AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifruR_ecoli_hinf_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 HI0050 74 conserved hypothetical transmembrane protein #21 HI0051 38 conserved hypothetical transmembrane protein #22 HI0052 26 conserved hypothetical protein #23 HI0053 109 zinc-type alcohol dehydrogenase #24 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #25 HI0449 86 H. influenzae predicted coding region HI0449 #26 HI0451 71 conserved hypothetical protein #27 HI0452 50 conserved hypothetical protein #28 HI0453 26 conserved hypothetical protein #29 HI0454 54 conserved hypothetical protein #30 HI0457 69 conserved hypothetical protein #31 HI0458 70 stationary phase survival protein SurA, putative #32 HI0459 131 pyrimidine operon regulatory protein (pyrR) #33 HI0524 110 fructose-bisphosphate aldolase (fba) #34 HI0525 101 phosphoglycerate kinase (pgk) #35 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #36 HI0982 95 6-phosphofructokinase (pfkA) #37 HI0985 300 DNA processing chain A (dprA) #38 HI1711 59 PTS system, glucose-specific IIA component (crr) #39 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #40 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 GCGGCGTAAGCGCCTTATCCGGCCTACAAGAAC 15 111 0 CGCTATCCGC 0.997883 -119 AAGGCGCTTACGCCGCATCCGGCGCTGCCCCTC 15 128 1 CGCCATCCGC 0.998355 -102 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 19 27 0 CGCTATCCGC 0.997883 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 19 44 1 CGCCATCCGC 0.998355 -139 GACGCGCAAGCGTCGCATCAGGCATCGTGCACC 19 71 0 CGCCATCAGC 0.991701 -112 GACGCTTGCGCGTCTTATCATGCCTACAGCCGT 19 90 1 CGCTATCAGC 0.989341 -93 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 19 125 0 CGCTATCCGC 0.997883 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 19 142 1 CGCCATCCGC 0.998355 -41 TTCAAATTGTGGGCTTATCCCGCTAAACATAAA 33 74 1 GGCTATCCGC 0.985609 -37 ** * ***** ** Masking position 7 Map Score: 27.3476 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 78 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 AGTCCAAAGTGCTGAAACCATTCAAGAGTCAA 2 84 0 GCTGAACCTT 0.956836 -217 AAATATATTTGCTTGAACGATTCACCGTTTTT 3 199 1 GCTTGACGTT 0.919661 -102 TATTACACTGACTGAAACGTTTTTGCCCTATG 5 122 1 ACTGAACGTT 0.956932 -113 AGGATTTATGACTGAAACGCCTGTAACCGGAG 