# 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 # --[3..337]--> unknown_A (49) <--[2..29]--> unknown_B (28) <--[13..101]--> unknown_D (31) <--[1..14]--> unknown_E (15) <--[2..6]--> unknown_F (12) <--[2..60]--> unknown_G (27) <--[11..37]--> unknown_H (30) <--[0..3]--> unknown_I (19) <--[0..37]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3611020180911_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 = 16781, name = Contig36110) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig36110 AUGUSTUS gene 84 12030 0.01 + . g1 Contig36110 AUGUSTUS transcript 84 12030 0.01 + . g1.t1 Contig36110 AUGUSTUS exon 84 92 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS start_codon 86 88 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 93 3137 0.15 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 3300 4732 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 4983 5073 0.75 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 5271 5372 0.89 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 5466 6276 0.73 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 6415 7337 0.86 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 7441 7618 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 7802 7928 0.44 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 8036 8193 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 8217 9190 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 9302 9778 0.18 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 9916 10179 0.55 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 10261 10352 0.54 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS intron 10425 11324 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 86 92 0.15 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 3138 3299 0.96 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 3138 3299 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 4733 4982 0.99 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 4733 4982 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 5074 5270 0.75 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 5074 5270 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 5373 5465 0.87 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 5373 5465 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 6277 6414 0.83 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 6277 6414 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 7338 7440 1 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 7338 7440 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 7619 7801 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 7619 7801 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 7929 8035 0.1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 7929 8035 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 8194 8216 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 8194 8216 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 9191 9301 0.06 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 9191 9301 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 9779 9915 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 9779 9915 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 10180 10260 0.55 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 10180 10260 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 10353 10424 0.07 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 10353 10424 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS CDS 11325 11406 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS exon 11325 12030 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS stop_codon 11404 11406 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS tts 12030 12030 . + . transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 5414 5465 2.62 + 0 target "unknown_A[1..18]"; target_start 219; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 6277 6371 4.27 + 2 target "unknown_A[18..49]"; target_start 219; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 6402 6414 0.882 + 0 target "unknown_B[1..5]"; target_start 278; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 7338 7408 1.96 + 2 target "unknown_B[5..28]"; target_start 278; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 7764 7801 2.57 + 0 target "unknown_D[1..13]"; target_start 365; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 7929 7983 3.05 + 1 target "unknown_D[13..31]"; target_start 365; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 8023 8035 0.66 + 0 target "unknown_E[1..5]"; target_start 409; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 8194 8216 3.27 + 1 target "unknown_E[5..13]"; target_start 408; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 9191 9199 2.1 + 0 target "unknown_E[13..15]"; target_start 409; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 9209 9244 4.04 + 0 target "unknown_F[1..12]"; target_start 427; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 9806 9886 4.99 + 0 target "unknown_G[1..27]"; target_start 467; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 10217 10260 7.14 + 0 target "unknown_H[1..15]"; target_start 516; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 10353 10398 8.3 + 1 target "unknown_H[15..30]"; target_start 516; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 10405 10424 3.42 + 0 target "unknown_I[1..7]"; target_start 548; transcript_id "g1.t1"; gene_id "g1"; Contig36110 AUGUSTUS protein_match 11325 11361 3.94 + 1 target "unknown_I[7..19]"; target_start 548; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggtgatcacctcagcgaaattaacagagaagggagagggtaatgatgagttcactcccttgccagccagtaaattaa # gacgaagagtcgcagttcaatccgcagacaccgaaaaaaagtacgctggacggaaaatctcacgacagaaacttacggacctagagtcagatgacagt # ggatctgagcaatctgtggagagcgagtctgttgatgatgaggaggaggatgactcaccaatggaagaggaatccatgaacattgagcaggaagagga # ggaagaagatgaggaggaggaggaagatgaaggggaagatgagccagtggaaagtttaacagaggaggagatgtctgcccttggatcattcagaatta # aaatgaagataaaaacaaaaccagaaaaagcggaagaaaagttcagtatggctgtggtttgtagttttgtagatgatggtgattacagtaagtattac # gactcggaagacgaagctgtggatcagagcgatgacgacgattacagtgatgacgacagtgatgatgttgatgatgatgacaatgatgatgacgatga # tggtggatttaaggaagggagtgaagaagaaatggaagatgatgaaggtccatcaccaactgagggaggggtgagcagtttctcaaagtccagactgg # atgaggagatccagaagggagaggcagccagacaacaactaggtctgtgggacagtttattggaaggaagaatcaagttccagaaaattctgacagct # gtcaatcaacttccccagccagacaactggggagattttgagaagccagggggagacaactttaaggaaaagacagtctcagttcagagattactgga # taatctcctgcagaaactgatccggctgcagtccgttctacttctacagaattcagaaactcagtacatcgagtccggacagaaaaaaccagtcaaga # agactgaggacccagatgatgaggagatcactagcgaatcagactcagagaaaaacaagcagtcaacagagacattcaaacagcagaagaagatcgca # gcaaaaaggaaactcactttggaggaaatcccggaatttctagttaagcggcaaaaagacttccagagttacaggaataacacgctagagaaatggta # tgacaagacacgccttctgggggtaaaatctccagtaaaagcttcagtgggtcgaacagtccgcgctgaaacaaatacaacagctgctctgaaacaaa # tacaacagattatgacagacaaggacagactgatcaaaagaactcagatgaagcgagcgagctaccgagttctggggaaatctgaggaaagccataca # tctgctgatcagaagcaagaggttgaggctgagagcaagaatacagagcttacacacgaccccgagatttttgatgacagtgacttttaccatcaaca # gcttcgggaactcatcgagaggaagacttcagacatcaatgatcctatcgccctcagcagacaatggctagacattcagagactgagaaacaaagtga # agagaaaagtggaaacaaaagcctccaaagggagaaaaatcagatatcatgtacactcaaaactcgtcaacttcatggcacccaaagacacctgcacc # tggaccaatgaagccagagatgacctattcaaatctctatttggccagagaagcacaacacaggcaccatcctcagacgagagtgtagtcggcagatg # a] # protein sequence = [MVITSAKLTEKGEGNDEFTPLPASKLRRRVAVQSADTEKKYAGRKISRQKLTDLESDDSGSEQSVESESVDDEEEDDS # PMEEESMNIEQEEEEEDEEEEEDEGEDEPVESLTEEEMSALGSFRIKMKIKTKPEKAEEKFSMAVVCSFVDDGDYSKYYDSEDEAVDQSDDDDYSDDD # SDDVDDDDNDDDDDGGFKEGSEEEMEDDEGPSPTEGGVSSFSKSRLDEEIQKGEAARQQLGLWDSLLEGRIKFQKILTAVNQLPQPDNWGDFEKPGGD # NFKEKTVSVQRLLDNLLQKLIRLQSVLLLQNSETQYIESGQKKPVKKTEDPDDEEITSESDSEKNKQSTETFKQQKKIAAKRKLTLEEIPEFLVKRQK # DFQSYRNNTLEKWYDKTRLLGVKSPVKASVGRTVRAETNTTAALKQIQQIMTDKDRLIKRTQMKRASYRVLGKSEESHTSADQKQEVEAESKNTELTH # DPEIFDDSDFYHQQLRELIERKTSDINDPIALSRQWLDIQRLRNKVKRKVETKASKGRKIRYHVHSKLVNFMAPKDTCTWTNEARDDLFKSLFGQRST # TQAPSSDESVVGR] # sequence of block unknown_A 219 [SRLDEEIQKGEAARQQLGLWDSLLEGRIKFQKILTAVNQLPQPDNWGDF] 268 # sequence of block unknown_B 278 [KTVSVQRLLDNLLQKLIRLQSVLLLQNS] 306 # sequence of block unknown_D 365 [FLVKRQKDFQSYRNNTLEKWYDKTRLLGVKS] 396 # sequence of block unknown_E 409 [TNTTAALKQIQQIMT] 424 # sequence of block unknown_F 427 [RLIKRTQMKRAS] 439 # sequence of block unknown_G 467 [LTHDPEIFDDSDFYHQQLRELIERKTS] 494 # sequence of block unknown_H 516 [KRKVETKASKGRKIRYHVHSKLVNFMAPKD] 546 # sequence of block unknown_I 548 [TWTNEARDDLFKSLFGQRS] 567 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370F1Q.prfl --predictionStart=0 --predictionEnd=30425 --species=fly ./tmp/Contig3611020180911_busco_2432604931_.temp