AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_hpyl_reg_300.orf -o00450_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 Purged sequences: HP1141 23 methionyl-tRNA formyltransferase (fmt) HP1132 22 ATP synthase F1, subunit beta (atpD) Input sequences: #1 HP0106 24 cystathionine gamma-synthase (metB) #2 HP0107 38 cysteine synthetase (cysK) #3 HP0194 214 triosephosphate isomerase (tpi) #4 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #5 HP0417 168 methionyl-tRNA synthetase (metS) #6 HP1118 210 gamma-glutamyltranspeptidase (ggt) #7 HP1120 128 H. pylori predicted coding region HP1120 #8 HP1121 161 cytosine specific DNA methyltransferase (BSP6IM) #9 HP1122 274 H. pylori predicted coding region HP1122 #10 HP1125 66 peptidoglycan associated lipoprotein precursor (omp18) #11 HP1129 52 biopolymer transport protein (exbD) #12 HP1137 110 ATP synthase F0, subunit b' (atpF') #13 HP1142 39 H. pylori predicted coding region HP1142 #14 HP1143 243 H. pylori predicted coding region HP1143 #15 HP1512 153 iron-regulated outer membrane protein (frpB) #16 HP1513 226 selenocystein synthase (selA) Motif number 1 GGTTTTTCCTTTTTTATTGAATTT 1 1 0 TTTTTAATTT 0.8267 -24 AATTTTGAGTTTTTAGGAGCAGTTTTT 3 3 0 TTTTGAGTTT 0.913682 -212 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 3 22 0 TTTTGATTTT 0.924357 -193 ATTCTACTACATTTGAAATAATTTTTCTTATAAAC 3 73 1 ATTTAATTTT 0.835281 -142 TTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 3 94 0 ATTTGTGTTT 0.834309 -121 ACAATAGCCCCTTTGAATTGAATTTTTTCTCAATT 3 116 0 CTTTAAATTT 0.66725 -99 TCAAAGGGGCTATTGTTTAAAATTTACATTTTTTA 3 135 1 TATTTAATTT 0.5336 -80 AAAATGGGCTTATTATAGCTTATTTCATTCT 4 7 0 TATTTTATTT 0.502956 -58 TCCTTGAACTCTTTTTCAATTTTTTGAGCGTTAAT 5 19 1 CTTTTTTTTT 0.871018 -150 TTTGAGCGTTAATTATAATGAATTTTAAGCTAAAA 5 41 1 AATTTAATTT 0.380932 -128 ATTTATGCTTATTTGTGGGGTGTTTTTAGCTTAAA 5 64 0 ATTTTTGTTT 0.843562 -105 ATGCAACCTCTATTCTCTAAATTTTTAAAAGCATG 5 97 1 TATTTATTTT 0.758368 -72 AATAAGCCTTATTTAACTTATTTTTTAAACTCTAT 6 37 1 ATTTATTTTT 0.817686 -174 TTAAAACTCATTTTTGAGCCTTTTTTATAGCTAGC 6 77 1 TTTTGTTTTT 0.915312 -134 AACAAATCCTTTAGCTCTTGTTTCAGCCGTATT 7 106 0 CTTTGTGTTT 0.845256 -23 GTGATTTTGCTTTTCATTAAATTTTAGTTTCTCTG 8 51 1 TTTTAATTTT 0.904108 -111 TTTCTCTGTGTTTTAAAATGAGTTTGTTGCTTTCT 8 78 1 TTTTAAGTTT 0.890913 -84 TATTCCCTACCATTTGCTTTTTTTTATTTTGTTAT 9 70 1 CATTGTTTTT 0.601969 -205 GCTTTTTTTTATTTTGTTATATTTTAATTTTTTTA 9 85 1 ATTTGATTTT 0.867941 -190 GTTAATGGATTTTTGAAATCTGTTTTTGCAATTCC 9 215 0 TTTTATGTTT 0.878396 -60 AATCCATTAACTTTTTTTCTTTTTTGCCGATACTT 