AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_bsub_mtub_300.orf -o005_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ileS 300 isoleucyl-tRNA synthetase #2 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #3 lsp 102 signal peptidase II #4 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #5 pyrP 171 uracil permease #6 pyrB 145 aspartate carbamoyltransferase Motif number 1 TCCCTTATGGGATGAGAGGGCTTTTTTTAT 1 251 1 GATGAGAGGG 0.95079 -50 TTAAAACAGTCCAGAGAGGCTGAGAAGGAT 4 148 1 CCAGAGAGGC 0.992429 -126 TCCTGCCAGAGCATAGAGGGGTTTTAGGAC 4 215 0 GCATAGAGGG 0.989539 -59 TTTAAGCAATCCAGAGAGGTTGCAAAGAGG 5 22 1 CCAGAGAGGT 0.988148 -150 CAGAGAGGTTGCAAAGAGGTGCACAACAAA 5 33 1 GCAAAGAGGT 0.981489 -139 GCTTTTTTACGCAAAGAGGCATACAAAGAC 5 84 0 GCAAAGAGGC 0.988148 -88 GCGTAAAAAAGCAAAGAGGTTTTTTTATAC 5 102 1 GCAAAGAGGT 0.981489 -70 TAATGAAAGTCCAGAGAGGCTTGGAAGGGT 6 18 1 CCAGAGAGGC 0.992429 -128 GAAGGGTTATGAAGAGAAGGAAGCTTCAAT 6 41 1 GAAGAGAAGG 0.922966 -105 GGGTATGGTTAAATAGAGGGCAGCATTGAA 6 65 0 AAATAGAGGG 0.888331 -81 CTTAAGTTGAAAAGAGAGGGGAAAGAAC 6 128 1 AAAGAGAGGG 0.972051 -18 ********** Masking position 5 Map Score: 23.6398 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 123 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 CAGAAAATAAAAAAAGCCCTCTCATCCCATA 1 256 0 AAAAACCCTC 0.995216 -45 TGCAAAAGAGCCCGGCGTAAAAGCC 2 5 1 AAAGACCCGG 0.968642 -73 CTTGGCACAAAAAAAGCCCGGCTTTTACGCC 2 24 0 AAAAACCCGG 0.993294 -54 TTTTATCAATAAAAAGCACTGGAGTAAAGAA 3 41 0 AAAAACACTG 0.947849 -62 TATTTCAGAAAAGAAACCCTCTGTCAACCGT 4 94 0 AAGAACCCTC 0.977469 -180 CACCTTGTCCTAAAACCCCTCTATGCTCTGG 4 209 1 TAAAACCCTC 0.966966 -65 ATATAGAAGAAAAAACCCCTCCTGCCAGAGC 4 233 0 AAAAACCCTC 0.995216 -41 AAAGAGGCATACAAAGACCTGCCGAATACTT 5 71 0 ACAAAACCTG 0.88235 -101 ATGACTGTATAAAAAAACCTCTTTGCTTTTT 5 107 0 AAAAAACCTC 0.972945 -65 AAGGCTGAAAAAAAACCCCGGTCTAAGATAG 6 100 0 AAAAACCCGG 0.993294 -46 ***** ***** Masking position 5 Map Score: 20.3711 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 109 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CTTTCAACCGTTTTTTCATCTGAATTTATG 1 19 0 TTTTTTCATC 0.945283 -282 CAAGCATACACTTTTTCCTCTTGAGCATCG 1 181 0 CTTTTTCCTC 0.892149 -120 GCGAGATAAGCTTTCTCGTCCCTTATGGGA 1 233 1 CTTTCTCGTC 0.763855 -68 CTCCACTGCATTTTTTCAGAAAATAAAAAA 1 273 0 TTTTTTCAGA 0.892698 -28 AAGCCGGGCTTTTTTTGTGCCAAGAGTGAC 2 31 1 TTTTTTGTGC 0.875915 -47 CTGTCAACCGTTTTTTCTGAGGTTTTCGAT 4 75 0 TTTTTTCTGA 0.858022 -199 ACAGAGGGTTTCTTTTCTGAAATAATAAAC 4 101 1 TCTTTTCTGA 0.818994 -173 TTTTAAAGAATCTATTCAGCTTCGTTTATT 4 124 0 TCTATTCAGC 0.776048 -150 TATCCGTTATCCTTCTCAGCCTCTCTGGAC 4 156 0 CCTTCTCAGC 0.939442 -118 GCAGGAGGGGTTTTTTCTTCTATATGAACT 4 239 1 TTTTTTCTTC 0.926194 -35 TAGATCACCTTTTTAAGCAATCCAGAGA 5 9 1 CTTTTTAAGC 0.86022 -163 CTGCCGAATACTTTTTGGGCCTTTGTTGTG 5 54 0 CTTTTTGGGC 0.823105 -118 ACCTCTTTGCTTTTTTACGCAAAGAGGCAT 5 92 0 TTTTTTACGC 0.754351 -80 ATTGAAGCTTCCTTCTCTTCATAACCCTTC 6 41 0 CCTTCTCTTC 0.782563 -105 GACCGGGGTTTTTTTTCAGCCTTAAGTTGA 6 108 1 TTTTTTCAGC 0.981848 -38 CTTTCCCCTCTCTTTTCAACTTAAGGCTGA 6 123 0 TCTTTTCAAC 0.761393 -23 ********** Masking position 6 Map Score: 15.4068 Number of sites scoring better than the average of aligned sites = 5328 Number in coding regions = 4831 Number