# 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 # --[7..131]--> unknown_B (17) <--[0..14]--> unknown_C (13) <--[0..1]--> unknown_D (61) <--[0..6]--> unknown_E (24) <--[0..3]--> unknown_F (91) <--[1..11]--> unknown_G (140) <--[0..9]--> unknown_H (6) <--[0..1]--> unknown_I (16) <--[0..180]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5088320180911_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 = 29868, name = Contig50883) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig50883 AUGUSTUS gene 1 4175 0.09 - . g1 Contig50883 AUGUSTUS transcript 1 4175 0.09 - . g1.t1 Contig50883 AUGUSTUS intron 1 396 0.47 - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS intron 449 564 0.32 - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS intron 640 3037 0.45 - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS intron 3127 3318 0.67 - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS CDS 397 448 0.4 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS exon 397 448 . - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS CDS 565 639 0.34 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS exon 565 639 . - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS CDS 3038 3126 0.67 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS exon 3038 3126 . - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS CDS 3319 3437 0.89 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS exon 3319 3500 . - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS start_codon 3435 3437 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS exon 4116 4175 . - . transcript_id "g1.t1"; gene_id "g1"; Contig50883 AUGUSTUS tss 4175 4175 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggccctgctgtgtggttgtgactacacggacggaattccaggggtgggacctgtcacagctatggaaattttgagtg # aatttccggctgctgatttttcctctctacaggccttcaaatcttggtgggaagaaagtcagaaaaagaaaaggaatccaaatatcagcaaagtccgt # tcaaaactaaggcgactggatgtttctgaagttttctccaagactgaggttggtgagatatccagtagcaagcgtgtagtcaccggcggctcccttga # gagaagcaacttacgcgtcaggaaacataggtgtctaaccggtggcgctgctgtggtggg] # protein sequence = [MALLCGCDYTDGIPGVGPVTAMEILSEFPAADFSSLQAFKSWWEESQKKKRNPNISKVRSKLRRLDVSEVFSKTEVGE # ISSSKRVVTGGSLERSNLRVRKHRCLTGGAAVV] # end gene g1 ### # start gene g2 Contig50883 AUGUSTUS gene 5874 13155 0.01 - . g2 Contig50883 AUGUSTUS transcript 5874 13155 0.01 - . g2.t1 Contig50883 AUGUSTUS tts 5874 5874 . - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS exon 5874 8028 . - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS stop_codon 7774 7776 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS intron 8029 11316 0.76 - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS intron 11559 11730 0.97 - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS CDS 7774 8028 0.76 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS CDS 11317 11558 0.66 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS exon 11317 11558 . - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS CDS 11731 12244 0.16 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS exon 11731 12505 . - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS start_codon 12242 12244 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS exon 13038 13155 . - . transcript_id "g2.t1"; gene_id "g2"; Contig50883 AUGUSTUS tss 13155 13155 . - . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgatggaggaatacaaggaggaagctaaaggtgaaggaaaagacaaaggaaaagaaaaggatgagagggatcaactgg # aggaaagtgacactgaagacagtgaatgtgttagagaaagtaaacagtttgaagatgtggagaggacaggagtgaaaaatgataaagttgaggtcaag # cataactcgggagagagtaactctcataaatctaatgacaaagagagaacatccatcaatgaactgagtgaagactcagatcaagaaaacaatgaagt # ggacaaaacgagttcaaacaaggaaatcagcgagatggagaacaaggggaaagttgaagatagtgtgaaatgtaacacaaacacctcttcctcgaggg # agataactcttgctaatggaaatagtaaacctttagaacttggtttgattgaggaggctgcaacagtggagagcgtaaggagacattcatcagaagac # aaaagaaataagtcatatcagaatgaatccagtgactctgaagatgagggatttattgaggtgtccattgaccccaacaaagttggtcctgatgaact # tttcccagcagatattttcaatactagatctacctccgaatctcagaaagagctggtcccaacaactgatgcagaaccacagttctcagctgaaccgg # aacatgtgaccgctgagttagaaccaatagaaaccaacacagaagaggagcccagagatctcgcccaacagttcacagaattggtggaggatctgctg # agactgttcggcgtgccttatgtagtgagtcccacagaggccgaggctcagtgtgcctggctagactcgctcaatctcactcacggcacagtcactga # cgacagcgacatctggttatttggagggaagcgagtttacaaaaacttcttcaaccaagaacgaacggtggaactctatttaaaggaaagcctccaga # gtcagcnnnnnnnnnnnnnnnnnnngtcagacaatagacctgtaatctaa] # protein