AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_ecoli_reg_100.orf -o00030_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 talB 278 transaldolase B #2 gcd 193 glucose dehydrogenase #3 seqA 184 negative modulator of initiation of replication #4 pgm 25 phosphoglucomutase #5 prsA 150 phosphoribosylpyrophosphate synthetase #6 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #7 edd 234 6-phosphogluconate dehydratase #8 zwf 300 glucose-6-phosphate dehydrogenase #9 gnd 300 gluconate-6-phosphate dehydrogenase, decarboxylating #10 talA 288 transaldolase A #11 rpiA 55 ribosephosphate isomerase, constitutive #12 yqfE 141 orf, hypothetical protein #13 fba 214 fructose-bisphosphate aldolase, class II #14 tktA 151 transketolase 1 isozyme #15 dam 106 DNA adenine methylase #16 gntK 230 gluconokinase 2, thermoresistant #17 rbsK 125 ribokinase #18 pfkA 180 6-phosphofructokinase I #19 pgi 300 glucosephosphate isomerase #20 rpiB 300 ribose 5-phosphate isomerase B #21 fbp 175 fructose-bisphosphatase #22 idnK 216 gluconate kinase, thermosensitive glucokinase #23 deoC 257 2-deoxyribose-5-phosphate aldolase #24 deoA 83 thymidine phosphorylase #25 deoB 51 phosphopentomutase Motif number 1 GTCGCGATGACTTTCCTGTGTAAACGTTAC 1 31 1 CTTTCCTGTG 0.752216 -248 CCGAAACAGTCTCGCCTGGCGATAACCGTC 1 168 1 CTCGCCTGGC 0.98894 -111 CGGATAGCGTCAAGCCTGGCTTGCAGAAAA 3 100 0 CAAGCCTGGC 0.896384 -85 TTTATTCATATACTCCTGGCGACTTGTATT 3 139 1 TACTCCTGGC 0.942055 -46 CGAAACTCAGCTTGCCCGGC 5 1 0 CTTGCCCGGC 0.932717 -150 AGGCATGATCCTTTCCAGGCGGTGTATTAA 5 71 0 CTTTCCAGGC 0.877915 -80 TGGAAAGGATCATGCCTGGCCCGCACAGTT 5 84 1 CATGCCTGGC 0.983995 -67 CCAATGGACGCATGCCTGAGGTTCTTCTC 5 132 1 CATGCCTGAG 0.723125 -19 AATTCGTTACCTTTCCAGGGACGCTAATCT 6 76 0 CTTTCCAGGG 0.724527 -211 TGTCAGATATTACGCCTGTGTGCCGTGTTA 8 35 1 TACGCCTGTG 0.739248 -266 TATTTGCGAACATTCCAGGCCGCGAGCATT 9 248 1 CATTCCAGGC 0.888435 -53 TACATACTCCTGTCAGGTGTGATC 9 287 0 TACTCCTGTC 0.812753 -14 CCAGCAATACCATGCCTGTCTGCTATGCTT 10 188 1 CATGCCTGTC 0.942576 -101 GATCGTTTCGCCTGTGGTATGAAATT 11 40 0 TTCGCCTGTG 0.719107 -16 GGCAACGCGCCTCTTCTGGCCTGCGCTAGC 19 52 1 CTCTTCTGGC 0.688481 -249 ATTTTTCATCCACTCCTGGCGGTCAGTAGT 19 144 1 CACTCCTGGC 0.982285 -157 GCGTTTCTCACTTGCCCGACATATGCGTAA 21 44 0 CTTGCCCGAC 0.61687 -132 GCTGCGATACTACGCCTGGCGGCATAATAA 22 171 0 TACGCCTGGC 