AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifruR_ecoli_bsub_100.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 icdA 201 isocitrate dehydrogenase, specific for NADP+ #2 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #3 ppsA 300 phosphoenolpyruvate synthase #4 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #5 edd 234 6-phosphogluconate dehydratase #6 fruB 300 PTS system, fructose-specific IIA/fpr component #7 ptsH 300 PTS system protein HPr #8 ptsI 44 PEP-protein phosphotransferase system enzyme I #9 crr 40 PTS system, glucose-specific IIA component #10 fba 214 fructose-bisphosphate aldolase, class II #11 pgk 49 phosphoglycerate kinase #12 epd 284 D-erythrose 4-phosphate dehydrogenase #13 pckA 300 phosphoenolpyruvate carboxykinase #14 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #15 mtlD 229 mannitol-1-phosphate dehydrogenase #16 pfkA 180 6-phosphofructokinase I #17 aceB 268 malate synthase A #18 aceA 29 isocitrate lyase #19 aceK 182 isocitrate dehydrogenase kinase/phosphatase #20 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #21 mtlD 52 mannitol-1-phosphate dehydrogenase #22 yjdD 147 similar to fructose phosphotransferase system enzyme II #23 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #24 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #25 fruR 279 transcriptional regulator (DeoR family) #26 pps 300 phosphoenolpyruvate synthase #27 kdgK 37 2-keto-3-deoxygluconate kinase #28 kdgR 221 transcriptional regulator (LacI family) #29 ypqE 137 similar to phosphotransferase system enzyme II #30 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #31 citC 163 isocitrate dehydrogenase #32 pykA 42 pyruvate kinase #33 pfk 183 6-phosphofructokinase #34 pckA 300 phosphoenolpyruvate carboxykinase #35 pgk 300 phosphoglycerate kinase #36 gap 46 glyceraldehyde-3-phosphate dehydrogenase #37 yvbQ 297 yvbQ #38 crh 23 catabolite repression HPr-like protein #39 yvcL 22 similar to hypothetical proteins #40 yvcJ 24 similar to hypothetical proteins #41 yvcI 300 similar to mutator MutT protein #42 yvkC 300 similar to pyruvate,water dikinase Motif number 1 GCGGCGTAAGCGCCTTATCCGGCCTACAAGAAC 15 111 0 CGCCATCCGC 0.997098 -119 AAGGCGCTTACGCCGCATCCGGCGCTGCCCCTC 15 128 1 CGCCATCCGC 0.997098 -102 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 19 27 0 CGCCATCCGC 0.997098 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 19 44 1 CGCCATCCGC 0.997098 -139 GACGCGCAAGCGTCGCATCAGGCATCGTGCACC 19 71 0 CGTCATCAGC 0.969568 -112 GACGCTTGCGCGTCTTATCATGCCTACAGCCGT 