# 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 # --[22..202]--> unknown_C (10) <--[2..15]--> unknown_D (25) <--[13..34]--> unknown_F (19) <--[1..12]--> unknown_G (15) <--[0..2]--> unknown_H (16) <--[11..59]--> unknown_J (35) <--[5..64]--> unknown_K (20) <--[0..1]--> unknown_L (10) <--[0..59]--> unknown_M (7) <--[0..8]--> unknown_N (14) <--[0..17]--> unknown_O (36) <--[1..87]--> unknown_P (25) <--[6..9]--> unknown_R (17) <--[8..102]--> unknown_T (16) <--[0..687]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig6458720180911_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 = 22323, name = Contig64587) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig64587 AUGUSTUS gene 12775 21923 0.01 - . g1 Contig64587 AUGUSTUS transcript 12775 21923 0.01 - . g1.t1 Contig64587 AUGUSTUS tts 12775 12775 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 12775 13320 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 13697 13770 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 13880 14466 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 17798 17891 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 19221 19557 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS stop_codon 19255 19257 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS intron 19558 20361 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS intron 21550 21872 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS CDS 19255 19557 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS CDS 20362 21549 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 20362 21549 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS CDS 21873 21875 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS exon 21873 21923 . - . transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS start_codon 21873 21875 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 19258 19305 5.64 - 0 target "unknown_T[1..16]"; target_start 481; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 19486 19536 3.78 - 0 target "unknown_R[1..17]"; target_start 404; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20362 20436 3.34 - 0 target "unknown_P[1..25]"; target_start 372; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20521 20628 3.27 - 0 target "unknown_O[1..36]"; target_start 308; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20629 20670 3.58 - 0 target "unknown_N[1..14]"; target_start 294; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20671 20691 4.14 - 0 target "unknown_M[1..7]"; target_start 287; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20773 20802 2.42 - 0 target "unknown_L[1..10]"; target_start 250; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20806 20865 2.71 - 0 target "unknown_K[1..20]"; target_start 229; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 20953 21057 2.57 - 0 target "unknown_J[1..35]"; target_start 165; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 21097 21144 3.77 - 0 target "unknown_H[1..16]"; target_start 136; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 21148 21192 3.84 - 0 target "unknown_G[1..15]"; target_start 120; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 21199 21255 2.1 - 0 target "unknown_F[1..19]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 21328 21402 4.08 - 0 target "unknown_D[1..25]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig64587 AUGUSTUS protein_match 21409 21438 7.99 - 0 target "unknown_C[1..10]"; target_start 38; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgataatattcaacaatttaatccccgaccatgatgctggtgtttttaatcctccaaccaacattccaagtggaattc # tggacaaatttgttgaaacaatgttaggtggactcaatcgctgggatgcagtgtatttcatgcatatatcggagcatggttatatatatcaaaacagt # ctagcttttttcccgatgtttccttttttgattagaatagttgcaaactctttgtgttatcctttgcagtttgttttgacatacaaaaatgtgttaat # gatttcagcaatggtttttaatgtgtttgtgtttctattaaccgtgaagctgttgttcagacttggaagaaatgttttaggcaatacttatacagcat # ataaagcttgtctcttgttttgtattaaccctgccagtatatttatgatggctttttattcagaaactttgtatttttgtttagtggtatatggactt # gttaattttgaaagcaacagaaaggtaatggctgtgtttctgtttgcgttaagttcattatgcaggtctaatggattgctcaatcttggatttatatt # ttatgatagtttcattttcattgtaatgattttcacaaattttttatcaggtgtatctaagccagatggaaacccatcttttagattgttcacctttt # ttggcttcatgataattcagttgatatacctacttattctcatacttttgtttgctgtaccatttattttatatcagttctattacatcaacacaatg # ttttgtaaatctggcattcatgaattgtcagacattcctaaatttttaattgactatggactagaaagaggttatcatatcattggcgacagtgtgcc # gaggtggtgtcattttaccattccattatcatatgctgacgtacaaaatactcactggggagtaggttttatgaaatattatgaatttaaacaaattc # ccaactttttgctggcattgccagtaactgtgaccagtggctgttgtgtaatgtgctattacgtgtggaacaaaaaggcatgctggacgttagggatc # aagtcaaacatgtcctgtctaaagaaaagtgatgagggatgcagatgtttgtggaacaatcctagactccttccttatgttgttcatctgctggccct # aacagtgtttggctggatgtttgttcatattcaggtacttaccagaatgctgttctcagcctccccactattgtactggtttgttgcctactgtacga # cagatgagaccaagaccaaagttccaattcggaatcaatatgatgtcatgaaaatttcagaggacatttctaaggttgaaaaggaagagaacctccag # cattcagtaaaaaacattgtcactgaccagataatggccttctggaagcagacagtaatcacgaaattcattctggcttattttctaatatattttat # tgttggaacttttatgtttagtaactttttaccatggacctga] # protein sequence = [MIIFNNLIPDHDAGVFNPPTNIPSGILDKFVETMLGGLNRWDAVYFMHISEHGYIYQNSLAFFPMFPFLIRIVANSLC # YPLQFVLTYKNVLMISAMVFNVFVFLLTVKLLFRLGRNVLGNTYTAYKACLLFCINPASIFMMAFYSETLYFCLVVYGLVNFESNRKVMAVFLFALSS # LCRSNGLLNLGFIFYDSFIFIVMIFTNFLSGVSKPDGNPSFRLFTFFGFMIIQLIYLLILILLFAVPFILYQFYYINTMFCKSGIHELSDIPKFLIDY # GLERGYHIIGDSVPRWCHFTIPLSYADVQNTHWGVGFMKYYEFKQIPNFLLALPVTVTSGCCVMCYYVWNKKACWTLGIKSNMSCLKKSDEGCRCLWN # NPRLLPYVVHLLALTVFGWMFVHIQVLTRMLFSASPLLYWFVAYCTTDETKTKVPIRNQYDVMKISEDISKVEKEENLQHSVKNIVTDQIMAFWKQTV # ITKFILAYFLIYFIVGTFMFSNFLPWT] # sequence of block unknown_T 481 [YFIVGTFMFSNFLPWT] 497 # sequence of block unknown_R 404 [SASPLLYWFVAYCTTDE] 421 # sequence of block unknown_P 372 [NPRLLPYVVHLLALTVFGWMFVHIQ] 397 # sequence of block unknown_O 308 [VGFMKYYEFKQIPNFLLALPVTVTSGCCVMCYYVWN] 344 # sequence of block unknown_N 294 [IPLSYADVQNTHWG] 308 # sequence of block unknown_M 287 [PRWCHFT] 294 # sequence of block unknown_L 250 [YINTMFCKSG] 260 # sequence of block unknown_K 229 [LIYLLILILLFAVPFILYQF] 249 # sequence of block unknown_J 165 [VMAVFLFALSSLCRSNGLLNLGFIFYDSFIFIVMI] 200 # sequence of block unknown_H 136 [SIFMMAFYSETLYFCL] 152 # sequence of block unknown_G 120 [TYTAYKACLLFCINP] 135 # sequence of block unknown_F 99 [VFVFLLTVKLLFRLGRNVL] 118 # sequence of block unknown_D 50 [EHGYIYQNSLAFFPMFPFLIRIVAN] 75 # sequence of block unknown_C 38 [NRWDAVYFMH] 48 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370VTP.prfl --predictionStart=584 --predictionEnd=40685 --species=fly ./tmp/Contig6458720180911_busco_2432604931_.temp