AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_hpyl_reg_100.orf -o00260_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HP0106 24 cystathionine gamma-synthase (metB) Input sequences: #1 HP0096 72 phosphoglycerate dehydrogenase #2 HP0098 203 threonine synthase (thrC) #3 HP0107 38 cysteine synthetase (cysK) #4 HP0122 186 H. pylori predicted coding region HP0122 #5 HP0123 39 threonyl-tRNA synthetase (thrS) #6 HP0133 180 serine transporter (sdaC) #7 HP0181 257 H. pylori predicted coding region HP0181 #8 HP0398 28 H. pylori predicted coding region HP0398 #9 HP0399 120 ribosomal protein S1 (rps1) #10 HP0653 296 nonheme iron-containing ferritin (pfr) #11 HP0820 173 H. pylori predicted coding region HP0820 #12 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #13 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #14 HP1050 53 homoserine kinase (thrB) #15 HP1051 72 H. pylori predicted coding region HP1051 #16 HP1054 63 H. pylori predicted coding region HP1054 #17 HP1057 148 H. pylori predicted coding region HP1057 #18 HP1067 290 chemotaxis protein (cheY) #19 HP1190 61 histidyl-tRNA synthetase (hisS) #20 HP1228 150 invasion protein (invA) #21 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #22 HP1361 56 competence locus E (comE3) #23 HP1365 83 response regulator #24 HP1368 300 type IIS restriction enzyme M2 protein (mod) #25 HP1483 26 gerC2 protein (gerC2) #26 HP1490 103 hemolysin Motif number 1 TAAACCACAAAATCCTTTTTTAAAAGAAACTAAG 1 12 0 AACTTTTAAA 0.93459 -61 ATAATACTATAATGCGGTTTAAAATTTTGCCGCA 2 46 0 AACTTTAAAA 0.921012 -158 TAAAAGAGCGAATGTAACCTTAAATGGTTTTTTA 2 132 0 AATCCTTAAA 0.939691 -72 TTCAAGTCGTAGCATACCCTAAAAGAGCGAATGT 2 151 0 AGTCCTAAAA 0.881217 -53 AAAACTCCCTTAAAATGATCATTA 4 1 1 AACCCTTAAA 0.970443 -186 ACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 7 62 0 AACTCTAAAA 0.943025 -196 AACTTAAAAAAAACTACCCTTAAAAAAATCAATC 7 77 0 AATCCTTAAA 0.939691 -181 TGAAAATAATAACACAACTTAAAAAAAACTACCC 7 92 0 AACCTTAAAA 0.949686 -166 AAAGATAGTCATAGCGTCTTAAAACAAACACCCA 7 170 0 ATCCTTAAAA 0.88853 -88 AGAGTGATTTTAAAAGCATGAGAA 8 1 1 AGTTTTTAAA 0.798232 -28 CACATTTTGAAAATTTTCTTTAAAAAAACCGCTA 9 11 1 AATCTTTAAA 0.916503 -110 TTTGGCTTACAAAATCGTTTAAAAACTAACAATT 9 44 0 AATTTTAAAA 0.846942 -77 TAATATGTAAAAAGCATTCTTAAATCTAAAAATG 10 50 0 AACTCTTAAA 0.953013 -247 CAGAATTTTTAAATCAGCCTTAAAA 11 2 0 AACCCTTAAA 0.970443 -172 TACATATTAAATAATATTTTAAAATTAAAAAGCG 12 11 0 