AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_ecoli_reg_300.orf -o00120_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 caiA 30 probable carnitine operon oxidoreductase #2 caiT 300 probable carnitine transporter #3 rpsB 300 30S ribosomal subunit protein S2 #4 tsf 257 protein chain elongation factor EF-Ts #5 pyrH 146 uridylate kinase #6 frr 291 ribosome releasing factor #7 yaeM 91 putative ATP-binding component of a transport system #8 yaeS 185 orf, hypothetical protein #9 cdsA 120 CDP-diglyceride synthetase #10 yaeT 29 orf, hypothetical protein #11 hlpA 121 histone-like protein, located in outer membrane or nucleoid #12 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #13 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #14 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #15 yaiN 166 putative alpha helix chain #16 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #17 ycjL 121 probable amidotransferase subunit #18 ycjC 26 orf, hypothetical protein #19 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #20 rspA 205 starvation sensing protein #21 b1582 134 orf, hypothetical protein #22 gatD 47 galactitol-1-phosphate dehydrogenase #23 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #24 gatZ 28 putative tagatose 6-phosphate kinase 1 #25 gatY 197 tagatose-bisphosphate aldolase 1 #26 BIME96 27 BIME #27 b2097 184 orf, hypothetical protein #28 pdxB 98 erythronate-4-phosphate dehyrogenase #29 pepP 25 proline aminopeptidase P II #30 ygfB 161 orf, hypothetical protein #31 yiaY 189 putative oxidoreductase #32 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #33 yibF 227 putative S-transferase #34 trxA 76 thioredoxin 1 #35 rhoL 140 rho operon leader peptide #36 rho 84 transcription termination factor Rho; polarity suppressor #37 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #38 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 AGCTCGAGAATTCCCGGGAGCTTACATCAGTA 4 60 1 TTCCCGGGCT 0.65106 -198 CTTCATATTTCGCGCCGCAGATGCGTTATCTT 4 113 0 CGCGCGCGAT 0.936124 -145 TGCGGTTTAATGCCGGGCAGATCACATCTCCG 4 225 1 TGCCGGCGAT 0.684482 -33 ACCAGACTTACGCCCCCGCGATACTTACGCGG 6 41 0 CGCCCCGGAT 0.959675 -251 TTTGCCATTTTGGCCCCGGGCAGTGCTCGCCA 6 149 0 TGGCCCGGCA 0.684925 -143 ACAAAAACGCCGCTCAGTAGATCCTTGCGGAT 7 22 1 CGCTCGTGAT 0.627773 -70 AAGCAAAACGCCGCCAGCCGATCCGCAAGGAT 7 42 0 CCGCCGCGAT 0.804324 -50 