AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_opreg_100.orf -g0.5 -x5 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 = 0 Input sequences: #1 rhaD 300 rhamnulose-phosphate aldolase #2 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #3 rhaT 284 rhamnose transport Motif number 1 CGACGCTGTCGCGTCTTATCAGGC 1 1 0 GGCTATCGGC 0.999405 -300 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 19 1 GGCCATCGGC 0.999547 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAATGCC 1 40 0 GGCCATCGGC 0.999548 -261 TGCGGCACAAGTGCCTTATCCGGCCTACAGGTCG 1 56 1 GGCTATCGGC 0.999446 -245 CGACGCTGTCGCGTCTTATCAGGCCTACAACTGT 1 93 0 GGCTATCGGC 0.999405 -208 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 111 1 GGCCATCGGC 0.999547 -190 ATAAGCGACTTGTGCGCATCCGGCAATCAATGCC 1 132 0 TTCCATCGGC 0.957384 -169 ATGCGCACAAGTCGCTTATCAGGCCTACAGGTCG 1 147 1 GCCTATCGGC 0.998395 -154 CGACGCTGTCGCGTCTTATCAGGCCTACAACTAT 1 184 0 GGCTATCGGC 0.999405 -117 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 202 1 GGCCATCGGC 0.999547 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 240 1 GGCTATCGGC 0.999405 -61 CGGCCTACGGGTCGTGCATCCGACAACACCGAAT 1 260 1 GCTCATCGAC 0.877088 -41 GGTGATTTGCTTCACATCTCGGGCATTTTCCTGC 3 135 0 TCCTCTCGGC 0.965508 -150 TTTTCGTCGCGTCACATCTCCGACGAGATGAGTG 3 244 0 GCCTCTCGAC 0.964848 -41 * * * **** *** Masking position 9 Map Score: 63.4727 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 163 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 GCCTGATAAGACGCGACAGCGTCGCATCAGG 1 10 1 GACGCGAGCG 0.993131 -291 GTCGCATCAGGCATTGATTGCCGGATGCGGCA 1 31 1 GCATTGAGCC 0.92052 -270 AACTGTTGCCGACCTGTAGGCCGGATAAGGCA 1 67 0 GACCTGTGCC 0.992221 -234 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 102 1 GACGCGAGCG 0.993131 -199 GTCGCATCAGGCATTGATTGCCGGATGCGCAC 1 123 1 GCATTGAGCC 0.92052 -178 CCTGATAAGCGACTTGTGCGCATCCGGCAATC 1 138 0 GACTTGTGCA 0.924443 -163 AACTATTGCCGACCTGTAGGCCTGATAAGCGA 1 158 0 GACCTGTGCC 0.992221 -143 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 193 1 GACGCGAGCG 0.993131 -108 GGCATTGATTGCCGTGGATGCGCGCGAGCGCC 1 223 1 GCCGTGGGCG 0.993125 -78 TCGGATGCACGACCCGTAGGCCGGATAAGGCG 1 251 0 GACCCGTGCC 0.991458 -50 TTACTATTTCGCCGTGTTGACGACATCAGGAG 2 17 0 GCCGTGTACG 0.9395 -271 CGTTCATCTTTCCCTGGTTGCCAATGGCCCAT 2 188 1 TCCCTGGGCC 0.876531 -100 GATTGTTAATGCCGCGTAAGCAGTTGGTTCAT 3 38 1 GCCGCGTGCA 0.984446 -247 CCCACTTAATGCCGTGATTGCCAGTAAATCGA 3 167 1 GCCGTGAGCC 0.997178 -118 ******* *** Masking position 11 Map Score: 32.3378 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1369 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 3 CCGCATCCGGCAATCAATGCCTGATGCGACGC 1 29 0 CTCAATGCCT 0.983235 -272 ATCAGGCCTACAACTGTTGCCGACCTGTAGGC 1 78 0 CCTGTTGCCG 0.985276 -223 GCGCATCCGGCAATCAATGCCTGATGCGACGC 1 121 0 CTCAATGCCT 0.983235 -180 ATCAGGCCTACAACTATTGCCGACCTGTAGGC 1 169 0 CCTATTGCCG 0.989263 -132 GCATCCACGGCAATCAATGCCTGATGCGACGC 1 212 0 CTCAATGCCT 0.983235 -89 ACTGGCCTCCTGATGTCGTCAACACGGC 2 7 1 CCTGATGTCG 0.928213 -281 GGGCGGCCGATTGTTAATGCCGCGTAAGCAGT 3 30 1 TTTAATGCCG 0.970732 -255 TTGAAAATGATTATCAATGCCGTACTTTTCGT 3 89 1 TTCAATGCCG 0.972924 -196 GCAAATCACCCACTTAATGCCGTGATTGCCAG 