# 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..165]--> unknown_A (24) <--[0..4]--> unknown_B (31) <--[9..25]--> unknown_C (17) <--[47..194]--> unknown_H (14) <--[0..4]--> unknown_I (17) <--[7..9]--> unknown_K (20) <--[8..13]--> unknown_L (72) <--[0..1]--> unknown_M (20) <--[2..4]--> unknown_N (20) <--[0..1]--> unknown_O (28) <--[0..2]--> unknown_P (14) <--[3..26]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig2090120180911_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 = 26062, name = Contig20901) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig20901 AUGUSTUS gene 5588 16629 0.01 + . g1 Contig20901 AUGUSTUS transcript 5588 16629 0.01 + . g1.t1 Contig20901 AUGUSTUS start_codon 5588 5590 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 5594 6222 0.23 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 6340 7615 0.11 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 7712 7995 0.15 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 8074 8941 0.38 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 9023 9666 0.44 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 9817 10072 0.92 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 10143 10228 0.76 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 10296 10621 0.05 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 10708 11977 0.05 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 12071 13370 0.39 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 13496 13630 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 13682 13791 0.16 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 13882 14681 0.18 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS intron 14793 16509 0.31 + . transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 5588 5593 0.26 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 6223 6339 0.68 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 7616 7711 0.16 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 7996 8073 0.93 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 8942 9022 0.42 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 9667 9816 0.96 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 10073 10142 0.98 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 10229 10295 0.27 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 10622 10707 0.04 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 11978 12070 0.44 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 13371 13495 0.36 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 13631 13681 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 13792 13881 0.34 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 14682 14792 0.22 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS CDS 16510 16629 0.98 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS stop_codon 16627 16629 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 7634 7705 3.11 + 0 target "unknown_A[1..24]"; target_start 47; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 8002 8073 3.67 + 0 target "unknown_B[1..24]"; target_start 75; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 8942 8962 2.52 + 0 target "unknown_B[25..31]"; target_start 75; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 9011 9022 3.77 + 0 target "unknown_C[1..4]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 9667 9705 3.17 + 0 target "unknown_C[5..17]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 10276 10295 1.42 + 0 target "unknown_H[1..7]"; target_start 215; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 10622 10643 4.34 + 1 target "unknown_H[7..14]"; target_start 215; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 10644 10694 7.9 + 0 target "unknown_I[1..17]"; target_start 229; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 11989 12048 5.76 + 0 target "unknown_K[1..20]"; target_start 254; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 13385 13495 2.54 + 0 target "unknown_L[1..37]"; target_start 286; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 13631 13681 6.25 + 2 target "unknown_L[38..55]"; target_start 285; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 13792 13845 2.35 + 0 target "unknown_L[55..72]"; target_start 286; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 