AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_hpyl_reg_300.orf -o00130_hpyl_300.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 Input sequences: #1 HP0012 286 DNA primase (dnaG) #2 HP0031 108 H. pylori predicted coding region HP0031 #3 HP0032 30 conserved hypothetical protein #4 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #5 HP0246 188 flagellar basal-body P-ring protein (flgI) #6 HP0282 50 H. pylori predicted coding region HP0282 #7 HP0289 66 toxin-like outer membrane protein #8 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #9 HP1067 290 chemotaxis protein (cheY) #10 HP1255 116 protein translocation protein, low temperature (secG) #11 HP1259 69 conserved hypothetical protein #12 HP1260 101 NADH-ubiquinone oxidoreductase, NQO7 subunit (NQO7) #13 HP1282 222 anthranilate synthase component I (trpE) #14 HP1283 97 H. pylori predicted coding region HP1283 #15 HP1284 69 conserved hypothetical protein #16 HP1285 169 conserved hypothetical secreted protein #17 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #18 HP1361 56 competence locus E (comE3) #19 HP1365 83 response regulator #20 HP1368 300 type IIS restriction enzyme M2 protein (mod) #21 HP1483 26 gerC2 protein (gerC2) #22 HP1490 103 hemolysin #23 HP1491 138 phosphate permease Motif number 1 TTTTGATAAATAAAATAGAAATTTAGCGCTTATT 1 26 1 TAAAGAATTT 0.88969 -261 AAATAAAATCTTAAAATAAGGTTTGTTAATAACG 1 202 0 TAAAAAGTTT 0.94013 -85 AGAACCAACCTTAAATGAAGTTTTGGTATTATAC 2 84 0 TAAAAATTTT 0.959682 -25 CTATCCCCCTTAAAAATGAGTTTTACTATAAAAC 4 20 1 TAAAGATTTT 0.981433 -186 AGTTTTACTATAAAACAAAATTTTAAAAAGATTA 4 38 1 TAAAAATTTT 0.959684 -168 AAAAATAAGATCAAAAAAATTTTTTATTAACTCT 4 110 1 TAAAAATTTT 0.959678 -96 AACAATTTTAAAAAAAGGACTTTTG 4 191 1 AAAAGATTTT 0.948048 -15 AAGTTTCAAATTAAATTGAGGTATGAATCTCCC 5 10 0 TAAAGAGTAT 0.664623 -179 CTTATAAACTTTAAATCAAAGATTTTAATTTTAG 5 64 0 TAAAAAGATT 0.619178 -125 TTTATCGCACTCAAAGAGTTATTTTATTACTTTT 9 59 1 TAAAGTATTT 0.556102 -232 ATCATAGCAAACAAACTGAATTTTTTTACAAATA 9 101 1 AAAAGATTTT 0.948492 -190 CGCTTGAAATTAAAACTAAATTTTAGTGTATTCT 10 32 1 TAAAAATTTT 0.959666 -85 GAAATGTTAAAATAATTTTTATTTTTTCAG 12 7 1 TAAAAATTTT 0.95881 -95 ACAAAGCCAATTAAACCATGTTTTTGCTAATCGT 12 44 0 TAAAATTTTT 0.787117 -58 TGTAAAAGCATAAAAAGGAATTTTCTAACCACCA 13 51 1 TAAAGATTTT 0.98163 -172 ATCCATCGCATAAGAACGATTTTTGCTAAAACAT 15 16 1 TAGAGATTTT 0.924598 -54 