3 159 1 CTTAATGCCG 0.994815 -126 ATTAACCTTTCGCCTGTTGCCGCCGTTGTCGA 3 195 0 CCTGTTGCCG 0.985032 -90 * ********* Masking position 8 Map Score: 20.4579 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 876 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 GCCTGATAAGACGCGACAGCGTCGCATCA 1 10 1 GACGCGACAG 0.983831 -291 AACTGTTGCCGACCTGTAGGCCGGATAAGG 1 69 0 GACCTGTAGG 0.951026 -232 GGCCTGATAAGACGCGACAGCGTCGCATCA 1 102 1 GACGCGACAG 0.983831 -199 AACTATTGCCGACCTGTAGGCCTGATAAGC 1 160 0 GACCTGTAGG 0.951026 -141 GGCCTGATAAGACGCGACAGCGTCGCATCA 1 193 1 GACGCGACAG 0.983831 -108 TCGGATGCACGACCCGTAGGCCGGATAAGG 1 253 0 GACCCGTAGG 0.973638 -48 TTACTATTTCGCCGTGTTGACGACATCAGG 2 19 0 GCCGTGTTGA 0.862012 -269 GGGAAAGATGAACGTGATGATGTTCACAAT 2 172 0 AACGTGATGA 0.674944 -116 TCCTGTCAGTAACGAGAAGGTCGCGAATTC 2 222 1 AACGAGAAGG 0.818276 -66 ATTTCATTACGACCAGTCTAAAAAGCGCCT 2 252 0 GACCAGTCTA 0.541654 -36 GATTGTTAATGCCGCGTAAGCAGTTGGTTC 3 38 1 GCCGCGTAAG 0.930228 -247 CCCACTTAATGCCGTGATTGCCAGTAAATC 3 167 1 GCCGTGATTG 0.800638 -118 TCACATCTCCGACGAGATGAGTGTAAAAAT 3 237 0 GACGAGATGA 0.917655 -48 TCGGAGATGTGACGCGACGAAAAATGATGA 3 255 1 GACGCGACGA 0.985252 -30 ********** Masking position 3 Map Score: 18.9039 Number of sites scoring better than the average of aligned sites = 2853 Number in coding regions = 2631 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 AGTGCCTTATCCGGCCTACAGGTCGGCAAC 1 65 1 CCGGCCTACA 0.996941 -236 CGCGTCTTATCAGGCCTACAACTGTTGCCG 1 88 0 CAGGCCTACA 0.997476 -213 AGTCGCTTATCAGGCCTACAGGTCGGCAAT 1 156 1 CAGGCCTACA 0.997476 -145 CGCGTCTTATCAGGCCTACAACTATTGCCG 1 179 0 CAGGCCTACA 0.997476 -122 AGCGCCTTATCCGGCCTACGGGTCGTGCAT 1 249 1 CCGGCCTACG 0.987039 -52 ACCGAATTTACAGGAACACAGAAC 1 287 1 CAGGAACACA 0.934103 -14 GTGAGCATCACATCACCACAATTCAGCAAA 2 143 1 CATCACCACA 0.791251 -145 TGAAATTCAGCAGGATCACATT 2 276 1 CAGGATCACA 0.934103 -12 TAACAATCGGCCGCCCGACAATACTGGAGA 3 16 0 CCGCCCGACA 0.97319 -269 ********** Masking position 8 Map Score: 19.6447 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 236 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TTCTGTGTTCCTGTAAATTCGGTGTTGTCGGA 1 278 0 CTGAAATTCG 0.964095 -23 ACCGCATTTCCTGAAAATTCACGCTGTATCTT 2 113 0 CTGAAATTCC 0.962652 -175 CACCACAATTCAGCAAATTGTGAACATCATCA 2 156 1 CAGAAATTGG 0.989604 -132 TCGTTACTGACAGGAAAATGGGCCATTGGCAA 2 205 0 CAGAAAATGG 0.98117 -83 TATGGTTTTGCAGGAAAATGCCCGAGATGTGA 3 126 1 CAGAAAATGC 0.981174 -159 CCGTGATTGCCAGTAAATCGACAACGGCGGCA 3 178 1 CAGAAATCGC 0.972642 -107 *** ****** * Masking position 6 Map Score: 4.24806 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 150 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ATCCGGCAATCAATGCCTGATGCGACGCTG 1 27 0 CAATGCCTGA 0.983763 -274 GATGCGGCACAAGTGCCTTATCCGGCCTAC 1 54 1 AAGTGCCTTA 0.980482 -247 ATCCGGCAATCAATGCCTGATGCGACGCTG 1 119 0 CAATGCCTGA 0.983763 -182 TAGGCCTGATAAGCGACTTGTGCGCATCCG 1 144 0 AAGCGACTTG 0.642808 -157 CCACGGCAATCAATGCCTGATGCGACGCTG 1 210 0 CAATGCCTGA 0.983763 -91 GGATGCGCGCGAGCGCCTTATCCGGCCTAC 1 238 1 GAGCGCCTTA 0.964702 -63 AATTTAAGGTAAGAACCTGACCTCGTGATT 2 47 0 AAGAACCTGA 0.813529 -241 CCAGTCTAAAAAGCGCCTGAATTCGCGACC 2 240 0 AAGCGCCTGA 0.993599 -48 ********** Masking position 2 Map Score: 8.72961 Number of sites scoring better than the average of aligned sites = 1826 Number in coding regions = 1675 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 8 TCGCGCGCATCCACGGCAATCAATGCCTGA 1 220 0 CCACGGCAAT 0.97418 -81 CTTAAATTTTCGACGGAAAACCACGTAAAA 2 69 1 CGACGGAAAA 0.991379 -219 CGACGGAAAACCACGTAAAAAACGTCGATT 2 79 1 CCACGTAAAA 0.956588 -209 CCATTGGCAACCAGGGAAAGATGAACGTGA 2 185 0 CCAGGGAAAG 0.939268 -103 AAATCGACAACGGCGGCAACAGGCGAAAGG 3 192 1 CGGCGGCAAC 0.953374 -93 AGATGTGACGCGACGAAAAATGATGAGGAT 3 259 1 CGACGAAAAA 0.956588 -26 ********** Masking position 8 Map Score: 1.66375 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 515 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 GCCTGATAAGACGCGACAGCGTCGCATCAG 1 11 1 ACGCGACAGC 0.981164 -290 GCCTGATAAGACGCGACAGCGTCGCATCAG 1 103 1 ACGCGACAGC 0.981164 -198 GCCTGATAAGACGCGACAGCGTCGCATCAG 1 194 1 ACGCGACAGC 0.981164 -107 CGCTCGCGCGCATCCACGGCAATCAATGCC 1 223 0 CATCCACGGC 0.978864 -78 CGGCATTAACAATCGGCCGCCCGACAATAC 3 22 0 AATCGGCCGC 0.942371 -263 GAACCAACTGCTTACGCGGCATTAACAATC 3 38 0 CTTACGCGGC 0.512769 -247 GATTTACTGGCAATCACGGCATTAAGTGGG 3 167 0 CAATCACGGC 0.73488 -118 AGTAAATCGACAACGGCGGCAACAGGCGAA 3 189 1 CAACGGCGGC 0.975448 -96 GCGAAAGGTTAATCGACAGCACGATTTTTA 3 214 1 AATCGACAGC 0.977782 -71 ********** Masking position 7 Map Score: 7.20738 Number of sites scoring better than the average of aligned sites = 3136 Number in coding regions = 3018 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 10 GTAATCACGAGGTCAGGTTCTTACCTTAAATTT 2 45 1 GGTCAGTCTA 0.765592 -243 CAGGAAATGCGGTGAGCATCACATCACCACAAT 2 132 1 GGTGAGTCAA 0.976122 -156 AGATGAACGTGATGATGTTCACAATTTGCTGAA 2 164 0 GATGATTCAA 0.909314 -124 ATTTCATTACGACCAGTCTAAAAAGCGCCTGAA 2 249 0 GACCAGTAAA 0.919938 -39 AAATGCCCGAGATGTGAAGCAAATCACCCACTT 3 141 1 GATGTGGCAA 0.914485 -144 TCTCCGACGAGATGAGTGTAAAAATCGTGCTGT 3 229 0 GATGAGTAAA 0.98286 -56 TCGGAGATGTGACGCGACGAAAAATGATGAGGA 3 255 1 GACGCGGAAA 0.849823 -30 GACGAAAAATGATGAGGATAAGAAG 3 270 1 GATGAGTAAA 0.98285 -15 ****** *** * Masking position 13 Map Score: 0.701061 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 321 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 TGTGGTGATGTGATGCTCACCGCATTTCCTGAA 2 130 0 TGACTCACCC 0.982944 -158 CAGCAAATTGTGAACATCATCACGTTCATCTTT 2 166 1 TGAATCATCC 0.984445 -122 GTGATCCTGCTGAATTTCATTACGACCAGTCTA 2 262 0 TGATTCATTC 0.907321 -26 AGTACGGCATTGATAATCATTTTCAATATCATT 3 82 0 TGAATCATTT 0.824855 -203 GTGGGTGATTTGCTTCACATCTCGGGCATTTTC 3 139 0 TGCCACATCC 0.922865 -146 AGCACGATTTTTACACTCATCTCGTCGGAGATG 3 231 1 TTACTCATCC 0.980803 -54 CTTCTTATCCTCATCATTTTTCGTCGC 3 268 0 TTACTCATCT 0.933055 -17 *** ****** * Masking position 9 Map Score: 0.589354 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 365 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 ********** No masking Map Score: -1.44708e-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 13 ********** No masking Map Score: -1.44708e-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 14 ********** No masking Map Score: -1.44708e-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