GTTCTTTGCGTGGCCCGGCGATCTTATATTGA 11 61 0 TGGCCGGGAT 0.967941 -61 AATAATAACACGGCCTGCCGCAATCGTAAGAA 12 51 0 CGGCCGCGCA 0.927037 -54 CCCCGGATAGCGGGCGGCAGAAGGAA 15 5 0 CGGGCGCGAA 0.846189 -162 CGGGGCGGCCTTCCCTGCCGATTAGCCCCCCC 15 32 1 TTCCCGCGAT 0.812921 -135 AATGCTCTCCTGATAATGTTAAAC 16 287 0 TGCTCCCGAT 0.736377 -14 TGTGTATAGATTGCCGGGCGCATTGCGCTTAC 19 32 0 TTGCCGGGCA 0.428306 -243 TGGCTGCGTTCGCTCCCCCGAATCACTTACCT 19 119 0 CGCTCCCGAA 0.670545 -156 AACGGGCATACGGCCCGGGGATCTCTGCGCCC 19 204 1 CGGCCGGGAT 0.981657 -71 GGCAAAAAAACGGCCTCCCGATAGGGAAGCCG 25 69 0 CGGCCCCGAT 0.960312 -129 CAAGTATGCCTGGCCGCGAGATTATGGCACAC 28 38 1 TGGCCCGGAT 0.924926 -61 AATATCAGTATGGCCTGGTGATGGGAAAAAGG 33 183 0 TGGCCGGGAT 0.96799 -45 CATGTTCGGGTGCCCCGTCGCTAAAAACTGGA 35 19 1 TGCCCGTGCT 0.726159 -122 ATCTTAATGCCGCGCTGGCGATGTTAGGAAAA 37 69 1 CGCGCGGGAT 0.929673 -171 GATCTGATCACGCTCGGCAGAAATCACGCTCT 38 69 0 CGCTCGCGAA 0.833259 -121 ***** ** *** Masking position 10 Map Score: 19.9067 Number of sites scoring better than the average of aligned sites = 2935 Number in coding regions = 2816 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 AAATTAACGAAAAAACGCCCTCTATTCACC 2 115 1 AAAAACGCCC 0.951474 -186 TGATGCTGTACACAGCGCCAACAATTATTG 3 86 1 CACAGCGCCA 0.556748 -215 CGAGTTGCAGAAAGGCGGCAAGCTCGAGAA 4 40 1 AAAGGCGGCA 0.851493 -218 TAAAAGTGAAAAAGGGGGCCATATGCAGGC 4 189 0 AAAGGGGGCC 0.564618 -69 TTATCAAAAAGGAGCCGCCTGAGGGCG 5 8 1 AAAGGAGCCG 0.833548 -139 ATGGGCACAAAAAGAAGCCGCCCTCAGGCG 5 26 0 AAAGAAGCCG 0.859326 -121 GGCTGCGCTGAAAAGCGACGTACAATGTCG 5 82 1 AAAAGCGACG 0.876346 -65 CTTGAACGACAAAAACGCCGCTCAGTAGAT 7 14 1 AAAAACGCCG 0.97946 -78 GAATAAAAAGCAAAACGCCGCCAGCCGATC 7 51 0 CAAAACGCCG 0.949577 -41 GCCTATACAAAAAAAAGCCGTGTAAAACCA 8 119 0 AAAAAAGCCG 0.921666 -67 ATACTTCAGCAAAAGCGACCCCCA 9 5 0 AAAAGCGACC 0.744515 -116 CGGCAACAGAAACAACGCCGCGATGACGAC 9 65 0 AACAACGCCG 0.898205 -56 CAAGTTGCATCAAGGCGGCAAGTGAGCGAA 19 72 1 CAAGGCGGCA 0.693667 -203 AGTGATCACAAAAAAAGGCGTATATTTGCG 20 98 0 AAAAAAGGCG 0.883177 -108 ATAAAGATCGAAAAAAGCCGGAGTGATCAC 20 119 0 AAAAAAGCCG 0.921666 -87 TGAAAGGCAAAAAAACGGCCTCCCGATAGG 25 76 0 AAAAACGGCC 0.926463 -122 TAACGATCACAAAAACGACAATATGAAAAT 25 117 0 AAAAACGACA 0.791713 -81 TGAAAGTGTAAAAAAGGGCGGGCAGCTTAC 31 160 0 AAAAAGGGCG 0.881096 -30 TGGTGATGGGAAAAAGGGCAGAAAATGTTG 33 170 0 AAAAAGGGCA 0.765152 -58 GTCTTATGCCAAAAACGCCACGTGTTTACG 37 15 1 AAAAACGCCA 0.954475 -225 