AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipdhR_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 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 metA 156 homoserine transsuccinylase #5 aceB 268 malate synthase A #6 aceA 29 isocitrate lyase #7 aceK 182 isocitrate dehydrogenase kinase/phosphatase Motif number 1 GTAAAATACCGACGGATAGAACGACCCGGTGGT 3 103 1 GAGGATAACG 0.926933 -198 CTGACTGTAGGCCGGATAAGGCGTTCACGCCGC 7 27 1 GCGGATGGCG 0.999358 -156 TGCACCGATTGCCGGATGCGGCGTGAACGCCTT 7 44 0 GCGGATGGCG 0.999358 -139 GGTGCACGATGCCTGATGCGACGCTTGCGCGTC 7 71 1 GCTGATGACG 0.995162 -112 ACGGCTGTAGGCATGATAAGACGCGCAAGCGTC 7 90 0 GCTGATGACG 0.995162 -93 CCGAACGTAGGCTGGATAAGGCGTTTACGCCGC 7 125 1 GCGGATGGCG 0.999358 -58 GCAGAGAATTGCCGGATGCGGCGTAAACGCCTT 7 142 0 GCGGATGGCG 0.999358 -41 ** **** **** Masking position 6 Map Score: 20.2274 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 73 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 GACCAATTGACTTCGGCAAGTGGCTTAAGACAGGAACTC 1 272 1 CCGAATGGCG 0.979372 -29 TTGAGCTTTCCGGCGAGAGTTCAATGGGACAGGTTCCAGAAAA 2 96 1 CCAAGTCAAG 0.813665 -65 TACCTTGCTGCACCCAGAAATCCATAGGGTATGTGAAGTAATA 3 144 0 CCAAATCGAG 0.896593 -157 GCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGT 3 191 1 CCGAGTTGAG 0.977321 -110 GGGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGACGGGTA 3 236 1 CAGCGTGGAG 0.973352 -65 ATAAAAAAGGCACCCGAAGGTGCCTGAGGTAAGGTGCTGAATC 5 37 0 CCGAGTGGAG 0.997332 -232 GCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGG 7 5 1 CCACGTGGAG 0.994427 -178 ACGCCGCATCCGGCAATCGGTGCACGATGCCTGATGCGACGCT 7 53 1 CCACGTGGCG 0.991644 -130 CTTATCATGCCTACAGCCGTTGCCGAACGTAGGCTGGATAAGG 7 103 1 CCGCGTGGAG 0.997614 -80 TTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGTA 7 150 0 CCGAGAGGCG 0.974763 -33 * * * ** ** * * * Masking position 1 Map Score: 10.6179 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 581 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TGATTTTTCTGGTAAAAATTATCC 2 5 1 TTTTCTGGTA 0.982063 -156 ATTTACAACATCTTCTGGATAATTTTTACC 2 21 0 TCTTCTGGAT 0.951799 -140 TAACGTTGAGTTTTCTGGAACCTGTCCCAT 2 119 0 TTTTCTGGAA 0.974497 -42 GCTTTTTTCTGGTAATCTCATGAA 3 5 1 TTTTCTGGTA 0.982063 -296 TACCCTATGGATTTCTGGGTGCAGCAAGGT 3 156 1 ATTTCTGGGT 0.904064 -145 CATTGGCAAATTTTCTGGTTATCTTCAGCT 4 90 1 TTTTCTGGTT 0.97677 -67 TCTTCTGTGATAGTCGATCG 5 1 1 TCTTCTGTGA 0.837632 -268 ********** Masking position 6 Map Score: 7.43886 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 184 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TCATACCCGTCGTCTTTCAGGCCGCAGCGGCGTTAG 3 246 0 CCTTCACGCA 0.995774 -55 TGAAACTTTCTCACCTTCAACATGCAGGCTCGACAT 4 57 1 TCTTCAAGCA 0.922765 -100 AGCGATTCAGCACCTTACCTCAGGCACCTTCGGGTG 5 34 1 CCTACCAGCA 0.925734 -235 AACTAAGACTACTCATTTAAAATGCAAAATCAAAAA 5 167 0 ACTTTAAGCA 0.856 -102 GATCGTTGTGCTCTTTTCGTTCAGCACAACTAAGAC 5 194 0 CTTTCGCGCA 0.928977 -75 ACGCCTTATCCGGCCTACAGTCAGCAACGGTTGTTG 7 15 0 CCTACACGCA 0.991975 -168 AGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATC 7 35 1 ACTTCACGCA 0.98926 -148 ACGCCTTATCCAGCCTACGTTCGGCAACGGCTGTAG 7 113 0 CCTACGCGCA 0.985915 -70 AGGCTGGATAAGGCGTTTACGCCGCATCCGGCAATT 7 133 1 ACTTTACGCA 0.947747 -50 * * **** * *** Masking position 6 Map Score: 6.90583 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 472 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 TTTTAAACAACAAACGGCAACCGATTTGTCTATTC 3 53 0 CACGCACCGT 0.996533 -248 AGTAATACCCTAACCACCACCGGGTCGTTCTATCC 3 116 0 TACCCACGGT 0.970977 -185 