# 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..312]--> unknown_A (17) <--[3..95]--> unknown_B (19) <--[1..8]--> unknown_C (13) <--[2..36]--> unknown_D (55) <--[0..1]--> unknown_E (59) <--[9..71]--> unknown_G (17) <--[0..1]--> unknown_H (13) <--[14..51]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig389320180911_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 = 10344, name = Contig3893) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig3893 AUGUSTUS gene 4438 10035 0.01 - . g1 Contig3893 AUGUSTUS transcript 4438 10035 0.01 - . g1.t1 Contig3893 AUGUSTUS tts 4438 4438 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 4438 4778 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS stop_codon 4731 4733 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 4779 4832 0.53 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 4981 5597 0.95 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 5759 5883 0.95 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 5974 6340 0.86 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 6465 7190 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 7343 9614 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS intron 9699 9850 0.03 - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 4731 4778 0.49 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 4833 4980 1 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 4833 4980 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 5598 5758 0.94 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 5598 5758 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 5884 5973 0.86 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 5884 5973 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 6341 6464 0.06 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 6341 6464 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 7191 7342 0.03 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 7191 7342 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 9615 9698 0.03 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 9615 9698 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS CDS 9851 9904 0.03 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS exon 9851 10035 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS start_codon 9902 9904 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS tss 10035 10035 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 4881 4919 3.09 - 0 target "unknown_H[1..13]"; target_start 242; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 4923 4973 6.18 - 0 target "unknown_G[1..17]"; target_start 224; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 5675 5758 5.79 - 0 target "unknown_E[32..59]"; target_start 137; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 5884 5973 5.37 - 0 target "unknown_E[2..31]"; target_start 137; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 6341 6343 2.32 - 0 target "unknown_E[1..1]"; target_start 137; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 6344 6464 5.66 - 1 target "unknown_D[15..55]"; target_start 82; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 7191 7234 3.9 - 0 target "unknown_D[1..15]"; target_start 82; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 7268 7306 5.37 - 0 target "unknown_C[1..13]"; target_start 58; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 7310 7342 2.53 - 0 target "unknown_B[9..19]"; target_start 38; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 9615 9638 2.59 - 0 target "unknown_B[1..8]"; target_start 38; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 9690 9698 4.73 - 0 target "unknown_A[15..17]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; Contig3893 AUGUSTUS protein_match 9851 9892 1.98 - 0 target "unknown_A[1..14]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggaatcagatgaatcgttttctggagtggaaagttccgattcagatgaagagttacaagaggcatttgctgctggaa # agttgaaaccagggttgaatcttgaattaccagcatcatcaaagactataaatgacacagcaggcttgaaacaaaagttttcggcactcaagaaagat # ctgccatgggtggaacgtttagatgtgaccagtaaacctgcagcgacccacaaagacctcattagtcagggtgaaacagacgtccatgatgacttcaa # acgagaactacgattctattgtcaagcacaggcgactgttctggaagccataccaaggctccacagtatgaagttacctaccaagagaccggaggact # actttgcacagatggctaaatcggatgaccacatgaaacgtgtaagggagaagttgttggaaaagcaaacagccatggacagatccgaaaaagctaag # aaattgcgagaacttcgaaaatatggtaaaaaggtccaagttgaagttcttcagaaacgacagaaggaaaagaaggacatgctggatgctgtgaaaaa # gtatcgcaagggacagaaagacaaactggatttcttagaagatctgccaggggagccaaaaggcaaacgaaacaagaataacacagataaactcagac # caaataaaaagagagaatttaaaaacaagaaatttggatttggaggacagaagaaaagatccaaactgaatacaaagaacagttctgtagatatgtct # agcttcaaccccaaaataaaccagaagaaaccgggaaaacccaaaccatttaaaacttatatttttatagatgtaaccacccatggtacaatgtga] # protein sequence = [MESDESFSGVESSDSDEELQEAFAAGKLKPGLNLELPASSKTINDTAGLKQKFSALKKDLPWVERLDVTSKPAATHKD # LISQGETDVHDDFKRELRFYCQAQATVLEAIPRLHSMKLPTKRPEDYFAQMAKSDDHMKRVREKLLEKQTAMDRSEKAKKLRELRKYGKKVQVEVLQK # RQKEKKDMLDAVKKYRKGQKDKLDFLEDLPGEPKGKRNKNNTDKLRPNKKREFKNKKFGFGGQKKRSKLNTKNSSVDMSSFNPKINQKKPGKPKPFKT # YIFIDVTTHGTM] # sequence of block unknown_H 242 [SKLNTKNSSVDMS] 255 # sequence of block unknown_G 224 [KKREFKNKKFGFGGQKK] 241 # sequence of block unknown_E 137 [RVREKLLEKQTAMDRSEKAKKLRELRKYGKKVQVEVLQKRQKEKKDMLDAVKKYRKGQK] 196 # sequence of block unknown_D 82 [GETDVHDDFKRELRFYCQAQATVLEAIPRLHSMKLPTKRPEDYFAQMAKSDDHMK] 137 # sequence of block unknown_C 58 [DLPWVERLDVTSK] 71 # sequence of block unknown_B 38 [SSKTINDTAGLKQKFSALK] 57 # sequence of block unknown_A 4 [ESFSGVESSDSDEELQE] 21 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OGU.prfl --predictionStart=0 --predictionEnd=26406 --species=fly ./tmp/Contig389320180911_busco_2432604931_.temp