AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_ecoli_reg_300.orf -o00280_ecoli_300.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 rpsB 300 30S ribosomal subunit protein S2 #2 tsf 257 protein chain elongation factor EF-Ts #3 pyrH 146 uridylate kinase #4 frr 291 ribosome releasing factor #5 yaeM 91 putative ATP-binding component of a transport system #6 yaeS 185 orf, hypothetical protein #7 cdsA 120 CDP-diglyceride synthetase #8 yaeT 29 orf, hypothetical protein #9 hlpA 121 histone-like protein, located in outer membrane or nucleoid #10 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #11 ybeX 89 putative transport protein #12 ybeZ 113 putative ATP-binding protein in pho regulon #13 yleA 145 orf, hypothetical protein #14 htrB 224 heat shock protein #15 ycjL 121 probable amidotransferase subunit #16 ycjC 26 orf, hypothetical protein #17 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #18 ydbO 284 orf, hypothetical protein #19 ydcH 72 orf, hypothetical protein #20 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #21 msbB 119 suppressor of htrB, heat shock protein #22 yebA 78 orf, hypothetical protein #23 yebL 24 putative adhesin #24 wcaA 34 putative regulator #25 BIME92 24 BIME #26 wza 300 putative polysaccharide export protein #27 iciA 141 replication initiation inhibitor, binds to 13-mers at oriC #28 sbm 203 methylmalonyl-CoA mutase (MCM) #29 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #30 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 CAAAGTGAGATTGTCGCTTCCGTCCAGTCT 1 176 0 TTGTCGCTTC 0.60648 -125 AGTTGGGGTTATGCCTCCACGTATCCCATA 1 261 0 ATGCCTCCAC 0.648145 -40 ATTCTCGAGCTTGCCGCCTTTCTGCAACTC 2 41 0 TTGCCGCCTT 0.929084 -217 TATCAAAAAGGAGCCGCCTGAGGGCGGCTT 3 12 1 GAGCCGCCTG 0.961438 -135 GCGACGTACAATGTCGCTAGTATTAATTCA 3 96 1 ATGTCGCTAG 0.780556 -51 AAAAAGCAAAACGCCGCCAGCCGATCCGCA 5 47 0 ACGCCGCCAG 0.957387 -45 GTTGTTTCTGTTGCCGCCGGTGGGGTTCGC 7 79 1 TTGCCGCCGG 0.932148 -42 ATTCGCTCACTTGCCGCCTTGATGCAACTT 17 73 0 TTGCCGCCTT 0.929084 -202 TTCATCCTTCAAGCCGCCTCTGCCTTGGCT 17 146 0 AAGCCGCCTC 0.938585 -129 TATATAAAGAATGTCGCCAGAAATAAACGG 17 179 1 ATGTCGCCAG 0.950184 -96 ACTTTCCTAAGCCGCCAGCCAGGCGGCT 20 9 1 AAGCCGCCAG 0.964335 -54 GTTGTTAAAAAAGCCGCCTGGCTGGCGGCT 20 20 0 AAGCCGCCTG 0.968095 -43 GGGGCAAGTTGCGCCGCTACACTATCACCA 21 66 1 GCGCCGCTAC 0.636787 -54 ATTAATAGCAATGTCGCCATGCACATTTAC 26 240 0 ATGTCGCCAT 0.790013 -61 ACGTCGTTTTTTGCCGCCTGAGATTTGTCT 28 90 0 TTGCCGCCTG 0.985044 -114 TTACGTGGGTTTGTCGCCAGCAAAAAAAAT 28 128 0 TTGTCGCCAG 0.935512 -76 ATGGTGTCGAGTGCCGCTTCAACCTGGTCT 29 170 0 GTGCCGCTTC 0.871236 -131 CTGGCCGCTGGTGCCGCCTGGCGCCAGTAA 29 257 1 GTGCCGCCTG 0.986106 -44 ********** Masking position 5 Map Score: 26.3824 Number of sites scoring better than the average of aligned sites = 2952 Number in coding regions = 2807 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 TGATGTAAGCTCCCGGGAATTCTCGAGCTT 2 59 0 TCCCGGGAAT 0.694632 -199 GATGTGATCTGCCCGGCATTAAACCGCACA 2 223 0 GCCCGGCATT 0.982103 -35 CAGACTTACGCCCCCGCGATACTTACGCGG 4 41 0 CCCCCGCGAT 0.762358 -251 AGCCTAATAATCCAGACGATTACCCGTAAT 4 187 1 TCCAGACGAT 0.578611 -105 GCAAAACGCCGCCAGCCGATCCGCAAGGAT 5 42 0 GCCAGCCGAT 0.929011 -50 CCCGTCGTCATCGCGGCGTTGTTTCTGTTG 7 62 1 TCGCGGCGTT 0.759935 -59 TCTTTGCGTGGCCCGGCGATCTTATATTGA 9 61 0 GCCCGGCGAT 0.992637 -61 TTTGCCAGGCATTTGACTGGCAG 11 4 1 GCCAGGCATT 0.93432 -86 TGGCAGACGTCCCCGCCGTTGGTGATTAAC 11 28 1 CCCCGCCGTT 0.950534 -62 TTCTCAGGCCTGCCGTTCCGGTGGGCC 12 8 1 GCCTGCCGTT 0.946964 -106 TACACTATGCGCCCTGCATTCCTGGCTACT 13 107 1 GCCCTGCATT 0.719341 -39 TTATTTACAAGCGCGGCAATTTCGCCCAGT 14 123 1 GCGCGGCAAT 0.863255 -102 AGCGCAATGCGCCCGGCAATCTATACACAA 17 35 1 GCCCGGCAAT 0.980218 -240 CGGGCATACGGCCCGGGGATCTCTGCGCCC 17 206 1 GCCCGGGGAT 0.973814 -69 GATCTCTGCGCCCTGACGTTCACAAACTGC 17 223 1 CCCTGACGTT 0.794629 -52 CGCTCTGTCGCCCTGGCGTTTAATAATTTA 22 41 1 CCCTGGCGTT 0.942496 -38 TCTGTCAATAGCCTGCGGATGAAATCAATT 26 164 1 GCCTGCGGAT 0.816426 -137 GTTTTTTGCCGCCTGAGATTTGTCTATTTT 28 85 0 GCCTGAGATT 0.53298 -119 GGCACCAGCGGCCAGACGTTCTCAAGTTCG 29 242 0 GCCAGACGTT 0.90135 -59 ********** Masking position 10 Map Score: 20.9577 Number of sites scoring better than the average of aligned sites = 3072 Number in coding regions = 2917 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TCTCCCCCTTCATATTTCGCGCCGCAGATGCGTTAT 2 116 0 CTTCGCCGCA 0.923894 -142 AGTTTGGTCACGGCCAGCGCGCAGCAACCGGAGCGT 4 96 1 CGGCGCCGCA 0.989978 -196 ATTTTGGCCCCGGGCAGTGCTCGCCATCCTCACGTA 4 139 0 CGGTGCCCCA 0.960132 -153 TACTTACGATCAGATGGCGCAGACTATATCACTGAA 6 56 0 CGGCGCGCTA 0.914675 -130 CAAAGCATTACACTATGCGCCCTGCATTCCTGGCTA 13 99 1 CCGCGCCGCA 0.987051 -47 GCCGGGTAAGCGCAATGCGCCCGGCAATCTATACAC 17 27 1 CCGCGCCGCA 0.986652 -248 GTAAGCTCATCGGGATTCGCTCACTTGCCGCCTTGA 17 81 0 CGTCGCCCTT 0.81373 -194 TCTGCCTTGGCTGCGTTCGCTCCCCCGAATCACTTA 17 122 0 CGTCGCCCCC 0.976423 -153 TGAACTGTGACGGATTTCGCACCCTATTTTTATAAA 18 152 0 CGTCGCCCTA 0.97172 -133 AGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAA 21 53 0 CCTTGCCGCA 0.859204 -67 CGACGCCTGCATTCGCACCGCCCC 25 7 1 CGTCGCCGCC 0.979656 -18 GCCATGGATGCCGAAGGCGCTGGCTAACATGAGGAA 29 117 0 CGGCGCGCTA 0.915019 -184 AAATGCCGATCTGATCACGCTCGGCAGAAATCACGC 30 72 0 CGACGCCGCA 0.966495 -118 * * **** * *** Masking position 10 Map Score: 17.0238 Number of sites scoring better than the average of aligned