19 90 1 CGTCATCAGC 0.969568 -93 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 19 125 0 CGCCATCCGC 0.997098 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 19 142 1 CGCCATCCGC 0.997098 -41 CGGAGGGACAGGCCCTATGAAGCCCAGCAACCG 34 65 0 GGCCATGAGC 0.772071 -236 CCGGCGCTTTCGCCTAAGGCCGCTGCCCTGGCT 35 155 1 CGCCAGGCGC 0.944345 -146 AACGTGAAACCGTCTGTTCAAGCGATAACTCCG 35 234 0 CGTCTTCAGC 0.772236 -67 ATACAGAAAGCGCCAAATGGTGCATCCCAATAT 37 54 0 CGCCATGGGC 0.939872 -244 CATGCCGCGTCGTTTTATCCAGCAATATTTTAT 37 105 0 CGTTATCCGC 0.866776 -193 **** **** ** Masking position 13 Map Score: 28.5488 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 392 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 2 TTGACTCTTGAATGGTTTCAGCACTTTGGACT 2 84 1 AAGGTTCAGC 0.936016 -217 CATAGGGCAAAAACGTTTCAGTCAGTGTAATA 5 122 0 AACGTTCAGT 0.968779 -113 CTCCGGTTACAGGCGTTTCAGTCATAAATCCT 5 156 1 AGCGTTCAGT 0.853875 -79 TGCTTTCTTGAAACGTTTCAGCGCGATCTTGT 6 203 1 AACGTTCAGC 0.99208 -98 TGCTGAATTGAAACGATTCAGCCTCTATGAGA 6 266 0 AACGTTCAGC 0.99208 -35 CAAATCATAAAATCGATTCAGCTTTGGCTTTT 7 82 0 AACGTTCAGC 0.99208 -219 TAATCGACTGAAACGCTTCAGCTAGGATAAGC 12 148 0 AACGTTCAGC 0.99208 -137 CTGGACAGTTAACCGATTCAGTGCCAGATTTC 14 182 1 AACGTTCAGT 0.968779 -119 GCCTGACCTGAATCAATTCAGCAGGAAGTGAT 16 64 1 AACATTCAGC 0.950735 -117 GTCGATCGTTAAGCGATTCAGCACCTTACCTC 17 23 1 AACGTTCAGC 0.99208 -246 AGCCAAAAAAAATCATTTCTGCTTTCTTTAAT 37 208 0 AACATTCTGC 0.710322 -90 ** ** ****** Masking position 1 Map Score: 21.5325 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 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 3 TGACTCTTGAATGGTTTCAGCACTTTGGACT 2 85 1 AGGTTTCAGC 0.914842 -216 TATTTGCTTGAACGATTCACCGTTTTTTTCA 3 204 1 ACGATTCACC 0.954251 -97 CAGGCCTCGTGCGGATTCACCCACGAGGCTT 5 87 1 GGGATTCACC 0.842949 -148 ATAGGGCAAAAACGTTTCAGTCAGTGTAATA 5 122 0 ACGTTTCAGT 0.833869 -113 TCCGGTTACAGGCGTTTCAGTCATAAATCCT 5 157 1 GCGTTTCAGT 0.73597 -78 GCTTTCTTGAAACGTTTCAGCGCGATCTTGT 6 204 1 ACGTTTCAGC 0.958613 -97 GCTGAATTGAAACGATTCAGCCTCTATGAGA 6 266 0 ACGATTCAGC 0.978247 -35 AAATCATAAAATCGATTCAGCTTTGGCTTTT 7 82 0 ACGATTCAGC 0.978247 -219 GTAAGCTCCTGGGGATTCACTCTCTTGTCGC 10 102 0 GGGATTCACT 0.537879 -113 GAATCAACGAGAGGATTCACC 11 39 1 GGGATTCACC 0.843076 -11 AATCGACTGAAACGCTTCAGCTAGGATAAGC 12 148 0 ACGCTTCAGC 0.894394 -137 CCGGTAAAGTATCGATTCACCACGCTAACTT 13 15 0 ACGATTCACC 0.954251 -286 TGGACAGTTAACCGATTCAGTGCCAGATTTC 14 183 1 ACGATTCAGT 0.906885 -118 CCTGACCTGAATCAATTCAGCAGGAAGTGAT 16 65 1 ACAATTCAGC 0.817755 -116 TCGATCGTTAAGCGATTCAGCACCTTACCTC 