9 239 1 CTTTTTTTTT 0.871018 -36 AGCTTTTAAGGGGATTTTATAAATATCT 11 4 1 TTTTAATTTT 0.904108 -49 TATTCTCAAATTTTAAGCGATTTTTTGTTAAGATA 12 19 1 TTTTATTTTT 0.892922 -92 AGTTTCAAATATTTTGTAGGATTTTAGGAAAGAAA 12 80 1 ATTTGATTTT 0.867941 -31 CGTTATCTCAATTTCTTCATTTTTTTTATTTATAA 14 62 1 ATTTTTTTTT 0.861594 -182 GCGAAGGGTATTTTTTGCCTTTTTTATTTTTTGTT 14 109 1 TTTTTTTTTT 0.920473 -135 TTAATCACATTTTTCTTGGTATTTTCTTAATCCTA 15 27 1 TTTTTATTTT 0.929009 -127 TTTTTCTAAAAATTTAGTCAAGTTTTAAACCTAAG 15 106 0 AATTAAGTTT 0.51302 -48 CTTTTAGCCTTTTTATTTACTTTTTTCTAAAAATT 15 127 0 TTTTTTTTTT 0.920473 -27 CTATAGGGCTTTTTCATGTTTGTTTCCATGTTCAA 16 44 0 TTTTATGTTT 0.878396 -183 AAAAAAGTAGTTTTATCAAAAATTTAGCGGGTTTA 16 148 1 TTTTTAATTT 0.8267 -79 CGTTTGATTCCTTTTTTGAGAGTTTAAAATAAGCG 16 194 0 CTTTTAGTTT 0.868658 -33 **** * ***** Masking position 4 Map Score: 36.3551 Number of sites scoring better than the average of aligned sites = 3173 Number in coding regions = 2530 Number in noncoding regions = 643 Number of orfs with sites within 600 bp upstream = 333 Fraction of orfs with sites within 600 bp upstream = 0.0534854 Motif number 2 GGTTTTTCCTTTTTTATTGAATTT 1 7 0 CTTTTTTATT 0.846423 -18 TTGAAATAATTTTTCTTATAAACAAAACCT 3 85 1 TTTTCTTATA 0.839691 -130 CAAAGGGGCTATTGTTTAAAATTTACATTT 3 136 1 ATTGTTTAAA 0.65682 -79 TAAAATTTACATTTTTTAAACGCTATTAGA 3 152 1 ATTTTTTAAA 0.88683 -63 TGAACGATCCTTATTTTATAGGTGGTAACT 3 195 0 TTATTTTATA 0.834551 -20 ATACGAATGATTATTTTAATAAGGACAATC 4 44 1 TTATTTTAAT 0.834551 -21 TGGGGTGTTTTTAGCTTAAAATTCATTATA 5 54 0 TTAGCTTAAA 0.470459 -115 TTACCTTAAATTTGTTTAAATCTCTTAATT 5 136 0 TTTGTTTAAA 0.827509 -33 TATTTAACTTATTTTTTAAACTCTATCTAT 6 46 1 ATTTTTTAAA 0.88683 -165 TAAACTCTATCTATTTTAAAACTCATTTTT 6 62 1 CTATTTTAAA 0.862903 -149 ATTTTTGAGCCTTTTTTATAGCTAGCGCTC 6 86 1 CTTTTTTATA 0.900629 -125 TACTATGCCATTTTTTTATTGTAAAAACCC 7 68 0 TTTTTTTATT 0.878985 -61 GAGTTTGTTGCTTTCTTAAATAGGGCATGT 8 97 1 CTTTCTTAAA 0.867302 -65 ACCATTTGCTTTTTTTTATTTTGTTATATT 9 78 1 TTTTTTTATT 0.878985 -197 TATATTTTAATTTTTTTAATGTTCTTTATG 9 102 1 TTTTTTTAAT 0.922747 -173 GATTTTATAAATATCTTAAATAGGGAGTTA 11 23 1 ATATCTTAAA 0.592034 -30 ATTTCTTCATTTTTTTTATTTATAATGTAG 14 72 1 TTTTTTTATT 0.878985 -172 TATTTTTTGCCTTTTTTATTTTTTGTTGTT 14 117 1 CTTTTTTATT 0.846423 -127 TTAAGATTTGATTTTTTATATTTTATAATA 14 215 0 ATTTTTTATA 0.826546 -29 ATGCTAAAACTTTTTTTAATCACATTTTTC 15 12 1 TTTTTTTAAT 0.922747 -142 TTTCTTGGTATTTTCTTAATCCTAAAACAA 15 38 1 TTTTCTTAAT 0.83969 -116 GATAAAACTACTTTTTTAAAATCCTTAAGA 16 135 0 CTTTTTTAAA 0.937124 -92 