ATTTTTAAAA 0.70031 -121 TTTGAATGTAAGGGCTATTTTAAACTTATTATTG 12 68 1 AGCTTTTAAA 0.892893 -64 AATCTCAATTCTCCCTAAAAAACAAAATCA 13 92 0 AACCCTAAAA 0.964021 -20 TGTATAATGCTAGTTTTAAAAATGAAAGGG 14 7 1 ATTTTTTAAA 0.741166 -47 ATAACCCCCTAAAATTAAAACGAC 16 50 0 ATCCCTAAAA 0.918798 -14 GTTTGCTATGATAATCGTTTAAAAGTAATAAAAT 18 79 0 ATTTTTAAAA 0.70031 -212 CATTTAAATTAGGCTCTTTTTAAACAGCCAAAGC 18 245 0 AGTTTTTAAA 0.798232 -46 GCCTAATTTAAATGCAATCTTAAAAGGAGAAGCA 18 265 1 AACTCTTAAA 0.953013 -26 CAATAGCCCTTTTTTAAAGATTTTAAGC 19 5 1 AGCTTTTAAA 0.892893 -57 GTATGCTAAAATTTTAGCTTAAAATCTTTAAAAA 19 21 0 ATTCTTAAAA 0.790916 -41 TTTGATTTTAATGGCATTCTTAAAGCTAGTATAC 20 79 1 ATCTCTTAAA 0.895454 -72 AAGAAGTTCAAACGCCCCCTGAAAAGTTTTGTCT 22 12 0 AACCCTGAAA 0.796271 -45 GTTATAAAAAAACACTCCCTTAAAAAAGACACCG 23 21 0 AACCCTTAAA 0.970443 -63 CTATGAAAAGGTTTTCTAAAACTTCATAAAA 24 8 1 AATTCTAAAA 0.887067 -293 TTTTCATTATAACGCTCCTTAAAAAACATAGGAA 24 56 1 AACCTTAAAA 0.949686 -245 TAAAAGATTAAGCCTAACTTTAAAAATCAAGCCT 26 20 0 AGTCTTTAAA 0.864942 -84 ** * ******* Masking position 10 Map Score: 46.1158 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 1022 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 GATTTTGTGGTTTAATTATATAACTTTAAAATTA 1 32 1 TTATTATAAC 0.738455 -41 GATTTATGCTTATAATACTATAATGCGGTTTAAA 2 57 0 TTATTATAAT 0.902097 -147 GATCAATCGTTCTCATTAAAAAACCATTTAAGGT 2 116 1 TTATAAAAAC 0.778778 -88 TACGACTTGAAATTATCCAAAAATAAAAAGGAAT 2 174 1 ATATAAAAAT 0.813046 -30 ACTAAAGCTCTATCATGCTATCATTGTTATATTT 4 50 0 TTATTATCAT 0.785472 -137 TGGTTTATGATTTTATTGTATAATGGGCGGTTAG 4 134 1 TTATTATAAT 0.902095 -53 AATCTAAAATTCTTAAATTAAAATATAGCTATAA 7 47 0 TTAATAAAAT 0.902096 -211 CCCTTAAAAAAATCAATCTAAAATTCTTAAATTA 7 61 0 ATAATAAAAT 0.777189 -197 TAAGTTGTGTTATTATTTTCAAATTTCAAGTCTA 7 105 1 TTATTCAAAT 0.739356 -153 CTTACTATAAAATAAATATAAAATCCTTAAGGGT 9 90 0 ATAATAAAAT 0.777188 -31 GCTTTTTACATATTATATAAAAATATCCCCTTTT 10 69 1 TTATAAAAAT 0.919926 -228 TTAAATAGATTTTTATGATAAAATCTAAGCTTTA 10 145 1 TTATTAAAAT 0.973667 -152 TTTCATTATCATTTATGCTATAATTATGGGACAA 10 248 1 ATATTATAAT 0.777067 -49 AAACTGATCTTAACATGCTTTTTAGC 11 158 0 ATATTAACAT 0.847619 -16 CGCTTTTTAATTTTAAAATATTATTTAAT 12 6 1 TTATTAAAAT 0.973668 -126 AAACGCTGTCTTTGATTGAAACATATACATATTA 12 36 0 TTATAAACAT 0.82031 -96 ATTTTAAACTTATTATTGTAAAATGGTGAGTTTT 12 84 1 TTATTAAAAT 0.973669 -48 TCCTAATCTCATTGATTGTAAAACTCACCATTTT 12 103 0 ATATTAAAAC 0.810944 -29 TAAATTCAAGTATAATTCTAACATGATTTAGTCT 13 52 1 