GATATAAAAGCAAAACGCCACGTAAACACG 37 35 0 CAAAACGCCA 0.892244 -205 ********** Masking position 2 Map Score: 20.4532 Number of sites scoring better than the average of aligned sites = 1790 Number in coding regions = 1572 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 3 AGAAGCCGCCCTCAGGCGGCTCCTTTTTGA 5 14 0 CTCAGGCGGC 0.833805 -133 CGTAAGTATCGCGGGGGCGTAAGTCTGGTT 6 44 1 GCGGGGGCGT 0.769717 -248 GGTTGCTGCGCGCTGGCCGTGACCAAACTG 6 95 0 CGCTGGCCGT 0.894599 -197 CCATTTTGGCCCCGGGCAGTGCTCGCCATC 6 147 0 CCCGGGCAGT 0.799743 -145 CTTGCGGATCGGCTGGCGGCGTTTTGCTTT 7 45 1 GGCTGGCGGC 0.967218 -47 TGGCGAACCCCACCGGCGGCAACAGAAACA 9 81 0 CACCGGCGGC 0.742288 -40 ATATAAGATCGCCGGGCCACGCAAAGAACT 11 64 1 GCCGGGCCAC 0.928482 -58 GTAAGAATGAGACAGGCCGTAAAGTTTGGC 12 28 0 GACAGGCCGT 0.856433 -77 TTACGATTGCGGCAGGCCGTGTTATTATTG 12 54 1 GGCAGGCCGT 0.948705 -51 CGCCCCGGATAGCGGGCGGCAGAAGGAA 15 9 0 AGCGGGCGGC 0.882275 -158 CGCCCGCTATCCGGGGCGGCCTTCCCTGCC 15 21 1 CCGGGGCGGC 0.955473 -146 AAGAGGAAAGGGGGGGGGGCTAATCGGCAG 15 46 0 GGGGGGGGGC 0.89891 -121 GCAGCCAAGGCAGAGGCGGCTTGAAGGATG 19 144 1 CAGAGGCGGC 0.750049 -131 CGCAGAGATCCCCGGGCCGTATGCCCGTTT 19 203 0 CCCGGGCCGT 0.966376 -72 GTTTGTGAACGTCAGGGCGCAGAGATCCCC 19 220 0 GTCAGGGCGC 0.668677 -55 CTTCCCTATCGGGAGGCCGTTTTTTTGCCT 25 72 1 GGGAGGCCGT 0.855677 -126 TCGCAAGTATGCCTGGCCGCGAGATTATGG 28 35 1 GCCTGGCCGC 0.966326 -64 TGTAAAAAAGGGCGGGCAGCTTACTGAGGA 31 154 0 GGCGGGCAGC 0.946045 -36 AGTTTTTAGCGACGGGGCACCCGAACATGA 35 18 0 GACGGGGCAC 0.539364 -123 CATGACTCACGCCGGGCGTCCAGTTTTTAG 35 39 0 GCCGGGCGTC 0.821123 -102 CTTAATGCCGCGCTGGCGATGTTAGGAAAA 37 71 1 CGCTGGCGAT 0.474617 -169 ********** Masking position 5 Map Score: 17.0404 Number of sites scoring better than the average of aligned sites = 4213 Number in coding regions = 4038 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 4 TCGCTTCCGTCCAGTCTGTGTATACGAAATGGATCGGAA 3 154 0 CCGCTAACAA 0.960238 -147 TACCGTAAACCCTGTCAGGGAATAAAAAACGC 8 164 1 CCGCAAAAAA 0.976979 -22 GATACTCTTCCTGTCAAAATATAAGAAACGACAATAAT 12 77 0 CCGCAAAAAA 0.976979 -28 TAAAATTTATCCGGTGAATGTGGTCGGAAAACAAAGAGG 15 70 0 CCGGAGTCAA 0.729056 -97 ATTGCGCTTACCCGGCTTACAGAACAAAAAGA 19 4 0 CCGCTGACAA 0.952078 -271 GCGCAATGCGCCCGGCAATCTATACACAAAATCATTCAA 19 36 1 CCGCAAACAA 0.985492 -239 TCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATAT 20 103 0 CCGGTAAAAA 0.764305 -103 TGATTCTACACCATCCACTGCGGACGCAAAACGTACCAG 