AAAATAAGCGTTATTTTAAACTAAACCCGC 16 174 0 TTATTTTAAA 0.892415 -53 AAAATAACGCTTATTTTAAACTCTCAAAAA 16 187 1 TTATTTTAAA 0.892415 -40 ********** Masking position 6 Map Score: 31.7603 Number of sites scoring better than the average of aligned sites = 1479 Number in coding regions = 1127 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 3 AATCGCAAAATTGAATTTTATTGTTTGTT 2 9 1 AATGAATTTT 0.910834 -30 TTTAGGTTAATTTTGAGTTTTTAGGAGCAGT 3 15 0 TTTGAGTTTT 0.866304 -200 AGCCCCTTTGAATTGAATTTTTTCTCAATTT 3 115 0 AATGAATTTT 0.910834 -100 GCGTTAATTATAATGAATTTTAAGCTAAAAA 5 46 1 TATGAATTTT 0.930809 -123 AAAGGCTCAAAAATGAGTTTTAAAATAGATA 6 69 0 AATGAGTTTT 0.871354 -142 CCCCTTAAGAAATTGGGTTTTTACAATAAAA 7 54 1 AATGGGTTTT 0.934827 -75 GAATGATTGATTGGGGATTTTAACTTTT 8 144 1 TTGGGATTTT 0.92044 -18 TTGGTGGTGGTGATGGGTTTTTTTCCGGTTT 9 172 0 TGTGGGTTTT 0.902283 -103 GAAAAAAAGTTAATGGATTTTTGAAATCTGT 9 227 0 TATGGATTTT 0.966089 -48 AGCTTTTAAGGGGATTTTATAAATATCT 11 8 1 AAGGGATTTT 0.923626 -45 TCAAATATTTTGTAGGATTTTAGGAAAGAAA 12 84 1 TGAGGATTTT 0.775542 -27 GTTCAGTAAAATAGGGATTTTAAATACAAAC 14 144 0 ATGGGATTTT 0.8978 -100 TAGGATTTCTTTTTGAATTTTGAACATGGAA 16 25 1 TTTGAATTTT 0.907168 -202 TAAGATGCTCTTAAGGATTTTAAAAAAGTAG 16 127 1 TTAGGATTTT 0.836992 -100 ** ******** Masking position 8 Map Score: 13.1341 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 645 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 AACCTCTATTCTCTAAATTTTTAAAAGCATGT 5 101 1 CCTAAATTTT 0.972351 -68 TTGTTTAAATCTCTTAATTTTAACATGCTTTT 5 123 0 CCTTAATTTA 0.837259 -46 AATCGTGTTACCTTAAATTTGTTTAAATCTCT 5 141 0 CTTAAATTTT 0.963243 -28 ATCAGTTACGCTTAAAATTTCTTTGTTATTAT 6 175 0 CTAAAATTTT 0.866705 -36 TTTTGCTTTTCATTAAATTTTAGTTTCTCTGT 8 55 1 CTTAAATTTA 0.939213 -107 TTCAAAAATCCATTAACTTTTTTTCTTTTTTG 9 233 1 CTTAACTTTT 0.831509 -42 AACTCACATTCGCTTAATTTAACC 10 3 0 CCTTAATTTA 0.837259 -64 CAAAAAATCGCTTAAAATTTGAGAATATTCAA 12 14 0 CTAAAATTTA 0.793119 -97 TTTAATAATACCTTAAATTTGTTTTAGGATTA 15 54 0 CTTAAATTTT 0.963243 -100 TTTAAAACTTGACTAAATTTTTAGAAAAAAGT 15 112 1 GCTAAATTTT 0.804186 -42 AAACTAAACCCGCTAAATTTTTGATAAAACTA 16 155 0 CCTAAATTTT 0.972351 -72 * ******** * Masking position 6 Map Score: 10.8353 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 82 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 AGTTTTTAGGAGCAGTTTTT 3 1 0 AGCAGTTTTT 0.708554 -214 GCTTATTTGTGGGGTGTTTTTAGCTTAAAA 5 63 0 GGGGTGTTTT 0.92181 -106 TATAAGCGAGAGAGTGTTTTGTAAAGCTTG 6 141 1 AGAGTGTTTT 0.893386 -70 TTAAGGGGATAGGGGGTATTTTGAAATCAT 7 32 0 AGGGGGTATT 0.913966 -97 CTTCATTTCTAGGGGGTTTATTCTTGCTGT 