# 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..88]--> unknown_A (11) <--[0..1]--> unknown_B (24) <--[1..3]--> unknown_C (12) <--[5..14]--> unknown_D (17) <--[16..25]--> unknown_G (12) <--[7..43]--> unknown_H (13) <--[6..36]--> unknown_I (31) <--[0..2]--> unknown_J (23) <--[0..1]--> unknown_K (17) <--[1..70]--> unknown_L (13) <--[3..5]--> unknown_M (12) <--[1..24]--> unknown_N (24) <--[0..41]--> unknown_O (36) <--[9..36]--> unknown_Q (8) <--[5..12]--> unknown_R (8) <--[0..1]--> unknown_S (12) <--[0..146]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig13789220180911_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 = 12890, name = Contig137892) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig137892 AUGUSTUS gene 49 11545 0.01 + . g1 Contig137892 AUGUSTUS transcript 49 11545 0.01 + . g1.t1 Contig137892 AUGUSTUS start_codon 49 51 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 52 182 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 257 694 0.2 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 774 897 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 991 1404 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 1546 2049 0.91 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 2111 2259 0.65 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 2356 6984 0.06 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 7066 7463 0.21 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 7632 7786 0.8 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 7857 8210 0.3 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 8238 8684 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 8711 9094 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 9112 9221 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 9248 9390 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 9419 10622 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 10681 10746 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 10811 10876 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS intron 10909 11528 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 49 51 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 183 256 0.4 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 695 773 0.2 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 898 990 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 1405 1545 0.93 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 2050 2110 0.91 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 2260 2355 0.31 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 6985 7065 0.19 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 7464 7631 0.77 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 7787 7856 0.9 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 8211 8237 0.54 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 8685 8710 0.08 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 9095 9111 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 9222 9247 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 9391 9418 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 10623 10680 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 10747 10810 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 10877 10908 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS CDS 11529 11545 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS stop_codon 11543 11545 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 183 215 2.93 + 0 target "unknown_A[1..11]"; target_start 1; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 216 256 3.25 + 0 target "unknown_B[1..14]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 695 725 5.28 + 1 target "unknown_B[14..24]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 729 764 2.07 + 0 target "unknown_C[1..12]"; target_start 37; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 916 966 2.64 + 0 target "unknown_D[1..17]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 1441 1476 3.29 + 0 target "unknown_G[1..12]"; target_start 95; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 1513 1545 3.51 + 0 target "unknown_H[1..11]"; target_start 119; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 2050 2055 4.65 + 0 target "unknown_H[12..13]"; target_start 119; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 2074 2110 1.94 + 0 target "unknown_I[1..13]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 2260 2315 4.25 + 2 target "unknown_I[13..31]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 2322 2355 4.96 + 0 target "unknown_J[1..12]"; target_start 171; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 6985 7019 2.52 + 2 target "unknown_J[12..23]"; target_start 171; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7020 