AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_bsub_mtub_300.orf -o326_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 yqfQ 168 yqfQ #5 yqfP 122 similar to penicillin tolerance #6 lspA 51 lspA #7 idsB 300 idsB Motif number 1 AGTGTATGCTTGCTTTTTCTAAAAGGGTGG 1 199 1 TGCTTTTTCT 0.965275 -102 GGGATGAGAGGGCTTTTTTTATTTTCTGAA 1 259 1 GGCTTTTTTT 0.976227 -42 ATTCCTCCACTGCATTTTTTCAGAAAATAA 1 277 0 TGCATTTTTT 0.962617 -24 GTAAAAGCCGGGCTTTTTTTGTGCCAAGAG 2 27 1 GGCTTTTTTT 0.976227 -51 AGAAATATCAGGCATATTAACCGGACAGAC 3 15 0 GGCATATTAA 0.807586 -88 TTTACTCCAGTGCTTTTTATTGATAAAATG 3 44 1 TGCTTTTTAT 0.976365 -59 TAATCCATTATGCATTTTATCAATAAAAAG 3 56 0 TGCATTTTAT 0.976365 -47 TCCTTAAAGCGGCACATTATGTGTCCATCA 4 21 1 GGCACATTAT 0.861511 -148 CCGCAGCCCATGCATATTCTAATAGCAGAG 4 127 1 TGCATATTCT 0.926346 -42 GTTTGATTACGGCTTTTTATATTGCCTTTA 5 74 1 GGCTTTTTAT 0.985047 -49 ********** Masking position 7 Map Score: 14.6189 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 571 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 AATTCAGATGAAAAAACGGTTGAAAGGGACAGTCATGTTTCCTT 1 23 1 AACGGGGGTC 0.997866 -278 AGGCCTTCATAGCGACCCGGAGATGGTGAGAGTCCGGGATGGCC 1 68 1 ACCGGTGGTC 0.997217 -233 TTCCTTGCTGAACTCACAGTAGGTTAGGACGTTCATCACGTTAC 1 138 1 AACGGGGTTC 0.978651 -163 TGCAAAAGAGCCCGGCGTAAAAGCCGGGCTTTTTTTGTG 2 6 1 ACCGGAGGGC 0.989711 -72 TTATCAATAAAAAGCACTGGAGTAAAGAAATATCAGGCATATTA 3 26 0 AACGGGAATC 0.925706 -77 ACCATCATCATCCCCTAGGGCCGATATGGCCCGCCCAGAC 6 22 0 ACCCGGAGGC 0.8833 -30 GTCGAAGGCAACCTACCCGCCGTGATGGGAAGTATAGGTCGCCG 7 48 1 ACCGGGGGTA 0.988482 -253 TGGGAAGTATAGGTCGCCGCAGGGTATGCGTGTCTTTCTGTAGT 7 73 1 AGCGGTGGTC 0.985729 -228 CGGAATTCGAGTTGTCCAGACGCCCCGGGTCATCCACTACAGAA 7 108 0 GCCGGGGATC 0.761072 -193 ATCATTGCTAACAACCCTGATGGTCGTGTTGGTCGACGGGCATA 7 154 1 ACCGGTGGTC 0.997197 -147 TCTTAACCTCACCGGAGCAACAGTGAGTCGCTATTTTCA 7 272 0 AACGGAGGTC 0.715181 -29 * ** * * ** *** Masking position 7 Map Score: 14.3673 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 208 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 TTTTCATCTGAATTTATGAACGTATT 1 5 0 ATTTATGAAG 0.831646 -296 GAGCATCGTAACGTGATGAACGTCCTAACCTA 1 157 0 AGTGATGAAG 0.972839 -144 AAGAGGAAAAAGTGTATGCTTGCTTTTTCTAA 1 189 1 ATGTATGCTG 0.706185 -112 CTCGTCCCTTATGGGATGAGAGGGCTTTTTTT 1 247 1 AGGGATGAGG 0.98191 -54 GAAAAAATGCAGTGGAGGAATGAAA 1 286 1 ATGGAGGAAG 0.982781 -15 AATAAAAAGCACTGGAGTAAAGAAATATCAGG 3 33 0 ATGGAGTAAG 0.926469 -70 TAAAATGCATAATGGATTAAAGTAACCGTAAA 3 67 1 ATGGATTAAG 0.938708 -36 GTAACCGTAAACTGGAGGAACGTTT 3 88 1 ATGGAGGAAG 0.982781 -15 ATCGGGTATAATGTGATGATGGACACATAATG 4 35 0 AGTGATGATG 0.941922 -134 TCCAATACTGAAGTGAGTAAAGGCAATATAAA 5 89 0 AGTGAGTAAG 0.866747 -34 TATCGGCCCTAGGGGATGATGATGGT 6 36 1 AGGGATGATA 0.782979 -16 AGGTCGCCGCAGGGTATGCGTGTCTTTCTGTA 7 83 1 AGGTATGCGG 0.80593 -218 * ******** * Masking position 6 Map Score: 11.2836 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 825 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 4 GTTTCCTTCAGGCCTTCATAGCGACCCGGAGA 1 59 1 GGCCTATAGC 0.929534 -242 GATGGTGAGAGTCCGGGATGGCCGGAATCATG 1 89 1 GTCCGATGGC 0.985903 -212 ATCCCATAAGGGACGAGAAAGCTTATCTCGCG 1 232 0 GGACGAAAGC 0.944124 -69 