# 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..552]--> unknown_A (14) <--[4..19]--> unknown_B (18) <--[4..39]--> unknown_C (34) <--[0..2]--> unknown_D (15) <--[0..1]--> unknown_E (18) <--[4..36]--> unknown_F (17) <--[0..1]--> unknown_G (31) <--[25..77]--> unknown_J (20) <--[18..78]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig5695820180911_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 = 22183, name = Contig56958) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig56958 AUGUSTUS gene 317 20149 0.01 - . g1 Contig56958 AUGUSTUS transcript 317 20149 0.01 - . g1.t1 Contig56958 AUGUSTUS stop_codon 317 319 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 404 685 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 711 9415 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 9524 11134 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 11160 11204 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 11338 11451 0.74 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 11530 11862 0.44 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 11915 13476 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 13560 15157 0.91 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 15309 16647 0.84 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 16757 17690 0.5 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS intron 17782 19330 0.87 - . transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 317 403 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 686 710 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 9416 9523 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 11135 11159 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 11205 11337 0.02 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 11452 11529 0.74 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 11863 11914 0.48 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 13477 13559 0.96 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 15158 15308 0.94 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 16648 16756 0.8 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 17691 17781 0.58 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS CDS 19331 20149 0.44 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS start_codon 20147 20149 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 392 403 0.669 - 0 target "unknown_J[17..20]"; target_start 542; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 686 710 1.31 - 1 target "unknown_J[8..16]"; target_start 542; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 9416 9438 1.22 - 0 target "unknown_J[1..8]"; target_start 542; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 9523 9523 1 - 1 target "unknown_G[31..31]"; target_start 483; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11135 11159 2.03 - 2 target "unknown_G[23..31]"; target_start 483; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11205 11271 4.53 - 0 target "unknown_G[1..23]"; target_start 483; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11275 11325 5.45 - 0 target "unknown_F[1..17]"; target_start 465; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11455 11508 4.34 - 0 target "unknown_E[1..18]"; target_start 442; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11509 11529 8.8 - 0 target "unknown_D[9..15]"; target_start 427; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11863 11886 3.63 - 0 target "unknown_D[1..8]"; target_start 427; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 11887 11914 3.37 - 1 target "unknown_C[25..34]"; target_start 393; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 13477 13550 3.35 - 0 target "unknown_C[1..25]"; target_start 393; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 15161 15214 4.37 - 0 target "unknown_B[1..18]"; target_start 371; transcript_id "g1.t1"; gene_id "g1"; Contig56958 AUGUSTUS protein_match 15260 15301 3.31 - 0 target "unknown_A[1..14]"; target_start 342; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaagatggtcctgtcttcgatccagcatctgctgatggccctttgtcccctacagacagttttggacccaggtctcc # agaccaggatgcaggaccagcatcaccagaaggcagttatgaagaaattgcatctccaacaggagctggtcccgcttcaccggatccagaaggaccag # catcaccagagatggatccagacagtcctctctctccagaggggcctacatctcccggatctcaatcacctaaatctcccgtgtatagtccaagtcct # gctagaagcagaagtggttcaccagatgaaaatgaaagaggttctcctgtcagaagtcgttcaggatcccaggccagaagcaggtctggatctccaag # aagtaggtcagcctcccctgcaaaaagtaggtcagcctcccctgctaggagtaggtcaggctctccagttagaagtcgatcaggctctccagttagaa # gtcgatcaggatcccctgcaagaagtggatcaggttctcctagaagcaggtcagggtcaccaagaagtaggtcagggatccccagttagaagtagtca # ggtcacccaagaagcaggtcaggatcaccaagaagcagatcaggttccccagttagaagtaggtcagggtcaccaagaagtaggtcagggtcacctag # aagcagatcaagatcaagaagtttttcacgttcaagatctggatccccaagaagtagatctggttccagaagcaggagtcgctcggggtctccgcgca # gcaggtcagcctctccagcagctagaagtgatgaagaaaaagagaagggaaaagggttttgaagaagctgatgtggaagctgcaaagaagaagaagga # gaaaaagaaaggaagtaagtggataagaatgtttgaacaatgcaatgaagagtctaaagccattgtttctgatgatgaagaagggggcggagttaccg # ggcaggtggagaaccaggaagttgtcccggatatgtcctcggatgaggaagttaacaaaaatgattttgtatccgattttgaattgatgttaatgaga # aagaaagaagaaatgaggaaaagaaaaaagcgtcgacgagatgtggacataattaatgacaatgacgaccttatagtcgacatgattgtcaaaatgaa # ggaggctgcagaggatgaccgtgcactcaatatgcagaagaaaccagccataaccaaactgaaaatgctgggtcatgtcatatctcaactgaaaaaag # ccgatcttcactacgccttcttggactgtggaatcctcagtgcaatgacggaatggctggctcctcttccagacaaaagcctcccccatttacagatc # cgggaacagtttttacgcgttctacacgagtttccagccatcagtaaagagggattgaaggccagtggaattggtaaagccatcatgtatctgtataa # acatccaaaggaaaccaaagaaaacaaagaccgggcgggaaaactcatcagtaagatgactcggttggtatttcacgtttgtattgattgaaaatgga # ctgacgattatttggaggaagggattgtttggaaagattcggaattaaaagtgccaaatcggccttatgttcgctaccaaagtggaaaaagagacaaa # agtaatgtaccactatcaccgcttatggtaacccgtttacttgtttcgactacaggctcacggcggtgtgaccggtcagcagaggatgctgtacgtcc # tcccatggcaccgtga] # protein sequence = [MKMVLSSIQHLLMALCPLQTVLDPGLQTRMQDQHHQKAVMKKLHLQQELVPLHRIQKDQHHQRWIQTVLSLQRGLHLP # DLNHLNLPCIVQVLLEAEVVHQMKMKEVLLSEVVQDPRPEAGLDLQEVGQPPLQKVGQPPLLGVGQALQLEVDQALQLEVDQDPLQEVDQVLLEAGQG # HQEVGQGSPVRSSQVTQEAGQDHQEADQVPQLEVGQGHQEVGQGHLEADQDQEVFHVQDLDPQEVDLVPEAGVARGLRAAGQPLQQLEVMKKKRREKG # FEEADVEAAKKKKEKKKGSKWIRMFEQCNEESKAIVSDDEEGGGVTGQVENQEVVPDMSSDEEVNKNDFVSDFELMLMRKKEEMRKRKKRRRDVDIIN # DNDDLIVDMIVKMKEAAEDDRALNMQKKPAITKLKMLGHVISQLKKADLHYAFLDCGILSAMTEWLAPLPDKSLPHLQIREQFLRVLHEFPAISKEGL # KASGIGKAIMYLYKHPKETKENKDRAGKLISKMTRLVFHVCIDXKWTDDYLEEGIVWKDSELKVPNRPYVRYQSGKRDKSNVPLSPLMVTRLLVSTTG # SRRCDRSAEDAVRPPMAP] # sequence of block unknown_J 542 [QSGKRDKSNVPLSPLMVTRL] 562 # sequence of block unknown_G 483 [KHPKETKENKDRAGKLISKMTRLVFHVCID] 513 # sequence of block unknown_F 465 [SKEGLKASGIGKAIMYL] 482 # sequence of block unknown_E 442 [DKSLPHLQIREQFLRVLH] 460 # sequence of block unknown_D 427 [CGILSAMTEWLAPLP] 442 # sequence of block unknown_C 393 [ALNMQKKPAITKLKMLGHVISQLKKADLHYAFLD] 427 # sequence of block unknown_B 371 [NDNDDLIVDMIVKMKEAA] 389 # sequence of block unknown_A 342 [FVSDFELMLMRKKE] 356 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370NBW.prfl --predictionStart=0 --predictionEnd=31532 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5695820180911_busco_2432604931_.temp