AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_hinf_300.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 0.993559 -291 GTCGCATCAGGCATTGATTGCCGGATGCGGCA 1 31 1 GCATTGAGCC 0.925132 -270 AACTGTTGCCGACCTGTAGGCCGGATAAGGCA 1 67 0 GACCTGTGCC 0.992699 -234 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 102 1 GACGCGAGCG 0.993559 -199 GTCGCATCAGGCATTGATTGCCGGATGCGCAC 1 123 1 GCATTGAGCC 0.925132 -178 CCTGATAAGCGACTTGTGCGCATCCGGCAATC 1 138 0 GACTTGTGCA 0.928844 -163 AACTATTGCCGACCTGTAGGCCTGATAAGCGA 1 158 0 GACCTGTGCC 0.992699 -143 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 193 1 GACGCGAGCG 0.993559 -108 GGCATTGATTGCCGTGGATGCGCGCGAGCGCC 1 223 1 GCCGTGGGCG 0.993554 -78 TCGGATGCACGACCCGTAGGCCGGATAAGGCG 1 251 0 GACCCGTGCC 0.991984 -50 TTACTATTTCGCCGTGTTGACGACATCAGGAG 2 17 0 GCCGTGTACG 0.943079 -271 CGTTCATCTTTCCCTGGTTGCCAATGGCCCAT 2 188 1 TCCCTGGGCC 0.883372 -100 GATTGTTAATGCCGCGTAAGCAGTTGGTTCAT 3 38 1 GCCGCGTGCA 0.985407 -247 CCCACTTAATGCCGTGATTGCCAGTAAATCGA 3 167 1 GCCGTGAGCC 0.997355 -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 GCGTCGCATCAGGCATTGATTGCCGGATGCGG 1 29 1 AGGCATTGAG 0.978943 -272 GCCTACAGGTCGGCAACAGTTGTAGGCCTGAT 1 78 1 CGGCAACAGG 0.987671 -223 GCGTCGCATCAGGCATTGATTGCCGGATGCGC 1 121 1 AGGCATTGAG 0.978943 -180 GCCTACAGGTCGGCAATAGTTGTAGGCCTGAT 1 169 1 CGGCAATAGG 0.991873 -132 GCGTCGCATCAGGCATTGATTGCCGTGGATGC 1 212 1 AGGCATTGAG 0.978943 -89 GCCGTGTTGACGACATCAGGAGGCCAGT 2 7 0 CGACATCAGG 0.954504 -281 ATCGGCCGCCCGACAATACTGGAGATGAAT 3 9 0 CGACAATACG 0.84869 -276 ACTGCTTACGCGGCATTAACAATCGGCCGCCC 3 30 0 CGGCATTAAA 0.96867 -255 ACGAAAAGTACGGCATTGATAATCATTTTCAA 3 89 0 CGGCATTGAA 0.966572 -196 CTGGCAATCACGGCATTAAGTGGGTGATTTGC 3 159 0 CGGCATTAAG 0.995042 -126 TCGACAACGGCGGCAACAGGCGAAAGGTTAAT 3 195 1 CGGCAACAGG 0.98748 -90 ********* * Masking position 5 Map Score: 20.9115 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1265 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 TGATGCGACGCTGTCGCGTCTTATCAGGC 1 10 0 CTGTCGCGTC 0.983659 -291 CCTTATCCGGCCTACAGGTCGGCAACAGTT 1 69 1 CCTACAGGTC 0.950522 -232 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 102 0 CTGTCGCGTC 0.983659 -199 GCTTATCAGGCCTACAGGTCGGCAATAGTT 1 160 1 CCTACAGGTC 0.950522 -141 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 193 0 CTGTCGCGTC 0.983659 -108 CCTTATCCGGCCTACGGGTCGTGCATCCGA 1 253 1 CCTACGGGTC 0.973361 -48 CCTGATGTCGTCAACACGGCGAAATAGTAA 2 19 1 TCAACACGGC 0.860728 -269 ATTGTGAACATCATCACGTTCATCTTTCCC 2 172 1 TCATCACGTT 0.67258 -116 GAATTCGCGACCTTCTCGTTACTGACAGGA 2 222 0 CCTTCTCGTT 0.816672 -66 AGGCGCTTTTTAGACTGGTCGTAATGAAAT 2 252 1 TAGACTGGTC 0.538983 -36 GAACCAACTGCTTACGCGGCATTAACAATC 3 38 0 CTTACGCGGC 0.929527 -247 GATTTACTGGCAATCACGGCATTAAGTGGG 3 167 0 CAATCACGGC 0.798916 -118 ATTTTTACACTCATCTCGTCGGAGATGTGA 3 237 1 TCATCTCGTC 0.916839 -48 TCATCATTTTTCGTCGCGTCACATCTCCGA 3 255 0 TCGTCGCGTC 0.985095 -30 ********** Masking position 5 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 0.996664 -236 CGCGTCTTATCAGGCCTACAACTGTTGCCG 1 88 0 CAGGCCTACA 0.997246 -213 AGTCGCTTATCAGGCCTACAGGTCGGCAAT 1 156 1 CAGGCCTACA 0.997246 -145 CGCGTCTTATCAGGCCTACAACTATTGCCG 1 179 0 