AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_hpyl_reg_100.orf -o00561_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 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0214 95 sodium-dependent transporter (huNaDC-1) #4 HP0497 228 sodium- and chloride-dependent transporter #5 HP0654 296 conserved hypothetical protein #6 HP0655 82 protective surface antigen D15 #7 HP0664 37 H. pylori predicted coding region HP0664 #8 HP0698 187 H. pylori predicted coding region HP0698 #9 HP0699 39 H. pylori predicted coding region HP0699 #10 HP0737 146 conserved hypothetical integral membrane protein #11 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #12 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #13 HP1015 111 H. pylori predicted coding region HP1015 #14 HP1067 290 chemotaxis protein (cheY) #15 HP1154 130 H. pylori predicted coding region HP1154 #16 HP1350 209 protease #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) Motif number 1 ATAAAGATAGTCATAGCGTCTTAAAACAAACACCCATTA 1 73 1 TAATTAAAAA 0.958789 -185 TTGAAAATAATAACACAACTTAAAAAAAACTACCCTTAA 1 152 1 TAATAAAAAA 0.969962 -106 AAAAACTGCTCCTAAAAACTCAAAATTAACCTAAAATC 2 10 1 TCATCAAAAA 0.812671 -205 TTATTATATCTAATAGCGTTTAAAAAATGTAAATTTTAA 2 151 0 TAATAAAAAG 0.927702 -64 AAGATTTTAGAAAAATCATATCAAAATAGGAAAAAGA 3 9 0 AAATCAAAAG 0.634206 -87 CATGCTACAATAAAACTTTTTCAAAACTAAGATTTTAGA 3 37 0 TAATCAAAAA 0.939123 -59 ACTTAAATAATGAAATTTTCTTAAAATTATACAATATGT 4 22 1 TAATTAAAAA 0.958787 -207 AAACCCACTTTAAAAATACCTAAAAAATACAGAGCAACG 4 87 0 TAATAAAAAA 0.969962 -142 CTTAAGATCTTTAAAGATTTTAAAAACTAATACAGCAAT 4 136 1 TAATAAAAAA 0.969962 -93 AATGAGAGTATGAAAATTTTTAAAAATTTACAAAAATGA 5 75 1 TAATAAAAAT 0.777798 -222 ATCTATTTAATGAGAATTAGGTAAAAAAAGGGGTTGGCA 5 163 1 TAAGTAAAAA 0.7666 -134 GGATATTTTTATATAATATGTAAAAAGCATTCTTAAATC 5 221 1 AAATAAAAAA 0.901314 -76 CTAATCATTCTTAAAAACGCTAAAAATTA 6 1 0 TAATAAAAAA 0.969962 -82 CGAAATTGGATACAATCAGCTTAAAAAGGATATAAA 7 12 1 TCATTAAAAG 0.722206 -26 ATACCTAGTATTAAATCAAAAAAAAAGAAAAAAGCTTAA 8 129 0 TAAAAAAAAA 0.625658 -59 CTTTTCCTTGTTAGGTGGAATTAAAATTATACCTAGTAT 8 157 0 TAGTTAAAAA 0.827117 -31 ATGATAACTTTTAAATTCTCTCAAAAATTAAAGGTTAAT 10 15 0 TAATCAAAAT 0.625783 -132 GTTATCATACTAAAACGTGCTTAAAATTAAGCCTTATTG 10 46 1 TAATTAAAAA 0.958789 -101 AATGCTAAAATGCCATGATTTAAAAAGAATTTAAGGCAA 10 115 1 TCATAAAAAA 0.900802 -32 