# 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 # --[2..646]--> unknown_A (43) <--[17..28]--> unknown_C (59) <--[0..1]--> unknown_D (48) <--[0..1]--> unknown_E (24) <--[22..276]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3620620180911_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 = 19982, name = Contig36206) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig36206 AUGUSTUS gene 774 8139 0.01 + . g1 Contig36206 AUGUSTUS transcript 774 8139 0.01 + . g1.t1 Contig36206 AUGUSTUS exon 774 868 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 2014 2588 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS start_codon 2077 2079 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 2589 3069 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 3191 4840 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 4968 5082 0.16 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 5237 5405 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 5599 6811 0.08 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 6927 7014 0.09 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS intron 7080 8051 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 2077 2588 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 3070 3190 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 3070 3190 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 4841 4967 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 4841 4967 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 5083 5236 0.94 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 5083 5236 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 5406 5598 0.65 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 5406 5598 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 6812 6926 0.08 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 6812 6926 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 7015 7079 0.09 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 7015 7079 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS CDS 8052 8069 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS exon 8052 8139 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS stop_codon 8067 8069 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS tts 8139 8139 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 4841 4967 4.22 + 0 target "unknown_A[1..43]"; target_start 211; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 5083 5084 1 + 2 target "unknown_A[43..43]"; target_start 211; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 5139 5236 4.75 + 0 target "unknown_C[1..33]"; target_start 272; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 5406 5484 5.08 + 1 target "unknown_C[33..59]"; target_start 272; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 5485 5598 5.27 + 0 target "unknown_D[1..38]"; target_start 331; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 6812 6841 1.93 + 0 target "unknown_D[39..48]"; target_start 331; transcript_id "g1.t1"; gene_id "g1"; Contig36206 AUGUSTUS protein_match 6842 6913 1.97 + 0 target "unknown_E[1..24]"; target_start 379; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggatagcaggatttggactgtgtttatatcctccgacttcctaaatgatcccttctgtaaactttacgggaaaattg # tagaggaggattgttttgttcttgttttagacaagcactatgttgatgccaagggctgtgataaaccaataggtacgtttcatcaagttggaacagtg # ttgaatggagaagaaagcagaaaatcacagaatccacccaacagcatattcatcgacctatattttagccatgatggaaatattttgtgcaaaatgat # aactaaacatcttgaaacactaaaatgcaacattgtgatatttgaaccacaagaattgttagaatcttactttctatgttgggatactttgtcaacaa # tcagcagtaaaaacgtaatagatattttgtcaaaagagattaacaccaaggcaccccatgtcagaacacccaggattcatcgactgcagattctttgg # ctgttcgtgttccagtttgttggatttttgttggataataggttagcgaatgcttgttggagacagttgttggactccctgctgggagtggttttgat # gtactttttcatgtactacagtatgtctgatgaagtcgcagcacatatcatcacatgggcttatgcggtagctgagtacctccattcactggtggagt # ggttgatgggtgccccggcaggtctcaaactaaacaaacaattgaccgaatttttaggacactttttcctctatcatatttacctctggaaaggatac # ctaggaatactacagcctgttctgggcggtgtgttgtggtactcttctctgtttggaattctgggattgacggcacagctgtgttttctgcgagacgt # cctgtcagtgatgactctgcatatatattgcttttatgtttatgctgcaagactgtatcaattccaagtatatgccttgtcggccttttggcgcttgt # ttcgcggtaaaaagtggaatacgctgcggcagcgattggactcggtccgctatgacgtggaccagcttttcctgggaactctgctgttcaccatactt # ctctttactctaccaacatctgcactttactatgtcgttttcacattgcttagactcattgtattaacagctcatcaaatgatttttaaaattgtcca # gactttagattcattgccaatattttcgattttgatgtggagtgtgaattcgagatgtgttaatggagatattttgtttaccattattccacagaaaa # atatagacatttcatcattattctcactgcagtatcagatctgtacttag] # protein sequence = [MDSRIWTVFISSDFLNDPFCKLYGKIVEEDCFVLVLDKHYVDAKGCDKPIGTFHQVGTVLNGEESRKSQNPPNSIFID # LYFSHDGNILCKMITKHLETLKCNIVIFEPQELLESYFLCWDTLSTISSKNVIDILSKEINTKAPHVRTPRIHRLQILWLFVFQFVGFLLDNRLANAC # WRQLLDSLLGVVLMYFFMYYSMSDEVAAHIITWAYAVAEYLHSLVEWLMGAPAGLKLNKQLTEFLGHFFLYHIYLWKGYLGILQPVLGGVLWYSSLFG # ILGLTAQLCFLRDVLSVMTLHIYCFYVYAARLYQFQVYALSAFWRLFRGKKWNTLRQRLDSVRYDVDQLFLGTLLFTILLFTLPTSALYYVVFTLLRL # IVLTAHQMIFKIVQTLDSLPIFSILMWSVNSRCVNGDILFTIIPQKNIDISSLFSLQYQICT] # sequence of block unknown_A 211 [AVAEYLHSLVEWLMGAPAGLKLNKQLTEFLGHFFLYHIYLWKG] 