TTATTAACAT 0.936281 -60 AGTTTCTTTCAATTATACTAAAATAATTAAAATG 17 94 0 ATATTAAAAT 0.933325 -55 TCAAGGTAATTTTAATCAAAACATGCTATTATTT 18 179 1 TTATAAACAT 0.82031 -112 TTTTTAAAGATTTTAAGCTAAAATTTTAGCATAC 19 21 1 TTAATAAAAT 0.90209 -41 GTAATCGTCTTCTAATAAAAAAATCTTTTTTTGC 24 134 0 TTATAAAAAT 0.919926 -167 AATACCCCCATTTCATTGTAAAATTCTTTCATGC 24 240 1 TTATTAAAAT 0.973669 -61 AGGCTTAATCTTTTATGTTAAAATTCTGAGATTT 26 39 1 TTATTAAAAT 0.973667 -65 AACTTTAAACCTAAAACCTAACGATAA 26 87 0 TTAATAAAAC 0.738455 -17 * * ** ****** Masking position 3 Map Score: 36.158 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 156 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 TATGCTTATAATACTATAATGCGGTTTAAA 2 57 0 ATACTATAAT 0.830223 -147 AAGCTCTATCATGCTATCATTGTTATATTT 4 50 0 ATGCTATCAT 0.810811 -137 TAACCCGCACAAGCTATAATAACGCTTAAA 6 36 0 AAGCTATAAT 0.884586 -145 AAAAAGCTTTATGCTACAATGAAAGCTCTT 6 133 1 ATGCTACAAT 0.975356 -48 AAATCTAAAAATGCTACAATGTTTATCTTT 10 33 0 ATGCTACAAT 0.975356 -264 ATTATCATTTATGCTATAATTATGGGACAA 10 252 1 ATGCTATAAT 0.971568 -45 AAAACGACTAACGCTAAAATTTTAAACCTT 16 28 0 ACGCTAAAAT 0.953287 -36 TAATAAAGTCATGCTACAATGCCACTATAT 17 30 0 ATGCTACAAT 0.975356 -119 TCTTTCAATTATACTAAAATAATTAAAATG 17 94 0 ATACTAAAAT 0.780224 -55 TAATCAAAACATGCTATTATTTGGAACGAT 18 191 1 ATGCTATTAT 0.74511 -100 TTGTATTTGTATGCTAAAATTTTAGCTTAA 19 33 0 ATGCTAAAAT 0.961093 -29 AAGCTAGTATACACTATAATACCATCTTAA 20 101 1 ACACTATAAT 0.800671 -50 AAACAAGAAAGAGCTAAAATAAAGACCT 20 133 1 GAGCTAAAAT 0.740906 -18 AAGGCAATTAGCGCTACAATACCCCC 23 68 1 GCGCTACAAT 0.943556 -16 TTTTTAAGGAGCGTTATAATGAAAACGAAC 24 51 0 GCGTTATAAT 0.57357 -250 CGCTCATTAAGCGCTACAATACCCCCATGC 24 106 1 GCGCTACAAT 0.943556 -195 TTAATCTTTTATGTTAAAATTCTGAGATTT 26 43 1 ATGTTAAAAT 0.695719 -61 ********** Masking position 5 Map Score: 20.5905 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 205 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 GAGATTAAGGGGTGGTTTTGGGCACGCATTT 6 86 0 GGTGGTTTGG 0.929796 -95 TTTTATGATTGGGGTTTTTTGAGATTAAGGG 6 106 0 GGGGTTTTTG 0.966843 -75 TTTTTTTAAGGGTAGTTTTTTTTAAGTTGTG 7 83 1 GGTAGTTTTT 0.783721 -175 CTAACAATTAGCGGTTTTTTTAAAGAAAATT 9 22 0 GCGGTTTTTT 0.888656 -99 GGGGTTAAAAGGGGATATTTTTATATAATAT 10 78 0 GGGGATTTTT 0.880534 -219 GCCATTAGCCGGTGTTCTTTCTCATTTTTGT 10 183 1 GGTGTTTTTC 0.815574 -114 GGTGCTGTTGGTGGGCGTTTGCATAGAAGAA 11 40 1 GTGGGCTTTG 0.695177 -134 AGTTTTTTTAGCGGGTTTTTCATTGAATGGA 11 85 1 GCGGGTTTTC 0.920997 -89 