AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifruR_ecoli_hinf_300.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 zwf 300 glucose-6-phosphate dehydrogenase #7 fruB 300 PTS system, fructose-specific IIA/fpr component #8 ptsH 300 PTS system protein HPr #9 ptsI 44 PEP-protein phosphotransferase system enzyme I #10 crr 40 PTS system, glucose-specific IIA component #11 fba 214 fructose-bisphosphate aldolase, class II #12 pgk 49 phosphoglycerate kinase #13 epd 284 D-erythrose 4-phosphate dehydrogenase #14 yggD 21 putative transcriptional regulator #15 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #16 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #17 pckA 300 phosphoenolpyruvate carboxykinase #18 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #19 mtlD 229 mannitol-1-phosphate dehydrogenase #20 b3913 146 orf, hypothetical protein #21 yiiP 148 putative transport system permease protein #22 pfkA 180 6-phosphofructokinase I #23 metA 156 homoserine transsuccinylase #24 aceB 268 malate synthase A #25 aceA 29 isocitrate lyase #26 aceK 182 isocitrate dehydrogenase kinase/phosphatase #27 HI0050 74 conserved hypothetical transmembrane protein #28 HI0051 38 conserved hypothetical transmembrane protein #29 HI0052 26 conserved hypothetical protein #30 HI0053 109 zinc-type alcohol dehydrogenase #31 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #32 HI0449 86 H. influenzae predicted coding region HI0449 #33 HI0451 71 conserved hypothetical protein #34 HI0452 50 conserved hypothetical protein #35 HI0453 26 conserved hypothetical protein #36 HI0454 54 conserved hypothetical protein #37 HI0457 69 conserved hypothetical protein #38 HI0458 70 stationary phase survival protein SurA, putative #39 HI0459 131 pyrimidine operon regulatory protein (pyrR) #40 HI0524 110 fructose-bisphosphate aldolase (fba) #41 HI0525 101 phosphoglycerate kinase (pgk) #42 HI0526 77 H. influenzae predicted coding region HI0526 #43 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #44 HI0810 144 conserved hypothetical protein #45 HI0811 134 argininosuccinate lyase (argH) #46 HI0812 21 glucosephosphate uridylyltransferase (galU) #47 HI0813 77 carbon storage regulator (csrA) #48 HI0814 187 alanyl-tRNA synthetase (alaS) #49 HI0815 101 universal stress protein A (uspA) #50 HI0817 170 conserved hypothetical protein #51 HI0819 37 galactokinase (galK) #52 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #53 HI0982 95 6-phosphofructokinase (pfkA) #54 HI0985 300 DNA processing chain A (dprA) #55 HI1711 59 PTS system, glucose-specific IIA component (crr) #56 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #57 HI1713 158 phosphocarrier protein HPr (ptsH) #58 HI1714 70 conserved hypothetical protein Motif number 1 GGTATAAACGAAACCATAAAAATGAAATGCTGTT 3 95 0 AAAAAAAATG 0.583104 -206 ATCAGTCTTAAAAAGTAAAAAAATATATTTGCTT 3 179 1 AAAAAAAAAT 0.943011 -122 ACGAGGCCTGAAAGTGTAAAAATTGTTCTACAAT 5 63 0 AAAAAAAATT 0.862332 -172 CAATTAGGAAAAATGGCAAAAAATTGTGCAGCAC 7 112 1 AAAAAAAAAT 0.943011 -189 AAGAACGTGCAAATTCAACAAATTGTGATGCATC 19 83 0 AAAACAAATT 0.791905 -147 CAATAAGAATAAACTACACAAAATAATAGTAACA 27 21 0 AAAACAAAAT 0.909524 -54 TTTTGTAGAGAAATGGATAAAAATTTACCGCACT 33 12 0 AAATAAAAAT 0.778345 -60 TTATGTTATAAAACCATAAAAAATTTGAGGTTAA 33 46 1 AAAAAAAAAT 0.943011 -26 CAAAGTATCAAAAATAAAGGGGCTT 37 2 1 AAACAAAAAT 0.744323 -68 AGAGAAAATAAAAAACAACAAAAGGGGCAATTAA 37 34 0 AAAACAAAAG 0.691795 -36 TCATCAATACAAATTCTTCAAATTGTGGGCTTAT 40 58 1 AAATCAAATT 0.446767 -53 TGATTGACAAAAACTAAACAAAATTT 42 62 1 AAAACAAAAT 0.909524 -16 GTTCTTAAAAAAATGTTTAAAAATGAGATCTACT 43 75 1 AAATAAAAAT 0.778345 -98 TAATGGATGTCAATATAAAAAAATGTTAAGTAGA 43 103 0 CAAAAAAAAT 0.708639 -70 TAATACAAATAAAATGGACAAAATGAAAGATTTT 45 18 1 AAAACAAAAT 0.909524 -117 TAATAAAACAAAAATGGACAAAATCTTTCATTTT 45 37 0 AAAACAAAAT 0.909524 -98 TAATTAAAACAAAAAGGAAAAATT 45 121 1 AAAAAAAATT 0.862338 -14 CATATTTTTGAAATTTATAAAAAGGCTTTTTGCC 48 108 0 AAATAAAAAG 0.439482 -80 TAAATTTCAAAAATATGCAAAAATAGGGCGACTT 48 125 1 AAACAAAAAT 0.744323 -63 AGTATGAACTAAATCATAAAAAATTTTGCTTATT 52 93 1 AAAAAAAAAT 0.943011 -115 TTTTAATATAAAATGCCAAAAAATAGTTTGACAG 54 25 0 AAAAAAAAAT 0.943011 -276 GTAAAAAATCCAATAAGAAAAATTTGTTGATTAG 54 137 0 CAAAAAAATT 0.479363 -164 TCTTATTTTGAAAATGTAAAAAATCCAATAAGAA 54 152 0 AAAAAAAAAT 0.943011 -149 TACATTTTCAAAATAAGAAAAATTTTGCAATTTT 54 168 1 AAAAAAAATT 0.862338 -133 ATTTTCAAATAAAAAGGAAAAAAT 54 287 1 AAAAAAAAAT 0.943011 -14 TGTTTTTGGTAAAATGAAAAAAATTTTTGCATAG 58 24 0 AAAAAAAAAT 0.943011 -47 *** ******* Masking position 10 Map Score: 32.3782 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 87 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 GGGAAAAGCGCGCAAAGTGCGGCAAAACTGATA 6 152 0 CGCATGCGGC 0.986202 -149 TCTGGTTAAATACCAGTTCCGACAGGCTGAATC 8 13 0 TACCTCCGAC 0.799362 -288 TCCACGAGATGCGGCCCAATTTACT 10 3 1 CACGTGCGGC 0.865053 -38 ACCAATCAGTCGCAGTTTGCGACAGGTAAGGTT 13 195 1 CGCATGCGAC 0.953586 -90 TCGCAGTATCTACAAGGTCCGGCTACCTCTGCC 18 