5 156 0 ACTGAACGCT 0.94805 -79 ACAAGATCGCGCTGAAACGTTTCAAGAAAGCA 6 203 0 GCTGAACGTT 0.992566 -98 TCTCATAGAGGCTGAATCGTTTCAATTCAGCA 6 266 1 GCTGAACGTT 0.992566 -35 AAAAGCCAAAGCTGAATCGATTTTATGATTTG 7 82 1 GCTGAACGTT 0.992566 -219 GCTTATCCTAGCTGAAGCGTTTCAGTCGATTA 12 148 1 GCTGAACGTT 0.992566 -137 GAAATCTGGCACTGAATCGGTTAACTGTCCAG 14 182 0 ACTGAACGTT 0.956932 -119 GCCGGATGCGGCGTAAGCGCCTTATCCGGCCT 15 119 0 GCGTAACGCT 0.936739 -111 ATCACTTCCTGCTGAATTGATTCAGGTCAGGC 16 64 0 GCTGAATGTT 0.8831 -117 GAGGTAAGGTGCTGAATCGCTTAACGATCGAC 17 23 0 GCTGAACGTT 0.992566 -246 GCCGGATGCGGCGTGAACGCCTTATCCGGCCT 19 35 0 GCGTGACGCT 0.799002 -148 GCCGGATGCGGCGTAAACGCCTTATCCAGCCT 19 133 0 GCGTAACGCT 0.936739 -50 AGGCTTCCTTGCTTAATCCCCTTTAGACAGTA 25 33 1 GCTTAACCCT 0.853262 -54 ****** ** ** Masking position 6 Map Score: 26.409 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 280 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 3 GGCAATTCATAATCTCTGAAAATACC 1 4 0 AATTGAAAAT 0.784568 -198 CTGTTTTCATAAAAAATAAAATTGAAGGTTCAT 3 67 0 AAATAAAATT 0.792944 -234 GGTATAAACGAAACCATAAAAATGAAATGCTGT 3 96 0 AAATAAAAAT 0.911665 -205 TCAGTCTTAAAAAGTAAAAAAATATATTTGCTT 3 180 1 AAAAAAAAAT 0.903096 -121 ACGAGGCCTGAAAGTGTAAAAATTGTTCTACAA 5 64 0 AAATAAAAAT 0.911664 -171 AATTAGGAAAAATGGCAAAAAATTGTGCAGCAC 6 113 1 AATAAAAAAT 0.91166 -188 GAGCAATTTATAAAATTGAACATAGGG 21 22 0 AATTAAAATT 0.758539 -17 TTTGTAGAGAAATGGATAAAAATTTACCGCACT 26 12 0 AATTAAAAAT 0.919543 -60 TTCTTAAAAAAATGTTTAAAAATGAGATCTACT 35 76 1 AATTAAAAAT 0.918638 -97 AATGGATGTCAATATAAAAAAATGTTAAGTAGA 35 103 0 AATAAAAAAT 0.911646 -70 TTTAATATAAAATGCCAAAAAATAGTTTGACAG 37 25 0 AATAAAAAAT 0.91166 -276 TAAAAAATCCAATAAGAAAAATTTGTTGATTAG 37 137 0 AATAAAAATT 0.792928 -164 CTTATTTTGAAAATGTAAAAAATCCAATAAGAA 37 152 0 AAAAAAAAAT 0.90308 -149 ACATTTTCAAAATAAGAAAAATTTTGCAATTTT 37 169 1 AATAAAAATT 0.792928 -132 TTTTCAAATAAAAAGGAAAAAAT 37 288 1 AAAAAAAAAT 0.903096 -13 CTTAGCCATAAAATTGTGAAATTTTATGGCTAT 39 17 1 AAATGAAATT 0.549331 -63 AGCCTGAATTAAATCATAAAAATAAGCTAAATA 40 39 0 AAATAAAAAT 0.911664 -120 TTAAAAATATAAAACCAGAAAATTGCCCTAGTA 40 112 0 AAAAGAAAAT 0.748363 -47 TCGACTAATCAATAATTAAAAATATAAAACCAG 40 127 0 AATTAAAAAT 0.919529 -32 *** ******* Masking position 13 Map Score: 20.6258 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 97 