TCCTGAATTAGGGTTTATTTTTTGGAATTGG 15 11 1 GGGTTTTTTT 0.667644 -62 CTTTAGGCGAGGGGGTCTTGCTCGGG 15 57 1 GGGGGTTTGC 0.970581 -16 AAACTTTTCAGGGGGCGTTTGAACTTCTTAC 22 17 1 GGGGGCTTTG 0.97579 -40 CAGGTATTCTTTGGGGGTCGTAA 22 44 0 GGTATTTTTG 0.507054 -13 AAAATAAAGCGGTGTCTTTTTTAAGGGAGTG 23 12 1 GGTGTCTTTT 0.807132 -72 TCTTTTTTAAGGGAGTGTTTTTTTATAACCG 23 26 1 GGGAGTTTTT 0.936249 -58 GGGGGTATTGTAGCGCTAATT 23 73 0 GGGGGTTTGT 0.984929 -11 CGCTTAATGAGCGGGCTTTGTTATAATACTT 24 88 0 GCGGGCTTGT 0.875292 -213 TTTTTTGCATGGGGGTATTGTAGCGCTTAAT 24 111 0 GGGGGTTTGT 0.984929 -190 ACAATGAAATGGGGGTATTTTAAAAAAATGA 24 228 0 GGGGGTTTTT 0.990359 -73 ****** **** Masking position 8 Map Score: 20.9297 Number of sites scoring better than the average of aligned sites = 1240 Number in coding regions = 1093 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 AAAAAGAATACACCCTCTTATTAAAAAGCTTAGT 4 101 0 CACCTCTTAA 0.776759 -86 AACCACCCTTTCTATTCAAAAATACCTAA 4 168 0 CCCTTCTCAA 0.975383 -19 CCCAAAACCACCCCTTAATCTCAAAAAACCCCAA 6 95 1 CCCTTATCAA 0.945715 -86 AAAACAAACACCCATTACTCTTAAATCATGCCAA 7 150 0 CCCTTATTAA 0.950382 -108 GGTTAAATTGCCCTTTCGTTTTAAAGATAAACAT 10 11 1 CCCTTCTTAA 0.97756 -286 CGGTTATAAAGCCCCTCCATTCAATGAAAAACCC 11 97 0 GCCCTCTCAA 0.970064 -77 GTTTAAAATAGCCCTTACATTCAAAACGCTGTCT 12 59 0 GCCTTATCAA 0.898441 -73 ATTGTTGATACCCTTTCATTTTTAAAACTAGCAT 14 17 0 CCCTTCTTTA 0.860528 -37 CCGAGCAAGACCCCCTCGCCTAAAGAGATAAGCG 15 48 0 CCCCTCTAAA 0.970132 -25 ATAACCCCCTAAAATTAAAACGACTAAC 16 46 0 CCCCTATTAA 0.968601 -18 ATGCTACAATGCCACTATATTTAACACTTAGGAT 17 16 0 GCCCTATTAA 0.939992 -133 AAAATTTTTACCCACCCTAATAAAGTCATGCTAC 17 43 0 CCCCCCTAAA 0.78463 -106 AGTGCTTCTCCTTTTAAGATTGCATTT 18 274 0 GCTCTCTTAA 0.624633 -17 ACCCTCTCCGTTTTAATAGCGTTAT 20 2 1 CCCCTCTTTA 0.908567 -149 GAGTTTCAAGCCCTTTTTTCTTAATTTTTGATTT 20 53 1 CCCTTTTTAA 0.774394 -98 CTTTAAGAATGCCATTAAAATCAAAAATTAAGAA 20 70 0 GCCTTATCAA 0.898441 -81 AGCGCTAATTGCCTTTATACTAAAAGCGGTTATA 23 49 0 GCCTTATAAA 0.81827 -35 AACTCCTTAACGCTCTCGCTTAAAAGGTAATCGT 24 160 0 CGCCTCTAAA 0.704787 -141 *** *** **** Masking position 11 Map Score: 19.6635 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 283 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AAAACTCCCTTAAAATGATCAT 4 2 1 AAACCCCTTA 0.501897 -185 AAAAGAATACACCCTCTTATTAAAAAGCTTA 4 103 0 ACCCCTTATT 0.741087 -84 ATACCTAACTAACCGCCCATTATACAATAAA 4 145 0 AACCCCCATT 0.987877 -42 AACCACCCTTTCTATTCAAAA 4 176 0 AACCCCCTTT 0.966133 -11 