# 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..16]--> unknown_A (9) <--[3..18]--> unknown_B (9) <--[5..26]--> unknown_C (24) <--[0..17]--> unknown_D (96) <--[0..8]--> unknown_E (21) <--[0..16]--> unknown_F (9) <--[0..6]--> unknown_G (11) <--[0..2]--> unknown_H (20) <--[0..36]--> unknown_I (11) <--[0..2]--> unknown_J (44) <--[0..19]--> unknown_K (20) <--[0..1]--> unknown_L (9) <--[0..3]--> unknown_M (52) <--[1..19]--> unknown_N (26) <--[0..18]--> unknown_O (42) <--[9..20]--> unknown_Q (17) <--[0..39]--> unknown_R (40) <--[15..581]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig8235520180911_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 = 11744, name = Contig82355) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig82355 AUGUSTUS gene 126 9374 0.01 + . g1 Contig82355 AUGUSTUS transcript 126 9374 0.01 + . g1.t1 Contig82355 AUGUSTUS tss 126 126 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS exon 126 536 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS exon 3990 4123 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS start_codon 4044 4046 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS intron 4124 6885 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS intron 8576 9133 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS CDS 4044 4123 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS CDS 6886 8575 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS exon 6886 8575 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS CDS 9134 9289 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS exon 9134 9374 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS stop_codon 9287 9289 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS tts 9374 9374 . + . transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 4056 4082 6.28 + 0 target "unknown_A[1..9]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 4092 4118 6.66 + 0 target "unknown_B[1..9]"; target_start 16; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 6908 6979 5.71 + 0 target "unknown_C[1..24]"; target_start 34; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 6980 7267 6.08 + 0 target "unknown_D[1..96]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7268 7330 6.22 + 0 target "unknown_E[1..21]"; target_start 154; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7334 7360 4.77 + 0 target "unknown_F[1..9]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7361 7393 5.93 + 0 target "unknown_G[1..11]"; target_start 185; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7394 7453 3.89 + 0 target "unknown_H[1..20]"; target_start 196; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7484 7516 4.5 + 0 target "unknown_I[1..11]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7517 7648 6.39 + 0 target "unknown_J[1..44]"; target_start 237; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7649 7708 4.74 + 0 target "unknown_K[1..20]"; target_start 281; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7709 7735 4.91 + 0 target "unknown_L[1..9]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7736 7891 5.91 + 0 target "unknown_M[1..52]"; target_start 310; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7898 7975 7.02 + 0 target "unknown_N[1..26]"; target_start 364; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 7976 8101 6.5 + 0 target "unknown_O[1..42]"; target_start 390; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 8138 8188 3.73 + 0 target "unknown_Q[1..17]"; target_start 444; transcript_id "g1.t1"; gene_id "g1"; Contig82355 AUGUSTUS protein_match 8210 8329 3.89 + 0 target "unknown_R[1..40]"; target_start 468; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcaggtttcaaatccaaataatgtgaagatatacaatctaagcgctggaaagtcactaccagaatggctgtcggata # gacagaggcgctctctacagaaacaggacatcgatgtaaggagaagaatcgaactcctccaggattttgaaatgcccacagccagtcaatgtgttggg # gtatcaccagatggacaatatatctgtgccacaggaacatacaaaccaagaatcaagtgcttcgacactgcgcaaatgtcactcaaatttgaaagagg # tcttgattcggatgttgtcaagtttcaatttcttggagaagattatgggaaactagtgtttctgcagtgtgatcggtacattgaactgcattcacaat # ttggaagatattacagactcagaatcccaaaatatggaagagacatggcgtatgatttcccaagttctgacttatacatcggtggaattggatcagag # gtgtacagaatcaatttagagcaaggccggtttttgagtcccctcaccactaagtctccagacattaattgttgtgagataaacccgtcacatggcct # gctagcttgtggaacagcatcaggaacggtggagtgctttgaccctcgtgtacgcaaagcttcgggaattttagacattacatatactggtcacattg # aagaaattcatgagctaccaaaagttactgcactgaagtttcgcgatgcattaaacatggctgtaggaacgagtactggtcatatcttgctgtatgat # attcgttctagtaaaccactgctagtgaaagatcatcagtatgaactgccaatcaaatcaatccagtttcaagactcgcttaatcttgttctctctat # ggacaaaaagatccttaagttgtgggattttgagactggaaaagctttcacgtcaatcgaaccaggcacaaatcttaacgatctaagtctactgccga # attcaggacttttattcatggcaaatgaagaccagaaaatcttgtcatattacattccaaccttaggaactgctcccaagtggtgctcatttctggac # aatttgacagaggagttggaagaaagcacggctcaaattgtgtatgatgattacaaatttgtaacgaggaaagaattggaggaactgggcctgacaca # cctgattggatcgacgttactgagagcctacatgcatggctttttcatggacaacaggctatacaataaggctaaaaccattgcagaaccatttgcct # atgaagactacagaaaaagcaagattcgggagaagattgaacaggagagagctaatcgagtcagattaaagaaacttccaaaagttaatagagacttg # gcagagaagcttatggatgtgaaagaaattggaaccaacaaaaagaaagtcaaagaaacaacatctttattggaggataacagattctccgccatgtt # ctccaatcccgagttccagatcaatgtgaatagcgatgaatacaagctggtcaacccggtggtttcaaagctggacaaagtacgcagaaagaagctgg # ccaagatggagcagtttgcagaagtcagtgatgaagaggacaaaggtccaagtgacagcgatagctcagacgatgaacatacatggacaaaagaactc # aaagaacagcacaagaagctacgcaaagaagcagctcaagtcaggcatgcagagtacttggaaaagaaaaatgcaccaaaattctacgaaattaaaga # tggagaggaacttgataataagaatatgaaaggagaaaatttttggcaggacctggaattgaacttgggatcccttcactactactcgggtgctccaa # ccacttggctatccaggtcgatgtccatggtccgtatagttcaaaccactgtattcctcctcctcaatggttttcacccttag] # protein sequence = [MQVSNPNNVKIYNLSAGKSLPEWLSDRQRRSLQKQDIDVRRRIELLQDFEMPTASQCVGVSPDGQYICATGTYKPRIK # CFDTAQMSLKFERGLDSDVVKFQFLGEDYGKLVFLQCDRYIELHSQFGRYYRLRIPKYGRDMAYDFPSSDLYIGGIGSEVYRINLEQGRFLSPLTTKS # PDINCCEINPSHGLLACGTASGTVECFDPRVRKASGILDITYTGHIEEIHELPKVTALKFRDALNMAVGTSTGHILLYDIRSSKPLLVKDHQYELPIK # SIQFQDSLNLVLSMDKKILKLWDFETGKAFTSIEPGTNLNDLSLLPNSGLLFMANEDQKILSYYIPTLGTAPKWCSFLDNLTEELEESTAQIVYDDYK # FVTRKELEELGLTHLIGSTLLRAYMHGFFMDNRLYNKAKTIAEPFAYEDYRKSKIREKIEQERANRVRLKKLPKVNRDLAEKLMDVKEIGTNKKKVKE # TTSLLEDNRFSAMFSNPEFQINVNSDEYKLVNPVVSKLDKVRRKKLAKMEQFAEVSDEEDKGPSDSDSSDDEHTWTKELKEQHKKLRKEAAQVRHAEY # LEKKNAPKFYEIKDGEELDNKNMKGENFWQDLELNLGSLHYYSGAPTTWLSRSMSMVRIVQTTVFLLLNGFHP] # sequence of block unknown_A 4 [NPNNVKIYN] 13 # sequence of block unknown_B 16 [GKSLPEWLS] 25 # sequence of block unknown_C 34 [QDIDVRRRIELLQDFEMPTASQCV] 58 # sequence of block unknown_D 58 [GVSPDGQYICATGTYKPRIKCFDTAQMSLKFERGLDSDVVKFQFLGEDYGKLVFLQCDRYIELHSQFGRYYRLRIPKYGRDMAYDFPSSDLYIGGI] 154 # sequence of block unknown_E 154 [GSEVYRINLEQGRFLSPLTTK] 175 # sequence of block unknown_F 176 [PDINCCEIN] 185 # sequence of block unknown_G 185 [PSHGLLACGTA] 196 # sequence of block unknown_H 196 [SGTVECFDPRVRKASGILDI] 216 # sequence of block unknown_I 226 [ELPKVTALKFR] 237 # sequence of block unknown_J 237 [DALNMAVGTSTGHILLYDIRSSKPLLVKDHQYELPIKSIQFQDS] 281 # sequence of block unknown_K 281 [LNLVLSMDKKILKLWDFETG] 301 # sequence of block unknown_L 301 [KAFTSIEPG] 310 # sequence of block unknown_M 310 [TNLNDLSLLPNSGLLFMANEDQKILSYYIPTLGTAPKWCSFLDNLTEELEES] 362 # sequence of block unknown_N 364 [QIVYDDYKFVTRKELEELGLTHLIGS] 390 # sequence of block unknown_O 390 [TLLRAYMHGFFMDNRLYNKAKTIAEPFAYEDYRKSKIREKIE] 432 # sequence of block unknown_Q 444 [PKVNRDLAEKLMDVKEI] 461 # sequence of block unknown_R 468 [KETTSLLEDNRFSAMFSNPEFQINVNSDEYKLVNPVVSKL] 508 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705KN.prfl --predictionStart=0 --predictionEnd=28323 --species=fly ./tmp/Contig8235520180911_busco_2432604931_.temp