# 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..812]--> unknown_A (22) <--[0..1]--> unknown_B (18) <--[1..5]--> unknown_C (13) <--[5..13]--> unknown_D (18) <--[6..12]--> unknown_F (21) <--[0..1]--> unknown_G (21) <--[10..42]--> unknown_I (10) <--[1..3]--> unknown_J (14) <--[6..11]--> unknown_K (9) <--[19..75]--> unknown_N (34) <--[0..81]--> unknown_O (26) <--[1..5]--> unknown_P (56) <--[0..1]--> unknown_Q (29) <--[11..74]--> unknown_R (25) <--[0..169]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4542920180911_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 = 17838, name = Contig45429) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig45429 AUGUSTUS gene 2766 9549 0.01 + . g1 Contig45429 AUGUSTUS transcript 2766 9549 0.01 + . g1.t1 Contig45429 AUGUSTUS tss 2766 2766 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 2766 3255 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 3299 3365 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 3779 3861 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS start_codon 3854 3856 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS intron 3862 7078 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS intron 7144 7520 0.06 + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS intron 7571 7856 0.08 + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS intron 7992 8300 0.09 + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS CDS 3854 3861 0.15 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS CDS 7079 7143 0.06 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 7079 7143 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS CDS 7521 7570 0.08 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 7521 7570 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS CDS 7857 7991 0.1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 7857 7991 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS CDS 8301 8399 0.09 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS exon 8301 9549 . + . transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS stop_codon 8397 8399 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig45429 AUGUSTUS tts 9549 9549 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaagccgaagacattgctgctctgggagctctactacaccgagggtatgacagagtgggaatgcctaccacatattc # tttcgcgctggcctttatttggatccacatttttcagtataagggaaacaattctcaagtatacgttcagtgaagtgttgtcaacgcgccgttatcga # agtgataatggcgacaattacctggacatgaagttgggaaatttaatggtgcagaaaattgtgaggattgaaacaaatcagggatcagatatttcgaa # tttgataggacaatacatgcaggttataaatcgacacaaaaagaggccaagtgacaagatgagcctacaacgataccactga] # protein sequence = [MKPKTLLLWELYYTEGMTEWECLPHILSRWPLFGSTFFSIRETILKYTFSEVLSTRRYRSDNGDNYLDMKLGNLMVQK # IVRIETNQGSDISNLIGQYMQVINRHKKRPSDKMSLQRYH] # end gene g1 ### # start gene g2 Contig45429 AUGUSTUS gene 10048 15675 0.01 - . g2 Contig45429 AUGUSTUS transcript 10048 15675 0.01 - . g2.t1 Contig45429 AUGUSTUS tts 10048 10048 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 10048 11992 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS stop_codon 11861 11863 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 11993 12117 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 12194 12321 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 12437 12628 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 12740 12923 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 12984 13093 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 13133 13374 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 13479 13574 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 13686 13803 0.03 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 13894 14688 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 14838 14920 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 15025 15235 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS intron 15317 15509 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 11861 11992 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 12118 12193 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 12118 12193 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 12322 12436 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 12322 12436 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 12629 12739 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 12629 12739 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 12924 12983 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 12924 12983 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 13094 13132 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 13094 13132 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 13375 13478 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 13375 13478 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 13575 13685 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 13575 13685 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 13804 13893 0.02 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 13804 13893 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 14689 14837 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 14689 14837 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 14921 15024 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 14921 15024 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 15236 15316 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 15236 15316 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS CDS 15510 15636 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS exon 15510 15675 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS start_codon 15634 