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 TGAACCTTCAATTTTATTTTTTATGAAAACAG 3 68 1 ATTTTATTTT 0.746296 -233 CAGCATTTCATTTTTATGGTTTCGTTTATACC 3 97 1 TTTTTATTTT 0.947505 -204 CAAATATATTTTTTTACTTTTTAAGACTGATC 3 178 0 TTTTTACTTT 0.917875 -123 TGTAGAACAATTTTTACACTTTCAGGCCTCGT 5 65 1 TTTTTACTTT 0.917875 -170 TGAAATGGCATTTTGACTATTCGTGGCGCTTT 6 17 0 TTTTGACTTC 0.56982 -284 CTGCACAATTTTTTGCCATTTTTCCTAATTGC 6 111 0 TTTTGCCTTT 0.705057 -190 AGCTGAATCGATTTTATGATTTGGTTCAATTC 7 91 1 ATTTTATTTT 0.746296 -210 CACATTTTTGTTTTGATGGTTTGTTGAA 14 7 0 TTTTGATTTT 0.893019 -294 CCAAAAAGAGTTTTTATGTTTCATAATCATAT 23 31 1 TTTTTATTTC 0.822237 -79 GTGCGGTAAATTTTTATCCATTTCTCTACAAA 26 13 1 TTTTTATATT 0.66177 -59 AACCTCAAATTTTTTATGGTTTTATAACATAA 26 46 0 TTTTTATTTT 0.947505 -26 GCCCCTTTATTTTTGATACTTTG 30 2 0 TTTTGATTTT 0.893019 -68 CTTTTGTTGTTTTTTATTTTCTCTTTCTTATA 30 44 1 TTTTTATTCT 0.611016 -26 ATTTGCACCATTTTTCTTGTTCGTTATACTAT 32 41 0 TTTTTCTTTC 0.681443 -91 AGGCGTATTTTCTTTATACTTTGTGCATTGAA 32 86 1 TCTTTATTTT 0.751643 -46 CTTATTGGATTTTTTACATTTTCAAAATAAGA 37 154 1 TTTTTACTTT 0.917875 -147 AATTGCAAAATTTTTCTTATTTTGAAAATGTA 37 168 0 TTTTTCTTTT 0.893019 -133 ATTTTGCAATTTTTTATTCATTAAAAAGAATT 37 189 1 TTTTTATATT 0.66177 -112 ATTTTTTCCTTTTTATTTGAAAAT 37 287 0 TTTTTCCTTT 0.837897 -14 ATTTAGCTTATTTTTATGATTTAATTCAGGCT 40 40 1 TTTTTATTTT 0.947505 -119 TAATTCAGGCTTTTTAGTGTTTATTCTTGATT 40 61 1 TTTTTAGTTT 0.682404 -98 TAGTGTTTATTCTTGATTATTTTGCTTTGAAA 40 75 1 TCTTGATTTT 0.583274 -84 TACTAGGGCAATTTTCTGGTTTTATATTTTTA 40 112 1 ATTTTCTTTT 0.576346 -47 ******* *** Masking position 4 Map Score: 16.8437 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 125 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 CCTTCAATTTTATTTTTTATGAAAACAGCATTTCATTT 3 72 1 TATTTTAAAG 0.957676 -229 CCTTTATGGTTATTTTACCGGTAACATGATCTTGCGCA 5 24 1 TATTTTAACG 0.886541 -211 ACTTGTGACTGATTTTTAAAAGAACCCGGGAAA 8 6 0 GATTTTAACG 0.913242 -39 ACAAGGCGGCGATTTTCGCTAAAAATGGCATTTAAATG 14 49 0 GATTTTAAAG 0.968115 -252 CAAATGGCGGTATTTTATACACAAAATGCGGGTCTGGC 16 26 0 TATTTTAAAG 0.941656 -155 AGTTATCAAGTATTTTTAATTAAAATGGAAATTGTTTT 17 133 1 TATTTTAAAG 0.957676 -136 AATTGTTTTTGATTTTGCATTTTAAATGAGTAGTCTTA 17 162 1 GATTTTTAAG 0.778323 -107 TTTATAACATAATTTTGTAGAGAAATGGATAAAAATTT 26 20 0 AATTTTAAAG 0.824514 -52 TAAGTAGGTTTATTTTTAATATAAAATGCCAAAAAATA 