8 23 1 AGGGGGTTTA 0.954012 -139 TCTTAAATAGGGCATGTTTTTAGTCGTGTG 8 110 1 GGCATGTTTT 0.777623 -52 AGCTTTTAAGGGGATTTTATAAATATCT 11 9 1 AGGGGATTTT 0.935289 -44 ATAGGGAGTTAGAAGGTTTTT 11 42 1 AGAAGGTTTT 0.893384 -11 TTTTATGCGAAGGGTATTTTTTGCCTTTTT 14 103 1 AGGGTATTTT 0.841526 -141 ATTTAACTTAAGCAGGTTTTATCCAATAAG 14 174 0 AGCAGGTTTT 0.961239 -70 TCAAAAATTTAGCGGGTTTAGTTTAAAATA 16 163 1 AGCGGGTTTA 0.943655 -64 ********** Masking position 7 Map Score: 8.31529 Number of sites scoring better than the average of aligned sites = 1229 Number in coding regions = 1064 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 TAGGTGGTAACTATCCCTTATTATATCTAA 3 177 0 CTATCCCTTA 0.964396 -38 CTGTCTATTCCTTGAACTCTTTTT 5 5 1 CTATTCCTTG 0.936379 -164 AATGCAACCTCTATTCTCTAAATTTTTAAA 5 96 1 CTATTCTCTA 0.815016 -73 AAAATACCCCCTATCCCCTTAAGAAATTGG 7 40 1 CTATCCCCTT 0.920317 -89 TTAAATACTCCTATACCTTA 9 1 0 CTATACCTTA 0.908513 -274 CAAAAATTGGCTATTCCCTACCATTTGCTT 9 59 1 CTATTCCCTA 0.975281 -216 TCTGTTTTTGCAATTCCTTACCAAATTTCT 9 202 0 CAATTCCTTA 0.87825 -73 AACCTATTTCTTTCCTAAAATCC 12 98 0 CTATTTCTTT 0.661642 -13 ********** Masking position 3 Map Score: 4.56353 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 82 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GGTTTTTCCTTTTTTATTGAA 1 14 0 GTTTTTCCTT 0.976383 -11 TTAAGGCAGTGTTTTTGCGTCAAGCGATTT 3 44 0 GTTTTTGCGT 0.916533 -171 TGATTGTCCTTATTAAAATAA 4 54 0 GATTGTCCTT 0.888014 -11 AAATGGCATAGTATTTGCTTGAATACGGCT 7 85 1 GTATTTGCTT 0.938022 -44 TTTCTAGGGGGTTTATTCTTGCTGTGATTT 8 28 1 GTTTATTCTT 0.792071 -134 TTCTTGCTGTGATTTTGCTTTTCATTAAAT 8 43 1 GATTTTGCTT 0.962646 -119 GATTTTCCTTTAAGATTTGA 14 234 0 GATTTTCCTT 0.962646 -10 ATTTTTCTTGGTATTTTCTTAATCCTAAAA 15 35 1 GTATTTTCTT 0.87042 -119 ********** Masking position 6 Map Score: 4.22936 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 131 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 TATAACAAACAATAAAATTCAATTTTGCGATT 2 10 0 AATAAATAAT 0.662042 -29 CCACCTATAAAATAAGGATCGTTCA 3 200 1 AATAAGTGTT 0.710335 -15 AGAATGAAATAAGCTATAATAAGCCCATTT 4 8 1 AATAAGAAAT 0.761538 -57 GCCCATTTTGAATACGAATGATTATTTTAATAA 4 33 1 AATACGTATT 0.832407 -32 ACACCCCACAAATAAGCATAAATGCAACCTCTA 5 76 1 AATAAGTAAT 0.964948 -93 AAATAAGTTAAATAAGGCTTATTTGATCAAAAC 6 27 0 AATAAGTATT 0.497877 -184 AAGGCTCAAAAATGAGTTTTAAAATAGATAGAG 6 66 0 AATGAGTAAA 0.710764 -145 GCTAGCTATAAAAAAGGCTCAAAAATGAGTTTT 6 79 0 AAAAAGTAAA 0.762691 -132 TATTTGCTTGAATACGGCTGAAACAAGAGCTAA 7 96 1 AATACGTAAA 0.832553 -33 ATCAAATTTTAATAAGTGTAAATATTAACTCAC 10 28 0 