# 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 # --[10..260]--> unknown_B (52) <--[7..15]--> unknown_C (20) <--[0..13]--> unknown_D (13) <--[2..3]--> unknown_E (23) <--[5..125]--> unknown_F (18) <--[1..2]--> unknown_G (12) <--[0..3]--> unknown_H (14) <--[1..24]--> unknown_I (17) <--[0..9]--> unknown_J (15) <--[2..3]--> unknown_K (14) <--[3..18]--> unknown_L (17) <--[0..13]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4433620180911_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 = 24451, name = Contig44336) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig44336 AUGUSTUS gene 1516 16265 0.01 + . g1 Contig44336 AUGUSTUS transcript 1516 16265 0.01 + . g1.t1 Contig44336 AUGUSTUS tss 1516 1516 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 1516 1664 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 3159 4459 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS start_codon 3192 3194 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 4460 8905 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 8948 9488 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 9504 9632 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 9668 11086 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 11143 11906 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS intron 11919 14456 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 3192 4459 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 8906 8947 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 8906 8947 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 9489 9503 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 9489 9503 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 9633 9667 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 9633 9667 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 11087 11142 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 11087 11142 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 11907 11918 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 11907 11918 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS CDS 14457 14510 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS exon 14457 16265 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS stop_codon 14508 14510 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS tts 16265 16265 . + . transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 3912 4067 4.12 + 0 target "unknown_B[1..52]"; target_start 240; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4089 4148 5.6 + 0 target "unknown_C[1..20]"; target_start 299; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4149 4187 9.77 + 0 target "unknown_D[1..13]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4197 4265 5.76 + 0 target "unknown_E[1..23]"; target_start 335; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4287 4340 5.87 + 0 target "unknown_F[1..18]"; target_start 365; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4344 4379 3.48 + 0 target "unknown_G[1..12]"; target_start 384; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4383 4424 7.7 + 0 target "unknown_H[1..14]"; target_start 397; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 4428 4459 2.75 + 0 target "unknown_I[1..11]"; target_start 412; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 8906 8924 1.04 + 1 target "unknown_I[11..17]"; target_start 412; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 8943 8947 1.23 + 0 target "unknown_J[1..2]"; target_start 435; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 9489 9503 2.43 + 0 target "unknown_J[3..7]"; target_start 434; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 