37 34 0 TATTTTAAAG 0.941656 -267 TTCCATACTAGATTTTCAAATAAAAAGGAAAAAAT 37 276 1 GATTTTAAAG 0.967703 -25 AAAATTATTTGATTTTACGTTAAAATAGCAACCATCTT 38 13 1 GATTTTAAAG 0.968115 -47 TATTCTTGATTATTTTGCTTTGAAAAAGGATACTAGGG 40 82 1 TATTTTAAAG 0.957269 -77 ****** *** * Masking position 14 Map Score: 13.796 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 33 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TAGCGCTCGAAGGAGAGGTGA 1 191 1 AGGAGAGGGA 0.983196 -11 CCTCGCTCTAAGGATAGGTGACATCGAAAAA 2 186 0 AGGATAGGGA 0.968516 -115 TAAGTTGAGAAGGATGGGAGAAACTTGCTTT 2 265 0 AGGATGGGGA 0.852794 -36 ATAACCATAAAGGATAAGCGCAGATA 5 6 0 AGGATAAGGC 0.942362 -229 TCAATTCAGCAAGAGAGGAGAACT 6 287 1 AAGAGAGGGA 0.793974 -14 TTTACTGCTTAGGAGAAGATC 9 30 1 AGGAGAAGTC 0.671939 -11 CCGACGATACAGGACAAGAGAC 10 203 1 AGGACAAGGA 0.890608 -12 CGCTTCAGCTAGGATAAGCGAAACGTGGAAT 12 136 0 AGGATAAGGA 0.957019 -149 ATATTGGCTAAGGAGCAGTGAA 13 289 1 AGGAGCAGGA 0.936212 -12 CCTCTCCGTGAGGAGAGGGGCAGCGCCGGAT 15 144 0 AGGAGAGGGC 0.977254 -86 CGCCCTCATCAGGAGCAGAGAATTGCCGGAT 19 158 0 AGGAGCAGGA 0.936212 -25 TATGTTATAGAGGAAAAGTGCGG 33 3 0 AGGAAAAGGC 0.801334 -108 CCATCTTGAATGGATAGGAGATTAAA 38 44 1 TGGATAGGGA 0.766009 -16 ******** ** Masking position 4 Map Score: 12.9241 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 52 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 TAAGCCAGGTTGGCGCTTTTTTTCTCATAGAG 6 244 1 TGGCGCTTTT 0.956759 -57 ACCTTACTTGTGACTGATTTTTAAAAGAACCC 8 17 0 TGACTGTTTT 0.903611 -28 GTGACAGGAATCACGGAGTTTTTTGTCAAATA 13 178 1 TCACGGTTTT 0.7654 -123 ATCGCCGCCTTGTTGCTTTTTTACACAAGCGT 14 74 1 TGTTGCTTTT 0.716633 -227 ACTGTCCAGTCGACGGCCTTTTGTGTGATATC 14 159 0 CGACGGTTTT 0.840641 -142 AATGCGGGTCTGGCTCTCTTTTATACTGA 16 8 0 TGGCTCTTTT 0.851541 -173 TCAGGCCAAATGGCGGTATTTTATACACAAAA 16 38 0 TGGCGGTTTT 0.975111 -143 GACAGTATAATGGCGGCGTTTTATTAACTTTA 25 58 1 TGGCGGTTTT 0.975111 -29 CCAACGTTATTGACTCTTTTTTGGATGAG 31 52 1 TGACTCTTTT 0.841125 -19 TTTGTATTGATGATGGCATTTTTGATGCCACC 33 39 0 TGATGGTTTT 0.867657 -72 ACTTGTGTTTCCTTTTTATGTTTAGCG 33 94 0 TGTTTCTTTT 0.395991 -17 CCCGACATTGTGTCGGGATTGTTT 35 3 0 TGTCGGTTGT 0.782758 -170 CCCGACACAATGTCGGGATTTTTGCTCTATAT 35 18 1 TGTCGGTTTT 0.96109 -155 TAGCAAAATTTGACGGGATTTTGATCTACA 36 9 0 TGACGGTTTT 0.973091 -87 ****** **** Masking position 9 Map Score: 