0.966703 -46 TTCATTCTCCTGGCTTGTCGCCAA 23 244 0 TTCTCCTGGC 0.936228 -14 ********** Masking position 6 Map Score: 21.8076 Number of sites scoring better than the average of aligned sites = 2041 Number in coding regions = 1907 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 GGTTTTGGCACCGCAACAAAGCGCAAGACACGCAGTAT 2 43 1 CGAACAACAA 0.910722 -151 CGCAGTATACCAGTAAAACTATTCATTCGCGGAATCTG 2 73 1 CGAAAATCAC 0.953964 -121 GCCTGGCTTGCAGAAAAACTCGGAATAAACCTTATTTG 3 79 0 CGAAAATAAA 0.89235 -106 ATATATTTATCTGCAAAATTTTAAATAAAGCTCCAATA 6 188 1 CGAAAATAAA 0.89235 -99 TCAGCGGAAAGTGAAGAAATTAACAATATGATTTATTG 6 221 0 GGAGAATCAA 0.50885 -66 GATCATGTTACCGGTAAAATAACCATAAAGGATAAGCG 7 17 0 CGTAAATCAA 0.565783 -218 GCGCAAAGTGCGGCAAAACTGATAAAAAAATCATCGTT 8 138 0 CGAAAATAAA 0.89235 -163 GCATGAAAAGCGGGAACATAATGAAGTC 9 1 0 CGAACAAAAC 0.840841 -300 AAGCATTTACCAGGAGCAGACAACAGCA 12 1 0 CGAGCAACAA 0.819982 -141 TTGGGCTACGCCGGAAAATTTGCCAACAATTTACCGCA 14 66 0 CGAAAATCAA 0.947949 -86 CGGACAATATCAGAAGCAATATCCATCCATGCCTTAAG 16 97 0 CGAGCATCAC 0.916194 -134 TAACTGTTATCGGTAACATTGTCCAGCCGGACAATATC 16 124 0 CGAACATCAC 0.960758 -107 TAACAGTTACCCGTAACATTTTTAATTCTTGTATTGTG 16 153 1 CGAACATAAC 0.917653 -78 AGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAA 18 138 1 CGAACAACAT 0.695639 -43 TCTAAAAAACCAGAAAAACAAATAACATCATGTTTTTA 20 107 0 CGAAAAAAAT 0.468226 -194 AGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATT 20 193 1 CGAAAAACAA 0.896201 -108 TTCCCCGTCCGTGCAAAACTTCACAATCAAAAAACATT 20 268 0 GGAAAATCAC 0.725276 -33 AGTAAAGCGACCGCAACAATCTTAACAAATAATCTCAA 21 123 0 CGAACATAAA 0.907354 -53 TAATTCTTATCAGTAGAAATAAAAAAACGTGAAATTAT 22 137 1 CGAGAATAAC 0.808121 -80 * * **** * ** * Masking position 8 Map Score: 15.49 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 410 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 CCGTCTTGTCGGCGGTTGCGCTGACGTTGCGT 1 193 1 GCGTTGCGCT 0.965218 -86 GGTATACTGCGTGTCTTGCGCTTTGTTGCGGT 2 52 0 GGCTTGCGCT 0.986053 -142 ACACTTTCAGGCCTCGTGCGGATTCACCCACG 7 80 1 GCCGTGCGGA 0.875228 -155 TGTGGGCAGGGGCTGTTGCCCACACACTTTAT 10 41 0 GCGTTGCCCA 0.832072 -248 TAAAAGATCAGGGATTTGCGCTA 12 129 1 GGTTTGCGCT 0.887577 -13 TACATGACGCGCGGCTTGCGGTAAATTGTTGG 14 50 1 GGCTTGCGGT 0.981618 -102 GTGTTAGGGTGGCGCGTGCCCTGCTTTTCTTT 17 76 0 GCCGTGCCCT 0.835816 -50 CACAAAATGCGGGTCTGGCTCTCTTTTATACT 