AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_hpyl_reg_300.orf -o00561_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: HP1350 209 protease 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 HP0695 300 hydantoin utilization protein A (hyuA) #9 HP0698 187 H. pylori predicted coding region HP0698 #10 HP0699 39 H. pylori predicted coding region HP0699 #11 HP0737 146 conserved hypothetical integral membrane protein #12 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #13 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #14 HP0966 220 conserved hypothetical protein #15 HP0967 285 virulence associated protein D (vapD) #16 HP0971 49 H. pylori predicted coding region HP0971 #17 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #18 HP1010 300 polyphosphate kinase (ppk) #19 HP1011 36 dihydroorotate dehydrogenase (pyrD) #20 HP1015 111 H. pylori predicted coding region HP1015 #21 HP1067 290 chemotaxis protein (cheY) #22 HP1154 130 H. pylori predicted coding region HP1154 #23 HP1352 300 adenine specific DNA methyltransferase (HINFIM) #24 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #25 HP1361 56 competence locus E (comE3) #26 HP1365 83 response regulator #27 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 ATAAAGATAGTCATAGCGTCTTAAAACAAACACCCA 1 73 1 TATCTTAAAA 0.926577 -185 TTTGAAAATAATAACACAACTTAAAAAAAACTACCC 1 151 1 AAACTTAAAA 0.928408 -107 CAACTTAAAAAAAACTACCCTTAAAAAAATCAATCT 1 167 1 AAACTTAAAA 0.928408 -91 AAAAACTGCTCCTAAAAACTCAAAATT 2 2 1 AAACCTAAAA 0.792414 -213 TTATTATATCTAATAGCGTTTAAAAAATGTAAATTT 2 154 0 TATTTAAAAA 0.794809 -61 TTTATTTTACCCTTTAAAATTACTAACCT 3 77 0 ATTTTTAAAA 0.379551 -19 ACTTAAATAATGAAATTTTCTTAAAATTATACAATA 4 22 1 TAACTTAAAA 0.955434 -207 AAACCCACTTTAAAAATACCTAAAAAATACAGAGCA 4 90 0 TAACTAAAAA 0.934995 -139 CTTAAGATCTTTAAAGATTTTAAAAACTAATACAGC 4 136 1 TAATTAAAAA 0.868065 -93 AATGAGAGTATGAAAATTTTTAAAAATTTACAAAAA 5 75 1 TAATTAAAAA 0.868081 -222 GTAAAAAGCATTCTTAAATCTAAAAATGCTACAATG 5 240 1 TCTCTAAAAA 0.699238 -57 CTAATCATTCTTAAAAACGCTAAAAATTA 6 4 0 TAACTAAAAA 0.934939 -79 CGAAATTGGATACAATCAGCTTAAAAAGGATATAAA 7 12 1 TCACTTAAAA 0.856926 -26 GATATTCATCTTAAATTACCCAAAAATATCATATAA 8 119 0 TAACCAAAAA 0.808938 -182 TTGAAATAAATGATTTCCATTTAAAAATCAGCCTTA 8 227 1 TATTTTAAAA 0.852365 -74 TGATAACTTTTAAATTCTCTCAAAAATTAAAGGTTA 11 17 0 TAATCAAAAA 0.659516 -130 GTTATCATACTAAAACGTGCTTAAAATTAAGCCTTA 11 46 1 TAACTTAAAA 0.955434 -101 TTTTAGCATTTTATTTGCATTAAAAAGCGATTTTCT 11 89 0 TATTTAAAAA 0.794728 -58 AAAGTCTATCTATATTTACCTAAAAAAAGGCTTTTG 12 24 0 TTACTAAAAA 0.715896 -54 GATCAAACTCCCTAAAAACGATTGCAAT 12 60 0 TAACTAAAAA 0.934995 -18 TATACATATTAAATAATATTTTAAAATTAAAAAGCG 13 11 0 AATTTTAAAA 0.7774 -121 ACCATTTTACAATAATAAGTTTAAAATAGCCCTTAC 13 75 0 ATATTTAAAA 0.509655 -57 TTTGTAATGATGATTATTCTTAAAAATTCGCTTTCT 14 49 1 TATTTAAAAA 0.794809 -172 AAAAATCCCCAAAAAATCCCCAAAAAAGGGTTTATA 14 155 0 AAACCAAAAA 