# 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 # --[0..60]--> unknown_A (10) <--[1..17]--> unknown_B (9) <--[3..20]--> unknown_C (13) <--[7..86]--> unknown_D (15) <--[0..24]--> unknown_E (19) <--[3..55]--> unknown_F (26) <--[0..1]--> unknown_G (17) <--[0..46]--> unknown_H (18) <--[0..19]--> unknown_I (16) <--[0..1]--> unknown_J (13) <--[0..822]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3643120180911_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 = 9760, name = Contig36431) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig36431 AUGUSTUS gene 1976 9716 0.01 + . g1 Contig36431 AUGUSTUS transcript 1976 9716 0.01 + . g1.t1 Contig36431 AUGUSTUS tss 1976 1976 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 1976 2671 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 3062 3245 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 3960 4054 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS start_codon 4027 4029 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 4055 4735 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 4858 5615 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 5688 5868 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 5958 6071 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 6106 6270 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 6322 6419 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS intron 6502 9155 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 4027 4054 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 4736 4857 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 4736 4857 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 5616 5687 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 5616 5687 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 5869 5957 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 5869 5957 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 6072 6105 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 6072 6105 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 6271 6321 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 6271 6321 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 6420 6501 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 6420 6501 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS CDS 9156 9271 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS exon 9156 9716 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS stop_codon 9269 9271 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS tts 9716 9716 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 4042 4054 6.93 + 0 target "unknown_A[1..5]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 4736 4752 4.05 + 2 target "unknown_A[5..10]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 4765 4791 2.65 + 0 target "unknown_B[1..9]"; target_start 19; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 4801 4839 4.01 + 0 target "unknown_C[1..13]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 5640 5684 2.97 + 0 target "unknown_D[1..15]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 5685 5687 7.08 + 0 target "unknown_E[1..1]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 5869 5922 4.64 + 0 target "unknown_E[2..19]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 5932 5957 4.48 + 0 target "unknown_F[1..9]"; target_start 95; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6072 6105 9.26 + 0 target "unknown_F[10..21]"; target_start 94; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6271 6288 8.36 + 0 target "unknown_F[21..26]"; target_start 95; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6289 6321 8.88 + 0 target "unknown_G[1..11]"; target_start 121; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6420 6437 5.76 + 0 target "unknown_G[12..17]"; target_start 121; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6441 6494 7.83 + 0 target "unknown_H[1..18]"; target_start 139; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 6495 6501 5.25 + 0 target "unknown_I[1..3]"; target_start 157; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 9156 9196 4.14 + 2 target "unknown_I[3..16]"; target_start 157; transcript_id "g1.t1"; gene_id "g1"; Contig36431 AUGUSTUS protein_match 9200 9238 4.27 + 0 target "unknown_J[1..13]"; target_start 174; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggctgcgcccacgatttgtgtcccaggtcaaagaatctgtcaactggaggagacgtgtgagggaggcagtggtactt # attccaggaacggttacatatactccagtctagcagggtatctccaaagttctcaaagtgagggtggaaagtcacttattcaagtgaaaacacaagaa # gaacagaatattgttccctcagtggatgctactgttacaacaaggattacaaatgtcaaccccagattctgtaagtgcatgattctaagcgtaggaag # gattccactcaaagaaccgttccgaggacagatcaggaaagaagatgttcgtgcaacagagaaagataaggtggaaatgtacaagtgctttaggccag # gagatatagtcgttgcaagagttctttcactaggagatgctcattcttatttgctaaccacagctgaaaatgaattgggtgttgtcatggcaacaagt # gaagcaggagctgccttggaacctattagctggtgcaagatgaaatgtccaaaaacattgagcgaagagttcagaaaagttgccaaggttcaaccgaa # atatgtacaatatgctgggacgtaa] # protein sequence = [MAAPTICVPGQRICQLEETCEGGSGTYSRNGYIYSSLAGYLQSSQSEGGKSLIQVKTQEEQNIVPSVDATVTTRITNV # NPRFCKCMILSVGRIPLKEPFRGQIRKEDVRATEKDKVEMYKCFRPGDIVVARVLSLGDAHSYLLTTAENELGVVMATSEAGAALEPISWCKMKCPKT # LSEEFRKVAKVQPKYVQYAGT] # sequence of block unknown_A 5 [ICVPGQRICQ] 15 # sequence of block unknown_B 19 [CEGGSGTYS] 28 # sequence of block unknown_C 31 [YIYSSLAGYLQSS] 44 # sequence of block unknown_D 58 [EEQNIVPSVDATVTT] 73 # sequence of block unknown_E 73 [RITNVNPRFCKCMILSVGR] 92 # sequence of block unknown_F 95 [KEPFRGQIRKEDVRATEKDKVEMYKC] 121 # sequence of block unknown_G 121 [FRPGDIVVARVLSLGDA] 138 # sequence of block unknown_H 139 [SYLLTTAENELGVVMATS] 157 # sequence of block unknown_I 157 [EAGAALEPISWCKMKC] 173 # sequence of block unknown_J 174 [KTLSEEFRKVAKV] 187 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UR1.prfl --predictionStart=0 --predictionEnd=26506 --species=fly ./tmp/Contig3643120180911_busco_2432604931_.temp