GATCAAACTCCCTAAAAACGATTGCAATAAA 11 57 0 TAATAAAAAA 0.969962 -21 TATACATATTAAATAATATTTTAAAATTAAAAAGCG 12 8 0 AAATTAAAAA 0.868077 -124 AACAAAGAGTTGCAATTCATTAAAAAATGCTTGTTGGGC 13 47 1 TCATAAAAAG 0.783007 -65 ATAGCCCCACACAAAGGGGCGAAAAAATAGCCCAACAAG 13 76 0 AAAGAAAAAA 0.5632 -36 TTGTTTGCTATGATAATCGTTTAAAAGTAATAAAATAAC 14 76 0 TAATTAAAAA 0.958789 -215 AGCCTAATTTAAATGCAATCTTAAAAGGAGAAGCACT 14 264 1 AAGTTAAAAA 0.575037 -27 GGTTATAAAAAAACACTCCCTTAAAAAAGACACCGCTTT 19 17 0 AAATTAAAAG 0.723356 -67 GTTTTCATTATAACGCTCCTTAAAAAACATAGGAAGTAT 20 55 1 TAGTAAAAAA 0.869117 -246 CATTGAAGTTTAATAAAAGGTAAAAATAAGA 20 280 1 TAATAAAAAA 0.969962 -21 * * * ****** * Masking position 13 Map Score: 37.4441 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 423 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 TTAAAAAAAACTACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 171 1 CTTAAATAAA 0.690988 -87 TCTAAAATTCTTAAATTAAAATATAGCTATAATACACTAAAACAAT 1 200 1 TTTAAATTCA 0.935773 -58 AAACTCAAAATTAACCTAAAATCGCTTGACGCAAAAACACTGCCTT 2 26 1 TTTAAACAAA 0.825507 -189 TCAATTTAGGTTTTGTTTATAAGAAAAATTATTTCAAATGTAGTAG 2 76 0 TTTATATTCA 0.714081 -139 TGAGAAAAAATTCAATTCAAAGGGGCTATTGTTTAAAATTTACATT 2 119 1 TTTAAATTAA 0.976266 -96 TTTGATATGATTTTTCTAAAATCTTAGTTTTGAAAAAGTTTTATTG 3 23 1 TTTAAATAAA 0.962531 -73 AATAATGAAATTTTCTTAAAATTATACAATATGTAACTTAACTATA 4 27 1 TTTAAATGAA 0.916999 -202 TAAAGTGGGTTTTTTCTTAAATCTTAAGATCTTTAAAGATTTTAAA 4 114 1 TTTAAATTAA 0.976277 -115 TTGTCAATGATTAAAATTAAAGAGCGATGTCCTTAATCGTCCAACT 4 175 0 TTTAAATTAA 0.976132 -54 AAATAGATTTTTATGATAAAATCTAAGCTTTATCAAGCCATTAGCC 5 125 0 TTTAAATTAA 0.976278 -172 TTAGGTGGAATTAAAATTATACCTAGTATTAAATCAAAAAAAAAGA 8 140 0 TTTATATACA 0.609266 -48 AGCATTTTATTTGCATTAAAAAGCGATTTTCTTAAACAATAAGGCT 10 75 0 TTTAAATTAA 0.97605 -72 AAACGCTGTCTTTGATTGAAACATATACATATTAAATAATATTTTA 12 24 0 TTTAAATTAA 0.976274 -108 TTTAAACTTATTATTGTAAAATGGTGAGTTTTACAATCAATGAGAT 12 86 1 TTTAAATAAA 0.962538 -46 AGTTATTTTATTACTTTTAAACGATTATCATAGCAAACAAACTGAA 14 75 1 TTTAAAAGAA 0.489885 -216 CCTTTTAAGATTGCATTTAAATTAGGCTCTTTTTAAACAGCCAAAG 14 246 0 TTTAAATTAA 0.976255 -45 TATTATCCTAAAATAGAGCGTTCCTTAAAAAATGGTTG 15 3 1 TTTAAATTAA 0.976277 -128 GACTATCCTTTTTAATTTAAATGCTTTGTTGTATAATTTTGAAAAA 15 93 0 TTTAAATAAA 0.961703 -38 CCATTTTTGAGATTAGAAAGAATCACCTTTAAGGTTTTATTC 16 178 0 TTTAGACTAA 0.433649 -32 