# 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..219]--> unknown_A (15) <--[0..4]--> unknown_B (9) <--[0..1]--> unknown_C (48) <--[0..2]--> unknown_D (15) <--[1..7]--> unknown_E (20) <--[13..26]--> unknown_F (19) <--[1..9]--> unknown_G (15) <--[2..15]--> unknown_H (22) <--[10..22]--> unknown_I (47) <--[0..9]--> unknown_J (14) <--[1..7]--> unknown_K (10) <--[1..4]--> unknown_L (8) <--[6..13]--> unknown_M (15) <--[1..2]--> unknown_N (11) <--[2..4]--> unknown_O (30) <--[0..88]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig6540320180911_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 = 13590, name = Contig65403) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig65403 AUGUSTUS gene 1 13498 0.01 - . g1 Contig65403 AUGUSTUS transcript 1 13498 0.01 - . g1.t1 Contig65403 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 1 697 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS stop_codon 668 670 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 698 3018 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 3031 3610 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 3639 3896 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 3910 4237 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 4276 4712 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 4734 4782 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 4808 5987 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 5998 8015 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 8072 8269 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 8283 8642 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 8690 9605 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 9633 10735 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 10956 11239 0.57 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 11427 12681 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS intron 12744 13120 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 668 697 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 3019 3030 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 3019 3030 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 3611 3638 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 3611 3638 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 3897 3909 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 3897 3909 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 4238 4275 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 4238 4275 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 4713 4733 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 4713 4733 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 4783 4807 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 4783 4807 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 5988 5997 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 5988 5997 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 8016 8071 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 8016 8071 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 8270 8282 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 8270 8282 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 8643 8689 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 8643 8689 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 9606 9632 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 9606 9632 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 10736 10955 0.02 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 10736 10955 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 11240 11426 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 11240 11426 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 12682 12743 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 12682 12743 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS CDS 13121 13447 0.03 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS exon 13121 13498 . - . transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS start_codon 13445 13447 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 677 697 1.49 - 0 target "unknown_O[24..30]"; target_start 339; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 3019 3030 3.23 - 0 target "unknown_O[20..23]"; target_start 339; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 3611 3638 1.28 - 1 target "unknown_O[10..19]"; target_start 339; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 3897 3909 0.79 - 2 target "unknown_O[6..10]"; target_start 339; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 4238 4253 0.894 - 0 target "unknown_O[1..6]"; target_start 339; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 4260 4275 0.905 - 1 target "unknown_N[6..11]"; target_start 326; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 4713 4729 2.21 - 0 target "unknown_N[1..6]"; target_start 326; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 