AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 sdhC 300 succinate dehydrogenase, cytochrome b556 Motif number 1 TCTCGCCGGAAAGCTCAATAAGACAGGTTCTACGTTT 2 77 0 AGCTATACGG 0.881507 -84 TCTATCTAATAACGTTGAGTTTTCTGGAACCTGTCCC 2 121 0 ACGTAGTCGG 0.96575 -40 GGATAGAACGACCCGGTGGTGGTTAGGGTATTACTTC 3 116 1 ACCGGGTTGG 0.970475 -185 TACTTCACATACCCTATGGATTTCTGGGTGCAGCAAG 3 147 1 ACCTGGTCGG 0.997129 -154 CGGCGGTCATACCCGTCGTCTTTCAGGCCGCAGCGGC 3 251 0 ACCGGTTCGG 0.990668 -50 CAGCCTATACTGCCGCCAGGTCTCCGGAACACCCTGC 4 72 1 TCCGAGTCGG 0.990726 -229 ACACGTTACAACGCTGGGTGGCTCGGGATTGCAGGGT 4 102 0 AGCTGTTCGG 0.963235 -199 ACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAA 4 190 1 ACCGAGACGG 0.990726 -111 AACTTTCTGTTACCTGGAGACGTCGGGATTTCCTTCC 4 218 0 TCCTAGTCGG 0.98996 -83 TTCTTATTATTCCCTGGGGACTACGGGCACAGAGGTT 4 255 0 TCCTGGACGG 0.986149 -46 * *** ** ** ** Masking position 16 Map Score: 13.7932 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 560 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 GGGTCGTTCTATCCGTCGGTATTTTACAAA 3 100 0 ATCCGTCGGT 0.964955 -201 GGATAGAACGACCCGGTGGTGGTTAGGGTA 3 116 1 ACCCGGTGGT 0.971531 -185 GTCTTTCAGGCCGCAGCGGCGTTAGCTTCA 3 241 0 CCGCAGCGGC 0.932718 -60 CGGCGGTCATACCCGTCGTCTTTCAGGCCG 3 258 0 ACCCGTCGTC 0.978821 -43 ATATATTTATCTCCGGCGGTCATACCCGTC 3 271 0 CTCCGGCGGT 0.975595 -30 TGTTCCGGAGACCTGGCGGCAGTATAGGCT 4 73 0 ACCTGGCGGC 0.98574 -228 ATCCCGAGCCACCCAGCGTTGTAACGTGTC 4 110 1 ACCCAGCGTT 0.96494 -191 CAGCGTTGTAACGTGTCGTTTTCGCATCTG 4 123 1 ACGTGTCGTT 0.792367 -178 ********** Masking position 8 Map Score: 6.7732 Number of sites scoring better than the average of aligned sites = 2696 Number in coding regions = 2540 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 ACCGATTCACTTACCAATTTTGTGATTTTT 1 41 0 TTACCAATTT 0.986235 -260 TTGTGCATAGTTACAACTTTGAAACGTTAT 1 134 1 TTACAACTTT 0.8985 -167 TGTGCACATTTTAACAACTTGACATATATA 1 161 0 TTAACAACTT 0.916009 -140 TCAATTGGTCTTACCAATTTCATGTCTGTG 1 252 0 TTACCAATTT 0.986235 -49 TACAAAATTGTTAACAATTTTTAAACAACA 3 76 0 TTAACAATTT 0.960333 -225 CGTCGGTATTTTACAAAATTGTTAACAATT 3 87 0 TTACAAAATT 0.88036 -214 ********** Masking position 6 Map Score: 4.59963 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 4 TGGATAATTTTTACCAGAAAAATCA 2 5 0 TTACCAGAAA 0.972068 -156 TGGTAAAAATTATCCAGAAGATGTTGTAAAT 2 20 1 TATCCAGAAA 0.953504 -141 AATGGGACAGGTTCCAGAAAACTCAACGTTA 2 118 1 GTTCCAGAAA 0.92519 -43 ATTCATGAGATTACCAGAAAAAAGC 3 5 0 TTACCAGAAA 0.972068 -296 TATTCGCTAATAACCTCAATACATTCATGAG 3 27 0 TAACCTCAAA 0.876512 -274 TGTCGGGTTTTATCCTGAACAGTGAT 4 6 0 TATCCTGAAA 0.940266 -295 TAACTTTCTGTTACCTGGAGACGTCGGGATT 4 225 0 TTACCTGGAA 0.898081 -76 ********* * Masking position 9 Map Score: 5.63544 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 156 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 CACAAAATTGGTAAGTGAATCGGTTCAATT 1 47 1 GTAAGTGAAT 0.965605 -254 