# 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..120]--> unknown_A (10) <--[8..16]--> unknown_B (12) <--[7..27]--> unknown_C (11) <--[3..23]--> unknown_D (20) <--[0..8]--> unknown_E (23) <--[74..326]--> unknown_J (43) <--[0..78]--> unknown_K (14) <--[1..5]--> unknown_L (23) <--[0..1]--> unknown_M (29) <--[0..54]--> unknown_N (19) <--[0..1]--> unknown_O (8) <--[3..23]--> unknown_P (35) <--[0..3]--> unknown_Q (14) <--[12..50]--> unknown_S (17) <--[0..3]--> unknown_T (20) <--[9..323]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2290020180911_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 = 28632, name = Contig22900) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig22900 AUGUSTUS gene 3936 11414 0.01 + . g1 Contig22900 AUGUSTUS transcript 3936 11414 0.01 + . g1.t1 Contig22900 AUGUSTUS tss 3936 3936 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 3936 4098 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 4936 4944 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS start_codon 4937 4939 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 4945 5954 0.27 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 6051 6548 0.62 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 6682 6845 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 6983 7095 0.99 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 7224 10831 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 10890 11037 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS intron 11247 11314 0.25 + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 4937 4944 0.53 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 5955 6050 0.37 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 5955 6050 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 6549 6681 0.8 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 6549 6681 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 6846 6982 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 6846 6982 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 7096 7223 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 7096 7223 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 10832 10889 1 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 10832 10889 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 11038 11246 0.91 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 11038 11246 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS CDS 11315 11346 0.25 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS exon 11315 11414 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS stop_codon 11344 11346 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22900 AUGUSTUS tts 11414 11414 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgatcagacataggtatatggtcatggaatattgcgttggagaattacaggaactgttggaagctgcacctgataaaa # agtttccaatttttcaggcacacaggtacttctcacagttggtgaacggattggaacaccttcatggacagggaatcgttcacaaagatatcaagccg # gggaacctgctactgacgacagaggaagtcctgaaaataaccgattttggtgtcgcggaggctatcggaccttttgcggaggacgatacgtgccacac # cagtcagggtactccagcattccagcctccggagatcgccaatggaatggaattcttctctggattcaaagtggacatctggtccagtggtgtcacac # tgtataatatgacgacaggcatttacccgtttgaaggagacaatatatttaaattatttgagaacattggcaaaggccagtaccagattcctgatggg # gtggaagacaatctcagagatctactcacaggcatgctacagtttgaggcagcaaaaagattagctttaccggagattaaaaaacacgattgggtaaa # gaggaaacacccagtgactcccggatttgtggcgtttaagccggtacagggacacgaggatttacttcgaggttttacagttataccgtacttagagg # actatcatttccacaacagtgaggaggaggaggagtatgaggaccactatttatctagtgtaacgcatcctccaacggaactccataacgctagtgct # catatatgcagtgatcccaaatcagtatgccagtga] # protein sequence = [MIRHRYMVMEYCVGELQELLEAAPDKKFPIFQAHRYFSQLVNGLEHLHGQGIVHKDIKPGNLLLTTEEVLKITDFGVA # EAIGPFAEDDTCHTSQGTPAFQPPEIANGMEFFSGFKVDIWSSGVTLYNMTTGIYPFEGDNIFKLFENIGKGQYQIPDGVEDNLRDLLTGMLQFEAAK # RLALPEIKKHDWVKRKHPVTPGFVAFKPVQGHEDLLRGFTVIPYLEDYHFHNSEEEEEYEDHYLSSVTHPPTELHNASAHICSDPKSVCQ] # end gene g1 ### # start gene g2 Contig22900 AUGUSTUS gene 14615 27385 0.01 - . g2 Contig22900 AUGUSTUS transcript 14615 27385 0.01 - . g2.t1 Contig22900 AUGUSTUS tts 14615 14615 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 14615 15135 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS stop_codon 14947 14949 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 15136 15280 0.12 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 15372 15673 0.1 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 15758 15872 0.1 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 15941 