212 1 TACATCCGGC 0.817204 -89 GCGGCGTAAGCGCCTTATCCGGCCTACAAGAAC 19 111 0 CGCCTCCGGC 0.997148 -119 AAGGCGCTTACGCCGCATCCGGCGCTGCCCCTC 19 128 1 CGCCTCCGGC 0.997148 -102 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 26 27 0 CGCCTCCGGC 0.997148 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 26 44 1 CGCCTCCGGC 0.997148 -139 CGGTGCACGATGCCTGATGCGACGCTTGCGCGT 26 70 1 TGCCTGCGAC 0.926908 -113 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 26 125 0 CGCCTCCAGC 0.95839 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 26 142 1 CGCCTCCGGC 0.997148 -41 AGAAAACGACCGCACTTTGCGACCGTTTGGGAT 34 12 0 CGCATGCGAC 0.953586 -39 **** ****** Masking position 8 Map Score: 25.9983 Number of sites scoring better than the average of aligned sites = 1126 Number in coding regions = 630 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 TTGACTCTTGAATGGTTTCAGCACTTTGGACT 2 84 1 AAGGTTCAGC 0.95221 -217 AAAAACGGTGAATCGTTCAAGCAAATATATTT 3 199 0 AACGTCAAGC 0.900941 -102 CATAGGGCAAAAACGTTTCAGTCAGTGTAATA 5 122 0 AACGTTCAGT 0.926855 -113 CTCCGGTTACAGGCGTTTCAGTCATAAATCCT 5 156 1 AGCGTTCAGT 0.918799 -79 TGCTTTCTTGAAACGTTTCAGCGCGATCTTGT 7 203 1 AACGTTCAGC 0.988843 -98 TGCTGAATTGAAACGATTCAGCCTCTATGAGA 7 266 0 AACGTTCAGC 0.988843 -35 CAAATCATAAAATCGATTCAGCTTTGGCTTTT 8 82 0 AACGTTCAGC 0.988843 -219 TAATCGACTGAAACGCTTCAGCTAGGATAAGC 13 148 0 AACGTTCAGC 0.988843 -137 CTGGACAGTTAACCGATTCAGTGCCAGATTTC 18 182 1 AACGTTCAGT 0.926855 -119 AGGCCGGATAAGGCGCTTACGCCGCATCCGGC 19 119 1 AGCGTTACGC 0.926776 -111 GCCTGACCTGAATCAATTCAGCAGGAAGTGAT 22 64 1 AACATTCAGC 0.814659 -117 CTGGATGTCTAAACGTATAAGCGTATGTAGTG 23 122 1 AACGATAAGC 0.854646 -35 GTCGATCGTTAAGCGATTCAGCACCTTACCTC 24 23 1 AACGTTCAGC 0.988843 -246 AGGCCGGATAAGGCGTTCACGCCGCATCCGGC 26 35 1 AGCGTCACGC 0.747085 -148 AGGCTGGATAAGGCGTTTACGCCGCATCCGGC 26 133 1 AGCGTTACGC 0.926776 -50 TACTGTCTAAAGGGGATTAAGCAAGGAAGCCT 32 33 0 AGGGTTAAGC 0.886659 -54 TTTTATGTTTAGCGGGATAAGCCCACAATTTG 40 76 0 AGGGATAAGC 0.541355 -35 ** ** ****** Masking position 1 Map Score: 21.8874 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 435 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 TGACTCTTGAATGGTTTCAGCACTTTGGACT 2 85 1 AGGTTTCAGC 0.937004 -216 TATTTGCTTGAACGATTCACCGTTTTTTTCA 3 204 1 ACGATTCACC 0.979754 -97 CAGGCCTCGTGCGGATTCACCCACGAGGCTT 5 87 1 GGGATTCACC 0.915978 -148 ATAGGGCAAAAACGTTTCAGTCAGTGTAATA 5 122 0 ACGTTTCAGT 0.903637 -113 TCCGGTTACAGGCGTTTCAGTCATAAATCCT 5 157 1 GCGTTTCAGT 0.850027 -78 GCTTTCTTGAAACGTTTCAGCGCGATCTTGT 