# 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..240]--> unknown_A (27) <--[0..5]--> unknown_B (24) <--[0..15]--> unknown_C (11) <--[1..1]--> unknown_D (10) <--[1..13]--> unknown_E (39) <--[1..3]--> unknown_F (24) <--[0..14]--> unknown_G (10) <--[7..54]--> unknown_H (28) <--[0..1]--> unknown_I (19) <--[2..28]--> unknown_J (23) <--[23..811]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2074420180911_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 = 16271, name = Contig20744) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig20744 AUGUSTUS gene 1796 16248 0.01 + . g1 Contig20744 AUGUSTUS transcript 1796 16248 0.01 + . g1.t1 Contig20744 AUGUSTUS tss 1796 1796 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 1796 1828 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 5860 6141 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS start_codon 6059 6061 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6142 6242 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6368 6413 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6451 6569 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6581 6641 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6673 6778 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 6882 7136 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 7260 9002 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 9156 12256 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 12367 14218 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS intron 14293 15887 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6059 6141 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6243 6367 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 6243 6367 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6414 6450 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 6414 6450 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6570 6580 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 6570 6580 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6642 6672 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 6642 6672 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 6779 6881 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 6779 6881 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 7137 7259 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 7137 7259 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 9003 9155 0.18 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 9003 9155 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 12257 12366 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 12257 12366 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 14219 14292 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 14219 14292 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS CDS 15888 15937 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS exon 15888 16248 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS stop_codon 15935 15937 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS tts 16248 16248 . + . transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6095 6141 3.15 + 0 target "unknown_A[1..16]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6243 6276 8.47 + 1 target "unknown_A[16..27]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6280 6351 7.34 + 0 target "unknown_B[1..24]"; target_start 40; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6364 6367 0.192 + 0 target "unknown_C[1..2]"; target_start 68; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6414 6442 1.07 + 2 target "unknown_C[2..11]"; target_start 68; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6446 6450 0.135 + 0 target "unknown_D[1..2]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6570 6580 4.3 + 0 target "unknown_D[3..6]"; target_start 79; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6642 6655 1.09 + 2 target "unknown_D[6..10]"; target_start 80; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 6789 6881 4.4 + 0 target "unknown_E[1..31]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 7137 7160 5.8 + 0 target "unknown_E[32..39]"; target_start 99; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 7167 7238 7.81 + 0 target "unknown_F[1..24]"; target_start 140; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 9006 9035 6.57 + 0 target "unknown_G[1..10]"; target_start 172; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 9057 9140 3.94 + 0 target "unknown_H[1..28]"; target_start 189; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 9144 9155 7.25 + 0 target "unknown_I[1..4]"; target_start 218; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 12257 12301 3.56 + 0 target "unknown_I[5..19]"; target_start 218; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 12332 12366 8.09 + 0 target "unknown_J[1..12]"; target_start 247; transcript_id "g1.t1"; gene_id "g1"; Contig20744 AUGUSTUS protein_match 14219 14252 4.05 + 1 target "unknown_J[12..23]"; target_start 247; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggatgtaaaacaagagaccgccagtggcgcacaagctctgggactgactatcccaacatatgtcctggacgatttat # gcagtcgatttatcattaacatcccagatgaagaaagacaagatctgatccgagtgttctttcaaatagaactggctcattggttttatttagacttc # tattgtgccgaaaacccagagcttagaacatgtaatttgctattgttaatttttagtttgttacaaattttacattgtgatattctatatacagataa # aaacgcgttgcttggacatgcgggagaagtggataaaattttggacaactggaaagcgtacaaaatgagtgtacctacgtacggtgcaatcctgctgg # acccggagatgaaatattgtttgcttgctcagggattttggactaagagcagttggggatttccaaagggcaaagtcaatgagaacgagattgcacat # gattgtgccattagagaggtattgtcagagtacttttatatggtttatgaagagacaggatttgacattacatcgctgatagacaagaatgagtttat # agaaaactactttaatgaccagctatccagactctatatcatcacgggggtggggctggagaccaaatttcaaccaaagaccaggaaagaaatcaaga # gtcttcagtggtttcccgtggatgccttgcctgcccaccgaagggaccaaacgccaaaatccctggacatgaatcccaacaacttctttatggtcatc # ccattcatcaaaccacttaggaaatggatttccaaaaagtcaggacagacttataacatagaatttgaatttgatatcaagggagtcgaatctcgtta # tctcaagctggatgggaacaaaaaaaatttgaggtag] # protein sequence = [MDVKQETASGAQALGLTIPTYVLDDLCSRFIINIPDEERQDLIRVFFQIELAHWFYLDFYCAENPELRTCNLLLLIFS # LLQILHCDILYTDKNALLGHAGEVDKILDNWKAYKMSVPTYGAILLDPEMKYCLLAQGFWTKSSWGFPKGKVNENEIAHDCAIREVLSEYFYMVYEET # GFDITSLIDKNEFIENYFNDQLSRLYIITGVGLETKFQPKTRKEIKSLQWFPVDALPAHRRDQTPKSLDMNPNNFFMVIPFIKPLRKWISKKSGQTYN # IEFEFDIKGVESRYLKLDGNKKNLR] # sequence of block unknown_A 12 [ALGLTIPTYVLDDLCSRFIINIPDEER] 39 # sequence of block unknown_B 40 [DLIRVFFQIELAHWFYLDFYCAEN] 64 # sequence of block unknown_C 68 [TCNLLLLIFSL] 79 # sequence of block unknown_D 80 [QILHCDILYT] 90 # sequence of block unknown_E 99 [GEVDKILDNWKAYKMSVPTYGAILLDPEMKYCLLAQGFW] 138 # sequence of block unknown_F 140 [SSWGFPKGKVNENEIAHDCAIREV] 164 # sequence of block unknown_G 172 [YEETGFDITS] 182 # sequence of block unknown_H 189 [IENYFNDQLSRLYIITGVGLETKFQPKT] 217 # sequence of block unknown_I 218 [KEIKSLQWFPVDALPAHRR] 237 # sequence of block unknown_J 247 [PNNFFMVIPFIKPLRKWISKKSG] 270 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705U4.prfl --predictionStart=0 --predictionEnd=29155 --species=fly ./tmp/Contig2074420180911_busco_2432604931_.temp