sites = 764 Number in coding regions = 732 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TTATCAAAAAGGAGCCGCCTGAGGG 3 6 1 AAAAAGGAGC 0.762435 -141 AGATGGGCACAAAAAGAAGCCGCCCTCAGG 3 28 0 AAAAAGAAGC 0.794711 -119 GCTGCGCTGAAAAGCGACGTACAATGTCGC 3 83 1 AAAGCGACGT 0.778865 -64 TTGAACGACAAAAACGCCGCTCAGTAGATC 5 15 1 AAAACGCCGC 0.988033 -77 AATAAAAAGCAAAACGCCGCCAGCCGATCC 5 50 0 AAAACGCCGC 0.988033 -42 CCTATACAAAAAAAAGCCGTGTAAAACCAC 6 118 0 AAAAAGCCGT 0.955766 -68 GGCAACAGAAACAACGCCGCGATGACGACG 7 64 0 ACAACGCCGC 0.912819 -57 TTAGTTAATCAAAACGCCGTCGTTAATCAC 11 49 0 AAAACGCCGT 0.972024 -41 ACGCCACAGGAAAAAGGCGCAAGCATTGCA 12 69 0 AAAAAGGCGC 0.916907 -45 ATGGGAAAGTAAAAATCCGCGGCATGATAT 14 30 1 AAAAATCCGC 0.730743 -195 AAGGTCATTTAAAGCGCAGTAATGGCGATA 15 88 1 AAAGCGCAGT 0.798038 -34 GCAGTTGTTAAAAAAGCCGCCTGGCTGGCG 20 23 0 AAAAAGCCGC 0.980896 -40 CACCAAATAAAAAAAGCCGGTACTGACTGC 21 35 0 AAAAAGCCGG 0.869256 -85 TCCGTGGTTAAAAGCGCAGCTTAAAAGATC 27 25 0 AAAGCGCAGC 0.903753 -117 CAAGGAATACAAAAAGAAGTGAGGACAACG 28 44 0 AAAAAGAAGT 0.619643 -160 CAGGCGGCAAAAAACGACGTCTGAATGCAT 28 100 1 AAAACGACGT 0.900071 -104 ********** Masking position 3 Map Score: 23.5165 Number of sites scoring better than the average of aligned sites = 1235 Number in coding regions = 1092 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 5 CTGGACGGAAGCGACAATCTCACTTTGTGTAAC 1 179 1 GCACATCCAC 0.8229 -122 GGATGAGCGAGCGAAGATAACGCATCTGCGGCG 2 100 1 GCAAATACGC 0.888451 -158 TTACGCCCCCGCGATACTTACGCGGAATCTTAC 4 33 0 GCATCTTCGC 0.899546 -259 CAAACTGCCTGCAACAATAACGCCTTATAACCA 4 69 0 GCACATACGC 0.985571 -223 GGTGGGGTTCGCCATTGTAACGCTGGTGGTCTG 7 97 1 GCATGTACGC 0.786845 -24 TAAAGTCATCGCTACACTACCACTACATTCCTT 9 23 0 GCACCTACAC 0.947633 -99 CATCTTTATTGCAATGCTTGCGCCTTTTTCCTG 12 60 1 GCATCTTCGC 0.933978 -54 TGCATTCCTGGCTACTATTTCGCAAGAGCAAGT 13 121 1 GCACATTCGC 0.983593 -25 CACATTTTACGCTACATTTGCGCATTAAAAATT 14 85 1 GCACTTTCGC 0.894302 -140 ATTTACAAGCGCGGCAATTTCGCCCAGTCTTCA 14 125 1 GCGCATTCGC 0.844275 -100 CTAAATTATCGCCATTACTGCGCTTTAAATGAC 15 91 0 GCATACTCGC 0.868321 -31 AAGTTGCGCCGCTACACTATCACCAGATTGATT 21 71 1 GCACCTACAC 0.947617 -49 ATAATTTACCGCGACCACACCGCGTT 22 63 1 GCACACACGC 0.966295 -16 TGGCTTTTTAGCTACCAATACACTGATTTAGTT 26 86 0 GCACAATCAC 0.650662 -215 CAGGCATCCAGACACGCTACCGCCCCTGGCTTT 26 112 0 GAACCTACGC 0.766841 -189 GGCATCCATGGCCAACACATCACCCGGAAAGAC 29 141 1 GCAAACACAC 0.538917 -160 ** ** *** *** Masking position 11 Map Score: 17.6202 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 862 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 CGTGTACTACCTGGTCTATAAGGGCTCTCCCCC 2 144 0 CGGCTATAGG 0.984097 -114 GGGTAATCGTCTGGATTATTAGGCTATTTTATT 4 