# 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 # --[8..110]--> unknown_B (19) <--[0..3]--> unknown_C (53) <--[0..2]--> unknown_D (16) <--[0..1]--> unknown_E (15) <--[9..33]--> unknown_G (12) <--[2..36]--> unknown_H (21) <--[5..24]--> unknown_I (16) <--[11..41]--> unknown_J (25) <--[2..8]--> unknown_K (16) <--[2..7]--> unknown_L (12) <--[0..8]--> unknown_M (23) <--[21..59]--> unknown_P (23) <--[0..30]--> unknown_Q (11) <--[0..8]--> unknown_R (31) <--[0..33]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2535820180911_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 = 29545, name = Contig25358) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig25358 AUGUSTUS gene 20973 32135 0.01 + . g1 Contig25358 AUGUSTUS transcript 20973 32135 0.01 + . g1.t1 Contig25358 AUGUSTUS tss 20973 20973 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 20973 21442 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS start_codon 21346 21348 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 21443 23734 0.18 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 23748 23813 0.33 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 23948 25442 0.48 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 25595 25796 0.32 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 25929 26126 0.77 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 26322 27092 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 27267 27488 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 27647 29613 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS intron 29746 31647 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 21346 21442 0.32 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 23735 23747 0.33 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 23735 23747 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 23814 23947 0.47 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 23814 23947 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 25443 25594 0.97 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 25443 25594 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 25797 25928 0.3 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 25797 25928 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 26127 26321 0.05 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 26127 26321 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 27093 27266 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 27093 27266 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 27489 27646 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 27489 27646 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 29614 29745 0.03 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 29614 29745 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS CDS 31648 31843 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS exon 31648 32135 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS stop_codon 31841 31843 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS tts 32135 32135 . + . transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 23848 23904 6.04 + 0 target "unknown_B[1..19]"; target_start 48; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 23911 23947 3.99 + 0 target "unknown_C[1..13]"; target_start 69; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 25443 25564 8.09 + 2 target "unknown_C[13..53]"; target_start 69; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 25565 25594 5.83 + 0 target "unknown_D[1..10]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 25797 25814 6.25 + 0 target "unknown_D[11..16]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 25818 25862 2.75 + 0 target "unknown_E[1..15]"; target_start 139; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 25893 25928 3.95 + 0 target "unknown_G[1..12]"; target_start 164; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 26133 26195 4.45 + 0 target "unknown_H[1..21]"; target_start 178; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 26211 26258 3.31 + 0 target "unknown_I[1..16]"; target_start 204; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 27102 27176 4.76 + 0 target "unknown_J[1..25]"; target_start 244; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 27183 27230 4.85 + 0 target "unknown_K[1..16]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 27246 27266 6.83 + 0 target "unknown_L[1..7]"; target_start 292; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 27489 27503 2.7 + 0 target "unknown_L[8..12]"; target_start 292; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 27510 27578 8.16 + 0 target "unknown_M[1..23]"; target_start 306; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 29714 29745 3.09 + 0 target "unknown_P[1..11]"; target_start 385; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 31648 31684 4.72 + 1 target "unknown_P[11..23]"; target_start 385; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 31688 31720 3.9 + 0 target "unknown_Q[1..11]"; target_start 409; transcript_id "g1.t1"; gene_id "g1"; Contig25358 AUGUSTUS protein_match 31733 31825 5.42 + 0 target "unknown_R[1..31]"; target_start 424; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgctgattatctgctgtggtcccaaccttttgtgttttacaaatagcactaatggactggacatcatgctgtttgtgg # cctccctcagtctggcagatgtacacggtatccacaatgccaatggagctgattatgatgtggcggtcattggagggggtattgttggtatggctacc # gctagagagatgaaagttcgacatccaaatctgtcatttgttgttctagaaaaggaaaaggaaatttccttccaccagagtggccacaacagtggggt # gatacacgccgggatttactacaccccgggatcactgaaggccaaactatgtgttcagggagtacaactgctctacgactactgcgaccagaacgata # ttccatacaataagtgtggaaagttgattgtagcagtggatcaagaggaaattcccaggttagaaggtttgctgtccagagggaatgaaaacggggta # aaggatttatgcttattaggtccaaaggagatcaaagaaatcgagccaaattgtgagggcttaaaagccgtgcactccccacacactggtatcattga # ttacaaagtggtgacccaatcctacggacaaacttttgagaaactaggaggacatatttatacaaactttgaggtgaccgacttctcagtgaccaagg # aaagcggccatggtattgactatcctgtcacaataagaggcagcggccatgatacgggtactccccgtgaggtgagatgtaaatacgtggttacttgt # ggtggtctgttctcagaccgactggcggaactgtcggggtgtaaccgagaacccagaattgtgcctttcaggggagactacttactattaaaaccaga # gaaaaccagccttgtcaatggaaatatctacccagtaccaaacccactattcccatttctaggggtccatttcacaccaagaatgaacggtgatgtat # ggcttggccctaacgcagtgctagcctttaaaagagagggctaccggctcttagacttcagtgctgctgatgcaacagatgcactctcttttagaggt # cttaggaaactagccataaggaacctgggatttggaattaaggaaatgtatcgtggttttaatgtagcatcccaagtcaaacagctccaaagatatgt # gccatctttaaaagtatcagatgttacaagaggtcctgctggagtaagagcccaggctttagatcatgatggcaatcttgtggatgattttgtctttg # atgtaggagatggagaattgggatctcgtatattacatgtgcgaaatgcaccatcaccagcagcaacttcctctctcgctattgccaaaatggtgtct # gataaagtacagaatacattcagtttatga] # protein sequence = [MLIICCGPNLLCFTNSTNGLDIMLFVASLSLADVHGIHNANGADYDVAVIGGGIVGMATAREMKVRHPNLSFVVLEKE # KEISFHQSGHNSGVIHAGIYYTPGSLKAKLCVQGVQLLYDYCDQNDIPYNKCGKLIVAVDQEEIPRLEGLLSRGNENGVKDLCLLGPKEIKEIEPNCE # GLKAVHSPHTGIIDYKVVTQSYGQTFEKLGGHIYTNFEVTDFSVTKESGHGIDYPVTIRGSGHDTGTPREVRCKYVVTCGGLFSDRLAELSGCNREPR # IVPFRGDYLLLKPEKTSLVNGNIYPVPNPLFPFLGVHFTPRMNGDVWLGPNAVLAFKREGYRLLDFSAADATDALSFRGLRKLAIRNLGFGIKEMYRG # FNVASQVKQLQRYVPSLKVSDVTRGPAGVRAQALDHDGNLVDDFVFDVGDGELGSRILHVRNAPSPAATSSLAIAKMVSDKVQNTFSL] # sequence of block unknown_B 48 [VIGGGIVGMATAREMKVRH] 67 # sequence of block unknown_C 69 [LSFVVLEKEKEISFHQSGHNSGVIHAGIYYTPGSLKAKLCVQGVQLLYDYCDQ] 122 # sequence of block unknown_D 122 [NDIPYNKCGKLIVAVD] 138 # sequence of block unknown_E 139 [EEIPRLEGLLSRGNE] 154 # sequence of block unknown_G 164 [PKEIKEIEPNCE] 176 # sequence of block unknown_H 178 [KAVHSPHTGIIDYKVVTQSYG] 199 # sequence of block unknown_I 204 [LGGHIYTNFEVTDFSV] 220 # sequence of block unknown_J 244 [REVRCKYVVTCGGLFSDRLAELSGC] 269 # sequence of block unknown_K 271 [EPRIVPFRGDYLLLKP] 287 # sequence of block unknown_L 292 [VNGNIYPVPNPL] 304 # sequence of block unknown_M 306 [FLGVHFTPRMNGDVWLGPNAVLA] 329 # sequence of block unknown_P 385 [VPSLKVSDVTRGPAGVRAQALDH] 408 # sequence of block unknown_Q 409 [GNLVDDFVFDV] 420 # sequence of block unknown_R 424 [LGSRILHVRNAPSPAATSSLAIAKMVSDKVQ] 455 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370LGH.prfl --predictionStart=5448 --predictionEnd=51822 --species=fly ./tmp/Contig2535820180911_busco_2432604931_.temp