AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifruR_ecoli_opreg_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 Motif number 1 ACTCTTGAATGGTTTCAGCACTTTGGACTGTA 2 87 1 GGTTTCAGCT 0.865338 -214 TTTGCTTGAACGATTCACCGTTTTTTTCATCC 3 206 1 CGATTCACCT 0.91896 -95 GGCCTCGTGCGGATTCACCCACGAGGCTTTTT 5 89 1 GGATTCACCC 0.865344 -146 AGGGCAAAAACGTTTCAGTCAGTGTAATAAAA 5 119 0 CGTTTCAGTG 0.941435 -116 CGGTTACAGGCGTTTCAGTCATAAATCCTCTG 5 159 1 CGTTTCAGTT 0.822085 -76 TCAGCAATTTCATTTCAGCAGCGTCAGCAGCC 6 61 0 CATTTCAGCC 0.886385 -240 ATAATACTTCTGTTTCAGCACGCAAGGAAAGC 6 172 0 TGTTTCAGCG 0.934285 -129 TTTCTTGAAACGTTTCAGCGCGATCTTGTCTT 6 206 1 CGTTTCAGCG 0.989297 -95 TGAATTGAAACGATTCAGCCTCTATGAGAAAA 6 263 0 CGATTCAGCC 0.989726 -38 TGAATCGTTTCAATTCAGCAAGAGAGGAGAAC 6 278 1 CAATTCAGCG 0.947148 -23 TTGATTCAGCCTGTCGGAACTGG 7 2 1 TGATTCAGCG 0.956516 -299 ATCATAAAATCGATTCAGCTTTGGCTTTTCCT 7 79 0 CGATTCAGCT 0.976252 -222 AACCTGCCCTTGTTTCAGCGCGCTTTTAGAGC 10 29 1 TGTTTCAGCG 0.934285 -186 AAGCTCCTGGGGATTCACTCTCTTGTCGCCTT 10 99 0 GGATTCACTC 0.52776 -116 TCGACTGAAACGCTTCAGCTAGGATAAGCGAA 12 145 0 CGCTTCAGCG 0.960863 -140 GGTAAAGTATCGATTCACCACGCTAACTTTTT 13 12 0 CGATTCACCG 0.975278 -289 GACAGTTAACCGATTCAGTGCCAGATTTCGCA 14 185 1 CGATTCAGTC 0.943669 -116 TGACCTGAATCAATTCAGCAGGAAGTGATTGT 16 67 1 CAATTCAGCG 0.947148 -114 GATCGTTAAGCGATTCAGCACCTTACCTCAGG 17 26 1 CGATTCAGCC 0.989726 -243 ********* * Masking position 5 Map Score: 34.7371 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 501 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 ATGAAAGATGCGCGTTATTAGGCTATAATGCGG 1 35 0 CGCGATTGGC 0.960231 -167 TTGTAGATACTGCGAAATCTGGCACTGAATCGG 14 194 0 TGCGATCGGC 0.960231 -107 GCGGCGTAAGCGCCTTATCCGGCCTACAAGAAC 15 111 0 CGCCATCGGC 0.999033 -119 AAGGCGCTTACGCCGCATCCGGCGCTGCCCCTC 15 128 1 CGCCATCGGC 0.999033 -102 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 19 27 0 CGCCATCGGC 0.999033 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 19 44 1 CGCCATCGGC 0.999033 -139 GACGCGCAAGCGTCGCATCAGGCATCGTGCACC 19 71 0 CGTCATCGGC 0.994434 -112 GACGCTTGCGCGTCTTATCATGCCTACAGCCGT 19 90 1 CGTCATCTGC 0.945991 -93 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 19 125 0 CGCCATCAGC 0.990227 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 19 142 1 CGCCATCGGC 0.999033 -41 **** *** *** Masking position 7 Map Score: 30.9201 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 38 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 TAGCGCTCGAAGGAGAGGTGA 1 191 1 AGGAGAGGGA 0.990329 -11 CCTCGCTCTAAGGATAGGTGACATCGAAAAA 2 186 0 AGGATAGGGA 0.977629 -115 TAAGTTGAGAAGGATGGGAGAAACTTGCTTT 2 265 0 AGGATGGGGA 0.910798 -36 ATAACCATAAAGGATAAGCGCAGATA 5 6 0 AGGATAAGGC 0.953262 -229 TCAATTCAGCAAGAGAGGAGAACT 6 287 1 AAGAGAGGGA 0.88973 -14 TTTACTGCTTAGGAGAAGATC 9 30 1 AGGAGAAGTC 0.79017 -11 CCGACGATACAGGACAAGAGAC 10 203 1 AGGACAAGGA 0.936183 -12 CGCTTCAGCTAGGATAAGCGAAACGTGGAAT 12 136 0 AGGATAAGGA 0.970207 -149 ATATTGGCTAAGGAGCAGTGAA 13 289 1 AGGAGCAGGA 0.970424 -12 CCTCTCCGTGAGGAGAGGGGCAGCGCCGGAT 15 144 0 AGGAGAGGGC 0.984648 -86 CGCCCTCATCAGGAGCAGAGAATTGCCGGAT 19 158 0 AGGAGCAGGA 0.970424 -25 ******** ** Masking position 4 Map Score: 15.0459 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 43 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CCACGTTGCATATGCGTTTGCGTCCTGCGATA 1 140 0 TAGCGTTGCG 0.89322 -62 TTTCATTTCAGCAGCGTCAGCAGCCAATCAGC 6 54 0 GCGCGTAGCA 0.989872 -247 AATGACGTACGAAACGTCAGCGGTCAACACCC 7 145 1 GAACGTAGCG 0.940992 -156 AGTTGCATGTGCTGCGTCTGCGTTCGCTCACC 10 149 0 GCGCGTTGCG 0.996174 -66 GACGCAAGCAGCGTCTGCAAAACTTTTAG 11 8 1 GCGCGTTGCA 0.980867 -42 AGCGCCGGATGCGGCGTAAGCGCCTTATCCGG 15 122 0 GCGCGTAGCG 0.997989 -108 ATTGCCGGATGCGGCGTGAACGCCTTATCCGG 19 38 0 GCGCGTAACG 0.989872 -145 GGCATGATAAGACGCGCAAGCGTCGCATCAGG 19 82 0 GAGCGCAGCG 0.974363 -101 ATTGCCGGATGCGGCGTAAACGCCTTATCCAG 19 136 0 GCGCGTAACG 0.989872 -47 ** **** **** Masking position 5 Map Score: 14.4926 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 5 GGAAAGCGAATCCGGTATTACGAAAGTGGTGG 2 219 0 TCCGGTATTG 0.684261 -82 GGATTCGCTTTCCGGCAGTGCGCCCAGAAAGC 2 238 1 TCCGGCAGTG 0.915895 -63 TTTTACACTTTCAGGCCTCGTGCGGATTCACC 5 76 1 TCAGGCCTCG 0.954983 -159 CTTGTCGCCTTCCTGCAACTCGAATTATTTAG 10 78 0 TCCTGCAACG 0.844244 -137 GACAGAGTAATCCAGCAAATCGTCCGGGGAAA 12 226 0 TCCAGCAAAG 0.739394 -59 ACTTTACTATTCAGGCAATACATATTGGCTAA 13 268 1 TCAGGCAATA 0.842871 -33 GCGTAGCGCATCAGGCAATTAACCCCACCTTC 15 36 0 TCAGGCAATA 0.842871 -194 GCTACGCTTATCAGGCCTACAGGATGCATCAC 15 61 1 TCAGGCCTAG 0.95141 -169 AAGCGCCTTATCCGGCCTACAAGAACGTGCAA 15 105 0 TCCGGCCTAA 0.904592 -125 TTGATTCAGGTCAGGCCAAATGGCGGTATTTT 16 48 0 TCAGGCCAAG 0.957006 -133 CAAGAAGACTTCCGGCAACAGATTTCATTTTG 16 136 1 TCCGGCAACA 0.922605 -45 GAACGCCTTATCCGGCCTACAGTCAGCAACGG 19 21 0 TCCGGCCTAG 0.975706 -162 TCACGCCGCATCCGGCAATCGGTGCACGATGC 19 51 1 TCCGGCAATG 0.978996 -132 AAGCGTCGCATCAGGCATCGTGCACCGATTGC 19 65 0 TCAGGCATCG 0.955861 -118 GCGCGTCTTATCATGCCTACAGCCGTTGCCGA 19 97 1 TCATGCCTAG 0.677602 -86 TTACGCCGCATCCGGCAATTCTCTGCTCCTGA 19 149 1 TCCGGCAATT 0.769814 -34 ********* * Masking position 1 Map Score: 14.5938 Number of sites scoring better than the average of aligned sites = 1241 Number in coding regions = 980 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 6 TGCGATACGGATGCTTTAGAGCAATTTTTTGTTAATGA 