AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipdhR_ecoli_bsub_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 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #2 aceE 160 pyruvate dehydrogenase (decarboxylase component) #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 aceB 268 malate synthase A #5 aceA 29 isocitrate lyase #6 aceK 182 isocitrate dehydrogenase kinase/phosphatase #7 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #8 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #9 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #10 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #11 yqiS 124 similar to phosphate butyryltransferase Motif number 1 TTAACAACTTGACATATATAACGTTTCAAAGTT 1 148 0 GACTATAACG 0.767404 -153 AGCTCAATAAGACAGGTTCTACGTTTAGTTGCC 2 70 0 GACGGTTACG 0.94142 -91 GTAAAATACCGACGGATAGAACGACCCGGTGGT 3 103 1 GACGATAACG 0.976675 -198 CCTGAAAGACGACGGGTATGACCGCCGGAGATA 3 261 1 GACGGTGACC 0.905041 -40 CTGACTGTAGGCCGGATAAGGCGTTCACGCCGC 6 27 1 GCCGATGGCG 0.997363 -156 TGCACCGATTGCCGGATGCGGCGTGAACGCCTT 6 44 0 GCCGATGGCG 0.997363 -139 GGTGCACGATGCCTGATGCGACGCTTGCGCGTC 6 71 1 GCCGATGACG 0.997534 -112 ACGGCTGTAGGCATGATAAGACGCGCAAGCGTC 6 90 0 GCAGATGACG 0.972479 -93 CCGAACGTAGGCTGGATAAGGCGTTTACGCCGC 6 125 1 GCTGATGGCG 0.970628 -58 GCAGAGAATTGCCGGATGCGGCGTAAACGCCTT 6 142 0 GCCGATGGCG 0.997363 -41 AAGATGAGAAGACTGATTTTACGGGCTCAAAAG 7 152 1 GACGATTACG 0.976675 -80 *** *** **** Masking position 7 Map Score: 21.2984 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 602 Number in noncoding regions = 766 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 GAGTTCCTGTCTTAAGCCACTTGCCGAAGTCAATTGGTC 1 272 0 CGCCATTCGG 0.981298 -29 TTTTCTGGAACCTGTCCCATTGAACTCTCGCCGGAAAGCTCAA 2 96 0 CTTGACTTGG 0.714539 -65 TATTACTTCACATACCCTATGGATTTCTGGGTGCAGCAAGGTA 3 144 1 CTCGATTTGG 0.887505 -157 ACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCTGGCGC 3 191 0 CTCAACTCGG 0.956916 -110 TACCCGTCGTCTTTCAGGCCGCAGCGGCGTTAGCTTCACGCCC 3 236 0 CTCCACGCTG 0.959929 -65 GATTCAGCACCTTACCTCAGGCACCTTCGGGTGCCTTTTTTAT 4 37 1 CTCCACTCGG 0.995544 -232 CCTTATCCGGCCTACAGTCAGCAACGGTTGTTGTTGC 6 5 0 CTCCACGTGG 0.993783 -178 AGCGTCGCATCAGGCATCGTGCACCGATTGCCGGATGCGGCGT 6 53 0 CGCCACGTGG 0.99294 -130 CCTTATCCAGCCTACGTTCGGCAACGGCTGTAGGCATGATAAG 6 103 0 CTCCACGCGG 0.996722 -80 TACGCCGCATCCGGCAATTCTCTGCTCCTGATGAGGGCGCTAA 6 150 1 CGCCTCTCGG 0.964173 -33 CGGATATCACCCGGCCTTTGACAATGATCGACGTATTTATTTC 7 24 0 CGCCATGTGG 0.973705 -208 * * * ** ** * * * Masking position 1 Map Score: 12.5982 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 698 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 TCAAGTTGTTAAAATGTGCACAGTTTCATGA 1 169 1 AAATGTGCAC 0.936241 -132 TTCTACGTTTAGTTGCCGCGCTTTTATATGC 2 56 0 AGTGCCGCGC 0.912349 -105 ATCCATGACGAGGAGCTGCACG 4 257 1 AGAGCTGCAC 0.993645 -12 ATAACTATGGAGCATCTGCAC 5 19 1 AGATCTGCAC 0.983902 -11 CGCATCCGGCAATCGGTGCACGATGCCTGAT 6 57 1 AACGGTGCAC 0.920375 -126 CCTAAATAGAAGGAGGCGCACAAA 7 218 1 AGAGGCGCAC 0.981955 -14 AGCAATTGGAGAAGCTGCGCTTGCCGCAGA 10 10 1 AGAGCTGCGC 0.988832 -64 AATAAACGCAAACATCTGCACGAATGTTTCG 11 18 1 AAATCTGCAC 0.959824 -107 ** ******** Masking position 1 Map Score: 8.23936 