# 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..197]--> unknown_A (23) <--[0..1]--> unknown_B (23) <--[0..5]--> unknown_C (13) <--[5..44]--> unknown_D (36) <--[0..21]--> unknown_E (15) <--[0..1]--> unknown_F (34) <--[2..27]--> unknown_G (13) <--[0..1]--> unknown_H (25) <--[0..6]--> unknown_I (28) <--[1..7]--> unknown_J (19) <--[27..753]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4414320180911_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 = 12500, name = Contig44143) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig44143 AUGUSTUS gene 1666 10784 0.01 + . g1 Contig44143 AUGUSTUS transcript 1666 10784 0.01 + . g1.t1 Contig44143 AUGUSTUS tss 1666 1666 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 1666 1905 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS start_codon 1744 1746 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 1906 3052 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 3290 3788 0.46 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 4001 4499 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 4724 7489 0.8 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 7626 8289 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS intron 8952 9005 0.5 + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 1744 1905 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 3053 3289 0.47 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 3053 3289 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 3789 4000 0.98 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 3789 4000 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 4500 4723 1 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 4500 4723 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 7490 7625 0.8 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 7490 7625 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 8290 8951 0.77 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 8290 8951 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS CDS 9006 10372 0.15 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS exon 9006 10784 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS stop_codon 10370 10372 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS tts 10784 10784 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 1756 1824 4.09 + 0 target "unknown_A[1..23]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 1825 1893 7.19 + 0 target "unknown_B[1..23]"; target_start 27; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 1894 1905 2.48 + 0 target "unknown_C[1..4]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3053 3079 1.23 + 0 target "unknown_C[5..13]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3098 3205 2.04 + 0 target "unknown_D[1..36]"; target_start 69; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3206 3250 2.38 + 0 target "unknown_E[1..15]"; target_start 105; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3251 3289 4.53 + 0 target "unknown_F[1..13]"; target_start 120; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3789 3851 4.59 + 0 target "unknown_F[14..34]"; target_start 120; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3864 3902 7.65 + 0 target "unknown_G[1..13]"; target_start 158; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3903 3977 7.81 + 0 target "unknown_H[1..25]"; target_start 171; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 3987 4000 7.47 + 0 target "unknown_I[1..5]"; target_start 199; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 4500 4569 5.8 + 1 target "unknown_I[5..28]"; target_start 199; transcript_id "g1.t1"; gene_id "g1"; Contig44143 AUGUSTUS protein_match 4585 4641 4.06 + 0 target "unknown_J[1..19]"; target_start 232; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggatcccgttgacagtgatttgtgccccgtttgccacgaggcggtagatatttttgcaatcggtcattgcgatcacc # cgatatgttaccgatgctcaacaagaatgcgtgtactgtgtaaccacatgtattgtcccatctgtaggactgacttaaatcaggtgtatatggttcac # aaaaaggttaaatgtgaagaaattcctcgctatggctacatcccaaacagaaggtacaaaatatttttggaagatggacagattcagaagaagtttga # gaagcttaatgaacaccgttgtcctaaatgcaaaatgttggagagaaacttaaaagcattgcagcaacatctttcaaaacagcatactttatttttct # gcaatttgtgtttggaccacttaaagatatttccatctgaacggaaggcttataaccgacaagatcttgcactgcatcgtcgccaaggagacaaggac # gacacgtcctataagggacacccgctgtgtcacttctgtgatgaacggtacctggacaatgatgagctcttcaagcatttgagaaaagaccactatta # ttgtcatttctgcgagacggatggcaaccaggattattacagtgattatgaagatctgaaagagcactttcgggccaagcacttcctgtgtgaggatg # gagactgtgtcaatactcagtttactcacgccttccgatccaaaatcgacttccaagctcaccagacgaatcaccactcgaggatgctgtccaaatct # caagtgaagcaagccaggaccatagaggtggacatccagttagcaccgaggaaccggaggagagataaaggagtagtgacagcagaggactatgagga # caagcctgtccaaaggacgggacctcctgctcaaaggacgggacctcctgctcaaaggactggacctccagtgaggggtcaggggagactagtgaagg # aacgattcagggaggaggacatgaatcgagcaatccaggcctccttaagtgtcatgacagaagagaagatgaagaagcctaggacagtggaggaggag # agaaaaacaccgtccccagaattactgcaggacactgagcaattcccaagcctcgggaaaatgagagaggaaccaaaaccgctacgtagtgattcgcc # tgcgactgtggactccgattctntcccaagcctcgggaaaatgagagaggaaccgaaaccgctacgtagtgattcgcccgcgactgtggactctgatt # cagagaagtctagtcggtcattggcacaaaggctcgccaagaagtccaagcaatcggttcaacatggagcaatgggcgaggaagattttccgacgctt # ttaatgaaaccgtccaaacctgaagtcacagttaatgttataaaaacttctaaaccagtaccgcatgcctacagtgtggcatcaaagtcggggcctgc # tggtgttcaggaagattttccaagtcttcccgttggtaaaacaaatagtgcatcatctgccattggccagtggggcaagaacagcgctgccagtggaa # aaggtttcaaaactgtgaaaactgtcacgtcagtttcatacccgtctcctttagatgtgatgatgagtgatcggtcaggcaaagagaatgactttcct # accttaacttcagttggggtagaaaatcgcaacactgactggctgaaaaatgtagccgagaaaaagaaagtaaaacaggttaaaccaattgattggtt # tgaggtaaataatgaatcgaatgaatttagtattgaaaatcttactggtgataaggataataaacaattaattacggaggcatataaagagactaaga # aaaagaaaaagactaaaaagactaagttgggtagtaatggtaacaaatgtgatgatgtgatgtctggtacagcatcactagataatatagctacgtcg # ctgttgggaaatggatttccagcttcaaaaaaaaaaactgtggtaaaggtggtggaagatatcccagtgaaggaagagaagcagacggttcctgcttc # agaaaaatttgagagcaacacaactacctcagagcccactgcacctgttggtccttctgtcaatccacctgttggtccatctattgatccacctgttg # atgatctgatcttggaaagaaatgttgaggaaagtttcattccagtgaaaatcaaggagaagaaaaccaaagagaagaagaatggaagtctggactcc # tcagattttccagctctgtctgcaccacaggccaagggacctccaccaggcttcagcaaagccaagaagccccctccaggatttgaaagttcacagac # ccctgcgtcagtttcccctactgtgatggcccctcccccagggtttgcctcttcatcgctggcgggtctcaaagacttgagtctgaagaatttgatgg # attctgtctcgaatgaaaatcgagtgccaaatgcagacgcaccggcagtgtttccagagagctatcgatatgaggaaccaaaggatttccaatctaga # aacaaagaccttgtgatgaaaatcaaagatgtgtttcaagaaaatgagggaaaattttcttcatttaaatcctgttcgagtgatttcagaggaggaac # tatatctgctgttgaatattacaacaagtgcacggagttgataggactggaacacttcacacagatcttcacagaactcttagttttacttcctgata # tcgaaaagcaacaggaacttctcaacgcgcataaaatgaatgagaaatcaaaaaacagtgctgaaaaagtgttgaagatcagcggaaaaagttcagct # gctccatggaatagtcaactagactttgtttcgtgtcccgtctgttgtcaaattttgctgcaaggcgactacaaccaacacgtaagcacacacaacct # agaagctgattatccttctctcggttctcaagtgacctcgcaaggaacaggaatgagggcgtggatcaaagccaactag] # protein sequence = [MDPVDSDLCPVCHEAVDIFAIGHCDHPICYRCSTRMRVLCNHMYCPICRTDLNQVYMVHKKVKCEEIPRYGYIPNRRY # KIFLEDGQIQKKFEKLNEHRCPKCKMLERNLKALQQHLSKQHTLFFCNLCLDHLKIFPSERKAYNRQDLALHRRQGDKDDTSYKGHPLCHFCDERYLD # NDELFKHLRKDHYYCHFCETDGNQDYYSDYEDLKEHFRAKHFLCEDGDCVNTQFTHAFRSKIDFQAHQTNHHSRMLSKSQVKQARTIEVDIQLAPRNR # RRDKGVVTAEDYEDKPVQRTGPPAQRTGPPAQRTGPPVRGQGRLVKERFREEDMNRAIQASLSVMTEEKMKKPRTVEEERKTPSPELLQDTEQFPSLG # KMREEPKPLRSDSPATVDSDSXPSLGKMREEPKPLRSDSPATVDSDSEKSSRSLAQRLAKKSKQSVQHGAMGEEDFPTLLMKPSKPEVTVNVIKTSKP # VPHAYSVASKSGPAGVQEDFPSLPVGKTNSASSAIGQWGKNSAASGKGFKTVKTVTSVSYPSPLDVMMSDRSGKENDFPTLTSVGVENRNTDWLKNVA # EKKKVKQVKPIDWFEVNNESNEFSIENLTGDKDNKQLITEAYKETKKKKKTKKTKLGSNGNKCDDVMSGTASLDNIATSLLGNGFPASKKKTVVKVVE # DIPVKEEKQTVPASEKFESNTTTSEPTAPVGPSVNPPVGPSIDPPVDDLILERNVEESFIPVKIKEKKTKEKKNGSLDSSDFPALSAPQAKGPPPGFS # KAKKPPPGFESSQTPASVSPTVMAPPPGFASSSLAGLKDLSLKNLMDSVSNENRVPNADAPAVFPESYRYEEPKDFQSRNKDLVMKIKDVFQENEGKF # SSFKSCSSDFRGGTISAVEYYNKCTELIGLEHFTQIFTELLVLLPDIEKQQELLNAHKMNEKSKNSAEKVLKISGKSSAAPWNSQLDFVSCPVCCQIL # LQGDYNQHVSTHNLEADYPSLGSQVTSQGTGMRAWIKAN] # sequence of block unknown_A 4 [DSDLCPVCHEAVDIFAIGHCDHP] 27 # sequence of block unknown_B 27 [ICYRCSTRMRVLCNHMYCPICRT] 50 # sequence of block unknown_C 50 [DLNQVYMVHKKVK] 63 # sequence of block unknown_D 69 [YGYIPNRRYKIFLEDGQIQKKFEKLNEHRCPKCKML] 105 # sequence of block unknown_E 105 [ERNLKALQQHLSKQH] 120 # sequence of block unknown_F 120 [TLFFCNLCLDHLKIFPSERKAYNRQDLALHRRQG] 154 # sequence of block unknown_G 158 [TSYKGHPLCHFCD] 171 # sequence of block unknown_H 171 [ERYLDNDELFKHLRKDHYYCHFCET] 196 # sequence of block unknown_I 199 [QDYYSDYEDLKEHFRAKHFLCEDGDCVN] 227 # sequence of block unknown_J 232 [AFRSKIDFQAHQTNHHSRM] 251 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CZT.prfl --predictionStart=0 --predictionEnd=24644 --species=fly ./tmp/Contig4414320180911_busco_2432604931_.temp