sequence = [MMEEYKEEAKGEGKDKGKEKDERDQLEESDTEDSECVRESKQFEDVERTGVKNDKVEVKHNSGESNSHKSNDKERTSI # NELSEDSDQENNEVDKTSSNKEISEMENKGKVEDSVKCNTNTSSSREITLANGNSKPLELGLIEEAATVESVRRHSSEDKRNKSYQNESSDSEDEGFI # EVSIDPNKVGPDELFPADIFNTRSTSESQKELVPTTDAEPQFSAEPEHVTAELEPIETNTEEEPRDLAQQFTELVEDLLRLFGVPYVVSPTEAEAQCA # WLDSLNLTHGTVTDDSDIWLFGGKRVYKNFFNQERTVELYLKESLQSQXXXXXXXSDNRPVI] # end gene g2 ### # start gene g3 Contig50883 AUGUSTUS gene 16246 27908 0.01 + . g3 Contig50883 AUGUSTUS transcript 16246 27908 0.01 + . g3.t1 Contig50883 AUGUSTUS tss 16246 16246 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 16246 16451 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS start_codon 16338 16340 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 16452 18212 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 18325 18685 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 18730 19459 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 19547 19755 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 19848 20285 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 20536 20902 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 21030 21275 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 21407 21640 0.04 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 21785 22143 0.45 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 22265 22593 0.85 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 22817 25408 1 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 25485 25828 1 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS intron 25979 27178 0.36 + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 16338 16451 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 18213 18324 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 18213 18324 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 18686 18729 0.01 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 18686 18729 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 19460 19546 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 19460 19546 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 19756 19847 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 19756 19847 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 20286 20535 0.01 + 1 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 20286 20535 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 20903 21029 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 20903 21029 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 21276 21406 0.01 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 21276 21406 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 21641 21784 0.04 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 21641 21784 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 22144 22264 0.53 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 22144 22264 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 22594 22816 0.85 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 22594 22816 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 25409 25484 1 + 1 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 25409 25484 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 25829 25978 0.94 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 25829 25978 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS CDS 27179 27244 0.36 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS exon 27179 27908 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS stop_codon 27242 27244 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS tts 27908 27908 . + . transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 19508 19546 7.24 + 0 target "unknown_B[1..13]"; target_start 106; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 19756 19767 11.3 + 0 target "unknown_B[14..17]"; target_start 106; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 19768 19806 8.97 + 0 target "unknown_C[1..13]"; target_start 123; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 19807 19847 9.23 + 0 target "unknown_D[1..14]"; target_start 136; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 20286 20427 12.2 + 1 target "unknown_D[14..61]"; target_start 136; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 20446 20517 8.59 + 0 target "unknown_E[1..24]"; target_start 203; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 