AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aceE 160 pyruvate dehydrogenase (decarboxylase component) #2 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #3 sdhC 300 succinate dehydrogenase, cytochrome b556 #4 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #5 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #6 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #7 HI1661 102 2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide succinyltransferase(sucB) #8 HI1662 157 2-oxoglutarate dehydrogenase E1 component (sucA) Motif number 1 TCATGAATGTATTGAGGTTATTAGCGAATA 2 28 1 ATTGAGGTTA 0.932516 -273 AGATAAATATATAGAGGTCATG 2 289 1 ATAGAGGTCA 0.831801 -12 GACTACGGGCACAGAGGTTAACTTTCTGTT 3 244 0 ACAGAGGTTA 0.855943 -57 AGACCGTAAAAGTGCGGTCAATATTTTTAA 4 76 1 AGTGCGGTCA 0.996382 -38 TTGATGAAAACTGCGGTCAAAAAACATTG 5 10 1 ACTGCGGTCA 0.989851 -53 TTCCTTTTAAAGTGCGGTCATAAAACACAA 5 37 0 AGTGCGGTCA 0.996382 -26 ATTATTTGAAAGTGCGGTAATTTTTTTGTG 6 104 0 AGTGCGGTAA 0.98142 -196 AGTGCGGTTAATTTAATAAA 7 1 1 AGTGCGGTTA 0.995351 -102 TCTTAAACAAAGTGCGGTTATTTTTACTTG 8 20 0 AGTGCGGTTA 0.995351 -138 TAAGAGATGAAGTGCGGTTTTTTATTGTTT 8 45 1 AGTGCGGTTT 0.967872 -113 ********** Masking position 8 Map Score: 23.7806 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 141 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 CGTTTAGTTGCCGCGCTTTTATATGCGCTTG 1 51 0 CCGCGCTTTA 0.990613 -110 AAAATATTGACCGCACTTTTACGGTCTTTAT 4 72 0 CCGCACTTTA 0.997093 -42 TGTTTTTTGACCGCAGTTTTCATCAA 5 6 0 CCGCAGTTTC 0.967429 -57 TGTTTTATGACCGCACTTTAAAAGGAACAAA 5 40 1 CCGCACTTTA 0.997093 -23 AAAAAAATTACCGCACTTTCAAATAATTATT 6 107 1 CCGCACTTTA 0.997093 -193 GTAAAAATAACCGCACTTTGTTTAAGAGATG 8 23 1 CCGCACTTTT 0.994588 -135 CAATAAAAAACCGCACTTCATCTCTTAAACA 8 41 0 CCGCACTTCT 0.982626 -117 ********* * Masking position 7 Map Score: 16.7631 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 26 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 AAACGTAGAACCTGTCTTATTGAGCTTTCCGGCGAGA 1 77 1 CCGTATAGCT 0.800269 -84 GGGACAGGTTCCAGAAAACTCAACGTTATTAGATAGA 1 121 1 CCGACTACGT 0.930639 -40 GAAGTAATACCCTAACCACCACCGGGTCGTTCTATCC 2 116 0 CCAACCCGGT 0.946963 -185 CTTGCTGCACCCAGAAATCCATAGGGTATGTGAAGTA 2 147 0 CCGACCAGGT 0.995445 -154 GCCGCTGCGGCCTGAAAGACGACGGGTATGACCGCCG 2 251 1 CCGAACCGGT 0.986857 -50 GCAGGGTGTTCCGGAGACCTGGCGGCAGTATAGGCTG 3 72 0 CCGACTCGGA 0.98446 -229 ACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGT 3 102 1 CCGAACAGCT 0.950329 -199 TTTCCTTCCTCCGGTCTGCTTGCGGGTCAGACAGCGT 3 190 0 CCGTCTCGGT 0.977168 -111 GGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGTT 3 218 1 CCGACTAGGA 0.985453 -83 AACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAA 3 255 1 CCGTCCAGGA 0.980887 -46 ATCTTGGCTCCCCTATTTACAGAGGAAAGCAAAGATA 7 37 0 CCTAACAGGA 0.805284 -66 ** ** ** *** * Masking position 2 Map Score: 11.5531 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 710 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 CGAATAGACAAATCGGTTGCCGTTTGTTGTTTAAAAA 2 52 1 ATCGTTTTGT 