16057 0.08 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 16203 16644 0.06 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 16680 17210 0.18 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 17311 18213 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 18286 18602 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 18908 18979 0.15 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 19259 19412 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 19533 19980 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 20104 20194 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS intron 20396 27301 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 14947 15135 0.12 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 15281 15371 0.19 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 15281 15371 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 15674 15757 0.1 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 15674 15757 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 15873 15940 0.1 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 15873 15940 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 16058 16202 0.07 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 16058 16202 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 16645 16679 0.18 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 16645 16679 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 17211 17310 0.22 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 17211 17310 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 18214 18285 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 18214 18285 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 18603 18907 0.16 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 18603 18907 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 18980 19258 0.02 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 18980 19258 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 19413 19532 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 19413 19532 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 19981 20103 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 19981 20103 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 20195 20395 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 20195 20395 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS CDS 27302 27328 0.02 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS exon 27302 27385 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS start_codon 27326 27328 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS tss 27385 27385 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 14998 15057 6.73 - 0 target "unknown_T[1..20]"; target_start 576; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15058 15108 3.67 - 0 target "unknown_S[1..17]"; target_start 559; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15299 15340 4.74 - 0 target "unknown_Q[1..14]"; target_start 530; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15341 15371 6.33 - 1 target "unknown_P[25..35]"; target_start 495; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15674 15747 5.77 - 0 target "unknown_P[1..25]"; target_start 495; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15757 15757 1 - 1 target "unknown_O[8..8]"; target_start 484; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15873 15895 5.32 - 0 target "unknown_O[1..8]"; target_start 484; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 15896 15940 6.78 - 0 target "unknown_N[5..19]"; target_start 465; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 16058 16069 3.69 - 0 target "unknown_N[1..4]"; target_start 465; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 16109 16195 6.29 - 0 target "unknown_M[1..29]"; target_start 423; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 16199 16202 1.79 - 1 target "unknown_L[22..23]"; target_start 399; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 16645 16679 2.99 - 0 target "unknown_L[11..22]"; target_start 399; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 17211 17240 5.1 - 0 target "unknown_L[1..10]"; target_start 399; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 17244 17285 5.18 - 0 target "unknown_K[1..14]"; target_start 384; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 18231 18285 3.58 - 1 target "unknown_J[25..43]"; target_start 327; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 18603 