21 40 1 CCTCAGACAA 0.80038 -95 CGCACCTGCCATTTAACAAGGAAAAAAC 24 5 1 CCGCAAAAAA 0.976979 -24 CCTTACATTACCTGTCATGAAGGAATTAAAAG 27 4 0 CCGCAGAAAA 0.972155 -181 TAGGGTTTCGCCTGTCAGCAGACAAATAACCCGATAAAA 33 23 0 CCGCAAAAAA 0.976979 -205 CATGGATGATCCTGCCATACCATTCACAACATTAAGTTC 36 22 1 CCGCAATCAA 0.938344 -63 ** * ** * ** ** Masking position 18 Map Score: 11.7893 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 96 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCGAGCTTGCCGCCTTTCTGCAACTCGAAC 4 37 0 CGCCTTTCTG 0.832429 -221 CAAAGAACTGCACCCTCCGGTGCAAATGGG 11 85 1 CACCCTCCGG 0.942743 -37 GCAAAGCTGACACCTTTCAGCATCGCTTTT 16 38 0 CACCTTTCAG 0.836112 -263 AGCAAGATTACTCACTTCTGGGTACTGATT 16 90 0 CTCACTTCTG 0.894389 -211 TCAATATAAACACCCTCCTGGTACGTTTTG 21 66 0 CACCCTCCTG 0.984125 -69 GCCACCTTCCTGCTGATTGACT 30 3 1 CACCTTCCTG 0.94592 -159 AACACACTCCTGAAAGTGTAAA 31 178 0 CACACTCCTG 0.945919 -12 TGATGGATATCTCACTTCAGGCTTTCTTAT 33 69 0 CTCACTTCAG 0.727979 -159 GGAACGGACTTTCCCTTCTGAATAAAGGTC 37 174 1 TTCCCTTCTG 0.838413 -66 TTTTTACCCTTCTGTTTTTTTGAC 38 5 1 TACCCTTCTG 0.908183 -185 ********** Masking position 6 Map Score: 6.37077 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 206 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 GATCCATAAAACAATATTGAAAATTTCTTTT 2 18 0 ACAATATTAA 0.733759 -283 TTTGGCGAACAAAAGATGGAACG 12 3 0 AAAAGATGAA 0.946866 -102 TATTTTGTTAAAAACATGTAA 13 1 0 AAAACATGAA 0.803381 -76 CTAGATTGAAAAAATATTGAACATAAAGGTC 17 63 1 AAAATATTAA 0.794693 -59 AATGGTTGACAAAAGATGAAATAGAATACCT 20 62 0 AAAAGATGAA 0.946866 -144 CACAAAAACGACAATATGAAAATTATTCGAG 25 109 0 ACAATATGAA 0.865916 -89 AAAAACATCCAAAAGATGGAAAAACTCGCCC 27 149 1 AAAAGATGAA 0.946866 -36 GTTGGAAATTACAAGATTCAAACTTAATAAG 35 101 0 ACAAGATTAA 0.844109 -40 ATATGCAAACAAAAGATTAAAGAAATGCCGA 38 99 0 AAAAGATTAA 0.883787 -91 TTTTGTGTTAAAAATATGCAAACAAAAGATT 38 112 0 AAAATATGAA 0.900697 -78 ******** ** Masking position 6 Map Score: 6.50947 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 33 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AACCTCGTGGACGCGTTAATGGCTAACTCATAAT 2 194 0 ACGAATGGCT 0.864804 -107 TTATATCTGTGCGGTTTAATGCCGGGCAGATCAC 4 216 1 GCGAATGCCG 0.949049 -42 GTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAG 6 33 1 GCGTATCGCG 0.897586 -259 GTACAAAAGTACGTGAGGATGGCGAGCACTGCCC 6 130 1 ACGGATGGCG 0.98575 -162 CCAACTACTTACGATCAGATGGCGCAGACTATAT 8 63 0 