CTAATTGCCTTTATACTAAAAGCGGTTATAAAAAAACACTCCCTTA 19 33 0 TTTAAAAAAA 0.726361 -51 GCTTCGTTCGTTTTCATTATAACGCTCCTTAAAAAACATAGGAAGT 20 46 1 TTTATATAAA 0.814921 -255 GGTAATCGTCTTCTAATAAAAAAATCTTTTTTTGCATGGGGGTATT 20 123 0 TTTAAATTCA 0.935767 -178 TGAAAGAATTTTACAATGAAATGGGGGTATTTTAAAAAAATGAGTC 20 225 0 TTTAAATTAA 0.976274 -76 ** * *** * * ** Masking position 7 Map Score: 34.9759 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 211 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 CAATTCAAAGGGGCTATTGTTTAAAATTTA 2 131 1 GGGCTATTGT 0.986515 -84 ATTTTTAAAGTGGGTTTTTTCTTAAATCTT 4 109 1 TGGGTTTTTT 0.763292 -120 GGGTTAAAAGGGGATATTTTTATATAATAT 5 210 1 GGGATATTTT 0.94081 -87 AATAAAATAAGGGGTTTTTT 9 30 1 GGGGTTTTTT 0.976148 -10 TTGAATGTAAGGGCTATTTTAAACTTATTA 12 69 1 GGGCTATTTT 0.990361 -63 AATGCTTGTTGGGCTATTTTTTCGCCCCTT 13 72 1 GGGCTATTTT 0.990361 -40 CCTTTGTGTGGGGCTATTCTGTTA 13 98 1 GGGCTATTCT 0.964651 -14 GGGGGTATTGTAGCGCTAATT 19 73 0 GGGGTATTGT 0.986515 -11 CTTAATGAGCGGGCTTTGTTATAATACTTC 20 87 0 GGGCTTTGTT 0.88515 -214 TTTTTGCATGGGGGTATTGTAGCGCTTAAT 20 111 0 GGGGTATTGT 0.986515 -190 CAATGAAATGGGGGTATTTTAAAAAAATGA 20 228 0 GGGGTATTTT 0.990361 -73 ********** Masking position 5 Map Score: 21.5458 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 185 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 ATTCAATTCAAAGGGGCTATTGTTTAAAAT 2 128 1 AAGGGGCTAT 0.561222 -87 CCTATAAAATAAGGATCGTTCA 2 203 1 AAGGATCGTT 0.711095 -12 TAGTATAATCTAAGGGCGTTGCTCTGTATT 4 71 1 TAAGGGCGTT 0.785742 -158 GATTAAAATTAAAGAGCGATGTCCTTAATC 4 183 0 AAAGAGCGAT 0.879166 -46 ATTAGGTAAAAAAAGGGGTTGGCATCAATA 5 178 1 AAAAGGGGTT 0.919702 -119 GTTGGCATCAATAGGGGGTTAAAAGGGGAT 5 195 1 ATAGGGGGTT 0.897501 -102 ATAGGGGGTTAAAAGGGGATATTTTTATAT 5 205 1 AAAAGGGGAT 0.751655 -92 CTTTTTATGAAAGAGGCTTTATGCCTCTTG 8 23 1 AAGAGGCTTT 0.750117 -165 TTTCAATAAAATAAGGGGTTTTTT 9 26 1 ATAAGGGGTT 0.844476 -14 TATTTGCATTAAAAAGCGATTTTCTTAAAC 10 84 0 AAAAAGCGAT 0.818746 -63 TTTACCTAAAAAAAGGCTTTTGAATTTTCT 11 16 0 AAAAGGCTTT 0.798219 -62 TGGAGCGTTCAATGAGCGTTCTTATTTGTA 14 127 0 AATGAGCGTT 0.73066 -164 CATTGGCTAAATGGAGCGTTCAATGAGCGT 14 138 0 ATGGAGCGTT 0.908385 -153 CCTTATAATAATAAATCGTTCCAAATAATA 14 205 0 ATAAATCGTT 0.488841 -86 ATTTATTATTATAAGGCGTTAGAGACGCTT 14 219 1 ATAAGGCGTT 0.940801 -72 TTATCCTAAAATAGAGCGTTCCTTAAAAAA 15 13 1 ATAGAGCGTT 0.928845 -118 GCGTTCCTTAAAAAATGGTTGGATTTGGAA 