179 0 CGGTTATAGG 0.98279 -113 TCACCGGCCTATAAGGAAATTATTCA 12 98 0 CGGCTATAGG 0.984096 -16 TTTAAGTTTACAGGATTTTTACCCCTAAGGGCT 13 37 1 CGGTTTTACC 0.842897 -109 GGTTGTTCTCCCGGCTTATGAGCTGGTTTGCTT 24 11 0 CGGTTATAGC 0.974787 -24 GCTACCGCCCCTGGCTTTTTAGCTACCAATACA 26 97 0 CGGTTTTAGC 0.978698 -204 ATAATTCAGACTGGTCTTTCAGGCATCCAGACA 26 131 0 CGGCTTTAGG 0.986583 -170 CTTAAAAGATCAGGGATTTGCGCTA 27 3 0 CGGATTTCGC 0.785439 -139 ATGGCAGCAACTGTTTTTTCAGGAACGATACAG 29 56 1 CGTTTTTAGG 0.842467 -245 ATGAGGAAATCGGGGTTATCAGTAAGGGTGGTT 29 92 0 CGGTTATAGT 0.881073 -209 CCGCTTCAACCTGGTCTTTCCGGGTGATGTGTT 29 154 0 CGGCTTTCGG 0.965776 -147 * ** **** *** Masking position 7 Map Score: 10.3783 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 206 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GAGATGTGATCTGCCCGGCATTAAACCGCA 2 225 0 CTGCCCGGCA 0.853184 -33 AAAAAGAAGCCGCCCTCAGGCGGCTCCTTT 3 18 0 CGCCCTCAGG 0.718642 -129 ACCAGACTTACGCCCCCGCGATACTTACGC 4 43 0 CGCCCCCGCG 0.978888 -249 ATGGCGAGCACTGCCCGGGGCCAAAATGGC 4 148 1 CTGCCCGGGG 0.96635 -144 GTTCTTTGCGTGGCCCGGCGATCTTATATT 9 63 0 TGGCCCGGCG 0.966987 -59 AACGGGCATACGGCCCGGGGATCTCTGCGC 17 204 1 CGGCCCGGGG 0.992675 -71 GGGATCTCTGCGCCCTGACGTTCACAAACT 17 221 1 CGCCCTGACG 0.959073 -54 CCTAAGCCGCCAGCCAGGCGGCTTTTTTAA 20 16 1 CAGCCAGGCG 0.919354 -47 CCCGCTCTGTCGCCCTGGCGTTTAATAATT 22 39 1 CGCCCTGGCG 0.885412 -40 GCGGCACCAGCGGCCAGACGTTCTCAAGTT 29 244 0 CGGCCAGACG 0.961854 -57 GCCGCTGGTGCCGCCTGGCGCCAGTAATTC 29 260 1 CCGCCTGGCG 0.968095 -41 ********** Masking position 5 Map Score: 13.7457 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 1137 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 ATAGAAAATTCGACGTCTGATGCTGTACACA 1 69 1 CGACGCTGAT 0.958364 -232 CTGAGACTGTCAACGATTGAAATGAATTAAT 3 117 0 CAACGTTGAA 0.79962 -30 CCAACGGCGGGGACGTCTGCCAGTCAAATGC 11 19 0 GGACGCTGCC 0.891886 -71 ATACTGGTCACAACGGCAGCAAAGCATTACA 13 80 1 CAACGCAGCA 0.952936 -66 CGACGCCTGCATTCGCACCGC 25 1 1 CGACGCTGCA 0.991464 -24 CCTTTCTCATCAACGACTGCATGCTGAGAGG 26 42 1 CAACGCTGCA 0.986457 -259 TAGCGTGTCTGGATGCCTGAAAGACCAGTCT 26 126 1 GGATGCTGAA 0.77101 -175 GAAGTGAGGACAACGCCTGATATGTGCTATC 28 28 0 CAACGCTGAT 0.935207 -176 CGGCAAAAAACGACGTCTGAATGCATTTTTT 28 104 1 CGACGCTGAA 0.986457 -100 GATGGTTCGACAATGGCAGCAACTGTTTTTT 29 44 1 CAATGCAGCA 0.777788 -257 ***** ***** Masking position 3 Map Score: 6.97507 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 662 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 CGGAAGTCCGGCGCGCTTTATACCACAAATACGT 1 125 0 GCCGTTTTCC 0.957238 -176 TAAGGCTTGATAACTCCCCCAAAATAGT 2 5 1 GCTGTAATCC 0.892605 -253 GCGTTTTTTATTCCCTGACAGGGT 6 172 0 GCTTTTTTCC 0.966927 -14 