GCGTGCCCAAAACCACCCCTTAATCTCAAAA 6 90 1 AACCCCCCTT 0.927816 -91 GCTATTAAACCGCCCTTTTATCGTGTTA 6 163 0 AACCCCCTTT 0.966127 -18 GTCTTAAAACAAACACCCATTACTCTTAAAT 7 158 0 AAACCCCATT 0.972845 -100 TCTTTAAAAAAACCGCTAATTGTTAGTTTTT 9 27 1 AACCCTAATT 0.851067 -94 ATCCCCTTTTAACCCCCTATTGATGCCAACC 10 93 1 AACCCCTATT 0.950588 -204 TATTGATGCCAACCCCTTTTTTTACCTAATT 10 110 1 AACCCTTTTT 0.788718 -187 AAAAATTTTCATACTCTCATTTACTTTTTCA 10 222 1 ATACCTCATT 0.775101 -75 ATTTTAAACCCCTATTGTTGATACCC 14 38 0 AAACCCTATT 0.894276 -16 TCCAAAAAATAAACCCTAATTCAGGA 15 6 0 AAACCTAATT 0.715305 -67 ACTCCATTTTAACCGGTCATTTTAATTATTT 17 77 1 AACCGTCATT 0.768498 -72 TTACAAATAAGAACGCTCATTGAACGCTCCA 18 126 1 GAACCTCATT 0.822526 -165 TTATAACAAAGCCCGCTCATTAAGCGCTACA 24 93 1 GCCCCTCATT 0.738889 -208 TTTTTTTAAAATACCCCCATTTCATTGTAAA 24 231 1 ATACCCCATT 0.861469 -70 **** ****** Masking position 10 Map Score: 16.682 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 435 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 TTTTGCCGCAAAGGGCAAAAAATTTCATCA 2 26 0 AAGGGCAAAA 0.905197 -178 ATCTTTTTTTAAGCGTTATTATAGCTTGTG 6 29 1 AAGCGTTATT 0.720455 -152 TCTTTAAAAAAACCGCTAATTGTTAGTTTT 9 27 1 AACCGCTAAT 0.779243 -94 TTTAAAACGAAAGGGCAATTTAACC 10 6 0 AAGGGCAATT 0.939813 -291 TTATTGCTACAAGCGCTAAAAAGCATGTTA 11 144 1 AAGCGCTAAA 0.95644 -30 TTTTGAATGTAAGGGCTATTTTAAACTTAT 12 67 1 AAGGGCTATT 0.967783 -65 CTAAAGAGATAAGCGCTAAATCCAATTCCA 15 33 0 AAGCGCTAAA 0.95644 -40 ATCTTTAAAAAAGGGCTATTG 19 2 0 AAGGGCTATT 0.967783 -60 TCAAACAAGAAAGAGCTAAAATAAAGACCT 20 131 1 AAGAGCTAAA 0.740123 -20 CTTTTAGTATAAAGGCAATTAGCGCTACAA 23 57 1 AAAGGCAATT 0.551707 -27 AAAACGAACGAAGCGCAATTTTATGAAGTT 24 30 0 AAGCGCAATT 0.949038 -271 CCCGCTCATTAAGCGCTACAATACCCCCAT 24 104 1 AAGCGCTACA 0.889238 -197 ********** Masking position 8 Map Score: 10.4838 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 430 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GTTATATAATTAAACCACAAAATCCTTTTT 1 26 0 TAAACCACAA 0.804128 -47 ATTATAAGCATAAATCAAAAATTAAACTGG 2 75 1 TAAATCAAAA 0.882284 -129 TTAAGTTTCTTAAAACAAAAATATAACAAT 4 32 1 TAAAACAAAA 0.93459 -155 ACAAACTAGCTAAAACTAAAGCTCTATCAT 4 68 0 TAAAACTAAA 0.890702 -119 AATAAAATCATAAACCAAAAAGAATACACC 4 121 0 TAAACCAAAA 0.968008 -66 ATTCAAACCCTAAACCCAAACCTTTCTCTC 7 217 0 TAAACCCAAA 0.920716 -41 AACGATTTTGTAAGCCAAAAAAGGATACAA 9 59 1 TAAGCCAAAA 0.883113 -62 TGTTTATCTTTAAAACGAAAGGGCAATTTA 10 14 0 TAAAACGAAA 0.748728 -283 AAAGCATTCTTAAATCTAAAAATGCTACAA 