ACTCCGCCTAAGAGATCAAATTTTTTGTCATGTT 15 45 0 AAGAAATTTT 0.666804 -25 TATTATACCTTAAAACAGATGATTAGGAGTGTTT 16 72 0 TAAAGAGATT 0.784998 -98 GTTGTTATGATAAAAAAGACCTTTGCATCAGTTT 16 129 1 TAAAGACTTT 0.871449 -41 TTGATCCCTAATAAAATGACTTTT 17 1 0 AAAAGATTTT 0.947647 -28 ACCCCCATGCAAAAAAAGATTTTTTTATTAGAAG 20 126 1 AAAAGATTTT 0.914822 -175 AAGTAAAATTTTAAAGAGAGTTTTAAAAA 23 6 0 TAAAGATTTT 0.981636 -133 AGCCACTCTTAAAAAGCGTTGTTTGATAAAAATG 23 60 0 AAAAGTGTTT 0.651163 -79 AAGACCACTATTAGAACAAGGTTTTTATGACGAT 23 115 1 TAGAAAGTTT 0.793187 -24 * *** ** **** Masking position 14 Map Score: 33.6594 Number of sites scoring better than the average of aligned sites = 813 Number in coding regions = 639 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 CTATAGCGCATTTTTAGGGATAAGTCAAGCC 1 77 1 TTTTTAGGAT 0.792198 -210 ACAAACCTTATTTTAAGATTTTATTTATTGA 1 210 1 TTTTAAGTTT 0.723418 -77 TGTGTCCTTTTTCTAAGCGAGATTGTAGCGC 2 13 1 TTCTAAGGAG 0.860305 -96 TAAAACTCATTTTTAAGGGGGATAGTTATCC 4 14 0 TTTTAAGGGG 0.947769 -192 AAAACAAAATTTTAAAAAGATTAAATAATAT 4 49 1 TTTAAAAGAT 0.607917 -157 AAAGTCCTTTTTTTAAAATTGTTTTAGGCTT 4 183 0 TTTTAAATTG 0.679313 -23 CTCAATTAGGTTTAAAGTTTTTATAAAAGGC 5 124 1 TTTAAAGTTT 0.45991 -65 ATTTTATTACTTTTAAACGATTATCATAGCA 9 79 1 TTTTAAAGAT 0.826461 -212 GCTTTGGCTGTTTAAAAAGAGCCTAATTTAA 9 245 1 TTTAAAAGAG 0.840172 -46 GTGCTTCTCCTTTTAAGATTGCATTTAAATT 9 269 0 TTTTAAGTTG 0.89866 -22 TTAGTTTTAATTTCAAGCGTGGTGCGTTAAA 10 20 0 TTTCAAGGTG 0.81547 -97 ACAACCACATTTTTAAGAGAGCAGAATGTCT 13 108 1 TTTTAAGGAG 0.985421 -115 CAGCTCCTATTTTTTAGTGTTCAACAATGTA 14 74 0 TTTTTAGGTT 0.676766 -24 TAATCATCTGTTTTAAGGTATAATACAAAAA 16 81 1 TTTTAAGTAT 0.826461 -89 AAGACAAAACTTTTCAGGGGGCGTTTGAACT 18 11 1 TTTTCAGGGG 0.789282 -46 GCGGTGTCTTTTTTAAGGGAGTGTTTTTTTA 19 20 1 TTTTAAGGAG 0.985421 -64 CTTCCTATGTTTTTTAAGGAGCGTTATAATG 20 60 0 TTTTTAAGAG 0.755351 -241 GACGATTACCTTTTAAGCGAGAGCGTTAAGG 20 159 1 TTTTAAGGAG 0.985421 -142 GCAATCTAAATTTTCAATGAGTCAAACTCCT 20 187 0 TTTTCAAGAG 0.769211 -114 AGGCTTGATTTTTAAAGTTAGGCTTAATCTT 22 20 1 TTTAAAGTAG 0.840172 -84 AAAGTAAAATTTTAAAGAGAGTTTTAAAAA 23 10 0 TTTAAAGGAG 0.956533 -129 AAACAACGCTTTTTAAGAGTGGCTCAAGGGC 23 70 1 TTTTAAGGTG 0.973769 -69 ******* *** Masking position 2 Map Score: 25.0453 Number of sites scoring better than the average of aligned sites = 1212 Number in coding regions = 1041 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 