in noncoding regions = 497 Number of orfs with sites within 600 bp upstream = 472 Fraction of orfs with sites within 600 bp upstream = 0.0758111 Motif number 4 AATACGTTCATAAATTCAGATGAAAA 1 5 1 CTTCATAAAT 0.689753 -296 ATGACTGTCCCTTTCAACCGTTTTTTCATCTG 1 27 0 CTTCAACCGT 0.969016 -274 TAGGTTAGGACGTTCATCACGTTACGATGCTC 1 157 1 CTTCATCACT 0.9225 -144 AAAAAAAGCCCTCTCATCCCATAAGGGACGAG 1 247 0 CCTCATCCCT 0.941566 -54 TTTCATTCCTCCACTGCATTTTTTC 1 286 0 CTTCCTCCAT 0.983241 -15 CCTGATATTTCTTTACTCCAGTGCTTTTTATT 3 33 1 CTTACTCCAT 0.955664 -70 TTTACGGTTACTTTAATCCATTATGCATTTTA 3 67 0 CTTAATCCAT 0.971764 -36 AAACGTTCCTCCAGTTTACGGTTAC 3 88 0 CTTCCTCCAT 0.983241 -15 AAGAAACCCTCTGTCAACCGTTTTTTCTGAGG 4 83 0 CGTCAACCGT 0.867062 -191 TGAATAGATTCTTTAAAACAGTCCAGAGAGGC 4 136 1 CTTAAAACAT 0.75764 -138 CGCACCTTGTCCTAAAACCCCTCTATGCTCTG 4 207 1 CTAAAACCCT 0.680169 -67 * ******** * Masking position 12 Map Score: 7.9357 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 783 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 TGAAGGAAACATGACTGTCCCTTTCAACCG 1 39 0 ATGACTGTCC 0.984804 -262 CCCGGAGATGGTGAGAGTCCGGGATGGCCG 1 83 1 GTGAGAGTCC 0.976654 -218 TCGTAACGTGATGAACGTCCTAACCTACTG 1 154 0 ATGAACGTCC 0.980567 -147 CAGTGTCTGTCCGGTTAATATG 3 3 1 GTGTCTGTCC 0.929849 -100 TCATCCTAAAATGAAAGTCAACAATCAGGG 5 142 1 ATGAAAGTCA 0.93011 -30 AACCTTTTAATGAAAGTCCAGAGAGGCTT 6 10 1 ATGAAAGTCC 0.988509 -136 ********** Masking position 8 Map Score: 5.12005 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 GATGAAAAAACGGTTGAAAGGGACAGTCAT 1 29 1 CGGTTGAAAG 0.96716 -272 AAAAATGCAGTGGAGGAATGAAA 1 288 1 TGGAGGAATG 0.944436 -13 TAAAAAGCACTGGAGTAAAGAAATATCAGG 3 33 0 TGGAGTAAAG 0.970895 -70 AAATGCATAATGGATTAAAGTAACCGTAAA 3 69 1 TGGATTAAAG 0.965064 -34 AACCGTAAACTGGAGGAACGTTT 3 90 1 TGGAGGAACG 0.961819 -13 TCAGAAAAAACGGTTGACAGAGGGTTTCTT 4 85 1 CGGTTGACAG 0.90046 -189 CTCTCTGGACTGTTTTAAAGAATCTATTCA 4 136 0 TGTTTTAAAG 0.733455 -138 ********** Masking position 7 Map Score: 3.12611 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 360 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TGAAGGCCTGAAGGAAACATGACTGTCCCT 1 47 0 AAGGAAACAT 0.978318 -254 TGAGTTCAGCAAGGAAACTAAAGGGCTGAT 1 124 0 AAGGAAACTA 0.803207 -177 CTTTTAGAAAAAGCAAGCATACACTTTTTC 1 194 0 AAGCAAGCAT 0.942741 -107 TTTAGAACGAAAGGAAAAATCTT 2 65 1 AAGGAAAAAT 0.924972 -13 TCCCGAGGATATGGCAGAATTAATCGAAAA 4 53 1 ATGGCAGAAT 0.808677 -221 TTATGAAGAGAAGGAAGCTTCAATGCTGCC 6 47 1 AAGGAAGCTT 0.975111 -99 GGTTAAATAGAGGGCAGCATTGAAGCTTCC 6 59 0 AGGGCAGCAT 0.958246 -87 ********** Masking position 6 Map Score: 2.60678 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 519 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 AAAAGCCCGGCTTTTACGCCGGGCTCTTTTGC 2 12 0 CTTTTCCCGG 0.965082 -66 AAATATCAGGCATATTAACCGGACAGACACTG 3 11 0 CATATACCGG 0.97 -92 TCAAATTCGACATATTCTCCTGTTCGTGGATG 4 12 0 CATATCCCTG 0.986036 -262 TTAATTCTGCCATATCCTCGGGAAGCGGCGCT 4 44 0 CATATCCGGG 0.99093 -230 GATGATTTCCCCCTGATTGTTGACT 5 157 0 GATTTCCCTG 0.95189 -15 CCCGGTCTAAGATAGACTCGGGGTATGGTTAA 6 83 0 GATAGCCGGG 0.954295 -63 ***** * **** Masking position 3 Map Score: 0.885831 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 292 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0