CCAATTTCATGTCTGTGACGCTAAAGTAAC 1 239 0 GTCTGTGACG 0.975248 -62 AATCCATAGGGTATGTGAAGTAATACCCTA 3 139 0 GTATGTGAAG 0.97749 -162 GCTTACATAAGTAAGTGACTGGGGTGAGGG 3 209 1 GTAAGTGACT 0.97749 -92 ********** Masking position 6 Map Score: 0.62786 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GCTTTTATATGCGCTTGATTTACAACATCTT 2 37 0 GCGCTTGATT 0.946094 -124 GGGGATTCTGGCGCTTGCTACCTTGCTGCAC 3 174 0 GCGCTTGCTC 0.976461 -127 ACTGGGGTGAGGGCGTGAAGCTAACGCCGCT 3 226 1 GGGCGTGAAC 0.977779 -75 ATAGTTTGTCGGGTTTTATCCTGAACAGTGA 4 12 0 GGGTTTTATC 0.88622 -289 TTCTATAACTGCGCGTCATGCAAAACACTGC 4 156 0 GCGCGTCATC 0.985143 -145 AACAGCATGTGGGCGTTATTC 4 290 1 GGGCGTTATC 0.987527 -11 ********* * Masking position 6 Map Score: 0.919366 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 628 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 CTGTCTTAAGCCACTTGCCGAAGTCAATTG 1 275 0 CCACTTGCCG 0.989227 -26 GGTTCTACGTTTAGTTGCCGCGCTTTTATA 2 59 0 TTAGTTGCCG 0.93155 -102 AATAGACAAATCGGTTGCCGTTTGTTGTTT 3 54 1 TCGGTTGCCG 0.970549 -247 AACACTGCTTCCAGATGCGAAAACGACACG 4 134 0 CCAGATGCGA 0.861702 -167 TTCCTCCGGTCTGCTTGCGGGTCAGACAGC 4 192 0 CTGCTTGCGG 0.845421 -109 GAATAACGCCCACATGCTGTTCTTATTAT 4 282 0 CCACATGCTG 0.898307 -19 ********** Masking position 6 Map Score: 0.658132 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1376 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 8 TGCACCCAGAAATCCATAGGGTATGTGAAG 3 149 0 AATCCATAGG 0.943999 -152 CAAGCGCCAGAATCCCCAGGAGCTTACATA 3 188 1 AATCCCCAGG 0.995849 -113 AACACCCTGCAATCCCGAGCCACCCAGCGT 4 99 1 AATCCCGAGC 0.985534 -202 GGAGGAAGGAAATCCCGACGTCTCCAGGTA 4 215 1 AATCCCGACG 0.985517 -86 CTGTGCCCGTAGTCCCCAGGGAATAATAAG 4 260 1 AGTCCCCAGG 0.990832 -41 ********** Masking position 3 Map Score: 4.67224 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 20 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: -1.94446e-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: -1.94446e-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 GAATGAATTTAAATTCGTTTTAATTGA 1 8 1 TTTAAATTCG 0.909732 -293 AAGTGAATCGGTTCAATTCGGATTTTTATA 1 59 1 GTTCAATTCG 0.961738 -242 TTGCCGCGCTTTTATATGCGCTTGATTTAC 2 45 0 TTTATATGCG 0.934063 -116 TCCGGCGAGAGTTCAATGGGACAGGTTCCA 2 104 1 GTTCAATGGG 0.839136 -57 GCAACCGATTTGTCTATTCGCTAATAACCT 3 42 0 TGTCTATTCG 0.892928 -259 CCACCGGGTCGTTCTATCCGTCGGTATTTT 3 105 0 GTTCTATCCG 0.972476 -196 CCTCTATATATTTATCTCCGGCGGTCATAC 3 276 0 TTTATCTCCG 0.813395 -25 ********** Masking position 7 Map Score: 0.0513771 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 310 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 ********** No masking Map Score: -1.94446e-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 13 ********** No masking Map Score: -1.94446e-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 14 ********** No masking Map Score: -1.94446e-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