18 13 0 GGCTGGCTCT 0.71938 -168 GCCAGAAGAGGCGCGTTGCCCAAGTAACGGTG 19 40 0 GGGTTGCCCA 0.915738 -261 AATAAAGGGTGAGCGGGGCGGTTGTCAACGAT 19 100 1 GGGGGGCGGT 0.914436 -201 GTCAACGATGGGGTCATGCGGATTTTTCATCC 19 123 1 GGCATGCGGA 0.794756 -178 ACATTTTTCTGTGACTGGCGCTACAATCTTCC 19 243 1 GGCTGGCGCT 0.97018 -58 TATTTGTTAAGATTGTTGCGGTCGCTTTACTC 21 130 1 GTGTTGCGGT 0.800762 -46 GTGTATCGAAGTGTGTTGCGGAGTAGATGTTA 23 181 1 GGGTTGCGGA 0.963286 -77 * * ******** Masking position 9 Map Score: 9.92923 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 905 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 GATAACTTCTGCGTAGCATACATGAGGTTTTG 1 97 1 GCGTACATCA 0.907234 -182 AACGTTGCAGACAAAGGACAAAG 4 2 1 ACGTTCAGCA 0.960866 -24 TAGGGCAAAAACGTTTCAGTCAGTGTAATAAA 7 120 0 ACGTTCAGCA 0.960866 -115 CCGGTTACAGGCGTTTCAGTCATAAATCCTCT 7 158 1 GCGTTCAGCA 0.990012 -77 GATTCACAACGCGTTTCATTCAGAGGATTTAT 7 179 0 GCGTTCATCA 0.960866 -56 CATCAAAAAAGCATAGCAGACAGGCATGGTAT 10 194 0 GCATACAGCA 0.907234 -95 ACAGCATCCAGCGCTTCAGGCAACTCCCGCAA 15 40 0 GCGCTCAGCA 0.974387 -67 CAGCGCAATAGCGTTAAAGACACTCACCATCC 20 159 0 GCGTTAAGCA 0.886494 -142 ATTCACCTGAGCGCAACATTGAGATTATTTGT 21 105 1 GCGCACATGA 0.593822 -71 TACTCCATAAACATTGCAGGGAAAGTTTT 21 157 1 ACATTCAGGA 0.703164 -19 GAACCAGATCGCATTACAGTGATGCAAACTTG 23 125 1 GCATTCAGGA 0.905332 -133 ***** *** ** Masking position 8 Map Score: 9.11501 Number of sites scoring better than the average of aligned sites = 803 Number in coding regions = 690 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 AAACCTATAATTAATTGCTACTAAAATATT 2 150 1 TTAATTGCTA 0.676856 -44 GCGCTTATCCTTTATGGTTATTTTACCGGT 7 16 1 TTTATGGTTA 0.454836 -219 CTTTGTATACTTATTTGCGAACATTCCAGG 9 237 1 TTATTTGCGA 0.904657 -64 CCCACACACTTTATTTGTGAACGTTACGTG 10 25 0 TTATTTGTGA 0.94436 -264 AAACATTATATTAATGGTGAGAGTTTGGAC 10 120 0 TTAATGGTGA 0.904657 -169 TAAATTTTATTTTTTTGTGAAGTCGCCAGC 20 15 0 TTTTTTGTGA 0.871141 -286 TAAAGTTTATTTTATTGTGAACAATGGCGA 20 45 1 TTTATTGTGA 0.871141 -256 CAAATGTTTTTTGATTGTGAAGTTTTGCAC 20 266 1 TTGATTGTGA 0.798612 -35 AACATTGAGATTATTTGTTAAGATTGTTGC 21 119 1 TTATTTGTTA 0.789328 -57 TTAACTGTCATTATTTGTGATGAAGATCAC 22 58 1 TTATTTGTGA 0.94436 -159 GTAGATTTCCTTAATTGTGATGTGTATCGA 23 160 1 TTAATTGTGA 0.94436 -98 AAGGTGAATTTTATTGGCGACAAGCCAGGA 23 231 1 TTATTGGCGA 0.841384 -27 ********** Masking position 