7 204 1 ACGTTTCAGC 0.975444 -97 GCTGAATTGAAACGATTCAGCCTCTATGAGA 7 266 0 ACGATTCAGC 0.989584 -35 AAATCATAAAATCGATTCAGCTTTGGCTTTT 8 82 0 ACGATTCAGC 0.989584 -219 GTAAGCTCCTGGGGATTCACTCTCTTGTCGC 11 102 0 GGGATTCACT 0.720882 -113 GAATCAACGAGAGGATTCACC 12 39 1 GGGATTCACC 0.916337 -11 AATCGACTGAAACGCTTCAGCTAGGATAAGC 13 148 0 ACGCTTCAGC 0.947075 -137 CCGGTAAAGTATCGATTCACCACGCTAACTT 17 15 0 ACGATTCACC 0.979754 -286 TGGACAGTTAACCGATTCAGTGCCAGATTTC 18 183 1 ACGATTCAGT 0.957173 -118 CCTGACCTGAATCAATTCAGCAGGAAGTGAT 22 65 1 ACAATTCAGC 0.843176 -116 TCGATCGTTAAGCGATTCAGCACCTTACCTC 24 24 1 ACGATTCAGC 0.989538 -245 * ********* Masking position 9 Map Score: 20.5053 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 213 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 GTGACATCGAAAAAGCGTGCAGAGGAATGT 2 170 0 AAAAGCGTGC 0.860859 -131 CGATTACGGGAAAAGCGCGCAAAGTGCGGC 6 162 0 AAAAGCGCGC 0.975743 -139 AAATCAAAAGCGCCACGAATAGTCA 7 6 1 AAAAGCGCCA 0.896885 -295 AAAATGGCAAAAAATTGTGCAGCACATCAA 7 121 1 AAAATTGTGC 0.5213 -180 CTATGAGAAAAAAAGCGCCAACCTGGCTTA 7 244 0 AAAAGCGCCA 0.896885 -57 TGCGTGCTCTAAAAGCGCGCTGAAACAAGG 11 36 0 AAAAGCGCGC 0.975743 -179 AAAAGGGGATAAAAGTGTGATGTGAGTCAG 13 70 1 AAAAGTGTGA 0.680047 -215 ATTTTTAGCGAAAATCGCCGCCTTGTTGCT 18 61 1 AAAATCGCCG 0.887528 -240 TCAGGAGCAGAGAATTGCCGGATGCGGCGT 26 151 0 AGAATTGCCG 0.618114 -32 CAAACGGTCGCAAAGTGCGGTCGTTTTCTT 34 16 1 CAAAGTGCGG 0.881685 -35 AATACGCCTAAAAAGCGACGGCATTTGCAC 39 65 0 AAAAGCGACG 0.705748 -67 GTTATAGAGGAAAAGTGCGG 40 1 0 AAAAGTGCGG 0.984277 -110 GATCAAGACAAAAAGTGCGGAAAAAACCAC 44 95 1 AAAAGTGCGG 0.984277 -50 AATTGAGATAAAAAGTGCGGTGGTTTTTTC 44 114 0 AAAAGTGCGG 0.984277 -31 ACGCTATTTGAGAAGTGCGGTTAAAATTTA 48 49 0 AGAAGTGCGG 0.935938 -139 ATAAAACCAGAAAATTGCCCTAGTATCCTT 57 107 0 AAAATTGCCC 0.796608 -52 AAAAGTGCGGTCGTTTTTTC 58 61 0 AAAAGTGCGG 0.984277 -10 ********** Masking position 4 Map Score: 16.1309 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 631 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 TTAGAGCAATTTTTTGTTAATGATTTGTAATTGGCT 1 96 0 TTTTTTATTT 0.911155 -106 TGAAACGCTGTTTTTGTTTTCCTTTTGGATTAATTT 2 28 1 TTTTTTTTTT 0.918369 -273 TTCTGTGCGTTTTTAATTTATGCTTTCA 3 3 0 TTTTTTATTT 0.911155 -298 GAAAACGATGATTTTTTTATCAGTTTTGCCGCACTT 6 135 1 ATTTTTTTTT 0.813172 -166 CACATCAAACTTTTGCTCATAACTTTACGGCTTTCC 7 143 1 TTTTTCTTTT 0.664348 -158 GTGGGGGTTTTTTTTATCCTCAATTTGCCTGCTGCT 21 63 1 TTTTTCTTTT 0.664348 -86 TAACGTAGTCTTTTCCTTGAAACTTTCTCACCTTCA 23 40 1 TTTTTTATTT 