# 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..152]--> unknown_A (14) <--[0..1]--> unknown_B (16) <--[1..9]--> unknown_C (15) <--[0..3]--> unknown_D (41) <--[0..6]--> unknown_E (50) <--[0..2]--> unknown_F (51) <--[19..41]--> unknown_H (18) <--[13..34]--> unknown_I (19) <--[1..17]--> unknown_J (50) <--[5..19]--> unknown_K (15) <--[0..59]--> unknown_L (16) <--[8..39]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4402020180911_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 = 21968, name = Contig44020) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig44020 AUGUSTUS gene 1 19135 0.01 - . g1 Contig44020 AUGUSTUS transcript 1 19135 0.01 - . g1.t1 Contig44020 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 1 728 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS stop_codon 651 653 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 729 821 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 848 2436 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 2496 4980 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 5051 5437 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 5577 6657 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 6752 7483 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 7607 8237 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 8300 9407 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 9545 9744 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 9819 10328 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 10436 12930 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS intron 13089 18979 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 651 728 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 822 847 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 822 847 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 2437 2495 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 2437 2495 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 4981 5050 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 4981 5050 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 5438 5576 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 5438 5576 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 6658 6751 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 6658 6751 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 7484 7606 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 7484 7606 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 8238 8299 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 8238 8299 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 9408 9544 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 9408 9544 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 9745 9818 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 9745 9818 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 10329 10435 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 10329 10435 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 12931 13088 0.03 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 12931 13088 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS CDS 18980 19091 0.31 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS exon 18980 19135 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS start_codon 19089 19091 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS tss 19135 19135 . - . transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 720 728 4.56 - 0 target "unknown_L[14..16]"; target_start 374; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 822 847 1.23 - 2 target "unknown_L[5..13]"; target_start 374; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 2437 2449 0.833 - 0 target "unknown_L[1..5]"; target_start 374; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 2468 2495 2.58 - 1 target "unknown_K[6..15]"; target_start 353; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 4981 4997 6.82 - 0 target "unknown_K[1..6]"; target_start 353; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 5025 5050 8.54 - 2 target "unknown_J[42..50]"; target_start 294; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 