# 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..111]--> unknown_A (42) <--[0..1]--> unknown_B (8) <--[0..2]--> unknown_C (8) <--[0..1]--> unknown_D (51) <--[0..18]--> unknown_E (16) <--[4..6]--> unknown_F (27) <--[0..1]--> unknown_G (9) <--[1..53]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig117520180911_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 = 23023, name = Contig1175) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig1175 AUGUSTUS gene 591 12394 0.01 - . g1 Contig1175 AUGUSTUS transcript 591 12394 0.01 - . g1.t1 Contig1175 AUGUSTUS stop_codon 591 593 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 640 1152 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 1169 1943 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 1970 2764 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 2777 3353 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 3376 3558 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 3603 3780 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 3792 4518 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 4529 5032 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 5066 5253 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 5267 5363 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 5378 7079 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 7091 8144 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 8305 10377 0.25 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS intron 10488 12382 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 591 639 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 1153 1168 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 1944 1969 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 2765 2776 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 3354 3375 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 3559 3602 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 3781 3791 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 4519 4528 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 5033 5065 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 5254 5266 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 5364 5377 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 7080 7090 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 8145 8304 0.96 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 10378 10487 0.81 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS CDS 12383 12394 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS start_codon 12392 12394 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 618 639 1.65 - 1 target "unknown_G[2..9]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 1153 1157 9.77 - 0 target "unknown_G[1..2]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 1161 1168 1.83 - 2 target "unknown_F[25..27]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 1944 1969 1.96 - 1 target "unknown_F[16..25]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 2765 2776 1.55 - 1 target "unknown_F[12..16]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 3354 3375 1.49 - 2 target "unknown_F[5..12]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 3559 3571 1.52 - 0 target "unknown_F[1..5]"; target_start 135; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 3584 3602 0.975 - 1 target "unknown_E[10..16]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 3781 3791 1.72 - 0 target "unknown_E[7..10]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 4519 4528 7.35 - 1 target "unknown_E[3..6]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 5033 5040 0.719 - 0 target "unknown_E[1..3]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 5056 5065 0.884 - 1 target "unknown_D[48..51]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 5254 5266 2.86 - 2 target "unknown_D[44..48]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 5364 5377 1.06 - 1 target "unknown_D[39..44]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 7080 7090 1.09 - 0 target "unknown_D[36..39]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 8145 8249 8.78 - 0 target "unknown_D[1..35]"; target_start 59; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 8250 8273 5.17 - 0 target "unknown_C[1..8]"; target_start 51; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 8274 8297 6.05 - 0 target "unknown_B[1..8]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 8301 8304 15.4 - 1 target "unknown_A[41..42]"; target_start 0; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 10378 10487 7.37 - 0 target "unknown_A[5..41]"; target_start 0; transcript_id "g1.t1"; gene_id "g1"; Contig1175 AUGUSTUS protein_match 12383 12394 16.1 - 0 target "unknown_A[1..4]"; target_start 0; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgttttaccatgtctcattagaacatgaaattcttcttcacccaagatattttggaccaaatttactcaatattgtga # agcagaaactgttcacagaggttgagggaacatgcactggaaaatatggatttgtgatagcagttacaactattgataatattggagcaggaacaata # caacccagtcgaggttttgtggtctatccagttaaatataaagccattgtgttccggccattcaaaggcgaagttcttgatgctgttgtcactcaggt # taacaagctttccttcaaacccacagtaggggtcctggaggtaggcttatctgataagaataaaatggacagttctaaaccccctactataaaactcc # atccttcgtaccaaaacaaagggttcttcgatgaggatttaaatgttcaaaatgatactagcccaaagacaaagctcagaggagcgcgtcccgacttc # tcccgaaacttctctgctatctgtaagcttaaacccagatttctctatcacaaacaacctacgcaccgttaa] # protein sequence = [MFYHVSLEHEILLHPRYFGPNLLNIVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGTIQPSRGFVVYPVKYKAIVFR # PFKGEVLDAVVTQVNKLSFKPTVGVLEVGLSDKNKMDSSKPPTIKLHPSYQNKGFFDEDLNVQNDTSPKTKLRGARPDFSRNFSAICKLKPRFLYHKQ # PTHR] # sequence of block unknown_G 163 [ICKLKPRFL] 172 # sequence of block unknown_F 135 [EDLNVQNDTSPKTKLRGARPDFSRNFS] 162 # sequence of block unknown_E 115 [SSKPPTIKLHPSYQNK] 131 # sequence of block unknown_D 59 [QPSRGFVVYPVKYKAIVFRPFKGEVLDAVVTQVNKLSFKPTVGVLEVGLSD] 110 # sequence of block unknown_C 51 [DNIGAGTI] 59 # sequence of block unknown_B 43 [FVIAVTTI] 51 # sequence of block unknown_A 0 [MFYHVSLEHEILLHPRYFGPNLLNIVKQKLFTEVEGTCTGKY] 42 # end gene g1 ### # start gene g2 Contig1175 AUGUSTUS gene 15884 21426 0.05 + . g2 Contig1175 AUGUSTUS transcript 15884 21426 0.05 + . g2.t1 Contig1175 AUGUSTUS start_codon 15884 15886 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS intron 15909 17268 0.17 + . transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS intron 17471 17712 0.22 + . transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS intron 17765 21246 0.22 + . transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS CDS 15884 15908 0.28 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS CDS 17269 17470 0.14 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS CDS 17713 17764 0.22 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS CDS 21247 21426 0.68 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig1175 AUGUSTUS stop_codon 21424 21426 . + 0 transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtgggaggcactgggagcgtgggatcagaccagccatgtaacaacactgtatgagaagttccagcagaatcctcaat # ctgtcccattggttacgtccagggagctagagtaccccaaccagtaccgctcccctcgccaggcctggctagaaacactcagcacagtggaggatcac # aaactcggcatgatcgatctccaccctgatgtctttgctgctcatcccaggcttgacatactgtatcacaatttaagatggcaggaattttataagaa # aatagattatgactggacaccaagtcgtggtgatctggatgtaaccactcggaaacagatgaaacagaagggatcaggaagagccaggaaccgcaaca # gagattcagtgatgttcaggacaggtatgtgtgtgcttatagatattgacactagtacaagaaataacccttcagccgaagcctaa] # protein sequence = [MWEALGAWDQTSHVTTLYEKFQQNPQSVPLVTSRELEYPNQYRSPRQAWLETLSTVEDHKLGMIDLHPDVFAAHPRLD # ILYHNLRWQEFYKKIDYDWTPSRGDLDVTTRKQMKQKGSGRARNRNRDSVMFRTGMCVLIDIDTSTRNNPSAEA] # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UV4.prfl --predictionStart=0 --predictionEnd=30481 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig117520180911_busco_2432604931_.temp