10 44 0 TAAATCTAAA 0.81042 -253 TGGGACAACTTAAACCAACACAAAGGAGAT 10 274 1 TAAACCAACA 0.782701 -23 GTTTATTTCTTAATACAAAAGGTAGGCGTT 13 11 0 TAATACAAAA 0.566724 -101 AAATCACTTTTAAGACTAAATCATGTTAGA 13 68 0 TAAGACTAAA 0.670494 -44 ATTCTCCCTAAAAAACAAAATCACTTTTAA 13 85 0 AAAAACAAAA 0.683125 -27 TTCCAAAAAATAAACCCTAATTCAGGA 15 8 0 TAAACCCTAA 0.652127 -65 GCTAAAATTTTAAACCTTAACTCCAAGATC 16 16 0 TAAACCTTAA 0.735857 -48 GAATGCCATTAAAATCAAAAATTAAGAAAA 20 68 0 AAAATCAAAA 0.530707 -83 AACTTTAAACCTAAAACCTAACGAT 26 89 0 TAAACCTAAA 0.945228 -15 ********** Masking position 3 Map Score: 13.5764 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 356 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 9 AATTAAACCACAAAATCCTTTTTTAAAAGA 1 19 0 CAAAATCCTT 0.966337 -54 AACCCTAAACCCAAACCTTTCTCTCATATA 7 212 0 CCAAACCTTT 0.741202 -46 TTTTGGCTTACAAAATCGTTTAAAAACTAA 9 49 0 CAAAATCGTT 0.788008 -72 AAAAAGGATACAATACCCTTAAGGATTTTA 9 76 1 CAATACCCTT 0.881665 -45 AAAATAAATATAAAATCCTTAAGGGTATTG 9 86 0 TAAAATCCTT 0.863705 -35 CCTATTGATGCCAACCCCTTTTTTTACCTA 10 108 1 CCAACCCCTT 0.888809 -189 AATCGCCAAATCCCTTGAATTGTTTG 17 133 0 CAAATCCCTT 0.90238 -16 TTACTTGTAAAATCCTTGTCTTTCTTT 18 8 1 TAAAATCCTT 0.863705 -283 AATTTTAGCTTAAAATCTTTAAAAAAGGGC 19 16 0 TAAAATCTTT 0.493997 -46 TCCATTTCCTTGTATTTGTAT 19 51 0 CCATTTCCTT 0.499881 -11 TTCAATGAGTCAAACTCCTTAACGCTCTCG 24 176 0 CAAACTCCTT 0.925056 -125 TTCTTTCATGCAAAACCCATTGAAGTTTAA 24 263 1 CAAAACCCAT 0.793884 -38 ********** Masking position 3 Map Score: 6.4336 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 535 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 GTTTCCTTTCTTCAAACCTTAAAAT 5 6 0 TTCAAACCTT 0.978557 -34 GGCTAAATTTTGAAACCTTGAGATTGTTT 7 10 1 TTGAAACCTT 0.89768 -248 ATCAATATAATTCAAACCCTAAACCCAAAC 7 226 0 TTCAAACCCT 0.974249 -32 TCTAAGCTTTATCAAGCCATTAGCCGGTGT 10 168 1 ATCAAGCCAT 0.897715 -129 ACGCTAAAATTTTAAACCTTAACTCCAAGA 16 18 0 TTTAAACCTT 0.855479 -46 TCTTTCTTTTTTCAAACCATCCAATGACCC 18 29 1 TTCAAACCAT 0.960721 -262 TAAAATGAGTTTCAAGCCCTTTTTTCTTAA 20 47 1 TTCAAGCCCT 0.973742 -104 AACTTTAAAAATCAAGCCTTCAAAAACC 26 9 0 ATCAAGCCTT 0.942447 -95 ********** Masking position 5 Map Score: 6.28396 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 157 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ATTTTTGTTTTAAGAAACTTAATGATCATT 4 24 0 TAAGAAACTT 0.844995 -163 ACCCTCTTATTAAAAAGCTTAGTAATACAA 4 94 0 TAAAAAGCTT 0.952553 -93 ATAACGCTTAAAAAAAGATTAATAAAGGAT 