# 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 # --[5..117]--> unknown_A (19) <--[5..21]--> unknown_B (15) <--[6..9]--> unknown_D (52) <--[0..12]--> unknown_E (21) <--[0..5]--> unknown_F (29) <--[0..1]--> unknown_G (23) <--[0..8]--> unknown_H (14) <--[6..15]--> unknown_J (28) <--[3..15]--> unknown_K (8) <--[5..146]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig140120180911_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 = 11689, name = Contig1401) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig1401 AUGUSTUS gene 756 10317 0.01 + . g1 Contig1401 AUGUSTUS transcript 756 10317 0.01 + . g1.t1 Contig1401 AUGUSTUS tss 756 756 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 756 1005 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 1649 1715 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS start_codon 1650 1652 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 1716 2612 0.59 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 2718 3014 0.96 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 3115 3670 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 3815 4328 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 4421 6382 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 6489 8273 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 8351 9321 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 9391 9506 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS intron 9585 10214 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 1650 1715 0.59 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 2613 2717 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 2613 2717 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 3015 3114 0.96 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 3015 3114 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 3671 3814 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 3671 3814 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 4329 4420 0.03 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 4329 4420 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 6383 6488 0.02 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 6383 6488 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 8274 8350 0.98 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 8274 8350 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 9322 9390 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 9322 9390 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 9507 9584 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 9507 9584 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS CDS 10215 10310 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS exon 10215 10317 . + . transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS stop_codon 10308 10310 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 2643 2699 5.04 + 0 target "unknown_A[1..19]"; target_start 32; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 3030 3074 2.5 + 0 target "unknown_B[1..15]"; target_start 62; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 3099 3114 2.89 + 0 target "unknown_D[1..6]"; target_start 85; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 3671 3810 8.03 + 2 target "unknown_D[6..52]"; target_start 85; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 3814 3814 1 + 0 target "unknown_E[1..1]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 4329 4390 6.31 + 2 target "unknown_E[1..21]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 4403 4420 3.33 + 0 target "unknown_F[1..6]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 6383 6451 11.8 + 0 target "unknown_F[7..29]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 6455 6488 10.2 + 0 target "unknown_G[1..12]"; target_start 193; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 8274 8308 6.49 + 2 target "unknown_G[12..23]"; target_start 193; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 8309 8350 5.03 + 0 target "unknown_H[1..14]"; target_start 216; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 9343 9390 6.21 + 0 target "unknown_J[1..16]"; target_start 237; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 9507 9542 2.38 + 0 target "unknown_J[17..28]"; target_start 237; transcript_id "g1.t1"; gene_id "g1"; Contig1401 AUGUSTUS protein_match 10215 10238 6.53 + 0 target "unknown_K[1..8]"; target_start 279; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgccaccgaagaaaaacgaaccagggaaaaagacaatagaaaagaaaaaagaaaaagttatagaggataaaacctttg # gattgaaaaacaagaagggagcaaaacagcaaaggttcatccaaaatgttacgcaacaggtcaagtttggaaaccagaagaccagcaaactgtcacag # ttggaggctgacaagaataaaaagaaattggacaagaagaaagaagccgatgaactgaacactttgtttagaccagtacagactgtttcaaaaggtgc # tgaccccaagtctgttttgtgtgcgtttttcaaacaaggacagtgttcaaagggagccaagtgtaaattttctcatgacttgaatattgacagaaagg # gagagaaaatcagcatttattctgattccagggacaaagaggaaacaatggaagactgggatgaggatcagctgagagatgtcgtaaacaaaaagcat # ggagagcatgagaaatccctgccaaagaccacgattatctgtaaatatttcctggaagcggtagaatcaagtaaatatggctggttttgggaatgtcc # aaacggagggaagaaatgccattacaaacacgctctacctccaggttttgttttgaaaaaagaccaaaagaaggaggaaaaagaagaccagattacaa # tagaggagttgatagaaaaagagcgtgccgcactagggggaggtacaacaaaagttaccttagagtcattcttgaagtggaaagaaagaaagagaaaa # gaaaagattcagcaagctaaagccgcacaggataagaagaaagctgattacaaagcaggccgggcttttggaatcagtggaagagagatgttcgagtt # taatcccgatctggtgggagaagacgatgatgaggccacagaaggggtgatagaacgagacgtattctga] # protein sequence = [MPPKKNEPGKKTIEKKKEKVIEDKTFGLKNKKGAKQQRFIQNVTQQVKFGNQKTSKLSQLEADKNKKKLDKKKEADEL # NTLFRPVQTVSKGADPKSVLCAFFKQGQCSKGAKCKFSHDLNIDRKGEKISIYSDSRDKEETMEDWDEDQLRDVVNKKHGEHEKSLPKTTIICKYFLE # AVESSKYGWFWECPNGGKKCHYKHALPPGFVLKKDQKKEEKEDQITIEELIEKERAALGGGTTKVTLESFLKWKERKRKEKIQQAKAAQDKKKADYKA # GRAFGISGREMFEFNPDLVGEDDDEATEGVIERDVF] # sequence of block unknown_A 32 [GAKQQRFIQNVTQQVKFGN] 51 # sequence of block unknown_B 62 [DKNKKKLDKKKEADE] 77 # sequence of block unknown_D 85 [QTVSKGADPKSVLCAFFKQGQCSKGAKCKFSHDLNIDRKGEKISIYSDSRDK] 137 # sequence of block unknown_E 138 [ETMEDWDEDQLRDVVNKKHGE] 159 # sequence of block unknown_F 163 [LPKTTIICKYFLEAVESSKYGWFWECPNG] 192 # sequence of block unknown_G 193 [KKCHYKHALPPGFVLKKDQKKEE] 216 # sequence of block unknown_H 216 [KEDQITIEELIEKE] 230 # sequence of block unknown_J 237 [TTKVTLESFLKWKERKRKEKIQQAKAAQ] 265 # sequence of block unknown_K 279 [ISGREMFE] 287 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RJN.prfl --predictionStart=0 --predictionEnd=26490 --species=fly ./tmp/Contig140120180911_busco_2432604931_.temp