AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_ecoli_bsub_300.orf -o193_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yacE 224 putative DNA repair protein #2 polA 300 DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease #3 ytaG 161 similar to hypothetical proteins #4 ytaF 171 ytaF #5 polA 243 DNA polymerase I #6 phoP 211 two-component response regulator #7 citH 43 malate dehydrogenase #8 citC 163 isocitrate dehydrogenase #9 citZ 300 citrate synthase II Motif number 1 GCAAGACTGCGAAATTGTCTTTTTTTACGCTACAAT 1 91 1 GAGTCTTTTT 0.879103 -134 CCACATTAGAAAAAATCCCATTATCTCAATTATTAG 2 42 1 AACCCATTTT 0.908557 -259 TTACAGCATGATGTTTGTCTTTGTTTTTCATGCAGT 2 95 0 ATGTCTTTTT 0.902 -206 AATGTCCGTGCCTGTTTATCAGATTATGG 2 282 0 GTGCCTGTTT 0.880573 -19 ATTGGAATCAATGCCGGCCATTTTCTGTCTAAGTGG 3 52 1 ATGCCATTTT 0.967257 -110 AAGCCCCGGCAAAAACGCCATTTTATCGATCCATTT 3 88 0 AAGCCATTTT 0.978816 -74 ACTCTGGATTAAGGATGCCATTTTCGAAACACGGAT 4 53 1 AAGCCATTTG 0.879398 -119 TTGCATATCCGTTTCTTCCTTTCTGTTGGTGCTCTT 4 146 0 GTTCCTTTTT 0.647753 -26 AGGCTGTATTAAGCAAGCCTTTCTCTCTTTTTA 6 8 0 AAGCCTTTTT 0.986367 -204 AGGCTTGCTTAATACAGCCTTTCTCTTTTTACTATA 6 24 1 AAGCCTTTTT 0.986367 -188 AAGCGCTATCATAAACGTCTTTATTTCTTTTAAAAA 6 65 1 ATGTCTTTTT 0.901996 -147 AATAAAAACCTCCCAGTATGTAATTCATATT 8 143 0 AACCCAGTTT 0.758397 -21 ATTTCCCCGAAAAAACGCCTTTATTTGCGGGTTTTT 9 12 0 AAGCCTTTTT 0.986363 -289 ** ****** * * Masking position 12 Map Score: 11.9728 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 268 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 TCAAAACGTTAAAAATGAGTGCACGAAAGC 1 174 0 AAAAATGAGT 0.832818 -51 ACGTTTTGATAATCATGATGAATTCCCGGG 1 195 1 AATCATGATG 0.685285 -30 AAACAAAGACAAACATCATGCTGTAAAAAG 2 105 1 AAACATCATG 0.90729 -196 ATCATGCTGTAAAAAGCATGATAATAAATT 2 119 1 AAAAAGCATG 0.921095 -182 GACAGGATGAAAACATGAGTTTTTCACCGC 2 237 0 AAACATGAGT 0.85198 -64 AGGATGCCACAGACAGGATGAAAACATGAG 2 248 0 AGACAGGATG 0.823878 -53 TGGAAATTGTAAAAAGGAGTGGATCTC 3 145 1 AAAAAGGAGT 0.87314 -17 AGAAGACACAAAAAAGGACGGGAACACAAA 5 116 0 AAAAAGGACG 0.926009 -128 TATTTCTTTTAAAAATGATGTAAAAGGCGA 6 86 1 AAAAATGATG 0.948795 -126 TAAAATAGAGAAATAGGATGTCGGGGAATT 6 173 1 AAATAGGATG 0.821056 -39 GAATGTTAGGAAAAATCATTTTATTTTCTA 8 88 1 AAAAATCATT 0.708336 -76 AGGCTTACTTAAAAAGCACGATGCAAGTAT 9 227 0 AAAAAGCACG 0.850881 -74 AGTGTTGTAAAAACATGAGGCTTACTTAAA 9 244 0 AAACATGAGG 0.952545 -57 ********** Masking position 5 Map Score: 10.9411 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 361 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 GTGCGGATTCCTGGGGTTAATGGCT 1 5 1 GGATTCCGGG 0.984508 -220 TAATCATGATGAATTCCCGGGAATATAAATT 1 204 1 GAATTCCGGG 0.947176 -21 TATGGGTAAAGGATGCCACAGACAGGATGAA 2 256 0 GGATGCCCAG 0.977281 -45 GCGAGCTCATGATTGCCACGGCGATGCTCA 3 10 0 GATTGCCCGG 0.908082 -152 CGTGATTAATAGAAGCCCCGGCAAAAACGCC 3 105 0 AGAAGCCCGG 0.951167 -57 