# 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 # --[1..140]--> unknown_A (9) <--[8..45]--> unknown_C (24) <--[0..2]--> unknown_D (19) <--[0..3]--> unknown_E (15) <--[2..15]--> unknown_F (14) <--[0..8]--> unknown_G (19) <--[16..448]--> unknown_H (42) <--[4..66]--> unknown_I (27) <--[4..11]--> unknown_J (9) <--[1..74]--> unknown_K (28) <--[3..6]--> unknown_L (8) <--[0..8]--> unknown_M (10) <--[0..2]--> unknown_N (21) <--[0..28]--> unknown_O (16) <--[0..1]--> unknown_P (26) <--[7..54]--> unknown_R (28) <--[12..29]--> unknown_T (29) <--[0..7]--> unknown_U (20) <--[2..6]--> unknown_V (21) <--[3..11]--> unknown_W (15) <--[0..1]--> unknown_X (20) <--[0..9]--> unknown_Y (45) <--[74..702]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig43620180911_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 = 27042, name = Contig436) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig436 AUGUSTUS gene 816 26855 0.01 - . g1 Contig436 AUGUSTUS transcript 816 26855 0.01 - . g1.t1 Contig436 AUGUSTUS tts 816 816 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 816 1407 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS stop_codon 1390 1392 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 1408 1841 0.18 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 2052 4989 0.98 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 5175 5821 0.75 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 6041 6779 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 6925 7076 0.77 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 7298 7550 0.23 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 7671 7765 0.27 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 7921 8402 0.54 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 8528 8973 0.96 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 9210 9559 0.26 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 10405 11555 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 11734 12261 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 12272 14048 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 14083 15705 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 15824 26622 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS intron 26656 26762 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 1390 1407 0.18 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 1842 2051 0.99 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 1842 2051 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 4990 5174 0.8 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 4990 5174 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 5822 6040 0.89 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 5822 6040 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 6780 6924 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 6780 6924 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 7077 7297 0.38 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 7077 7297 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 7551 7670 0.27 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 7551 7670 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 7766 7920 0.54 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 7766 7920 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 8403 8527 0.96 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 8403 8527 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 8974 9209 0.46 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 8974 9209 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 9560 10404 0.16 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 9560 10404 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 11556 11733 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 11556 11733 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 12262 12271 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 12262 12271 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 14049 14082 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 14049 14082 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 15706 15823 0.03 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 15706 15823 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 26623 26655 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 26623 26655 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS CDS 26763 26802 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS exon 26763 26855 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS start_codon 26800 26802 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS tss 26855 26855 . - . transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 5862 5996 2.85 - 0 target "unknown_Y[1..45]"; target_start 768; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 5997 6040 4.42 - 2 target "unknown_X[6..20]"; target_start 748; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 6780 6795 7.54 - 0 target "unknown_X[1..6]"; target_start 748; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 6799 6843 4.89 - 0 target "unknown_W[1..15]"; target_start 732; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 6853 6915 4.33 - 0 target "unknown_V[1..21]"; target_start 708; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 6922 6924 0.804 - 0 target "unknown_U[20..20]"; target_start 686; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7077 7133 7.21 - 0 target "unknown_U[1..19]"; target_start 686; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7134 7220 3.84 - 0 target "unknown_T[1..29]"; target_start 657; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7260 7297 3.8 - 2 target "unknown_R[16..28]"; target_start 616; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7551 7596 3.24 - 0 target "unknown_R[1..16]"; target_start 616; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7621 7670 7.66 - 2 target "unknown_P[10..26]"; target_start 582; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7766 7793 6.29 - 0 target "unknown_P[1..10]"; target_start 582; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7794 7841 2.02 - 0 target "unknown_O[1..16]"; target_start 566; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7851 7913 5.44 - 0 target "unknown_N[1..21]"; target_start 542; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 7914 7920 7.02 - 1 target "unknown_M[8..10]"; target_start 532; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 8403 8425 3.34 - 0 target "unknown_M[1..8]"; target_start 532; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 8450 8473 7.79 - 0 target "unknown_L[1..8]"; target_start 516; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 8483 8527 7.19 - 0 target "unknown_K[14..28]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 8974 9012 10.2 - 0 target "unknown_K[1..13]"; target_start 485; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 9181 9207 5.93 - 0 target "unknown_J[1..9]"; target_start 420; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 9570 9650 6.17 - 0 target "unknown_I[1..27]"; target_start 389; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 9753 9878 3.62 - 0 target "unknown_H[1..42]"; target_start 313; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 10347 10403 4.11 - 0 target "unknown_G[1..19]"; target_start 138; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 11561 11602 4.91 - 0 target "unknown_F[1..14]"; target_start 122; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 11612 11656 5.01 - 0 target "unknown_E[1..15]"; target_start 104; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 11660 11716 4.38 - 0 target "unknown_D[1..19]"; target_start 84; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 11717 11733 5.14 - 2 target "unknown_C[19..24]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 12262 12271 0.96 - 0 target "unknown_C[16..19]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 14049 14082 2.42 - 1 target "unknown_C[4..15]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 15706 15716 0.679 - 0 target "unknown_C[1..4]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 26633 26655 2.56 - 2 target "unknown_A[2..9]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; Contig436 AUGUSTUS protein_match 26763 26766 3.59 - 0 target "unknown_A[1..2]"; target_start 12; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcccattgggccgaggtctttccgtcaaacttccggagggtttgtcaggaaaatatacaaacttaaccgaggcgtta # attttaccaggaggcagattgactacattttcaacatcatggccgaatcaaagacaaatcaaccaacaaagaagagtagacagggccagggagatttg # gaatgggaaagcggtataattatgcattatgtagtgatttacattgaaaaatattgtaagccatcctcagatgaattgaaaaggattatgtaccagca # tggtggtcattatgagcactacctttctaagagaagagttacacatataatagcgaccagtcttcccaacagtaaaatcacaaagggacttaaacact # gcaaggtggtcaagccagagtggatcactgaaaggcaagttgttgctgcgggaaggctcttgtcctacatcccctatcaactgtacacagggcagact # aaaatccaacagggcatgtcttcatacgccacccaatcttccacaaaaatatgcaactccaccatagcaggtatatgtaccaagaatgccctgagtag # aaatctggttggtgaaagtagtagatgtggaaatttggtggaaaaagcagacgaggaagaagatgtgatagataaggagatgcagaggagaatggaaa # agattgtaaaagaagtggagagcgaatcagaggagagcgattcagacagcgagttcgggagatatgcagtggagactgaacggaaacaagccatcctt # gatgattcgttgactaatgttaatgttagggaggacgttaccaccacgccaaggaagttagatgttaaaaatagcactggaagtaccgatacatcgtg # tatatcaaataaaaatgtaggcatggaaggtccaaagccatccatttccagtgaaacaaagagtccttcaccgaacagcaagctccatgggcgagcag # gtgatccacactacctgaatgaattctataacaattcacggctccaccatctctccacgtggaaatctgagtggagagaatatgtcaacaaaaaatcc # aaagagttgacaaattatccggggagacaagccctgattagggttgtgagcaagcaggcagcagacttaacatcacgggacatgggtggtgagggcat # tagaaggacgaggtcggggaaacctaaacgtgtcgtaatgcatgttgacatggattgtttcttcgtgtctgttggtttgcggaaaaagcctgatctaa # ttggcaagcctgttgctgttacacattgcaaaaaccaaggcaggaaagggcctataccaggatctgatattgaatatgaacaaaaaatgtggagaatt # aaaaaagacaaaggtatatccaccaatccagacctgcaggccaatccagacagcagcactttaggatttgggaggaacggaaatctagatgcattttc # ctccatgtctgaaatagcttcctgcagctatgaggcaagacaggcaggggttaaaaatggtatgttcatgggtcctgccaagaaactgtgcccggatc # tgcaaacaatcccgtatgactttgaaggctaccaagaagtgtcccagattctctatgacactgtgttaagttatacccatgatattgaggcagtgagc # tgtgatgaaatgctggttgattgcacagatctcctagcgagcactggagcggaaccagaacaatttgcttctctgctacggaaacagatacagttgaa # gaccggctgttctgcctccgctgggatgggaggaaatattttactcgcaaaaatggccaccaagaaggcgaagcctaatggacagttttacttggagg # aagcagatgtcatggactttatgaaggaacagtctgttcaaaatatccctggtgtaggatggtctatgaatagaaaactgaaatctttgggggtcacg # acttgtgggcagcttcaagaggtaccccagtctaccctacagaaggaatttggccctaaaacagggctgtccttgtataggggctgtaggggacagga # tgaccgccagatcaaatctaaccaggaaagaaagtcggtgtctgctgaagtcaattatggcatcaggttcaaatcgaatactgaggcggagaagttca # tcatggatttgtcagaagaagtccacaaccgtctgcgcgacattggaatgaaggggaaatccgtgacgatgaaattaatggttagaagagaagatgct # cctctggaaacagccaagtttatgggtcatgggatttgtaacaacatctccaagtccagcatgttgcccatcccaacagatgatgccagtttgatata # tcaggagtgtatgacgatcttacgcgggctgcggctgaactgctcggacctgaggggtataggaatacagatccagagactcgagtcggcaacagtgg # gcgggaacaatcaaaagaaaccccagagcattctcaattttacgacaaaagtgtcatctacgaaaacaagtcctctcgaacaaagagttgtggagacc # agcaatcataatcactcttcagcactcggtggaaacttggaaatttcaacggtcagccatgacggtcaaggtagtccccggattgatggagaagagag # gcactggacagacactctgatgaatctggatcgagaaattgatccgaatgtgttgaaggaactgccaccagaaatccaagctcagattaagaccgagc # tccagactctgagacgagagcctcgccaggcgagacagagggtgtccagttacagtgaggagccgggatgttctcactggacctcgagggaacctccg # gtaaccgaggatatctcgtctgccatcgtacctctaccacatctgtcccagggatgtcaaaatgagtaa] # protein sequence = [MPIGPRSFRQTSGGFVRKIYKLNRGVNFTRRQIDYIFNIMAESKTNQPTKKSRQGQGDLEWESGIIMHYVVIYIEKYC # KPSSDELKRIMYQHGGHYEHYLSKRRVTHIIATSLPNSKITKGLKHCKVVKPEWITERQVVAAGRLLSYIPYQLYTGQTKIQQGMSSYATQSSTKICN # STIAGICTKNALSRNLVGESSRCGNLVEKADEEEDVIDKEMQRRMEKIVKEVESESEESDSDSEFGRYAVETERKQAILDDSLTNVNVREDVTTTPRK # LDVKNSTGSTDTSCISNKNVGMEGPKPSISSETKSPSPNSKLHGRAGDPHYLNEFYNNSRLHHLSTWKSEWREYVNKKSKELTNYPGRQALIRVVSKQ # AADLTSRDMGGEGIRRTRSGKPKRVVMHVDMDCFFVSVGLRKKPDLIGKPVAVTHCKNQGRKGPIPGSDIEYEQKMWRIKKDKGISTNPDLQANPDSS # TLGFGRNGNLDAFSSMSEIASCSYEARQAGVKNGMFMGPAKKLCPDLQTIPYDFEGYQEVSQILYDTVLSYTHDIEAVSCDEMLVDCTDLLASTGAEP # EQFASLLRKQIQLKTGCSASAGMGGNILLAKMATKKAKPNGQFYLEEADVMDFMKEQSVQNIPGVGWSMNRKLKSLGVTTCGQLQEVPQSTLQKEFGP # KTGLSLYRGCRGQDDRQIKSNQERKSVSAEVNYGIRFKSNTEAEKFIMDLSEEVHNRLRDIGMKGKSVTMKLMVRREDAPLETAKFMGHGICNNISKS # SMLPIPTDDASLIYQECMTILRGLRLNCSDLRGIGIQIQRLESATVGGNNQKKPQSILNFTTKVSSTKTSPLEQRVVETSNHNHSSALGGNLEISTVS # HDGQGSPRIDGEERHWTDTLMNLDREIDPNVLKELPPEIQAQIKTELQTLRREPRQARQRVSSYSEEPGCSHWTSREPPVTEDISSAIVPLPHLSQGC # QNE] # sequence of block unknown_Y 768 [IPTDDASLIYQECMTILRGLRLNCSDLRGIGIQIQRLESATVGGN] 813 # sequence of block unknown_X 748 [TAKFMGHGICNNISKSSMLP] 768 # sequence of block unknown_W 732 [SVTMKLMVRREDAPL] 747 # sequence of block unknown_V 708 [AEKFIMDLSEEVHNRLRDIGM] 729 # sequence of block unknown_U 686 [NQERKSVSAEVNYGIRFKSN] 706 # sequence of block unknown_T 657 [STLQKEFGPKTGLSLYRGCRGQDDRQIKS] 686 # sequence of block unknown_R 616 [DVMDFMKEQSVQNIPGVGWSMNRKLKSL] 644 # sequence of block unknown_P 582 [TGCSASAGMGGNILLAKMATKKAKPN] 608 # sequence of block unknown_O 566 [EPEQFASLLRKQIQLK] 582 # sequence of block unknown_N 542 [HDIEAVSCDEMLVDCTDLLAS] 563 # sequence of block unknown_M 532 [ILYDTVLSYT] 542 # sequence of block unknown_L 516 [LQTIPYDF] 524 # sequence of block unknown_K 485 [MSEIASCSYEARQAGVKNGMFMGPAKKL] 513 # sequence of block unknown_J 420 [KPVAVTHCK] 429 # sequence of block unknown_I 389 [RSGKPKRVVMHVDMDCFFVSVGLRKKP] 416 # sequence of block unknown_H 313 [SKLHGRAGDPHYLNEFYNNSRLHHLSTWKSEWREYVNKKSKE] 355 # sequence of block unknown_G 138 [VAAGRLLSYIPYQLYTGQT] 157 # sequence of block unknown_F 122 [KHCKVVKPEWITER] 136 # sequence of block unknown_E 104 [VTHIIATSLPNSKIT] 119 # sequence of block unknown_D 84 [LKRIMYQHGGHYEHYLSKR] 103 # sequence of block unknown_C 60 [WESGIIMHYVVIYIEKYCKPSSDE] 84 # sequence of block unknown_A 12 [GGFVRKIYK] 21 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093702DP.prfl --predictionStart=0 --predictionEnd=29860 --species=fly ./tmp/Contig43620180911_busco_2432604931_.temp