# 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 # --[26..168]--> unknown_B (11) <--[0..13]--> unknown_C (10) <--[2..46]--> unknown_D (11) <--[4..5]--> unknown_E (12) <--[1..8]--> unknown_F (30) <--[0..34]--> unknown_G (23) <--[2..22]--> unknown_H (59) <--[43..197]--> unknown_I (13) <--[2..11]--> unknown_J (13) <--[3..12]--> unknown_K (47) <--[10..182]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig128420180911_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 = 26389, name = Contig1284) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig1284 AUGUSTUS gene 1 23935 0.01 - . g1 Contig1284 AUGUSTUS transcript 1 23935 0.01 - . g1.t1 Contig1284 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 1 417 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS stop_codon 403 405 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 418 711 0.08 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 883 3026 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 3182 3387 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 3461 3555 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 3628 3863 0.75 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 4056 4317 0.57 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 4426 5205 0.67 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 5425 15141 0.04 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 15217 15319 0.06 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS intron 15441 23506 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 403 417 0.1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 712 882 0.92 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 712 882 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 3027 3181 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 3027 3181 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 3388 3460 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 3388 3460 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 3556 3627 0.95 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 3556 3627 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 3864 4055 0.75 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 3864 4055 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 4318 4425 0.67 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 4318 4425 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 5206 5424 0.93 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 5206 5424 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 15142 15216 0.06 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 15142 15216 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 15320 15440 0.02 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 15320 15440 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS CDS 23507 23517 0.02 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 23507 23517 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS start_codon 23515 23517 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS exon 23598 23935 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS tss 23935 23935 . - . transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 3039 3179 3.65 - 0 target "unknown_K[1..47]"; target_start 291; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 3395 3433 4.5 - 0 target "unknown_J[1..13]"; target_start 275; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 3449 3460 5.52 - 0 target "unknown_I[10..13]"; target_start 257; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 3556 3582 5.1 - 0 target "unknown_I[1..9]"; target_start 257; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 3963 4055 4.02 - 0 target "unknown_H[29..59]"; target_start 150; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 4318 4401 4.11 - 0 target "unknown_H[1..28]"; target_start 150; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 4420 4425 5.6 - 0 target "unknown_G[22..23]"; target_start 121; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 5206 5268 4.47 - 0 target "unknown_G[1..21]"; target_start 121; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 5281 5370 7.71 - 0 target "unknown_F[1..30]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 5374 5409 5.37 - 0 target "unknown_E[1..12]"; target_start 74; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 5422 5424 0.419 - 0 target "unknown_D[11..11]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 15142 15171 8.01 - 0 target "unknown_D[1..10]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 15181 15210 7.09 - 0 target "unknown_C[1..10]"; target_start 46; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 15211 15216 7.98 - 0 target "unknown_B[10..11]"; target_start 35; transcript_id "g1.t1"; gene_id "g1"; Contig1284 AUGUSTUS protein_match 15320 15346 7.75 - 0 target "unknown_B[1..9]"; target_start 35; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcacgctcgagatgcacctccaattatacccactgatacaaaccaaggttacaagcaaatgaaggccaagataggga # gcagcaaagtccggccatggaagtggatgccattcacaaatcctgcaagaaaggacggtgcagtgttttatcactggagaagagtagcagatgaagga # aaggattacccgtttgcaagatttaacaaggctgtggacataccagtgtactcagatctggagtatcagcaacatctccatgacgacaattggaccag # acaggaaaccgattttctgtttgacctgtgtaaacgttttgacttgcgcttcattttaattcatgatcgctgggaccgggacaagtttcctaacagaa # gtgtggaggacataaaggagagatactatggtatctgtaacactctgtcaaaggtcagaatatcacaaggcactgagccaaaaattcgagcttttgat # gcagagcatgaaaggaaacgaaaacagcagctcatcaaactgtttgacagaactcctgagcaggttgaggaggaagaccatttgattgcggaactgaa # gaaaattgaactacggaagaaagagcgtgaaaagaaaacacaagacttacagaaactgattacagcagccgacagcaactttgacagcagacggtcag # agaagaagcagaccaagaaaaagatccacaccccccatcagaagataaatccaacaattgctacgccagagccaagtggaattaaatttgcagatttc # aagacatctggggtgtctttgcgaagtcagaggatgaaattaccagcatcaattggacagaaaaagatgaaagcaattgaacaagttctggaagagct # cggcattgaatataatccaattcccacagaagacacagtgacacatttcaatgaattgcggcaggacgtcgttttgctttatgaactgaaaattgcct # tagcaacctgtgattatgaactggagtccttaaaacacagatttgaaacattagcccctggaaagcctcttccaatagaagccacagttaaatctgag # ccgatgtcctctgtgttgggatcagaagcagcagaatctcttatcactcccaacatctcgcctgagtccccgtccaaactgaagaagctgtccgaggc # tattgatgtggtcaacgccaaccccccaggaacacccaatagacaatgcttgtag] # protein sequence = [MHARDAPPIIPTDTNQGYKQMKAKIGSSKVRPWKWMPFTNPARKDGAVFYHWRRVADEGKDYPFARFNKAVDIPVYSD # LEYQQHLHDDNWTRQETDFLFDLCKRFDLRFILIHDRWDRDKFPNRSVEDIKERYYGICNTLSKVRISQGTEPKIRAFDAEHERKRKQQLIKLFDRTP # EQVEEEDHLIAELKKIELRKKEREKKTQDLQKLITAADSNFDSRRSEKKQTKKKIHTPHQKINPTIATPEPSGIKFADFKTSGVSLRSQRMKLPASIG # QKKMKAIEQVLEELGIEYNPIPTEDTVTHFNELRQDVVLLYELKIALATCDYELESLKHRFETLAPGKPLPIEATVKSEPMSSVLGSEAAESLITPNI # SPESPSKLKKLSEAIDVVNANPPGTPNRQCL] # sequence of block unknown_K 291 [YNPIPTEDTVTHFNELRQDVVLLYELKIALATCDYELESLKHRFETL] 338 # sequence of block unknown_J 275 [KKMKAIEQVLEEL] 288 # sequence of block unknown_I 257 [SGVSLRSQRMKLP] 270 # sequence of block unknown_H 150 [PKIRAFDAEHERKRKQQLIKLFDRTPEQVEEEDHLIAELKKIELRKKEREKKTQDLQKL] 209 # sequence of block unknown_G 121 [PNRSVEDIKERYYGICNTLSKVR] 144 # sequence of block unknown_F 87 [DNWTRQETDFLFDLCKRFDLRFILIHDRWD] 117 # sequence of block unknown_E 74 [VYSDLEYQQHLH] 86 # sequence of block unknown_D 59 [KDYPFARFNKA] 70 # sequence of block unknown_C 46 [AVFYHWRRVA] 56 # sequence of block unknown_B 35 [MPFTNPARKDG] 46 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DXT.prfl --predictionStart=0 --predictionEnd=33280 --species=fly ./tmp/Contig128420180911_busco_2432604931_.temp