# 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..153]--> unknown_A (22) <--[3..5]--> unknown_B (25) <--[0..2]--> unknown_C (16) <--[4..14]--> unknown_D (15) <--[0..2]--> unknown_E (63) <--[0..3]--> unknown_F (28) <--[5..8]--> unknown_G (12) <--[0..2]--> unknown_H (15) <--[1..7]--> unknown_I (10) <--[0..1]--> unknown_J (74) <--[0..1]--> unknown_K (10) <--[1..9]--> unknown_L (7) <--[0..14]--> unknown_M (19) <--[0..1]--> unknown_N (24) <--[0..8]--> unknown_O (12) <--[14..49]--> unknown_Q (18) <--[26..61]--> unknown_U (16) <--[0..119]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig4978220180911_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 = 30356, name = Contig49782) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig49782 AUGUSTUS gene 4826 28529 0.01 + . g1 Contig49782 AUGUSTUS transcript 4826 28529 0.01 + . g1.t1 Contig49782 AUGUSTUS tss 4826 4826 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 4826 5004 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 5167 5470 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS start_codon 5462 5464 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 5471 12656 0.35 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 12770 13848 0.51 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 14080 14778 0.02 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 14828 14969 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 15065 15220 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 15345 16765 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 16946 17265 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 17428 18543 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 18703 20769 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 20779 20934 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 20946 21036 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 21056 21393 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 21410 22033 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 22069 22197 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 22211 22341 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 22412 22485 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 22503 23555 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 23583 25397 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 25426 26929 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 26958 27241 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 27289 27347 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 27438 27752 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 27809 27975 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS intron 28064 28372 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 5462 5470 0.35 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 12657 12769 0.53 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 12657 12769 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 13849 14079 0.17 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 13849 14079 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 14779 14827 0.02 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 14779 14827 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 14970 15064 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 14970 15064 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 15221 15344 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 15221 15344 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 16766 16945 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 16766 16945 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 17266 17427 0.05 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 17266 17427 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 18544 18702 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 18544 18702 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 20770 20778 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 20770 20778 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 20935 20945 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 20935 20945 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 21037 21055 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 21037 21055 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 21394 21409 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 21394 21409 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 22034 22068 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 22034 22068 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 22198 22210 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 22198 22210 