0.83003 -249 TATTTTACAAAATTGTTAACAATTTTTAAACAACAAA 2 74 0 ATTTTTTTTT 0.967753 -227 ACCTACATATAGTTTGTCGGGTTTTATCCTGAACAGT 3 14 0 ATTGTTTTAT 0.808306 -287 TATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTA 3 42 1 ATTTATTTGT 0.928212 -259 TATTGACCGCACTTTTACGGTCTTTATAGGATGGGTT 4 62 0 ATTTATTTAT 0.779115 -52 AGTGCGGTCAATATTTTTAACGTTTTTACGAGGTAAA 4 86 1 AATTTTTTTT 0.761548 -28 TTTGTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGG 6 19 0 ATTTTTTTTT 0.967754 -281 AAAATATTGCATTCCATCGGGCTTTGTTTTAAAGTTT 6 41 0 ATCATTTTGT 0.759445 -259 AAAGTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTA 6 89 0 ATTTTTTTTT 0.967754 -211 AAATCTTGTAAATTTTAGAAGATTTTTTGAGATAAAG 6 184 0 ATTTATTTTT 0.905971 -116 AATTTACAAGATTTGTTAAATGTTTGTGAAAAGCAAA 6 207 1 ATTTTTTTGT 0.975772 -93 AGTGCGGTTAATTTAATAAAGGTTTTTATCTTTGCTT 7 11 1 ATTATTTTTT 0.881606 -92 TCTTATCGGAAATTGTTACAAATTTGTGATCTAGTTC 8 91 0 ATTTTTTTGT 0.975771 -67 * ** ** ***** Masking position 1 Map Score: 10.7598 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 75 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 TTTGTTGTTTAAAAATTGTTAACAATTTTGTAAAA 2 74 1 AAAAAAACAA 0.9395 -227 TAGGCTGTTCACAAAATCATTACAATTAACCTACA 3 44 0 ACAAATACAA 0.796909 -257 AACCCATCCTATAAAGACCGTAAAAGTGCGGTCAA 4 62 1 ATAAATAAAA 0.554361 -52 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGC 4 89 0 TAAAAAAAAA 0.929735 -25 GACCGCACTTTAAAAGGAACAAAAA 5 48 1 TAAAAAAAAA 0.929735 -15 TCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 6 18 1 AAAAAAAAAA 0.962534 -282 TTGTTCGCTAAAATAACCAGTAAAATATTGCATTC 6 64 0 AAATATAAAA 0.629512 -236 TTTAGCGAACAAAAAAACACAAAAAAATTACCGCA 6 87 1 AAAAAAAAAA 0.962534 -213 CTTTATCTCAAAAAATCTTCTAAAATTTACAAGAT 6 184 1 AAAAATAAAA 0.907324 -116 TTTGCTTTTCACAAACATTTAACAAATCTTGTAAA 6 209 0 ACAAAAACAA 0.91148 -91 AAGATATAGTAAAAAAGAAGAAAAGGAAAAATAAA 7 78 1 AAAAAAAAAG 0.777072 -25 ATTTTAATACAAGTAAAAATAACCGCACT 8 5 1 TAATAAAAAA 0.696641 -153 TCTTTAGATTTCAAACAATAAAAAACCGCACTTCA 8 52 0 TCAAAAAAAA 0.897684 -106 GAACTAGATCACAAATTTGTAACAATTTCCGATAA 8 91 1 ACAAAAACAA 0.91148 -67 CAATCCTATGTATAATGCGTAAAAA 8 143 1 TATAAAAAAA 0.547776 -15 ***** ***** Masking position 5 Map Score: 12.5026 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 212 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 6 CATTGAACTCTCGCCGGAAAGCTCAATAAGA 1 91 0 TCGCCGGAAG 0.923028 -70 TTGTAAAATACCGACGGATAGAACGACCCGG 2 101 1 CCGACGGAAG 0.954844 -200 ACCCTAACCACCACCGGGTCGTTCTATCCGT 2 114 0 CCACCGGGCG 0.971657 -187 GCGCCAGAATCCCCAGGAGCTTACATAAGTA 2 191 1 CCCCAGGACT 0.92566 -110 GTCTTTCAGGCCGCAGCGGCGTTAGCTTCAC 2 240 0 CCGCAGCGCG 0.928237 -61 GGCCTGAAAGACGACGGGTATGACCGCCGGA 2 259 1 ACGACGGGAT 0.782774 -42 ACGGGTATGACCGCCGGAGATAAATATATAG 2 272 1 CCGCCGGAAT 0.988147 -29 GCCTATACTGCCGCCAGGTCTCCGGAACACC 3 74 1 CCGCCAGGCT 0.953801 -227 TGCCCGTAGTCCCCAGGGAATAATAAGAACA 3 263 1 CCCCAGGGAT 0.950005 -38 ******** ** Masking position 2 Map Score: 4.54374 Number of sites scoring better than the average of aligned sites = 2255 Number in coding regions = 2136 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 TGATTTTTCTGGTAAAAATTATC 1 4 1 TTTTTCTGGT 0.985107 -157 GCTTTTTTCTGGTAATCTCATGA 2 4 1 TTTTTCTGGT 0.985107 -297 GTTTTAAAGTTTTTTCAGATTTTTTTCAAA 6 23 0 TTTTTCAGAT 0.906745 -277 GAATGCAATATTTTACTGGTTATTTTAGCG 6 64 1 TTTTACTGGT 0.966415 -236 TGCGGTAATTTTTTTGTGTTTTTTTGTTCG 6 92 0 TTTTTGTGTT 0.842483 -208 TTTAGAAGATTTTTTGAGATAAAGATAGTG 6 178 0 TTTTTGAGAT 0.804033 -122 GTGCGGTTATTTTTACTTGTATTAAAAT 8 9 0 TTTTACTTGT 0.788694 -149 ********** Masking position 4 Map Score: 4.40538 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 298 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 AAGATGTTGTAAATCAAGCGCATATAAAAGC 1 37 1 AATCAAGCGC 0.9259 -124 GTGCAGCAAGGTAGCAAGCGCCAGAATCCCC 2 174 1 GAGCAAGCGC 0.94385 -127 AGCGGCGTTAGCTTCACGCCCTCACCCCAGT 2 226 0 GTTCACGCCC 0.969597 -75 TCACTGTTCAGGATAAAACCCGACAAACTAT 3 12 1 GATAAAACCC 0.891527 -289 GCAGTGTTTTGCATGACGCGCAGTTATAGAA 3 156 1 GATGACGCGC 0.952297 -145 GAATAACGCCCACATGCTGTT 3 290 0 GATAACGCCC 0.986328 -11 TAATCGGTGGGCTTAAAGCCCACCTACAGA 4 10 0 GTTAAAGCCC 0.964214 -104 AAAAACTTTAAAACAAAGCCCGATGGAATGC 6 39 1 AACAAAGCCC 0.838186 -261 * ********* Masking position 6 Map Score: 3.02399 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 597 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 9 TTGCCGCGCTTTTATATGCGCTTGATTTACAA 1 43 0 TTTATTGGCT 0.964135 -118 GCAACCGATTTGTCTATTCGCTAATAACCTCA 2 40 0 TGTCTTTGCT 0.947615 -261 AGAGGTTAACTTTCTGTTACCTGGAGACGTCG 3 230 0 TTTCTTTCCT 0.918712 -71 TCTGTAGGTGGGCTTTAAGCCCAC 4 3 1 TGTAGTGGCT 0.801713 -111 TTTTTGTGTTTTTTTGTTCGCTAAAATAACCA 6 80 0 TTTTTTTGCT 0.921332 -220 AATAAAGGTTTTTATCTTTGCTTTCCTCTGTA 7 25 1 TTTATTTGCT 0.97937 -78 CTATATCTTAATTATCTTGGCTCCCCTATTTA 7 55 0 ATTATTTGCT 0.894818 -48 TTTATTTTTCCTTTTCTTCTTT 7 91 0 TTTATTTCCT 0.943806 -12 ***** ** *** Masking position 7 Map Score: 3.00146 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 71 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 TGATTTTTCTGGTAAAAATTATCCAGAA 1 9 1 CTGGTAAAAA 0.683482 -152 TGTTAACAATTTTTAAACAACAAACGGCAA 2 68 0 TTTTAAACAA 0.692396 -233 TGTTTAAAAATTGTTAACAATTTTGTAAAA 2 79 1 TTGTTAACAA 0.496506 -222 TCCGTCGGTATTTTACAAAATTGTTAACAA 2 89 0 TTTTACAAAA 0.632554 -212 GCAGTATAGGCTGTTCACAAAATCATTACA 3 55 0 CTGTTCACAA 0.933616 -246 TTTTCAGATTTTTTTCAAAAAGGACTCAGC 6 12 0 TTTTTCAAAA 0.73688 -288 TTTTCACAAACATTTAACAAATCTTGTAAA 6 209 0 CATTTAACAA 0.726656 -91 GCAATATTTGCTTTTCACAAACATTTAACA 6 220 0 CTTTTCACAA 0.951773 -80 AGATCACAAATTTGTAACAATTTCCGATAA 8 96 1 TTTGTAACAA 0.78417 -62 ********** Masking position 7 Map Score: 1.49205 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 199 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 11 ********** No masking Map Score: -9.4259e-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 12 ********** No masking Map Score: -9.4259e-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 13 ********** No masking Map Score: -9.4259e-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