# 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..48]--> unknown_A (22) <--[10..42]--> unknown_C (42) <--[0..19]--> unknown_D (44) <--[15..144]--> unknown_F (21) <--[46..790]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4540420180911_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 = 25881, name = Contig45404) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig45404 AUGUSTUS gene 4676 23150 0.01 + . g1 Contig45404 AUGUSTUS transcript 4676 23150 0.01 + . g1.t1 Contig45404 AUGUSTUS tss 4676 4676 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 4676 4822 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 5988 6142 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS start_codon 6013 6015 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 6143 14009 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 14049 15234 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 15306 15542 0.25 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 15687 16139 0.17 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 16323 19808 0.12 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 19874 20029 0.17 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 20127 20767 0.15 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS intron 20858 21760 0.17 + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 6013 6142 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 14010 14048 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 14010 14048 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 15235 15305 0.02 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 15235 15305 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 15543 15686 0.1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 15543 15686 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 16140 16322 0.31 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 16140 16322 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 19809 19873 0.17 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 19809 19873 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 20030 20126 0.17 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 20030 20126 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 20768 20857 0.36 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 20768 20857 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS CDS 21761 21778 0.17 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS exon 21761 23150 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS stop_codon 21776 21778 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS tts 23150 23150 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 6037 6102 4.04 + 0 target "unknown_A[1..22]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 14042 14048 6.06 + 0 target "unknown_C[1..3]"; target_start 54; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 15235 15305 8.82 + 1 target "unknown_C[3..27]"; target_start 53; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 15543 15590 2.55 + 0 target "unknown_C[27..42]"; target_start 54; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 15600 15686 5.65 + 0 target "unknown_D[1..29]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 16140 16184 1.96 + 0 target "unknown_D[30..44]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig45404 AUGUSTUS protein_match 16245 16307 3.02 + 0 target "unknown_F[1..21]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcagcaccctgcccatcagctgaggtgcattttgcacaaaaacttgctgcaaatgaaaaaagaacgagagacagtg # catttaaaaaactaaagaaatggctccaatctcgatcgagtgttggaaaggtttacgcttatagtccgcgaagcggatctatattcagcgaagcagat # tttttgaaaatatggaaaggtctacactattgcatgtggatgcaggacaagccattaatccaggaggaactctcagacaacatgtgtaagatgctaag # tgtctttggcaatgtggacatttcattgatgttcctcggagtgtttttccagactgagtcccgggaatggagtggaatagatcgatggagaatggata # aatttatgatgttgtccagggagatgctgggtcaggccatggctctaatgaagaaggccaagtggaagaaggcacaccttgatttgtttgctcagatc # ctcaaggaccgggttctaatggcagaaaatgacggatacaaattccatatcaccgacatttacctagatgagcttgaaaaagctggagcggaaatact # ttcaccaagtcagattgttcattttctggagccattctcgacattcctagtggagtccaaaaatacgacgctagtgaagcgagtcatatccagaatat # ttgacgccattatacaacagaccgtggatgatgctacgcggagagcagagaggcttcttcagaaggaagacgaagaaaacaacaatggtgcagacatg # gaagatgaggatgatgaagacgaggaggaagatgacacgcctccaagactggatttcacaaattttggttaa] # protein sequence = [MAAPCPSAEVHFAQKLAANEKRTRDSAFKKLKKWLQSRSSVGKVYAYSPRSGSIFSEADFLKIWKGLHYCMWMQDKPL # IQEELSDNMCKMLSVFGNVDISLMFLGVFFQTESREWSGIDRWRMDKFMMLSREMLGQAMALMKKAKWKKAHLDLFAQILKDRVLMAENDGYKFHITD # IYLDELEKAGAEILSPSQIVHFLEPFSTFLVESKNTTLVKRVISRIFDAIIQQTVDDATRRAERLLQKEDEENNNGADMEDEDDEDEEEDDTPPRLDF # TNFG] # sequence of block unknown_A 8 [EVHFAQKLAANEKRTRDSAFKK] 30 # sequence of block unknown_C 54 [FSEADFLKIWKGLHYCMWMQDKPLIQEELSDNMCKMLSVFGN] 96 # sequence of block unknown_D 99 [SLMFLGVFFQTESREWSGIDRWRMDKFMMLSREMLGQAMALMKK] 143 # sequence of block unknown_F 163 [MAENDGYKFHITDIYLDELEK] 184 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370S1Z.prfl --predictionStart=0 --predictionEnd=35305 --species=fly ./tmp/Contig4540420180911_busco_2432604931_.temp