# 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..217]--> unknown_A (12) <--[0..9]--> unknown_B (19) <--[0..1]--> unknown_C (24) <--[0..2]--> unknown_D (64) <--[3..22]--> unknown_E (34) <--[2..7]--> unknown_F (53) <--[0..22]--> unknown_G (26) <--[0..7]--> unknown_H (138) <--[0..76]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2111020180911_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 = 15736, name = Contig21110) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig21110 AUGUSTUS gene 686 15615 0.01 - . g1 Contig21110 AUGUSTUS transcript 686 15615 0.01 - . g1.t1 Contig21110 AUGUSTUS tts 686 686 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 686 911 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS stop_codon 856 858 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 912 964 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 987 1140 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 1152 1775 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 1792 1874 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 1889 2591 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 2609 2734 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 2754 4070 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 4091 4146 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 4159 5235 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 5258 5332 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 5345 6616 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 6643 7547 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 7559 8727 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 8751 10015 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 10033 10288 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 10303 11269 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 11453 11627 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 11842 12867 0.93 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 13051 13202 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 13323 14265 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 14346 14498 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 14521 14909 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 14925 15025 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 15039 15132 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 15153 15260 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS intron 15287 15444 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 856 911 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 965 986 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 965 986 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 1141 1151 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 1141 1151 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 1776 1791 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 1776 1791 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 1875 1888 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 1875 1888 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 2592 2608 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 2592 2608 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 2735 2753 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 2735 2753 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 4071 4090 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 4071 4090 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 4147 4158 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 4147 4158 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 5236 5257 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 5236 5257 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 5333 5344 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 5333 5344 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 6617 6642 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 6617 6642 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 7548 7558 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 7548 7558 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 8728 8750 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 8728 8750 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 10016 10032 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 10016 10032 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 10289 10302 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 10289 10302 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 11270 11452 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 11270 11452 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 11628 11841 0.81 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 11628 11841 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 12868 13050 0.99 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 12868 13050 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 13203 13322 0.03 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 13203 13322 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 14266 14345 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 14266 14345 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 14499 14520 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 14499 14520 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 14910 14924 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 14910 14924 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 15026 15038 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 15026 15038 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 15133 15152 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 15133 15152 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 15261 15286 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 15261 15286 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS CDS 15445 15501 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS exon 15445 15615 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS start_codon 15499 15501 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS tss 15615 15615 . - . transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 892 911 1.36 - 2 target "unknown_H[132..138]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 965 986 1.1 - 0 target "unknown_H[125..132]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 1141 1151 1.1 - 2 target "unknown_H[121..124]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 1776 1791 1.91 - 0 target "unknown_H[116..121]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 1875 1888 0.722 - 2 target "unknown_H[111..115]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 2592 2608 1.2 - 1 target "unknown_H[105..111]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 2735 2753 1.63 - 2 target "unknown_H[99..105]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 4071 4090 1.11 - 1 target "unknown_H[92..99]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 4147 4158 1.15 - 1 target "unknown_H[88..92]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 5236 5257 1.36 - 2 target "unknown_H[81..88]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 5333 5344 1.64 - 2 target "unknown_H[77..81]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 6617 6642 1.64 - 1 target "unknown_H[68..77]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 7548 7558 1.38 - 0 target "unknown_H[65..68]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 8728 8750 1.04 - 2 target "unknown_H[57..64]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 10016 10032 1.56 - 1 target "unknown_H[51..57]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 10289 10302 1.85 - 0 target "unknown_H[47..51]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 11270 11407 6.12 - 0 target "unknown_H[1..46]"; target_start 265; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 11408 11452 12 - 0 target "unknown_G[12..26]"; target_start 239; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 11628 11660 12.4 - 0 target "unknown_G[1..11]"; target_start 239; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 11670 11828 6.56 - 0 target "unknown_F[1..53]"; target_start 183; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 12870 12971 6.47 - 0 target "unknown_E[1..34]"; target_start 144; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 12981 13050 12.4 - 1 target "unknown_D[41..64]"; target_start 77; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 13203 13322 8.79 - 1 target "unknown_D[1..41]"; target_start 77; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 14266 14267 1 - 0 target "unknown_D[1..1]"; target_start 77; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 14274 14345 6.84 - 0 target "unknown_C[1..24]"; target_start 51; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 14502 14520 1.08 - 1 target "unknown_B[13..19]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 14910 14924 0.947 - 1 target "unknown_B[8..13]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 15026 15038 0.863 - 2 target "unknown_B[4..8]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 15133 15142 0.667 - 0 target "unknown_B[1..4]"; target_start 31; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 15149 15152 0.152 - 1 target "unknown_A[11..12]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 15261 15286 1.49 - 0 target "unknown_A[3..11]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig21110 AUGUSTUS protein_match 15445 15450 1.17 - 0 target "unknown_A[1..2]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgctacataaattttcaaattttgctatacagcttccatcgtcggctttcaatacagtgccaattatagctccataca # atcaatttgagttctttgccatggtatatgtgggatgttcaacgcgcataatatcacgtgcttttagggatgtcgccttgataaaaagaatagaaaaa # gtcacagggaagcctgtccaccatcttcttcggaggggcatcttcttctcgcagagggacatggagatgatattggatgtctatgagcagcggaaacc # cttctatctctacacaggaagagggccatcttcagaagccatgcatatggggcatctgattccattcattttcactaagtggctgcaggatacttttg # acgtaccactggtcatccaactgaccgatgatgaaaaatttttgtggaaggacctaaccctagaacaaaccaaccacttggcctttgagaatgcaaaa # gacatcatagcttgtggttttgaccttgataagacatttatcttcagcgatctagactttttaacgaacagcccggcgttttacagaactatttgccg # aatccagaagctggtgacctataatcaggttaaaggcatctttggcttctcggatagcgatagtataggaaaaatcagctttcccgccatccaggctg # ctcccagctttagctgtatgttcccggaaatattcaatggaaaacctgatatcccttgtttcattccatgtgcaatagaccaggatccttatttccga # atgacgagagacgtggcgccccggatggggtgtataaagccagccctcattcactccacatttttcccagccctacaaggggcacagaccaagatgag # cgccagcgaccctaattcatccatatttgtcaccgacacagaccaacaaatcaaagataaggtagacacacatgcgcacacacttggaggatccagga # tttgtgggatcaggtgcctaggaggaaacagttctgtagatgttacgatatcctaccactcttgtcaattagaacccaataatgaatatgaagaaagg # gctaggggtgtgattcttggcaatttgtcaacaggggccctcattaagttgcttgccgtatttctatatcagctgacagctcaacatcaacatcattc # aaagtgtgttggcaaaaatactctgaaaaaagtgttcgagatatcaaagttcaactgtacttttatttcactatcagatgtaatctaa] # protein sequence = [MLHKFSNFAIQLPSSAFNTVPIIAPYNQFEFFAMVYVGCSTRIISRAFRDVALIKRIEKVTGKPVHHLLRRGIFFSQR # DMEMILDVYEQRKPFYLYTGRGPSSEAMHMGHLIPFIFTKWLQDTFDVPLVIQLTDDEKFLWKDLTLEQTNHLAFENAKDIIACGFDLDKTFIFSDLD # FLTNSPAFYRTICRIQKLVTYNQVKGIFGFSDSDSIGKISFPAIQAAPSFSCMFPEIFNGKPDIPCFIPCAIDQDPYFRMTRDVAPRMGCIKPALIHS # TFFPALQGAQTKMSASDPNSSIFVTDTDQQIKDKVDTHAHTLGGSRICGIRCLGGNSSVDVTISYHSCQLEPNNEYEERARGVILGNLSTGALIKLLA # VFLYQLTAQHQHHSKCVGKNTLKKVFEISKFNCTFISLSDVI] # sequence of block unknown_H 265 [CIKPALIHSTFFPALQGAQTKMSASDPNSSIFVTDTDQQIKDKVDTHAHTLGGSRICGIRCLGGNSSVDVTISYHSCQLEPNNEYEERARGVILGNLSTGALIKLLAVFLYQLTAQHQHHSKCVGKNTLKKVFEISKF] 403 # sequence of block unknown_G 239 [IPCFIPCAIDQDPYFRMTRDVAPRMG] 265 # sequence of block unknown_F 183 [FYRTICRIQKLVTYNQVKGIFGFSDSDSIGKISFPAIQAAPSFSCMFPEIFNG] 236 # sequence of block unknown_E 144 [LEQTNHLAFENAKDIIACGFDLDKTFIFSDLDFL] 178 # sequence of block unknown_D 77 [RDMEMILDVYEQRKPFYLYTGRGPSSEAMHMGHLIPFIFTKWLQDTFDVPLVIQLTDDEKFLWK] 141 # sequence of block unknown_C 51 [ALIKRIEKVTGKPVHHLLRRGIFF] 75 # sequence of block unknown_B 31 [FAMVYVGCSTRIISRAFRD] 50 # sequence of block unknown_A 17 [NTVPIIAPYNQF] 29 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E0Y.prfl --predictionStart=0 --predictionEnd=33324 --species=fly ./tmp/Contig2111020180911_busco_2432604931_.temp