AGGTTTGTTAATAACGCCCCTTTCTCTAATC 1 187 0 AAACGCCCCT 0.979818 -100 TTTACAAATAAGAACGCTCATTGAACGCTCC 9 125 1 AAACGCTCAT 0.909915 -166 GGAATTTTTGAAAACGCTCACTCATTAGCGT 13 140 1 AAACGCTCAC 0.97233 -83 TTTTGAATTAAAAACGCTAACTATACAGCAA 16 26 1 AAACGCTAAC 0.734663 -144 GTTAATGGTAAAAACACTCCTAATCATCTGT 16 61 1 AAACACTCCT 0.96217 -109 TTTTATCATAACAACACCTACCTAATGGGGA 16 113 0 AAACACCTAC 0.830001 -57 GTAAGAAGTTCAAACGCCCCCTGAAAAGTTT 18 17 0 CAACGCCCCC 0.96382 -40 CGGTTATAAAAAAACACTCCCTTAAAAAAGA 19 26 0 AAACACTCCC 0.988825 -58 AATTAGCGCTACAATACCCCC 19 73 1 AAATACCCCC 0.97233 -11 CGTTTTCATTATAACGCTCCTTAAAAAACAT 20 54 1 AAACGCTCCT 0.97233 -247 GGGCTTTGTTATAATACTTCCTATGTTTTTT 20 76 0 AAATACTTCC 0.779437 -225 ATTAAGCGCTACAATACCCCCATGCAAAAAA 20 111 1 AAATACCCCC 0.97233 -190 TCATTTTTTTAAAATACCCCCATTTCATTGT 20 228 1 AAATACCCCC 0.97233 -73 * ********* Masking position 4 Map Score: 16.3496 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 695 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 ACTCAATAAATAAAATCTTAAAATAAGGTTT 1 212 0 TAAAACTTAA 0.909745 -75 AACAAAATTTTAAAAAGATTAAATAATATTA 4 51 1 TAAAAGATTA 0.601277 -155 TTTATTTTCATAAAAACCTTGATCGCTATCC 4 153 0 TAAAACCTTG 0.945102 -53 TTTATGAAAATAAAAGCCTAAAACAATTTTA 4 170 1 TAAAACCTAA 0.96608 -36 TGAAACTTTATAAAAAGCTAATAAAAGGCTA 5 36 1 TAAAAGCTAA 0.90732 -153 AAAAAGCTAATAAAAGGCTAAAATTAAAATC 5 47 1 TAAAAGCTAA 0.90732 -142 AGGCTAAAATTAAAATCTTTGATTTAAAGTT 5 61 1 TAAAACTTTG 0.859036 -128 AAGCCTTTTATAAAAACTTTAAACCTAATTG 5 126 0 TAAAACTTTA 0.906923 -63 AAAGTTTTTATAAAAGGCTTATGCTAAAATA 5 137 1 TAAAAGCTTA 0.907266 -52 AGAAAAACCTAACCATAAAATT 8 36 0 GAAAACCTAA 0.783175 -12 TTACTTGTAAAATCCTTGTCTTTCTTTT 9 8 1 TAAAACCTTG 0.945102 -283 TGATTCCTTAAATGCCTAAAATTTAGAAA 10 98 0 TAAATCCTAA 0.709053 -19 AAAGCGGGATTAAAACCTTTAGAGACGCTG 11 50 1 TAAAACTTTA 0.906923 -20 AGTTATCCTCTAAAAACTTATAACGCAA 13 8 0 TAAAACTTAT 0.538806 -215 CTTTAGATTGTAAAAGCATAAAAAGGAATTT 13 43 1 TAAAACATAA 0.814398 -180 ATCGTCATAAAAACCTTGTTCTAATAGT 23 121 0 TAAAACCTTG 0.945102 -18 ***** ***** Masking position 4 Map Score: 19.3299 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 458 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 5 TTTTATAGTAAAACTCATTTTTAAGGGGGATA 4 21 0 AAATCTTTTT 0.967363 -185 CAAAAGTCCTTTTTTTAAAATTGT 4 192 0 AAATCTTTTT 0.967363 -14 GGCTAAAATTAAAATCTTTGATTTAAAGTTTA 5 62 1 AAATCTTGAT 0.764242 -127 GCTATACTCAAAAATCTTATAAACTTTAAATC 