# 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..114]--> unknown_A (13) <--[0..2]--> unknown_B (26) <--[0..2]--> unknown_C (40) <--[0..2]--> unknown_D (12) <--[2..8]--> unknown_E (28) <--[0..4]--> unknown_F (20) <--[1..23]--> unknown_G (13) <--[0..15]--> unknown_H (10) <--[0..2]--> unknown_I (16) <--[7..22]--> unknown_K (16) <--[0..4]--> unknown_L (33) <--[1..26]--> unknown_M (31) <--[1..2]--> unknown_N (27) <--[3..16]--> unknown_O (16) <--[9..46]--> unknown_Q (17) <--[1..11]--> unknown_R (35) <--[5..38]--> unknown_S (18) <--[1..18]--> unknown_T (32) <--[24..345]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2896620180911_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 = 22802, name = Contig28966) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig28966 AUGUSTUS gene 12316 22076 0.01 + . g1 Contig28966 AUGUSTUS transcript 12316 22076 0.01 + . g1.t1 Contig28966 AUGUSTUS tss 12316 12316 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 12316 12538 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 12831 13874 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS start_codon 12848 12850 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 13875 15094 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 15192 16253 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 16268 16725 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 16746 16884 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 16916 17957 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 18022 19121 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 19169 19254 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 19297 19846 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 19876 20441 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS intron 20480 21810 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 12848 13874 0.88 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 15095 15191 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 15095 15191 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 16254 16267 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 16254 16267 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 16726 16745 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 16726 16745 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 16885 16915 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 16885 16915 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 17958 18021 0.04 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 17958 18021 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 19122 19168 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 19122 19168 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 19255 19296 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 19255 19296 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 19847 19875 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 19847 19875 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 20442 20479 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 20442 20479 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS CDS 21811 21919 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS exon 21811 22076 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS stop_codon 21917 21919 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS tts 22076 22076 . + . transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 12872 12910 5.42 + 0 target "unknown_A[1..13]"; target_start 8; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 12911 12988 4.4 + 0 target "unknown_B[1..26]"; target_start 21; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 12989 13108 5.58 + 0 target "unknown_C[1..40]"; target_start 47; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13109 13144 3.36 + 0 target "unknown_D[1..12]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13163 13246 8.45 + 0 target "unknown_E[1..28]"; target_start 105; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13250 13309 6.52 + 0 target "unknown_F[1..20]"; target_start 134; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13313 13351 4.55 + 0 target "unknown_G[1..13]"; target_start 155; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13352 13381 8.36 + 0 target "unknown_H[1..10]"; target_start 168; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13382 13429 5.41 + 0 target "unknown_I[1..16]"; target_start 178; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13457 13504 8.37 + 0 target "unknown_K[1..16]"; target_start 203; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13505 13603 7.97 + 0 target "unknown_L[1..33]"; target_start 219; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13616 13708 6.37 + 0 target "unknown_M[1..31]"; target_start 256; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13712 13792 5.54 + 0 target "unknown_N[1..27]"; target_start 288; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 13811 13858 2.57 + 0 