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 285 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 TGTCTTAAGCCACTTGCCGAAGTCAATTGG 1 274 0 CACTTGCCGA 0.945736 -27 GTTCTACGTTTAGTTGCCGCGCTTTTATAT 2 58 0 TAGTTGCCGC 0.859605 -103 ATAGACAAATCGGTTGCCGTTTGTTGTTTA 3 55 1 CGGTTGCCGT 0.949429 -246 GGCGCTTGCTACCTTGCTGCACCCAGAAAT 3 166 0 ACCTTGCTGC 0.742306 -135 GAAGCTAACGCCGCTGCGGCCTGAAAGACG 3 242 1 CCGCTGCGGC 0.977521 -59 AAAATTTATTCACCTGCTGAGGTACGTTTC 4 84 0 CACCTGCTGA 0.769055 -185 GCAACAACAACCGTTGCTGACTGTAGGCCG 6 11 1 CCGTTGCTGA 0.96023 -172 CACCGATTGCCGGATGCGGCGTGAACGCCT 6 45 0 CGGATGCGGC 0.965651 -138 ATGCCTACAGCCGTTGCCGAACGTAGGCTG 6 109 1 CCGTTGCCGA 0.984068 -74 AGAGAATTGCCGGATGCGGCGTAAACGCCT 6 143 0 CGGATGCGGC 0.965651 -40 GGAGAAGCTGCGCTTGCCGCAGATGGCAAA 10 18 1 CGCTTGCCGC 0.988283 -56 ********** Masking position 5 Map Score: 12.6555 Number of sites scoring better than the average of aligned sites = 2608 Number in coding regions = 2265 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 5 CGATCGTTAAGCGATTCAGCACCTTACCTCA 4 25 1 GCGATTAGCA 0.874213 -244 GAAATTGTTTTTGATTTTGCATTTTAAATGA 4 160 1 TTGATTTGCA 0.987205 -109 ATATCCGGTCTTTTTTTTGCATGCTGTAAAA 7 60 1 TTTTTTTGCA 0.885791 -172 ATCTTCCCTCTCGATTATGCAGTTTGA 8 7 0 TCGATTTGCA 0.981098 -108 ACCTCCTAGTTTGATTAAGCAATTTTAAAGT 8 86 0 TTGATTAGCA 0.971069 -29 GATGTTTGCGTTTATTCTGCAAA 11 3 0 TTTATTTGCA 0.97393 -122 GACTCCGCCTTTTATTATGCAAGTTCCATGC 11 82 0 TTTATTTGCA 0.973924 -43 ****** **** Masking position 11 Map Score: 5.79054 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 52 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ATTGAGCTTTCCGGCGAGAGTTCAATGGGA 2 95 1 CCGGCGAGAG 0.923513 -66 GACTGGGGTGAGGGCGTGAAGCTAACGCCG 3 225 1 AGGGCGTGAA 0.932026 -76 TCAGGCCGCAGCGGCGTTAGCTTCACGCCC 3 236 0 GCGGCGTTAG 0.975149 -65 TAACGCCGCTGCGGCCTGAAAGACGACGGG 3 247 1 GCGGCCTGAA 0.988843 -54 GGCACCCGAAGGTGCCTGAGGTAAGGTGCT 4 42 0 GGTGCCTGAG 0.854188 -227 ATTGCCGGATGCGGCGTGAACGCCTTATCC 6 40 0 GCGGCGTGAA 0.995262 -143 ATTGCCGGATGCGGCGTAAACGCCTTATCC 6 138 0 GCGGCGTAAA 0.970144 -45 ********** Masking position 9 Map Score: 5.35959 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 805 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 7 CCGGAAAGCTCAATAAGACAGGTTCTACGTTT 2 77 0 CAAAAACAGG 0.948179 -84 AACAATTTTTAAACAACAAACGGCAACCGATT 3 62 0 AAAAAAAACG 0.944601 -239 TACGTTTCGGAAATAAAAAAGGCACCCGAAGG 4 60 0 AAAAAAAAGG 0.97585 -209 GCAACAACAACCGTTGCTGACTG 6 2 1 CAAAAAACCG 0.885331 -181 CAGCATGCAAAAAAAAGACCGGATATCACCCG 7 54 0 AAAAAACCGG 0.948179 -178 TTCATTTTTAAAAGCATAAAGGAGGGGCTTGA 10 52 1 AAACAAAAGG 0.925559 -22 GGCGGAGTCGAAACAAGAAAGGTGGTAACAG 11 104 1 AAAAAAAAGG 0.97585 -21 *** ** ***** Masking position 6 Map Score: 2.41218 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 95 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 AAAAATCACAAAATTGGTAAGTGAATCGGT 1 41 1 AAATTGGTAA 0.974198 -260 ATAACGTTTCAAAGTTGTAACTATGCACAA 1 134 0 AAAGTTGTAA 0.873912 -167 TATATATGTCAAGTTGTTAAAATGTGCACA 1 161 1 AAGTTGTTAA 0.895168 -140 CACAGACATGAAATTGGTAAGACCAATTGA 1 252 1 AAATTGGTAA 0.974198 -49 TGTTGTTTAAAAATTGTTAACAATTTTGTA 3 76 1 AAATTGTTAA 0.911504 -225 AATTGTTAACAATTTTGTAAAATACCGACG 3 87 1 AATTTTGTAA 0.757906 -214 CGAAACAAGAAAGGTGGTAACAG 