6 18 0 AAAAAAGATT 0.786664 -163 ACCCCAATCATAAAAAGCTTTATGCTACAA 6 122 1 TAAAAAGCTT 0.952553 -59 TTTATCGTGTTAAAGAGCTTTCATTGTAGC 6 145 0 TAAAGAGCTT 0.759988 -36 CGGTTTTTTTAAAGAAAATTTTCAAAATGT 9 12 0 AAAGAAAATT 0.50032 -109 ATATAATATGTAAAAAGCATTCTTAAATCT 10 57 0 TAAAAAGCAT 0.865688 -240 AAAACCCGCTAAAAAAACTTCAAACAGCTC 11 74 0 AAAAAAACTT 0.873421 -100 CTACAAGCGCTAAAAAGCATGTTAAGATCA 11 150 1 TAAAAAGCAT 0.865688 -24 AGTATAATTGAAAGAAACTTTTAACAAACA 17 109 1 AAAGAAACTT 0.776955 -40 TTCTTATTTGTAAAAAAATTCAGTTTGTTT 18 109 0 TAAAAAAATT 0.756336 -182 TAACGCTCCTTAAAAAACATAGGAAGTATT 24 65 1 TAAAAAACAT 0.77613 -236 CCCCCATGCAAAAAAAGATTTTTTTATTAG 24 127 1 AAAAAAGATT 0.786664 -174 ********** Masking position 6 Map Score: 10.5376 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 613 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 12 AAAGGATTTTGTGGTTTAATTATATAACTT 1 28 1 GTGGTTTAAT 0.731042 -45 ATACTATAATGCGGTTTAAAATTTTGCCGC 2 47 0 GCGGTTTAAA 0.982342 -157 TATAGCTTGTGCGGGTTAAATCGTGGATTT 6 48 1 GCGGGTTAAA 0.95526 -133 CGATAAAAGGGCGGTTTAATAGC 6 168 1 GCGGTTTAAT 0.932448 -13 GCATCAATAGGGGGTTAAAAGGGGATATTT 10 89 0 GGGGTTAAAA 0.934467 -208 ATTCAAGCTTGCGGTTATAAAGCCCCTCCA 11 112 0 GCGGTTATAA 0.920734 -62 ATCAACAATAGGGGTTTAAAAT 14 42 1 GGGGTTTAAA 0.944274 -12 CTTTATTAGGGTGGGTAAAAATTTTACTCC 17 52 1 GTGGGTAAAA 0.779641 -97 ATTAAAATGACCGGTTAAAATGGAGTAAAA 17 73 0 CCGGTTAAAA 0.845372 -76 AGACGCTTTGGCTGTTTAAAAAGAGCCTAA 18 241 1 GCTGTTTAAA 0.814243 -50 TATACTAAAAGCGGTTATAAAAAAACACTC 23 38 0 GCGGTTATAA 0.920734 -46 ********** Masking position 9 Map Score: 12.0225 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 239 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 AAGCATAAATCAAAAATTAAACTGGATTAA 2 80 1 CAAAAATTAA 0.766204 -124 TTGAAATTATCCAAAAATAAAAAGGAATCA 2 180 1 CCAAAAATAA 0.835236 -24 TCTCCTATAACAAACAATAAAATTCAATTT 3 18 0 CAAACAATAA 0.850284 -21 AAATCATAAACCAAAAAGAATACACCCTCT 4 117 0 CCAAAAAGAA 0.90603 -70 TTTTGTAAGCCAAAAAAGGATACAATACCC 9 64 1 CAAAAAAGGA 0.825508 -57 AATCCAATTCCAAAAAATAAACCCTAATTC 15 15 0 CAAAAAATAA 0.929618 -58 TGGATGGTTTGAAAAAAGAAAGACAAGGAT 18 22 0 GAAAAAAGAA 0.856868 -269 AATTTTTTTACAAATAAGAACGCTCATTGA 18 119 1 CAAATAAGAA 0.798396 -172 CCATTAAAATCAAAAATTAAGAAAAAAGGG 20 63 0 CAAAAATTAA 0.766204 -88 CCATCTTAATCAAACAAGAAAGAGCTAAAA 20 122 1 CAAACAAGAA 0.915268 -29 GACAAGCCATGAAAAAAGAAAAGTC 25 12 1 GAAAAAAGAA 0.856868 -15 ********** Masking position 