17 24 1 ACGATTCAGC 0.978233 -245 CCCCTTGGTTAGGATTTCAGCATCACTTGAA 28 19 1 AGATTTCAGC 0.517343 -203 * ********* Masking position 6 Map Score: 21.6541 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 363 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 TCTACAATCTGCGCAAGATCATGTTACCGGTAA 5 38 0 GCGCAATCTG 0.888095 -197 TGCGGCGTAAGCGCCTTATCCGGCCTACAAGAA 15 112 0 GCGCCATCGG 0.995681 -118 TAAGGCGCTTACGCCGCATCCGGCGCTGCCCCT 15 127 1 ACGCCATCGG 0.993107 -103 TGCGGCGTGAACGCCTTATCCGGCCTACAGTCA 19 28 0 ACGCCATCGG 0.993105 -155 TAAGGCGTTCACGCCGCATCCGGCAATCGGTGC 19 43 1 ACGCCATCGG 0.993107 -140 AGACGCGCAAGCGTCGCATCAGGCATCGTGCAC 19 72 0 GCGTCATCGG 0.969732 -111 CGACGCTTGCGCGTCTTATCATGCCTACAGCCG 19 89 1 GCGTCATCTG 0.888095 -94 TGCGGCGTAAACGCCTTATCCAGCCTACGTTCG 19 126 0 ACGCCATCAG 0.93388 -57 TAAGGCGTTTACGCCGCATCCGGCAATTCTCTG 19 141 1 ACGCCATCGG 0.993107 -42 GCAATTCTCTGCTCCTGATGAGGGCGCTAA 19 163 1 GCTCCATGGG 0.780499 -20 TCTGGCATAGACGCATAATCTGGTTAAAAAAGG 29 22 0 ACGCAATCGG 0.952419 -116 TATACAGAAAGCGCCAAATGGTGCATCCCAATA 37 55 0 GCGCCATGTG 0.924675 -243 ***** *** ** Masking position 8 Map Score: 20.7191 Number of sites scoring better than the average of aligned sites = 593 Number in coding regions = 264 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 ACCCACGAGGCTTTTTTTATTACACTGACTGA 5 105 1 CTTTTTTTTA 0.89845 -130 CAGGTTGGCGCTTTTTTTCTCATAGAGGCTGA 6 249 1 CTTTTTTTCA 0.9345 -52 CGCCTTGTTGCTTTTTTACACAAGCGTTTTGT 14 79 1 CTTTTTTACA 0.566362 -222 CTTCGGGTGCCTTTTTTATTTCCGAAACGTAC 17 61 1 CTTTTTTTTC 0.830319 -208 GATCGTTGTGCTCTTTTCGTTCAGCACAACTA 17 198 0 CTCTTTTTTC 0.730206 -71 TTATTCCTTGCTTTTTTTGTTATAGGGAAAAA 22 20 1 CTTTTTTTTA 0.89845 -128 ATTAAAATCGCTTTTTTTACCATAGGTTCCGG 22 63 0 CTTTTTTCCA 0.894096 -85 ATGAACTTCCCGTTTTTTTCCCTCAATCACTG 23 64 0 CGTTTTTCCC 0.476781 -175 AATTGACCTCCTCTTTTTACTAGTCTGACCTT 23 214 0 CTCTTTTCTA 0.743304 -25 TAACTTAAAGCTTTATTACTTCACAATATTAT 24 59 0 CTTTATTTTC 0.381707 -39 TGAAAAAAGTCTTTTATATTCATAGTAGAAAT 25 49 0 CTTTTATTCA 0.491841 -231 ATATAAAAGACTTTTTTCATTAAAATAAGAAG 25 62 1 CTTTTTTTTA 0.89845 -218 TTTTCGTTGACTCTTTTCACTATTTATCCTAA 28 84 0 CTCTTTTCTA 0.743304 -138 TCGCCACCGCCTTTTTTAACCAGATTATGCGT 29 13 1 CTTTTTTCCA 0.894096 -125 TATGACGGGACGTTTTTTGTCATAGCGGGACA 37 239 1 CGTTTTTTCA 0.735743 -59 GGGTCAATTACTTTATTAATCATAACCGAAAA 41 63 0 CTTTATTTCA 0.64285 -238 TATCCGTGTCCTTTTTTTGTCCATAAATAAAA 41 138 1 CTTTTTTTCC 0.887528 -163 AACTGGAATTCTCTTTTATTTATGGACAAAAA 41 151 0 CTCTTTTTTA 0.830319 -150 ATCAGCGGCACTTTTTTTATTACATCATCAAG 42 38 1 CTTTTTTTTA 0.89845 -263 TTTGAAACCCCTCTTTTCTTCATTCATTTTGT 42 278 0 CTCTTTTTCA 0.887528 -23 ******* *** Masking position 7 Map Score: 15.0519 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 113 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 TCACCTCTCCTTCGAGCGCTAC 1 190 0 TCCCTTCCTT 0.972502 -12 TTTTTCGATGTCACCTATCCTTAGAGCGAGGC 2 186 1 TCCCTTCCTT 0.972502 -115 AAAGCAAGTTTCTCCCATCCTTCTCAACTTAA 2 265 1 TCCCCTCCTT 0.847981 -36 TATCTGCGCTTATCCTTTATGGTTATT 5 6 1 GCCTTTCCTT 0.815614 -229 AGTTCTCCTCTCTTGCTGAATTGAA 6 286 0 TCCCTTCTTG 0.607009 -15 GATTCAGCTTTGGCTTTTCCTGTAACGATTAA 7 68 0 TGCTTTCCTG 0.644492 -233 GTCTCTTGTCCTGTATCGTCGGG 10 202 0 TCCTTTCCTG 0.955786 -13 ATTCCACGTTTCGCTTATCCTAGCTGAAGCGT 12 136 1 TCCTTTCCTA 0.805539 -149 TTCACTGCTCCTTAGCCAATATG 13 288 0 TCCTGTCCTT 0.904426 -13 ATCCGGCAATTCTCTGCTCCTGATGAGGGCGC 19 158 1 TCCTGTCCTG 0.862539 -25 TGTATTTTCTCCCTTCTCATTCACTTCAACC 29 117 0 TCCTTTCATT 0.79108 -21 AGGATGGAGATCCCTTTTCATTGTTTTTAGGG 33 113 1 TCCTTTCATT 0.79108 -71 AGGGAGTCCGTCCCCTTCCCTTGTCCGCTTTC 35 48 0 TCCCTCCCTT 0.90471 -253 GGGGACGGACTCCCTTTCCCTTTTTCCATGAA 35 65 1 TCCTTCCCTT 0.897458 -236 AAGATCTCCCCTTTTCTTTACGG 38 6 0 TCCCTTTCTT 0.66679 -18 ** *** ***** Masking position 11 Map Score: 10.3467 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 85 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 AACCGGATGAAAAAAACGGTGAATCGTTCAAG 3 210 0 AAAAACGTGA 0.815278 -91 CTCTATGAGAAAAAAAGCGCCAACCTGGCTTA 6 244 0 AAAAAGGCCA 0.820569 -57 GGGTTCTTTTAAAAATCAGTCACAAGTAAGGT 8 17 1 AAAATCGTCA 0.807147 -28 TATTTGACAAAAAACTCCGTGATTCCTGTCAC 13 178 0 AAAATCGTGA 0.698358 -123 TAAAAAAGCAACAAGGCGGCGATTTTCGCTAA 14 65 0 ACAAGCGCGA 0.667507 -236 GATATCACACAAAAGGCCGTCGACTGGACAGT 14 159 1 AAAAGCGTCG 0.920778 -142 TCAGTATAAAAGAGAGCCAGACCCGCATT 16 8 1 AAAAAGGCCA 0.820569 -173 TTTTGTGTATAAAATACCGCCATTTGGCCTGA 16 38 1 AAAAACGCCA 0.935049 -143 ATCTGGTTAAAAAAGGCGGTGGCGATA 29 6 0 AAAAGCGTGG 0.865399 -132 CGTAAGAACCAAAAAGCAGCCAGCGCTCCGCA 30 28 0 AAAAGCGCCA 0.968241 -178 AAAGCTGCTTAAAACGCGGTCGTTTCTCTATC 35 122 0 AAAAGCGTCG 0.920778 -179 CCTGTGCCGAAAAAGACTGCGATCTGCCCTAG 35 202 1 AAAAACGCGA 0.888438 -99 ACGCGGCATGAAAACTCTGCGAATATTGTCGA 37 128 1 AAAATCGCGA 0.806854 -170 ATTCATTATAAAAAGGGGGTCAATTACTTTAT 41 79 0 AAAAGGGTCA 0.842949 -222 TGATGTAATAAAAAAAGTGCCGCTGATTAGAA 42 33 0 AAAAAGGCCG 0.758794 -268 ATTATCCTGAAAAATGCGGCCGTACTGGTACT 42 110 0 AAAAGCGCCG 0.954487 -191 GGTTTTCAGGAAAATGCTGTCAAACGCAGAAA 42 175 0 AAAAGCGTCA 0.944122 -126 **** ** **** Masking position 4 Map Score: 15.9495 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 