11 112 1 AAGGTGGTAA 0.954677 -13 ********** Masking position 2 Map Score: 4.78462 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 63 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TGATTTTTCTGGTAAAAATTAT 2 2 1 GATTTTCTGG 0.83747 -159 CTGTCTTATTGAGCTTTCCGGCGAGAGTTCA 2 88 1 GAGTTTCCGG 0.988951 -73 TAATAACGTTGAGTTTTCTGGAACCTGTCCC 2 121 0 GAGTTTCTGG 0.953428 -40 CCGACGGATAGAACGACCCGGTGGTGGTTAG 3 111 1 GAAGACCCGG 0.875993 -190 ACCTGCTGAGGTACGTTTCGGAAATAAAAAA 4 72 0 GTAGTTTCGG 0.91225 -197 TCACAGTGGGGAAGTTTTCGGATCCATGACG 4 236 1 GAATTTTCGG 0.966636 -33 CAAAGGCCGGGTGATATCCGGTCTTTTTTTT 7 47 1 GTGTATCCGG 0.92305 -185 ACATCTGCACGAATGTTTCGGTATACCTGGT 11 29 1 GAAGTTTCGG 0.965984 -96 *** ******* Masking position 10 Map Score: 2.65384 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 648 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 AATTTTTACCAGAAAAATCA 2 1 0 AGAAAAATCA 0.939321 -160 GACAGGTTCCAGAAAACTCAACGTTATTAG 2 123 1 AGAAAACTCA 0.912411 -38 ATTAGCGAATAGACAAATCGGTTGCCGTTT 3 47 1 AGACAAATCG 0.974751 -254 AGCACAACTAAGACTACTCATTTAAAATGC 4 178 0 AGACTACTCA 0.903374 -91 CTGTAAAACGAGACAAATGAATCAGTTTGA 7 83 1 AGACAAATGA 0.86008 -149 AATCAGTTTGAGACAAAACGAGACACACGT 7 102 1 AGACAAAACG 0.943812 -130 TTTGCAGAATAAACGCAAACATCTG 11 6 1 AGAATAAACG 0.779638 -119 ********** Masking position 6 Map Score: 1.86538 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 129 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 TTGCTACCTTGCTGCACCCAGAAATCCATA 3 161 0 GCTGCACCCA 0.949638 -140 AGCGGCGTTAGCTTCACGCCCTCACCCCAG 3 227 0 GCTTCACGCC 0.845955 -74 GTGCTGAATCGCTTAACGATCGACTATCAC 4 17 0 GCTTAACGAT 0.857585 -252 TCTTAGTTGTGCTGAACGAAAAGAGCACAA 4 195 1 GCTGAACGAA 0.971656 -74 ACTTCCCCACTGTGAACGAAGGATCGTTGT 4 221 0 TGTGAACGAA 0.828161 -48 TCCGGCAATCGGTGCACGATGCCTGATGCG 6 61 1 GGTGCACGAT 0.962501 -122 CATTTATAATGGTGAACCCTAAATAGAAGG 7 201 1 GGTGAACCCT 0.848751 -31 AACGCAAACATCTGCACGAATGTTTCGGTA 11 22 1 TCTGCACGAA 0.925579 -103 ********** Masking position 6 Map Score: 1.91962 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 1187 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 12 ATCCGAATTGAACCGATTCACTTACCAATT 1 52 0 AACCGATTCA 0.986882 -249 GTCGATCGTTAAGCGATTCAGCACCTTACC 4 23 1 AAGCGATTCA 0.986882 -246 TTTTGTCTCAAACTGATTCATTTGTCTCGT 7 90 0 AACTGATTCA 0.949837 -142 GCAGATGGCAAAGCCATTCATTTTTAAAAG 10 36 1 AAGCCATTCA 0.965593 -38 ********** Masking position 6 Map Score: 1.1748 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 GATTTTTAATTCAATTAAAACGAATTTAAA 1 18 0 TCAATTAAAA 0.790247 -283 TAAATCAAGCGCATATAAAAGCGCGGCAAC 2 46 1 GCATATAAAA 0.917678 -115 CTAAGACTACTCATTTAAAATGCAAAATCA 4 171 0 TCATTTAAAA 0.938524 -98 CACACTTCTTGCATTTATAATGGTGAACCC 7 190 1 GCATTTATAA 0.91769 -42 TACATCGTAAGCATTGAAAACAGATATATA 8 55 0 GCATTGAAAA 0.94294 -60 CCTCCTTTATGCTTTTAAAAATGAATGGCT 10 47 0 GCTTTTAAAA 0.91769 -27 ********** Masking position 7 Map Score: 0.593056 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 89 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 ********** No masking Map Score: -1.79524e-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 15 ********** No masking Map Score: -1.79524e-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