6 Map Score: 8.00432 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 310 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 14 TATCATGCTATCATTGTTATATTTTTGTTTT 4 43 0 TCATTGTTTA 0.891083 -144 TAAAGAGCTTTCATTGTAGCATAAAGCTTTT 6 134 0 TCATTGTACA 0.570804 -47 AATTTTAGATTGATTTTTTTAAGGGTAGTTT 7 70 1 TGATTTTTTA 0.65493 -188 GTGTTCTTTCTCATTTTTGTAAATTTTTAAA 10 194 1 TCATTTTTTA 0.928889 -103 TATTTTAAACTTATTATTGTAAAATGGTGAG 12 83 1 TTATTATTTA 0.53942 -49 TGATACCCTTTCATTTTTAAAACTAGCATTA 14 15 0 TCATTTTTAA 0.745334 -39 GTCATTTTAATTATTTTAGTATAATTGAAAG 17 92 1 TTATTTTATA 0.784335 -57 ACTCAAAGAGTTATTTTATTACTTTTAAACG 18 67 1 TTATTTTATA 0.784328 -224 TTGGAACGATTTATTATTATAAGGCGTTAGA 18 211 1 TTATTATTTA 0.53942 -80 GGCTTGAAACTCATTTTAATAGCGCCCAAAT 20 34 0 TCATTTTATA 0.918537 -117 AAAAGTCATTTTATTAGGGATCAAAT 21 6 1 TCATTTTATA 0.918536 -23 CTTGACTGACTCATTTTTTTAAAATACCCCC 24 218 1 TCATTTTTTA 0.928889 -83 TACCCCCATTTCATTGTAAAATTCTTTCATG 24 242 1 TCATTGTAAA 0.612748 -59 ******** ** Masking position 3 Map Score: 7.45564 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 78 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 15 CTTTGCGGCAAAATTTTAAACCGCATTATA 2 43 1 AAATTTTAAA 0.710003 -161 AAGGAAACATAAGTTTTAAAGA 5 28 1 AAGTTTTAAA 0.84654 -12 GGCTAAATTTTGAAACCTTGAGATT 7 6 1 AATTTTGAAA 0.726523 -252 ATCAATCTAAAATTCTTAAATTAAAATATA 7 54 0 AATTCTTAAA 0.61275 -204 GTTGTGTTATTATTTTCAAATTTCAAGTCT 7 108 1 TATTTTCAAA 0.683908 -150 TTTTAAAGAAAATTTTCAAAATGTG 9 6 0 AATTTTCAAA 0.903419 -115 GCTAATTGTTAGTTTTTAAACGATTTTGTA 9 41 1 AGTTTTTAAA 0.61275 -80 AATTTTTAAAAATTTACAAAAATGAGAAAG 10 199 0 AATTTACAAA 0.414485 -98 AGAGTATGAAAATTTTTAAAAATTTACAAA 10 209 0 AATTTTTAAA 0.933805 -88 ACCACGCCAGAATTTTTAAATCAGCCTTAA 11 13 0 AATTTTTAAA 0.933805 -161 CGCTTTTTAATTTTAAAATATTATTTAA 12 9 1 AATTTTAAAA 0.819135 -123 TTACAATAATAAGTTTAAAATAGCCCTTAC 12 75 0 AAGTTTAAAA 0.639122 -57 TGTATAATGCTAGTTTTAAAAATGAAAGGG 14 11 1 TAGTTTTAAA 0.560628 -43 ACTAACGCTAAAATTTTAAACCTTAACTCC 16 22 0 AAATTTTAAA 0.710003 -42 TTTAGCTTAAAATCTTTAAAAAAGGGCTAT 19 13 0 AATCTTTAAA 0.61275 -49 AGGCAATCTAAATTTTCAATGAGTCAAACT 24 190 0 AATTTTCAAT 0.414485 -111 GAAATGGGGGTATTTTAAAAAAATGAGTCA 24 224 0 TATTTTAAAA 0.51162 -77 TTGAAGGCTTGATTTTTAAAGTTAGGCTTA 26 16 1 GATTTTTAAA 0.656833 -88 ********** Masking position 8 Map Score: 10.8911 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 535 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346