9633 9657 1.62 + 1 target "unknown_J[7..15]"; target_start 435; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 9667 9667 1 + 0 target "unknown_K[1..1]"; target_start 453; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 11087 11127 1.6 + 2 target "unknown_K[1..14]"; target_start 453; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 11137 11142 1.25 + 0 target "unknown_L[1..2]"; target_start 470; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 11907 11918 1.44 + 2 target "unknown_L[3..7]"; target_start 469; transcript_id "g1.t1"; gene_id "g1"; Contig44336 AUGUSTUS protein_match 14457 14489 1.73 + 0 target "unknown_L[7..17]"; target_start 470; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcggtgaatgacatatcaagcagaagagaatctttgatattagaactttacaaagtggaagcgcttaagtttggaa # attttaaactgaagagtggaatagactcccccgtgtactttgacttgcgtgtcattgtgtcctacccgtctcttctgaatgaggtagcggagctgacg # tgggagactgcgagagcagctggctgtcagtttgactctgtatgcggagtcccatacacagcgctacctatagcagcgtgtatgtctgtgcatcacaa # tgtgccaatgttaattcgtcgaaaagaagcgaaggattatgggacaaagaagatggttgaaggtcattacaaggaaggagaaaactgtctggttgttg # aggatgttgtcaccagtggagggtctgtgatggacacgatacacactctacagtctatactggtaaaagtatctgatgctgttgttttgctggacaga # gaacaaggaggaaaatctgctctgcggaagaaaggaatacaccttcacagtgtgtgtattttgacgacagtactggaagttttggaatcaaatggcaa # acttgataaaaacattgtagagaggacgagaaaatttattcaggagaacagatttgatgtggatacttccattaatggtgcggagaaaattgtagggg # atcaggcgaagaaatcaaaatttacagtcttcagtcatgccgaagcaatgtgcaaaaatgccaaacttcgttcattgtactcaattatggacacaaag # aaaacaaaccttgctgtgtctgttgatctcactacctctgatgacgtgttgaagcttttggatgctgtggggccgtacatatgcttagcgaagacaca # tgttgacatcatcgcagacttctcgcagtccttcaccaactcgctgacggccttggctaggaaacacaatttccttctgtttgaggacaggaaattcg # cagatattggtaacaccgtgaaacatcagtatgaaggtgggctgtaccacatcagctcctgggcagacattgtaaattgtcaccctgtctctggggaa # ggagtcattcagggtctgaaagagattggtcatccattaaacagagcttgtttgttggtggctgagatgagttctaagggcagccttgcaaaaaatga # atacacaaaatctacacttgcaatggcacaaaagcacaaagattttgtgattggatttatctgtcagtcaaagttgacctctgatcccgatctcattc # atatgatgcaggtaatttttctcgagagctcgcgcttctggcgttcgcaggtcaacttttttggccagtgttggttgaatattggcccagtggttctt # gagagaagactggatatcattacaattggtagagatatcaaaagaggcaaaaccaatgaaaagcaagccaatacgtacaatgaacaaggcatgtcttt # gcatcatgaacctcaaagtacacttcagtga] # protein sequence = [MAVNDISSRRESLILELYKVEALKFGNFKLKSGIDSPVYFDLRVIVSYPSLLNEVAELTWETARAAGCQFDSVCGVPY # TALPIAACMSVHHNVPMLIRRKEAKDYGTKKMVEGHYKEGENCLVVEDVVTSGGSVMDTIHTLQSILVKVSDAVVLLDREQGGKSALRKKGIHLHSVC # ILTTVLEVLESNGKLDKNIVERTRKFIQENRFDVDTSINGAEKIVGDQAKKSKFTVFSHAEAMCKNAKLRSLYSIMDTKKTNLAVSVDLTTSDDVLKL # LDAVGPYICLAKTHVDIIADFSQSFTNSLTALARKHNFLLFEDRKFADIGNTVKHQYEGGLYHISSWADIVNCHPVSGEGVIQGLKEIGHPLNRACLL # VAEMSSKGSLAKNEYTKSTLAMAQKHKDFVIGFICQSKLTSDPDLIHMMQVIFLESSRFWRSQVNFFGQCWLNIGPVVLERRLDIITIGRDIKRGKTN # EKQANTYNEQGMSLHHEPQSTLQ] # sequence of block unknown_B 240 [KNAKLRSLYSIMDTKKTNLAVSVDLTTSDDVLKLLDAVGPYICLAKTHVDII] 292 # sequence of block unknown_C 299 [TNSLTALARKHNFLLFEDRK] 319 # sequence of block unknown_D 319 [FADIGNTVKHQYE] 332 # sequence of block unknown_E 335 [YHISSWADIVNCHPVSGEGVIQG] 358 # sequence of block unknown_F 365 [LNRACLLVAEMSSKGSLA] 383 # sequence of block unknown_G 384 [NEYTKSTLAMAQ] 396 # sequence of block unknown_H 397 [HKDFVIGFICQSKL] 411 # sequence of block unknown_I 412 [SDPDLIHMMQVIFLESS] 429 # sequence of block unknown_J 435 [VNFFGQCWLNIGPVV] 450 # sequence of block unknown_K 453 [RLDIITIGRDIKRG] 467 # sequence of block unknown_L 470 [EKQANTYNEQGMSLHHE] 487 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OUS.prfl --predictionStart=0 --predictionEnd=24451 --species=fly ./tmp/Contig4433620180911_busco_2432604931_.temp