0.911155 -117 TGGAAATTGTTTTTGATTTTGCATTTTAAATGAGTA 24 158 1 TTTTTTTTTT 0.918369 -111 AGTGCGGTCGTTTTCTTTTATATTTTTGAGTA 34 29 1 TTTTTTATTT 0.911155 -22 CTTTTGTTGTTTTTTATTTTCTCTTTCTTATAGCTT 37 44 1 TTTTTTTTTT 0.918369 -26 ATTTGCACCATTTTTCTTGTTCGTTATACTATCCAA 39 37 0 TTTTTTTTTA 0.775338 -95 TTTTAGGCGTATTTTCTTTATACTTTGTGCATTGAA 39 82 1 ATTTTTATTT 0.798698 -50 AAGTTTTCAATTTTAATTTTAATTTTAACTTAACAA 41 65 1 TTTTTTTTTT 0.918369 -37 AAATTTTGTTTAGTTTTTGTCAATCAAG 42 60 0 ATTTTTATTT 0.798698 -18 GTCTTGATCGTTTTATTTAAGTGTTTTTGCTTATAA 44 68 0 TTTTTTATTT 0.911155 -77 TTTTGTCCATTTTTGTTTTATTATTAATATAGAATA 45 48 1 TTTTTTATTA 0.758803 -87 AATTTTTCCTTTTTGTTTTAATTAATTAT 45 116 0 TTTTTTTTTT 0.918369 -19 TGAAGTGCGGTTTTATTTTGGAGTTTTGGCAAAAAG 48 81 1 TTTTTTGTTT 0.658858 -107 ATTTTTTATGATTTAGTTCATACTTATGAAAGTAAC 52 81 0 ATTTTTATTA 0.548964 -127 ACAAAATTATTTGATTTTACGTTAAAATAGCAAC 55 9 1 ATTTTTTTTA 0.571766 -51 TATTTTTATGATTTAATTCAGGCTTTTTAGTGTTTA 57 48 1 ATTTTTATTT 0.798698 -111 GGTTTTATATTTTTAATTATTGATTAGTCGAGGTAG 57 129 1 TTTTTTTTTA 0.775338 -30 **** ** * *** Masking position 7 Map Score: 21.7028 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 49 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 TCATAAAAAATAAAATTGAAGGTTCATTTT 3 64 0 TAAAATTGAA 0.868748 -237 AACGAAACCATAAAAATGAAATGCTGTTTT 3 93 0 TAAAAATGAA 0.881179 -208 GGATCAGTCTTAAAAAGTAAAAAAATATAT 3 177 1 TAAAAAGTAA 0.651388 -124 CGTCCGGCGGTAAAAATAAAATACTCGTGC 16 252 0 TAAAAATAAA 0.822101 -49 GACGGTACCCTAAAAATAAAATAAGGATAA 16 278 1 TAAAAATAAA 0.822101 -23 TATTTTTAATTAAAATGGAAATTGTTTTTG 24 143 1 TAAAATGGAA 0.855302 -126 GAGCAATTTATAAAATTGAACATAGGGGAT 28 19 0 TAAAATTGAA 0.868748 -20 CTTAATAATTTAAAAAGAAAGCTGCGGATG 31 44 0 TAAAAAGAAA 0.804937 -28 CCGCTAAACATAAAAAGGAAACACAAGT 40 93 1 TAAAAAGGAA 0.868805 -18 AAATTAAAATTAAAATTGAAAACTTTTCGT 41 60 0 TAAAATTGAA 0.868748 -42 CTTGTTAAGTTAAAATTAAAATTAAAATTG 41 72 0 TAAAATTAAA 0.804862 -30 TATATAAGATTAAAATTTAACTGTGGCTTA 43 140 0 TAAAATTTAA 0.650902 -33 GAAGTGCGGTTAAAATTTAAGTTATTTCAG 48 38 0 TAAAATTTAA 0.650902 -150 TTACCCATAATAAAAATAAAAACTAAGTCG 48 153 0 TAAAAATAAA 0.822101 -35 CATTTTATATTAAAAATAAACCTACTTACA 54 44 1 TAAAAATAAA 0.822101 -257 GATTTTCAAATAAAAAGGAAAAAAT 54 286 1 TAAAAAGGAA 0.868805 -15 TTGTTTTTGGTAAAATGAAAAAAATTTTTG 58 29 0 TAAAATGAAA 0.786476 -42 ********** Masking position 5 Map Score: 18.4207 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 44 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 CGATGGTTTATGTGGAAATTGTCGAAGAGAGC 3 