CTGAAGTATCGCCTGATATCTGCTTTTGTGTTAA 7 26 1 GCTGTATTCT 0.938132 -95 GTTCCGGTGGGCCTTGTTTTTTCTCTCTTTATCC 12 25 1 GCTTTTTTCT 0.929744 -89 ATGTATTGTCGCATTTTTTCGCCCGCAACCAAAA 14 166 0 GCTTTTTGCC 0.833859 -59 CGGGCCGTATGCCCGTTTATTTCTGGCGACATTC 17 187 0 GCCGTTATCT 0.715431 -88 ACTATCACCAGATTGATTTTTGCCTTATCCGAAA 21 86 1 GATGTTTTCC 0.822521 -34 ACCGCCCCTGGCTTTTTAGCTACCAATACACTGA 26 93 0 GCTTTAGTCC 0.759748 -208 TGAGGACAACGCCTGATATGTGCTATCAGGCATT 28 21 0 GCTGTATTCT 0.938132 -183 ACGTCTGAATGCATTTTTTTTGCTGGCGACAAAC 28 116 1 GCTTTTTTCT 0.929744 -88 TTCATCCAGAGCGTGATTTCTGCCGAGCGTGATC 30 62 1 GCTGTTTTCC 0.984754 -128 ** ** *** * ** Masking position 7 Map Score: 7.03044 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 363 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 TTCGTATACACAGACTGGACGGAAGCGACA 1 165 1 CAGACTGGAC 0.893847 -136 TTCGCTCGCTCATCCCGGTCACTTACTGAT 2 85 0 CATCCCGGTC 0.868954 -173 CAAACGTGTACTACCTGGTCTATAAGGGCT 2 151 0 CTACCTGGTC 0.927802 -107 TTGTTGCAGGCAGTTTGGTCACGGCCAGCG 4 85 1 CAGTTTGGTC 0.839653 -207 CTGTGTGTGACTGTCTGGTCTGACTGAGAC 4 251 1 CTGTCTGGTC 0.944069 -41 TGATAACGCTCATACTGGTCACAACGGCAG 13 69 1 CATACTGGTC 0.947503 -77 AGGCAAAAATCAATCTGGTGATAGTGTAGC 21 81 0 CAATCTGGTG 0.789816 -39 CAGAATAATTCAGACTGGTCTTTCAGGCAT 26 138 0 CAGACTGGTC 0.981623 -163 AGTGCCGCTTCAACCTGGTCTTTCCGGGTG 29 161 0 CAACCTGGTC 0.976 -140 ********** Masking position 1 Map Score: 4.87966 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 365 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 CGCCAAACGTGCCACTGAAGGTTTTCTATA 1 39 1 GCCACTGAAG 0.778691 -262 CCGCCTTTCTGCAACTCGAACTATTTTGGG 2 28 0 GCAACTCGAA 0.819432 -230 CCAGCGCGCAGCAACCGGAGCGTACAAAAG 4 109 1 GCAACCGGAG 0.901224 -183 CCCACCGGCGGCAACAGAAACAACGCCGCG 7 73 0 GCAACAGAAA 0.927933 -48 AACCGAAACTGGATAGATAACTAC 10 5 1 GAAACTGGAT 0.60872 -20 AATTATTCACGCCACAGGAAAAAGGCGCAA 12 77 0 GCCACAGGAA 0.930799 -37 CCGCCTTGATGCAACTTGAATGATTTTGTG 17 60 0 GCAACTTGAA 0.753809 -215 TGATAGACGTGAAACAGGAGTCATA 17 260 1 GAAACAGGAG 0.860743 -15 TTAACTATTAGCAACAGAAATGTGAAACAT 18 24 0 GCAACAGAAA 0.927933 -261 TGCCTTATCCGAAACTGGAAAAGC 21 106 1 GAAACTGGAA 0.896706 -14 GTGATTACGTGCAACAGATAGCCCGCTCTG 22 18 1 GCAACAGATA 0.620643 -61 ********** Masking position 4 Map Score: 3.21767 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 929 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 12 TCCCATATTACCGACCCCAAAGGGCACCCCG 1 237 0 CCGCCCCAAA 0.957976 -64 TATGCAGGCCCCCTAACCAAACGTGTACTAC 2 167 0 CCCAACCAAA 0.944467 -91 TGCGCGCTGGCCGTGACCAAACTGCCTGCAA 4 88 0 CCGGACCAAA 0.989108 -204 CGAGCACTGCCCGGGGCCAAAATGGCAAATA 4 152 1 CCGGGCCAAA 0.970764 -140 ATTTTTTCGCCCGCAACCAAAATTTGTGGCT 14 157 0 CCGAACCAAA 