5 81 0 AAATCTATAA 0.574462 -108 TAGTAGCCAAAAACTCTCTCATTTGATTAAAT 7 19 0 AAATCCTCAT 0.805876 -48 GAAATGTTAAAATAATTTTTATTTTTTCAG 12 9 1 AAATATTTTT 0.580556 -93 CAGACTCTCAAACTCCTTTAATTACTAGCAA 12 81 0 AAATCTTTAA 0.905048 -21 GGTGGTTAGAAAATTCCTTTTTATGCTTTTAC 13 52 0 AAATCTTTTT 0.967349 -171 CGCTAAAAATAAACTCGTATTTTACAAGAAAT 13 190 0 AAATCTATTT 0.807459 -33 ATTATAGTAGAAAGTCTCTTATCAAAT 14 6 0 AAATCCTTAT 0.919444 -92 CTATAATCACACATTCGTTTATTCTTAATGTT 14 31 1 ACATCTTTAT 0.839593 -67 TGTTTTAGCAAAAATCGTTCTTATGCGATGGA 15 17 0 AAATCTTCTT 0.914006 -53 AACTGATGCAAAGGTCTTTTTTATCATAACAA 16 130 0 AAGTCTTTTT 0.768772 -40 AAAAGTCATTTTATTAGGGATCA 17 2 1 AAATCTTTTA 0.922031 -27 TTATAAAAAAACACTCCCTTAAAAAAGACACC 19 22 0 ACATCCTTAA 0.499393 -62 TTCTAATAAAAAAATCTTTTTTTGCATGGGGG 20 127 0 AAATCTTTTT 0.966874 -174 TTTCATTGTAAAATTCTTTCATGCAAAACCCA 20 250 1 AAATCTTCAT 0.896798 -51 TTTTTAAAACTCTCTTTAAAATTTTACT 23 7 1 AAATCCTTTA 0.849611 -132 *** ** ***** Masking position 5 Map Score: 18.6049 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 470 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 TATTTTATTTATCAAAACTTAGGAGAACTAA 1 12 0 ATCAAACTTA 0.288223 -275 AAGTCAAGCCATAAAAACAAAGCTAATAATA 1 98 1 ATAAAACAAA 0.497022 -189 ATCCTTGTATTTTTAAACTAATGAAACTTGA 1 159 0 TTTTAACTAA 0.657016 -128 GAAAGGGGCGTTATTAACAAACCTTATTTTA 1 194 1 TTATTACAAA 0.451432 -93 AAGTTTTGGTATTATACCAAATAAACCCTAA 2 70 0 ATTATACAAA 0.919235 -39 TCTTATAAACTTTAAATCAAAGATTTTAATT 5 68 0 TTTAAACAAA 0.838162 -121 TTATAAAAACTTTAAACCTAATTGAGCGTAT 5 119 0 TTTAAACTAA 0.712065 -70 AATTCTAATTATTTTAGCATAAGCCTTTTAT 5 146 0 ATTTTACATA 0.718844 -43 TGATTACGCCATTATATCCAAGATTAAGGCT 6 17 0 ATTATACCAA 0.590731 -34 CTCTCATTTGATTAAATCAAAGGGA 7 5 0 ATTAAACAAA 0.88102 -62 TGAACGAAGCATTATAGCAAAAAAG 8 5 0 ATTATACAAA 0.919235 -43 TTAAACGATTATCATAGCAAACAAACTGAAT 9 91 1 ATCATACAAA 0.818015 -200 GTCAAGGTAATTTTAATCAAAACATGCTATT 9 178 1 TTTTAACAAA 0.800469 -113 CACGCTTGAAATTAAAACTAAATTTTAGTGT 10 30 1 ATTAAACTAA 0.779518 -87 TTTTAGTGTATTCTTAGCAAATTTTAGATAA 10 52 1 TTCTTACAAA 0.708917 -65 ATCACGCTTGATCTTATCTAAAATTTGCTAA 10 65 0 ATCTTACTAA 0.624407 -52 TTTTTGTCATGTTTTAGCAAAAATCGTTCTT 15 27 0 GTTTTACAAA 0.562565 -43 GATTTTTTGTATTATACCTTAAAACAGATGA 16 84 0 ATTATACTTA 0.611798 -86 GCAAAGGTCTTTTTTATCATAACAACACCTA 16 124 0 TTTTTACATA 0.641369 -46 CATAGGAAGTATTATAACAAAGCCCGCTCAT 20 82 1 ATTATACAAA 0.919234 -219 