461 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 ATTTATCACAAAAGGATTGTTCG 3 288 1 AAAGGAGTTC 0.883264 -13 ACGTGGAATAAAAGGAATGTTTGTCCAGCCGA 12 113 0 AAAGGAGTTT 0.902023 -172 GCAAACATAAGAAGGGGTGTTTTT 14 287 1 GAAGGGGTTT 0.969318 -14 CACTGTGAACGAAGGATCGTTGTGCTCTTTTC 17 212 0 GAAGGAGTTG 0.827881 -57 GAGGGAAAAAAACGGGAAGTTCATTCTCGTTC 23 72 1 AACGGGGTTC 0.861268 -167 ATTTTTTTTTGAAGGGGAGATGTAGA 26 285 1 GAAGGGGATG 0.718268 -16 AAAAAACGATAAAGGAAGGTTTCAT 34 286 1 AAAGGAGTTT 0.902027 -15 CTTTTTCGGCACAGGGCAGTTCGTCTAAAAGC 35 185 0 ACAGGGGTTC 0.757276 -116 CTTCCCGTAGAAAGGGCTGTTTCATTAAAGCG 37 14 0 AAAGGGGTTT 0.962688 -284 CTTTCTACGGGAAGGGCTGTTTATATTGGGAT 37 32 1 GAAGGGGTTT 0.969096 -266 TTTTGGCTATGACGGGACGTTTTTTGTCATAG 37 232 1 GACGGGGTTT 0.901684 -66 AGCAAAAAAGGAAGGAACGTTTGAGTC 37 281 1 GAAGGAGTTT 0.91789 -17 CCGTAAAGAAAAGGGGAGATCTT 38 10 1 AAAGGGGATC 0.800538 -14 TGAATGAAGAAAAGAGGGGTTTCAAAT 42 284 1 AAAGAGGTTT 0.61279 -17 ****** **** Masking position 11 Map Score: 10.6365 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 115 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TATCGCAGGACGCAAACGCATATGCAACGTGG 1 140 1 CGCAACGCTA 0.787697 -62 GCTGATTGGCTGCTGACGCTGCTGAAATGAAA 6 54 1 TGCTACGCGC 0.977451 -247 GGGTGTTGACCGCTGACGTTTCGTACGTCATT 7 145 0 CGCTACGTTC 0.876131 -156 GGTGAGCGAACGCAGACGCAGCACATGCAACT 10 149 1 CGCAACGCGC 0.991415 -66 CTAAAAGTTTTGCAGACGCTGCTTGCGTC 11 8 0 TGCAACGCGC 0.957875 -42 CCGGATAAGGCGCTTACGCCGCATCCGGCGCT 15 122 1 CGCTACGCGC 0.995478 -108 CCGGATAAGGCGTTCACGCCGCATCCGGCAAT 19 38 1 CGTTACGCGC 0.977451 -145 CCTGATGCGACGCTTGCGCGTCTTATCATGCC 19 82 1 CGCTGCGCTC 0.943999 -101 CTGGATAAGGCGTTTACGCCGCATCCGGCAAT 19 136 1 CGTTACGCGC 0.977451 -47 **** **** ** Masking position 7 Map Score: 8.17898 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 480 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 10 ATATTTTTTGAAACGCTGTTTTTGTTTTCCTT 2 20 1 AAAGCGTTTT 0.923385 -281 CATAAAAATGAAATGCTGTTTTCATAAAAAAT 3 83 0 AAAGCGTTTT 0.923385 -218 CGAATAGTCAAAATGCCATTTCACTGTTGCTG 6 26 1 AAAGCATTTC 0.905176 -275 TCCACACCTAAAATGCTATTTCTGCGATAATA 13 135 1 AAAGCATTTC 0.905175 -166 ACTCACATTTAAATGCCATTTTTAGCGAAAAT 14 44 1 AAAGCATTTT 0.903545 -257 TTCCGGTAATAAAGGCATTTTTCCCTATAACA 22 37 0 AAAGCTTTTT 0.883767 -111 CTATGGTAAAAAAAGCGATTTTAATGAGCTGA 22 70 1 AAAGCATTTT 0.896546 -78 TTCACACTTTAAAGGAGGTTTCCT 22 134 1 AAAGAGTTTC 0.779373 -14 CTATGAATATAAAAGACTTTTTTCATTAAAAT 25 56 1 AAAGATTTTT 0.685979 -224 ATTTCATTGTAAACGCTATTTTCGGTTTAGGC 25 219 0 AAAGCATTTT 0.9035 -61 ATAGAAAATAAAATGATTTTTCCTAACATTCA 31 87 0 AAAGATTTTC 0.690129 -77 TTCCCGTAGAAAGGGCTGTTTCATTAAAGCGT 37 13 0 AAGGCGTTTC 0.659676 -285 AAGAAAGCAGAAATGATTTTTTTTGGCTATGA 37 212 1 AAAGATTTTT 0.686054 -86 *** ** ***** Masking position 2 Map Score: 9.65956 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 153 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 CAGAGTTTTCTCTCGCCTGATTACAAATT 4 18 0 CTCTCGCCTG 0.9154 -19 TGTCTTTAACCCTAAGCCAGGTTGGCGCTT 6 232 1 CCTAAGCCAG 0.760332 -69 CAGCGGTCAACACCCGCCAGCAATGGACTG 7 162 1 CACCCGCCAG 0.89168 -139 GGCGGTTCGACTTTAGCCTGTATTGTTAGC 7 231 0 CTTTAGCCTG 0.58472 -70 TCTGCGTTCGCTCACCCCAGTCACTTACTT 10 135 0 CTCACCCCAG 0.914679 -80 GTTATTATTACGCCAGCCTGGAATAAAGCT 12 34 1 CGCCAGCCTG 0.84788 -251 AGGGAAAAGCCTCACCCCAGCCCTCTCGGG 15 184 1 CTCACCCCAG 0.914679 -46 AACTGGAAGACTTACGCCTGTGAATTCGTT 23 166 1 CTTACGCCTG 0.930452 -73 CTTTTTGGTTCTTACGCCTGATATTCTGTG 30 44 1 CTTACGCCTG 0.930452 -162 ACCTCATTGACGCAAGCCAGCCTCCAATGG 31 15 0 CGCAAGCCAG 0.82793 -149 AGGGCCTGTCCCTCCGCCAGCTCGGGATAA 34 82 1 CCTCCGCCAG 0.936751 -219 CTTTCTCCCCCCTGACTTGTCTTT 40 11 0 CTCCCCCCTG 0.925477 -14 ATCATCAAGTCCGCCGCCAGATTCCGAGAA 42 61 1 CCGCCGCCAG 0.843987 -240 ********** Masking position 7 Map Score: 6.69468 Number of sites scoring better than the average of aligned sites = 2155 Number in coding regions = 2052 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 12 CAGGGCAGGGAAACCTGCCCTTGTTTCAGC 10 18 1 AAACCTGCCC 0.879543 -197 AGCCTGGAATAAAGCTTCCCACAAAAGGGG 12 48 1 AAAGCTTCCC 0.932055 -237 TCGTCCGGGGAAACCTTACCTGTCGCAAAC 12 209 0 AAACCTTACC 0.856597 -76 TCCCTCACCCAAACCCTCTCCGTGAGGAGA 15 159 0 AAACCCTCTC 0.785869 -71 GGGTGAGGGAAAAGCCTCACCCCAGCCCTC 15 179 1 AAAGCCTCAC 0.564923 -51 CATGGATCCGAAAACTTCCCCACTGTGAAC 17 234 0 AAAACTTCCC 0.927047 -35 ATATAAACCCTCCCTGTTTTGTTT 20 159 0 AAACCCTCCC 0.976748 -14 AATAAAAACCTCCCAGTATGTAAT 31 150 0 AAAACCTCCC 0.932283 -14 CCTCCCTATGAAACCTTACCTATTATACAA 33 86 0 AAACCTTACC 0.856597 -98 ATGAAACCTTCCTTTATCGTTTT 34 288 0 AAACCTTCCT 0.753394 -13 GCTATGACAAAAAACGTCCCGTCATAGCCA 37 235 0 AAAACGTCCC 0.796337 -63 ********** Masking position 3 Map Score: 6.30366 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 115 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 CTGGTTTATAAAATGAACCTTCAATTTTATT 3 55 1 AAAGAACCTT 0.741032 -246 AAAGGCTCCTGAAATTGAGTT 5 224 0 AAAGCTCCTG 0.945371 -11 ACTGATTTTTAAAAGAACCCGGGAAA 8 6 0 AAAGAACCCG 0.954825 -39 CGGAAATAAAAAAGGCACCCGAAGGTGCCTG 17 54 0 AAAGCACCCG 0.964554 -215 TTAAAAATAAAAAGGCTCCTGGTT 20 4 0 AAAGCTCCTG 