1 109 0 ATTTGCTTTT 0.876545 -93 ATAACGTTCTACGCTTCTGTGCGTTTTTAATTTATGCT 3 15 0 ACTTGCTTTT 0.985107 -286 ATTTGCTTGAACGATTCACCGTTTTTTTCATCCGGTTA 3 205 1 ACTTGTTTTT 0.789151 -96 TTTGAGAAACACATTTCTGCGCATTTATCTTTGCATAT 3 244 0 ACTTGCTTAT 0.858264 -57 TGGCATTTTGACTATTCGTGGCGCTTTTGATTT 6 6 0 ACTTGCTTTT 0.985107 -295 GATGTGCTGCACAATTTTTTGCCATTTTTCCTAATTGC 6 111 0 ACTTGCTTTT 0.985107 -190 CTTTCTTGAAACGTTTCAGCGCGATCTTGTCTTTAACC 6 205 1 ACTTGCTCTT 0.899747 -96 TAACCCTAAGCCAGGTTGGCGCTTTTTTTCTCATAGAG 6 238 1 CCGTGCTTTT 0.853638 -63 TTTAGCCTGTATTGTTAGCGCCAGTTTTTAACAGACGC 7 212 0 ATTTCCTTTT 0.541047 -89 GACTCACATCACACTTTTATCCCCTTTTGTGGGAAGCT 12 60 0 ACTTCCTTTT 0.916546 -225 CGACAATTAACCAATCAGTCGCAGTTTGCGACAGGTAA 12 186 1 CCTCGCTTTG 0.819432 -99 GACACTACTCACATTTAAATGCCATTTTTAGCGAAAAT 14 38 1 ACTTGCTTTT 0.985107 -263 GCGAAAATCGCCGCCTTGTTGCTTTTTTACACAAGCGT 14 68 1 CCCTGCTTTT 0.853638 -233 GGTTAACTGTCCAGTCGACGGCCTTTTGTGTGATATCA 14 158 0 CCTCGCTTTG 0.819435 -143 TACCTCAGGCACCTTCGGGTGCCTTTTTTATTTCCGAA 17 49 1 ACTCGCTTTT 0.965478 -220 ** ** ** **** Masking position 15 Map Score: 13.7546 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 288 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 AGTCGAACCGCCAGGCTAGACTTTAGTTCC 7 249 1 CCAGGCTAGA 0.800465 -52 TCTCTTGTCGCCTTCCTGCAACTCGAATTA 10 83 0 CCTTCCTGCA 0.7971 -132 TATTATTACGCCAGCCTGGAATAAAGCTTC 12 36 1 CCAGCCTGGA 0.957936 -249 CCTCGGGCTTCCAGCCTGCGCGACAGCAAA 14 262 1 CCAGCCTGCG 0.973367 -39 CTACGCTTATCAGGCCTACAGGATGCATCA 15 62 1 CAGGCCTACA 0.955663 -168 AGCGCCTTATCCGGCCTACAAGAACGTGCA 15 106 0 CCGGCCTACA 0.990947 -124 AACGCCTTATCCGGCCTACAGTCAGCAACG 19 22 0 CCGGCCTACA 0.990947 -161 CGCGTCTTATCATGCCTACAGCCGTTGCCG 19 98 1 CATGCCTACA 0.905362 -85 AACGCCTTATCCAGCCTACGTTCGGCAACG 19 120 0 CCAGCCTACG 0.977929 -63 ********** Masking position 7 Map Score: 9.06046 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 269 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 AAACAAAAACAGCGTTTCAAAAAATATACAAC 2 15 0 ACGTTTCAAA 0.831548 -286 AAAGTGCTGAAACCATTCAAGAGTCAATTGGC 2 79 0 ACCATTCAGA 0.718912 -222 GACTGATCCCAGCGTTGCGCAAATCTGCTCTC 3 154 0 ACGTTGCGAA 0.831892 -147 GTGATAAATGAACGGTTTGAGAAACACATTTC 3 265 0 ACGGTTTGGA 0.875613 -36 CGAACAATCCTTTTGTGATAAATGAACG 3 283 0 ACCTTTTGGA 0.903694 -18 ATCGCGCTGAAACGTTTCAAGAAAGCATAATA 6 198 0 ACGTTTCAGA 0.972624 -103 CGCGAAATTAATCGTTACAGGAAAAGCCAAAG 7 61 1 ACGTTACAGA 0.848504 -240 GCTCAGGGAAAACCTTGCAGGAGATCT 12 268 1 ACCTTGCAGA 0.919253 -17 ACCAAGATTTAACCTTTTGAGAACATTTTCCA 13 107 1 ACCTTTTGGA 0.903694 -194 GATAATAGCAACCGTTTCGTGACAGGAATCAC 13 160 1 ACGTTTCGGA 0.982719 -141 TTTTTACACAAGCGTTTTGTGATGAACGTCAC 