5438 5561 7.33 - 0 target "unknown_J[1..42]"; target_start 294; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 6658 6714 1.81 - 0 target "unknown_I[1..19]"; target_start 270; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 7525 7578 2.14 - 0 target "unknown_H[1..18]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 8288 8299 3.85 - 0 target "unknown_F[48..51]"; target_start 149; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 9408 9544 7.95 - 2 target "unknown_F[2..47]"; target_start 149; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 9745 9748 1.09 - 0 target "unknown_F[1..2]"; target_start 149; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 9749 9818 7.02 - 1 target "unknown_E[27..50]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 10329 10408 10.3 - 0 target "unknown_E[1..27]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 10418 10435 8.06 - 0 target "unknown_D[36..41]"; target_start 55; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 12931 13035 2.94 - 0 target "unknown_D[1..35]"; target_start 55; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 13036 13080 3.84 - 0 target "unknown_C[1..15]"; target_start 40; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 18981 19028 6.37 - 0 target "unknown_B[1..16]"; target_start 21; transcript_id "g1.t1"; gene_id "g1"; Contig44020 AUGUSTUS protein_match 19029 19070 3.49 - 0 target "unknown_A[1..14]"; target_start 7; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgacagaaaaaaataagtacgatgcggcgtgtcttccagatttactacctttatactacaagaaattgtttccatatg # gattgtactacagatggttaaactatggaggagttccaaactactacttcaccaatcgagagttctctttcactttgaagatgatgtgtatatccgat # atcagtcttttttctgaccaacaggaactggaaaaggaaattcaaaagagatgtccatataaaatagacattggtgctgtattctctcacaagcccaa # agatcacaaaaccgtgaaagctgcagcatttcaggcccaggaaaaagaacttgtgtttgatatcgacatgacggattatgatgatgtgcggacatgtt # gctcaggagcagatatatgcgaaaaatgttggccccttatgcaggtagcagtcaaagtcttggatcgagcattggaagaggattttggatttgagcac # agactgtgggtgtactccgggaggcgaggggtgcactgctgggtgtgtgatgaaactgccaggaaactctcccagaacgggaggacagccgtggcaga # gtatctcagtctggtcaaaggtggagaacatcagaataaaaaagtcagtctggatacaccaacacttcaccctttcattagccaatccttagaaatca # tcaaggatagatttgatgattatgcagtgaagaaacaagagtttttgggcgatgatgaaggacggaagaaagtcctgtcgcttatcacagaagaaaat # atccttttatcaccgttagaagaaaactttgaacaggaattccaaggtgctgtttcaaagacagcatgggatgttatgaaaaaatatataaatgctga # aaagagtaaccctaaatttaaagggtgcaggtatgtgctagaagagattatgttgcagtacacgtaccctcgactggacgttaacgtcagtaaaggcg # tcaaccatttactgaaaagtccattctgtgtgcatcccaaaacaggaagactttgtgttcccattgatcccaagaaaattgatgattttgatccaatg # gctgtacccacaataagtgagattttagaagaagtgaacgcagcagaaaaggaagattccaataagaggacaaaagtacagagcatgcagaatttagt # gaagaattttgagattgtgcagggtagatcaggtcatgacaggtgtgaaaatctaccacctggtgttcagaagagtggataa] # protein sequence = [MTEKNKYDAACLPDLLPLYYKKLFPYGLYYRWLNYGGVPNYYFTNREFSFTLKMMCISDISLFSDQQELEKEIQKRCP # YKIDIGAVFSHKPKDHKTVKAAAFQAQEKELVFDIDMTDYDDVRTCCSGADICEKCWPLMQVAVKVLDRALEEDFGFEHRLWVYSGRRGVHCWVCDET # ARKLSQNGRTAVAEYLSLVKGGEHQNKKVSLDTPTLHPFISQSLEIIKDRFDDYAVKKQEFLGDDEGRKKVLSLITEENILLSPLEENFEQEFQGAVS # KTAWDVMKKYINAEKSNPKFKGCRYVLEEIMLQYTYPRLDVNVSKGVNHLLKSPFCVHPKTGRLCVPIDPKKIDDFDPMAVPTISEILEEVNAAEKED # SNKRTKVQSMQNLVKNFEIVQGRSGHDRCENLPPGVQKSG] # sequence of block unknown_L 374 [KRTKVQSMQNLVKNFE] 390 # sequence of block unknown_K 353 [AVPTISEILEEVNAA] 368 # sequence of block unknown_J 294 [KGCRYVLEEIMLQYTYPRLDVNVSKGVNHLLKSPFCVHPKTGRLCVPIDP] 344 # sequence of block unknown_I 270 [GAVSKTAWDVMKKYINAEK] 289 # sequence of block unknown_H 226 [FDDYAVKKQEFLGDDEGR] 244 # sequence of block unknown_F 149 [EEDFGFEHRLWVYSGRRGVHCWVCDETARKLSQNGRTAVAEYLSLVKGGEH] 200 # sequence of block unknown_E 99 [AAFQAQEKELVFDIDMTDYDDVRTCCSGADICEKCWPLMQVAVKVLDRAL] 149 # sequence of block unknown_D 55 [CISDISLFSDQQELEKEIQKRCPYKIDIGAVFSHKPKDHKT] 96 # sequence of block unknown_C 40 [YYFTNREFSFTLKMM] 55 # sequence of block unknown_B 21 [KLFPYGLYYRWLNYGG] 37 # sequence of block unknown_A 7 [DAACLPDLLPLYYK] 21 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DV4.prfl --predictionStart=0 --predictionEnd=30438 --species=fly ./tmp/Contig4402020180911_busco_2432604931_.temp