10.4233 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 444 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 8 TAAATGTCTTCTTCGGCTGGACAAACATTCC 12 101 1 CTTCGGCGGA 0.903551 -184 CACAAAAGGCCGTCGACTGGACAGTTAACCG 14 166 1 CGTCGACGGA 0.903551 -135 TTTGCTGTCGCGCAGGCTGGAAGCCCGAGGT 14 261 0 CGCAGGCGGA 0.975202 -40 TGATGCATCCTGTAGGCCTGATAAGCGTAGC 15 61 0 TGTAGGCTGA 0.955284 -169 TGCACGTTCTTGTAGGCCGGATAAGGCGCTT 15 106 1 TGTAGGCGGA 0.989406 -124 CGTTGCTGACTGTAGGCCGGATAAGGCGTTC 19 22 1 TGTAGGCGGA 0.989406 -161 CGGCAACGGCTGTAGGCATGATAAGACGCGC 19 97 0 TGTAGGCTGA 0.955284 -86 CGTTGCCGAACGTAGGCTGGATAAGGCGTTT 19 120 1 CGTAGGCGGA 0.993295 -63 ******* *** Masking position 11 Map Score: 8.9804 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 100 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 TAGGCTATAATGCGGCAATTCATAATCTCTG 1 19 0 TGCGGCAATC 0.929629 -183 TGCGTTTGCGTCCTGCGATACGGATGCTTTA 1 129 0 TCCTGCGATC 0.871103 -73 GGATTCGCTTTCCGGCAGTGCGCCCAGAAAG 2 238 1 TCCGGCAGTC 0.955041 -63 CTTGTCGCCTTCCTGCAACTCGAATTATTTA 10 79 0 TCCTGCAACC 0.91797 -136 ACTTTACTATTCAGGCAATACATATTGGCTA 13 268 1 TCAGGCAATC 0.888185 -33 TTACGCCGCATCCGGCGCTGCCCCTCTCCTC 15 135 1 TCCGGCGCTC 0.901322 -95 CAAGAAGACTTCCGGCAACAGATTTCATTTT 16 136 1 TCCGGCAACG 0.966354 -45 TCACGCCGCATCCGGCAATCGGTGCACGATG 19 51 1 TCCGGCAATG 0.975809 -132 CCAGCCTACGTTCGGCAACGGCTGTAGGCAT 19 109 0 TTCGGCAACG 0.737921 -74 TTACGCCGCATCCGGCAATTCTCTGCTCCTG 19 149 1 TCCGGCAATC 0.989121 -34 ********* * Masking position 1 Map Score: 7.13358 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 539 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 CTGCCACCACGTTGCATATGCGTTTGCGTCC 1 147 0 GTTGCATTGC 0.972584 -55 TAATTTCAGCGTATAATGCGCGCCAATTGAC 2 58 1 GTATAATCGC 0.483005 -243 TTTTCATCCGGTTAAATATGCAAAGATAAAT 3 229 1 GTTAAATTGC 0.838847 -72 AAGCCTCGTGGGTGAATCCGCACGAGGCCTG 5 87 0 GGTGAATCGC 0.892028 -148 ATGAGCAAAAGTTTGATGTGCTGCACAATTT 6 132 0 GTTTGATTGC 0.696513 -169 CATACTTCAAGTTGCATGTGCTGCGTCTGCG 10 159 0 GTTGCATTGC 0.972584 -56 TACTTTACCGGTTGAATTTGCATCAATTTCA 13 35 1 GTTGAATTGC 0.963549 -266 ATCACAATTTGTTGAATTTGCACGTTCTTGT 15 88 1 GTTGAATTGC 0.963549 -142 ACATAACTATGGAGCATCTGCAC 18 17 1 GGAGCATTGC 0.816291 -13 TGGTCGATTTGTTTCATCCGCAGCTTTCTTT 24 30 1 GTTTCATCGC 0.848387 -42 CAAGAAAAATGGTGCAAATGCCGTCGCTTTT 32 