20521 20535 2.24 + 0 target "unknown_F[1..5]"; target_start 228; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 20903 21029 6.49 + 2 target "unknown_F[6..48]"; target_start 227; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 21276 21406 12.2 + 2 target "unknown_F[48..91]"; target_start 228; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 21644 21784 8.96 + 0 target "unknown_G[1..47]"; target_start 320; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 22144 22264 9.07 + 2 target "unknown_G[48..88]"; target_start 319; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 22594 22751 8.53 + 2 target "unknown_G[88..140]"; target_start 320; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 22752 22769 11.3 + 0 target "unknown_H[1..6]"; target_start 460; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 22770 22816 5.05 + 0 target "unknown_I[1..16]"; target_start 466; transcript_id "g3.t1"; gene_id "g3"; Contig50883 AUGUSTUS protein_match 25409 25409 1 + 1 target "unknown_I[16..16]"; target_start 466; transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atggagatgggcattgggcagtgggctcccatctttgtctctcattcccttcacagcctggtgcagccatatgctcaca # tctgtttaatgcttgtaaaggcttttatcaaaaaggaagtctttgatctacagattaggaaaaacgttttgaagactttcatattttcggaactcctc # tgctattttatggaacacgtgcttcacaaaataacaatggcggatactgaacacaaaaagaaaaagaggaaaagtggtgctgttgatgttgcggaagt # tcaacacacagaaaattttcttctgaagccctccagtgttgtggaacagttggatacgtcacaatggccactactgcttaagaattttgacaaattga # atgtgcggactgctcactacacccccattccagccgggtgttccccactaaagagaccaatacaggaatacataaagagtggattcattaatcttgac # aaaccagcaaatccatcatctcatgaagttgtatcttgggtgaagagaattcttagggtacagaagacgggtcacagtggtacactagaccccaaggt # cacgggctgtctcattgtgtgtgtagagcgagccacgcgactggtcaaatcgcagcagggagctggcaaagagtatgtttgtatcttcaagcttcaca # gtgctgtcaatgatgaaaagcttgtcgcgcaaaaaatagagatgatgacaggggcactcttccagagaccgcccctaatttcagccgtcaagcgacag # ctgagaattcgaacgatttatgaatgcaagatgctagagtacgaaaaagaagatgcaatgggtattttctgggtgagctgcgaggcaggcacatacat # taggaccatgtgtgtacatctgggtctctttttgggggtcgggggacaaatgcaggagctcagacgagttcgatctggtatcatgtcggaaaaggcaa # atctatacaccatgcatgacgttttggatgcgcagtggatgtatgacaaccataaggatgagtcgtacttaagacgagtgatcaatccattggaagca # ttactaacatcacacaaaagaatcatcatgaaagacacagcagttaatgcagtgtgctatggggctaaaatcatgttgcctggtgttctcagatatga # ggacggaattgaagtagatgagcaaatcgtcatagtaacgacaaaaggagaagcagttgctttagccattgcccagatgacaacagcagtcatggcta # cgtgtgatcacggtatggtggccaagataaaaagggtcgtcatggagagggacacgtatccaaggaaatgggggctgggtcctatggcactgcagaag # aaaaaaatgattctagcaggaacactggataaatatggcaaaccgaatgagaaaacaccagccaactggaaaaagggttatgaagacttcaacataaa # gaaagaacctgtatgtagcataaagaaagaacctgtagatggtattccagaaccagtcaactcgcacaagagaaagaaggaagctagcagctctgatg # agagtgagcctccctcacccacgccagctgtgatggaagatgaccaggcagagaagaagaaaaagaaaaagaagaacaaggaccaggaagcagaggct # gatgaagctggggatgctacagaggaatcacctgaaaagaagaagaaaaagaaaaagaagcataagaaaataaaaacagaatctgactga] # protein sequence = [MEMGIGQWAPIFVSHSLHSLVQPYAHICLMLVKAFIKKEVFDLQIRKNVLKTFIFSELLCYFMEHVLHKITMADTEHK # KKKRKSGAVDVAEVQHTENFLLKPSSVVEQLDTSQWPLLLKNFDKLNVRTAHYTPIPAGCSPLKRPIQEYIKSGFINLDKPANPSSHEVVSWVKRILR # VQKTGHSGTLDPKVTGCLIVCVERATRLVKSQQGAGKEYVCIFKLHSAVNDEKLVAQKIEMMTGALFQRPPLISAVKRQLRIRTIYECKMLEYEKEDA # MGIFWVSCEAGTYIRTMCVHLGLFLGVGGQMQELRRVRSGIMSEKANLYTMHDVLDAQWMYDNHKDESYLRRVINPLEALLTSHKRIIMKDTAVNAVC # YGAKIMLPGVLRYEDGIEVDEQIVIVTTKGEAVALAIAQMTTAVMATCDHGMVAKIKRVVMERDTYPRKWGLGPMALQKKKMILAGTLDKYGKPNEKT # PANWKKGYEDFNIKKEPVCSIKKEPVDGIPEPVNSHKRKKEASSSDESEPPSPTPAVMEDDQAEKKKKKKKNKDQEAEADEAGDATEESPEKKKKKKK # KHKKIKTESD] # sequence of block unknown_B 106 [EQLDTSQWPLLLKNFDK] 123 # sequence of block unknown_C 123 [LNVRTAHYTPIPA] 136 # sequence of block unknown_D 136 [GCSPLKRPIQEYIKSGFINLDKPANPSSHEVVSWVKRILRVQKTGHSGTLDPKVTGCLIVC] 197 # sequence of block unknown_E 203 [LVKSQQGAGKEYVCIFKLHSAVND] 227 # sequence of block unknown_F 228 [KLVAQKIEMMTGALFQRPPLISAVKRQLRIRTIYECKMLEYEKEDAMGIFWVSCEAGTYIRTMCVHLGLFLGVGGQMQELRRVRSGIMSEK] 319 # sequence of block unknown_G 320 [NLYTMHDVLDAQWMYDNHKDESYLRRVINPLEALLTSHKRIIMKDTAVNAVCYGAKIMLPGVLRYEDGIEVDEQIVIVTTKGEAVALAIAQMTTAVMATCDHGMVAKIKRVVMERDTYPRKWGLGPMALQKKKMILAGTL] 460 # sequence of block unknown_H 460 [DKYGKP] 466 # sequence of block unknown_I 466 [NEKTPANWKKGYEDFN] 482 # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370BBR.prfl --predictionStart=0 --predictionEnd=44710 --species=fly ./tmp/Contig5088320180911_busco_2432604931_.temp