10 Map Score: 8.15471 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 99 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 CCGCGATGGTCTCTTTTTTTGTTGTACGGAC 6 20 0 CTCTTTTTTG 0.84516 -267 TCAGTTTTGCCGCACTTTGCGCGCTTTTCCC 8 154 1 CGCACTTTCG 0.887272 -147 GCACTTTGCGCGCTTTTCCCGTAATCGCACG 8 165 1 CGCTTTTCCG 0.956588 -136 ATTATGTTCCCGCTTTTCATGCGATACATTA 9 17 1 CGCTTTTCTG 0.957412 -284 ATCGCTTTTTTTGTATATAATGC 11 3 1 CGCTTTTTTG 0.969301 -53 TTGACGACAGCGCGTTTTGGGCTACGCCGGA 14 89 0 CGCGTTTTGG 0.905387 -63 AACACGGTGGCGCATTTTATGGACATCCCGA 17 103 1 CGCATTTTTG 0.974937 -23 GAGCCAGACCCGCATTTTGTGTATAAAATAC 18 24 1 CGCATTTTTG 0.974911 -157 TAATCTGCCGCTCATTTTACGCATATGTCGG 21 28 1 CTCATTTTCG 0.86827 -148 AAGTGAGAAACGCATTTCAGGATAATCCGTA 21 61 1 CGCATTTCGG 0.949077 -115 ******** ** Masking position 6 Map Score: 7.6606 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 287 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 GGATTTCTGACACTGCGTTGATATCGCCCG 1 140 0 CACTGCGTTG 0.864735 -139 ACCATTGTGCCACAGGGCTGCAACAAATAA 3 56 1 CACAGGGCTG 0.983375 -129 TCAGCTAAGACACTGCACTGGATTAAG 3 168 1 CACTGCACTG 0.952649 -17 TCTTACGGTGCACTGTACTGCTTTTACGAG 8 225 0 CACTGTACTG 0.828183 -76 CAGGTGTGATCACCGCGCTGAATGCTCGCG 9 268 0 CACCGCGCTG 0.962229 -33 AAAATCACAGGGCAGGGAAACCTGC 13 6 1 CACAGGGCAG 0.949357 -209 TTCACCTTGTCACCGGGCGGATCTATTTAA 16 34 1 CACCGGGCGG 0.944463 -197 AGGTGTTATCACAGGACTGGCTCCTCCAA 19 10 1 CACAGGACTG 0.951014 -291 ATAAATGCTTCACTGCGCTAAGGGTTTACA 19 181 1 CACTGCGCTA 0.870235 -120 AAATTCCTCACTGGTCAGGTAGACACCT 22 9 1 CACTGGTCAG 0.795951 -208 ********** Masking position 2 Map Score: 7.90766 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 545 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 AACCATAAAGGATAAGCGCAGATA 7 4 0 GAAAGCGCAG 0.848154 -231 CCGTGTTAATGACAAAAGCAGATAAAAAAGT 8 57 1 GAAAAAGCAG 0.616187 -244 TTCGCAAGCTCGTAAAAGCAGTACAGTGCAC 8 217 1 CGAAAAGCAG 0.81588 -84 CTAAACGCATCAAAAAAGCATAGCAGACAGG 10 202 0 CAAAAAGCAT 0.687226 -87 GAGAAATTTCGCTAAACGCATCAAAAAAGCA 10 213 0 GCAAACGCAT 0.780219 -76 TCATAGTGCAGGAAAAAGCATTTACCAGGAG 12 23 0 GGAAAAGCAT 0.733432 -119 GGTGAGCGAACGCAGACGCAGCACATGCAAC 13 149 1 CGAGACGCAG 0.939088 -66 CACCCTAACACGGTGGCGCATTTTATGGACA 17 97 1 CGTGGCGCAT 0.857384 -29 GTACTACCTGCGCTAGCGCAGGCCAGAAGAG 19 62 0 CGTAGCGCAG 0.888147 -239 