ATCAGATGTGAAATGCCCGGGATTCATCACA 4 113 0 AAATGCCGGG 0.947176 -59 CCAACAGAAAGGAAGAAACGGATATGCAA 4 153 1 GGAAGAACGG 0.793194 -19 TTGGCTCCTTGGATGAAGGGGTTCTACTACA 5 66 0 GGATGAAGGG 0.926 -178 AGAGATGAATGGAAGCCTGAGGCTTCTTAGG 5 213 1 GGAAGCCGAG 0.966415 -31 TAGAGAAATAGGATGTCGGGGAATTATAATA 6 178 1 GGATGTCGGG 0.976219 -34 ******* *** Masking position 11 Map Score: 8.58094 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 917 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 CATCCTGTCTGTGGCATCCTTTACCCATAATCT 2 258 1 GTGGCATCTA 0.979049 -43 GAGCATCGCCGTGGCAATCATGAGCTCGCTGTT 3 12 1 GTGGCAACTA 0.949015 -150 CGTTTTTGCCGGGGCTTCTATTAATCACGATTG 3 107 1 GGGGCTTTTA 0.899417 -55 TGTTTCGAAAATGGCATCCTTAATCCAGAGTTA 4 51 0 ATGGCATCTA 0.938709 -121 GTCCTTTTTTGTGTCTTCTCTTATAGTTCACGT 5 127 1 GTGTCTTTTA 0.696032 -117 TAAGAAGCCTCAGGCTTCCATTCATCTCTTACA 5 209 0 CAGGCTTCTC 0.842251 -35 AAAAGAGAGAAAGGCTTGCTTAATACAGCCTTT 6 13 1 AAGGCTTCTA 0.963321 -199 CTTCTCCTTTATGGCTAGTTTTAGGCTTTTTCC 7 15 0 ATGGCTATTA 0.791395 -29 CCATTGGAGGCTGGCTTGCGTCAATGAGGTTAG 8 15 1 CTGGCTTCTA 0.976475 -149 GTCTGAACAAGAGGCTAACCTCATTGACGCAAG 8 29 0 GAGGCTACTA 0.969622 -135 GTAAAAACATGAGGCTTACTTAAAAAGCACGAT 9 235 0 GAGGCTTCTA 0.987675 -66 ******* * * * Masking position 11 Map Score: 8.54912 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 322 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AGCATGATAATAAATTAAAAGCGATGTAAAT 2 133 1 TAAATAAAAG 0.796045 -168 GGAAATTGTAAAAAGGAGTGGATCTC 3 146 1 AAAAGAGTGG 0.677206 -16 GAACTTTGTTAAAATAAGAGGAGCTAATGAC 5 176 1 AAAATAGAGG 0.94606 -68 ATTTATAGTAAAAAGAGAAAGGCTGTATTAA 6 32 0 AAAAGGAAAG 0.767098 -180 CTTTTTACTATAAATGAAAGCGCTATCATAA 6 48 1 TAAATAAAGC 0.642074 -164 TGCTTTCGCTAAAATAAAATCATGAAACATG 6 131 1 AAAATAAATC 0.76177 -81 AAACTAGCCATAAAGGAGAAGAGAGAC 7 27 1 TAAAGAGAAG 0.776943 -17 GGTTACACTTTAAATTGAATGTTAGGAAAAA 8 72 1 TAAATGAATG 0.683517 -92 TCTTATATAGAAAATAAAATGATTTTTCCTA 8 94 0 AAAATAAATG 0.946805 -70 CTATATAAGAAAAATAAAATGTTTTCTAAAT 8 115 1 AAAATAAATG 0.946805 -49 ATGGAAAAAAAAAATTATAGGTAAACATTTA 9 54 1 AAAATATAGG 0.770689 -247 ATGTTCTTTCAAAAGCAAAGGGTTTTAGTTC 9 152 1 AAAAGAAAGG 0.966699 -149 CTCTCCCCCAAAAAGAAAATGCTTACATTTT 9 194 0 AAAAGAAATG 0.955814 -107 AAATTTATTGAAAAGGAGATGTTATAT 9 284 1 AAAAGAGATG 0.940772 -17 ***** ***** Masking position 4 Map Score: 8.78637 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 308 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 6 GTAAAAAAAGACAATTTCGCAGTCTTGCGC 1 89 0 ACAATTTCGC 0.915424 -136 TACAATCCCATAAATTTACCTGGTAAATAG 1 121 1 TAAATTTACC 0.680967 -104 GAACGTTTCATCAATTTCGCTTTCGTGCAC 1 156 1 TCAATTTCGC 0.967284 -69 ATTTTATCGATCCATTTCCACTTAGACAGA 3 75 0 TCCATTTCCA 0.858257 -87 ACTCCTTTTTACAATTTCCAGAGCCCAATC 3 135 0 ACAATTTCCA 0.892998 -27 CACGGATTTTTCACTTTCCCATATATATGA 4 82 1 TCACTTTCCC 0.95689 -90 TCAATTTCCTCCTAAGAAGC 5 234 0 TCAATTTCCT 