAMMGSAHVYDTTAV # IAGKKDKPGTEGIEVALNPEELDLDTAAMQAKYDQTMREQQSQLEKEDLSDMVAEHAAKQKENHKVTRWEILLHIRFA] # sequence of block unknown_N 709 [LEKEDLSDMVAEHAAKQKENHK] 731 # sequence of block unknown_M 690 [DTAAMQAKYDQTMREQ] 706 # sequence of block unknown_L 675 [TEGIEVALNPEE] 687 # sequence of block unknown_K 651 [GAMMGSAHVYDTTA] 665 # sequence of block unknown_J 635 [TPALYTILPEKKS] 648 # sequence of block unknown_I 612 [METPDMIELRKK] 624 # sequence of block unknown_H 597 [EGLVTPSGITS] 608 # sequence of block unknown_G 555 [IPEEDVDKSLWGEMDEESSSEEESE] 580 # sequence of block unknown_F 542 [DVFGTQSS] 550 # sequence of block unknown_E 485 [FPPPWLIAMQRYGPPPSYPNLKIPGLSAPIPESCSFGYHAGGWGKPPVDENGKPLYG] 542 # sequence of block unknown_D 403 [QKNLKAKMREKVRPKMGKIDIDYQKLHDAFFRWQTKPKMTIHGDLYYEGKEFETRLKEKKPGNLSDELKTALGMPLG] 480 # sequence of block unknown_C 370 [GKRGIEKPPFELPDYIKATGIMEMREALAEKE] 402 # sequence of block unknown_B 302 [DGQKLSKKKLKKMTRLSVAQLKQLVSRPDVVEMHDVTAQDPRLLVHLKATRNTVPVPRHWCFKRKYLQ] 370 # sequence of block unknown_A 241 [TDPNYFIFSKIFEAFKISEEKRE] 264 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BJE.prfl --predictionStart=0 --predictionEnd=30055 --species=fly ./tmp/Contig4295120180911_busco_2432604931_.temp