# 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..24]--> unknown_A (9) <--[0..1]--> unknown_B (43) <--[0..6]--> unknown_C (59) <--[1..5]--> unknown_D (33) <--[29..289]--> unknown_E (18) <--[17..65]--> unknown_G (13) <--[3..14]--> unknown_H (12) <--[3..6]--> unknown_I (12) <--[3..17]--> unknown_J (12) <--[0..14]--> unknown_K (12) <--[4..25]--> unknown_L (29) <--[4..13]--> unknown_M (23) <--[0..61]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5248120180911_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 = 11123, name = Contig52481) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig52481 AUGUSTUS gene 4906 9225 0.1 + . g1 Contig52481 AUGUSTUS transcript 4906 9225 0.1 + . g1.t1 Contig52481 AUGUSTUS tss 4906 4906 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 4906 5055 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS start_codon 4981 4983 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 5056 5216 0.9 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 5299 5412 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 5586 5879 0.94 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 5997 6123 0.98 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 6289 6395 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 6564 6736 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 6896 7042 0.97 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 7211 7310 0.97 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS intron 7443 7625 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 4981 5055 0.91 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 5217 5298 0.95 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 5217 5298 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 5413 5585 0.95 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 5413 5585 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 5880 5996 0.98 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 5880 5996 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 6124 6288 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 6124 6288 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 6396 6563 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 6396 6563 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 6737 6895 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 6737 6895 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 7043 7210 0.94 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 7043 7210 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 7311 7442 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 7311 7442 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS CDS 7626 7742 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS exon 7626 9225 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS stop_codon 7740 7742 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS tts 9225 9225 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 4984 5010 3.95 + 0 target "unknown_A[1..9]"; target_start 1; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5011 5055 10.6 + 0 target "unknown_B[1..15]"; target_start 10; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5217 5298 9.23 + 2 target "unknown_B[16..43]"; target_start 9; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5413 5414 1 + 2 target "unknown_B[43..43]"; target_start 10; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5415 5585 7.89 + 0 target "unknown_C[1..57]"; target_start 53; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5880 5885 0.223 + 0 target "unknown_C[58..59]"; target_start 53; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 5895 5993 6.99 + 0 target "unknown_D[1..33]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6399 6452 3.05 + 0 target "unknown_E[1..18]"; target_start 205; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6531 6563 4.1 + 0 target "unknown_G[1..11]"; target_start 249; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6737 6742 0.83 + 0 target "unknown_G[12..13]"; target_start 249; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6770 6805 3.62 + 0 target "unknown_H[1..12]"; target_start 271; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6815 6850 3.25 + 0 target "unknown_I[1..12]"; target_start 286; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 6860 6895 4.02 + 0 target "unknown_J[1..12]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 7070 7105 5.43 + 0 target "unknown_K[1..12]"; target_start 322; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 7124 7210 5.24 + 0 target "unknown_L[1..29]"; target_start 340; transcript_id "g1.t1"; gene_id "g1"; Contig52481 AUGUSTUS protein_match 7344 7412 5.46 + 0 target "unknown_M[1..23]"; target_start 380; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggccacaattaacatcaacagcgaggtcactgaccagttctaccgctataagatgcctaggctcatagctaaggttg # aggggaaagggaatgggattaaaactgtaattgtgaatatgcctgaaattgccaaggcgttatcaagaccaccaacatatccaacaaagtattttgga # tgtgaattaggagcacaaaccatgtttgactttaaaaatgaacgctttattgtcaatggttctcatgatgccagcaagcttcagttgcttttggacgg # cttcatcaaacgttttgtactgtgtcctgagtgttctaacccagaaactcaactaaattgctctcaaaagaaacagaccatctcgcaacggtgtattg # cttgtggtaactccggtatgattgatatgcggcacaaactgacgactttcatcctgaaaaatcctcctgatcaggaccctgctgcaacacccaccaag # cagactaagaaggacaagaagaagaataaggctgtaaatggagaaaagaaggatgacagagccagtcctgaagctaatgcacaggagcaaatggcagc # ccagagagccagtgggggtgtggttgatgctccccctgttgtggaaactagtaagaatgaagaagaagatgactggggcgaagacttcagtgaggaag # cagtgagaaatagaatggaggagctcagtacagcggcaaaacagatggccttcactgatgacttggagaaaacacaggaggaacgactcaatatgttc # tacaagtttgttgagttaaagcgtgaaacctttccaggaggaggagacaaagaggttgttgctgaagccgaacgtctggaaatcaaggacaaggcacc # tttgatactggtcgaggttcttcttgatgtgaaggtgctacaacagttgaaacagcaccgcaatctgttcttacggttttgccatgaaaatcccaaat # cacaaaagtatatgcttggaggtattgaacaacttgtgggaaatgtacacagagaggaattattgcctaaagtaccccatatcttcaaagcattatat # gaccttgatattattgatgaggaggtcttgctggagtgggacaaaaaggtatctaaaaagtatgttgacaagaaggtttcagctgaaattcatgagaa # agcgactcctttcattaactggctgaaggaagcggaagaggatgactccgaggaggacgaagatgaagaggaccaagtggaggtggtctattccaact # ttgagggagttggccaaaaggaagtgcagagaccagtagccagggaagcccctcctgcacaggatgaggaagatgatgatcttgatattgatgacatc # taa] # protein sequence = [MATININSEVTDQFYRYKMPRLIAKVEGKGNGIKTVIVNMPEIAKALSRPPTYPTKYFGCELGAQTMFDFKNERFIVN # GSHDASKLQLLLDGFIKRFVLCPECSNPETQLNCSQKKQTISQRCIACGNSGMIDMRHKLTTFILKNPPDQDPAATPTKQTKKDKKKNKAVNGEKKDD # RASPEANAQEQMAAQRASGGVVDAPPVVETSKNEEEDDWGEDFSEEAVRNRMEELSTAAKQMAFTDDLEKTQEERLNMFYKFVELKRETFPGGGDKEV # VAEAERLEIKDKAPLILVEVLLDVKVLQQLKQHRNLFLRFCHENPKSQKYMLGGIEQLVGNVHREELLPKVPHIFKALYDLDIIDEEVLLEWDKKVSK # KYVDKKVSAEIHEKATPFINWLKEAEEDDSEEDEDEEDQVEVVYSNFEGVGQKEVQRPVAREAPPAQDEEDDDLDIDDI] # sequence of block unknown_A 1 [ATININSEV] 10 # sequence of block unknown_B 10 [TDQFYRYKMPRLIAKVEGKGNGIKTVIVNMPEIAKALSRPPTY] 53 # sequence of block unknown_C 53 [PTKYFGCELGAQTMFDFKNERFIVNGSHDASKLQLLLDGFIKRFVLCPECSNPETQLNC] 112 # sequence of block unknown_D 115 [KQTISQRCIACGNSGMIDMRHKLTTFILKNPPD] 148 # sequence of block unknown_E 205 [TSKNEEEDDWGEDFSEEA] 223 # sequence of block unknown_G 249 [ERLNMFYKFVELK] 262 # sequence of block unknown_H 271 [KEVVAEAERLEI] 283 # sequence of block unknown_I 286 [APLILVEVLLDV] 298 # sequence of block unknown_J 301 [QQLKQHRNLFLR] 313 # sequence of block unknown_K 322 [KYMLGGIEQLVG] 334 # sequence of block unknown_L 340 [LLPKVPHIFKALYDLDIIDEEVLLEWDKK] 369 # sequence of block unknown_M 380 [AEIHEKATPFINWLKEAEEDDSE] 403 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MHI.prfl --predictionStart=0 --predictionEnd=25588 --species=fly ./tmp/Contig5248120180911_busco_2432604931_.temp