# 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 # --[6..260]--> unknown_B (36) <--[6..103]--> unknown_C (28) <--[30..120]--> unknown_D (36) <--[0..1]--> unknown_E (14) <--[0..15]--> unknown_F (11) <--[0..20]--> unknown_G (9) <--[0..11]--> unknown_H (14) <--[0..2]--> unknown_I (16) <--[0..17]--> unknown_J (14) <--[0..1]--> unknown_K (21) <--[5..7]--> unknown_L (12) <--[6..13]--> unknown_M (37) <--[1..20]--> unknown_N (24) <--[7..50]--> unknown_O (10) <--[29..155]--> unknown_Q (26) <--[0..77]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2366720180911_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 = 44854, name = Contig23667) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig23667 AUGUSTUS gene 14 44289 0.01 + . g1 Contig23667 AUGUSTUS transcript 14 44289 0.01 + . g1.t1 Contig23667 AUGUSTUS start_codon 14 16 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 20 63 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 94 144 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 368 612 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 815 19442 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 19527 19965 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 20057 22721 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 22805 24655 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 24852 26896 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 26975 27578 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 27699 39709 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 39724 41281 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 41421 43702 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS intron 43881 44010 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 14 19 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 14 19 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 64 93 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 64 93 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 145 367 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 145 367 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 613 814 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 613 814 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 19443 19526 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 19443 19526 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 19966 20056 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 19966 20056 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 22722 22804 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 22722 22804 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 24656 24851 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 24656 24851 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 26897 26974 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 26897 26974 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 27579 27698 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 27579 27698 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 39710 39723 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 39710 39723 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 41282 41420 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 41282 41420 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 43703 43880 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 43703 43880 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS CDS 44011 44036 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS exon 44011 44289 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS stop_codon 44034 44036 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS tts 44289 44289 . + . transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 82 93 2 + 0 target "unknown_B[1..4]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 145 240 1.38 + 0 target "unknown_B[5..36]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 328 367 1.02 + 0 target "unknown_C[1..14]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 613 656 2.18 + 2 target "unknown_C[14..28]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 19447 19526 3.29 + 0 target "unknown_D[1..27]"; target_start 155; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 19966 19993 8.97 + 1 target "unknown_D[27..36]"; target_start 155; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 19994 20035 6.29 + 0 target "unknown_E[1..14]"; target_start 191; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 20048 20056 9.36 + 0 target "unknown_F[1..3]"; target_start 209; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 22722 22745 3.06 + 0 target "unknown_F[4..11]"; target_start 209; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 22749 22775 4.27 + 0 target "unknown_G[1..9]"; target_start 221; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 22776 22804 4.4 + 0 target "unknown_H[1..10]"; target_start 230; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 24656 24668 3.2 + 1 target "unknown_H[10..14]"; target_start 230; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 24669 24716 5.3 + 0 target "unknown_I[1..16]"; target_start 244; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 24717 24758 2.62 + 0 target "unknown_J[1..14]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 24762 24824 3.38 + 0 target "unknown_K[1..21]"; target_start 275; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 24840 24851 4.9 + 0 target "unknown_L[1..4]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 26897 26920 3.88 + 0 target "unknown_L[5..12]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 26945 26974 2.63 + 0 target "unknown_M[1..10]"; target_start 321; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 27579 27659 2.69 + 0 target "unknown_M[11..37]"; target_start 321; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 27696 27698 1.93 + 0 target "unknown_N[1..1]"; target_start 370; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 39710 39723 1.61 + 2 target "unknown_N[2..6]"; target_start 369; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 41282 41336 2.77 + 1 target "unknown_N[6..24]"; target_start 370; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 41367 41396 4.58 + 0 target "unknown_O[1..10]"; target_start 404; transcript_id "g1.t1"; gene_id "g1"; Contig23667 AUGUSTUS protein_match 43787 43864 2.48 + 0 target "unknown_Q[1..26]"; target_start 450; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcttaagaagaaggaacaaaagaagaaggagaaacgaagtatcgaaagacggaaaaatatggaggagaaaaaggaca # acaaaaaattctctgccctcacagacctcatgaagaaacgcgaggaaaaaaagaaaattggtaagcttagtttgtgtgatgttatgattctggcttgt # gtaatttgtattgcaatatctagtagatgtacagtaagttcacctatggctgtatgtaagcacatctacagcaactgtatgcagcagataaaaaaaca # agaagaaaaacaagaacaaaaaaagaaactgctgaaaacaagtgatatatactctgatgatgatgatgacgaagaggaggatccaaaatctgaaccag # aaaaggaacggggagaagattctggatctgaatcggagagcagcagcagttcaaggtcgtctgcaaggtcggactccgagggagaagagacctatgaa # tcacgaaaaccaaaatttataacctgcaaagaagatctgtctaaaatccgtttatcccgacacaagttagaaaaatggtgtcatatgcctttcttcaa # gaagacggtttgtggttgttttgtcagaatcggtattggtaatcatgagggaagagccgtgtacagaattgcagaaattgttgacacttgggagacag # caaaaatttatcagctcggtacaacacgcaccaataagggagtcaaattaaaacatggacattctgagcgtgtgtatcgattggaatttgtatccaac # caagacttcacagattccgaattctcaaagtggcgagaggcaatgactctcggagacatcgctatccccaccatacaggaagtagacaggaagcaaaa # agccattcaagaggccatgaattataaattcaaagaaaatgatatcgaggagattgtcgcagagaagcagaaattcaagaagaaccctcataattatg # ctattaagaaaacctttttgctcaaacaaaaggaaatggcagatttggagggtgacacagcatcacagtacaaaatatcccaggaactggaggaatta # gaagagagggccaacgaactggacaggagacggaccaacaatatatcatccaacatcgatcttgatatttacataaaccaaagaaatcgtttgaggaa # tcaaatattggcagaggaagcatcgaagaaagagtttttggagatgaagaacgctgtagccgatccctttactcgacggtcgtgccgtcccacactcg # tcacaaagcaagaagaaaccgcaaacagagataagagagaagagaccagtgatcaaaaccaatttcccgtcagattatcaggaacatcacccgagaaa # atggacaggggcgaccgtcgccggacgtcagaagatttgttcgcagtccacgattttaacattgaaattgatttggatgtccctaccaccagattcta # tatacctgtcagagtgtag] # protein sequence = [MLKKKEQKKKEKRSIERRKNMEEKKDNKKFSALTDLMKKREEKKKIGKLSLCDVMILACVICIAISSRCTVSSPMAVC # KHIYSNCMQQIKKQEEKQEQKKKLLKTSDIYSDDDDDEEEDPKSEPEKERGEDSGSESESSSSSRSSARSDSEGEETYESRKPKFITCKEDLSKIRLS # RHKLEKWCHMPFFKKTVCGCFVRIGIGNHEGRAVYRIAEIVDTWETAKIYQLGTTRTNKGVKLKHGHSERVYRLEFVSNQDFTDSEFSKWREAMTLGD # IAIPTIQEVDRKQKAIQEAMNYKFKENDIEEIVAEKQKFKKNPHNYAIKKTFLLKQKEMADLEGDTASQYKISQELEELEERANELDRRRTNNISSNI # DLDIYINQRNRLRNQILAEEASKKEFLEMKNAVADPFTRRSCRPTLVTKQEETANRDKREETSDQNQFPVRLSGTSPEKMDRGDRRRTSEDLFAVHDF # NIEIDLDVPTTRFYIPVRV] # sequence of block unknown_B 8 [KKEKRSIERRKNMEEKKDNKKFSALTDLMKKREEKK] 44 # sequence of block unknown_C 73 [PMAVCKHIYSNCMQQIKKQEEKQEQKKK] 101 # sequence of block unknown_D 155 [YESRKPKFITCKEDLSKIRLSRHKLEKWCHMPFFKK] 191 # sequence of block unknown_E 191 [TVCGCFVRIGIGNH] 205 # sequence of block unknown_F 209 [VYRIAEIVDTW] 220 # sequence of block unknown_G 221 [TAKIYQLGT] 230 # sequence of block unknown_H 230 [TRTNKGVKLKHGHS] 244 # sequence of block unknown_I 244 [ERVYRLEFVSNQDFTD] 260 # sequence of block unknown_J 260 [SEFSKWREAMTLGD] 274 # sequence of block unknown_K 275 [AIPTIQEVDRKQKAIQEAMNY] 296 # sequence of block unknown_L 301 [DIEEIVAEKQKF] 313 # sequence of block unknown_M 321 [IKKTFLLKQKEMADLEGDTASQYKISQELEELEERAN] 358 # sequence of block unknown_N 370 [NIDLDIYINQRNRLRNQILAEEAS] 394 # sequence of block unknown_O 404 [VADPFTRRSC] 414 # sequence of block unknown_Q 450 [KMDRGDRRRTSEDLFAVHDFNIEIDL] 476 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FKI.prfl --predictionStart=0 --predictionEnd=44854 --species=fly ./tmp/Contig2366720180911_busco_2432604931_.temp