# 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 # --[17..86]--> unknown_B (25) <--[15..57]--> unknown_E (31) <--[11..30]--> unknown_G (18) <--[8..16]--> unknown_H (9) <--[0..2]--> unknown_I (21) <--[5..40]--> unknown_J (12) <--[3..8]--> unknown_K (16) <--[4..15]--> unknown_L (20) <--[2..29]--> unknown_M (17) <--[0..15]--> unknown_N (15) <--[0..1]--> unknown_O (19) <--[0..21]--> unknown_P (15) <--[0..26]--> unknown_Q (20) <--[6..33]--> unknown_R (31) <--[0..13]--> unknown_S (19) <--[0..23]--> unknown_T (35) <--[0..101]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3876420180911_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 = 16106, name = Contig38764) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig38764 AUGUSTUS gene 48 15697 0.01 + . g1 Contig38764 AUGUSTUS transcript 48 15697 0.01 + . g1.t1 Contig38764 AUGUSTUS exon 48 110 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS start_codon 56 58 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 111 385 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 408 607 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 630 706 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 718 814 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 865 1032 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 1155 2716 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 2759 2896 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 3003 4637 0.69 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 4759 4948 0.94 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 5145 5241 0.19 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 5323 5565 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 5724 6815 0.76 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 6944 8101 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS intron 8204 11660 0.06 + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 56 110 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 386 407 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 386 407 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 608 629 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 608 629 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 707 717 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 707 717 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 815 864 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 815 864 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 1033 1154 0.08 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 1033 1154 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 2717 2758 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 2717 2758 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 2897 3002 0.66 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 2897 3002 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 4638 4758 0.81 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 4638 4758 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 4949 5144 0.89 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 4949 5144 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 5242 5322 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 5242 5322 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 5566 5723 0.7 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 5566 5723 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 6816 6943 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 6816 6943 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 8102 8203 0.05 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 8102 8203 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS CDS 11661 11800 0.07 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 11661 11894 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS stop_codon 11798 11800 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 13590 13673 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 14783 14894 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS exon 15371 15697 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS tts 15697 15697 . + . transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 110 110 1 + 0 target "unknown_B[1..1]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 386 407 0.997 + 1 target "unknown_B[1..8]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 608 629 1.31 + 0 target "unknown_B[9..16]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 707 717 0.839 + 2 target "unknown_B[16..19]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 815 833 1.83 + 1 target "unknown_B[19..25]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 1071 1154 5.91 + 0 target "unknown_E[1..28]"; target_start 66; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 2717 2725 2.56 + 0 target "unknown_E[29..31]"; target_start 66; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 2927 2980 