7065 4.1 + 0 target "unknown_K[1..16]"; target_start 194; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7464 7468 3.66 + 2 target "unknown_K[16..17]"; target_start 194; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7511 7549 3.47 + 0 target "unknown_L[1..13]"; target_start 225; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7562 7597 2.27 + 0 target "unknown_M[1..12]"; target_start 242; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7604 7631 7.28 + 0 target "unknown_N[1..10]"; target_start 256; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 7787 7830 4.36 + 2 target "unknown_N[10..24]"; target_start 256; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 8686 8710 1.07 + 0 target "unknown_O[1..9]"; target_start 298; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 9095 9111 0.847 + 1 target "unknown_O[9..15]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 9222 9247 1.01 + 2 target "unknown_O[15..23]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 9391 9418 1.37 + 0 target "unknown_O[24..33]"; target_start 297; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10623 10634 3.38 + 0 target "unknown_O[33..36]"; target_start 298; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10668 10680 1.04 + 0 target "unknown_Q[1..5]"; target_start 345; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10747 10757 1.51 + 2 target "unknown_Q[5..8]"; target_start 345; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10788 10810 1.62 + 0 target "unknown_R[1..8]"; target_start 363; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10877 10877 1 + 1 target "unknown_R[8..8]"; target_start 363; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 10881 10908 1.39 + 0 target "unknown_S[1..10]"; target_start 372; transcript_id "g1.t1"; gene_id "g1"; Contig137892 AUGUSTUS protein_match 11529 11536 4.68 + 2 target "unknown_S[10..12]"; target_start 372; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtgtccatttctcaagcttactttaccctcagaaacagaggccaaacaactggcaagtcggagtgtattgataaaat # cagttattgagttgtggggccacggaaacacacatgaagatctgtatgaggatttaagaaaatccaaagattcaatagtgccatatttgtcaagtctt # tcttcattcaagattgttgttgatggtttcaaccgatctctcccgcataaatacaaaatcaagatgattgagaaactaacagatgacgctctaccttt # tgaagggaaaatagatttaaagactcctgatgagatctattatctattagaggattatgggaaacagtcaaaaaatgccactgctgatgctgagcatg # tgtattttggtaggtggatagcagatggaaacagaggtgaaattcagaaccagcatataaccaaaagatcctttattggaaataccagtatggaatcc # agtctttcacttctgatggccaatttatcgaaagtccagaaaaacatgctcgtgattgatccattcgtgggaacgggtagcatactagtaccgtgtgc # ctaccatcatgcctatgtcatgggaacggacattaattatttacttctacatgcaaaagctaagcccagccgatctaatcagaaagcgcgagctgcga # acgaaagcatccggaacaacctggcagagtacggtttggagtcgtattactgcgacatcatggtggctgatgcctcaaaacatgccatgtggagagag # aaggaaatattcgacgccatcatcacagaccctccttatggtattagggaaggagccaagaaagttggtaaagaagacccagttttacttacagagga # acacttgtttatggatccaacattgaagatcatggatgcatcaatcatgcgacgattgaacttcaacgttgaggaaagcgtggactcacagttccacc # aagcagataagtacctatatactggtcctagaaatgtattttcaaagcggtatgaaaatctcataactctcccaagtctcgatagaccacttgtacct # aagagcatgtatctactccaagaaattaaatatccatgtacaagaccaacgattcatcgaacctcgaccaacgctttgattatgtctaagatcctgtt # ttga] # protein sequence = [MCPFLKLTLPSETEAKQLASRSVLIKSVIELWGHGNTHEDLYEDLRKSKDSIVPYLSSLSSFKIVVDGFNRSLPHKYK # IKMIEKLTDDALPFEGKIDLKTPDEIYYLLEDYGKQSKNATADAEHVYFGRWIADGNRGEIQNQHITKRSFIGNTSMESSLSLLMANLSKVQKNMLVI # DPFVGTGSILVPCAYHHAYVMGTDINYLLLHAKAKPSRSNQKARAANESIRNNLAEYGLESYYCDIMVADASKHAMWREKEIFDAIITDPPYGIREGA # KKVGKEDPVLLTEEHLFMDPTLKIMDASIMRRLNFNVEESVDSQFHQADKYLYTGPRNVFSKRYENLITLPSLDRPLVPKSMYLLQEIKYPCTRPTIH # RTSTNALIMSKILF] # sequence of block unknown_A 1 [CPFLKLTLPSE] 12 # sequence of block unknown_B 12 [TEAKQLASRSVLIKSVIELWGHGN] 36 # sequence of block unknown_C 37 [HEDLYEDLRKSK] 49 # sequence of block unknown_D 58 [LSSFKIVVDGFNRSLPH] 75 # sequence of block unknown_G 95 [IDLKTPDEIYYL] 107 # sequence of block unknown_H 119 [ADAEHVYFGRWIA] 132 # sequence of block unknown_I 138 [IQNQHITKRSFIGNTSMESSLSLLMANLSKV] 169 # sequence of block unknown_J 171 [NMLVIDPFVGTGSILVPCAYHHA] 194 # sequence of block unknown_K 194 [YVMGTDINYLLLHAKAK] 211 # sequence of block unknown_L 225 [IRNNLAEYGLESY] 238 # sequence of block unknown_M 242 [MVADASKHAMWR] 254 # sequence of block unknown_N 256 [EIFDAIITDPPYGIREGAKKVGKE] 280 # sequence of block unknown_O 298 [MDASIMRRLNFNVEESVDSQFHQADKYLYTGPRNVF] 334 # sequence of block unknown_Q 345 [SLDRPLVP] 353 # sequence of block unknown_R 363 [YPCTRPTI] 371 # sequence of block unknown_S 372 [RTSTNALIMSKI] 384 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AS9.prfl --predictionStart=0 --predictionEnd=22357 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig13789220180911_busco_2432604931_.temp