4785 4807 2.03 - 2 target "unknown_M[8..15]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 5988 5997 0.927 - 0 target "unknown_M[5..8]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 8016 8027 1.18 - 0 target "unknown_M[1..4]"; target_start 309; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 8061 8071 3.39 - 2 target "unknown_L[5..8]"; target_start 290; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 8270 8282 1.37 - 0 target "unknown_L[1..5]"; target_start 290; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 8649 8678 3.42 - 0 target "unknown_K[1..10]"; target_start 278; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 8682 8689 2.28 - 2 target "unknown_J[12..14]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 9606 9632 1.62 - 2 target "unknown_J[3..12]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 10736 10742 0.145 - 0 target "unknown_J[1..3]"; target_start 263; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 10755 10895 6.26 - 0 target "unknown_I[1..47]"; target_start 212; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 10938 10955 4.21 - 0 target "unknown_H[17..22]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 11240 11287 10.4 - 0 target "unknown_H[1..16]"; target_start 176; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 11300 11344 3.52 - 0 target "unknown_G[1..15]"; target_start 157; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 11351 11407 2.01 - 0 target "unknown_F[1..19]"; target_start 136; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 12741 12743 4.02 - 0 target "unknown_E[20..20]"; target_start 90; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 13121 13177 4.73 - 0 target "unknown_E[1..19]"; target_start 90; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 13184 13228 5.05 - 0 target "unknown_D[1..15]"; target_start 73; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 13229 13372 5.04 - 0 target "unknown_C[1..48]"; target_start 25; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 13373 13399 5.85 - 0 target "unknown_B[1..9]"; target_start 16; transcript_id "g1.t1"; gene_id "g1"; Contig65403 AUGUSTUS protein_match 13403 13447 9.89 - 0 target "unknown_A[1..15]"; target_start 0; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggttccgtttgcgggctggagcatgcctgtccagtacgcagaaggaatcacggagtctcacctccacgtccggtccg # ccgctggactgtttgatgtctcccacatgctgcagaccagggtgaccgggaaagaccgagtgtcgtttgtagagagtatgattgtcggggacgtaagg # ggcctccgggacaaccagggaaccctgtctgtgttcaccaatgagagaggaggaattctggatgatctgatcgtgtccaagacggaggagggagatct # gtatgttgtgtccaatgctggctgtgccgagcaagactataaaaatatgcaggaggagggggatggatgtggagtagcagctgatctgcgaacggact # gctggccgttggcaaggtctataaacattatcattgttttacttgatccactcctaggtccatcaatggccaaggtgctacaggagggggttgatttc # gacctgaatagtctccctttcatgacaaacaaaatggctactgtgtttggtattcctgactgcagagtgacgagatgtggctacacaggagaggacgg # ggtcgagatttccgtaagtccagaaaagactgagactttggccaatgcactgactggatcctctaaggcggacgtcatgatgattggtctgggggcgc # gtgacaccctacgactggaggccgggctctgtctctatggaagtgacatcgatgagactaccacacccgtagaggcttcactaacatggacaataggt # aaaaataccgcaacagctaaaaatacaaccaatatctctaccagaatcagcagacaaaataaaggaaagtcagagaggcgccgagtgggttttctcgt # cctcgggggtcagccaaaaggtcaacatacgggcaatactatttttaaaatgaaggtattgcgtcaaagtgtgaatgacaagacctgtcactgtattt # ttccatgtttagaacagaaaaatatctgctatcacagagttccgagtttgagtatgaatcagacaaaaagtttcttgcaaccaagaaatgtacaagtt # aatgggaagttaactaaaatgcttagacaacctacaacctacatgaggaaggcctaa] # protein sequence = [MVPFAGWSMPVQYAEGITESHLHVRSAAGLFDVSHMLQTRVTGKDRVSFVESMIVGDVRGLRDNQGTLSVFTNERGGI # LDDLIVSKTEEGDLYVVSNAGCAEQDYKNMQEEGDGCGVAADLRTDCWPLARSINIIIVLLDPLLGPSMAKVLQEGVDFDLNSLPFMTNKMATVFGIP # DCRVTRCGYTGEDGVEISVSPEKTETLANALTGSSKADVMMIGLGARDTLRLEAGLCLYGSDIDETTTPVEASLTWTIGKNTATAKNTTNISTRISRQ # NKGKSERRRVGFLVLGGQPKGQHTGNTIFKMKVLRQSVNDKTCHCIFPCLEQKNICYHRVPSLSMNQTKSFLQPRNVQVNGKLTKMLRQPTTYMRKA] # sequence of block unknown_O 339 [NQTKSFLQPRNVQVNGKLTKMLRQPTTYMR] 369 # sequence of block unknown_N 326 [KNICYHRVPSL] 337 # sequence of block unknown_M 309 [QSVNDKTCHCIFPCL] 324 # sequence of block unknown_L 290 [GQPKGQHT] 298 # sequence of block unknown_K 278 [SERRRVGFLV] 288 # sequence of block unknown_J 263 [TTNISTRISRQNKG] 277 # sequence of block unknown_I 212 [ADVMMIGLGARDTLRLEAGLCLYGSDIDETTTPVEASLTWTIGKNTA] 259 # sequence of block unknown_H 176 [DCRVTRCGYTGEDGVEISVSPE] 198 # sequence of block unknown_G 157 [DLNSLPFMTNKMATV] 172 # sequence of block unknown_F 136 [VLLDPLLGPSMAKVLQEGV] 155 # sequence of block unknown_E 90 [DLYVVSNAGCAEQDYKNMQE] 110 # sequence of block unknown_D 73 [ERGGILDDLIVSKTE] 88 # sequence of block unknown_C 25 [SAAGLFDVSHMLQTRVTGKDRVSFVESMIVGDVRGLRDNQGTLSVFTN] 73 # sequence of block unknown_B 16 [ITESHLHVR] 25 # sequence of block unknown_A 0 [MVPFAGWSMPVQYAE] 15 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370IF5.prfl --predictionStart=0 --predictionEnd=33447 --species=fly ./tmp/Contig6540320180911_busco_2432604931_.temp