0.945371 -169 AGTAAGTTCAAAAAGAACCCAACTTTAGGAT 26 41 1 AAAGAACCCA 0.702404 -260 GGAAATTAAGAAAAGAACCTGGTGAAATTTC 26 125 1 AAAGAACCTG 0.962441 -176 GTGCAATATAAAAAGAACCTGGGAAATTTCA 26 147 0 AAAGAACCTG 0.962441 -154 TCAAGTGCTCCTGTATCTCATAT 28 209 0 AAGGCTCCTG 0.801717 -13 *** ******* Masking position 2 Map Score: 4.30839 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 90 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 TGGTTCAATTCTTCCTTTAGCGGCATAATG 7 112 1 CTTCCTTTAG 0.805342 -189 ATAACAATCACTTCCTGCTGAATTGATTCA 16 72 0 CTTCCTGCTG 0.776875 -109 GAGAATGATGCTTCCCTTTGACTCTATGTT 20 101 0 CTTCCCTTTG 0.914565 -72 ATATAAACCCTCCCTGTTTTGTTTGTCGC 20 154 0 CTCCCTGTTT 0.845197 -19 CGAGAATGAACTTCCCGTTTTTTTCCCTCA 23 71 0 CTTCCCGTTT 0.935542 -168 AGGCGTAAGTCTTCCAGTTTAACCGTTTAC 23 155 0 CTTCCAGTTT 0.79836 -84 AATAAAAACCTCCCAGTATGTAATTCATA 31 145 0 CTCCCAGTAT 0.509001 -19 TTGGTTCACTTCCTTCTGAAATCTTCAG 32 25 0 CTTCCTTCTG 0.715919 -18 ATGAAACCTTCCTTTATCGTTTTTTGT 34 284 0 CTTCCTTTAT 0.802374 -17 AGTCCGTCCCCTTCCCTTGTCCGCTTTCAT 35 46 0 CTTCCCTTGT 0.71052 -255 ATAAACAGCCCTTCCCGTAGAAAGGGCTGT 37 26 0 CTTCCCGTAG 0.884666 -272 TCAAACGTTCCTTCCTTTTTTGCTGGACAT 37 275 0 CTTCCTTTTT 0.886726 -23 AAGATCTCCCCTTTTCTTTACGG 38 9 0 CTCCCCTTTT 0.841352 -15 ********** Masking position 2 Map Score: 3.64048 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 262 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 CCCTATTGTTTGCCGTCATGAAAGATGCGCGTTATTA 1 48 0 TCGTGAAGAG 0.841961 -154 GCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATA 1 125 1 ACGCGCAGAG 0.966936 -77 AGTTTTTAACAGACGCGACGCACGAAGAGCGCAATAC 7 191 0 ACGCGCAGAG 0.966936 -110 CGTGCTCTAAAAGCGCGCTGAAACAAGGGCAGGTTTC 10 27 0 ACGTGAACAG 0.900113 -188 ACTCTAAATAATTCGAGTTGCAGGAAGGCGACAAGAG 10 75 1 ACGTGCAGAG 0.98303 -140 GACGCAGCACATGCAACTTGAAGTATGACGAGTATAA 10 163 1 ACATGAATAG 0.567629 -52 TAGGCCTGATAAGCGTAGCGCATCAGGCAATTAACCC 15 43 0 ACGCGCACAG 0.862732 -187 CGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCA 16 116 1 CCGTGCAGAG 0.952551 -65 CCGAAAACTTCCCCACTGTGAACGAAGGATCGTTGTG 17 220 0 CCATGAAGAG 0.852384 -49 AAAAAACCTCATGCATGTTGCATGAGG 25 1 0 ACATGCAGAG 0.958366 -279 AGTGTGGTTAAATAGTGGTGAATGAAGGGATAACGGT 29 83 1 AAGTGAAGAG 0.734159 -55 GCTGTATGCAAACCATTTTGAAGGAGGATCTCCTAGG 35 273 1 ACATGAAGAG 0.94338 -28 CTAGAGAGAAAAACAAAATGAATGAAGAAAAGAGGGG 42 266 1 ACATGAAGAG 0.94338 -35 * ** **** ** * Masking position 12 Map Score: 7.97645 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 192 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727