15 28 1 AAAAATGGTT 0.408031 -103 GCGTAAAAGCAAAAGGCGTTCCAAATCCAA 15 46 0 AAAAGGCGTT 0.971033 -85 AAAACTTTTCAGGGGGCGTTTGAACTTCTT 18 16 1 AGGGGGCGTT 0.856804 -41 TATGTTTTTTAAGGAGCGTTATAATGAAAA 20 56 0 AAGGAGCGTT 0.954345 -245 ********** Masking position 10 Map Score: 18.859 Number of sites scoring better than the average of aligned sites = 2328 Number in coding regions = 2100 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 ATTCTTAAATTAAAATATAGCTATAATACACT 1 206 1 TAAATATGCT 0.635593 -52 TTACCACCTATAAAATAAGGATCGTTCA 2 197 1 TAAATAAGAT 0.700302 -18 ACCTCCATGCTACAATAAAACTTTTTCAAAAC 3 49 0 TAAATAAACT 0.606372 -47 TTTAAAAATTTACAAAAATGAGAAAGAACACC 5 93 1 TAAAAAAGAG 0.805368 -204 GAGAATTAGGTAAAAAAAGGGGTTGGCATCAA 5 174 1 TAAAAAAGGG 0.774291 -123 CATTCTTAAATCTAAAAATGCTACAATGTTTA 5 248 1 TCAAAAAGCT 0.643843 -49 AATGATTAGTTATAATAACGCTACTAACAACA 6 31 1 TAAATAAGCT 0.941487 -52 ATCAAAAAAAAAGAAAAAAGCTTAAATTTTTT 8 122 0 AAAAAAAGCT 0.913671 -66 ATACTTTCAATAAAATAAGGGGTTTTTT 9 22 1 TAAATAAGGG 0.726572 -18 GATTTTCTTAAACAATAAGGCTTAATTTTAAG 10 65 0 AAAATAAGCT 0.891281 -82 CTTATTGTTTAAGAAAATCGCTTTTTAATGCA 10 78 1 AAAAAATGCT 0.534289 -69 TTTTTAATGCAAATAAAATGCTAAAATGCCAT 10 99 1 AATAAAAGCT 0.633006 -48 TATATTTACCTAAAAAAAGGCTTTTGAATTTT 11 18 0 TAAAAAAGCT 0.95407 -60 AATATTTTAAAATTAAAAAGCG 12 1 0 AATAAAAGCG 0.702909 -131 CTCACCATTTTACAATAATAAGTTTAAAATAG 12 82 0 TAAATAAAAG 0.234811 -50 TTGCAATTCATTAAAAAATGCTTGTTGGGCTA 13 56 1 TTAAAAAGCT 0.54949 -56 TTTTTTTACAAATAAGAACGCTCATTGAACGC 14 121 1 AAAAGAAGCT 0.606896 -170 AACGATTTATTATTATAAGGCGTTAGAGACGC 14 215 1 TATATAAGCG 0.782468 -76 TATTATCCTAAAATAGAGCGTTCCTTAAAA 15 9 1 TAAATAGGCG 0.667876 -122 AAAAGCGTAAAAGCAAAAGGCGTTCCAAATCC 15 48 0 AACAAAAGCG 0.581209 -83 TAAACGATACAACAAAAACGCGTAACTCCCCG 16 82 0 AAAAAAAGCG 0.935556 -128 TAAAATAAAGCGGTGTCTTTTT 19 1 1 TAAATAAGCG 0.956656 -83 AAAGCGGTTATAAAAAAACACTCCCTTAAAAA 19 29 0 TAAAAAAACT 0.665408 -55 GGGGGTATTTTAAAAAAATGAGTCAGTCAAGG 20 217 0 TAAAAAAGAG 0.805368 -84 ** ***** *** Masking position 7 Map Score: 18.3713 Number of sites scoring better than the average of aligned sites = 1474 Number in coding regions = 1289 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 6 AAAAAGTTTTATTGTAGCATGGAGGTTAGT 3 55 1 ATTGTAGCAT 0.973282 -41 TTGTCCCATAATTATAGCATAAATGATAAT 5 36 1 ATTATAGCAT 0.849308 -261 TAAAGCTTAGATTTTATCATAAAAATCTAT 