128 1 TGGGAATTGT 0.49472 -173 GTGACAGGAATCACGGAGTTTTTTGTCAAATA 17 178 1 TCCGGGTTTT 0.764907 -123 CCCCACATGCTGTGGGGGTTTTTTTTATCCTC 21 52 1 TGGGGGTTTT 0.97087 -97 TCAGGCCAAATGGCGGTATTTTATACACAAAA 22 38 0 TGCGGATTTT 0.947167 -143 TCGTTCACAGTGGGGAAGTTTTCGGATCCATG 24 232 1 TGGGAGTTTT 0.852107 -37 GACAGTATAATGGCGGCGTTTTATTAACTTTA 32 58 1 TGCGGGTTTT 0.97087 -29 GGTCGCAAAGTGCGGTCGTTTTCTTTTATATT 34 21 1 TGGGTGTTTT 0.89196 -30 TTTGTATTGATGATGGCATTTTTGATGCCACC 40 39 0 TGTGGATTTT 0.699281 -72 CCCGACATTGTGTCGGGATTGTTT 43 3 0 TGCGGATTGT 0.849935 -170 CCCGACACAATGTCGGGATTTTTGCTCTATAT 43 18 1 TGCGGATTTT 0.947167 -155 AGATAAAAAGTGCGGTGGTTTTTTCCGCACTT 44 107 0 TGGGTGTTTT 0.89196 -38 TAGCAAAATTTGACGGGATTTTGATCTACA 53 9 0 TGCGGATTTT 0.947167 -87 AAAAGTGCGGTCGTTTTTTCCCTTGTT 58 54 0 TGGGTGTTTT 0.89196 -17 ** *** ***** Masking position 9 Map Score: 10.4634 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 152 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 TCACCTCTCCTTCGAGCGCTA 1 191 0 TCCCTCTCCT 0.979165 -11 TTTTTCGATGTCACCTATCCTTAGAGCGAGG 2 186 1 TCCCTATCCT 0.967181 -115 AAAGCAAGTTTCTCCCATCCTTCTCAACTTA 2 265 1 TCCCCATCCT 0.860061 -36 TATCTGCGCTTATCCTTTATGGTTAT 5 6 1 GCCTTATCCT 0.911454 -229 AGTTCTCCTCTCTTGCTGAATTGA 7 287 0 TCCCTCTCTT 0.771276 -14 GTCTCTTGTCCTGTATCGTCGG 11 203 0 TCCTTGTCCT 0.870675 -12 ATTCCACGTTTCGCTTATCCTAGCTGAAGCG 13 136 1 TCCTTATCCT 0.948487 -149 TTCACTGCTCCTTAGCCAATAT 17 289 0 TCCTGCTCCT 0.918496 -12 ATCCGGCGCTGCCCCTCTCCTCACGGAGAGG 19 144 1 GCCCTCTCCT 0.963334 -86 ATCCGGCAATTCTCTGCTCCTGATGAGGGCG 26 158 1 TCCTGCTCCT 0.918496 -25 CCGCACTTTTCCTCTATAACATA 40 3 1 GCCTTTTCCT 0.717471 -108 TTTAATCTCCTATCCATTCAAGATGG 55 44 0 TCCCTATCCA 0.77342 -16 ** ******** Masking position 8 Map Score: 8.53632 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 40 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GGGATAAAAGTGTGATGTGAGTCAGATAAATGTCT 13 75 1 TGTGATTCAG 0.862899 -210 TATAAATATTTGTGATCTACAACACGCCTTATCTA 16 71 0 TGTGATACAC 0.930422 -230 ATATCAATTATGTAATATGCATCACGATATGCGGT 16 114 1 TGTAATTCAC 0.809398 -187 CATTCAGGAATGCGATTCCACTCACAATATTCCCG 17 64 1 TGCGATTCAC 0.953885 -237 CAAAAAACTCCGTGATTCCTGTCACGAAACGGTTG 17 168 0 CGTGATTCAC 0.91031 -133 AAAACAAAAATGTGACACTACTCACATTTAAATGC 18 25 1 TGTGACTCAC 0.953885 -276 ACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 18 98 1 TGTGATTCAC 0.981783 -203 CGGCCTTTTGTGTGATATCAATCACATAAATATAG 18 143 0 TGTGATTCAC 0.981783 -158 ATGTTTAAATTGTGATCTAGTACACAGTTTTTTAT 49 16 1 TGTGATACAC 