GAGTGTAAACCCTTAGCGCAGTGAAGCATTT 19 183 0 CCTAGCGCAG 0.707478 -118 TCGGGCAAGTGAGAAACGCATTTCAGGATAA 21 55 1 GAAAACGCAT 0.862431 -121 AAACTTCTTACAATGGCGCATCACCTTCGGC 23 27 0 CATGGCGCAT 0.7638 -231 CGTCAGTGGTGGCAAACGCATCAGGATCAAA 23 70 0 GGAAACGCAT 0.92098 -188 CGTTTGCCACCACTGACGCATTCATTTGAAA 23 83 1 CATGACGCAT 0.797454 -175 CCGGATAAGGCGTAGACGCATCCGGCAAAAG 24 31 1 CGAGACGCAT 0.934262 -53 ** ******** Masking position 10 Map Score: 8.17921 Number of sites scoring better than the average of aligned sites = 1412 Number in coding regions = 1326 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 9 CAGTCTCGCCTGGCGATAACCGTCTTGTCGGC 1 174 1 TGCGATAACG 0.956392 -105 AACTATTCATTCGCGGAATCTGTTAATAAAGC 2 89 1 TGCGGAATCG 0.877159 -105 GGAAAGAATCTGCCGAAAACTGTGCGGGCCAG 5 99 0 TCCGAAAACG 0.977568 -52 ACCATCGCGGTCCCGGAAACTTTCTTAAGGAT 6 41 1 TCCGGAAACT 0.917 -246 AATAAGCATGTGGCGAAAACAGATTTTTATTT 6 154 1 TGCGAAAACG 0.972363 -133 ATGGTTATTTTACCGGTAACATGATCTTGCGC 7 29 1 TCCGGTAACT 0.873208 -206 TTTTACGAGCTTGCGAAAACTGTAAACGCTTA 8 202 0 TGCGAAAACG 0.972363 -99 TGGACAATGTTACCGATAACAGTTACCCGTAA 16 137 1 TCCGATAACG 0.964496 -94 GCAAGAAGACTTCCGGCAACAGATTTCATTTT 18 135 1 TCCGGCAACG 0.953521 -46 * ******** * Masking position 8 Map Score: 7.23464 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 299 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 GATATCAACGCAGTGTCAGAAATCCGAAAC 1 145 1 CAGTGTCAGA 0.676551 -134 CGCTTTGTTGCGGTGCCAAAACCTGCCCGT 2 36 0 CGGTGCCAAA 0.616389 -158 CTTTTTTTCGCGTTGTCGGGTTAGGGTATT 3 20 1 CGTTGTCGGG 0.860891 -165 TGACGCTATCCGCTGCCGGGATTTATTCAT 3 118 1 CGCTGCCGGG 0.94642 -67 GAGACCATCGCGGTCCCGGAAACTTTCTTA 6 38 1 CGGTCCCGGA 0.891165 -249 TCCGCTGATTCGGTGCCAGACTGAAATCAG 6 251 1 CGGTGCCAGA 0.968152 -36 ATAACATGATCAGTGTCAGATTTTTACCCA 8 102 1 CAGTGTCAGA 0.676551 -199 CACATTATTACCCTGCCGGAGTCTACAGAC 10 81 1 CCCTGCCGGA 0.882576 -208 AACGATAAACCATTGCGGGAGATAACCTTG 15 12 0 CATTGCGGGA 0.680202 -95 AATGGTTTATCGTTGCGGGAGTTGCCTGAA 15 28 1 CGTTGCGGGA 0.921457 -79 AAGCGCTGGATGCTGTCGGAGCTTTCTCCA 15 56 1 TGCTGTCGGA 0.853348 -51 AAATGAAATCTGTTGCCGGAAGTCTTCTTG 18 136 0 TGTTGCCGGA 0.933998 -45 GCCCAAGTAACGGTGTTGGAGGAGCCAGTC 19 25 0 CGGTGTTGGA 0.821662 -276 AGATGATAGATGTTGCTGGATGGTGAGTGT 20 142 1 TGTTGCTGGA 0.621728 -159 AACGCTATTGCGCTGTCAGATGTAACTCTG 20 176 1 CGCTGTCAGA 0.886487 -125 