AAATCTCAGAATTTTAACATAAAAGATTAAG 22 42 0 ATTTTACATA 0.718844 -62 AACTTTAAACCTAAAACCTAACGA 22 90 0 TTTAAACTAA 0.712065 -14 TAATGAGCCATTTTTATCAAACAACGCTTTT 23 52 1 TTTTTACAAA 0.860455 -87 ****** **** Masking position 2 Map Score: 18.5332 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 411 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 7 CTTATTGTTATTAAGCGACATAACTATAGCG 1 54 1 TTAAGCGCAT 0.900386 -233 TATAATTCATTCAAGCGAGTTAAAACAAGAA 1 242 1 TCAAGCGGTT 0.91138 -45 TGTCCTTTTTCTAAGCGAGATTGTAGCGCTT 2 15 1 CTAAGCGGAT 0.862378 -94 AGCTCAAAGATAAAGCGCTACAATCTCGCTT 2 27 0 TAAAGCGTAC 0.780106 -82 AAACTCATTTTTAAGGGGGATAGTTATCCAA 4 12 0 TTAAGGGGAT 0.929409 -194 TTGAGTGCGATAAAGGGTCATTGGATGGTTT 9 42 0 TAAAGGGCAT 0.622143 -249 AGTTTTAATTTCAAGCGTGGTGCGTTAAAGG 10 18 0 TCAAGCGGGT 0.955037 -99 TTAGATAAGATCAAGCGTGATTTTTTCTAAA 10 75 1 TCAAGCGGAT 0.966584 -42 TTTAGTAATCTTAAGCGGGGCTGGTATTTCA 11 15 1 TTAAGCGGGC 0.957423 -55 TATTTCAGCAGAAAGCGGGATTAAAACCTTT 11 39 1 GAAAGCGGAT 0.800163 -31 TAAAATAAAGCGGTGTCTTTTTTAAG 19 6 1 TAAAGCGTGT 0.797107 -78 GGTGTCTTTTTTAAGGGAGTGTTTTTTTATA 19 22 1 TTAAGGGGTG 0.618653 -62 AGCCCGCTCATTAAGCGCTACAATACCCCCA 20 102 1 TTAAGCGTAC 0.847374 -199 CGATTACCTTTTAAGCGAGAGCGTTAAGGAG 20 161 1 TTAAGCGGAG 0.941198 -140 AGTAAAATTTTAAAGAGAGTTTTAAAAA 23 8 0 TAAAGAGGTT 0.570357 -131 ACAACGCTTTTTAAGAGTGGCTCAAGGGCTA 23 72 1 TTAAGAGGGC 0.739932 -67 ******* *** Masking position 4 Map Score: 9.63467 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 459 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 TATTTGTATCAAGTTTCATTAGTTTAAAAATACAA 1 151 1 AATTATTATT 0.607212 -136 ATAATACCAAAACTTCATTTAAGGTTGGTTCTT 2 86 1 AATTTTTAGT 0.75322 -23 AAATAATATTAAATTGAATGGGGTTTATCAATATT 4 71 1 AATTATGGGT 0.915866 -135 AGTTAATAAAAAATTTTTTTGATCTTATTTTTGTC 4 107 0 AATTTTTGTT 0.682115 -99 CCTTTTTTTAAAATTGTTTTAGGCTTTTATTTTCA 4 174 0 AATTTTTAGT 0.832566 -32 ATAAAGTTTCAAATTAAATTGAGGTATGAATCTCC 5 12 0 AATTATTGGT 0.922429 -177 TAAAAAAATTCAGTTTGTTTGCTATGATAATCGTT 9 94 0 CATTTTTGTT 0.796852 -197 TTTAAGATTGCATTTAAATTAGGCTCTTTTTAAAC 9 254 0 CATTATTAGT 0.922903 -37 AAGAAGCTTTCAATTTGGTGGTGGTTAGAAAATTC 13 68 0 CATTGTGGGT 0.823017 -155 CAATTTCTTTACGCTAAAAATAAAC 13 208 0 CATTTTTAGT 0.900889 -15 ACCTTTGCATCAGTTTTATTAGGATTGAGTTTG 16 147 1 CATTATTAGT 0.922904 -23 AAAAGTCATTTTATTAGGGATCAAATCA 17 7 1 CATTTTAGGT 0.700421 -22 GAACGAAGCGCAATTTTATGAAGTTTTAGAAAACC 