3.55 + 0 target "unknown_G[1..18]"; target_start 118; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 4640 4666 5.27 + 0 target "unknown_H[1..9]"; target_start 144; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 4673 4735 2.78 + 0 target "unknown_I[1..21]"; target_start 155; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 4950 4985 3.84 + 0 target "unknown_J[1..12]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 4998 5045 3.76 + 0 target "unknown_K[1..16]"; target_start 200; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5070 5129 3.73 + 0 target "unknown_L[1..20]"; target_start 224; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5269 5319 2.87 + 0 target "unknown_M[1..17]"; target_start 258; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5569 5613 7.08 + 0 target "unknown_N[1..15]"; target_start 277; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5614 5670 7.33 + 0 target "unknown_O[1..19]"; target_start 292; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5671 5715 4.31 + 0 target "unknown_P[1..15]"; target_start 311; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 5716 5723 6.06 + 0 target "unknown_Q[1..3]"; target_start 326; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 6816 6867 4.47 + 1 target "unknown_Q[3..20]"; target_start 326; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 6892 6943 6.27 + 0 target "unknown_R[1..18]"; target_start 354; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 8102 8142 6.59 + 2 target "unknown_R[18..31]"; target_start 354; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 8143 8199 4.32 + 0 target "unknown_S[1..19]"; target_start 385; transcript_id "g1.t1"; gene_id "g1"; Contig38764 AUGUSTUS protein_match 11666 11770 3.9 + 0 target "unknown_T[1..35]"; target_start 407; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaaattatctttacatcataattcagttaagtacagaacccgtgggggtccggacagtaaattcgcaatagaaatca # tgacaatttattttatgcatgtcaaggtcagaaaaactgtctctctgaagtttgttaagcaggaagatcacaaacattgcagaaaggatgtttgtatt # agaaagttacacgaactgaagagtgatgaaagctgcgttgtgattgggacactgtttaaacacatggaactgaaaccaagcatattacaagaaatcag # tgaagagcatcacgatcaagatcaaacgtgtaacctcccgttgtccaaaccagttagaacaaagtttgtgtcgatacagaccagcttttatctggagg # atgagctacagaggattattttagtaggagacctggacgtccaaacagctgttacaggtgttatcatagctgtgtatggcaaagagccggatgatgac # cgtggcaagttccatgtacaggattactgttttcgaatgttaaaagaacagatccccaggccagtgttagagaatgacaaatatttaatcctgatatc # cggactagaaataggcagtaaggaagagcagatcttgaccctgcagctctttgttgacatggtgacaggaatgctgggtaatagttcagaacagggtc # actgttcggagatttccagaatcattgtagcagggaattccttgagttctagcacacaagacagagacagtttacaaaaggcaaagtacctgagtaag # aaaacggcagcaggaagcgtggatgcggttaaaacactagatgatgtcttcactcaactagcaagttcggtggatgtagacctgatgccgggtgagta # tgaccctgccaattatacgctaccccagcagccactccacaagtgtatgttcccgcaggcctcgcgttatccgaccttccagaccgtgaccaacccgt # acgacttcatcgtagaaggagtcaggattcttgggacatcaggtcagcctgtgcaggacatcattaagtacagtaccaatgaagactcgctggatatc # ctgcagaagactgttgagtgggggcacctggcacccacagcaccagacacactgggttgttatcctttctataaggaggatcccttcatcattggtga # ttgtccacatatactttttgctggaaacatgacaaagtatgactccaaaatcttcaaagatcctggtggacaggaagtcctattagtgagtgttccca # aattctgccagacctcaacagcagtgatgattaatctaaggactcaagagtgtcaccccatgcaattctcagcctctttcacaccagaacccaacaga # tag] # protein sequence = [MKLSLHHNSVKYRTRGGPDSKFAIEIMTIYFMHVKVRKTVSLKFVKQEDHKHCRKDVCIRKLHELKSDESCVVIGTLF # KHMELKPSILQEISEEHHDQDQTCNLPLSKPVRTKFVSIQTSFYLEDELQRIILVGDLDVQTAVTGVIIAVYGKEPDDDRGKFHVQDYCFRMLKEQIP # RPVLENDKYLILISGLEIGSKEEQILTLQLFVDMVTGMLGNSSEQGHCSEISRIIVAGNSLSSSTQDRDSLQKAKYLSKKTAAGSVDAVKTLDDVFTQ # LASSVDVDLMPGEYDPANYTLPQQPLHKCMFPQASRYPTFQTVTNPYDFIVEGVRILGTSGQPVQDIIKYSTNEDSLDILQKTVEWGHLAPTAPDTLG # CYPFYKEDPFIIGDCPHILFAGNMTKYDSKIFKDPGGQEVLLVSVPKFCQTSTAVMINLRTQECHPMQFSASFTPEPNR] # sequence of block unknown_B 18 [DSKFAIEIMTIYFMHVKVRKTVSLK] 43 # sequence of block unknown_E 66 [SDESCVVIGTLFKHMELKPSILQEISEEHHD] 97 # sequence of block unknown_G 118 [TSFYLEDELQRIILVGDL] 136 # sequence of block unknown_H 144 [VIIAVYGKE] 153 # sequence of block unknown_I 155 [DDRGKFHVQDYCFRMLKEQIP] 176 # sequence of block unknown_J 184 [YLILISGLEIGS] 196 # sequence of block unknown_K 200 [ILTLQLFVDMVTGMLG] 216 # sequence of block unknown_L 224 [SEISRIIVAGNSLSSSTQDR] 244 # sequence of block unknown_M 258 [AGSVDAVKTLDDVFTQL] 275 # sequence of block unknown_N 277 [SVDVDLMPGEYDPAN] 292 # sequence of block unknown_O 292 [YTLPQQPLHKCMFPQASRY] 311 # sequence of block unknown_P 311 [PTFQTVTNPYDFIVE] 326 # sequence of block unknown_Q 326 [GVRILGTSGQPVQDIIKYST] 346 # sequence of block unknown_R 354 [QKTVEWGHLAPTAPDTLGCYPFYKEDPFIIG] 385 # sequence of block unknown_S 385 [DCPHILFAGNMTKYDSKIF] 404 # sequence of block unknown_T 407 [GGQEVLLVSVPKFCQTSTAVMINLRTQECHPMQFS] 442 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DO5.prfl --predictionStart=0 --predictionEnd=28202 --species=fly ./tmp/Contig3876420180911_busco_2432604931_.temp