ATGAGGCGGCTTTTGCCGGATGCGTCTACG 24 41 0 TTTTGCCGGA 0.503813 -43 ********** Masking position 4 Map Score: 8.91627 Number of sites scoring better than the average of aligned sites = 2986 Number in coding regions = 2769 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 11 GTGATATCATCAGGGCAGACCGGTTACATCC 1 226 1 CAGGGCAGAC 0.856528 -53 ATCACTTCGCACGGGCAGGTTTTGGCACCGC 2 26 1 ACGGGCAGGT 0.77447 -168 ATTGAGTTGTCAGAGCAGGATGATTCACAAC 7 201 0 CAGAGCAGGT 0.928539 -34 CGCAGCTTAAAAGATCAGGGATTTGCGCTA 12 122 1 AAGATCAGGA 0.776113 -20 AAAATCACAGGGCAGGGAAACCTGCCCT 13 8 1 CAGGGCAGGA 0.981293 -207 GCGCTGAAACAAGGGCAGGTTTCCCTGCCCT 13 19 0 AAGGGCAGGT 0.948011 -196 TCGGATGATGAAGGGCACGCCCTTAACGACT 14 119 0 AAGGGCACGC 0.928942 -33 TAAAGAAAAGCAGGGCACGCGCCACCCTAAC 17 75 1 CAGGGCACGG 0.891335 -51 TGAATTGATTCAGGTCAGGCCAAATGGCGGT 18 53 0 CAGGTCAGGC 0.974135 -128 CTCTGTAAAACAGATCAGGAAGGCGTAATTC 20 201 1 CAGATCAGGA 0.884506 -100 AAATTCCTCACTGGTCAGGTAGACACCTCGG 22 11 1 CTGGTCAGGA 0.751054 -206 ATTTGTGATGAAGATCACGTCAGAAAATTGT 22 70 1 AAGATCACGC 0.656193 -147 ********* * Masking position 7 Map Score: 5.91193 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 681 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 CGTTGATATCGCCCGCCATTTTTATACAAAA 1 124 0 GCCCGCCATT 0.938911 -155 ATCATGCCTGGCCCGCACAGTTTTCGGCAGA 5 92 1 GCCCGCACGT 0.969247 -59 TACGGGAAAAGCGCGCAAAGTGCGGCAAAAC 8 157 0 GCGCGCAAGT 0.914322 -144 AGGGGCTGTTGCCCACACACTTTATTTGTGA 10 35 0 GCCCACACCT 0.85682 -254 AACAGCCCCTGCCCACAACGTGGCGCACATT 10 56 1 GCCCACAAGT 0.97043 -233 CGCTTTTAGAGCACGCAATTTTTCATACTCT 13 49 1 GCACGCAATT 0.88018 -166 CGGAAAATTTGCCAACAATTTACCGCAAGCC 14 62 0 GCCAACAATT 0.868301 -90 ATCTATTTAAGCCCACAAATTTGAAGTAGCT 16 54 1 GCCCACAATT 0.970999 -177 GGTGAATCGCGCCAGCAAATTACGGATTATC 21 81 0 GCCAGCAATT 0.928333 -95 ******** ** Masking position 11 Map Score: 5.1623 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 267 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 TTGTATAAAAATGGCGGGCGATATCAACGC 1 126 1 ATGGCGGGCG 0.926069 -153 CATTATATTAATGGTGAGAGTTTGGACTTG 10 117 0 ATGGTGAGAG 0.91269 -172 GTAAGTGACTGGGGTGAGCGAACGCAGACG 13 137 1 GGGGTGAGCG 0.930157 -78 CCGTGTTAGGGTGGCGCGTGCCCTGCTTTT 17 80 0 GTGGCGCGTG 0.85452 -46 TTATAAATAAAGGGTGAGCGGGGCGGTTGT 19 95 1 AGGGTGAGCG 0.959215 -206 CGTTAGCGTAATGTTGAGTGTAAACCCTTA 19 199 0 ATGTTGAGTG 