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 22342 22411 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 22342 22411 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 22486 22502 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 22486 22502 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 23556 23582 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 23556 23582 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 25398 25425 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 25398 25425 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 26930 26957 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 26930 26957 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 27242 27288 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 27242 27288 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 27348 27437 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 27348 27437 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 27753 27808 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 27753 27808 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 27976 28063 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 27976 28063 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS CDS 28373 28439 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS exon 28373 28529 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS stop_codon 28437 28439 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS tts 28529 28529 . + . transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 14006 14071 5.44 + 0 target "unknown_A[1..22]"; target_start 93; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 14783 14827 8.34 + 0 target "unknown_B[1..15]"; target_start 119; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 14970 14999 4.72 + 0 target "unknown_B[16..25]"; target_start 119; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 15006 15053 7 + 0 target "unknown_C[1..16]"; target_start 146; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 15234 15278 5.25 + 0 target "unknown_D[1..15]"; target_start 170; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 15279 15344 11.7 + 0 target "unknown_E[1..22]"; target_start 185; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 16766 16888 7.55 + 0 target "unknown_E[23..63]"; target_start 185; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 16889 16945 8.33 + 0 target "unknown_F[1..19]"; target_start 248; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 17266 17292 1.53 + 0 target "unknown_F[20..28]"; target_start 248; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 17308 17343 2.62 + 0 target "unknown_G[1..12]"; target_start 281; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 17344 17388 5.81 + 0 target "unknown_H[1..15]"; target_start 293; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 17392 17421 4.97 + 0 target "unknown_I[1..10]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 17425 17427 3.35 + 0 target "unknown_J[1..1]"; target_start 320; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 18544 18702 4.36 + 2 target "unknown_J[2..55]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 20770 20778 0.299 + 2 target "unknown_J[55..58]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 20935 20945 1.22 + 2 target "unknown_J[58..61]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 21037 21055 1.42 + 0 target "unknown_J[62..68]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 21394 21409 1.82 + 2 target "unknown_J[68..73]"; target_start 319; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22034 22038 2.13 + 2 target "unknown_J[73..74]"; target_start 320; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22042 22068 1.29 + 0 target "unknown_K[1..9]"; target_start 395; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22198 22200 0.228 + 0 target "unknown_K[10..10]"; target_start 395; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22359 22379 2.37 + 0 target "unknown_L[1..7]"; target_start 414; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22392 22411 1.33 + 0 target "unknown_M[1..7]"; target_start 425; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 22486 22502 1.45 + 0 target "unknown_M[8..13]"; target_start 424; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 23556 23575 1 + 2 target "unknown_M[13..19]"; target_start 425; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 23576 23582 0.681 + 0 target "unknown_N[1..3]"; target_start 444; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 25398 25425 1.95 + 1 target "unknown_N[3..12]"; target_start 443; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 