14 91 1 ACGTTTTGGA 0.948298 -210 GCATCCGGCAATCGGTGCACGATGCCTGATGC 19 58 1 ACGGTGCAGA 0.895183 -125 * ******* ** Masking position 1 Map Score: 7.68294 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 338 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 TCAGCCCAACGTGAGTGCCTGTTTTTGAGTC 2 128 0 GTAGTGCCTG 0.974273 -173 GATTTATGACTGAAACGCCTGTAACCGGAGC 5 155 0 TGAACGCCTG 0.844234 -80 AGCCTGTATTGTTAGCGCCAGTTTTTAACAG 7 216 0 GTAGCGCCAG 0.977011 -85 ACTTACTTATGTAAGCTCCTGGGGATTCACT 10 112 0 GTAGCTCCTG 0.92335 -103 GCTTACATAAGTAAGTGACTGGGGTGAGCGA 10 127 1 GTAGTGACTG 0.767907 -88 AGTTAACCGATTCAGTGCCAGATTTCGCAGT 14 188 1 TTAGTGCCAG 0.618583 -113 CGGATGCGGCGTAAGCGCCTTATCCGGCCTA 15 118 0 GTAGCGCCTT 0.974273 -112 TGAGGAGAGGGGCAGCGCCGGATGCGGCGTA 15 136 0 GGAGCGCCGG 0.957215 -94 CGGATGCGGCGTGAACGCCTTATCCGGCCTA 19 34 0 GTAACGCCTT 0.932947 -149 GCCTACGTTCGGCAACGGCTGTAGGCATGAT 19 106 0 GGAACGGCTG 0.819997 -77 CGGATGCGGCGTAAACGCCTTATCCAGCCTA 19 132 0 GTAACGCCTT 0.932947 -51 ** ******** Masking position 4 Map Score: 6.82907 Number of sites scoring better than the average of aligned sites = 1598 Number in coding regions = 1513 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 10 CGTCTGCCACCACGTTGCATATGCGTTTGC 1 151 0 CACGTTGCAT 0.789105 -51 CTCTCTTCGACAATTTCCACATAAACCATC 3 129 0 CAATTTCCAC 0.931478 -172 CGTCATACTTCAAGTTGCATGTGCTGCGTC 10 163 0 CAAGTTGCAT 0.924014 -52 TTTACCGGTTGAATTTGCATCAATTTCATT 13 38 1 GAATTTGCAT 0.926185 -263 CTTTTGAGAACATTTTCCACACCTAAAATG 13 120 1 CATTTTCCAC 0.877012 -181 ACAATTTGTTGAATTTGCACGTTCTTGTAG 15 91 1 GAATTTGCAC 0.931478 -139 GATTGTTATACTATTTGCACATTCGTTGGA 16 93 1 CTATTTGCAC 0.811721 -88 CAACAGATTTCATTTTGCATTCCAAAGTTC 16 151 1 CATTTTGCAT 0.936849 -30 AAATCAAAAACAATTTCCATTTTAATTAAA 17 147 0 CAATTTCCAT 0.926185 -122 AATTGTTTTTGATTTTGCATTTTAAATGAG 17 162 1 GATTTTGCAT 0.868107 -107 ********** Masking position 5 Map Score: 5.31875 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 172 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 TGGAAATTGTCGAAGAGAGCAGATTTGCGC 3 140 1 CGAAGAGAGC 0.96647 -161 TAACCATAAAGGATAAGCGCAGATA 5 6 0 GGATAAGCGC 0.880936 -229 ACGCGACGCACGAAGAGCGCAATACAGTCC 7 186 0 CGAAGAGCGC 0.98348 -115 ATTGCGTGCTCTAAAAGCGCGCTGAAACAA 10 38 0 CTAAAAGCGC 0.919842 -177 GCTATTTCTGCGATAATAGCAACCGTTTCG 13 149 1 CGATAATAGC 0.835617 -152 CCATTTTTAGCGAAAATCGCCGCCTTGTTG 14 59 1 CGAAAATCGC 0.960213 -242 TTGTGCTGAACGAAAAGAGCACAACGATCC 17 201 1 CGAAAAGAGC 0.977187 -68 ********** Masking position 6 Map Score: 4.40178 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 342 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 