# 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..480]--> unknown_A (19) <--[48..198]--> unknown_C (28) <--[9..19]--> unknown_E (22) <--[0..3]--> unknown_F (6) <--[0..2]--> unknown_G (14) <--[0..2]--> unknown_H (7) <--[0..24]--> unknown_I (8) <--[0..2]--> unknown_J (37) <--[1..72]--> unknown_K (21) <--[4..7]--> unknown_L (24) <--[0..14]--> unknown_M (17) <--[8..124]--> unknown_N (23) <--[0..23]--> unknown_O (18) <--[13..97]--> unknown_Q (19) <--[7..302]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig7324320180911_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 = 9770, name = Contig73243) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig73243 AUGUSTUS gene 1158 3945 0.01 + . g1 Contig73243 AUGUSTUS transcript 1158 3945 0.01 + . g1.t1 Contig73243 AUGUSTUS exon 1158 1662 . + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS start_codon 1176 1178 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS intron 1663 2571 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS intron 2761 3115 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS CDS 1176 1662 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS CDS 2572 2760 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS exon 2572 2760 . + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS CDS 3116 3729 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS exon 3116 3945 . + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS stop_codon 3727 3729 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS tts 3945 3945 . + . transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 1233 1289 3.2 + 0 target "unknown_A[1..19]"; target_start 19; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 1488 1571 2.46 + 0 target "unknown_C[1..28]"; target_start 104; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 1602 1662 4.86 + 0 target "unknown_E[1..21]"; target_start 142; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2572 2576 10.2 + 2 target "unknown_E[21..22]"; target_start 142; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2577 2594 6.9 + 0 target "unknown_F[1..6]"; target_start 164; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2595 2636 3.03 + 0 target "unknown_G[1..14]"; target_start 170; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2637 2657 6.41 + 0 target "unknown_H[1..7]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2658 2681 7.06 + 0 target "unknown_I[1..8]"; target_start 191; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 2682 2760 6.94 + 0 target "unknown_J[1..27]"; target_start 199; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3116 3147 4.58 + 2 target "unknown_J[27..37]"; target_start 199; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3151 3213 5.22 + 0 target "unknown_K[1..21]"; target_start 237; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3226 3297 4.37 + 0 target "unknown_L[1..24]"; target_start 262; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3310 3360 4.62 + 0 target "unknown_M[1..17]"; target_start 290; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3412 3480 4.12 + 0 target "unknown_N[1..23]"; target_start 324; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3502 3555 3.54 + 0 target "unknown_O[1..18]"; target_start 354; transcript_id "g1.t1"; gene_id "g1"; Contig73243 AUGUSTUS protein_match 3610 3666 4.4 + 0 target "unknown_Q[1..19]"; target_start 390; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgacagaaggtgactcaattttggatcccccggacgctgttcgtggtatgaagattttagacaggagtttgtttaaga # agactgtgtcaattccaggacttgcagttccacataagagtgttacaaagcttacaaagtcattgaaaaacgaaatcttgcgtttcaggtctattcaa # cccgtagtggacctaaatattcaagacaaatggtctaaaagtcataaattggtactgtttaatccacttaagataaagacagtggatgatttcaatga # aaagcagaaatgtatattggaaaacctagaagctgaaattgaaagtttcagtctgtacaactttgacatgaaatatgaaaattggggccatgcagaaa # ttatcaaagctgtgttaccaaaggaatttgaaacagtagcaggctttgcaatagttggtcatattgctcacctaaacctgagggatgggacagaggat # tacaaacagttaattgggcaagtgattctagacaaacacaagttaattaagacagttgtcaacaagatgaagtccattgacacagagttcagaaactt # tcagatggaattacttgcaggagagaacaattacactaccactgtgaaagaacatggatgtacattcaccttcgatttttcaaaagtttattggaata # ccaaattaagcacagaacacactcgagtggtttcgcagatgcagatggatgatgtagcctttgatgtgtttgctggggttggaccttttgctgtacct # tgtggaaagaagggagtcactgtgtttgcaaatgacttgaacccggattcatatgagagtttgaaattgaatgtgactaaaaataaagcaaataagca # ggacaatgtgaagtgttacaatatggacggcagagacttcataaaacaggttttctttaaagaaatggaaaagagatggacagatccattgagcaaag # ggacagttcatgtcttgatgaatttacctgccttagctgtagaattcctagacagttttgttggactgtttactcagacaagcctaagaccatcagat # cacagctgtatgcctttcattcactgttattatttcagtaaaagtgatgactttgaaaaggacaccaaagaggcagtagaaagggttttaggttgcac # tttgggagatgagctcgagatcagacaagttcgtaatgtggctcctggaaaagaaatgatgtgcataaaattcagactcccagaatctgttttattcc # aaaaaatcaaggaaatagatggtaagatttgctag] # protein sequence = [MTEGDSILDPPDAVRGMKILDRSLFKKTVSIPGLAVPHKSVTKLTKSLKNEILRFRSIQPVVDLNIQDKWSKSHKLVL # FNPLKIKTVDDFNEKQKCILENLEAEIESFSLYNFDMKYENWGHAEIIKAVLPKEFETVAGFAIVGHIAHLNLRDGTEDYKQLIGQVILDKHKLIKTV # VNKMKSIDTEFRNFQMELLAGENNYTTTVKEHGCTFTFDFSKVYWNTKLSTEHTRVVSQMQMDDVAFDVFAGVGPFAVPCGKKGVTVFANDLNPDSYE # SLKLNVTKNKANKQDNVKCYNMDGRDFIKQVFFKEMEKRWTDPLSKGTVHVLMNLPALAVEFLDSFVGLFTQTSLRPSDHSCMPFIHCYYFSKSDDFE # KDTKEAVERVLGCTLGDELEIRQVRNVAPGKEMMCIKFRLPESVLFQKIKEIDGKIC] # sequence of block unknown_A 19 [LDRSLFKKTVSIPGLAVPH] 38 # sequence of block unknown_C 104 [IESFSLYNFDMKYENWGHAEIIKAVLPK] 132 # sequence of block unknown_E 142 [VGHIAHLNLRDGTEDYKQLIGQ] 164 # sequence of block unknown_F 164 [VILDKH] 170 # sequence of block unknown_G 170 [KLIKTVVNKMKSID] 184 # sequence of block unknown_H 184 [TEFRNFQ] 191 # sequence of block unknown_I 191 [MELLAGEN] 199 # sequence of block unknown_J 199 [NYTTTVKEHGCTFTFDFSKVYWNTKLSTEHTRVVSQM] 236 # sequence of block unknown_K 237 [MDDVAFDVFAGVGPFAVPCGK] 258 # sequence of block unknown_L 262 [VFANDLNPDSYESLKLNVTKNKAN] 286 # sequence of block unknown_M 290 [VKCYNMDGRDFIKQVFF] 307 # sequence of block unknown_N 324 [VLMNLPALAVEFLDSFVGLFTQT] 347 # sequence of block unknown_O 354 [SCMPFIHCYYFSKSDDFE] 372 # sequence of block unknown_Q 390 [LEIRQVRNVAPGKEMMCIK] 409 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CZ0.prfl --predictionStart=0 --predictionEnd=23687 --species=fly ./tmp/Contig7324320180911_busco_2432604931_.temp