0.930422 -86 TTTCTTATTTTGTGACAAAGATCACGGTTTATTTA 52 126 1 TGTGACTCAC 0.953885 -82 AAAAGCATTTTGCGATGCAGATCGCAAAAATTCTT 54 214 0 TGCGATTCGC 0.795724 -87 ****** **** Masking position 5 Map Score: 8.54317 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 25 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 CGCGTTATTAGGCTATAATGCGGCAATTCATAATC 1 23 0 GGCTAGCGCA 0.988873 -179 CAGCAGCGTCAGCAGCCAATCAGCAACAGTGAAAT 7 43 0 AGCCATCGCA 0.802348 -258 TGTGTAAAAAAGCAACAAGGCGGCGATTTTCGCTA 18 66 0 AGCCAGCGCG 0.931481 -235 AAAAACCTCGGGCTTCCAGCCTGCGCGACAGCAAA 18 257 1 GGCCACCGCG 0.948138 -44 ACGCTTATCAGGCCTACAGGATGCATCACAATTTG 19 64 1 GGCAAGAGCA 0.780361 -166 GGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTG 19 120 1 GGCTAGCGCA 0.988873 -110 TTACGATTCAGGCTGCAAACATGCGTCAGGGGGTG 20 80 0 GGCCACAGCG 0.698158 -67 CGCCTTATCCGGCCTACAGTCAGCAACGGTTGTTG 26 15 0 GGCAATCGCA 0.874315 -168 GGCCGGATAAGGCGTTCACGCCGCATCCGGCAATC 26 36 1 GGCTAGCGCA 0.98887 -147 GGCTGGATAAGGCGTTTACGCCGCATCCGGCAATT 26 134 1 GGCTAGCGCA 0.98887 -49 CAACAAAAGGGGCAATTAAGCCCCTTTATTTTTGA 37 18 0 GGCTAGCCCT 0.81434 -52 AGTTTTTGTCGGCTATAATTCGCCGCTTTCAACTC 42 27 0 GGCTATCCCG 0.850073 -51 TAGCGTTAAAAGCTGTGACGCACCACCAGCCTCTT 50 65 1 AGCTAGCCCA 0.847079 -106 *** * * ** *** Masking position 8 Map Score: 8.21122 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 752 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 12 AATTAATCCAAAAGGAAAACAAAAACAGCG 2 33 0 AAAGGAAAAC 0.628739 -268 CGTGCGATTACGGGAAAAGCGCGCAAAGTG 6 166 0 CGGGAAAAGC 0.660311 -135 TTTCAGCACGCAAGGAAAGCCGTAAAGTTA 7 162 0 CAAGGAAAGC 0.945311 -139 TTAATCGTTACAGGAAAAGCCAAAGCTGAA 8 68 1 CAGGAAAAGC 0.835115 -233 AATCACAGGGCAGGGAAACCTGCCCTTGTT 11 13 1 CAGGGAAACC 0.981647 -202 GCAAATCGTCCGGGGAAACCTTACCTGTCG 13 214 0 CGGGGAAACC 0.95355 -71 CAAATTTGCTCAGGGAAAACCTTGCAGGAG 13 261 1 CAGGGAAAAC 0.954354 -24 AGCAATTGAGCAGGGAAACCGGTGTTTTGA 16 211 0 CAGGGAAACC 0.981647 -90 GTGTCTATGGCAAGGAAAACAGGGTTTA 21 9 0 CAAGGAAAAC 0.916616 -140 GGGGATTAAGCAAGGAAGCCTGTAAGGCTT 32 24 0 CAAGGAAGCC 0.841168 -63 ACATTCCATCAAAGGAAACCAAATT 39 6 0 AAAGGAAACC 0.81247 -126 ********** Masking position 6 Map Score: 8.99161 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 174 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 CAGTCAGTGTAATAAAAAAAGCCTCGTGGG 5 106 0 AATAAAAAAA 0.72097 -129 GACAAAAGCAGATAAAAAAGTTGTTATTTT 6 67 1 GATAAAAAAG 0.844314 -234 CGGCAAAACTGATAAAAAAATCATCGTTTT 6 136 0 GATAAAAAAA 0.63995 -165 ATATCAAGGTAATAAAAAAGGTCGCCGAAG 