# 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..51]--> unknown_A (15) <--[15..55]--> unknown_B (14) <--[13..154]--> unknown_D (25) <--[29..108]--> unknown_H (16) <--[0..3]--> unknown_I (19) <--[1..2]--> unknown_J (27) <--[0..1]--> unknown_K (21) <--[0..5]--> unknown_L (50) <--[1..3]--> unknown_M (31) <--[23..76]--> unknown_N (26) <--[7..25]--> unknown_O (20) <--[0..1]--> unknown_P (18) <--[26..72]--> unknown_R (10) <--[42..209]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig9701720180911_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 = 22565, name = Contig97017) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig97017 AUGUSTUS gene 3326 21820 0.01 + . g1 Contig97017 AUGUSTUS transcript 3326 21820 0.01 + . g1.t1 Contig97017 AUGUSTUS tss 3326 3326 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 3326 3670 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 3817 3928 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS start_codon 3875 3877 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 3929 8904 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 9067 9660 0.94 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 9792 9970 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 10037 10140 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 10230 10489 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 10621 10824 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 10925 11855 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 11950 12622 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 12716 12820 0.75 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 12927 13364 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 13476 14288 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 14408 15165 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 15325 17759 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 17815 20890 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS intron 20982 21397 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 3875 3928 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 8905 9066 0.15 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 8905 9066 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 9661 9791 0.96 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 9661 9791 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 9971 10036 0.04 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 9971 10036 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 10141 10229 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 10141 10229 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 10490 10620 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 10490 10620 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 10825 10924 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 10825 10924 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 11856 11949 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 11856 11949 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 12623 12715 0.75 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 12623 12715 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 12821 12926 0.97 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 12821 12926 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 13365 13475 0.8 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 13365 13475 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 14289 14407 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 14289 14407 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 15166 15324 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 15166 15324 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 17760 17814 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 17760 17814 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 20891 20981 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 20891 20981 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS CDS 21398 21462 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS exon 21398 21820 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS stop_codon 21460 21462 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS tts 21820 21820 . + . transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 3905 3928 1.45 + 0 target "unknown_A[1..8]"; target_start 10; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 8905 8925 1.45 + 0 target "unknown_A[9..15]"; target_start 10; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 9031 9066 1.16 + 0 target "unknown_B[1..12]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 9661 9666 5.17 + 0 target "unknown_B[13..14]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 9781 9791 5.18 + 0 target "unknown_D[1..4]"; target_start 112; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 9971 10034 4.72 + 1 target "unknown_D[4..25]"; target_start 112; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 10516 10563 2.49 + 0 target "unknown_H[1..16]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 