target "unknown_O[1..16]"; target_start 321; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 15115 15165 5.34 + 0 target "unknown_Q[1..17]"; target_start 349; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 15172 15191 2.37 + 0 target "unknown_R[1..7]"; target_start 368; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 16254 16267 2.03 + 0 target "unknown_R[8..12]"; target_start 367; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 16726 16745 1.2 + 1 target "unknown_R[12..19]"; target_start 367; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 16885 16915 1.38 + 2 target "unknown_R[19..29]"; target_start 367; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 17958 17977 0.915 + 2 target "unknown_R[29..35]"; target_start 368; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 19132 19168 1.1 + 0 target "unknown_S[1..13]"; target_start 421; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 19255 19271 1.09 + 2 target "unknown_S[13..18]"; target_start 421; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 19287 19296 2.38 + 0 target "unknown_T[1..4]"; target_start 444; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 19847 19875 1.12 + 1 target "unknown_T[4..14]"; target_start 443; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 20442 20479 1.2 + 2 target "unknown_T[14..26]"; target_start 443; transcript_id "g1.t1"; gene_id "g1"; Contig28966 AUGUSTUS protein_match 21811 21829 1.16 + 1 target "unknown_T[26..32]"; target_start 444; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgccagaagaatccacagaagacatattcaaaatcattgtcgcaacagatatacacctaggttatggggagaaagatg # ttatcagaggcaatgactcgcttgtggcttttgaagaaatattagaaaatgctaaaaagcatgaggctgattttattctcctgggtggagatcttttc # catgaaaataaaccaccaagaagaataatgcatggatgcatagcactgcttaggaagtactgttttggagacaaaccaattctttttgaatatttgag # tgatcaatcagcagattttcagcactgtcagttcccaaccttgaactatgaggacacaaatttaaatgtttcaataccagtgttttctattcatggga # atcatgatgatccttcaggacaaggcaatttatgttcgttagatcttcttcacagtgcaggactaatgaactattttggcaaaactacaagtttagag # aaaatagaaatgtcgccacttctcatgcagaaggggaatacaaagttggctctctatggtctagggtcagtaagagatgaacggctacatcgtttgtt # tgtccataaaaatgtgacgatgctacggccaaaggagaatcaagaagattggttcaacgtttttgtcattcatcaaaatcgtgccaagcactcgacaa # ctagttatatcccggaacagtttttggatgatttcttggaccttgttatttggggacatgaacacgagtgcagacttgagccagagtggaacagctca # caaaatttttttgtaagccagcctggtagcagtgtagccacatccctgagtgagggagagaccgctaaaaaacacattggtctgttgcaaattaaggg # aaagaatttcaagatgaccaagatccccttgcagactgtcaggcagttttacatggaagacattgtactcagcgacacagatctaaacccagaagacc # atgatatagccaagaaagtggaagcgtattgtttggaaaaagtggattccattttagagaaggcaactttggaacactcaggcaacagaagacaacca # gacaagcctttagtcagacttcgcatagactacagtggagggtttgaaccatttagtggatacagtttcgaagctagaattgggaacatcatcggaaa # tatcaagtcaatgataccctttaatgctatataccgtgtagtaatatcatctcaggaactcatctgtcccgctgtattcaacatagataaattgataa # atcattcaacaactaagatactagacgaggtcgatataccaaatgggttcgagtattattttatcctcttactaaataacatgactcgtgtttactac # aacaagttagttgaagtattaatgcgaaaatgtaatcgccacgatctacacaaatgctccggaaaatataactttatctttcttatgattgaaacaga # tttacccggtagtgaaagaaagggtattttccatttcagaacaggatctcactttttaaccccctaa] # protein sequence = [MPEESTEDIFKIIVATDIHLGYGEKDVIRGNDSLVAFEEILENAKKHEADFILLGGDLFHENKPPRRIMHGCIALLRK # YCFGDKPILFEYLSDQSADFQHCQFPTLNYEDTNLNVSIPVFSIHGNHDDPSGQGNLCSLDLLHSAGLMNYFGKTTSLEKIEMSPLLMQKGNTKLALY # GLGSVRDERLHRLFVHKNVTMLRPKENQEDWFNVFVIHQNRAKHSTTSYIPEQFLDDFLDLVIWGHEHECRLEPEWNSSQNFFVSQPGSSVATSLSEG # ETAKKHIGLLQIKGKNFKMTKIPLQTVRQFYMEDIVLSDTDLNPEDHDIAKKVEAYCLEKVDSILEKATLEHSGNRRQPDKPLVRLRIDYSGGFEPFS # GYSFEARIGNIIGNIKSMIPFNAIYRVVISSQELICPAVFNIDKLINHSTTKILDEVDIPNGFEYYFILLLNNMTRVYYNKLVEVLMRKCNRHDLHKC # SGKYNFIFLMIETDLPGSERKGIFHFRTGSHFLTP] # sequence of block unknown_A 8 [IFKIIVATDIHLG] 21 # sequence of block unknown_B 21 [YGEKDVIRGNDSLVAFEEILENAKKH] 47 # sequence of block unknown_C 47 [EADFILLGGDLFHENKPPRRIMHGCIALLRKYCFGDKPIL] 87 # sequence of block unknown_D 87 [FEYLSDQSADFQ] 99 # sequence of block unknown_E 105 [LNYEDTNLNVSIPVFSIHGNHDDPSGQG] 133 # sequence of block unknown_F 134 [LCSLDLLHSAGLMNYFGKTT] 154 # sequence of block unknown_G 155 [LEKIEMSPLLMQK] 168 # sequence of block unknown_H 168 [GNTKLALYGL] 178 # sequence of block unknown_I 178 [GSVRDERLHRLFVHKN] 194 # sequence of block unknown_K 203 [QEDWFNVFVIHQNRAK] 219 # sequence of block unknown_L 219 [HSTTSYIPEQFLDDFLDLVIWGHEHECRLEPEW] 252 # sequence of block unknown_M 256 [NFFVSQPGSSVATSLSEGETAKKHIGLLQIK] 287 # sequence of block unknown_N 288 [KNFKMTKIPLQTVRQFYMEDIVLSDTD] 315 # sequence of block unknown_O 321 [DIAKKVEAYCLEKVDS] 337 # sequence of block unknown_Q 349 [RRQPDKPLVRLRIDYSG] 366 # sequence of block unknown_R 368 [EPFSGYSFEARIGNIIGNIKSMIPFNAIYRVVISS] 403 # sequence of block unknown_S 421 [TTKILDEVDIPNGFEYYF] 439 # sequence of block unknown_T 444 [NMTRVYYNKLVEVLMRKCNRHDLHKCSGKYNF] 476 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093706PM.prfl --predictionStart=0 --predictionEnd=33759 --species=fly ./tmp/Contig2896620180911_busco_2432604931_.temp