# 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..166]--> unknown_A (17) <--[5..17]--> unknown_B (37) <--[0..78]--> unknown_C (21) <--[8..77]--> unknown_E (10) <--[0..3]--> unknown_F (17) <--[10..22]--> unknown_H (19) <--[41..144]--> unknown_M (12) <--[17..25]--> unknown_O (13) <--[4..36]--> unknown_P (9) <--[0..240]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig1712620180911_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 = 2958, name = Contig17126) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig17126 AUGUSTUS gene 1 2785 0.01 - . g1 Contig17126 AUGUSTUS transcript 1 2785 0.01 - . g1.t1 Contig17126 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 1 25 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS stop_codon 4 6 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 26 388 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 451 573 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 656 810 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 915 994 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 1118 1537 0.07 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 1650 1924 0.08 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 2020 2120 0.07 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS intron 2277 2635 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 4 25 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 389 450 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 389 450 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 574 655 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 574 655 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 811 914 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 811 914 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 995 1117 0.05 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 995 1117 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 1538 1649 0.11 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 1538 1649 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 1925 2019 0.07 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 1925 2019 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 2121 2276 0.07 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 2121 2276 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS CDS 2636 2746 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS exon 2636 2785 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS start_codon 2744 2746 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS tss 2785 2785 . - . transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 10 25 0.882 - 1 target "unknown_P[4..9]"; target_start 278; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 389 399 0.751 - 0 target "unknown_P[1..4]"; target_start 278; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 415 450 1.47 - 0 target "unknown_O[2..13]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 574 576 0.167 - 0 target "unknown_O[1..1]"; target_start 260; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 640 655 0.914 - 1 target "unknown_M[7..12]"; target_start 227; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 811 830 1.42 - 0 target "unknown_M[1..7]"; target_start 227; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1079 1117 5.16 - 0 target "unknown_H[7..19]"; target_start 152; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1538 1555 7.26 - 0 target "unknown_H[1..6]"; target_start 152; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1592 1642 4.02 - 0 target "unknown_F[1..17]"; target_start 123; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1643 1649 5.49 - 1 target "unknown_E[8..10]"; target_start 113; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1925 1947 4.99 - 0 target "unknown_E[1..8]"; target_start 113; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 1990 2019 4.69 - 0 target "unknown_C[12..21]"; target_start 78; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 2121 2153 3.87 - 0 target "unknown_C[1..11]"; target_start 78; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 2157 2267 3.23 - 0 target "unknown_B[1..37]"; target_start 40; transcript_id "g1.t1"; gene_id "g1"; Contig17126 AUGUSTUS protein_match 2654 2704 3.11 - 0 target "unknown_A[1..17]"; target_start 14; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtccctatcaacacagcgagacgatagtgaaagtcattatgtattacttgccaagctagacaacgcaaggaatgttt # ctaacatactgaaagcgatccatttcaaagagacagctacactctttgcaagctctcttgggatcaaggtgactgttgaggattcaaaatgtgtacag # gccaatgcattcatccaggaaggagtgttccatcacttcagtgttaaagatgaacagatcacattcaaaatcaatcttacagtccttttggaatgttt # gacgatatttgggaacacttctgtaccgggtattacaaccagtttgaaaatgtgttacgctggctatggatgtccacttgttctggttcttgaggaag # atggtgtgctgacagactgtacaataaagacgttagaaccagatgaagttttggacttcaacttttgtagtacgaatgtcatcaacaaaatcatcatg # aaatcggagtgtttaaaggaagccttcagtgaactagacatgaccagtgatgtcttacagattttaatgtcaccggatcagccttattttagactgtc # cacttttggtaatgctggcagcacacatctgatatttctggtacctaaatcactttattcgaaaatacacagagatcaaacaacaatttcacttcttt # cttcttcttttttttttcgtaaacaatattcattttctgtctttatttcagtccgactttccaaaagactcggatatggtcgagtcctttgtatgcac # acagacacaaacaaacaggtgttgtactgtaaaattgtgatgcccaccctcactttgttttgttgtaaatatatttaccagttttctactgtaaaagt # gtga] # protein sequence = [MSLSTQRDDSESHYVLLAKLDNARNVSNILKAIHFKETATLFASSLGIKVTVEDSKCVQANAFIQEGVFHHFSVKDEQ # ITFKINLTVLLECLTIFGNTSVPGITTSLKMCYAGYGCPLVLVLEEDGVLTDCTIKTLEPDEVLDFNFCSTNVINKIIMKSECLKEAFSELDMTSDVL # QILMSPDQPYFRLSTFGNAGSTHLIFLVPKSLYSKIHRDQTTISLLSSSFFFRKQYSFSVFISVRLSKRLGYGRVLCMHTDTNKQVLYCKIVMPTLTL # FCCKYIYQFSTVKV] # sequence of block unknown_P 278 [YIYQFSTVK] 287 # sequence of block unknown_O 260 [QVLYCKIVMPTLT] 273 # sequence of block unknown_M 227 [FRKQYSFSVFIS] 239 # sequence of block unknown_H 152 [NKIIMKSECLKEAFSELDM] 171 # sequence of block unknown_F 123 [EDGVLTDCTIKTLEPDE] 140 # sequence of block unknown_E 113 [YGCPLVLVLE] 123 # sequence of block unknown_C 78 [ITFKINLTVLLECLTIFGNTS] 99 # sequence of block unknown_B 40 [LFASSLGIKVTVEDSKCVQANAFIQEGVFHHFSVKDE] 77 # sequence of block unknown_A 14 [VLLAKLDNARNVSNILK] 31 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370F3T.prfl --predictionStart=0 --predictionEnd=22279 --species=fly ./tmp/Contig1712620180911_busco_2432604931_.temp