AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iiclR_ecoli_opreg_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 metA 156 homoserine transsuccinylase #2 aceB 268 malate synthase A #3 aceA 29 isocitrate lyase #4 aceK 182 isocitrate dehydrogenase kinase/phosphatase #5 iclR 160 repressor of aceBA operon Motif number 1 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 4 27 0 CGCCATCCGC 0.999664 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 4 44 1 CGCCATCCGC 0.999664 -139 GACGCGCAAGCGTCGCATCAGGCATCGTGCACC 4 71 0 CGTCATCAGC 0.997061 -112 GACGCTTGCGCGTCTTATCATGCCTACAGCCGT 4 90 1 CGTCATCAGC 0.997061 -93 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 4 125 0 CGCCATCCGC 0.999664 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 4 142 1 CGCCATCCGC 0.999664 -41 **** **** ** Masking position 7 Map Score: 23.079 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 55 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 CTGGATGTCTAAACGTATAAGCGTATGTAGTGA 1 122 1 AACGTTAGCG 0.976283 -35 AGGCCGGATAAGGCGTTCACGCCGCATCCGGCA 4 35 1 AGCGTCAGCC 0.997724 -148 AGGCATGATAAGACGCGCAAGCGTCGCATCAGG 4 82 0 AACGCCAGCG 0.986085 -101 GCGTCTTATCATGCCTACAGCCGTTGCCGAACG 4 99 1 AGCCTCACCG 0.964797 -84 AGGCTGGATAAGGCGTTTACGCCGCATCCGGCA 4 133 1 AGCGTTAGCC 0.994197 -50 CTTGCTCCCGACACGCTCAACCCAGATTTAATA 5 12 1 AACGCCACCC 0.986085 -149 TTTACCACAGATGCGTTTATGCCAGTATGGTTT 5 55 0 AGCGTTAGCC 0.994197 -106 TCTGTGGTAAAAGCGACCACCACGCAACATGAG 5 77 1 AGCGACACAC 0.881264 -84 * **** ** *** Masking position 9 Map Score: 9.47463 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 432 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 CCTGAGGTAAGGTGCTGAATCGCTTAACGA 2 28 0 GGTGCTGAAT 0.989374 -241 TAGTCTTAGTTGTGCTGAACGAAAAGAGCA 2 192 1 TGTGCTGAAC 0.981296 -77 TCCATGACGAGGAGCTGCACG 2 258 1 GGAGCTGCAC 0.924739 -11 AACAACAACCGTTGCTGACTGTAGGCCGGA 4 13 1 GTTGCTGACT 0.959555 -170 GCCTACAGCCGTTGCCGAACGTAGGCTGGA 4 111 1 GTTGCCGAAC 0.979813 -72 GCCAGTATGGTTTGTTGAATTTTTATTAAA 5 38 0 TTTGTTGAAT 0.731819 -123 TAATGCAATAGTTACTGAACTGATCCGATG 5 128 0 GTTACTGAAC 0.953646 -33 ********** Masking position 7 Map Score: 4.97599 Number of sites scoring better than the average of aligned sites = 1297 Number in coding regions = 1241 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 CCTTCAACATGCAGGCTCGACATTGGCAAA 1 70 1 GCAGGCTCGA 0.988052 -87 GTTGCTGACTGTAGGCCGGATAAGGCGTTC 4 23 1 GTAGGCCGGA 0.995115 -160 GGCAACGGCTGTAGGCATGATAAGACGCGC 4 97 0 GTAGGCATGA 0.982256 -86 GTTGCCGAACGTAGGCTGGATAAGGCGTTT 4 121 1 GTAGGCTGGA 0.996304 -62 ********** Masking position 3 Map Score: 4.10976 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 39 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 ACTTTCTCACCTTCAACATGCAGGCTCGAC 