# 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..234]--> unknown_A (43) <--[0..1]--> unknown_B (18) <--[0..3]--> unknown_C (8) <--[2..11]--> unknown_D (25) <--[0..8]--> unknown_E (33) <--[3..13]--> unknown_F (19) <--[0..65]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig5563320180911_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 = 9981, name = Contig55633) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig55633 AUGUSTUS gene 2591 9913 0.01 - . g1 Contig55633 AUGUSTUS transcript 2591 9913 0.01 - . g1.t1 Contig55633 AUGUSTUS stop_codon 2591 2593 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 2652 3708 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 3923 6176 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 6198 6502 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 6630 6950 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 6962 7629 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 7642 8196 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 8211 9465 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 9495 9612 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS intron 9622 9730 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 2591 2651 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 3709 3922 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 6177 6197 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 6503 6629 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 6951 6961 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 7630 7641 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 8197 8210 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 9466 9494 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 9613 9621 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS CDS 9731 9913 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS start_codon 9911 9913 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 2624 2651 1.29 - 1 target "unknown_F[10..19]"; target_start 197; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 3709 3737 1.6 - 0 target "unknown_F[1..10]"; target_start 197; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 3768 3866 5.44 - 0 target "unknown_E[1..33]"; target_start 154; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 3867 3922 4.02 - 2 target "unknown_D[7..25]"; target_start 129; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 6177 6195 1.2 - 0 target "unknown_D[1..7]"; target_start 129; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 6519 6542 2.53 - 0 target "unknown_C[1..8]"; target_start 115; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 6552 6605 2.14 - 0 target "unknown_B[1..18]"; target_start 94; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 6609 6629 7.56 - 0 target "unknown_A[37..43]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 6951 6961 2.95 - 2 target "unknown_A[33..36]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 7630 7641 0.963 - 2 target "unknown_A[29..33]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 8197 8210 0.831 - 1 target "unknown_A[24..29]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 9466 9494 1.78 - 0 target "unknown_A[15..24]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 9613 9621 0.875 - 0 target "unknown_A[12..14]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; Contig55633 AUGUSTUS protein_match 9731 9763 1.22 - 0 target "unknown_A[1..11]"; target_start 50; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgattttagactcatccgaaaatataactatattccaggaattttctaccgtcagtcatctcttttccctgcaccaag # acaaccttttcttcttcttggcttccatcacaaccactttcttcgtagacacacgcccctcaagttcttgcaaaaaccctaacctttccaacgaggcc # aaacagagacgaagcactccaaactattttttcaacatcgcctgtaattctggatgttggtcacgtggaggaaaaagcacagttggagcatgtattat # caacgctgagaatcgaattgttgcaacaggatataacggcttcgttgaactcgatgggatgaaaaacgacgaaatattttcgtgggcaagagaaaaaa # aacatccatatggatctttaaaggtatactttttctgccatgcagaaatgaatgcagtggtgaacagacatggtaccagtttaaagggctgcacagtg # tacgtcactctgtttccctgcaatgaatgcgcgaagcttctgatgcaatcaggaatcaaggaagtgatctactatgctgatgataaagctgagaaaaa # agaatttaaaatttcccgagagatgatggctcagaaaaatattacattgactaaacatcccagtcagcatgcacatgttggcccaacgttaccgccaa # caaagttcgtttag] # protein sequence = [MILDSSENITIFQEFSTVSHLFSLHQDNLFFFLASITTTFFVDTRPSSSCKNPNLSNEAKQRRSTPNYFFNIACNSGC # WSRGGKSTVGACIINAENRIVATGYNGFVELDGMKNDEIFSWAREKKHPYGSLKVYFFCHAEMNAVVNRHGTSLKGCTVYVTLFPCNECAKLLMQSGI # KEVIYYADDKAEKKEFKISREMMAQKNITLTKHPSQHAHVGPTLPPTKFV] # sequence of block unknown_F 197 [MMAQKNITLTKHPSQHAHV] 216 # sequence of block unknown_E 154 [CTVYVTLFPCNECAKLLMQSGIKEVIYYADDKA] 187 # sequence of block unknown_D 129 [SLKVYFFCHAEMNAVVNRHGTSLKG] 154 # sequence of block unknown_C 115 [EIFSWARE] 123 # sequence of block unknown_B 94 [ENRIVATGYNGFVELDGM] 112 # sequence of block unknown_A 50 [KNPNLSNEAKQRRSTPNYFFNIACNSGCWSRGGKSTVGACIIN] 93 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KGV.prfl --predictionStart=0 --predictionEnd=23923 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5563320180911_busco_2432604931_.temp