# 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 # --[4..107]--> unknown_A (10) <--[0..20]--> unknown_B (15) <--[3..57]--> unknown_C (28) <--[1..17]--> unknown_D (19) <--[7..14]--> unknown_F (8) <--[9..28]--> unknown_G (34) <--[0..13]--> unknown_H (59) <--[0..49]--> unknown_I (19) <--[0..12]--> unknown_J (33) <--[0..47]--> unknown_K (18) <--[0..1]--> unknown_L (11) <--[0..19]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3180020180911_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 = 5805, name = Contig31800) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig31800 AUGUSTUS gene 162 5069 0.01 + . g1 Contig31800 AUGUSTUS transcript 162 5069 0.01 + . g1.t1 Contig31800 AUGUSTUS exon 162 356 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS start_codon 269 271 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 357 650 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 672 752 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 772 1206 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 1291 1553 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 1623 2250 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 2364 2503 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 2620 2973 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 3000 3313 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 3534 3755 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS intron 3861 4684 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 269 356 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 651 671 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 651 671 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 753 771 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 753 771 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 1207 1290 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 1207 1290 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 1554 1622 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 1554 1622 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 2251 2363 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 2251 2363 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 2504 2619 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 2504 2619 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 2974 2999 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 2974 2999 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 3314 3533 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 3314 3533 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 3756 3860 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 3756 3860 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS CDS 4685 4822 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS exon 4685 5069 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS stop_codon 4820 4822 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS tts 5069 5069 . + . transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 344 356 1.97 + 0 target "unknown_A[1..5]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 651 667 1.69 + 2 target "unknown_A[5..10]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 668 671 0.121 + 0 target "unknown_B[1..2]"; target_start 35; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 753 771 1.04 + 1 target "unknown_B[2..8]"; target_start 34; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 1207 1228 1.06 + 1 target "unknown_B[8..15]"; target_start 35; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 1265 1290 6.59 + 0 target "unknown_C[1..9]"; target_start 62; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 1554 1611 6.4 + 1 target "unknown_C[9..28]"; target_start 62; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 1621 1622 1 + 0 target "unknown_D[1..1]"; target_start 93; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 2251 2305 8.33 + 1 target "unknown_D[1..19]"; target_start 93; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 2327 2350 4.74 + 0 target "unknown_F[1..8]"; target_start 119; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 2518 2619 5.96 + 0 target "unknown_G[1..34]"; target_start 136; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 3324 3500 6.21 + 0 target "unknown_H[1..59]"; target_start 182; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 3501 3533 7.86 + 0 target "unknown_I[1..11]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 3756 3779 6.35 + 0 target "unknown_I[12..19]"; target_start 241; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 3780 3860 6.18 + 0 target "unknown_J[1..27]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 4685 4702 2.12 + 0 target "unknown_J[28..33]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 4718 4771 5.18 + 0 target "unknown_K[1..18]"; target_start 298; transcript_id "g1.t1"; gene_id "g1"; Contig31800 AUGUSTUS protein_match 4772 4804 6.49 + 0 target "unknown_L[1..11]"; target_start 316; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgctggtgtactacgtggtaagcatcaaacgattatcttcacacctcgctcgaggcacgaggtttactagatatacac # atggattagagatgtatggtcacaattttttgaaaatgactgagtctcacgaaggagctaaacaatcatgttggaacgagtgtttgtctaaagctaat # ccttcatattccccagcgagggccattattgctccccatgcaggatatgtgtactgtggggcatgtggtggccatgcctacagacagatcgatccatc # caccattaagagagtctttgtacttggaccatctcatcatgtccgtttgtctggttgtgccctcacagaaacttcacactatcaaacaccattgtatg # atctgattatagaccagaaagtaaatgaagagctaaatgccacgaaagcttttgagaaaatgaagttgagcacagatgaagatgaacatagcatagag # atgcatttaccatacattgccaaagtcatggagaggcaacaaaacttggacttttcctatatttttcaacgtggccacttcaccgtggtaccagtttt # ggttggttctctatcatctgacaaggagaggctgtatggatctatatttagccaatatttagctgaccctgccaatttctttgtgatatcctccgact # tttgtcactggggacaacgattccgttacacattctatgataaatcttgtggcgacatctggcagtccatcgaggccttagataaaatgggaatggat # gcaatagaacaaatggatcctgttaaattttctcaatacttgaaagattatgaaaacactatatgtggtcgttatccaataggtgttctcttaaacgc # aattgattctctgcgacgaaatggaaatggccacagaatgtcatttaaatttctgaattacgctcagtccagtcgctgcaaaaagatgagcgattcct # cggtcagttacgctgctggtgccctgctaatgcagtaa] # protein sequence = [MLVYYVVSIKRLSSHLARGTRFTRYTHGLEMYGHNFLKMTESHEGAKQSCWNECLSKANPSYSPARAIIAPHAGYVYC # GACGGHAYRQIDPSTIKRVFVLGPSHHVRLSGCALTETSHYQTPLYDLIIDQKVNEELNATKAFEKMKLSTDEDEHSIEMHLPYIAKVMERQQNLDFS # YIFQRGHFTVVPVLVGSLSSDKERLYGSIFSQYLADPANFFVISSDFCHWGQRFRYTFYDKSCGDIWQSIEALDKMGMDAIEQMDPVKFSQYLKDYEN # TICGRYPIGVLLNAIDSLRRNGNGHRMSFKFLNYAQSSRCKKMSDSSVSYAAGALLMQ] # sequence of block unknown_A 25 [THGLEMYGHN] 35 # sequence of block unknown_B 35 [FLKMTESHEGAKQSC] 50 # sequence of block unknown_C 62 [SPARAIIAPHAGYVYCGACGGHAYRQID] 90 # sequence of block unknown_D 93 [IKRVFVLGPSHHVRLSGCA] 112 # sequence of block unknown_F 119 [QTPLYDLI] 127 # sequence of block unknown_G 136 [NATKAFEKMKLSTDEDEHSIEMHLPYIAKVMERQ] 170 # sequence of block unknown_H 182 [HFTVVPVLVGSLSSDKERLYGSIFSQYLADPANFFVISSDFCHWGQRFRYTFYDKSCGD] 241 # sequence of block unknown_I 241 [IWQSIEALDKMGMDAIEQM] 260 # sequence of block unknown_J 260 [DPVKFSQYLKDYENTICGRYPIGVLLNAIDSLR] 293 # sequence of block unknown_K 298 [HRMSFKFLNYAQSSRCKK] 316 # sequence of block unknown_L 316 [MSDSSVSYAAG] 327 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370IH5.prfl --predictionStart=0 --predictionEnd=23530 --species=fly ./tmp/Contig3180020180911_busco_2432604931_.temp