16 21 0 AATAAAAAAG 0.887436 -280 ATTCATATTTGACAAAAAACTCCGTGATTC 17 185 0 GACAAAAAAC 0.59517 -116 CCGCCACATTAACAAAAAACCTCGGGCTTC 18 243 1 AACAAAAAAC 0.681248 -58 GCAAATTGAGGATAAAAAAAACCCCCACAG 21 61 0 GATAAAAAAA 0.63995 -88 ACGTTTCGGAAATAAAAAAGGCACCCGAAG 24 61 0 AATAAAAAAG 0.887436 -208 TACTCAAAAATATAAAAGAAAACGACCG 34 33 0 AATATAAAAG 0.54328 -18 AGAAAGAGAAAATAAAAAACAACAAAAGGG 37 42 0 AATAAAAAAC 0.90155 -28 CATTTTGAGCAATAAAAAACTGTGTACTAG 49 32 0 AATAAAAAAC 0.90155 -70 CATTATTTATAATAAAAATGTCATTACAAG 50 13 1 AATAAAAATG 0.387712 -158 AACCTTTGTAAATAAAAAAGCCATCGCTTG 50 117 0 AATAAAAAAG 0.887436 -54 CGTTTACATTGATAAAAAACAGGAGTCAAA 52 188 1 GATAAAAAAC 0.863 -20 GAATAAAAAACTGGCTGTCAA 54 2 1 AATAAAAAAC 0.90155 -299 CTTTTTAATGAATAAAAAATTGCAAAATTT 54 187 0 AATAAAAAAT 0.505589 -114 AATAATTAAAAATATAAAACCAGAAAATTG 57 120 0 AATATAAAAC 0.58013 -39 ********** Masking position 6 Map Score: 13.6699 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 127 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 14 CTGCCACCACGTTGCATATGCGTTTGCGTCC 1 147 0 GTTGCATTGC 0.969677 -55 TTTTCATCCGGTTAAATATGCAAAGATAAAT 3 229 1 GTTAAATTGC 0.928743 -72 CATACTTCAAGTTGCATGTGCTGCGTCTGCG 11 159 0 GTTGCATTGC 0.969677 -56 TACTTTACCGGTTGAATTTGCATCAATTTCA 17 35 1 GTTGAATTGC 0.974728 -266 ATCACAATTTGTTGAATTTGCACGTTCTTGT 19 88 1 GTTGAATTGC 0.974728 -142 GGTTGTATTGGTTAAATATGCTAATTTTATT 54 106 0 GTTAAATTGC 0.928743 -195 ******* *** Masking position 6 Map Score: 4.48123 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 44 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 15 GATGGGAGAAACTTGCTTTCTGGGCGCACTGCCG 2 250 0 ACGCTTCTGG 0.928091 -51 CGAACAATCCTTTTGTGATAAATGAAC 3 284 0 ACTCTTTTGG 0.892818 -17 GCAACAGTGAAATGGCATTTTGACTATTCGTGGC 7 22 0 AAGCTTTTGC 0.933359 -279 TTATCGCAGAAATAGCATTTTAGGTGTGGAAAAT 17 131 0 AAGCTTTTAG 0.739127 -170 CCTGAATAGTAAAGTCTTTTTGGGGGTGTTAACC 17 249 0 AATCTTTTGG 0.899062 -52 GCTTTTTTACACAAGCGTTTTGTGATGAACGTCA 18 88 1 ACGCTTTTGG 0.971122 -213 CTGTCCAGTCGACGGCCTTTTGTGTGATATCAAT 18 156 0 GAGCTTTTGG 0.871328 -145 TTGCTCCCAAAATCTTTCTGTCGCGATTCAAC 20 125 0 AATCTTCTGC 0.571095 -22 AGAGAGCCAGACCCGCATTTTGTGTATAAAATAC 22 21 1 ACGCTTTTGG 0.971122 -160 AAATTTATAAAAAGGCTTTTTGCCAAAACTCCAA 48 98 0 AAGCTTTTGC 0.933359 -90 CGATTAATTTAAAAGCATTTTGCGATGCAGATCG 54 225 0 AAGCTTTTGG 0.972943 -76 ** ** ***** * Masking position 8 Map Score: 5.65873 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 119 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727