AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_hinf_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 0.999421 -300 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 19 1 GGCCATCGGC 0.999561 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAATGCC 1 40 0 GGCCATCGGC 0.999563 -261 TGCGGCACAAGTGCCTTATCCGGCCTACAGGTCG 1 56 1 GGCTATCGGC 0.999463 -245 CGACGCTGTCGCGTCTTATCAGGCCTACAACTGT 1 93 0 GGCTATCGGC 0.999421 -208 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 111 1 GGCCATCGGC 0.999561 -190 ATAAGCGACTTGTGCGCATCCGGCAATCAATGCC 1 132 0 TTCCATCGGC 0.958665 -169 ATGCGCACAAGTCGCTTATCAGGCCTACAGGTCG 1 147 1 GCCTATCGGC 0.99842 -154 CGACGCTGTCGCGTCTTATCAGGCCTACAACTAT 1 184 0 GGCTATCGGC 0.999421 -117 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 202 1 GGCCATCGGC 0.999561 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 240 1 GGCTATCGGC 0.999421 -61 CGGCCTACGGGTCGTGCATCCGACAACACCGAAT 1 260 1 GCTCATCGAC 0.880481 -41 GGTGATTTGCTTCACATCTCGGGCATTTTCCTGC 3 135 0 TCCTCTCGGC 0.966554 -150 TTTTCGTCGCGTCACATCTCCGACGAGATGAGTG 3 244 0 GCCTCTCGAC 0.965871 -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 0.992642 -291 GTCGCATCAGGCATTGATTGCCGGATGCGGCA 1 31 1 GCATTGAGCC 0.915305 -270 AACTGTTGCCGACCTGTAGGCCGGATAAGGCA 1 67 0 GACCTGTGCC 0.991674 -234 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 102 1 GACGCGAGCG 0.992642 -199 GTCGCATCAGGCATTGATTGCCGGATGCGCAC 1 123 1 GCATTGAGCC 0.915305 -178 CCTGATAAGCGACTTGTGCGCATCCGGCAATC 1 138 0 GACTTGTGCA 0.919463 -163 AACTATTGCCGACCTGTAGGCCTGATAAGCGA 1 158 0 GACCTGTGCC 0.991674 -143 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 193 1 GACGCGAGCG 0.992642 -108 GGCATTGATTGCCGTGGATGCGCGCGAGCGCC 1 223 1 GCCGTGGGCG 0.992636 -78 TCGGATGCACGACCCGTAGGCCGGATAAGGCG 1 251 0 GACCCGTGCC 0.990858 -50 TTACTATTTCGCCGTGTTGACGACATCAGGAG 2 17 0 GCCGTGTACG 0.935443 -271 CGTTCATCTTTCCCTGGTTGCCAATGGCCCAT 2 188 1 TCCCTGGGCC 0.868842 -100 GATTGTTAATGCCGCGTAAGCAGTTGGTTCAT 3 38 1 GCCGCGTGCA 0.98335 -247 CCCACTTAATGCCGTGATTGCCAGTAAATCGA 3 167 1 GCCGTGAGCC 0.996977 -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 TGATGCGACGCTGTCGCGTCTTATCAGGC 1 10 0 CTGTCGCGTC 0.983716 -291 CCTTATCCGGCCTACAGGTCGGCAACAGTT 1 69 1 CCTACAGGTC 0.95069 -232 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 102 0 CTGTCGCGTC 0.983716 -199 GCTTATCAGGCCTACAGGTCGGCAATAGTT 1 160 1 CCTACAGGTC 0.95069 -141 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 