54 1 GGTGCAATGC 0.696701 -78 GGTTGTATTGGTTAAATATGCTAATTTTATT 37 106 0 GTTAAATTGC 0.838847 -195 ******* *** Masking position 6 Map Score: 8.31497 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 249 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TTTAGAGCAATTTTTTGTTAATGATTTGTAATT 1 100 0 TTTTTTAATG 0.881148 -102 CTTCTGTGCGTTTTTAATTTATGCTTTCA 3 7 0 TTTTTTTATG 0.527993 -294 AACCTTCAATTTTATTTTTTATGAAAACAGCAT 3 70 1 TTTTTTTATG 0.527993 -231 GAACAATCCTTTTGTGATAAATGAACGGTTTGA 3 277 0 TTTTTAAATG 0.705945 -24 GCGCTTATCCTTTATGGTTATTTTACCGGTAAC 5 16 1 TTTTTTATTT 0.397231 -219 TTTTTTGCCATTTTTCCTAATTGCTGATGGGAA 6 102 0 TTTTTAATTG 0.811429 -199 AAGCCCGAGGTTTTTTGTTAATGTGGCGGCAGA 14 239 0 TTTTTTAATG 0.881148 -62 GTGAATAAATTTTATTCATATTGTTATCAACAA 17 101 1 TTTTATATTG 0.82309 -168 TTTTGTGTAGTTTATTCTTATTGTTATTTCTTG 20 32 1 TTTTTTATTG 0.930014 -43 CCTATGTTCAATTTTATAAATTGCTC 21 23 1 ATTTAAATTG 0.327893 -16 AACTTTCTCCTTATTGATTATGTTTT 22 11 0 TTTTTTATTG 0.930014 -16 ATCAATACAAATTCTTCAAATTGTGGGCTTATC 33 60 1 ATTTAAATTG 0.327893 -51 CTACTTAACATTTTTTTATATTGACATCCATTA 35 104 1 TTTTATATTG 0.82309 -69 TAATCAACAAATTTTTCTTATTGGATTTTTTAC 37 138 1 ATTTTTATTG 0.811429 -163 GATCGCAAAAATTCTTTTTAATGAATAAAAAAT 37 197 0 ATTTTTAATG 0.705945 -104 ATTGTGAAATTTTATGGCTATTGTTTATTTATT 39 29 1 TTTTCTATTG 0.676993 -51 TGGTTTTATATTTTTAATTATTGATTAGTCGAG 40 128 1 TTTTTTATTG 0.930014 -31 *** * ****** Masking position 5 Map Score: 9.07714 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 112 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 GGAACTAAAGTCTAGCCTGGCGGTTCGACT 7 249 0 TCTAGCCTGG 0.679143 -52 TAATTCGAGTTGCAGGAAGGCGACAAGAGA 10 83 1 TGCAGGAAGG 0.674562 -132 GAAGCTTTATTCCAGGCTGGCGTAATAATA 12 36 0 TCCAGGCTGG 0.923171 -249 TTTGCTGTCGCGCAGGCTGGAAGCCCGAGG 14 262 0 CGCAGGCTGG 0.950698 -39 TGATGCATCCTGTAGGCCTGATAAGCGTAG 15 62 0 TGTAGGCCTG 0.919178 -168 TGCACGTTCTTGTAGGCCGGATAAGGCGCT 15 106 1 TGTAGGCCGG 0.98298 -124 CGTTGCTGACTGTAGGCCGGATAAGGCGTT 19 22 1 TGTAGGCCGG 0.98298 -161 CGGCAACGGCTGTAGGCATGATAAGACGCG 19 98 0 TGTAGGCATG 0.834644 -85 CGTTGCCGAACGTAGGCTGGATAAGGCGTT 19 120 1 CGTAGGCTGG 0.958979 -63 ********** Masking position 4 Map Score: 5.48638 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 13 CCATTTCACTGTTGCTGATTGGCTGCTGACG 6 41 1 GTTGCTGATG 0.916971 -260 