20 20 0 CATTATGAGT 0.91582 -281 AAGAATTTTACAATGAAATGGGGGTATTTTAAAAA 20 233 0 CATGATGGGT 0.729764 -68 CCTTTTATTAAACTTCAATGGGTTTTGCATGAAAG 20 265 0 AATTATGGTT 0.718492 -36 ** ** **** * * Masking position 2 Map Score: 6.36488 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 201 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 9 CTTCATCTTGCTTTCTTGTTTTAACTCGCT 1 255 0 CTTTCTTGTT 0.606194 -32 TTTTCATGCTTTCTTCATCT 1 277 0 TTTTCATGCT 0.915426 -10 TAATAAAAAATTTTTTTGATCTTATTTTTG 4 109 0 TTTTTTTGAT 0.769958 -97 GCGATCAAGGTTTTTATGAAAATAAAAGCC 4 158 1 TTTTTATGAA 0.543373 -48 ATTGAGCGTATTTTTATGCTATACTCAAAA 5 100 0 TTTTTATGCT 0.950888 -89 CTTTTTTGCTATAATGCTTC 8 1 1 CTTTTTTGCT 0.940926 -47 AAAAATTCAGTTTGTTTGCTATGATAATCG 9 96 0 TTTGTTTGCT 0.768721 -195 AATTAAACCATGTTTTTGCTAATCGTTAGC 12 40 0 TGTTTTTGCT 0.768721 -62 AGAAAATTCCTTTTTATGCTTTTACAATCT 13 47 0 TTTTTATGCT 0.950888 -176 TAAAAAAATCTTTTTTTGCATGGGGGTATT 20 123 0 TTTTTTTGCA 0.873155 -178 TTGTAAAATTCTTTCATGCAAAACCCATTG 20 255 1 CTTTCATGCA 0.759952 -46 TAGGCTTAATCTTTTATGTTAAAATTCTGA 22 38 1 CTTTTATGTT 0.73358 -66 ********** Masking position 7 Map Score: 6.1244 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 424 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 CAAATAAACCCTAATGACCCGCTGAAAGCT 2 54 0 CTAATGACCC 0.888834 -55 CCAAGTAGCCAAATAGCATG 3 1 1 CCAAGTAGCC 0.901841 -30 TTCAAACCATCCAATGACCCTTTATCGCAC 9 39 1 CCAATGACCC 0.946421 -252 AATGGAGCGTTCAATGAGCGTTCTTATTTG 9 129 0 TCAATGAGCG 0.962004 -162 ATTGAACGCTCCATTTAGCCAATGATTATT 9 144 1 CCATTTAGCC 0.754332 -147 AATAAATACGCTAATGAGTGAGCGTTTTCA 13 148 0 CTAATGAGTG 0.788636 -75 TAGTATAAAGGCAATTAGCGCTACAATACC 19 61 1 GCAATTAGCG 0.786268 -23 CCTATGTTTTTTAAGGAGCGTTATAATGAA 20 58 0 TTAAGGAGCG 0.798866 -243 ATTGTAGCGCTTAATGAGCGGGCTTTGTTA 20 96 0 TTAATGAGCG 0.919745 -205 ATCTAAATTTTCAATGAGTCAAACTCCTTA 20 185 0 TCAATGAGTC 0.82974 -116 AAGATACCATATAATGAGCCATTTTTATCA 23 41 1 ATAATGAGCC 0.828344 -98 CTTATTCTATCCAATTAGCCCTTGAGCCAC 23 88 0 CCAATTAGCC 0.963649 -51 ********** Masking position 7 Map Score: 6.41921 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 371 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 ATATTATTAGCTTTGTTTTTATGGCTTGAC 1 100 0 CTTTGTTTTT 0.960708 -187 CTTCATCTTGCTTTCTTGTTTTAACTCGCT 1 255 0 CTTTCTTGTT 0.769007 -32 CTTTTTAAAATTTTGTTTTATAGTAAAACT 4 38 0 TTTTGTTTTA 0.711628 -168 AAATTAAAATCTTTGATTTAAAGTTTATAA 