0.928203 -10 TCCTTTTCAATAAATTTCCCCTTTAAGAGT 9 271 0 TAAATTTCCC 0.950284 -30 ********** Masking position 5 Map Score: 4.25073 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 239 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 TTTGTCTTTGTTTTTCATGCAGTTAAAAAT 2 88 0 TTTTTCATGC 0.841077 -213 TAATGCTTCATTGTCCAAGCTGTCGGTGCA 4 13 1 TTGTCCAAGC 0.845239 -159 CATATCCGTTTCTTCCTTTCTGTTGGTGCT 4 149 0 TCTTCCTTTC 0.912252 -23 AGTTCACGTATTTTCCTTTCAAATTGAACT 5 151 1 TTTTCCTTTC 0.971254 -93 GTTTTAGGCTTTTTCCTTGC 7 1 0 TTTTCCTTGC 0.981525 -43 ATAAAATGATTTTTCCTAACATTCAATTTA 8 82 0 TTTTCCTAAC 0.853312 -82 ATAATTTTTTTTTTCCATTCTGTGATTTCC 9 42 0 TTTTCCATTC 0.962892 -259 ********** Masking position 4 Map Score: 3.1744 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 190 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 TTGTTTTTCATGCAGTTAAAAATAAATCCA 2 81 0 TGCAGTTAAA 0.81216 -220 ACAAACATCATGCTGTAAAAAGCATGATAA 2 113 1 TGCTGTAAAA 0.949859 -188 GGGCTCTGGAAATTGTAAAAAGGAGTGGAT 3 139 1 AATTGTAAAA 0.663568 -23 TGCATGAAGATATTGTTAAACCTTTGTAAA 5 13 0 TATTGTTAAA 0.801144 -231 GCTGGTAGGATGTAGTAGAACCCCTTCATC 5 56 1 TGTAGTAGAA 0.823371 -188 CGCTTTCATTTATAGTAAAAAGAGAAAGGC 6 40 0 TATAGTAAAA 0.872774 -172 CTTTTAAAAATGATGTAAAAGGCGAATTGT 6 91 1 TGATGTAAAA 0.874156 -121 CCTTTAAGAGTGTTGTAAAAACATGAGGCT 9 252 0 TGTTGTAAAA 0.965671 -49 ********** Masking position 9 Map Score: 1.79887 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 163 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 ATGGCTATAAGGGTAAGAGCGCAACTCCAGTGA 1 30 1 GGTAGACGCA 0.93608 -195 ATTGATTAGTGCGTATGATAGCGTCACTGGAGT 1 53 0 GGTAGAAGCG 0.992382 -172 AATCAATGCGGCGCAAGACTGCGAAATTGTCTT 1 79 1 GGCAGATGCG 0.993054 -146 TTAAAAATGAGTGCACGAAAGCGAAATTGATGA 1 163 0 GGCAGAAGCG 0.995142 -62 CAAACAGCGAGCTCATGATTGCCACGGCGATGC 3 14 0 GTCAGATGCC 0.932068 -148 AAATAAAGACGTTTATGATAGCGCTTTCATTTA 6 58 0 GTTAGAAGCG 0.977788 -154 * *** ** **** Masking position 8 Map Score: 2.15562 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 99 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CCACATTAGAAAAAATCCCATTATCTCAAT 2 42 1 AAAAATCCCA 0.920916 -259 AAGCCCCGGCAAAAACGCCATTTTATCGAT 3 94 0 AAAAACGCCA 0.947402 -68 TGGGAAAGTGAAAAATCCGTGTTTCGAAAA 4 73 0 AAAAATCCGT 0.858884 -99 AATAAAAACCTCCCAGTATGTAA 8 151 0 AAAAACCTCC 0.891852 -13 CAAAAACCCGCAAATAAAGGC 9 2 1 AAAAACCCGC 0.965352 -299 ATTTCCCCGAAAAAACGCCTTTATTTGCGG 9 18 0 AAAAACGCCT 0.947402 -283 ********** Masking position 5 Map Score: 0.0953508 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 186 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 ********** No masking Map Score: 1.0114e-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 12 ********** No masking Map Score: 1.0114e-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: 1.0114e-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