CAGGCCTACA 0.997246 -122 AGCGCCTTATCCGGCCTACGGGTCGTGCAT 1 249 1 CCGGCCTACG 0.985874 -52 ACCGAATTTACAGGAACACAGAAC 1 287 1 CAGGAACACA 0.928528 -14 GTGAGCATCACATCACCACAATTCAGCAAA 2 143 1 CATCACCACA 0.776482 -145 TGAAATTCAGCAGGATCACATT 2 276 1 CAGGATCACA 0.928528 -12 TAACAATCGGCCGCCCGACAATACTGGAGA 3 16 0 CCGCCCGACA 0.970819 -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 0.968215 -23 ACCGCATTTCCTGAAAATTCACGCTGTATCTT 2 113 0 CTGAAATTCC 0.966566 -175 CACCACAATTCAGCAAATTGTGAACATCATCA 2 156 1 CAGAAATTGG 0.990806 -132 TCGTTACTGACAGGAAAATGGGCCATTGGCAA 2 205 0 CAGAAAATGG 0.983431 -83 TATGGTTTTGCAGGAAAATGCCCGAGATGTGA 3 126 1 CAGAAAATGC 0.983436 -159 CCGTGATTGCCAGTAAATCGACAACGGCGGCA 3 178 1 CAGAAATCGC 0.975903 -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 CGACGCTGTCGCGTCTTATCAGGC 1 5 0 GCGTCTTATC 0.991405 -296 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 19 1 GCGTCGCATC 0.99824 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAA 1 44 0 GTGCCGCATC 0.939356 -257 CGACGCTGTCGCGTCTTATCAGGCCTACAA 1 97 0 GCGTCTTATC 0.991405 -204 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 111 1 GCGTCGCATC 0.99824 -190 CGACGCTGTCGCGTCTTATCAGGCCTACAA 1 188 0 GCGTCTTATC 0.991405 -113 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 202 1 GCGTCGCATC 0.99824 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGG 1 240 1 GCGCCTTATC 0.975595 -61 AATGCGGTGAGCATCACATCACCACAATTC 2 137 1 GCATCACATC 0.982173 -151 AAATTCAGCAGGATCACATT 2 278 1 GGATCACATT 0.315842 -10 TGGGTGATTTGCTTCACATCTCGGGCATTT 3 141 0 GCTTCACATC 0.968986 -144 ATTTTTCGTCGCGTCACATCTCCGACGAGA 3 250 0 GCGTCACATC 0.997212 -35 ********** Masking position 8 Map Score: 38.505 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 373 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 GGAAAACCACGTAAAAAACGTCGATTTTTC 2 83 1 GTAAAAAACG 0.962387 -205 CGCTGTATCTTGAAAAATCGACGTTTTTTA 2 94 0 TGAAAAATCG 0.949558 -194 TACGACCAGTCTAAAAAGCGCCTGAATTCG 2 245 0 CTAAAAAGCG 0.953716 -43 TTACGCGGCATTAACAATCGGCCGCCCGAC 3 27 0 TTAACAATCG 0.949566 -258 CGAGATGAGTGTAAAAATCGTGCTGTCGAT 3 225 0 GTAAAAATCG 0.984767 -60 ********** Masking position 6 Map Score: 1.6715 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 98 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 CAGGCATTGATTGCCGTGGATGCGCGCGAG 1 221 1 TTGCCGTGGA 0.984745 -80 GATTACTATTTCGCCGTGTTGACGACATCA 2 21 0 TCGCCGTGTT 0.844909 -267 TTTACGTGGTTTTCCGTCGAAAATTTAAGG 2 68 0 TTTCCGTCGA 0.985124 -220 ATCGACGTTTTTTACGTGGTTTTCCGTCGA 2 78 0 TTTACGTGGT 0.91937 -210 CACGTTCATCTTTCCCTGGTTGCCAATGGC 2 186 1 TTTCCCTGGT 0.935698 -102 CTTTCGCCTGTTGCCGCCGTTGTCGATTTA 3 191 0 TTGCCGCCGT 0.963605 -94 TCGCGTCACATCTCCGACGAGATGAGTGTA 3 242 0 TCTCCGACGA 0.878715 -43 TCCTCATCATTTTTCGTCGCGTCACATCTC 3 258 0 TTTTCGTCGC 0.837026 -27 ********** Masking position 1 Map Score: 3.5945 Number of sites scoring better than the average of aligned sites = 1436 Number in coding regions = 1365 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 ********** 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 11 ********** 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 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