ACGGATGGCG 0.98575 -123 AACAGAAACAACGCCGCGATGACGACGGGTATTA 9 57 0 ACGGATGACG 0.885381 -64 CAGACCACCAGCGTTACAATGGCGAACCCCACCG 9 96 0 GCGAATGGCG 0.991193 -25 GTCATTTAAAGCGCAGTAATGGCGATAATTTAGT 17 91 1 GCGAATGGCG 0.991193 -31 ATGCCTGGCCGCGAGATTATGGCACACTTGTCCG 28 43 1 GCGTATGGCA 0.87073 -56 *** ******* Masking position 9 Map Score: 5.75117 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 325 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TGTTACACAAAGTGAGATTGTCGCTTCCGTC 3 182 0 AGTGAATTGT 0.930942 -119 AATTAATACTAGCGACATTGTACGTCGCTTT 5 93 0 AGCGAATTGT 0.805749 -54 AGTCACACACAGTGGAAGTGTGCTAAGTATA 6 232 0 AGTGGAGTGT 0.982047 -60 GTAGGGCTTCAGTGATATAGTCTGCGCCATC 8 49 1 AGTGAATAGT 0.707244 -137 AAAGGAATGTAGTGGTAGTGTAGCGATGACT 11 22 1 AGTGGAGTGT 0.982047 -100 CAATAAGATAAGAGGAAGTGTCAGCTGACAA 20 30 1 AGAGGAGTGT 0.919071 -176 GGTATTATTAAGTGGTATTGTCATCGCGTAC 27 42 0 AGTGGATTGT 0.971821 -143 GTACCAGATGAGTCGAAGTGTGTATTTTGTG 38 136 0 AGTCGAGTGT 0.900533 -54 ***** ***** Masking position 7 Map Score: 3.74999 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 42 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TTAACCCCCAAAATATCAAGAGGTTGAAAG 1 5 1 CCCAACAAGG 0.950035 -26 TGATAACTCCCCCAAAATAGTTCGAGTTGCAGAAAGGCG 4 18 1 CCCATCGAGG 0.94905 -240 GATGTAAGCTCCCGGGAATTCTCGAGCTTGCCGCCTTTC 4 49 0 CCCAACGAGT 0.900804 -209 AGGGCTCTCCCCCTTCATATTTCGCGCCGCAGATGCGTT 4 118 0 CCCATCGCGG 0.83186 -140 AAGGGGGAGAGCCCTTATAGACCAGGTAGTACACGTTTG 4 142 1 GCCATCAGGG 0.96827 -116 GCAATCTATACACAAAATCATTCAAGTTGCATCAAGGCG 19 50 1 CACATCAAGG 0.67117 -225 TCTTTATATACACTTCATCCTTCAAGCCGCCTCTGCCTT 19 150 0 CACATCAAGG 0.67117 -125 AAAGAATGTCGCCAGAAATAAACGGGCATACGGCCCGGG 19 184 1 GCCAACGGGT 0.935787 -91 GGAGGTTATCCCCCTTAACAATCAGGAGTTTTT 22 25 1 CCCAACAGGT 0.944273 -23 GGAAAAACTCGCCCGTAACGACCAGGATT 27 166 1 GCCAACAGGT 0.937016 -19 GGACAAGTGTGCCATAATCTCGCGGCCAGGCATACTTGC 28 37 0 GCCATCGGCG 0.700761 -62 GTTTGTGTTACCTGTATGAGACGAGAGTTAACCGGACA 28 71 0 ACCATCGAGT 0.470972 -28 CGAAGGCAGCGCAGTCAATCAGCAGGAAGGTGGC 30 6 0 GCAAACAGGG 0.617295 -156 GTGTGAGAGGGCCTTGATCAGCCAGGTTTCCT 32 76 1 GCCATCAGGT 0.937016 -22 TGCATAACATGCCAGCAAATTCCAGGAATTTTCCTAACA 37 90 0 GCCAACAGGT 0.937016 -150 GTCAGTCTCCTGAATCCGCAAGGTGATCTGGTCGT 38 165 0 CTCAACAAGG 0.5365 -25 *** ** **** * Masking position 7 Map Score: 7.62593 Number of sites scoring better than the average of aligned sites = 892 