# 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..25]--> unknown_A (18) <--[0..6]--> unknown_B (55) <--[0..11]--> unknown_C (38) <--[0..53]--> unknown_D (21) <--[0..4]--> unknown_E (10) <--[11..44]--> unknown_F (47) <--[0..1]--> unknown_G (49) <--[0..1]--> unknown_H (8) <--[0..16]--> unknown_I (24) <--[0..2]--> unknown_J (7) <--[0..230]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2367720180911_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 = 25036, name = Contig23677) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig23677 AUGUSTUS gene 121 8435 0.01 - . g1 Contig23677 AUGUSTUS transcript 121 8435 0.01 - . g1.t1 Contig23677 AUGUSTUS exon 121 193 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS stop_codon 177 179 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 194 335 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 366 621 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 653 716 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 730 838 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 856 925 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 942 1003 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 1035 1079 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 1109 1209 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 1227 1578 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 1596 1863 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 1878 2112 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 2129 2569 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 2592 2649 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 2796 3379 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 3417 3470 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 3529 3857 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 4007 4412 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS intron 4493 4810 0.39 - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 177 193 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 336 365 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 336 365 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 622 652 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 622 652 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 717 729 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 717 729 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 839 855 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 839 855 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 926 941 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 926 941 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 1004 1034 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 1004 1034 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 1080 1108 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 1080 1108 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 1210 1226 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 1210 1226 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 1579 1595 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 1579 1595 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 1864 1877 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 1864 1877 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 2113 2128 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 2113 2128 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 2570 2591 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 2570 2591 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 2650 2795 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 2650 2795 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 3380 3416 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 3380 3416 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 3471 3528 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 3471 3528 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 3858 4006 0.93 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 3858 4006 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 4413 4492 0.99 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 4413 4492 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS CDS 4811 5048 0.33 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 4811 5071 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS start_codon 5046 5048 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS exon 8250 8435 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS tss 8435 8435 . - . transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 180 193 1.07 - 2 target "unknown_J[3..7]"; target_start 318; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 336 342 2.02 - 0 target "unknown_J[1..3]"; target_start 318; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 346 365 1.02 - 2 target "unknown_I[18..24]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 622 652 1.27 - 0 target "unknown_I[8..18]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 717 729 1.82 - 1 target "unknown_I[3..7]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 839 846 0.184 - 0 target "unknown_I[1..3]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 847 855 1.07 - 0 target "unknown_H[6..8]"; target_start 285; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 926 940 1.27 - 0 target "unknown_H[1..5]"; target_start 285; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 1006 1034 1.26 - 2 target "unknown_G[40..49]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 1080 1108 1.2 - 1 target "unknown_G[30..40]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 1210 1226 1.11 - 0 target "unknown_G[25..30]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 1579 1595 1.58 - 2 target "unknown_G[19..24]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 1864 1877 4.25 - 1 target "unknown_G[14..19]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 2113 2128 1.48 - 2 target "unknown_G[9..14]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 2570 2591 1.26 - 0 target "unknown_G[2..9]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 2650 2652 1.58 - 0 target "unknown_G[1..1]"; target_start 235; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 2656 2795 1.34 - 2 target "unknown_F[1..47]"; target_start 187; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 3380 3380 1 - 0 target "unknown_F[1..1]"; target_start 187; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 3528 3528 1 - 1 target "unknown_E[10..10]"; target_start 146; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 3858 3886 6.88 - 0 target "unknown_E[1..10]"; target_start 146; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 3896 3958 5.45 - 0 target "unknown_D[1..21]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 3971 4006 6.37 - 0 target "unknown_C[27..38]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 4413 4490 9.16 - 0 target "unknown_C[1..26]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 4491 4492 1 - 2 target "unknown_B[55..55]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 4811 4973 11.1 - 0 target "unknown_B[1..55]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig23677 AUGUSTUS protein_match 4983 5036 10 - 0 target "unknown_A[1..18]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggtgttgtcgtgtagattttacaagaacaggtacccggaagttgaggatgttgttatggttaacgtccgctccattg # ctgagatgggagcctatgttcacttactggagtacaacaacatcgagggcatgatcctgctctccgagttatccagaagacgtatcagatccatcaac # aaactcatccgtattgggcgaagtgaatgtgtggtggtcatcagagtggataaagacaaaggatacattgatttgtccaaaagaagagtttcccccga # ggaagttacgaagtgtgaggaaaaatatgcgaaagcgaaagcagtaaacagtattctacgtcatgtgggagagttgatgaaatacaactgtgatgaac # agatggaggagttatacactaaaacagcctggttctttgatgacaagtacaagaaacccggagcttcatatgaagcatttaaacatgctgtaacgaaa # actatatatacagttgaacctcgtcatcacgaactcgatgggaccaataaaaaggtggttggtacctccaaattagttcgacataaccatgaaacgaa # aaatgttctcctgcaaaatattaagaggaggctgacaccacaagcagtaaagatcagagcaggtaagctaaatagagtgagtaagttaatcagagtgg # gtaagctaatcagagtgggtaagctagagtgtaagatcagaagtgtaaaatcaaagcaggtaaatgtgttattgctattacctccgcttttaattgtc # aagtccactccagtagatgatcagacggcagttgtcatatcaagacccgctatcgagtatgtgagatcagaagtgagtaaagctagagttggtaagct # tagagctggtaaagcaataagtggagttaatgctagagaaggtaaagtcaagagtggtaagctagagttgagatcagagtgggtagctaaatcagaga # ctaatcagagtgagtag] # protein sequence = [MVLSCRFYKNRYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRIGRSECVVVIRVDKD # KGYIDLSKRRVSPEEVTKCEEKYAKAKAVNSILRHVGELMKYNCDEQMEELYTKTAWFFDDKYKKPGASYEAFKHAVTKTIYTVEPRHHELDGTNKKV # VGTSKLVRHNHETKNVLLQNIKRRLTPQAVKIRAGKLNRVSKLIRVGKLIRVGKLECKIRSVKSKQVNVLLLLPPLLIVKSTPVDDQTAVVISRPAIE # YVRSEVSKARVGKLRAGKAISGVNAREGKVKSGKLELRSEWVAKSETNQSE] # sequence of block unknown_J 318 [SETNQSE] 325 # sequence of block unknown_I 293 [ISGVNAREGKVKSGKLELRSEWVA] 317 # sequence of block unknown_H 285 [GKLRAGKA] 293 # sequence of block unknown_G 235 [RSVKSKQVNVLLLLPPLLIVKSTPVDDQTAVVISRPAIEYVRSEVSKAR] 284 # sequence of block unknown_F 187 [ETKNVLLQNIKRRLTPQAVKIRAGKLNRVSKLIRVGKLIRVGKLECK] 234 # sequence of block unknown_E 146 [SYEAFKHAVT] 156 # sequence of block unknown_D 122 [DEQMEELYTKTAWFFDDKYKK] 143 # sequence of block unknown_C 80 [YIDLSKRRVSPEEVTKCEEKYAKAKAVNSILRHVGELM] 118 # sequence of block unknown_B 25 [IAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRIGRSECVVVIRVDKDKG] 80 # sequence of block unknown_A 4 [CRFYKNRYPEVEDVVMVN] 22 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MAO.prfl --predictionStart=0 --predictionEnd=25036 --species=fly ./tmp/Contig2367720180911_busco_2432604931_.temp