0.97579 -68 CGCAACTTGCCCCGCACCAAATAAAAAAAGC 21 48 0 CCCCACCAAA 0.96338 -72 TAATAATTTACCGCGACCACACCGCGTT 22 61 1 CCGGACCACA 0.965449 -18 *** ******* Masking position 9 Map Score: 5.28421 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 58 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 13 TTGCGGATCGGCTGGCGGCGTTTTGCTTTT 5 46 1 GCTGGCGGCG 0.984363 -46 GGCGAACCCCACCGGCGGCAACAGAAACAA 7 80 0 ACCGGCGGCA 0.952804 -41 GTCGTTAATCACCAACGGCGGGGACGTCTG 11 31 0 ACCAACGGCG 0.918982 -59 GTTGGTGATTAACGACGGCGTTTTGATTAA 11 45 1 AACGACGGCG 0.918982 -45 AAGCCGCCTGGCTGGCGGCTTAGGAAAGT 20 10 0 GCTGGCGGCT 0.860557 -53 CTGACTGCGTACCGGCTGCGAATGGATGTT 21 13 0 ACCGGCTGCG 0.972676 -107 AAAAGCCGGTACTGACTGCGTACCGGCTGC 21 24 0 ACTGACTGCG 0.863624 -96 ATATACCGAAGCCGTCGGCGGGTAACATTT 27 58 0 GCCGTCGGCG 0.986909 -84 TAAAAAGCTCACCGTAGGCGCAAATACCCT 28 155 1 ACCGTAGGCG 0.923248 -49 GGCCATGGATGCCGAAGGCGCTGGCTAACA 29 124 0 GCCGAAGGCG 0.960499 -177 ********** Masking position 9 Map Score: 10.7964 Number of sites scoring better than the average of aligned sites = 1618 Number in coding regions = 1571 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 14 CGACAATCTCACTTTGTGTAACAACACACAC 1 190 1 ACTTTGTGTA 0.946512 -111 GCACACTTCCACTGTGTGTGACTGTCTGGTC 4 240 1 ACTGTGTGTA 0.844841 -52 CTGATATCTGCTTTTGTGTTAATACCCGTCG 7 38 1 CTTTTGTGTA 0.946512 -83 AACTTGAATGATTTTGTGTATAGATTGCCGG 17 47 0 ATTTTGTGTT 0.84519 -228 TTTTACTTAACTATTGTGTAACTTTCATAAA 18 206 1 CTATTGTGTA 0.786041 -79 CTATGACACAATTTTGTGTCAGGTTGCATAT 27 84 0 ATTTTGTGTA 0.963367 -58 CGAAGTGTGTATTTTGTGTTAAAAATATGCA 30 123 0 ATTTTGTGTA 0.963367 -67 ********* * Masking position 5 Map Score: 0.736131 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 7 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 TCTGAATTTCGCCAAACGTGCCACTGAAGGT 1 30 1 GCCAAACTGC 0.86305 -271 CATATTTCGCGCCGCAGATGCGTTATCTTCG 2 111 0 GCCGCAGTGC 0.973617 -147 AGACGTCCCCGCCGTTGGTGATTAACGACGG 11 32 1 GCCGTTGTGA 0.789517 -58 CATCTTTATTGCAATGCTTGCGCCTTTTTCC 12 60 1 GCAATGCTGC 0.691483 -54 GGGCGAAATTGCCGCGCTTGTAAATAACAAA 14 119 0 GCCGCGCTGT 0.893814 -106 AGCCGCCTCTGCCTTGGCTGCGTTCGCTCCC 17 134 0 GCCTTGGTGC 0.911416 -141 ATTAATGTTTTCCGCAGTTGCTATACAGATC 18 104 0 TCCGCAGTGC 0.800646 -181 TGATGTGTTGGCCATGGATGCCGAAGGCGCT 29 132 0 GCCATGGTGC 0.971353 -169 ACAGTGATGGGCCATACCTGCTTCATGTCTC 29 205 1 GCCATACTGC 0.935349 -96 AGAACGTCTGGCCGCTGGTGCCGCCTGGCGC 29 250 1 GCCGCTGTGC 0.962129 -51 CGTGATTTCTGCCGAGCGTGATCAGATCGGC 30 73 1 GCCGAGCTGA 0.833765 -117 ******* *** Masking position 9 Map Score: 3.66036 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1318 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331