GGCAGTGCGCCCAGAAAGCAAGTTTCTCCCA 2 251 1 CCAGAAGCAA 0.849835 -50 GCGTCAGCAGCCAATCAGCAACAGTGAAATG 6 42 0 CCAACAGCAA 0.920582 -259 TCATTTCAGCAGCGTCAGCAGCCAATCAGCA 6 53 0 AGCGCAGCAG 0.892166 -248 AACGGATTTTCCCATCAGCAATTAGGAAAAA 6 94 1 CCCACAGCAA 0.967378 -207 GCGGTCAACACCCGCCAGCAATGGACTGTAT 7 164 1 CCCGCAGCAA 0.992346 -137 GACGCAAGCAGCGTCTGCAAAACTTTTAGA 11 10 1 AGCGCTGCAA 0.848076 -40 TTCCAGCCTGCGCGACAGCAAACATAAGAAG 14 270 1 CGCGCAGCAA 0.987607 -31 TATCCGGCCTACAGTCAGCAACGGTTGTTGT 19 14 0 ACAGCAGCAA 0.951946 -169 **** ****** Masking position 10 Map Score: 4.5569 Number of sites scoring better than the average of aligned sites = 809 Number in coding regions = 773 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 TTTTTCATCCGGTTAAATATGCAAAGATAAA 3 228 1 GGTTAATATG 0.871401 -73 TCATGTTACCGGTAAAATAACCATAAAGGAT 5 22 0 GGTAAATAAC 0.822843 -213 TAATTAGTCTGGTTAAATACCAGTTCCGACA 7 22 0 GGTTAATACC 0.965975 -279 GCGACTGATTGGTTAATTGTCGAACATTTAA 12 177 0 GGTTAATGTC 0.977021 -108 AAATTCAACCGGTAAAGTATCGATTCACCAC 13 23 0 GGTAAATATC 0.93821 -278 GCACTGAATCGGTTAACTGTCCAGTCGACGG 14 175 0 GGTTAATGTC 0.977045 -126 GAGAAGGTGGGGTTAATTGCCTGATGCGCTA 15 34 1 GGTTAATGCC 0.971502 -196 ****** **** Masking position 6 Map Score: 2.62904 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 AAGCCAATTACAAATCATTAACAAAAAATTG 1 95 1 CAAACATTAA 0.671663 -107 AATCCAAAAGGAAAACAAAAACAGCGTTTCA 2 28 0 GAAACAAAAA 0.944862 -273 TGAAAGCATAAATTAAAAACGC 3 2 1 GAAACATAAA 0.954777 -299 CGGTATAAACGAAACCATAAAAATGAAATGC 3 99 0 GAAACATAAA 0.954777 -202 AACGTTTCAAGAAAGCATAATACTTCTGTTT 6 189 0 GAAACATAAT 0.768957 -112 AGAATTGAACCAAATCATAAAATCGATTCAG 7 93 0 CAAACATAAA 0.928452 -208 AACAAACCATCAAAACAAAAATGTGACACTA 14 14 1 CAAACAAAAA 0.913291 -287 GTACGTTTCGGAAATAAAAAAGGCACCCGAA 17 62 0 GAAAAAAAAA 0.626861 -207 TTTAAAATGCAAAATCAAAAACAATTTCCAT 17 157 0 AAAACAAAAA 0.726105 -112 **** ****** Masking position 7 Map Score: 3.71869 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 104 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 TCTGCGTTCGCTCACCCCAGTCACTTACTTAT 10 133 0 CTCACCCATC 0.971558 -82 TCCAATCCCACCCTCTCCACATGGAGAA 15 7 1 CCCACCCCCC 0.990268 -223 GGCAATTAACCCCACCTTCTCCATGTGGAGAG 15 23 0 CCCACCTCCC 0.965227 -207 GCATCCGGCGCTGCCCCTCTCCTCACGGAGAG 15 142 1 CTGCCCCCCC 0.951535 -88 AGGCTTTTCCCTCACCCAAACCCTCTCCGTGA 15 164 0 CTCACCCACC 0.992077 -66 AGGGAAAAGCCTCACCCCAGCCCTCTCGGGTA 15 184 1 CTCACCCACC 0.992077 -46 GCCATTTGGCCTGACCTGAATCAATTCAGCAG 16 56 1 CTGACCTATC 0.797245 -125 ******* * ** Masking position 6 Map Score: 3.63839 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 112 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789