5 67 1 CTTTGATTTA 0.799175 -122 TCAAACCCTTTCTTATTCCCTAAATTC 5 172 0 CTTTCTTATT 0.850199 -17 TCCCTTTGATTTAATCAAATGAG 7 4 1 CTTTGATTTA 0.799175 -63 AAATCCTTGTCTTTCTTTTTTCAAACCATC 9 20 1 CTTTCTTTTT 0.934421 -271 GTTTAATTGGCTTTGTCATTTGCTAGTAAT 12 62 1 CTTTGTCATT 0.625736 -40 AAAGACACCGCTTTATTTTA 19 1 0 CTTTATTTTA 0.664809 -83 ATAATACTTCCTATGTTTTTTAAGGAGCGT 20 67 0 CTATGTTTTT 0.739043 -234 AATGAGCGGGCTTTGTTATAATACTTCCTA 20 84 0 CTTTGTTATA 0.876154 -217 GACTTTTCTTTTTTCATGGCTTG 21 14 0 TTTTCTTTTT 0.6644 -13 ********** Masking position 4 Map Score: 4.23203 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 541 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 12 TGTCGCTTAATAACAATAAGCGCTAAATTT 1 44 0 TAACAATAAG 0.846808 -243 GACTTATCCCTAAAAATGCGCTATAGTTAT 1 73 0 TAAAAATGCG 0.517612 -214 AGTCAAGCCATAAAAACAAAGCTAATAATA 1 99 1 TAAAAACAAA 0.522752 -188 GCTAATAATATAACTATAAGGATTATTAAG 1 119 1 TAACTATAAG 0.486529 -168 TTCATTAGTTTAAAAATACAAGGATTAGAG 1 165 1 TAAAAATACA 0.85339 -122 AAATAAAATCTTAAAATAAGGTTTGTTAAT 1 206 0 TTAAAATAAG 0.447731 -81 CTATCCCCCTTAAAAATGAGTTTTACTATA 4 20 1 TAAAAATGAG 0.698811 -186 CAATATTTGACAAAAATAAGATCAAAAAAA 4 99 1 CAAAAATAAG 0.54578 -107 AAGGTTTTTATGAAAATAAAAGCCTAAAAC 4 164 1 TGAAAATAAA 0.534178 -42 AATAAAAGGCTAAAATTAAAATCTTTGATT 5 55 1 TAAAATTAAA 0.436213 -134 GAGTATAGCATAAAAATACGCTCAATTAGG 5 104 1 TAAAAATACG 0.859137 -85 AGAAAAACCTAACCATAAAATTTGAACGA 8 29 0 TAACCATAAA 0.346593 -19 TGAATTTTTTTACAAATAAGAACGCTCATT 9 117 1 TACAAATAAG 0.534389 -174 TAACGCCTTATAATAATAAATCGTTCCAAA 9 210 0 TAATAATAAA 0.502713 -81 CGCTTGAAATTAAAACTAAATTTTAGTGTA 10 32 1 TAAAACTAAA 0.534179 -85 TAAAATTTGCTAAGAATACACTAAAATTTA 10 48 0 TAAGAATACA 0.56048 -69 TCGTTAGCTGAAAAAATAAAAATTATTTTA 12 18 0 AAAAAATAAA 0.436213 -84 TTCTTTACGCTAAAAATAAACTCGTATTTT 13 199 0 TAAAAATAAA 0.926396 -24 ACGCAAACATTAAGAATAAACGAATGTGTG 14 38 0 TAAGAATAAA 0.733856 -60 TTAAAAACGCTAACTATACAGCAATTCGGT 16 33 1 TAACTATACA 0.294887 -137 TAATAAAAGGTAAAAATAAGA 20 290 1 TAAAAATAAG 0.929518 -11 AGCCTAACTTTAAAAATCAAGCCTTCAAAA 22 14 0 TAAAAATCAA 0.546116 -90 AACCTAACGATAAATATAAAATATATAAAA 22 70 0 TAAATATAAA 0.683289 -34 ********** Masking position 7 Map Score: 7.99061 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 361 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 13 TTAGCTTTGTTTTTATGGCTTGACTTATCC 1 94 0 TTTTATGGCT 0.326208 -193 