5 139 1 ATTTTATCAT 0.660809 -158 AAAGATAAACATTGTAGCATTTTTAGATTT 5 255 0 ATTGTAGCAT 0.973282 -42 TAATTTTTAGCGTTTTTAAGAAT 6 4 1 TTTTTAGCGT 0.808463 -79 TCCTTAATAGATTTTAGCTTGAGTGTTGTT 6 56 0 ATTTTAGCTT 0.849343 -27 AAATCATGGCATTTTAGCATTTTATTTGCA 10 106 0 ATTTTAGCAT 0.964473 -41 GGAACGCTCTATTTTAGGATAATA 15 5 0 ATTTTAGGAT 0.742779 -126 TACGCTTTTAATTGTTGCGTATTTTTTCAA 15 71 1 ATTGTTGCGT 0.916368 -60 GTTTTATTCAATTTTTGCGTTTATTCTATC 16 157 0 ATTTTTGCGT 0.890888 -53 GGGGGTATTGTAGCGCTAATTGCCTT 19 68 0 ATTGTAGCGC 0.944286 -16 GCATGGGGGTATTGTAGCGCTTAATGAGCG 20 106 0 ATTGTAGCGC 0.944286 -195 ********** Masking position 5 Map Score: 11.7846 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 180 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 AAGAGTGTGAATTGGCATGATTTAAGAGTAATGG 1 106 0 ATTGCATGAA 0.957415 -152 ATTAACCTAAAATCGCTTGACGCAAAAACACTGC 2 35 1 AATGCTTGAA 0.926697 -180 GTCCCATAATTATAGCATAAATGATAATGAAAAA 5 38 1 TATGCATAAA 0.533581 -259 AACACCGGCTAATGGCTTGATAAAGCTTAGATTT 5 119 1 AATGCTTGAA 0.926597 -178 CTTAATAGATTTTAGCTTGAGTGTTGTTAGTAGC 6 50 0 TTTGCTTGAT 0.61 -33 ACTGATTTCCTTAATAGATTTTAGCTTG 6 65 0 ATTCCTTAAA 0.814131 -18 ATTGAAGAAAATTTGCTTGAGTTAAATCAACCCA 8 65 0 ATTGCTTGAA 0.970737 -123 TTAGCATTTTATTTGCATTAAAAAGCGATTTTCT 10 89 0 ATTGCATTAA 0.639196 -58 AAAATGCTAAAATGCCATGATTTAAAAAGAATTT 10 113 1 AATCCATGAA 0.81357 -34 TCTATCTATATTTACCTAAAAAAAGGCTTTTGAA 11 22 0 TTTCCTAAAA 0.377555 -56 GTGGATAATGTTTTGCAAGAAATATCT 13 4 0 TTTGCAAGAA 0.755063 -108 GACAATAATCATTGGCTAAATGGAGCGTTCAATG 14 143 0 ATTGCTAAAA 0.698105 -148 TTTGATTAAAATTACCTTGACCGACAATAATCAT 14 165 0 ATTCCTTGAA 0.944123 -126 GAAAATTTAGATTGCCTTGACTGACTCATTTTTT 20 203 1 ATTCCTTGAA 0.944123 -98 CTTCAATGGGTTTTGCATGAAAGAATTTTACAAT 20 254 0 TTTGCATGAA 0.9204 -47 *** ****** * Masking position 10 Map Score: 7.84418 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 309 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 TTAATTTAAGAATTTTAGATTGATTTTTTT 1 189 0 AATTTTAGAT 0.898609 -69 GGCTAAATTTTGAAACCTTGAGAT 1 244 0 AAATTTTGAA 0.498875 -14 CTATTGTTTAAAATTTACATTTTTTAAACG 2 144 1 AAATTTACAT 0.836004 -71 TCAAAACTAAGATTTTAGAAAAATCATATC 3 26 0 GATTTTAGAA 0.761923 -70 ATTTTCTTAAAATTATACAATATGTAACTT 4 36 1 AATTATACAA 0.768872 -193 AAATTTTTAAAAATTTTCATACTCTCATTT 5 74 0 AAATTTTCAT 0.419277 -223 AAATTTTTAAAAATTTACAAAAATGAGAAA 5 88 1 AAATTTACAA 