193 0 CTGTCGCGTC 0.983716 -108 CCTTATCCGGCCTACGGGTCGTGCATCCGA 1 253 1 CCTACGGGTC 0.973454 -48 CCTGATGTCGTCAACACGGCGAAATAGTAA 2 19 1 TCAACACGGC 0.861156 -269 ATTGTGAACATCATCACGTTCATCTTTCCC 2 172 1 TCATCACGTT 0.673366 -116 GAATTCGCGACCTTCTCGTTACTGACAGGA 2 222 0 CCTTCTCGTT 0.817206 -66 AGGCGCTTTTTAGACTGGTCGTAATGAAAT 2 252 1 TAGACTGGTC 0.53987 -36 GAACCAACTGCTTACGCGGCATTAACAATC 3 38 0 CTTACGCGGC 0.929761 -247 GATTTACTGGCAATCACGGCATTAAGTGGG 3 167 0 CAATCACGGC 0.799489 -118 ATTTTTACACTCATCTCGTCGGAGATGTGA 3 237 1 TCATCTCGTC 0.917111 -48 TCATCATTTTTCGTCGCGTCACATCTCCGA 3 255 0 TCGTCGCGTC 0.985147 -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 4 GCGTCGCATCAGGCATTGATTGCCGGATGCGG 1 29 1 AGGCATTGAG 0.977371 -272 GCCTACAGGTCGGCAACAGTTGTAGGCCTGAT 1 78 1 CGGCAACAGG 0.986746 -223 GCGTCGCATCAGGCATTGATTGCCGGATGCGC 1 121 1 AGGCATTGAG 0.977371 -180 GCCTACAGGTCGGCAATAGTTGTAGGCCTGAT 1 169 1 CGGCAATAGG 0.991315 -132 GCGTCGCATCAGGCATTGATTGCCGTGGATGC 1 212 1 AGGCATTGAG 0.977371 -89 GCCGTGTTGACGACATCAGGAGGCCAGT 2 7 0 CGACATCAGG 0.951197 -281 ATCGGCCGCCCGACAATACTGGAGATGAAT 3 9 0 CGACAATACG 0.838991 -276 ACTGCTTACGCGGCATTAACAATCGGCCGCCC 3 30 0 CGGCATTAAA 0.966357 -255 ACGAAAAGTACGGCATTGATAATCATTTTCAA 3 89 0 CGGCATTGAA 0.964109 -196 CTGGCAATCACGGCATTAAGTGGGTGATTTGC 3 159 0 CGGCATTAAG 0.994665 -126 TCGACAACGGCGGCAACAGGCGAAAGGTTAAT 3 195 1 CGGCAACAGG 0.986568 -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 5 GTTGCCGACCTGTAGGCCGGATAAGGCACT 1 65 0 TGTAGGCCGG 0.996825 -236 CGGCAACAGTTGTAGGCCTGATAAGACGCG 1 88 1 TGTAGGCCTG 0.99738 -213 ATTGCCGACCTGTAGGCCTGATAAGCGACT 1 156 0 TGTAGGCCTG 0.99738 -145 CGGCAATAGTTGTAGGCCTGATAAGACGCG 1 179 1 TGTAGGCCTG 0.99738 -122 ATGCACGACCCGTAGGCCGGATAAGGCGCT 1 249 0 CGTAGGCCGG 0.986552 -52 GTTCTGTGTTCCTGTAAATTCGGT 1 287 0 TGTGTTCCTG 0.931767 -14 TTTGCTGAATTGTGGTGATGTGATGCTCAC 2 143 0 TGTGGTGATG 0.785016 -145 AATGTGATCCTGCTGAATTTCA 2 276 0 TGTGATCCTG 0.931767 -12 TCTCCAGTATTGTCGGGCGGCCGATTGTTA 3 16 1 TGTCGGGCGG 0.972199 -269 ********** Masking position 3 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 0.963975 -23 ACCGCATTTCCTGAAAATTCACGCTGTATCTT 2 113 0 CTGAAATTCC 0.962537 -175 CACCACAATTCAGCAAATTGTGAACATCATCA 2 156 1 CAGAAATTGG 0.989569 -132 TCGTTACTGACAGGAAAATGGGCCATTGGCAA 2 205 0 CAGAAAATGG 0.981104 -83 TATGGTTTTGCAGGAAAATGCCCGAGATGTGA 3 126 1 CAGAAAATGC 0.981108 -159 CCGTGATTGCCAGTAAATCGACAACGGCGGCA 3 178 1 CAGAAATCGC 0.972547 -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 GCCTGATAAGACGCGACAGCGTCG 1 5 1 GATAAGACGC 0.992148 -296 ATCAATGCCTGATGCGACGCTGTCGCGTCT 1 19 0 GATGCGACGC 0.998393 -282 TTGATTGCCGGATGCGGCACAAGTGCCTTA 1 44 1 GATGCGGCAC 0.944349 -257 TTGTAGGCCTGATAAGACGCGACAGCGTCG 1 97 1 GATAAGACGC 0.992148 -204 ATCAATGCCTGATGCGACGCTGTCGCGTCT 1 111 0 GATGCGACGC 0.998393 -190 TTGTAGGCCTGATAAGACGCGACAGCGTCG 1 188 1 GATAAGACGC 0.992148 -113 ATCAATGCCTGATGCGACGCTGTCGCGTCT 1 202 0 GATGCGACGC 0.998393 -99 CCGTAGGCCGGATAAGGCGCTCGCGCGCAT 1 240 0 GATAAGGCGC 0.977675 -61 GAATTGTGGTGATGTGATGCTCACCGCATT 2 137 0 GATGTGATGC 0.983702 -151 AATGTGATCCTGCTGAATTT 2 278 0 AATGTGATCC 0.335874 -10 AAATGCCCGAGATGTGAAGCAAATCACCCA 3 141 1 GATGTGAAGC 0.971613 -144 TCTCGTCGGAGATGTGACGCGACGAAAAAT 3 250 1 GATGTGACGC 0.997454 -35 ********** Masking position 2 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 GTAGGCCGGATAAGGCACTTGTGCCGCATC 1 54 0 TAAGGCACTT 0.973314 -247 CGGATGCGCACAAGTCGCTTATCAGGCCTA 1 144 1 CAAGTCGCTT 0.925984 -157 GTAGGCCGGATAAGGCGCTCGCGCGCATCC 1 238 0 TAAGGCGCTC 0.984911 -63 AATCACGAGGTCAGGTTCTTACCTTAAATT 2 47 1 TCAGGTTCTT 0.882982 -241 GGTCGCGAATTCAGGCGCTTTTTAGACTGG 2 240 1 TCAGGCGCTT 0.993649 -48 ********** Masking position 3 Map Score: 1.80996 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 372 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 GAAAAATCGACGTTTTTTACGTGGTTTTCC 2 83 0 CGTTTTTTAC 0.959746 -205 TAAAAAACGTCGATTTTTCAAGATACAGCG 2 94 1 CGATTTTTCA 0.946068 -194 CGAATTCAGGCGCTTTTTAGACTGGTCGTA 2 245 1 CGCTTTTTAG 0.950498 -43 GTCGGGCGGCCGATTGTTAATGCCGCGTAA 3 27 1 CGATTGTTAA 0.946075 -258 ATCGACAGCACGATTTTTACACTCATCTCG 3 225 1 CGATTTTTAC 0.983671 -60 ********** Masking position 5 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 10 CAGGCATTGATTGCCGTGGATGCGCGCGAG 1 221 1 TTGCCGTGGA 0.984116 -80 GATTACTATTTCGCCGTGTTGACGACATCA 2 21 0 TCGCCGTGTT 0.839184 -267 TTTACGTGGTTTTCCGTCGAAAATTTAAGG 2 68 0 TTTCCGTCGA 0.984504 -220 ATCGACGTTTTTTACGTGGTTTTCCGTCGA 2 78 0 TTTACGTGGT 0.91612 -210 CACGTTCATCTTTCCCTGGTTGCCAATGGC 2 186 1 TTTCCCTGGT 0.933057 -102 CTTTCGCCTGTTGCCGCCGTTGTCGATTTA 3 191 0 TTGCCGCCGT 0.962068 -94 TCGCGTCACATCTCCGACGAGATGAGTGTA 3 242 0 TCTCCGACGA 0.874796 -43 TCCTCATCATTTTTCGTCGCGTCACATCTC 3 258 0 TTTTCGTCGC 0.831068 -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 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 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