AATAAGTAAT 0.964948 -39 AAAAGTAAATAAAAAGGCTAAAAGAA 15 138 1 AAAAAGTAAA 0.762718 -16 GAGAGTTTAAAATAAGCGTTATTTTAAACTAAA 16 179 0 AATAAGTATT 0.783443 -48 ****** * *** Masking position 2 Map Score: 6.35041 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 171 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 TATTATATCTAATAGCGTTTAAAAAATGTA 3 159 0 AATAGCGTTT 0.945922 -56 AAATTTAGAGAATAGAGGTTGCATTTATGC 5 91 0 AATAGAGGTT 0.754324 -78 GTTTTCTACCCATAGCGTTTTGATCAAATA 6 11 1 CATAGCGTTT 0.909101 -200 TTTTAAAATAGATAGAGTTTAAAAAATAAG 6 53 0 GATAGAGTTT 0.956293 -158 AAAGGCTCAAAAATGAGTTTTAAAATAGAT 6 70 0 AAATGAGTTT 0.721033 -141 TTATAAGCGAGAGAGTGTTTTGTAAAGCTT 6 140 1 GAGAGTGTTT 0.635485 -71 CCCCTTAAGAAATTGGGTTTTTACAATAAA 7 54 1 AATTGGGTTT 0.855056 -75 CTGTGTTTTAAAATGAGTTTGTTGCTTTCT 8 83 1 AAATGAGTTT 0.721033 -79 AGAGCCAAACGATTGCGATTGCAAACTTTT 9 135 0 GATTGCGATT 0.772365 -140 TTTTTGTTAAGATAGAGTTAATGTTTTTAT 12 40 1 GATAGAGTTA 0.699556 -71 AGTTCAGTAAAATAGGGATTTTAAATACAA 14 146 0 AATAGGGATT 0.674098 -98 GAACTTTTTCCATAGAGTTTGGCGGTTTCT 16 77 0 CATAGAGTTT 0.902273 -150 GATGAGTGCGTTTGATTCCTTTT 16 214 0 GAGTGCGTTT 0.85323 -13 ********** Masking position 2 Map Score: 5.54187 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 572 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 GGTTTTTCCTTTTTTATTGAATT 1 12 0 TTTTCCTTTT 0.611044 -13 ATTGAATTTTATTGTTTGTTATAGGAGAA 2 20 1 ATTGTTTGTT 0.634939 -19 TACGCTTAAAATTTCTTTGTTATTATAACA 6 171 0 ATTTCTTTGT 0.879696 -40 ATACTATGCCATTTTTTTATTGTAAAAACC 7 69 0 ATTTTTTTAT 0.370201 -60 TTCCCTACCATTTGCTTTTTTTTATTTTGT 9 72 1 TTTGCTTTTT 0.772851 -203 TCCTTACCAAATTTCTTGGTGGTGGTGATG 9 188 0 ATTTCTTGGT 0.888047 -87 CATTAACTTTTTTTCTTTTTTGCCGATACT 9 243 1 TTTTCTTTTT 0.915034 -32 ATTTTAAGCGATTTTTTGTTAAGATAGAGT 12 28 1 ATTTTTTGTT 0.846278 -83 CAATTTCTTCATTTTTTTTATTTATAATGT 14 70 1 ATTTTTTTTA 0.31721 -174 TGCCTTTTTTATTTTTTGTTGTTTGTATTT 14 124 1 ATTTTTTGTT 0.846278 -120 TTAATCACATTTTTCTTGGTATTTTCTTAA 15 27 1 TTTTCTTGGT 0.843168 -127 AGCCTTTTTATTTACTTTTTTCTAAAAATT 15 127 0 TTTACTTTTT 0.55504 -27 GAATCTTAGGATTTCTTTTTGAATTTTGAA 16 19 1 ATTTCTTTTT 0.940792 -208 CTATAGGGCTTTTTCATGTTTGTTTCCATG 16 49 0 TTTTCATGTT 0.534849 -178 AGTGCGTTTGATTCCTTTTTTGAGAGTTTA 16 203 0 ATTCCTTTTT 0.731743 -24 ********** Masking position 7 Map Score: 6.08514 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 933 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 11 AAACTCTATCTATTTTAAAACTCATTTTTG 6 63 1 TATTTTAAAA 0.79566 -148 ATTTCTTTGTTATTATAACACAAGCTTTAC 6 161 0 TATTATAACA 