CGTCGTCTTTCAGGCCGCAGCGGCGTTAGCTTCAC 3 240 0 CACGCACGGG 0.994207 -61 CACCTTACCTCAGGCACCTTCGGGTGCCTTTTTTA 5 44 1 CACCCTCGGT 0.964006 -225 ATCCGGCCTACAGTCAGCAACGGTTGTTGTTGC 7 9 0 CACGCACGGT 0.99821 -174 ATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 7 42 1 CACGCACCGC 0.993894 -141 TCGCATCAGGCATCGTGCACCGATTGCCGGATGCG 7 57 0 CAGGCACGAT 0.888209 -126 ATCCAGCCTACGTTCGGCAACGGCTGTAGGCATGA 7 107 0 CGCGCACGGT 0.992385 -76 ATAAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 7 140 1 TACGCACCGC 0.969746 -43 ** * *** *** * Masking position 8 Map Score: 13.0104 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 477 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 ACCGATTCACTTACCAATTTTGTGATTTTT 1 41 0 TTACCAATTT 0.980216 -260 TTGTGCATAGTTACAACTTTGAAACGTTAT 1 134 1 TTACAACTTT 0.859582 -167 TGTGCACATTTTAACAACTTGACATATATA 1 161 0 TTAACAACTT 0.88293 -140 TCAATTGGTCTTACCAATTTCATGTCTGTG 1 252 0 TTACCAATTT 0.980216 -49 TACAAAATTGTTAACAATTTTTAAACAACA 3 76 0 TTAACAATTT 0.943636 -225 CGTCGGTATTTTACAAAATTGTTAACAATT 3 87 0 TTACAAAATT 0.835759 -214 ********** Masking position 6 Map Score: 3.00996 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 49 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TTGAAATCATGAAACTGTGCACATTTTAAC 1 176 0 GAAACTGTGC 0.971246 -125 ACTAAACGTAGAACCTGTCTTATTGAGCTT 2 74 1 GAACCTGTCT 0.950313 -87 GAGTTTTCTGGAACCTGTCCCATTGAACTC 2 112 0 GAACCTGTCC 0.98023 -49 TCTTTTCCTTGAAACTTTCTCACCTTCAAC 4 48 1 GAAACTTTCT 0.936228 -109 AAGATAACCAGAAAATTTGCCAATGTCGAG 4 85 0 GAAAATTTGC 0.857721 -72 TCATGGATCCGAAAACTTCCCCACTGTGAA 5 235 0 GAAAACTTCC 0.839417 -34 ********** Masking position 3 Map Score: 1.13732 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 131 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TGTGCACATTTTAACAACTTGACATATATAACGTT 1 156 0 TTACACGAAT 0.881395 -145 CTATTCGCTAATAACCTCAATACATTCATGAGATT 3 24 0 ATACCCTAAT 0.991597 -277 GACGACGGGTATGACCGCCGGAGATAAATATATAG 3 268 1 ATACCCGAAT 0.976906 -33 CATGACCTCTATATATTTATCTCCGG 3 285 0 ATACCCTAAT 0.991597 -16 AACCTGATTACCTCACTACATACGCTTATAC 4 136 0 ATACCCTAAT 0.991597 -21 ** *** * ** ** Masking position 4 Map Score: 0.636185 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 TTTTTAATTCAATTAAAACGAATTTAAATT 1 16 0 AATTAAAACG 0.929189 -285 GTTTTAATTGAATTAAAAATCACAAAATTG 1 27 1 AATTAAAAAT 0.910899 -274 TCATGATTTCAATCAAAACCTGTATGGACA 1 194 1 AATCAAAACC 0.934064 -107 ACGTTTCGGAAATAAAAAAGGCACCCGAAG 5 61 0 AATAAAAAAG 0.862348 -208 TTTCCATTTTAATTAAAAATACTTGATAAC 5 134 0 AATTAAAAAT 0.910899 -135 TAAAATGCAAAATCAAAAACAATTTCCATT 5 156 0 AATCAAAAAC 0.944713 -113 ********** Masking position 5 Map Score: 0.997764 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 121 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 AATTGAACCGATTCACTTACCAATTTTGTG 1 47 0 ATTCACTTAC 0.963839 -254 GTTACTTTAGCGTCACAGACATGAAATTGG 1 239 1 CGTCACAGAC 0.898647 -62 TCCTGTCTTAAGCCACTTGCCGAAGTCAAT 1 277 0 AGCCACTTGC 0.927033 -24 TAGGGTATTACTTCACATACCCTATGGATT 3 139 1 CTTCACATAC 0.939104 -162 CCCTCACCCCAGTCACTTACTTATGTAAGC 3 209 0 AGTCACTTAC 0.976696 -92 AATAAAATTTATTCACCTGCTGAGGTACGT 5 87 0 ATTCACCTGC 0.928376 -182 ********** Masking position 5 Map Score: 0.533803 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 85 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 ********** No masking Map Score: 1.80068e-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: 1.80068e-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: 1.80068e-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