# 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..72]--> unknown_A (30) <--[0..1]--> unknown_B (12) <--[0..33]--> unknown_C (21) <--[0..1]--> unknown_D (8) <--[0..2]--> unknown_E (22) <--[0..87]--> unknown_F (19) <--[0..1]--> unknown_G (45) <--[0..1]--> unknown_H (23) <--[0..28]--> unknown_I (8) <--[9..20]--> unknown_K (25) <--[0..19]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3954320180911_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 = 31875, name = Contig39543) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig39543 AUGUSTUS gene 1366 17465 0.01 + . g1 Contig39543 AUGUSTUS transcript 1366 17465 0.01 + . g1.t1 Contig39543 AUGUSTUS tss 1366 1366 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 1366 1471 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 4032 4216 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS start_codon 4055 4057 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 4217 6096 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 6113 6183 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 6198 6605 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 6622 8288 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 8311 9063 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 9132 9837 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 9892 10317 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 10336 13222 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 13238 15487 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 15673 16618 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 16733 16898 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS intron 17001 17273 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 4055 4216 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 6097 6112 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 6097 6112 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 6184 6197 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 6184 6197 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 6606 6621 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 6606 6621 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 8289 8310 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 8289 8310 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 9064 9131 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 9064 9131 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 9838 9891 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 9838 9891 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 10318 10335 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 10318 10335 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 13223 13237 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 13223 13237 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 15488 15672 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 15488 15672 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 16619 16732 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 16619 16732 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 16899 17000 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 16899 17000 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS CDS 17274 17423 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS exon 17274 17465 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS stop_codon 17421 17423 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS tts 17465 17465 . + . transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 4187 4216 1.43 + 0 target "unknown_A[1..10]"; target_start 44; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 6097 6112 2.17 + 2 target "unknown_A[11..16]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 6184 6197 0.983 + 1 target "unknown_A[16..21]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 6606 6621 1.81 + 2 target "unknown_A[21..26]"; target_start 43; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 8289 8302 1.42 + 2 target "unknown_A[26..30]"; target_start 44; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 8306 8310 0.225 + 0 target "unknown_B[1..2]"; target_start 75; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 9064 9094 1.15 + 1 target "unknown_B[2..12]"; target_start 75; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 9876 9891 2.02 + 0 target "unknown_C[1..6]"; target_start 112; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 10318 10335 2.18 + 1 target "unknown_C[6..12]"; target_start 111; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 13223 13237 1.47 + 1 target "unknown_C[12..17]"; target_start 111; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 15488 15501 4.42 + 2 target "unknown_C[17..21]"; target_start 112; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 15502 15525 3.59 + 0 target "unknown_D[1..8]"; target_start 133; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 15526 15591 4.89 + 0 target "unknown_E[1..22]"; target_start 141; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 15595 15651 6.83 + 0 target "unknown_F[1..19]"; target_start 164; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 15652 15672 7.61 + 0 target "unknown_G[1..7]"; target_start 183; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 16619 16732 9.05 + 0 target "unknown_G[8..45]"; target_start 183; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 16899 16967 7 + 0 target "unknown_H[1..23]"; target_start 228; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 16968 16991 6.16 + 0 target "unknown_I[1..8]"; target_start 251; transcript_id "g1.t1"; gene_id "g1"; Contig39543 AUGUSTUS protein_match 17301 17375 6.77 + 0 target "unknown_K[1..25]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgatggaatctgaaattggaggatacgacaatttggtgaaagtccagttgactttgaagagaaagtctctgtacttcg # tcataaacatgttggctcccatgcttcttttgtccctattgaatcctctggtttttgctttgccagtggacagtggagagcgtgaccaaggtcactca # gccgttcaaatagacacaacatttcacattccactgtcaacatcaaatcacatcttatctgagctaaaagctgatatttgtcgaatgaattttcagtc # tttcacaagtcgtgcaaattcatatcatgccaaaacagagtttatcggagactgtcgaggtttctctgtatccatattggatattggtgggaactgct # tcggtttcaccgtgtctttgtcgccaatatttccttccaccctgatgcttgggattgaaattcgagtgaaggtgctagactatgtaaaggatagaatt # gaagccctcagagttcaaaatcctgggcaatataccaacatttcctgcatccgatccaacgccatgaagtatcttcctaatttctttcaaaaaggaca # gttgtcgaagatgttctttcttttccctgacccacacttcaaaaagacgaagcacaaatggagaattattagtccaagccttttggcggagtatgcac # acgtcatacgcgttgggggactagtgtacacaattactgacgtcaaagatcttcacgattggatgacttcccatttcgaccagtttccattgtttgaa # agagtaactggtgatgagttggatgatgacccggttgtttccaaattgtacgaaagtacggaggaaggacagaaagtgacgagaaacaagggggacaa # gcatctagccgtgtaccggagaatagcggaccccgccctttctaattcatccatctctcattcaatatcatga] # protein sequence = [MMESEIGGYDNLVKVQLTLKRKSLYFVINMLAPMLLLSLLNPLVFALPVDSGERDQGHSAVQIDTTFHIPLSTSNHIL # SELKADICRMNFQSFTSRANSYHAKTEFIGDCRGFSVSILDIGGNCFGFTVSLSPIFPSTLMLGIEIRVKVLDYVKDRIEALRVQNPGQYTNISCIRS # NAMKYLPNFFQKGQLSKMFFLFPDPHFKKTKHKWRIISPSLLAEYAHVIRVGGLVYTITDVKDLHDWMTSHFDQFPLFERVTGDELDDDPVVSKLYES # TEEGQKVTRNKGDKHLAVYRRIADPALSNSSISHSIS] # sequence of block unknown_A 44 [FALPVDSGERDQGHSAVQIDTTFHIPLSTS] 74 # sequence of block unknown_B 75 [HILSELKADICR] 87 # sequence of block unknown_C 112 [FSVSILDIGGNCFGFTVSLSP] 133 # sequence of block unknown_D 133 [IFPSTLML] 141 # sequence of block unknown_E 141 [GIEIRVKVLDYVKDRIEALRVQ] 163 # sequence of block unknown_F 164 [PGQYTNISCIRSNAMKYLP] 183 # sequence of block unknown_G 183 [NFFQKGQLSKMFFLFPDPHFKKTKHKWRIISPSLLAEYAHVIRVG] 228 # sequence of block unknown_H 228 [GLVYTITDVKDLHDWMTSHFDQF] 251 # sequence of block unknown_I 251 [PLFERVTG] 259 # sequence of block unknown_K 271 [YESTEEGQKVTRNKGDKHLAVYRRI] 296 # end gene g1 ### # start gene g2 Contig39543 AUGUSTUS gene 21456 30376 0.01 + . g2 Contig39543 AUGUSTUS transcript 21456 30376 0.01 + . g2.t1 Contig39543 AUGUSTUS tss 21456 21456 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 21456 21648 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 26200 26280 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS start_codon 26208 26210 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS intron 26281 26355 0.71 + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS intron 26752 27189 0.39 + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS CDS 26208 26280 0.29 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS CDS 26356 26751 0.69 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 26356 26751 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS CDS 27190 27263 0.39 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 27190 27290 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS stop_codon 27261 27263 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 29471 29611 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS exon 29879 30376 . + . transcript_id "g2.t1"; gene_id "g2"; Contig39543 AUGUSTUS tts 30376 30376 . + . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggaagccgttggagatgaagactttatgggaagaatatcttaccaaggagttgtgagctgggtacctggagctttat # ggggatattcgccatttgaggctaaattgattccacagaacaatatgtcgaacatggatacggcatactattctccaaacgcccagtggacgcttatg # ggaacagctatgaagactgctactttgggagactacgataatctgcttgaactccagttgattttgaagagaaaatccttatactttgtgataaatat # gttggcccctatccttctcctgtccttactgaatcctctggtgtttgttctgccggttgctagcggagaacgcgtatcctacgccatcacgatcttct # tatcctttgccgtttttatgacactgctcagcgacaacattccaaaatcgtcagagccaatgtctttgatgtcctatttcctgatagaaactatggta # cttgcttatgaatctgaattattaggcggacgggaatgcgttcaagatcgtacagcggctacgtacatgtag] # protein sequence = [MEAVGDEDFMGRISYQGVVSWVPGALWGYSPFEAKLIPQNNMSNMDTAYYSPNAQWTLMGTAMKTATLGDYDNLLELQ # LILKRKSLYFVINMLAPILLLSLLNPLVFVLPVASGERVSYAITIFLSFAVFMTLLSDNIPKSSEPMSLMSYFLIETMVLAYESELLGGRECVQDRTA # ATYM] # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TCX.prfl --predictionStart=0 --predictionEnd=35654 --species=fly ./tmp/Contig3954320180911_busco_2432604931_.temp