# 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 # --[9..364]--> unknown_B (21) <--[14..96]--> unknown_D (16) <--[10..126]--> unknown_F (18) <--[2..27]--> unknown_G (26) <--[16..40]--> unknown_H (26) <--[0..1]--> unknown_I (36) <--[0..1]--> unknown_J (20) <--[0..192]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3012820180911_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 = 16439, name = Contig30128) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig30128 AUGUSTUS gene 6 15100 0.01 + . g1 Contig30128 AUGUSTUS transcript 6 15100 0.01 + . g1.t1 Contig30128 AUGUSTUS start_codon 6 8 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 61 1494 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 1507 2156 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 2176 2900 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 2931 3190 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 3339 8408 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 8435 8613 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 8639 9834 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 9888 10546 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 10644 10852 0.12 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 11013 12693 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 12724 13152 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS intron 13173 13898 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 6 60 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 6 60 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 1495 1506 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 1495 1506 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 2157 2175 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 2157 2175 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 2901 2930 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 2901 2930 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 3191 3338 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 3191 3338 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 8409 8434 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 8409 8434 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 8614 8638 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 8614 8638 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 9835 9887 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 9835 9887 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 10547 10643 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 10547 10643 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 10853 11012 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 10853 11012 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 12694 12723 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 12694 12723 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 13153 13172 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 13153 13172 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS CDS 13899 13979 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS exon 13899 15100 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS stop_codon 13977 13979 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS tts 15100 15100 . + . transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 60 60 1 + 0 target "unknown_B[1..1]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 1495 1506 1.49 + 1 target "unknown_B[1..5]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 2157 2175 1.58 + 1 target "unknown_B[5..11]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 2901 2930 1.27 + 0 target "unknown_B[12..21]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 3191 3191 1 + 1 target "unknown_B[21..21]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 3255 3302 2.06 + 0 target "unknown_D[1..16]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 8421 8434 1.06 + 0 target "unknown_F[1..5]"; target_start 92; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 8614 8638 1.13 + 0 target "unknown_F[6..14]"; target_start 91; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 9835 9849 1.2 + 0 target "unknown_F[14..18]"; target_start 92; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 9865 9887 2.49 + 0 target "unknown_G[1..8]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 10547 10601 2.38 + 1 target "unknown_G[8..26]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 10862 10939 2.56 + 0 target "unknown_H[1..26]"; target_start 158; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 10940 11012 3.31 + 0 target "unknown_I[1..25]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 12694 12723 1.59 + 1 target "unknown_I[25..35]"; target_start 183; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 13153 13157 0.19 + 2 target "unknown_I[35..36]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 13158 13172 1.52 + 0 target "unknown_J[1..5]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; Contig30128 AUGUSTUS protein_match 13899 13943 1.23 + 0 target "unknown_J[6..20]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgttaagattgtattgtttcatccccattgttatttttgtacatgatatgaccggatataacgtatatgttgtgttca # tccccttcgctatcaaaaaatcctggggagaacactggttccctggtcagaaacccaaggtgaccttcacaattgatgaggaattagcaaaaggctca # ccaggagacatgccgatcccgcgggaacacaacatgattctgacggggctggggaaccagaacttagtagttttctctcagaacccggttgtgaggaa # cttgcgtaccgtttggtgtgaggaacttgtgtaccgtttggagggcaggactgccagccagcatcggaaccgcagttatctgaatctcaaacgaatgc # agcttgaagccaaaaacaaacctcagcgagaagtcattcagattacaaaggtggttccgatgtataaacccgtcaaagaccatgtacacaacgcaccg # tcatcagacaaaaataaagtggagaagagactcagggaagataaagaaaaagtcatggacattttgtttaatgcatttgagaaacatcagtattacaa # tgtgaaggaccttgtttccattaccaaacagccaatagtaagtcttgttactttatcattaacggtcgcaaatcaaaatgagaaagatgtatataaaa # agctacattgttttacaggggtaatacggaaatatatatggtccatgaaaaaagcctttattgggcttggcttggtttgcaatccttag] # protein sequence = [MLRLYCFIPIVIFVHDMTGYNVYVVFIPFAIKKSWGEHWFPGQKPKVTFTIDEELAKGSPGDMPIPREHNMILTGLGN # QNLVVFSQNPVVRNLRTVWCEELVYRLEGRTASQHRNRSYLNLKRMQLEAKNKPQREVIQITKVVPMYKPVKDHVHNAPSSDKNKVEKRLREDKEKVM # DILFNAFEKHQYYNVKDLVSITKQPIVSLVTLSLTVANQNEKDVYKKLHCFTGVIRKYIWSMKKAFIGLGLVCNP] # sequence of block unknown_B 18 [GYNVYVVFIPFAIKKSWGEHW] 39 # sequence of block unknown_D 60 [GDMPIPREHNMILTGL] 76 # sequence of block unknown_F 92 [LRTVWCEELVYRLEGRTA] 110 # sequence of block unknown_G 115 [RSYLNLKRMQLEAKNKPQREVIQITK] 141 # sequence of block unknown_H 158 [SDKNKVEKRLREDKEKVMDILFNAFE] 184 # sequence of block unknown_I 184 [KHQYYNVKDLVSITKQPIVSLVTLSLTVANQNEKDV] 220 # sequence of block unknown_J 220 [YKKLHCFTGVIRKYIWSMKK] 240 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DS4.prfl --predictionStart=0 --predictionEnd=31050 --species=fly ./tmp/Contig3012820180911_busco_2432604931_.temp