ATTTTTCCTAATTGCTGATGGGAAAATCCGT 6 95 0 ATTGCTGAGG 0.971046 -206 AATACAGTCCATTGCTGGCGGGTGTTGACCG 7 165 0 ATTGCTGGGG 0.969102 -136 GTGGAATCGCATTCCTGAATGAAATTGATGC 13 54 0 ATTCCTGATG 0.673118 -247 GGGTAAAAACATTGATGAAGGTTAATACT 15 211 1 ATTGATGAGG 0.924935 -19 AACAACAACCGTTGCTGACTGTAGGCCGGAT 19 13 1 GTTGCTGATG 0.916971 -170 TCGTGCACCGATTGCCGGATGCGGCGTGAAC 19 49 0 ATTGCCGGTG 0.863556 -134 GGAGCAGAGAATTGCCGGATGCGGCGTAAAC 19 147 0 ATTGCCGGTG 0.863556 -36 TCTATAACATATTGATGGTGGCATCAAAAAT 33 23 1 ATTGATGGGG 0.920149 -88 AAGAATTTGTATTGATGATGGCATTTTTGAT 33 45 0 ATTGATGAGG 0.924935 -66 AGAAAAATTTGTTGATTAGGGTTGTATTGGT 37 125 0 GTTGATTAGG 0.37814 -176 ******** ** Masking position 3 Map Score: 7.10194 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 643 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 TGGTGGCAGACGAGCAAACCAGTAGCGCTC 1 169 1 CGAGCAAACC 0.748774 -33 AATTAATCCAAAAGGAAAACAAAAACAGCG 2 33 0 AAAGGAAAAC 0.664317 -268 TTTCAGCACGCAAGGAAAGCCGTAAAGTTA 6 162 0 CAAGGAAAGC 0.939561 -139 TTAATCGTTACAGGAAAAGCCAAAGCTGAA 7 68 1 CAGGAAAAGC 0.690878 -233 AATCACAGGGCAGGGAAACCTGCCCTTGTT 10 13 1 CAGGGAAACC 0.979352 -202 GCAAATCGTCCGGGGAAACCTTACCTGTCG 12 214 0 CGGGGAAACC 0.958651 -71 CAAATTTGCTCAGGGAAAACCTTGCAGGAG 12 261 1 CAGGGAAAAC 0.928258 -24 GGGGATTAAGCAAGGAAGCCTGTAAGGCTT 25 24 0 CAAGGAAGCC 0.895917 -63 ACATTCCATCAAAGGAAACCAAATT 32 6 0 AAAGGAAACC 0.878854 -126 ********** Masking position 6 Map Score: 2.54413 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 234 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 ACTGATCCCAGCGTTGCGCAAATCTGCTCTCT 3 153 0 GCGTGCGCAA 0.761346 -148 TGAATGAAACGCGTTGTGAATCATCCTGCTCT 5 189 1 GCGTGTGAAC 0.981028 -46 GGCTTTCCTTGCGTGCTGAAACAGAAGTATTA 6 171 1 GCGTCTGAAC 0.976606 -130 AAAGACAAGATCGCGCTGAAACGTTTCAAGAA 6 207 0 TCGCCTGAAC 0.698568 -94 TGCTCTAAAAGCGCGCTGAAACAAGGGCAGGT 10 30 0 GCGCCTGAAC 0.959415 -185 AAAAAAGTTAGCGTGGTGAATCGATACTTTAC 13 11 1 GCGTGTGAAC 0.981028 -290 GGCCTGATAAGCGTAGCGCATCAGGCAATTAA 15 46 0 GCGTGCGCAC 0.970186 -184 GTCGCATCAGGCATCGTGCACCGATTGCCGGA 19 61 0 GCATGTGCAC 0.867135 -122 AAGAATTTTTGCGATCTGCATCGCAAAATGCT 37 214 1 GCGACTGCAC 0.91775 -87 **** ***** * Masking position 10 Map Score: 4.0483 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 408 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577