1 61 1 CTTCAACATG 0.926485 -96 CAACATGCAGGCTCGACATTGGCAAATTTT 1 74 1 GCTCGACATT 0.657212 -83 CCGAAACGTACCTCAGCAGGTGAATAAATT 2 82 1 CCTCAGCAGG 0.979448 -187 CGTGCAGCTCCTCGTCATGGATCCGAAAA 2 250 0 CCTCGTCATG 0.974695 -19 GGCGTTCACGCCGCATCCGGCAATCGGTGC 4 46 1 CCGCATCCGG 0.9634 -137 CGCGCAAGCGTCGCATCAGGCATCGTGCAC 4 72 0 TCGCATCAGG 0.952199 -111 GGCGTTTACGCCGCATCCGGCAATTCTCTG 4 144 1 CCGCATCCGG 0.9634 -39 TTAGCGCCCTCATCAGGAGCAGAGAAT 4 166 0 CCTCATCAGG 0.948108 -17 AGCGACCACCACGCAACATGAGATTTGTTC 5 88 1 ACGCAACATG 0.91107 -73 CATGAGATTTGTTCAACATTAACTCATCGG 5 104 1 GTTCAACATT 0.435287 -57 ********** Masking position 4 Map Score: 10.5921 Number of sites scoring better than the average of aligned sites = 2329 Number in coding regions = 1797 Number in noncoding regions = 532 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 6 CTGAAGATAACCAGAAAATTTGCCAATGTC 1 88 0 CCAGAAAATT 0.759477 -69 GCACCTTACCTCAGGCACCTTCGGGTGCCT 2 43 1 TCAGGCACCT 0.938487 -226 CTTTTTTATTTCCGAAACGTACCTCAGCAG 2 71 1 TCCGAAACGT 0.957308 -198 TCGTCATGGATCCGAAAACTTCCCCACTGT 2 238 0 TCCGAAAACT 0.948899 -31 TCACGCCGCATCCGGCAATCGGTGCACGAT 4 51 1 TCCGGCAATC 0.966521 -132 TTACGCCGCATCCGGCAATTCTCTGCTCCT 4 149 1 TCCGGCAATT 0.977222 -34 ACTTGCTCCCGACACGCTCAACCCAGA 5 8 1 CCCGACACGC 0.954485 -153 ********** Masking position 7 Map Score: 1.88526 Number of sites scoring better than the average of aligned sites = 1458 Number in coding regions = 1268 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 CATGTTGAAGGTGAGAAAGTTTCAAGGAAA 1 51 0 GTGAGAAAGT 0.966951 -106 AGCGTATGTAGTGAGGTAATCAGGTT 1 141 1 GTGAGGTAAT 0.935269 -16 TTATCAACAAGTTATCAAGTATTTTTAATT 2 124 1 GTTATCAAGT 0.858681 -145 TTCGTTCACAGTGGGGAAGTTTTCGGATCC 2 231 1 GTGGGGAAGT 0.966866 -38 TGAGCGTGTCGGGAGCAAGT 5 1 0 GGGAGCAAGT 0.977014 -160 TTTTATTGTTAGCTAATGCAATAGTTA 5 144 0 GTTAGCTAAT 0.867556 -17 ********** Masking position 8 Map Score: 1.02373 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 232 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 CTTCGGGTGCCTTTTTTATTTCCGAAACGT 2 61 1 CTTTTTTATT 0.915713 -208 GCAGGTGAATAAATTTTATTCATATTGTTA 2 97 1 AAATTTTATT 0.828192 -172 AAACAATTTCCATTTTAATTAAAAATACTT 2 140 0 CATTTTAATT 0.959365 -129 TTTGATTTTGCATTTTAAATGAGTAGTCTT 2 169 1 CATTTTAAAT 0.882934 -100 TGGTTTGTTGAATTTTTATTAAATCTGGGT 5 31 0 AATTTTTATT 0.938665 -130 ********** Masking position 5 Map Score: 0.0348597 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 177 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 9 ********** No masking Map Score: -1.71708e-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: -1.71708e-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: -1.71708e-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