10564 10620 4.17 + 0 target "unknown_I[1..19]"; target_start 192; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 10828 10908 5.11 + 0 target "unknown_J[1..27]"; target_start 212; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 10909 10924 6.19 + 0 target "unknown_K[1..6]"; target_start 239; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 11856 11902 4.53 + 2 target "unknown_K[6..21]"; target_start 239; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 11903 11949 5.11 + 0 target "unknown_L[1..16]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 12623 12715 6.29 + 0 target "unknown_L[17..47]"; target_start 259; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 12821 12830 9.39 + 1 target "unknown_L[47..50]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 12837 12926 4.85 + 0 target "unknown_M[1..30]"; target_start 312; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 13365 13367 1.39 + 0 target "unknown_M[31..31]"; target_start 312; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 13464 13475 1.64 + 0 target "unknown_N[1..4]"; target_start 375; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 14289 14354 4.31 + 0 target "unknown_N[5..26]"; target_start 375; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 15173 15232 2.84 + 0 target "unknown_O[1..20]"; target_start 421; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 15233 15286 3.59 + 0 target "unknown_P[1..18]"; target_start 441; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 17800 17814 1.05 + 0 target "unknown_R[1..5]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; Contig97017 AUGUSTUS protein_match 20891 20905 1.42 + 0 target "unknown_R[6..10]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaatataaagtacaactttcatggcaagatgcagaagagtgcaaatattcagctaggagaagaggaagatgatgtca # gtgaagaagataaagaggacacaatgccccaggatcagccgtccaaaacagatgtagaggaaaagggtgctaacaaaaagaaaaagaagaaaaagaaa # aagaagaagaaatcagctgaaagagaaattgacaatgaggaagatgaaattgatgccagtattaaggaggtcaatcgcattttggaaaattcgggtca # tggtgccgaattcatcacaagggtagacactgccaatgaatccacaaaggcccttctgacagtcgagcataagaatttgaatccagataatgaaatga # agaggatatttggatctcgagtagtgcaagctgaagtgtcaagaaggagacaaagaaatgtgcaagtccgtagacggacaagctggctggccacacct # aaagatacctggcctcacataggaaaatcagggttgacaatgtcggtaacagagacaggaggaaatgtgatccactttgtatacgaacacaatcatca # gtaccaacaagtgcaattcaaattctacgatgcagtggaatctttgaaccctcagaacatcatggatatcatcagaacacatccatatcatgtagatt # ctctgatccagatgagtgaagtgttccgcatgagtgaggacatgcaaacagcggccgatttgatagagagagctttgttttcctttgagatgtctttc # cattccttatttagtttaactaccggcaactgtcgactggatttcaggcagacagaaaacagaccattttatttggctctgttcaagcaccttgtgaa # tgtaggacagagaggttgctaccggacagctctggaattctgtaaattgctgttgagccttgaccctgataatgatcccatgtgtgttcttctgttga # ttgacttctatgcactaagagctgcagaatattccttcttgatccgactctaccaagaatgggaggatcacaggaacttgtctcagttaccaaacttt # gccttctcagtgccactggccatgtttcttctgggagaatctcaaagctcagaggatacaacagaggctgatgaaaagcttcaacaagctctgattat # gtttcctggtttattgatgccgctcctggataaatgcagtatcaaccctgacaacacggtttctagtcatgctttctttggagacaaaactcaataca # gtcaaaccgctgctctgaaacagctggttggattatacatcggacgctgccatgcctgctggaaacaacccgaggttgtacagtggttagaaagaaat # gtcaaggaagtgctgaagagagtggatgaactagatccatttattgaagaatgtaacaaaaatgttaatcaatatgacaattacagtgtatcaatatt # agaaatttaccccccaatggagacaggtgagataccagggaactccaaggaacatcttaagacacatcctcatctcagagatcaaggacgcaattaca # gcactccctcaatatctaaatataacagcttcagaaatttttgctgttccatgtactacagcaatgttgaaaactga] # protein sequence = [MNIKYNFHGKMQKSANIQLGEEEDDVSEEDKEDTMPQDQPSKTDVEEKGANKKKKKKKKKKKKSAEREIDNEEDEIDA # SIKEVNRILENSGHGAEFITRVDTANESTKALLTVEHKNLNPDNEMKRIFGSRVVQAEVSRRRQRNVQVRRRTSWLATPKDTWPHIGKSGLTMSVTET # GGNVIHFVYEHNHQYQQVQFKFYDAVESLNPQNIMDIIRTHPYHVDSLIQMSEVFRMSEDMQTAADLIERALFSFEMSFHSLFSLTTGNCRLDFRQTE # NRPFYLALFKHLVNVGQRGCYRTALEFCKLLLSLDPDNDPMCVLLLIDFYALRAAEYSFLIRLYQEWEDHRNLSQLPNFAFSVPLAMFLLGESQSSED # TTEADEKLQQALIMFPGLLMPLLDKCSINPDNTVSSHAFFGDKTQYSQTAALKQLVGLYIGRCHACWKQPEVVQWLERNVKEVLKRVDELDPFIEECN # KNVNQYDNYSVSILEIYPPMETGEIPGNSKEHLKTHPHLRDQGRNYSTPSISKYNSFRNFCCSMYYSNVEN] # sequence of block unknown_A 10 [MQKSANIQLGEEEDD] 25 # sequence of block unknown_B 60 [KKKSAEREIDNEED] 74 # sequence of block unknown_D 112 [VEHKNLNPDNEMKRIFGSRVVQAEV] 137 # sequence of block unknown_H 176 [GGNVIHFVYEHNHQYQ] 192 # sequence of block unknown_I 192 [QVQFKFYDAVESLNPQNIM] 211 # sequence of block unknown_J 212 [IIRTHPYHVDSLIQMSEVFRMSEDMQT] 239 # sequence of block unknown_K 239 [AADLIERALFSFEMSFHSLFS] 260 # sequence of block unknown_L 260 [LTTGNCRLDFRQTENRPFYLALFKHLVNVGQRGCYRTALEFCKLLLSLDP] 310 # sequence of block unknown_M 312 [DPMCVLLLIDFYALRAAEYSFLIRLYQEWED] 343 # sequence of block unknown_N 375 [ADEKLQQALIMFPGLLMPLLDKCSIN] 401 # sequence of block unknown_O 421 [AALKQLVGLYIGRCHACWKQ] 441 # sequence of block unknown_P 441 [PEVVQWLERNVKEVLKRV] 459 # sequence of block unknown_R 485 [IYPPMETGEI] 495 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093709JG.prfl --predictionStart=0 --predictionEnd=32998 --species=fly ./tmp/Contig9701720180911_busco_2432604931_.temp