13846 13881 2.44 + 0 target "unknown_M[1..12]"; target_start 358; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 14682 14705 3.08 + 0 target "unknown_M[13..20]"; target_start 358; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 14712 14771 2.81 + 0 target "unknown_N[1..20]"; target_start 380; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 14772 14792 3.53 + 0 target "unknown_O[1..7]"; target_start 400; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 16510 16572 4.49 + 0 target "unknown_O[8..28]"; target_start 400; transcript_id "g1.t1"; gene_id "g1"; Contig20901 AUGUSTUS protein_match 16573 16614 4.01 + 0 target "unknown_P[1..14]"; target_start 428; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaagttcattaaatgtcagcgctgcacgacaccacaccgtcagtatcatctttggagaggtgtttatgataaaggat # tgcaacagccattactgaaaaaccctcacacgcaattcaagcagattcaacagtattcagaaaatcaacaaccaaagaatttctttcaaaaattattt # gaccaagtgcaagaggatctaaaaaagaataaagaaatcaaggaaaacttaaagaagtttagagaagaaagaaaaaagttggaggaggcagatgcttt # gatgaaagcaagagagaagtttaaaaaagttcaagaagaaactaagaagagttccaccgtcttccaaaagacattcgaggatgtcaaggaaaaagtgt # cagagacggtggatgaagtcagtaagtcagactttggtaagagaagtaaagaatttaccgaggaactggggaaaactgctgggaaagccgcagagacg # atcgggagtgcaggggaacacctggcaaaatctcagccaatgaaaaaagtcgcagagggtgttagaacagtttcagaagaattggatgaacttgcttt # ttcgagacacaggatttataaatctccagagaaaccactgaagaggtcagagttcaggaccctgatgaaagaggagagagaaataaaagtggacgacg # agaccacaggagttacacttcataaagattccaagttttatcagagttggcagaattttaaagagaataatgcatatgtaaataaggtgtttgagtta # aagatgaagtatgatgaaagtgataatcctgcagtccgggtgacgagggcggtgacagatttaatcgggagagcgctaggtagcgtacttacaccgtc # aacgttaagcgaggccttgacagaaatcaataaatacgatccatcattcacaccagaaggattcgcttcattttgtgaaaccattgttgttccacata # tattagaggccatggttcgagctgacactgaagttttaaaggactggcttcatgaagctgcttacaatgtgacatccgcgatattgaaaccttacata # gaggccagatataagtcctgttcacagatcattgatatcggacgagtggacgttcttggcggacaggtaatggagcaggggccagtcttactaatcca # gtttcacgctcatcagatcgagtgctggcgggattttaaaaatgaagtggttgtgggtagtcctgacgatattttcaaaatgacctacacctgggcgc # tgtgccgagatcaggaggaagtggatcctaaagctgcctggaagttgttagaatttagtgccacgaaaaccaatgtagtgatataa] # protein sequence = [MKFIKCQRCTTPHRQYHLWRGVYDKGLQQPLLKNPHTQFKQIQQYSENQQPKNFFQKLFDQVQEDLKKNKEIKENLKK # FREERKKLEEADALMKAREKFKKVQEETKKSSTVFQKTFEDVKEKVSETVDEVSKSDFGKRSKEFTEELGKTAGKAAETIGSAGEHLAKSQPMKKVAE # GVRTVSEELDELAFSRHRIYKSPEKPLKRSEFRTLMKEEREIKVDDETTGVTLHKDSKFYQSWQNFKENNAYVNKVFELKMKYDESDNPAVRVTRAVT # DLIGRALGSVLTPSTLSEALTEINKYDPSFTPEGFASFCETIVVPHILEAMVRADTEVLKDWLHEAAYNVTSAILKPYIEARYKSCSQIIDIGRVDVL # GGQVMEQGPVLLIQFHAHQIECWRDFKNEVVVGSPDDIFKMTYTWALCRDQEEVDPKAAWKLLEFSATKTNVVI] # sequence of block unknown_A 47 [NQQPKNFFQKLFDQVQEDLKKNKE] 71 # sequence of block unknown_B 75 [LKKFREERKKLEEADALMKAREKFKKVQEET] 106 # sequence of block unknown_C 122 [KVSETVDEVSKSDFGKR] 139 # sequence of block unknown_H 215 [REIKVDDETTGVTL] 229 # sequence of block unknown_I 229 [HKDSKFYQSWQNFKENN] 246 # sequence of block unknown_K 254 [LKMKYDESDNPAVRVTRAVT] 274 # sequence of block unknown_L 286 [PSTLSEALTEINKYDPSFTPEGFASFCETIVVPHILEAMVRADTEVLKDWLHEAAYNVTSAILKPYIEARYK] 358 # sequence of block unknown_M 358 [SCSQIIDIGRVDVLGGQVME] 378 # sequence of block unknown_N 380 [PVLLIQFHAHQIECWRDFKN] 400 # sequence of block unknown_O 400 [EVVVGSPDDIFKMTYTWALCRDQEEVDP] 428 # sequence of block unknown_P 428 [KAAWKLLEFSATKT] 442 # end gene g1 ### # start gene g2 Contig20901 AUGUSTUS gene 25671 26062 0.97 - . g2 Contig20901 AUGUSTUS transcript 25671 26062 0.97 - . g2.t1 Contig20901 AUGUSTUS stop_codon 25671 25673 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig20901 AUGUSTUS intron 25889 26062 0.97 - . transcript_id "g2.t1"; gene_id "g2"; Contig20901 AUGUSTUS CDS 25671 25888 0.97 - 2 transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [gaacattttttcgtctgcaacagcaaggaaagttaacaaaggagcaactggaaggggccggtttggagatggatgatgt # ggaaggggccggtttggagatggatgatggtgattttgatgattctgatgatgaaactgaacacgaggatcaagagaaaacggagaacattggtagtg # aaaatgacgagactgaacaagaaaaaagctgtaatccctaa] # protein sequence = [TFFRLQQQGKLTKEQLEGAGLEMDDVEGAGLEMDDGDFDDSDDETEHEDQEKTENIGSENDETEQEKSCNP] # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370LYY.prfl --predictionStart=0 --predictionEnd=32060 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2090120180911_busco_2432604931_.temp