# 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..82]--> unknown_A (14) <--[0..17]--> unknown_B (16) <--[1..3]--> unknown_C (8) <--[0..1]--> unknown_D (17) <--[0..1]--> unknown_E (13) <--[0..9]--> unknown_F (14) <--[0..3]--> unknown_G (30) <--[0..11]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2265420180911_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 = 33480, name = Contig22654) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig22654 AUGUSTUS gene 32510 40624 0.09 + . g1 Contig22654 AUGUSTUS transcript 32510 40624 0.09 + . g1.t1 Contig22654 AUGUSTUS exon 32510 32564 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS start_codon 32516 32518 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS intron 32565 33621 0.56 + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS intron 33842 34474 0.32 + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS intron 34619 38969 0.52 + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS CDS 32516 32564 0.72 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS CDS 33622 33841 0.47 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS exon 33622 33841 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS CDS 34475 34618 0.33 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS exon 34475 34618 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS CDS 38970 39177 0.7 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS exon 38970 40624 . + . transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS stop_codon 39175 39177 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig22654 AUGUSTUS tts 40624 40624 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggagaatattcctgagttggactgtactgttatgatgcatatcaaagttttattgtccatacagggcctaaaggggc # ggggaaggaagagtccaaaaaagaaaaacaaggaaaataacacgtctgtgaaggagcgacgagattcagacaatagcagccgatcagcgaatgagagt # gtgcctactgaaaagccagagaaaaaacgagggaaagatctggagaaaaagaaacaggcagccgaacagtcggaggacatgaccgtgtgcaggttgat # actcacggagatggacaagcatgaagatgggtggccattcttaaagcccgtcaatttcaaacaatttcccgcatacaaaaagtatatacgacaaccaa # tggacttcaccaccatgaaaaataaactcagggacaaccagtacaaaactcgaggtgattttgcgtcagatgtgagactggtattcaataactgtcag # accttcaatgaggacgactcagaggtgggtcgttccggccacaacatgaggaagttcttcgaggcacgatggaagcagctgatgttatcgtcacctcc # ctcaccgtcatccaccagcaatgaggagaaaacggaggaggggacggactag] # protein sequence = [MENIPELDCTVMMHIKVLLSIQGLKGRGRKSPKKKNKENNTSVKERRDSDNSSRSANESVPTEKPEKKRGKDLEKKKQ # AAEQSEDMTVCRLILTEMDKHEDGWPFLKPVNFKQFPAYKKYIRQPMDFTTMKNKLRDNQYKTRGDFASDVRLVFNNCQTFNEDDSEVGRSGHNMRKF # FEARWKQLMLSSPPSPSSTSNEEKTEEGTD] # end gene g1 ### # start gene g2 Contig22654 AUGUSTUS gene 44358 47337 0.01 - . g2 Contig22654 AUGUSTUS transcript 44358 47337 0.01 - . g2.t1 Contig22654 AUGUSTUS tts 44358 44358 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS exon 44358 45234 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS stop_codon 44847 44849 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS intron 45235 46212 0.91 - . transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS CDS 44847 45234 0.85 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS CDS 46213 46994 0.73 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS exon 46213 47036 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS start_codon 46992 46994 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS exon 47226 47337 . - . transcript_id "g2.t1"; gene_id "g2"; Contig22654 AUGUSTUS tss 47337 47337 . - . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtctcttatagagggatttggtgatgaagtgaccatttttttggtcgttgtgctgattctactcatagtgtgcttag # catggatatcaacaaacataagagacattccattctttagtgtgataataattgaattaactcacagaagaaatagagatacagaaaacaccaatcag # actgaagttcagagttcaaccgaggtcactccatcaaattcagaaagccaaacaagttctgaaattgatgttcaaagtaatgtggatgggccaggtgt # aagaaccactgaaactgatcctgtcacaccaagtgaaatttcatcagaaaatagtccaaatggtgagagtagtgaaacccctcatgaggagaggacag # atgagaaatcagatacctcacagacacaactgccacaggaaagcaaaacagacagtatagaccactcgagggatttaagtgaatcagaacttcgacaa # aggcgattaaatttctttcagggaaataaagaaggtgctaccatttcgaatgcccaaattttgacagacagttcaaactcaactcggagatctagttc # acaggaattttcaggctctacttcagaacctactagcataccacaggaagcaactcctgattcaaatccaccggtctcagttcagagtgaagctattc # agacccaagaaactgatactgttacagggctgatcaccgtgagattaaaatatttgaatgacacccaaagaaatgttacagctgcaccaaatgtcact # ataggacaattcaggagagacaactttgccacggaactttcagagaataagctggtgagattcatcttcaatggacaagatttacgcaatgactccag # caccctccagaattacaacattggagacaacagtgttgtccactgcctgatcactcagatcaatcagcaggccccccaacagagacaggaaatcgacg # gaagctgtgacctgggggtcatcatcctgcccatctttggggtcatcctgtgttttgtgtggtatctacgattcgagtacagacacttttttactgcc # acatccacgtttatgttaattggactgacatttttgttcattgcagccgttttagcatcttgggacagtcagagacatcgggaacaggttccccatga # gcattttgagtga] # protein sequence = [MSLIEGFGDEVTIFLVVVLILLIVCLAWISTNIRDIPFFSVIIIELTHRRNRDTENTNQTEVQSSTEVTPSNSESQTS # SEIDVQSNVDGPGVRTTETDPVTPSEISSENSPNGESSETPHEERTDEKSDTSQTQLPQESKTDSIDHSRDLSESELRQRRLNFFQGNKEGATISNAQ # ILTDSSNSTRRSSSQEFSGSTSEPTSIPQEATPDSNPPVSVQSEAIQTQETDTVTGLITVRLKYLNDTQRNVTAAPNVTIGQFRRDNFATELSENKLV # RFIFNGQDLRNDSSTLQNYNIGDNSVVHCLITQINQQAPQQRQEIDGSCDLGVIILPIFGVILCFVWYLRFEYRHFFTATSTFMLIGLTFLFIAAVLA # SWDSQRHREQVPHEHFE] # end gene g2 ### # start gene g3 Contig22654 AUGUSTUS gene 47508 55356 0.01 + . g3 Contig22654 AUGUSTUS transcript 47508 55356 0.01 + . g3.t1 Contig22654 AUGUSTUS tss 47508 47508 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 47508 47678 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS start_codon 47628 47630 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS intron 47679 49154 0.02 + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS intron 49197 51570 0.02 + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS intron 51653 51904 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS intron 51988 52375 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS intron 52505 55172 0.01 + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 47628 47678 0.03 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 49155 49196 0.02 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 49155 49196 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 51571 51652 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 51571 51652 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 51905 51987 0.01 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 51905 51987 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 52376 52504 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 52376 52504 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS CDS 55173 55181 0.01 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS exon 55173 55356 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS stop_codon 55179 55181 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS tts 55356 55356 . + . transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 47637 47678 5.8 + 0 target "unknown_A[1..14]"; target_start 3; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 51571 51618 8.56 + 0 target "unknown_B[1..16]"; target_start 31; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 51622 51645 7.56 + 0 target "unknown_C[1..8]"; target_start 48; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 51646 51652 7.95 + 0 target "unknown_D[1..3]"; target_start 56; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 51905 51948 3.28 + 2 target "unknown_D[3..17]"; target_start 56; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 51949 51987 6.43 + 0 target "unknown_E[1..13]"; target_start 73; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 52376 52417 5.39 + 0 target "unknown_F[1..14]"; target_start 86; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 52418 52504 3.55 + 0 target "unknown_G[1..29]"; target_start 100; transcript_id "g3.t1"; gene_id "g3"; Contig22654 AUGUSTUS protein_match 55173 55175 5.36 + 0 target "unknown_G[30..30]"; target_start 100; transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgtcgcactcggcagtgaaaggaaagttgatagctgtaattggtgatgagattgagacttcggctgctctagctttag # tagactctagcactgacacctgcaccggattcttgttaggggggattggtgaactgaacaagaagagagaacctaactttcttgtggtggacaaagga # acaagccgacatgacatagaggaaacattcagaggatttctgaagagagaagacatagctatcattctcatcaatcagaccatcgcagaagaaatccg # ttacgttattgattcccatgaccagccagttccagcagtgttagaaattcctagtaaagatgctccctacgattccagcaaagannnnnnnnnnnnnn # nnnnnnnnnnnaaaatgagttag] # protein sequence = [MSHSAVKGKLIAVIGDEIETSAALALVDSSTDTCTGFLLGGIGELNKKREPNFLVVDKGTSRHDIEETFRGFLKREDI # AIILINQTIAEEIRYVIDSHDQPVPAVLEIPSKDAPYDSSKXXXXXXXXXKMS] # sequence of block unknown_A 3 [SAVKGKLIAVIGDE] 17 # sequence of block unknown_B 31 [DTCTGFLLGGIGELNK] 47 # sequence of block unknown_C 48 [REPNFLVV] 56 # sequence of block unknown_D 56 [DKGTSRHDIEETFRGFL] 73 # sequence of block unknown_E 73 [KREDIAIILINQT] 86 # sequence of block unknown_F 86 [IAEEIRYVIDSHDQ] 100 # sequence of block unknown_G 100 [PVPAVLEIPSKDAPYDSSKXXXXXXXXXKM] 130 # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093711LC.prfl --predictionStart=32373 --predictionEnd=72474 --species=fly ./tmp/Contig2265420180911_busco_2432604931_.temp