# 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..41]--> unknown_A (15) <--[2..11]--> unknown_B (35) <--[0..3]--> unknown_C (37) <--[0..11]--> unknown_D (19) <--[0..2]--> unknown_E (85) <--[0..1]--> unknown_F (155) <--[0..2]--> unknown_G (13) <--[0..1]--> unknown_H (17) <--[0..101]--> unknown_I (62) <--[1..2]--> unknown_J (8) <--[0..25]--> unknown_K (56) <--[0..4]--> unknown_L (18) <--[0..60]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2683820180911_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 = 18616, name = Contig26838) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig26838 AUGUSTUS gene 2 16113 0.01 + . g1 Contig26838 AUGUSTUS transcript 2 16113 0.01 + . g1.t1 Contig26838 AUGUSTUS tss 2 2 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 2 106 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS start_codon 59 61 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 107 181 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 244 724 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 737 856 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 981 1090 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 1139 1504 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 1576 2061 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 2126 10391 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 10461 11289 0.07 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 11445 12340 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 12422 12553 0.06 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 12635 12809 0.03 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 12937 13071 0.29 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 13145 13240 0.28 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 13362 13503 0.12 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 13661 14074 0.05 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 14303 14598 0.12 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS intron 14681 14881 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 59 106 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 182 243 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 182 243 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 725 736 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 725 736 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 857 980 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 857 980 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 1091 1138 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 1091 1138 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 1505 1575 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 1505 1575 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 2062 2125 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 2062 2125 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 10392 10460 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 10392 10460 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 11290 11444 0.15 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 11290 11444 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 12341 12421 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 12341 12421 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 12554 12634 0.03 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 12554 12634 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 12810 12936 0.27 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 12810 12936 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 13072 13144 0.29 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 13072 13144 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 13241 13361 0.2 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 13241 13361 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 13504 13660 0.1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 13504 13660 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 14075 14302 0.07 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 14075 14302 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 14599 14680 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 14599 14680 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS CDS 14882 14958 0.02 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS exon 14882 16113 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS stop_codon 14956 14958 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS tts 16113 16113 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 215 243 1.58 + 0 target "unknown_A[1..10]"; target_start 27; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 725 736 2.25 + 0 target "unknown_A[11..14]"; target_start 26; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 857 860 0.264 + 1 target "unknown_A[14..15]"; target_start 27; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 867 971 3.03 + 0 target "unknown_B[1..35]"; target_start 44; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 975 980 7.69 + 0 target "unknown_C[1..2]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 1091 1138 9.77 + 2 target "unknown_C[3..19]"; target_start 79; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 1505 1561 16.3 + 0 target "unknown_C[19..37]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 1562 1575 18.5 + 0 target "unknown_D[1..5]"; target_start 117; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 2062 2104 11.4 + 1 target "unknown_D[5..19]"; target_start 117; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 2111 2125 15.9 + 0 target "unknown_E[1..5]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 10392 10460 