# 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 # --[10..126]--> unknown_B (24) <--[1..12]--> unknown_C (34) <--[2..7]--> unknown_D (21) <--[3..13]--> unknown_E (24) <--[3..30]--> unknown_F (15) <--[1..9]--> unknown_G (19) <--[3..40]--> unknown_H (13) <--[1..29]--> unknown_I (15) <--[7..43]--> unknown_J (23) <--[0..39]--> unknown_K (12) <--[0..2]--> unknown_L (41) <--[1..11]--> unknown_M (29) <--[1..22]--> unknown_N (10) <--[1..18]--> unknown_O (11) <--[0..36]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3414320180911_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 = 27177, name = Contig34143) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig34143 AUGUSTUS gene 2119 26495 0.01 - . g1 Contig34143 AUGUSTUS transcript 2119 26495 0.01 - . g1.t1 Contig34143 AUGUSTUS exon 2119 2161 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS stop_codon 2131 2133 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 2162 2239 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 2334 2415 0.02 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 2484 2820 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 2879 3021 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 3061 3193 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 3223 5924 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 5936 6158 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 6192 7100 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 7126 7956 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 7968 14570 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 14637 14982 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 15136 16190 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 16299 16616 0.89 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 16875 17324 0.3 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 17376 17437 0.05 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 17455 17702 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 17720 20761 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 20773 23572 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 23596 23730 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 23746 24342 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 24360 25003 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 25060 25102 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 25113 25272 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 25286 25868 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS intron 25891 26385 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 2131 2161 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 2240 2333 0.02 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 2240 2333 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 2416 2483 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 2416 2483 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 2821 2878 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 2821 2878 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 3022 3060 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 3022 3060 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 3194 3222 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 3194 3222 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 5925 5935 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 5925 5935 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 6159 6191 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 6159 6191 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 7101 7125 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 7101 7125 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 7957 7967 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 7957 7967 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 14571 14636 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 14571 14636 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 14983 15135 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 14983 15135 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 16191 16298 0.75 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 16191 16298 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 16617 16874 0.37 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 16617 16874 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 17325 17375 0.21 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 17325 17375 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 17438 17454 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 17438 17454 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 17703 17719 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 17703 17719 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 20762 20772 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 20762 20772 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 23573 23595 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 23573 23595 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 23731 23745 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 23731 23745 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 24343 24359 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 24343 24359 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 25004 25059 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 25004 25059 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 25103 25112 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 25103 25112 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 25273 25285 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 25273 25285 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 25869 25890 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 25869 25890 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS CDS 26386 26427 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS exon 26386 26495 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS start_codon 26425 26427 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS tss 26495 26495 . - . transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 2317 2333 1.49 - 2 target "unknown_O[6..11]"; target_start 379; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 