AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_mthe_reg_100.orf -o00550_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH332 119 LPS biosynthesis RfbU related protein #2 MTH338 190 LPS biosynthesis RfbU related protein #3 MTH343 48 rhamnosyl transferase #4 MTH347 60 O-antigen transporter #5 MTH348 194 rhamnosyl transferase #6 MTH447 109 sensory transduction regulatory protein #7 MTH448 74 unknown #8 MTH449 38 unknown #9 MTH531 291 UDP-N-acetylmuramyl tripeptide synthetase related protein #10 MTH532 28 UDP-N-acetylmuramyl tripeptide synthetase related protein #11 MTH533 41 unknown #12 MTH735 88 phospho-N-acetylmuramoyl-pentapeptide-transferase #13 MTH736 133 conserved protein #14 MTH1570 74 glutamine synthetase #15 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog Motif number 1 CCAGTCCAGTCCAGTCCAGTCCATCCTATC 5 104 0 CCAGTCCAGT 0.985331 -91 CCAGTCCAGTCCAGTCCAGTCCAGTCCAGT 5 114 0 CCAGTCCAGT 0.985331 -81 TTTTATCAGTCCAGTCCAGTCCAGTCCAGT 5 124 0 CCAGTCCAGT 0.985331 -71 CTATCAGATCCCGGGTCAGGCATCTGGCTC 9 47 0 CCGGGTCAGG 0.943134 -245 ACATATCCTCCCGGGTGAGGATCTTTAGGT 9 127 1 CCGGGTGAGG 0.944198 -165 ACCAGTTCAAGCAGTTCAGGATCATTGGCC 12 24 0 GCAGTTCAGG 0.968961 -65 TTAATCTTGACCGGTTCAGGTAAAATTCAT 13 65 0 CCGGTTCAGG 0.992062 -69 GAAAAACAGTTCGGTTCAGGGAAGGGGTTT 15 89 0 TCGGTTCAGG 0.979476 -212 GAAAGATTCTTCAGATCAGTGAAAAGCAGA 15 154 0 TCAGATCAGT 0.797498 -147 ********** Masking position 8 Map Score: 14.6154 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 197 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 ATAGATTTCAAGAGAGCCTCTGAAAAACCTTAA 1 77 1 AGGGCCTTGA 0.936531 -43 TCCTCACGATAGTGTTCATTTGGACTTGTAGTT 2 164 0 AGGTCATTGG 0.937714 -27 TGAAGTCAAAGAGCGTCCTCTGGCCCG 8 5 0 GACTCCTTGG 0.938436 -34 CTTTATAGGTAGAGTGTCTATGGGTGGATACAT 9 98 1 AGGGTCTTGG 0.936534 -194 ATCTTTAGGTAGACTGCCTCTGGTAGATATCCC 9 147 1 AGCGCCTTGG 0.987273 -145 CGAGGTAGTGGGTGTACCTATGGATCATTCGGT 9 180 0 GGGACCTTGG 0.986743 -112 AGATGTCTGGGGCGGTCCTCTGGAGCCATTCTG 15 124 0 GGGTCCTTGG 0.996697 -177 GCCTATCACTGGAGATCCTGTGGGAAAGATTCT 15 174 0 GGGTCCTTGG 0.996696 -127 ATCATGAGGGGGTCATCCTGTAGGACCACAGCC 15 228 0 GGCTCCTTAG 0.938436 -73 ** * **** *** Masking position 9 Map Score: 11.1616 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 303 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TTGATCAATCAAAACTTGATTTCTGGGTGAATCCATGA 2 14 1 AAAGATCGGT 0.98553 -177 GTAGCCCCTCAAAATGCGAGTGGGGGGTAAAGACTGCT 2 66 0 AAAGAGGGGT 0.95649 -125 GCACCTAGTAAAAAGAGGACATGAGGTTTTCGTAATAA 2 128 1 AAAGATGGGT 0.972298 -63 TAAACTTTTCGTATGATGATGTGGGGTGCGACAGATTT 5 37 1 GATGATGGGG 0.924499 -158 CAGAGCAAGTATAAAGAGACGTCAGGCTGAAGTTATGA 7 37 1 AAAGATCGGT 0.98553 -38 TGATCTTGATGTACACAGAAGGCAGGTGAT 12 69 1 GACGAGCGGG 0.92597 -20 TATTTTGAGGGTATTGAGAATTCTGGATGAATTTTACC 13 39 1 GATGATCGGT 0.962131 -95 ACCAGTAGAAGGAAAGTTACTTCCGGTGAAGTTAAGCT 14 26 1 GAATATCGGG 0.870715 -49 CAGATCAGTGAAAAGCAGATGTCTGGGGCGGTCCTCTG 15 135 0 AAAGATCGGG 0.984542 -166 GGCTCATGCTGCAAGCAGATATAAGGCTGTGGTCCTAC 15 204 1 GAAGATAGGT 0.954348 -97 GTATTATGCAAGAACATGAAAGAGGGTTTGA 15 280 1 AAAGAGAGGT 0.907034 -21 * ** ** ** ** * Masking position 9 Map Score: 9.86933 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 137 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TCAAGTTTTGATTGATCAAGAG 2 3 0 ATTGATCAAG 0.474402 -188 ATTTTCATGGATTCACCCAGAAATCAAGTT 2 26 0 ATTCACCCAG 0.950285 -165 ATATTCCTCACGATAGTGTTCA 2 179 0 ATTCCTCACG 0.795162 -12 ATCCTATCCTATTCCTCCCTTAAACCTACA 5 82 0 ATTCCTCCCT 0.942858 -113 ATGTCTGGACATTGCCCCTGATACTTTGAT 6 51 0 ATTGCCCCTG 0.765185 -59 GAGGATATGTATCCACCCATAGACACTCTA 9 107 0 ATCCACCCAT 0.731962 -185 GAGTCACCTGATGGCACCCGTCCTGACCGA 9 210 0 ATGGCACCCG 0.869386 -82 TTAAATGCACCCATAAACGTTTTT 9 278 0 ATGCACCCAT 0.91961 -14 GGCTGATTGAATTCAACCCTAAAAA 13 6 0 ATTCAACCCT 0.76468 -128 TTCAGGTAAAATTCATCCAGAATTCTCAAT 13 51 0 ATTCATCCAG 0.934231 -83 GGGTTATGCCTCCATGGCATGAGCT 14 60 0 ATGCCTCCAT 0.939857 -15 CGATTTCAGAATGGCTCCAGAGGACCGCCC 15 118 1 ATGGCTCCAG 0.935274 -183 GTCCTACAGGATGACCCCCTCATGATTTAT 15 235 1 ATGACCCCCT 0.715506 -66 ********** Masking position 1 Map Score: 7.26122 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 740 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 GGTAATTATGATCTTAAGGTTTTTCAGAGG 1 93 0 ATCTTAAGGT 0.88204 -27 CCCCACTCGCATTTTGAGGGGCTACAGGAG 2 79 1 ATTTTGAGGG 0.956878 -112 AATGAACACTATCGTGAGGAATAT 2 177 1 ATCGTGAGGA 0.966638 -14 AAGGGAGTTAAGCGTGAGGAGATGATGCC 3 30 1 AGCGTGAGGA 0.885001 -19 CCGGGTGAGGATCTTTAGGTAGACTGCCTC 9 137 1 ATCTTTAGGT 0.888663 -155 AAACTTGGTGATCTTGATGTACACAGAAGG 12 61 1 ATCTTGATGT 0.873246 -28 TCAGCCCTGTATTTTGAGGGTATTGAGAAT 13 30 1 ATTTTGAGGG 0.956878 -104 GTTGATATAAATCATGAGGGGGTCATCCTG 15 241 0 ATCATGAGGG 0.959894 -60 ********** Masking position 7 Map Score: 4.21251 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 394 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TCAATCATCCTTTCTCTGATGAGTTAATCCCT 4 39 0 CTTCTCTGGA 0.952808 -22 TCGAGGATCTGCATTCACTGTCTACTCCAGGATC 5 154 0 GATCACTGTA 0.882537 -41 CTGATACTTTGATGTCACTGCAGAATAAGGTTTA 6 30 0 GTTCACTGGA 0.99372 -80 TTATGGAACCGCTATCACTGAGGACTAATGTCTG 6 74 0 GTTCACTGGA 0.99372 -36 TTACCGGGTTTCAGTGTTGAGCGTATCAGA 7 7 1 GTTCAGTGGA 0.963218 -68 AGTAATCCATGAACTCCCTGGAGTGTTAGAGGTG 9 13 0 GATCCCTGGT 0.867106 -279 CAGACATCTGCTTTTCACTGATCTGAAGAATCTT 15 148 1 CTTCACTGCT 0.872521 -153 GCAGCATGAGCCTATCACTGGAGATCCTGTGGGA 15 182 0 CTTCACTGGA 0.989822 -119 * * ****** ** Masking position 9 Map Score: 3.98553 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 157 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ATTAAAATAGCATCATTTATAAAGGTATAA 1 13 1 CATCATTTAT 0.894656 -107 ATTACGAAAACCTCATGTCCTCTTTTTACT 2 134 0 CCTCATGTCC 0.824762 -57 GGCATCATCTCCTCACGCTTAA 3 37 0 CATCATCTCC 0.905915 -12 TCAATCATCCTTTCTCTGATGAGTT 4 46 0 CATCCTTTCT 0.976248 -15 CAGTCCAGTCCATCCTATCCTATTCCTCCC 5 93 0 CATCCTATCC 0.963013 -102 GATAAACCTCCTTTATGGAACCGCTA 6 94 0 CCTCCTTTAT 0.868153 -16 GCGTGTACCATCATAACTTCAGCCTGAC 7 57 0 CATCATAACT 0.758289 -18 GATATGTTCTCATCCTATATAGCTATCAGA 9 69 0 CATCCTATAT 0.911858 -223 CAGAAGAATTCATCTTTTCTGTTTTAAGGA 15 20 0 CATCTTTTCT 0.887338 -281 ********** Masking position 6 Map Score: 3.47887 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 272 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TATGAGGAATGCCGGGACCTCCAGAAGTG 4 10 0 GCCGGGACCT 0.970026 -51 CACTGTCTACTCCAGGATCTTTTATCAGTC 5 143 0 TCCAGGATCT 0.964482 -52 CTCTCCATGTTCGAGGATCTGCATTCACTG 5 168 0 TCGAGGATCT 0.943472 -27 GTCCAGGACATTGAAGTCAAA 8 28 0 TCCAGGACAT 0.767142 -11 AGATGCCTGACCCGGGATCTGATAGCTATA 9 52 1 CCCGGGATCT 0.969474 -240 ATCCTCACCCGGGAGGATATGTATCCACCC 9 119 0 GGGAGGATAT 0.881024 -173 ATCCTCCCGGGTGAGGATCTTTAGGTAGAC 9 131 1 GTGAGGATCT 0.868517 -161 TGGATCATTCGGTGGGATATCTACCAGAGG 9 163 0 GGTGGGATAT 0.780735 -129 TTTACTCTTTGGTGGGATCTTATAAAAACT 13 94 0 GGTGGGATCT 0.926576 -40 GAATCTTTCCCACAGGATCTCCAGTGATAG 15 175 1 CACAGGATCT 0.819326 -126 ********** Masking position 7 Map Score: 5.57383 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 382 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TTTTCATGGATTCACCCAGAAATCAAGTTTT 2 24 0 TTCACCCGAA 0.980108 -167 CCTATCCTATTCCTCCCTTAAACCTACAGCA 5 79 0 TCCTCCCTAA 0.918309 -116 AGGATATGTATCCACCCATAGACACTCTACC 9 105 0 TCCACCCTAG 0.943382 -187 TTAAATGCACCCATAAACGTTTTTAT 9 276 0 TGCACCCTAA 0.971499 -16 TGATTCACCGTTAACTGCTCTTTA 10 15 0 TTCACCGTAA 0.934159 -14 GCTGATTGAATTCAACCCTAAAAA 13 4 0 TTCAACCTAA 0.935158 -130 TCAGGTAAAATTCATCCAGAATTCTCAATAC 13 49 0 TTCATCCGAA 0.934872 -85 ACTTTTTTATCCTTAAAACAGAAAAG 15 6 1 TTTATCCTAA 0.739578 -295 ******* *** Masking position 10 Map Score: 3.05961 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 134 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 ********** No masking Map Score: 6.13499e-13 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: 6.13499e-13 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 12 ********** No masking Map Score: 6.13499e-13 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