Number in coding regions = 813 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 TCGGGTGAATAGAGGGCGTTTTTTCGTTAA 2 118 0 AGAGGGCGTT 0.774618 -183 CGAACTATTTTGGGGGAGTTATCAAGCCTT 4 12 0 TGGGGGAGTT 0.632648 -246 CGAAATATGAAGGGGGAGAGCCCTTATAGA 4 133 1 AGGGGGAGAG 0.941081 -125 ACGTTTGGTTAGGGGGCCTGCATATGGCCC 4 174 1 AGGGGGCCTG 0.926308 -84 AAAGTGAAAAAGGGGGCCATATGCAGGCCC 4 187 0 AGGGGGCCAT 0.963042 -71 GAGCCGCCTGAGGGCGGCTTCTTTTTGTGC 5 22 1 AGGGCGGCTT 0.843804 -125 ATATTGAGGAAGAGCGAGAG 14 25 1 AGAGCGAGAG 0.452209 -10 CAAAGAGGAAAGGGGGGGGGGCTAATCGGC 15 48 0 AGGGGGGGGG 0.894277 -119 TATATACTATAGGGGGGTATGCATTGACAT 15 120 1 AGGGGGGTAT 0.856511 -47 AATATACTATAGGGGGGTATTCTATATGTC 15 145 0 AGGGGGGTAT 0.856511 -22 GTATAGTTATAGGGCGACATAATATCATCA 21 93 0 AGGGCGACAT 0.872835 -42 TTTTTACCTGAGGGGGAGGTTATCCCCCTT 22 11 1 AGGGGGAGGT 0.921719 -37 GAGATGGGTCAGGAGGACATATCGCGCA 32 9 0 AGGAGGACAT 0.594538 -89 TCTCCGTGTGAGAGGGCCTTGATCAGCCAG 32 71 1 AGAGGGCCTT 0.774609 -27 ********** Masking position 6 Map Score: 6.87418 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 195 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 CACATATTCCGGGGTGCCCTTTGGGGTCGG 3 228 1 GGGGTGCCCT 0.967677 -73 AACCCTTGTGGGGCTGCGCTGAAAAGCGAC 5 71 1 GGGCTGCGCT 0.965738 -76 TGGGGGTCGCTTTTGCTGAAG 9 2 1 GGGGGTCGCT 0.930434 -119 TGCCGCCGGTGGGGTTCGCCATTGTAACGC 9 90 1 GGGGTTCGCC 0.967456 -31 TATCCGGGGCGGCCTTCCCTGCCGATTAGC 15 28 1 GGCCTTCCCT 0.877526 -139 TAAGCTCATCGGGATTCGCTCACTTGCCGC 19 86 0 GGGATTCGCT 0.908803 -189 CTGCCTTGGCTGCGTTCGCTCCCCCGAATC 19 127 0 TGCGTTCGCT 0.657939 -148 CACTTTGCTACGGCTTCCCTATCGGGAGGC 25 59 1 CGGCTTCCCT 0.890872 -139 TAAATCTGTAGGGTTTCGCCTGTCAGCAGA 33 40 0 GGGTTTCGCC 0.876287 -188 ATTTCATGTTCGGGTGCCCCGTCGCTAAAA 35 15 1 CGGGTGCCCC 0.868427 -126 ********** Masking position 7 Map Score: 4.67696 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 250 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 ACGCCCTCTATTCACCCGAAACAAAAATGTG 2 129 1 TTCACCCGAA 0.800162 -172 TGCCCGGCATTAAACCGCACAGATATAAAAG 4 213 0 TAAACCGCAA 0.737123 -45 TACGTCGCTTTTCAGCGCAGCCCCACAAGGG 5 73 0 TTCAGCGCAC 0.872126 -74 CCATCCCATTTGCACCGGAGGGTGCAGTTCT 11 88 0 TGCACCGGAG 0.745395 -34 GCGCGCACAGTACAGCGCAACTTATTTTGTT 13 23 0 TACAGCGCAC 0.781547 -54 TCCGACCACATTCACCGGATAAATTTTATTC 15 81 1 TTCACCGGAA 0.968674 -86 CACGTATGTTTACACCGCATCCGGCATAAAA 25 21 1 TACACCGCAC 0.930456 -177 