0.887478 -209 ACATTGTAGCATTTTTAGATTTAAGAATGC 5 247 0 ATTTTTAGAT 0.431281 -50 TTTTTTAGGTAAATATAGATAGACTTTATT 11 33 1 AAATATAGAT 0.495507 -45 CGCTTTTTAATTTTAAAATATTATTTAA 12 9 1 AATTTTAAAA 0.573433 -123 TAAAACTCACCATTTTACAATAATAAGTTT 12 89 0 CATTTTACAA 0.661169 -43 TAAAATGGTGAGTTTTACAATCAATGAGAT 12 102 1 AGTTTTACAA 0.782187 -30 GAAAGACAAGGATTTTACAAGTAA 14 5 0 GATTTTACAA 0.782187 -286 ATTTTTTCAAAATTATACAACAAAGCATTT 15 91 1 AATTATACAA 0.768872 -40 ATGTTATCTAAATTTTAGATAGAATAAACG 16 140 1 AATTTTAGAT 0.898609 -70 AATTTTATGAAGTTTTAGAAAACCTTTTCA 20 14 0 AGTTTTAGAA 0.761923 -287 GACTCATTGAAAATTTAGATTGCCTTGACT 20 195 1 AAATTTAGAT 0.819592 -106 TGCATGAAAGAATTTTACAATGAAATGGGG 20 245 0 AATTTTACAA 0.938975 -56 ********** Masking position 6 Map Score: 9.26314 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 265 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 AACTACCCTTAAAAAAATCAATCTAAAATT 1 179 1 AAAAAAATCA 0.764983 -79 TTTGTTTATAAGAAAAATTATTTCAAATGT 2 81 0 AGAAAAATTA 0.811252 -134 CTAAATTGAGAAAAAATTCAATTCAAAGGG 2 113 1 AAAAAATTCA 0.917476 -102 CTAAGATTTTAGAAAAATCATATCAAAATA 3 20 0 AGAAAAATCA 0.839321 -76 TATAATTTTAAGAAAATTTCATTATTTAAG 4 23 0 AGAAAATTTC 0.698463 -206 AAAAATACCTAAAAAATACAGAGCAACGCC 4 85 0 AAAAAATACA 0.522596 -144 TGAAAATTTTTAAAAATTTACAAAAATGAG 5 85 1 TAAAAATTTA 0.631478 -212 TTAGGATTGAAGAAAATTTGCTTGAGTTAA 8 74 0 AGAAAATTTG 0.698463 -114 GCTGCAAATTAAAAAATTTAAGCTTTTTTC 8 112 1 AAAAAATTTA 0.901474 -76 TTAATTTTTGAGAGAATTTAAAAGTTATCA 10 23 1 AGAGAATTTA 0.80999 -124 CATGATTTAAAAAGAATTTAAGGCAATGA 10 128 1 AAAGAATTTA 0.726502 -19 TTTTAAGAAAATTCAAAAGCCTTTT 11 6 1 AGAAAATTCA 0.946909 -72 CTTATTTGTAAAAAAATTCAGTTTGTTTGC 14 107 0 AAAAAATTCA 0.917476 -184 TTTGACTCATTGAAAATTTAGATTGCCTTG 20 192 1 TGAAAATTTA 0.733035 -109 ********** Masking position 5 Map Score: 9.53941 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 303 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 GATTTAAGAGTAATGGGTGTTTGTTTTAAG 1 92 0 TAATGGGTGT 0.849476 -166 ATTTCAAGTCTAAAGAGTGTGAATTGGCAT 1 122 0 TAAAGAGTGT 0.610115 -136 ACCTATAAAATAAGGATCGTTCA 2 202 1 TAAGGATCGT 0.54233 -13 GGTATTTTTAAAGTGGGTTTTTTCTTAAAT 4 106 1 AAGTGGGTTT 0.4688 -123 TAATCATTGACAAGGAGTTTGGTAGTTAAG 4 208 1 CAAGGAGTTT 0.938984 -21 ATGAAAAAGTAAATGAGAGTATGAAAATTT 5 64 1 AAATGAGAGT 0.433335 -233 TTCAATAAAATAAGGGGTTTTTT 9 27 1 TAAGGGGTTT 