254 # sequence of block unknown_C 272 [FGILGLTAQLCFLRDVLSVMTLHIYCFYVYAARLYQFQVYALSAFWRLFRGKKWNTLRQ] 331 # sequence of block unknown_D 331 [RLDSVRYDVDQLFLGTLLFTILLFTLPTSALYYVVFTLLRLIVLTAHQ] 379 # sequence of block unknown_E 379 [MIFKIVQTLDSLPIFSILMWSVNS] 403 # end gene g1 ### # start gene g2 Contig36206 AUGUSTUS gene 8586 16533 0.01 + . g2 Contig36206 AUGUSTUS transcript 8586 16533 0.01 + . g2.t1 Contig36206 AUGUSTUS tss 8586 8586 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 8586 8760 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS start_codon 8748 8750 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 8761 9042 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 9076 10857 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 10952 11065 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 11219 11388 0.16 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 11582 12428 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 12467 13059 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS intron 13120 16000 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 8748 8760 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 9043 9075 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 9043 9075 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 10858 10951 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 10858 10951 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 11066 11218 0.13 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 11066 11218 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 11389 11581 0.12 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 11389 11581 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 12429 12466 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 12429 12466 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 13060 13119 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 13060 13119 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS CDS 16001 16082 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS exon 16001 16533 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS stop_codon 16080 16082 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS tts 16533 16533 . + . transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 8760 8760 1 + 0 target "unknown_A[1..1]"; target_start 4; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 9043 9075 1.17 + 1 target "unknown_A[1..12]"; target_start 3; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 10858 10951 1.89 + 1 target "unknown_A[12..43]"; target_start 3; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 11066 11066 1 + 1 target "unknown_A[43..43]"; target_start 4; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 11121 11218 4.75 + 0 target "unknown_C[1..33]"; target_start 65; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 11389 11467 5.08 + 1 target "unknown_C[33..59]"; target_start 65; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 11468 11581 5.27 + 0 target "unknown_D[1..38]"; target_start 124; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 12429 12458 1.36 + 0 target "unknown_D[39..48]"; target_start 124; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 12462 12466 2.35 + 0 target "unknown_E[1..2]"; target_start 173; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 13060 13119 1.3 + 0 target "unknown_E[3..22]"; target_start 172; transcript_id "g2.t1"; gene_id "g2"; Contig36206 AUGUSTUS protein_match 16001 16007 0.9 + 1 target "unknown_E[22..24]"; target_start 173; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgctgtctgttcaaagttgcgatcttcttacccccatgtgcttgttggttgatgggtgcccggcaggtctcaaactaa # acaaacaattgaccgaatttttaggacactttttccctatcatatttacctctggaaaggtgttacctaggaatactacagcctgttctggcggtgtg # ttgtggtacttcttctcttttggaattctgggattgacggcacagctgtgttttctgcgagacgtcctgtcagtgatgactctgcatatatattgctt # ttatgtttatgctgcaagactgtatcaattccaagtatatgccttgtcggccttttggcgcttgtttcgcggtaaaaagtggaatacgctgcggcagc # gattggactcggtccgctatgacgtggaccagcttttcctgggaactctgctgttcaccatacttctctttactctaccaacatctgcactttactat # gtcgttttcacattgttccgtgcgtttacgttgtttgttttcatgcgcgtattatgtgtatgtatctggtatctagaaaaatatagacatttcatcat # tattctccactgcaatggtgtagacgacatctgcgattcgtcgagttggggagcggtaccaggacgcttgtgttgtaaaacgtcgacaattcggtga] # protein sequence = [MLSVQSCDLLTPMCLLVDGCPAGLKLNKQLTEFLGHFFPIIFTSGKVLPRNTTACSGGVLWYFFSFGILGLTAQLCFL # RDVLSVMTLHIYCFYVYAARLYQFQVYALSAFWRLFRGKKWNTLRQRLDSVRYDVDQLFLGTLLFTILLFTLPTSALYYVVFTLFRAFTLFVFMRVLC # VCIWYLEKYRHFIIILHCNGVDDICDSSSWGAVPGRLCCKTSTIR] # sequence of block unknown_A 4 [QSCDLLTPMCLLVDGCPAGLKLNKQLTEFLGHFFPIIFTSGKV] 47 # sequence of block unknown_C 65 [FGILGLTAQLCFLRDVLSVMTLHIYCFYVYAARLYQFQVYALSAFWRLFRGKKWNTLRQ] 124 # sequence of block unknown_D 124 [RLDSVRYDVDQLFLGTLLFTILLFTLPTSALYYVVFTLFRAFTLFVFM] 172 # sequence of block unknown_E 173 [VLCVCIWYLEKYRHFIIILHCNGV] 197 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SPQ.prfl --predictionStart=0 --predictionEnd=24966 --species=fly ./tmp/Contig3620620180911_busco_2432604931_.temp