12.6 + 2 target "unknown_E[6..29]"; target_start 137; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 11290 11444 9.93 + 2 target "unknown_E[29..80]"; target_start 137; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 12341 12356 7.76 + 1 target "unknown_E[80..85]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 12357 12421 9.54 + 0 target "unknown_F[1..22]"; target_start 223; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 12554 12634 13.7 + 0 target "unknown_F[23..49]"; target_start 222; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 12810 12936 10.5 + 0 target "unknown_F[50..92]"; target_start 222; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13072 13144 12.6 + 2 target "unknown_F[92..116]"; target_start 222; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13241 13359 11.3 + 2 target "unknown_F[116..155]"; target_start 223; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13360 13361 1 + 0 target "unknown_G[1..1]"; target_start 378; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13504 13540 12.8 + 1 target "unknown_G[1..13]"; target_start 378; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13541 13591 11.4 + 0 target "unknown_H[1..17]"; target_start 391; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 13592 13660 10.8 + 0 target "unknown_I[1..23]"; target_start 408; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14075 14191 10.6 + 0 target "unknown_I[24..62]"; target_start 408; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14195 14218 5.66 + 0 target "unknown_J[1..8]"; target_start 471; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14219 14302 11.4 + 0 target "unknown_K[1..28]"; target_start 479; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14599 14680 10.6 + 2 target "unknown_K[29..56]"; target_start 478; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14882 14883 1 + 2 target "unknown_K[56..56]"; target_start 479; transcript_id "g1.t1"; gene_id "g1"; Contig26838 AUGUSTUS protein_match 14896 14949 9.44 + 0 target "unknown_L[1..18]"; target_start 539; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgacttaccaagaggtgctaaacagtcttcaaaatagtcctcacaagcaattgtgcctggggcgtctcgtgaggaact # gctggtgtgaagttgcagagatcgtcaaccaccttattggcaaaaatatttatttattgttcatattctgttatagaatcaaatgcaaaatttcgtca # aagtatgggctttcaagtcagccaagattggtggatatcatagcagcagtaccacaggaatacaaaaaaattctgctgccaaagttgaaagctaaacc # agtccgcactgctagtgggatagctgttgtagcagtgatgtgcaagccacatagatgtccacatattgccatgactggaaatatctgtgtatattgtc # ctggaggccctgactccgattttgaatactccacacagtcttatacaggatatgagcctacttctatgcgagccatccgagccaggtacaatccatat # ctacaaacaagacacagagtagagcagctaaagcagctgggccacagtgtggataaggtggagttcattgtgatgggtggcacgtttatgagtctggc # agacgactacagggactactttatcagaaacttgcacgacgcactgtctggacacacaagcagtggtgtggatgaggcggtcaaatattcagagaaaa # gtatgacaaaatgcattggtattactatagagacacgacccgattactgtcttcgtaaacacatcagtgatatgcttcggtatggctgtactcggctg # gaaatcggggtccagagtgtgtatgaagacgtggctcgggatacaaacaggggacacacagtgaaggcggtgaccgagtcctttcagatggctaagga # tgctggttttaaggttgtggctcacatgatgccagatctccccaatgttggctgggagagagacgtagaacagtttatagaattctttgaaaacccag # cattcagagcagatggcctcaaaatctaccctacacttgtcatccgaggaacaggtttatatgaattatggaagactggtagatacaaaagttaccct # cctagtggccttatagatctgatcgccagaattctagctcttgtccctccatggacacgagtctatcgagtccagagagatattccgatgcctttggt # aagttctggagttgaacatggaaatttacgagagctggctttggcgaggatgaaggacctagggactcagtgtcgggatgttaggacccgggaagtgg # ggattcaggagatacacaacaaagtcaagccctacgaggcagaattaatcagaagagattattgtgccaatggaggatgggagacattcttgtcatat # gaagaccctgagcaagatattctcataggtctactccgattacgcaaatgttcacccgacacgttcagatcagaactgaagtccagctgctctattgt # acgggaactccacgtctacggtagtgtagtgccggtccatgcaagggatcccactaaattccagcatcagggttttggaatgttgctgatggaagaag # ctgaaagaatagccagagaggaacacggatcctctaaaatagccgtgatatcaggtgtgggcacaaggaattattaccggaagattgggtatgaactg # gatggaccttatatgtcaaagtcacttgtttga] # protein sequence = [MTYQEVLNSLQNSPHKQLCLGRLVRNCWCEVAEIVNHLIGKNIYLLFIFCYRIKCKISSKYGLSSQPRLVDIIAAVPQ # EYKKILLPKLKAKPVRTASGIAVVAVMCKPHRCPHIAMTGNICVYCPGGPDSDFEYSTQSYTGYEPTSMRAIRARYNPYLQTRHRVEQLKQLGHSVDK # VEFIVMGGTFMSLADDYRDYFIRNLHDALSGHTSSGVDEAVKYSEKSMTKCIGITIETRPDYCLRKHISDMLRYGCTRLEIGVQSVYEDVARDTNRGH # TVKAVTESFQMAKDAGFKVVAHMMPDLPNVGWERDVEQFIEFFENPAFRADGLKIYPTLVIRGTGLYELWKTGRYKSYPPSGLIDLIARILALVPPWT # RVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTQCRDVRTREVGIQEIHNKVKPYEAELIRRDYCANGGWETFLSYEDPEQDILIGLLRLRKCSP # DTFRSELKSSCSIVRELHVYGSVVPVHARDPTKFQHQGFGMLLMEEAERIAREEHGSSKIAVISGVGTRNYYRKIGYELDGPYMSKSLV] # sequence of block unknown_A 27 [WCEVAEIVNHLIGKN] 42 # sequence of block unknown_B 44 [LLFIFCYRIKCKISSKYGLSSQPRLVDIIAAVPQE] 79 # sequence of block unknown_C 80 [KKILLPKLKAKPVRTASGIAVVAVMCKPHRCPHIAMT] 117 # sequence of block unknown_D 117 [GNICVYCPGGPDSDFEYST] 136 # sequence of block unknown_E 138 [YTGYEPTSMRAIRARYNPYLQTRHRVEQLKQLGHSVDKVEFIVMGGTFMSLADDYRDYFIRNLHDALSGHTSSGVDEAVKYSEKS] 223 # sequence of block unknown_F 223 [MTKCIGITIETRPDYCLRKHISDMLRYGCTRLEIGVQSVYEDVARDTNRGHTVKAVTESFQMAKDAGFKVVAHMMPDLPNVGWERDVEQFIEFFENPAFRADGLKIYPTLVIRGTGLYELWKTGRYKSYPPSGLIDLIARILALVPPWTRVYRVQ] 378 # sequence of block unknown_G 378 [RDIPMPLVSSGVE] 391 # sequence of block unknown_H 391 [HGNLRELALARMKDLGT] 408 # sequence of block unknown_I 408 [QCRDVRTREVGIQEIHNKVKPYEAELIRRDYCANGGWETFLSYEDPEQDILIGLLRLRKCSP] 470 # sequence of block unknown_J 471 [TFRSELKS] 479 # sequence of block unknown_K 479 [SCSIVRELHVYGSVVPVHARDPTKFQHQGFGMLLMEEAERIAREEHGSSKIAVISG] 535 # sequence of block unknown_L 539 [NYYRKIGYELDGPYMSKS] 557 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705Z6.prfl --predictionStart=0 --predictionEnd=34952 --species=fly ./tmp/Contig2683820180911_busco_2432604931_.temp