15636 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS tss 15675 15675 . - . transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 11870 11944 3.46 - 0 target "unknown_R[1..25]"; target_start 405; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12118 12193 4.9 - 1 target "unknown_Q[4..29]"; target_start 360; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12322 12332 2.26 - 0 target "unknown_Q[1..4]"; target_start 360; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12333 12436 10.1 - 2 target "unknown_P[22..56]"; target_start 304; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12629 12692 5.31 - 0 target "unknown_P[1..22]"; target_start 304; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12696 12739 4.11 - 2 target "unknown_O[12..26]"; target_start 277; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12924 12957 5.03 - 0 target "unknown_O[1..12]"; target_start 277; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 12970 12983 3.22 - 2 target "unknown_N[30..34]"; target_start 239; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 13094 13132 5.85 - 2 target "unknown_N[17..30]"; target_start 239; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 13375 13423 6.45 - 0 target "unknown_N[1..17]"; target_start 239; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 13655 13681 5.82 - 0 target "unknown_K[1..9]"; target_start 185; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 13821 13862 4.69 - 0 target "unknown_J[1..14]"; target_start 164; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 13866 13893 4.41 - 1 target "unknown_I[1..10]"; target_start 153; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 14689 14690 1 - 0 target "unknown_I[1..1]"; target_start 153; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 14727 14789 7.76 - 0 target "unknown_G[1..21]"; target_start 120; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 14793 14837 6.15 - 0 target "unknown_F[7..21]"; target_start 98; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 14921 14938 3.62 - 0 target "unknown_F[1..6]"; target_start 98; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 14960 15013 2.78 - 0 target "unknown_D[1..18]"; target_start 73; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 15246 15284 2.79 - 0 target "unknown_C[1..13]"; target_start 53; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 15297 15316 3.63 - 2 target "unknown_B[12..18]"; target_start 31; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 15510 15543 3.02 - 0 target "unknown_B[1..12]"; target_start 31; transcript_id "g2.t1"; gene_id "g2"; Contig45429 AUGUSTUS protein_match 15544 15609 6.64 - 0 target "unknown_A[1..22]"; target_start 9; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atggtacgaggaaagaagtccgtgtgtgttgttgttctgggggacataggacgcagtccacgcatgcagtaccacgcgt # catcttttggggcagaagggtttttcgtgggtatagtaggttatggaggttcaattccacattctgctgtaaggaattcagaaaaaattacaattcat # gagctatgggagcccccagcattcctaaagactgtacctcgtctactgggctatgttcttaaggtcttgttccagtgctttacccttggtataaagtt # attacttcttcccaaatttggattaatattactacagaacccaccctctattcccacaatggctgtgtgcagggttgtttgtttgttgaggggaagta # aactacttattgattggcataactatggctacacaatcctcagtttgtctttgaaaaatacccatccattggtcaaattttccaattggtatgaacat # gcatttggaaggatgtcccacttaaacatctgtgtaacaaatgcgatgaagaaagatttggaagaaaactggaaaattagagctgagacactgtatga # cagaccagcggaaatgttccagtgtacatcactcccagaagctcaccagctgtttttaaaactctcacaacaatatgaagtgttcactaacagagatt # tacaaaacagtacagtctttacaacacagacagaggatggaaaggtgacatggctgaaggacagaccagcactaattataagcagtaccagctggaca # gaggatgaagattttggaatccttttatctgcattaacagagtatgatgaagaccagaaggaagaccattctcttccaccgttaatatgtgtgattac # aggaaaaggacctcagaaagaattttatagatccaaaatagaaaatcacaattggaatggggtcaagttttgtctgccttggttggaagcacaggact # atcctaaacttttaggagctgctgacctaggaatttgtctccatacttcctcaagtggccttgacctcccaatgaaggtggtggacatgtttggttgt # ggtatcccagtctgtgcactcagatttaattgcatatctgaattggtgaaagatggacaaaatgggttgctctttcaggactcacaagaactctgtca # acaacttaagactttaatggtggactataaaggaggaaagacaaagttgtcgctgatgaaacgtaacttggaacaatttcaaaagctacggtggcatg # aatcttggaaaaatgttgtattgcaaatgatagagcatgaataa] # protein sequence = [MVRGKKSVCVVVLGDIGRSPRMQYHASSFGAEGFFVGIVGYGGSIPHSAVRNSEKITIHELWEPPAFLKTVPRLLGYV # LKVLFQCFTLGIKLLLLPKFGLILLQNPPSIPTMAVCRVVCLLRGSKLLIDWHNYGYTILSLSLKNTHPLVKFSNWYEHAFGRMSHLNICVTNAMKKD # LEENWKIRAETLYDRPAEMFQCTSLPEAHQLFLKLSQQYEVFTNRDLQNSTVFTTQTEDGKVTWLKDRPALIISSTSWTEDEDFGILLSALTEYDEDQ # KEDHSLPPLICVITGKGPQKEFYRSKIENHNWNGVKFCLPWLEAQDYPKLLGAADLGICLHTSSSGLDLPMKVVDMFGCGIPVCALRFNCISELVKDG # QNGLLFQDSQELCQQLKTLMVDYKGGKTKLSLMKRNLEQFQKLRWHESWKNVVLQMIEHE] # sequence of block unknown_R 405 [KRNLEQFQKLRWHESWKNVVLQMIE] 430 # sequence of block unknown_Q 360 [RFNCISELVKDGQNGLLFQDSQELCQQLK] 389 # sequence of block unknown_P 304 [NWNGVKFCLPWLEAQDYPKLLGAADLGICLHTSSSGLDLPMKVVDMFGCGIPVCAL] 360 # sequence of block unknown_O 277 [HSLPPLICVITGKGPQKEFYRSKIEN] 303 # sequence of block unknown_N 239 [WLKDRPALIISSTSWTEDEDFGILLSALTEYDED] 273 # sequence of block unknown_K 185 [ETLYDRPAE] 194 # sequence of block unknown_J 164 [LNICVTNAMKKDLE] 178 # sequence of block unknown_I 153 [WYEHAFGRMS] 163 # sequence of block unknown_G 120 [LRGSKLLIDWHNYGYTILSLS] 141 # sequence of block unknown_F 98 [GLILLQNPPSIPTMAVCRVVC] 119 # sequence of block unknown_D 73 [LLGYVLKVLFQCFTLGIK] 91 # sequence of block unknown_C 53 [EKITIHELWEPPA] 66 # sequence of block unknown_B 31 [EGFFVGIVGYGGSIPHSA] 49 # sequence of block unknown_A 9 [VVVLGDIGRSPRMQYHASSFGA] 31 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AI8.prfl --predictionStart=0 --predictionEnd=35618 --species=fly ./tmp/Contig4542920180911_busco_2432604931_.temp