CAAAAGAGCCCGGCGTAAAAGCCGGGCTTTTT 2 13 1 CGGCGAAAGC 0.981883 -65 CAATACTGAAGTGAGTAAAGGCAATATAAAAA 5 87 0 GTGAGAAGGC 0.773818 -36 CATCCCCTAGGGCCGATATGGCCCGCCCAGAC 6 22 0 GGCCGATGGC 0.995334 -30 CTCCGAGAAAGGCCAGGCAATT 7 1 1 CTCCGAAAGG 0.897983 -300 GCAACCTACCCGCCGTGATGGGAAGTATAGGT 7 55 1 CGCCGATGGG 0.981302 -246 AACGAGCAATCGGCGATATTGCTTCACTTCGG 7 237 0 CGGCGATTGC 0.95304 -64 ***** ***** Masking position 8 Map Score: 6.35426 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 769 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 GCAAGGAAACTAAAGGGCTGATCTACATGA 1 116 0 TAAAGGGCTG 0.956786 -185 CTTATGGGATGAGAGGGCTTTTTTTATTTT 1 254 1 GAGAGGGCTT 0.927074 -47 TGTGCCGCTTTAAGGAGCTGGGAAAA 4 7 0 TAAGGAGCTG 0.904737 -162 ATTAGAATATGCATGGGCTGCGGTATTTGC 4 120 0 GCATGGGCTG 0.974868 -49 TCTAATAGCAGAGAGAGCTGAAAGGAGGTA 4 144 1 GAGAGAGCTG 0.963944 -25 CCGGCCGCGGGGTCTGGGCGGGCCAT 6 7 1 GCGGGGTCTG 0.980684 -45 ATAGGTCGCCGCAGGGTATGCGTGTCTTTC 7 81 1 GCAGGGTATG 0.84504 -220 ********** Masking position 9 Map Score: 2.23715 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 883 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 AATCATGTAGATCAGCCCTTTAGTTTCCTT 1 114 1 ATCAGCCCTT 0.799783 -187 GTAAAGAAATATCAGGCATATTAACCGGAC 3 19 0 ATCAGGCATA 0.93329 -84 TTTAAGCAAAATCGGGTATAATGTGATGAT 4 47 0 ATCGGGTATA 0.967337 -122 CTTAAGTGAGATTGGCTATAATGAGATCAG 5 24 1 ATTGGCTATA 0.843054 -99 GCCGTAATCAAACGGCTCTATTCTTGCATT 5 57 0 AACGGCTCTA 0.945232 -66 GGCGGGCCATATCGGCCCTAGGGGATGATG 6 27 1 ATCGGCCCTA 0.989836 -25 CGTGTTGGTCGACGGGCATAGGTACATGTT 7 178 1 GACGGGCATA 0.856056 -123 CGAACGAGCAATCGGCGATATTGCTTCACT 7 241 0 ATCGGCGATA 0.965826 -60 ********** Masking position 9 Map Score: 4.71242 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 415 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TGAAGGCCTGAAGGAAACATGACTGTCCCT 1 47 0 AAGGAAACAT 0.976027 -254 TTTAGAACGAAAGGAAAAATCTT 2 65 1 AAGGAAAAAT 0.886393 -13 GAAGTGAGTAAAGGCAATATAAAAAGCCGT 5 82 0 AAGGCAATAT 0.95849 -41 CTTCGACAATACTGCAACATTCAATTGCCT 7 25 0 ACTGCAACAT 0.8941 -276 AGTATTGTCGAAGGCAACCTACCCGCCGTG 7 42 1 AAGGCAACCT 0.977806 -259 TTCAAATATCAACGCAACATGTACCTATGC 7 193 0 AACGCAACAT 0.971609 -108 ********** Masking position 6 Map Score: 3.61832 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 201 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GTCCGGGATGGCCGGAATCATGTAGATCAG 1 99 1 GCCGGAATCA 0.976023 -202 TAGTTTCCTTGCTGAACTCACAGTAGGTTA 1 134 1 GCTGAACTCA 0.965114 -167 CGGCTTTTACGCCGGGCTCTTTTGCA 2 7 0 GCCGGGCTCT 0.949602 -71 TCTCATTATAGCCAATCTCACTTAAGATAT 5 20 0 GCCAATCTCA 0.901769 -103 CTTGCATTCTTCTGATCTCATTATAGCCAA 5 35 0 TCTGATCTCA 0.840411 -88 AATATAAAAAGCCGTAATCAAACGGCTCTA 5 67 0 GCCGTAATCA 0.937202 -56 CAACTCGAATTCCGAGATCATTGCTAACAA 7 138 1 TCCGAGATCA 0.935315 -163 ********** Masking position 8 Map Score: 2.38134 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 806 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 ********** No masking Map Score: -1.29786e-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: -1.29786e-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: -1.29786e-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