26930 26957 1.25 + 0 target "unknown_N[13..22]"; target_start 443; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 27242 27250 1.6 + 0 target "unknown_N[22..24]"; target_start 444; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 27257 27288 1.31 + 0 target "unknown_O[1..11]"; target_start 470; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 27348 27351 0.18 + 1 target "unknown_O[11..12]"; target_start 470; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 27409 27437 1.09 + 0 target "unknown_Q[1..10]"; target_start 501; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 27753 27777 1.19 + 1 target "unknown_Q[10..18]"; target_start 501; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 28038 28063 1.13 + 0 target "unknown_U[1..9]"; target_start 550; transcript_id "g1.t1"; gene_id "g1"; Contig49782 AUGUSTUS protein_match 28373 28394 1.31 + 1 target "unknown_U[9..16]"; target_start 550; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtacgaggtgcagaaggagtttggtttgggcgacactggttggaatgtctacaaatcacgagataaaaaagattgga # tcagaacttccagagctaaaactcttgaaacttacaaagtcaagcatggggacatgttgtttctgctatcatcagaccgtaaacagagcaacgctagt # gtggacagtatgagcagtgggtctggtacctctaatatcacaggcgatatgggatctgtcagtatatcaggctcctcaatgtcctcaggctcctcaaa # ctctgttgttgaggatgaggtggatcagatcctgtataaagaagatggcaaaatctacagggagaggaatgaacaactttgtcgtcatggacctcaag # gcaaatgtctgcactgtgttcccctagagccatatgatgaagaatttttgaaaagctgtgaccctccaataaaatttctatcatttcattcacacatc # agaaaactgactggcggtgttgataaaggaaaatttgtttccttggagaatttaagttgtaagattaaaccagggtgtactgagcatcccccatggcc # aggaggcatctgtaccaagtgtcagccaaacgcagtcacactcaatagacagagatacagacatgtagactatgtgatgtttgaaaatgcttcaatag # tcgacagatttttgaactattggcgaagaacaggaaatcagagattaggaattatgtatggtcgatatgaacctcacaaagacacaccgctaggaatc # aaggccacagtagctgctatttatgaacctccacaaaaaagtcacaaaaacgttctccagctgttggcggaccccgcagaagagctggtaaaccgagt # ggccgactctcttggtattcgcccagtgggatggatatttacagatctactggccgaagatcttagcaaaggcagtgtaaagcacttcagaggaaata # ttaattctcattttctaagtgcccaggagtgcatcatggctgctgatttccaaaacaaatacaccaatccctgtaaattgtcttcagatggacatttt # ggatccaagtttgttactgttgtagttacaggtatttccactaattcatatgcaaataaacattatggcttgaacgagatttctttgtctttggttga # acttgtggtaattctcgcagatgcgttttttatcacatgtatgttcattaatgagattcactttgagggaggttcttttacaggaaacaacaatatgg # ttcccgattgtattttacaagtattgttgtccaaagtcccaatgtatgtaattgaagttgttcaactgcttccaccgctctttagtgtgaccctaatt # gtaactatgactattggcacaccacaacttgaatcatatcatttcattaggaacttacccaaaagatcaccctacaatagacagcacaatacaagctc # aagacaagatataatttatttccagaaatacgtgcaattagtagctcatagaattgtgcaattgtggttgtgctggattattgtttttagctatatta # agttcattttaaataaatatcatttgctatttttgaagacgttctactttgcatctcggaatttcgtggaaaagatcaccgtggcaggacgccacaaa # cagaagacactcttttatcagcacctactcgccattttaactgtctcgtgcaaaagcgtagttgcggtctcgattctcgtagttttaaaatattga] # protein sequence = [MYEVQKEFGLGDTGWNVYKSRDKKDWIRTSRAKTLETYKVKHGDMLFLLSSDRKQSNASVDSMSSGSGTSNITGDMGS # VSISGSSMSSGSSNSVVEDEVDQILYKEDGKIYRERNEQLCRHGPQGKCLHCVPLEPYDEEFLKSCDPPIKFLSFHSHIRKLTGGVDKGKFVSLENLS # CKIKPGCTEHPPWPGGICTKCQPNAVTLNRQRYRHVDYVMFENASIVDRFLNYWRRTGNQRLGIMYGRYEPHKDTPLGIKATVAAIYEPPQKSHKNVL # QLLADPAEELVNRVADSLGIRPVGWIFTDLLAEDLSKGSVKHFRGNINSHFLSAQECIMAADFQNKYTNPCKLSSDGHFGSKFVTVVVTGISTNSYAN # KHYGLNEISLSLVELVVILADAFFITCMFINEIHFEGGSFTGNNNMVPDCILQVLLSKVPMYVIEVVQLLPPLFSVTLIVTMTIGTPQLESYHFIRNL # PKRSPYNRQHNTSSRQDIIYFQKYVQLVAHRIVQLWLCWIIVFSYIKFILNKYHLLFLKTFYFASRNFVEKITVAGRHKQKTLFYQHLLAILTVSCKS # VVAVSILVVLKY] # sequence of block unknown_A 93 [VVEDEVDQILYKEDGKIYRERN] 115 # sequence of block unknown_B 119 [RHGPQGKCLHCVPLEPYDEEFLKSC] 144 # sequence of block unknown_C 146 [PIKFLSFHSHIRKLTG] 162 # sequence of block unknown_D 170 [SLENLSCKIKPGCTE] 185 # sequence of block unknown_E 185 [HPPWPGGICTKCQPNAVTLNRQRYRHVDYVMFENASIVDRFLNYWRRTGNQRLGIMYGRYEPH] 248 # sequence of block unknown_F 248 [KDTPLGIKATVAAIYEPPQKSHKNVLQL] 276 # sequence of block unknown_G 281 [EELVNRVADSLG] 293 # sequence of block unknown_H 293 [IRPVGWIFTDLLAED] 308 # sequence of block unknown_I 309 [SKGSVKHFRG] 319 # sequence of block unknown_J 320 [INSHFLSAQECIMAADFQNKYTNPCKLSSDGHFGSKFVTVVVTGISTNSYANKHYGLNEISLSLVELVVILADA] 394 # sequence of block unknown_K 395 [FITCMFINEI] 405 # sequence of block unknown_L 414 [NNNMVPD] 421 # sequence of block unknown_M 425 [VLLSKVPMYVIEVVQLLPP] 444 # sequence of block unknown_N 444 [LFSVTLIVTMTIGTPQLESYHFIR] 468 # sequence of block unknown_O 470 [PKRSPYNRQHNT] 482 # sequence of block unknown_Q 501 [IVQLWLCWIIVFSYIKFI] 519 # sequence of block unknown_U 550 [KTLFYQHLLAILTVSC] 566 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370HKV.prfl --predictionStart=0 --predictionEnd=38672 --species=fly ./tmp/Contig4978220180911_busco_2432604931_.temp