AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iiclR_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 aceB 268 malate synthase A #2 aceA 29 isocitrate lyase #3 aceK 182 isocitrate dehydrogenase kinase/phosphatase #4 iclR 160 repressor of aceBA operon Motif number 1 CTGACTGTAGGCCGGATAAGGCGTTCACGCCGC 3 27 1 GCGGATGGCG 0.99976 -156 TGCACCGATTGCCGGATGCGGCGTGAACGCCTT 3 44 0 GCGGATGGCG 0.99976 -139 GGTGCACGATGCCTGATGCGACGCTTGCGCGTC 3 71 1 GCTGATGACG 0.997904 -112 ACGGCTGTAGGCATGATAAGACGCGCAAGCGTC 3 90 0 GCTGATGACG 0.997904 -93 CCGAACGTAGGCTGGATAAGGCGTTTACGCCGC 3 125 1 GCGGATGGCG 0.99976 -58 GCAGAGAATTGCCGGATGCGGCGTAAACGCCTT 3 142 0 GCGGATGGCG 0.99976 -41 ** **** **** Masking position 7 Map Score: 24.4049 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 GTCGATCGTTAAGCGATTCAGCACCTTACCTCAGG 1 23 1 AGCGTAGCAC 0.95265 -246 TAAAAAAGGCACCCGAAGGTGCCTGAGGTAAGGTG 1 44 0 ACCGATGCCG 0.990865 -225 CTCGTCATGGATCCGAAAACTTCCCCACTGTGAAC 1 234 0 ACCGACTTCC 0.809832 -35 CGGATCCATGACGAGGAGCTGCACG 1 254 1 AGAGATGCAG 0.797986 -15 GCAACAACAACCGTTGCTGACTGTAGGCCGGAT 3 9 1 ACCGTTGACG 0.973206 -174 AGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAT 3 35 1 AGCGTCGCCC 0.997835 -148 GCATGATAAGACGCGCAAGCGTCGCATCAGGCATC 3 78 0 AGCGACGTCC 0.986303 -105 TCATGCCTACAGCCGTTGCCGAACGTAGGCTGGAT 3 107 1 ACCGTCGAAG 0.952685 -76 AGGCTGGATAAGGCGTTTACGCCGCATCCGGCAAT 3 133 1 AGCGTCGCCC 0.997835 -50 TTTACCACAGATGCGTTTATGCCAGTATGGTTTGT 4 53 0 AGCGTTGCCG 0.995755 -108 * *** * **** * Masking position 1 Map Score: 12.2155 Number of sites scoring better than the average of aligned sites = 2321 Number in coding regions = 1970 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 GCTTAACGATCGACTATCACAGAAGA 1 6 0 CGACTACACA 0.936198 -263 GTGCTCTTTTCGTTCAGCACAACTAAGACTA 1 192 0 CGTTCACACA 0.989385 -77 CCGGATAAGGCGTTCACGCCGCATCCGGCAA 3 38 1 CGTTCAGCCG 0.988859 -145 CTGGATAAGGCGTTTACGCCGCATCCGGCAA 3 136 1 CGTTTAGCCG 0.982551 -47 GCTCCCGACACGCTCAACCCAGATTTAATAA 4 15 1 CGCTCACCCA 0.982079 -146 ACCACAGATGCGTTTATGCCAGTATGGTTTG 4 54 0 CGTTTAGCCA 0.983069 -107 GTGGTGGTCGCTTTTACCACAGATGCGTTTA 4 69 0 CTTTTACACA 0.869322 -92 GTGGTAAAAGCGACCACCACGCAACATGAGA 4 80 1 CGACCACACG 0.957685 -81 ****** **** Masking position 6 Map Score: 9.74919 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 742 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 CGTTAAGCGATTCAGCACCTTACCTCAGGC 1 29 1 TTCAGCACCT 0.972093 -240 GCACCTTACCTCAGGCACCTTCGGGTGCCT 1 43 1 TCAGGCACCT 0.969997 -226 CCGGCCTACAGTCAGCAACGGTTGTTGTTG 3 12 0 GTCAGCAACG 0.943193 -171 TCACGCCGCATCCGGCAATCGGTGCACGAT 3 51 1 TCCGGCAATC 0.955837 -132 AAGCGTCGCATCAGGCATCGTGCACCGATT 3 67 0 TCAGGCATCG 0.934698 -116 CCAGCCTACGTTCGGCAACGGCTGTAGGCA 3 110 0 TTCGGCAACG 0.993786 -73 TTACGCCGCATCCGGCAATTCTCTGCTCCT 3 149 1 TCCGGCAATT 0.979611 -34 ATCGGATCAGTTCAGTAACTATTGCATTAG 4 129 1 TTCAGTAACT 0.852521 -32 ********** Masking position 7 Map Score: 6.35114 Number of sites scoring better than the average of aligned sites = 3095 Number in coding regions = 2858 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 GTTGCTGACTGTAGGCCGGATAAGGCGTTC 3 23 1 GTAGGCCGGA 0.997127 -160 GGCAACGGCTGTAGGCATGATAAGACGCGC 3 97 0 GTAGGCATGA 0.989947 -86 GTTGCCGAACGTAGGCTGGATAAGGCGTTT 3 121 1 GTAGGCTGGA 0.996367 -62 ********** Masking position 3 Map Score: 2.81074 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 13 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 CAGGTGAATAAATTTTATTCATATTGTTATC 1 98 1 AATTTTATTA 0.853668 -171 TTTTATTCATATTGTTATCAACAAGTTATCA 1 110 1 ATTGTTATCA 0.958043 -159 GTTATCAAGTATTTTTAATTAAAATGGAAAT 1 134 1 ATTTTTAATA 0.937733 -135 TAAAATGGAAATTGTTTTTGATTTTGCATTT 1 153 1 ATTGTTTTTA 0.875697 -116 TTGATTTTGCATTTTAAATGAGTAGTCTTAG 1 170 1 ATTTTAAATA 0.757672 -99 GGTTTGTTGAATTTTTATTAAATCTGGGTTG 4 29 0 ATTTTTATTA 0.965635 -132 TTTTATTGTTAGCTAATGCAATAGT 4 146 0 ATTGTTAGCA 0.911398 -15 ********* * Masking position 1 Map Score: 1.67128 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 139 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 AAAATTTATTCACCTGCTGAGGTACGTTTCG 1 83 0 CACCTGTGAG 0.981473 -186 GTGCACCGATTGCCGGATGCGGCGTGAACGC 3 47 0 TGCCGGTGCG 0.992228 -136 CGGTGCACGATGCCTGATGCGACGCTTGCGC 3 70 1 TGCCTGTGCG 0.992664 -113 AGCAGAGAATTGCCGGATGCGGCGTAAACGC 3 145 0 TGCCGGTGCG 0.992228 -38 CAATTCTCTGCTCCTGATGAGGGCGCTAA 3 164 1 CTCCTGTGAG 0.966757 -19 TTGAACAAATCTCATGTTGCGTGGTGGTCGC 4 89 0 CTCATGTGCG 0.909497 -72 ****** **** Masking position 8 Map Score: 11.6933 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 441 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 ********** No masking Map Score: 3.64809e-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 9 ********** No masking Map Score: 3.64809e-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 10 ********** No masking Map Score: 3.64809e-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