18676 3.93 - 0 target "unknown_J[1..25]"; target_start 327; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 19461 19529 4.22 - 0 target "unknown_E[1..23]"; target_start 118; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 19530 19532 1.6 - 0 target "unknown_D[20..20]"; target_start 98; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 19981 20037 4.62 - 0 target "unknown_D[1..19]"; target_start 98; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 20056 20088 3.48 - 0 target "unknown_C[1..11]"; target_start 81; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 20204 20239 5.69 - 0 target "unknown_B[1..12]"; target_start 61; transcript_id "g2.t1"; gene_id "g2"; Contig22900 AUGUSTUS protein_match 20273 20302 5.58 - 0 target "unknown_A[1..10]"; target_start 40; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgaacgcggatggtctccagtcgaaggattgtgccagtacttgtacaagattacaaaaccgaggtccagatgtaactt # cccagtgtgacgtgataattgattgtcagaatcgtctggttttcacggggcacgtgctgcacatgagggggccactcactcctcaaccagcgaggaac # gaacgaggatgttgtcttctgtggaatggggagatctttgggggcttgcaggtcactgaagaggaaaatgatacagctctactgttggaaaagttgtc # tgagaagtcgaatgtggaacacattctgagtactttgtcaaacttacatggaccatgggcatgtatttactggcaggaagaaaagaaaacgctgtggt # ttgggagggacttttttggaagacggagcttatgttggcagttaccgagaactagaggagattcttttcttctaacatcagtgagacagaacacagag # gatttacgggaggttccatccatcgggatgtactctgtgacgtggacgcagacggactgtttgaacataacagtgtacagctggacagatgccgtgtg # gccaggaacaatggagcctgtgacgagcgacaacctccagtcgagactagcaggggacgtcgactgtgacgtgaaatttaaccttcatcctcaaggtc # atctcactagaaatattccaccattaaacaaatgtattccagaccttgaaccctccaagatctcggttgataatccagaatcgagtgtcaaagtccga # gtgttcaatcagattctgttgtcgcaaaacgaacacaaaaatgacagtgacctgaagttaacatccgatttctctcattatcagcctaatgatgaaaa # tgcatcatgtgattgtgtaggacctgaaactcagaaatgtgtagaacctaaaacacagaaatgtttgtctgatggactgagggatgtaaaactaggcc # ctccagaaggtggagttgtgagaggctgtgcgaaaattgccattctgttttctggtggtgtggactcggcagtgttaacagcactagtggacaagtgt # cttccaggccaagagtcagtcgatttaataaatgtcgcctttgagaggaccccttcacagaacaaaaggaagcccagcgaggaggagaaatggaatgt # tccggatcgacagactggactccaggctttacaagaacttaatccagaccggaagtggaattttgttatggtgaatgtaagcatagcagaactacaaa # aacagagatcagaacacattcgccatctggtgtatcccttggagacggtgctggatgatagtattggttgtgctgtgtggtttgctgccagaggggag # ggaattctgggaaatggagagcatgctgggactgaatacaaaagcagtgccaaggttatactctgtggtatgggagctgatgaacagtttgctgggta # ttctcgacatagagggaaatttgaagaatctggatggcaaggccttatcgatgaagtggacatggaggtgcagagaatatctgcccgaaatctgggac # gggacgacagagttataacagatcacggcaaggaggccagatttccatttctggatgagaatgtggtgtcctatctccaaacactccctgttcaagtt # aaggctaatctttgttaccctcgtggtctcggggagaagattctcctgagggtgtgtgctgtacagctgggcctgactaaagctgctctttttcccaa # aagagctatacagtttggatccagaatagctaaaactgaaaacaacaaagagaaggcatcagagaagtgtgcccggctagcagatcccacgtag] # protein sequence = [MNADGLQSKDCASTCTRLQNRGPDVTSQCDVIIDCQNRLVFTGHVLHMRGPLTPQPARNERGCCLLWNGEIFGGLQVT # EEENDTALLLEKLSEKSNVEHILSTLSNLHGPWACIYWQEEKKTLWFGRDFFGRRSLCWQLPRTRGDSFLLTSVRQNTEDLREVPSIGMYSVTWTQTD # CLNITVYSWTDAVWPGTMEPVTSDNLQSRLAGDVDCDVKFNLHPQGHLTRNIPPLNKCIPDLEPSKISVDNPESSVKVRVFNQILLSQNEHKNDSDLK # LTSDFSHYQPNDENASCDCVGPETQKCVEPKTQKCLSDGLRDVKLGPPEGGVVRGCAKIAILFSGGVDSAVLTALVDKCLPGQESVDLINVAFERTPS # QNKRKPSEEEKWNVPDRQTGLQALQELNPDRKWNFVMVNVSIAELQKQRSEHIRHLVYPLETVLDDSIGCAVWFAARGEGILGNGEHAGTEYKSSAKV # ILCGMGADEQFAGYSRHRGKFEESGWQGLIDEVDMEVQRISARNLGRDDRVITDHGKEARFPFLDENVVSYLQTLPVQVKANLCYPRGLGEKILLRVC # AVQLGLTKAALFPKRAIQFGSRIAKTENNKEKASEKCARLADPT] # sequence of block unknown_T 576 [AALFPKRAIQFGSRIAKTEN] 596 # sequence of block unknown_S 559 [GEKILLRVCAVQLGLTK] 576 # sequence of block unknown_Q 530 [FPFLDENVVSYLQT] 544 # sequence of block unknown_P 495 [WQGLIDEVDMEVQRISARNLGRDDRVITDHGKEAR] 530 # sequence of block unknown_O 484 [SRHRGKFE] 492 # sequence of block unknown_N 465 [SSAKVILCGMGADEQFAGY] 484 # sequence of block unknown_M 423 [HIRHLVYPLETVLDDSIGCAVWFAARGEG] 452 # sequence of block unknown_L 399 [NPDRKWNFVMVNVSIAELQKQRS] 422 # sequence of block unknown_K 384 [NVPDRQTGLQALQE] 398 # sequence of block unknown_J 327 [RGCAKIAILFSGGVDSAVLTALVDKCLPGQESVDLINVAFERT] 370 # sequence of block unknown_E 118 [EKKTLWFGRDFFGRRSLCWQLPR] 141 # sequence of block unknown_D 98 [HILSTLSNLHGPWACIYWQE] 118 # sequence of block unknown_C 81 [NDTALLLEKLS] 92 # sequence of block unknown_B 61 [GCCLLWNGEIFG] 73 # sequence of block unknown_A 40 [FTGHVLHMRG] 50 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ER5.prfl --predictionStart=0 --predictionEnd=36222 --species=fly ./tmp/Contig2290020180911_busco_2432604931_.temp