CGGTCAAGTTTTCACCGCAAAGGTATTTAAA 27 74 0 TTCACCGCAA 0.968673 -111 GAGACGAGAGTTAACCGGACAAGTGTGCCAT 28 61 0 TTAACCGGAA 0.842408 -38 TTGACTTTATTTCACCGGATACGCTTTCGTA 34 42 0 TTCACCGGAA 0.968674 -35 ********* * Masking position 4 Map Score: 3.82639 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 347 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 TATATTAAATGTTAACAAAAATAAAACAAA 2 237 1 GTTAACAAAA 0.723981 -64 AGCAACCGGAGCGTACAAAAGTACGTGAGG 6 118 1 GCGTACAAAA 0.81885 -174 GAAGCCCTACGCTAACAAATAGCGCGACTC 8 29 0 GCTAACAAAT 0.808346 -157 GTAAAGTTTGGCGAACAAAAGATGGAACG 12 10 0 GCGAACAAAA 0.936996 -95 ACCTCACGACTCGGACAAAATGTCGTTGCG 13 51 0 TCGGACAAAA 0.718533 -26 GGAAGTGTCAGCTGACAAAAGGTATTCTAT 20 43 1 GCTGACAAAA 0.967543 -163 GCTGTGAATGGTTGACAAAAGATGAAATAG 20 69 0 GTTGACAAAA 0.837486 -137 AACAGAAAACGCTGAAAAAACATCCAAAAG 27 134 1 GCTGAAAAAA 0.722565 -51 TCGCCTGTCAGCAGACAAATAACCCGATAA 33 25 0 GCAGACAAAT 0.782841 -203 TTAAAAATATGCAAACAAAAGATTAAAGAA 38 106 0 GCAAACAAAA 0.868432 -84 ********** Masking position 5 Map Score: 2.16104 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 273 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 14 TGAACGACAAAAACGCCGCTCAGTAGATCC 7 16 1 AAACGCCGCT 0.94005 -76 ATAAAAAGCAAAACGCCGCCAGCCGATCCG 7 49 0 AAACGCCGCC 0.958747 -43 GCAACAGAAACAACGCCGCGATGACGACGG 9 63 0 CAACGCCGCG 0.988238 -58 ATAGCACTGCCACGTATGTTTACA 25 5 1 CACTGCCACG 0.773504 -193 CTTATGCCAAAAACGCCACGTGTTTACGTG 37 17 1 AAACGCCACG 0.980031 -223 TATAAAAGCAAAACGCCACGTAAACACGTG 37 33 0 AAACGCCACG 0.980031 -207 TCTGTAATCTTAATGCCGCGCTGGCGATGT 37 63 1 TAATGCCGCG 0.893665 -177 ********** Masking position 2 Map Score: 3.75027 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 351 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 TGTGATTGGTATCACATTTTTGTTTCGGGTG 2 141 0 ATCACATTTT 0.918553 -160 CGTGATCCAAATCAAATTTTTGCAAAGCTGA 16 58 0 ATCAAATTTT 0.754681 -243 ATTTAAAAAAAGCACATTGTTTAATGAATAC 31 60 1 AGCACATGTT 0.965636 -130 TCTAATAAAAAGCACATTGTATTCATTAAAC 31 78 0 AGCACATGTA 0.853794 -112 TTCCAAATAAATCACATATTTATCATGGTGA 33 127 0 ATCACATTTT 0.918554 -101 CAATTTGCATATCAAATGGTTAATTTTTGCA 37 127 1 ATCAAATGTT 0.863994 -113 TCCGCATCTTAGCACATCGTTCATCCAGAGC 38 43 1 AGCACATGTT 0.965668 -147 ******* *** Masking position 6 Map Score: 0.119655 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 51 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419