CCAAAACTTCATTTAAGGTTGGTTCTT 2 92 1 ATTTAAGGTT 0.558326 -17 TTTTAAAATTGTTTTAGGCTTTTATTTTCA 4 174 0 GTTTTAGGCT 0.959203 -32 AAAGATTTTAATTTTAGCCTTTTATTAGCT 5 51 0 ATTTTAGCCT 0.896245 -138 AATTCTAATTATTTTAGCATAAGCCTTTTA 5 147 0 ATTTTAGCAT 0.629761 -42 CGTTTAAGCCTTAATCTTGGA 6 2 1 GTTTAAGCCT 0.924209 -49 AAATGAGAGAGTTTTTGGCTACTATCTAGG 7 27 1 GTTTTTGGCT 0.893152 -40 TTTTTTCTAAATTTTAGGCATTTAAGGAAT 10 95 1 ATTTTAGGCA 0.754368 -22 ATTAAACCATGTTTTTGCTAATCGTTAGCT 12 39 0 GTTTTTGCTA 0.456092 -63 TTTTTGTCATGTTTTAGCAAAAATCGTTCT 15 28 0 GTTTTAGCAA 0.622072 -42 TAACATAAAAGATTAAGCCTAACTTTAAAA 22 29 0 GATTAAGCCT 0.585479 -75 TTATCGTTAGGTTTTAGGTTTAAAGTT 22 87 1 GTTTTAGGTT 0.869006 -17 ********** Masking position 4 Map Score: 1.95082 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 769 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 14 TAAAAACAAAGCTAATAATATAACTATAAG 1 109 1 GCTAATAATA 0.936834 -178 CTACAATCTCGCTTAGAAAAAGGACACAAA 2 11 0 GCTTAGAAAA 0.593801 -98 TGGTATTATACCAAATAAACCCTAATGACC 2 65 0 CCAAATAAAC 0.642727 -44 TTTATAAAAAGCTAATAAAAGGCTAAAATT 5 42 1 GCTAATAAAA 0.927549 -147 ATAAATCGTTCCAAATAATAGCATGTTTTG 9 195 0 CCAAATAATA 0.868363 -96 GTCTCTAACGCCTTATAATAATAAATCGTT 9 215 0 CCTTATAATA 0.807563 -76 TCTAAAATTTGCTAAGAATACACTAAAATT 10 50 0 GCTAAGAATA 0.892377 -67 ATTTCTTTACGCTAAAAATAAACTCGTATT 13 201 0 GCTAAAAATA 0.676057 -22 TAAAAACACTCCTAATCATCTGTTTTAAGG 16 69 1 CCTAATCATC 0.505895 -101 CAAACTCAATCCTAATAAAACTGATGCAAA 16 150 0 CCTAATAAAA 0.946628 -20 TGATTTGATCCCTAATAAAATGACTTTT 17 9 0 CCTAATAAAA 0.946628 -20 CTTACGACCCCCAAAGAATACCTG 18 43 1 CCAAAGAATA 0.786683 -14 GTAATCGTCTTCTAATAAAAAAATCTTTTT 20 138 0 TCTAATAAAA 0.664495 -163 ********** Masking position 5 Map Score: 6.5279 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 214 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 15 ACTCATTTTTAAGGGGGATAGTTATCCAAA 4 11 0 AAGGGGGATA 0.904735 -195 TATTAAATTGAATGGGGTTTATCAATATTT 4 77 1 AATGGGGTTT 0.962925 -129 ACACCTACCTAATGGGGATTTTTTGTATTA 16 101 0 AATGGGGATT 0.9629 -69 TCTTTTTTTGCATGGGGGTATTGTAGCGCT 20 115 0 CATGGGGGTA 0.936266 -186 TTTACAATGAAATGGGGGTATTTTAAAAAA 20 232 0 AATGGGGGTA 0.975714 -69 ATTAAACTTCAATGGGTTTTGCATGAAAGA 20 264 0 AATGGGTTTT 0.800721 -37 ********** Masking position 2 Map Score: 1.58554 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 137 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604