0.870525 -50 GCCATTTTTTTATTGTAAAAACCCAATTTC 7 62 0 TATTGTAAAA 0.767196 -67 TTTAAGGGGATTTTATAAATATCTTAAATA 11 15 1 TTTTATAAAT 0.485725 -38 GAGTTAATGTTTTTATAACAAATGCGAGTT 12 54 1 TTTTATAACA 0.637498 -57 GATCTCATTCTATTATAAAATATAAAAAAT 14 205 1 TATTATAAAA 0.723379 -39 AAATTTAAGGTATTATTAAATAGAATAATG 15 66 1 TATTATTAAA 0.774933 -88 AACCTAAGGTTATTATTACATTATTCTATT 15 84 0 TATTATTACA 0.693408 -70 TTATTTACTTTTTTCTAAAAATTTAGTCAA 15 120 0 TTTTCTAAAA 0.613063 -34 ATAAAACTACTTTTTTAAAATCCTTAAGAG 16 134 0 TTTTTTAAAA 0.637801 -93 AAAAAAGTAGTTTTATCAAAAATTTAGCGG 16 148 1 TTTTATCAAA 0.593378 -79 ********** Masking position 8 Map Score: 4.00573 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 214 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 12 CATTATAATTAACGCTCAAAAAATTGAAAA 5 31 0 AACGCTCAAA 0.976697 -138 AGCTATAAAAAAGGCTCAAAAATGAGTTTT 6 79 0 AAGGCTCAAA 0.955752 -132 TTTTATAGCTAGCGCTCAAACCATTAATAG 6 99 1 AGCGCTCAAA 0.947429 -112 TTCAATCAGTTACGCTTAAAATTTCTTTGT 6 181 0 TACGCTTAAA 0.720553 -30 CTAGAAATGAAGCCCTTAAACCCC 8 5 0 AGCCCTTAAA 0.699994 -157 TTAACAAAAAATCGCTTAAAATTTGAGAAT 12 20 0 ATCGCTTAAA 0.761852 -91 AAAAATAAAAAAGGCAAAAAATACCCTTCG 14 110 0 AAGGCAAAAA 0.633737 -134 AATGCTAAAACTTTTTTTAA 15 1 1 AATGCTAAAA 0.858033 -153 GTATTTTCTTAATCCTAAAACAAATTTAAG 15 45 1 AATCCTAAAA 0.617756 -109 AGTAAATAAAAAGGCTAAAAGAA 15 141 1 AAGGCTAAAA 0.93159 -13 GCTTATTTTAAACTCTCAAAAAAGGAATCA 16 195 1 AACTCTCAAA 0.804264 -32 ********** Masking position 8 Map Score: 6.29019 Number of sites scoring better than the average of aligned sites = 1302 Number in coding regions = 1182 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 13 TTCTACTACATTTGAAATAATTTTTCTTAT 3 74 1 TTTGAAATAA 0.698265 -141 CAAAACCTAAATTGAGAAAAAATTCAATTC 3 107 1 ATTGAGAAAA 0.88973 -108 TTTTAAAAATTTAGAGAATAGAGGTTGCAT 5 97 0 TTAGAGAATA 0.715037 -72 ATAGCCAATTTTTGAGATTAGAACTATTCA 9 43 0 TTTGAGATTA 0.92816 -232 TCGCTTAAAATTTGAGAATATTCAAGCG 12 9 0 TTTGAGAATA 0.940881 -102 TGTGGTGTGCTTTGAGATGATATTGTGAAT 13 15 1 TTTGAGATGA 0.88343 -25 AAATGAAGAAATTGAGATAACGATCGATCA 14 54 0 ATTGAGATAA 0.867544 -190 TTGACTAAATTTTTAGAAAAAAGTAAATAA 15 120 1 TTTTAGAAAA 0.708056 -34 CCGCTAAATTTTTGATAAAACTACTTTTTT 16 148 0 TTTGATAAAA 0.733621 -79 ********** Masking position 5 Map Score: 3.04636 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 188 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 ********** No masking Map Score: 9.6877e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 9.6877e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0