2416 2431 1.1 - 0 target "unknown_O[1..6]"; target_start 379; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 2471 2483 1.62 - 1 target "unknown_N[6..10]"; target_start 356; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 2821 2837 1.92 - 0 target "unknown_N[1..6]"; target_start 356; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 3035 3060 1.29 - 2 target "unknown_M[21..29]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 3194 3222 1.52 - 1 target "unknown_M[11..21]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 5925 5935 0.877 - 0 target "unknown_M[8..11]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 6159 6179 1.23 - 0 target "unknown_M[1..7]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 7104 7125 0.995 - 1 target "unknown_L[34..41]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 7957 7967 2.83 - 0 target "unknown_L[31..34]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 14571 14636 6.36 - 0 target "unknown_L[9..30]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 14983 15006 5.97 - 0 target "unknown_L[1..8]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 15007 15042 5.67 - 0 target "unknown_K[1..12]"; target_start 251; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 15046 15114 3.87 - 0 target "unknown_J[1..23]"; target_start 227; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16203 16247 2.57 - 0 target "unknown_I[1..15]"; target_start 201; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16251 16289 3.49 - 0 target "unknown_H[1..13]"; target_start 187; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16617 16673 6.24 - 0 target "unknown_G[1..19]"; target_start 165; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16677 16721 3.59 - 0 target "unknown_F[1..15]"; target_start 149; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16776 16847 3.02 - 0 target "unknown_E[1..24]"; target_start 107; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 16863 16874 5.06 - 0 target "unknown_D[18..21]"; target_start 81; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 17325 17375 7.4 - 0 target "unknown_D[1..17]"; target_start 81; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 17450 17454 3.32 - 2 target "unknown_C[33..34]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 17703 17719 0.839 - 1 target "unknown_C[27..33]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 20762 20772 1.51 - 0 target "unknown_C[24..27]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 23573 23595 1.16 - 2 target "unknown_C[16..23]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 23731 23745 1.02 - 2 target "unknown_C[11..16]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 24343 24359 2.05 - 1 target "unknown_C[5..11]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 25004 25017 1.2 - 0 target "unknown_C[1..5]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 25039 25059 1.24 - 0 target "unknown_B[18..24]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 25103 25112 0.6 - 1 target "unknown_B[14..17]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 25273 25285 0.848 - 2 target "unknown_B[10..14]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 25869 25890 1.34 - 0 target "unknown_B[3..10]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig34143 AUGUSTUS protein_match 26386 26391 0.16 - 0 target "unknown_B[1..2]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgctaatttacgtcccacatgtgtccgaacacctcatttattacttgacatgcccatcatacatgaagacgagatttg # ctggagatattcatggtagattctcgtttcgaaacgccgagaaacaccagcacggcgaacatatagggtatattacagctaaattagtcagcagatac # ttcgcaaaacttacctctattcgtttcatttcaatcatactagcaattgctcgtttagtcatgctaatcgtggaactgggacccggcagagggaccct # ggcagcggacatgatgagggttttttcacagtttcaagagttcaacaaagctgtatccctgcatttggtggaggtcagtccgaaaatgattcagcatc # aatccgaggctctcacaggggttatgccccctgataacacagtggcagagtaccagagccagaaaaccaaatttggaccggatgttcactggcaccgg # ttcctggaccaggttcctaaggagtgttcctgcttcatcgctcacgagttctttgatgtgttaccaatctataaatttcagaagaaagacggcgaatg # gaacgagattttggtggatatccaagaaggaggaggtctacgtttcatcatgtccagaggaccaaccacaaattctaaggcatttctcacacatatga # cagacttggatgagagagaccatgtagaggtgagcccagaaagtgggacgttagtacagaaaatgtcgcagaggatcagtgatcatggaggtcgagcg # atgattatagactacggccatgacggaacaaagacagacacatttaggggttttaaagatcacaagctgcacgacccgttacagaacccgggctctgc # tgatctcaccgccgatgtgctgttcttattactgatgaatattcacaaggagaacatgatacaagtgagtcaatacattacactgacagtggctttct # ttctgattctgatgaggggagtccaaaatttgaaaaaagtaagtgatcagaacaattcagccagggtatggtgcaaactgttacaggaaaaacccgga # tcatttcaacgaattctcacatccatcttctttcttacaaaggttcatggaatctctagtgaatacaatggtgcttttacaatgagtctcaaagacta # cttcatggaagtgaaaaacatcttagaaaacaaaattattttccagatattttatcagagagtatgggcaatttgcaagagtcttgtcagttgcaaaa # aaaaagaaaactttcttgtgtaa] # protein sequence = [MLIYVPHVSEHLIYYLTCPSYMKTRFAGDIHGRFSFRNAEKHQHGEHIGYITAKLVSRYFAKLTSIRFISIILAIARL # VMLIVELGPGRGTLAADMMRVFSQFQEFNKAVSLHLVEVSPKMIQHQSEALTGVMPPDNTVAEYQSQKTKFGPDVHWHRFLDQVPKECSCFIAHEFFD # VLPIYKFQKKDGEWNEILVDIQEGGGLRFIMSRGPTTNSKAFLTHMTDLDERDHVEVSPESGTLVQKMSQRISDHGGRAMIIDYGHDGTKTDTFRGFK # DHKLHDPLQNPGSADLTADVLFLLLMNIHKENMIQVSQYITLTVAFFLILMRGVQNLKKVSDQNNSARVWCKLLQEKPGSFQRILTSIFFLTKVHGIS # SEYNGAFTMSLKDYFMEVKNILENKIIFQIFYQRVWAICKSLVSCKKKENFLV] # sequence of block unknown_O 379 [TMSLKDYFMEV] 390 # sequence of block unknown_N 356 [RILTSIFFLT] 366 # sequence of block unknown_M 309 [VSQYITLTVAFFLILMRGVQNLKKVSDQN] 338 # sequence of block unknown_L 263 [GTKTDTFRGFKDHKLHDPLQNPGSADLTADVLFLLLMNIHK] 304 # sequence of block unknown_K 251 [GGRAMIIDYGHD] 263 # sequence of block unknown_J 227 [RDHVEVSPESGTLVQKMSQRISD] 250 # sequence of block unknown_I 201 [GLRFIMSRGPTTNSK] 216 # sequence of block unknown_H 187 [GEWNEILVDIQEG] 200 # sequence of block unknown_G 165 [CSCFIAHEFFDVLPIYKFQ] 184 # sequence of block unknown_F 149 [GPDVHWHRFLDQVPK] 164 # sequence of block unknown_E 107 [KAVSLHLVEVSPKMIQHQSEALTG] 131 # sequence of block unknown_D 81 [IVELGPGRGTLAADMMRVFSQ] 102 # sequence of block unknown_C 43 [HGEHIGYITAKLVSRYFAKLTSIRFISIILAIAR] 77 # sequence of block unknown_B 12 [IYYLTCPSYMKTRFAGDIHGRFSF] 36 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QMM.prfl --predictionStart=0 --predictionEnd=34642 --species=fly ./tmp/Contig3414320180911_busco_2432604931_.temp