0.89293 -13 CAATCGTTTTTAGGGAGTTTGATC 11 64 1 TAGGGAGTTT 0.860838 -14 GTTTTACAATCAATGAGATTAGGAATTTA 12 113 1 CAATGAGATT 0.592008 -19 AAAAGAAAGACAAGGATTTTACAAGTAA 14 9 0 CAAGGATTTT 0.605594 -282 ATGGAGCGTTCAATGAGCGTTCTTATTTGT 14 128 0 CAATGAGCGT 0.873501 -163 CAAAACTTTTCAGGGGGCGTTTGAACTTCT 18 15 1 CAGGGGGCGT 0.872165 -42 TGTCTTTTTTAAGGGAGTGTTTTTTTATAA 19 24 1 AAGGGAGTGT 0.818315 -60 CTATGTTTTTTAAGGAGCGTTATAATGAAA 20 57 0 TAAGGAGCGT 0.922339 -244 GCGAGAGCGTTAAGGAGTTTGACTCATTGA 20 175 1 TAAGGAGTTT 0.917619 -126 TATTAAACTTCAATGGGTTTTGCATGAAAG 20 265 0 CAATGGGTTT 0.829025 -36 ********** Masking position 2 Map Score: 8.54288 Number of sites scoring better than the average of aligned sites = 789 Number in coding regions = 648 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 11 CAAAGACAGCGTTTTGAATGTAAGGGCTAT 12 56 1 GTTTTGAATG 0.944823 -76 TGTGGATAATGTTTTGCAAGAAATATCT 13 9 0 GTTTTGCAAG 0.964492 -103 CATGCTTTGCGATTTGCATGTGAATGGATC 16 53 1 GATTTGCATG 0.964492 -157 AAAAAATCTTTTTTTGCATGGGGGTATTGT 20 121 0 TTTTTGCATG 0.944828 -180 ACTTCAATGGGTTTTGCATGAAAGAATTTT 20 259 0 GTTTTGCATG 0.988934 -42 ********** Masking position 5 Map Score: 3.08559 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 59 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ACTTAAAAAAAACTACCCTTAAAAAAATCA 1 169 1 AACTACCCTT 0.838639 -89 TAATTCCCCTTACTTAAATAA 4 2 1 AATTCCCCTT 0.903058 -227 GGTTAAATTGCCCTTTCGTTTTAAA 5 282 0 AATTGCCCTT 0.975876 -15 TAAAATTAACCTTTAATTTTTGA 10 4 1 AATTAACCTT 0.684772 -143 ATAAGTTTAAAATAGCCCTTACATTCAAAA 12 67 0 AATAGCCCTT 0.851032 -65 CAAACCATCCAATGACCCTTTATCGCACTC 14 41 1 AATGACCCTT 0.863183 -250 TTTTGATTAAAATTACCTTGACCGACAATA 14 170 0 AATTACCTTG 0.826069 -121 GATTAGAAAGAATCACCTTTAAGGTTTTAT 16 180 0 AATCACCTTT 0.740785 -30 TTGTAGCGCTAATTGCCTTTATACTAAAAG 19 57 0 AATTGCCTTT 0.948329 -27 AACTTCATAAAATTGCGCTTCGTTCGTTTT 20 30 1 AATTGCGCTT 0.811969 -271 ATTAGAAGACGATTACCTTTTAAGCGAGAG 20 152 1 GATTACCTTT 0.826069 -149 TGAAAATTTAGATTGCCTTGACTGACTCAT 20 202 1 GATTGCCTTG 0.688368 -99 ********** Masking position 2 Map Score: 5.62501 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 195 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 GTAATGGGTGTTTGTTTTAAGACGCTATGA 1 83 0 TTTGTTTTAA 0.385586 -175 AGACTTGAAATTTGAAAATAATAACACAAC 1 141 1 TTTGAAAATA 0.497513 -117 TTCTACTACATTTGAAATAATTTTTCTTAT 2 74 