0.793415 -102 ATTGTGAACAATGGCGAGTGGCTTAAAATT 20 58 1 ATGGCGAGTG 0.971191 -243 ATGTTGCTGGATGGTGAGTGTCTTTAACGC 20 151 1 ATGGTGAGTG 0.971746 -150 ********** Masking position 6 Map Score: 3.62418 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 265 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 GGCAAAGTTCTTTTTTTCGCGTTGTCGGGTT 3 4 1 AAATTTTTGG 0.962875 -181 AACTCGGAATAAACCTTATTTGTTGCAGCCCTGTGGCA 3 63 0 AAATTTTTCG 0.751788 -122 GCGGGCCAGGCATGATCCTTTCCAGGCGGTGTATTAAA 5 70 0 CATTTTTAGG 0.705635 -81 AAGAAATTAACAATATGATTTATTGGAGCTTTATTTAA 6 208 0 CAATTTTTGG 0.960404 -79 CTAAATATCTAAAAGTACTTTTTAAGTGCCATCTGAAG 9 84 0 AAATTTTAGG 0.865505 -217 CAACCTGACACAAAATTGTGTCATAGTGCAGGAAAAAG 12 36 0 CAATTGTTGG 0.834937 -106 TAACATTTTTAATTCTTGTATTGTGGGGGCACCACTTT 16 166 1 AATTTATTGG 0.592437 -65 TAAACTTTATAAATTTTATTTTTTTGTGAAGTCGCCAG 20 16 0 AAATTTTTGG 0.962875 -285 TAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCG 20 36 1 AAATTTTTGG 0.962874 -265 TTAACATCACAAATGTTTTTTGATTGTGAAGTTTTGCA 20 257 1 AAATTTTTGG 0.962875 -44 AAAGCCGCCTCATACTCTTTTCCTCGGGAGGTTACC 24 58 1 CATTTTTTGG 0.906202 -26 *** * *** * * * Masking position 2 Map Score: 3.8112 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 31 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 CCAGGCTTGACGCTATCCGCTGCCGGGATT 3 111 1 CGCTATCCGC 0.917037 -74 TTAATTTCTTCACTTTCCGCTGATTCGGTG 6 236 1 CACTTTCCGC 0.858296 -51 CATGCTTATATGCTTACGGCTTTATATTAC 9 180 0 TGCTTACGGC 0.835652 -121 GTGATCACCGCGCTGAATGCTCGCGGCCTG 9 263 0 CGCTGAATGC 0.658941 -38 TGAGAAATTTCGCTAAACGCATCAAAAAAG 10 215 0 CGCTAAACGC 0.858092 -74 AAATGTTACCCGCCGACGGCTTCGGTATAT 12 75 0 CGCCGACGGC 0.932228 -67 GCCCAAAACGCGCTGTCGTCAAGTCGTTAA 14 98 1 CGCTGTCGTC 0.800063 -54 CAGCATCCAGCGCTTCAGGCAACTCCCGCA 15 41 0 CGCTTCAGGC 0.809216 -66 CACACTTATACACTTAAGGCATGGATGGAT 16 85 1 CACTTAAGGC 0.821111 -146 TTAGCTGAACTACTGACCGCCAGGAGTGGA 19 152 0 TACTGACCGC 0.533364 -149 CTCAACATTACGCTAACGGCACTAAAACCA 19 211 1 CGCTAACGGC 0.954712 -90 TTGTTGCGGTCGCTTTACTCCATAAACATT 21 142 1 CGCTTTACTC 0.514432 -34 AATGGCGCATCACCTTCGGCATAAAAGGAA 23 17 0 CACCTTCGGC 0.726101 -241 ********** Masking position 3 Map Score: 2.54176 Number of sites scoring better than the average of aligned sites = 2993 Number in coding regions = 2838 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894