# 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 # --[1..165]--> unknown_A (22) <--[2..22]--> unknown_B (14) <--[0..1]--> unknown_C (33) <--[0..1]--> unknown_D (29) <--[0..3]--> unknown_E (14) <--[4..6]--> unknown_F (7) <--[0..1]--> unknown_G (18) <--[9..19]--> unknown_I (18) <--[0..3]--> unknown_J (34) <--[0..13]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig346120180911_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 = 16113, name = Contig3461) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig3461 AUGUSTUS gene 171 12610 0.01 + . g1 Contig3461 AUGUSTUS transcript 171 12610 0.01 + . g1.t1 Contig3461 AUGUSTUS exon 171 1185 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 8855 8974 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS start_codon 8855 8857 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS intron 8975 9122 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS intron 9225 9564 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS intron 9707 9819 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS intron 9879 10546 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS intron 10697 10956 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 8855 8974 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 9123 9224 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 9123 9224 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 9565 9706 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 9565 9706 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 9820 9878 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 9820 9878 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 10547 10696 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 10547 10696 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS CDS 10957 11070 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS exon 10957 12610 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS stop_codon 11068 11070 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS tts 12610 12610 . + . transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 8912 8974 4.72 + 0 target "unknown_A[1..21]"; target_start 19; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9123 9125 7.32 + 0 target "unknown_A[22..22]"; target_start 19; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9132 9173 4.63 + 0 target "unknown_B[1..14]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9174 9224 6.61 + 0 target "unknown_C[1..17]"; target_start 57; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9565 9612 10.8 + 0 target "unknown_C[18..33]"; target_start 57; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9613 9699 11.9 + 0 target "unknown_D[1..29]"; target_start 90; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 9822 9863 7.03 + 0 target "unknown_E[1..14]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 10547 10567 9.65 + 0 target "unknown_F[1..7]"; target_start 141; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 10568 10621 5.25 + 0 target "unknown_G[1..18]"; target_start 148; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 10652 10696 5 + 0 target "unknown_I[1..15]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 10957 10965 4.01 + 0 target "unknown_I[16..18]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig3461 AUGUSTUS protein_match 10966 11067 7.22 + 0 target "unknown_J[1..34]"; target_start 194; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcggcgcccgttgagcacgagaaaaacgcaaacaaagtcattaaaagtgtttcaaggcaaagcaatgaaaagaggt # tgatagttgttttagaaaaggcttcgttagaatcagtaaaggtggggaagcagtttgagttgttaaactgcgataagcacaaaggattagcaaagaaa # ttcaaacgggacataacgctttgtcgtccagacataacacatcagtgcttgttaatgttgatggacagcccactgaacagagcagggcttctccaagt # atatattcatacagaaaagaacgtcctgatagaaatcaacccgcaaacaagaattcctcgaacgtttgatagattctgtggtcttatggtacagttat # tacacaagtacagtattcatgcagcagacggaccacaaaaacttttaaaagtgataaaaaaccctgttagtgaccattttcctctgggttgtaagaaa # tatgggacgtcgtttcatgtcgaaaaagtcacagatcctcgtgaaattgtgccagaaaaagaacctgttgttgtcgtggtaggagctctttcacatgg # aagtgtggatgttgactacacggaggacgaaatctccattagcagttaccccctgtctgcagctctcacctgtgcaaagatctgttcagcttttgaag # aaaaatggaatgttgtctga] # protein sequence = [MAAPVEHEKNANKVIKSVSRQSNEKRLIVVLEKASLESVKVGKQFELLNCDKHKGLAKKFKRDITLCRPDITHQCLLM # LMDSPLNRAGLLQVYIHTEKNVLIEINPQTRIPRTFDRFCGLMVQLLHKYSIHAADGPQKLLKVIKNPVSDHFPLGCKKYGTSFHVEKVTDPREIVPE # KEPVVVVVGALSHGSVDVDYTEDEISISSYPLSAALTCAKICSAFEEKWNVV] # sequence of block unknown_A 19 [RQSNEKRLIVVLEKASLESVKV] 41 # sequence of block unknown_B 43 [QFELLNCDKHKGLA] 57 # sequence of block unknown_C 57 [KKFKRDITLCRPDITHQCLLMLMDSPLNRAGLL] 90 # sequence of block unknown_D 90 [QVYIHTEKNVLIEINPQTRIPRTFDRFCG] 119 # sequence of block unknown_E 122 [QLLHKYSIHAADGP] 136 # sequence of block unknown_F 141 [VIKNPVS] 148 # sequence of block unknown_G 148 [DHFPLGCKKYGTSFHVEK] 166 # sequence of block unknown_I 176 [KEPVVVVVGALSHGSVDV] 194 # sequence of block unknown_J 194 [DYTEDEISISSYPLSAALTCAKICSAFEEKWNVV] 228 # end gene g1 ### # start gene g2 Contig3461 AUGUSTUS gene 12692 16113 0.01 - . g2 Contig3461 AUGUSTUS transcript 12692 16113 0.01 - . g2.t1 Contig3461 AUGUSTUS tts 12692 12692 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 12692 12901 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS stop_codon 12754 12756 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 12902 13030 0.92 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 13135 13247 1 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 13346 13444 1 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 13565 13713 0.99 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 13844 13942 0.62 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 14147 14332 0.22 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS intron 14397 16113 0.21 - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 12754 12901 0.92 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 13031 13134 0.98 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 13031 13134 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 13248 13345 1 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 13248 13345 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 13445 13564 1 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 13445 13564 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 13714 13843 0.91 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 13714 13843 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 13943 14146 0.62 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 13943 14146 . - . transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS CDS 14333 14396 0.34 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig3461 AUGUSTUS exon 14333 14396 . - . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtgaatctaacgttggacgaattggtgggcaacaggttgtaaatgtttccaatggatgcggggctggcagcattgct # catgagcttgggcatacctttgggtttgtacacgaacaatctcgttccgaccgagaccaacacatccttattgtcggtggcaatataagtcccgggag # cgaaaagaacttcgagaaatactccaacaagaaagtctacacttataacctctcgtatgatatcggatccatcatgcattatagcgacaaggcatttt # caagagatggagaatcaaagacaattgtcgcacgtgatgctctggttcagtcgtggatgggacaaagggacggaccaagctttctagatatcaagctc # gccaatgaggcttaccagtgcgacaggcattgcaaaaccaactttgtctgtcaaaatggtggatttatcggacccaactgtcgctgcatttgtcccta # tggagttagtggcttcacgtgcgacaacgtggcgccctctacaccaaattgtgggggaactttccggggagaaaatggcacgattctctctcctaatt # accccaacgaatataacagtaacgcggaatgccactggcttattgaaggtccgtttgaattcttaaaactgaccttccgtgactttcattcggaattc # gagtatgatgtcctcgacattcgtgtatacggaccagaaagggttgggcagatgatttctgggaataattttggagacgaggtcatctattttagcag # caataaacttcttctgcattttacctccgacaagaacacaaacttccgaggattccgaattgattattctagcattcacagaatagacatggattctc # actaa] # protein sequence = [CESNVGRIGGQQVVNVSNGCGAGSIAHELGHTFGFVHEQSRSDRDQHILIVGGNISPGSEKNFEKYSNKKVYTYNLSY # DIGSIMHYSDKAFSRDGESKTIVARDALVQSWMGQRDGPSFLDIKLANEAYQCDRHCKTNFVCQNGGFIGPNCRCICPYGVSGFTCDNVAPSTPNCGG # TFRGENGTILSPNYPNEYNSNAECHWLIEGPFEFLKLTFRDFHSEFEYDVLDIRVYGPERVGQMISGNNFGDEVIYFSSNKLLLHFTSDKNTNFRGFR # IDYSSIHRIDMDSH] # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370USJ.prfl --predictionStart=0 --predictionEnd=31064 --species=fly ./tmp/Contig346120180911_busco_2432604931_.temp