1 TTTGAAATAA 0.797675 -141 AAATCTTAGTTTTGAAAAAGTTTTATTGTA 3 41 1 TTTGAAAAAG 0.594929 -55 ATAATGAAATTTTCTTAAAATTATACAATA 4 28 1 TTTCTTAAAA 0.630096 -201 AATAGATTTTTATGATAAAATCTAAGCTTT 5 140 0 TATGATAAAA 0.497061 -157 ATAAAGCCTCTTTCATAAAAAGGATTGAGC 8 15 0 TTTCATAAAA 0.80252 -173 TTTCTTTTTTTTTGATTTAATACTAGGTAT 8 138 1 TTTGATTTAA 0.61128 -50 ATCACTATACTTTCAATAAAATAAGGGGTT 9 16 1 TTTCAATAAA 0.637327 -24 GCTTTTGAATTTTCTTAAAA 11 1 0 TTTCTTAAAA 0.630096 -77 CATTGGATGGTTTGAAAAAAGAAAGACAAG 14 25 0 TTTGAAAAAA 0.921746 -266 AGCGTTCTTATTTGTAAAAAAATTCAGTTT 14 113 0 TTTGTAAAAA 0.832763 -178 AATAGCATGTTTTGATTAAAATTACCTTGA 14 179 0 TTTGATTAAA 0.823221 -112 GTTGTATAATTTTGAAAAAATACGCAACAA 15 82 0 TTTGAAAAAA 0.921746 -49 AAACGCAAAAATTGAATAAAACCTTAAAGG 16 165 1 ATTGAATAAA 0.283358 -45 ATGAGCGGGCTTTGTTATAATACTTCCTAT 20 83 0 TTTGTTATAA 0.61128 -218 AATGGGGGTATTTTAAAAAAATGAGTCAGT 20 222 0 TTTTAAAAAA 0.386788 -79 CCCATTGAAGTTTAATAAAAGGTAAAAATA 20 278 1 TTTAATAAAA 0.386788 -23 ********** Masking position 3 Map Score: 6.12935 Number of sites scoring better than the average of aligned sites = 1366 Number in coding regions = 1152 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 14 ACTATAGTATAATCTAAGGGCGTTGCTCTGT 4 67 1 AATCTAGGGC 0.959 -162 TTATCTTTAAAACGAAAGGGCAATTTAACC 5 277 1 AACGAAGGGC 0.981536 -20 CAGCGTTTTGAATGTAAGGGCTATTTTAAAC 12 62 1 AATGTAGGGC 0.988003 -70 AAAATGAGTGAATGAATGGGCATGTTATCTA 16 119 1 AATGAAGGGC 0.991597 -91 TGTAGCGCTTAATGAGCGGGCTTTGTTATAA 20 93 0 AATGAGGGGC 0.981536 -208 ****** **** Masking position 2 Map Score: 2.20211 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 TAAAAAAAACTACCCTTAAAAAAATCAATC 1 172 1 TACCCTTAAA 0.859409 -86 TTTATTTTACCCTTTAAAATTACTAAC 3 79 0 TACCCTTTAA 0.97486 -17 TATAAAAATATCCCCTTTTAACCCCCTATT 5 204 0 TCCCCTTTTA 0.749246 -93 TAAAATTAACCTTTAATTTTTGAGAG 10 7 1 TAACCTTTAA 0.927053 -140 TTTAGTATGATAACTTTTAAATTCTCTCAA 10 30 0 TAACTTTTAA 0.806394 -117 ACCATCCAATGACCCTTTATCGCACTCAAA 14 44 1 GACCCTTTAT 0.741133 -247 TTAGAAAGAATCACCTTTAAGGTTTTATTC 16 178 0 TCACCTTTAA 0.861343 -32 AGAAGACGATTACCTTTTAAGCGAGAGCGT 20 155 1 TACCTTTTAA 0.927053 -146 TCTTATTTTTACCTTTTATTAAACTTCAA 20 282 0 TACCTTTTAT 0.800638 -19 ********** Masking position 6 Map Score: 4.14623 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 190 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097