0.719187 -66 GCTCACCTGCTCTTTTTGGCTTAAAAGCAGCGAAGA 15 60 0 TTTCTTAAAA 0.688554 -226 AGGTAAAGCGACTTCCTCGCTTAAAAAAAGCTTGAA 15 116 0 ATTCTTAAAA 0.572162 -170 CTTTACCTCTAGCAAAAGCTTTAAAAAATCAGTTCG 15 144 1 ACATTTAAAA 0.623707 -142 AATTCTAACATGATTTAGTCTTAAAAGTGATTTTGT 17 65 1 TATCTTAAAA 0.926577 -47 AATCTCAATTCTCCCTAAAAAACAAAATCA 17 92 0 TAACCTAAAA 0.863213 -20 ATTTAACCCTAAAAGATCGCTTAAAATTTTTTTAGC 18 15 0 AAACTTAAAA 0.928408 -286 TGATAATCATTGAAGCTTTTTTAAAAAGTCATGGTC 18 213 0 TAATTTAAAA 0.907476 -88 ATCCTTTAAATCATCATGTTTAAAAATCAGTTTGTT 18 270 0 TATTTAAAAA 0.79481 -31 AACAAAGAGTTGCAATTCATTAAAAAATGCTTGTTG 20 47 1 TCATTAAAAA 0.647689 -65 TTGTTTGCTATGATAATCGTTTAAAAGTAATAAAAT 21 79 0 TATTTTAAAA 0.852364 -212 AGCCTAATTTAAATGCAATCTTAAAAGGAGAAGCAC 21 264 1 AATCTTAAAA 0.884174 -27 ATCCTAAAATAGAGCGTTCCTTAAAAAATGGTTGGA 22 15 1 AAGCTTAAAA 0.655896 -116 GATTAAACATTAAGATAACCTTAAAACGCTTGTGTT 23 236 1 TAGCTTAAAA 0.7591 -65 GTTATAAAAAAACACTCCCTTAAAAAAGACACCGCT 26 19 0 ACATTAAAAA 0.526526 -65 CTATGAAAAGGTTTTCTAAAACTTCATAAAA 27 6 1 AAATCTAAAA 0.635887 -295 CGTTTTCATTATAACGCTCCTTAAAAAACATAGGAA 27 54 1 AAACTTAAAA 0.928408 -247 * ** ******* Masking position 13 Map Score: 42.0941 Number of sites scoring better than the average of aligned sites = 1819 Number in coding regions = 1445 Number in noncoding regions = 374 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 2 TTAAGGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCAAATTT 1 148 0 TTTTAAGTAT 0.388533 -110 TCTAAAATTCTTAAATTAAAATATAGCTATAATACACTAAAAC 1 200 1 TTATAAATAT 0.895783 -58 TGAGAAAAAATTCAATTCAAAGGGGCTATTGTTTAAAATTTAC 2 119 1 TTATAAATTT 0.957815 -96 TTTGATATGATTTTTCTAAAATCTTAGTTTTGAAAAAGTTTTA 3 23 1 TTTTAAATGA 0.478242 -73 TAAAGTGGGTTTTTTCTTAAATCTTAAGATCTTTAAAGATTTT 4 114 1 TTTTAAATTT 0.930063 -115 TTGTCAATGATTAAAATTAAAGAGCGATGTCCTTAATCGTCCA 4 178 0 TTATAAATCT 0.807745 -51 TAAATAGATTTTTATGATAAAATCTAAGCTTTATCAAGCCATT 5 129 0 TTTAAAATTA 0.562502 -168 TTTTTACATATTATATAAAAATATCCCCTTTTAACCCCCTATT 5 204 0 TTAAAAATTA 0.68703 -93 AAATTGCCCTTTCGTTTTAAAGATAAACATTGTAGCATTTTTA 5 260 0 TTTTAAATGT 0.71105 -37 ATGGAAATCATTTATTTCAAAGTTGTTTGTAATAAGGGAAAAT 8 204 0 TTTTAAATAT 0.834281 -97 AATAAATGATTTCCATTTAAAAATCAGCCTTATACTTCTAATA 8 231 1 TTATAAATAT 0.895783 -70 ATCACTATACTTTCAATAAAATAAGGGGTTTTTT 10 16 1 TTATAAATTT 0.957815 -24 AGCATTTTATTTGCATTAAAAAGCGATTTTCTTAAACAATAAG 11 78 0 TTATAAATTT 0.957815 -69 TTGCCTTAAATTCTTTTTAAATCATGGCATTTTAGCATTTTAT 11 111 0 TTTTAAATTT 0.930063 -36 CTAAAAACGATTGCAATAAAGTCTATCTATATTTACCTAAAAA 12 34 0 TTATAAGTTT 0.741319 -44 AAACGCTGTCTTTGATTGAAACATATACATATTAAATAATATT 13 27 0 TTATAAATTT 0.957815 -105 TTTAAACTTATTATTGTAAAATGGTGAGTTTTACAATCAATGA 13 86 1 TTTTAAATTA 0.832031 -46 GTAATGATGATTATTCTTAAAAATTCGCTTTCTCTCTCTCTCT 14 52 1 TTTTAAATCT 0.71105 -169 CAATCCTTTAAAATTAAAAACTAAAATCTAAATAAGACGC 14 191 0 TTATAAATTA 0.894259 -30 ATTTATAGCATTCCACATAAAAAAAATCATCAAAGCCTTTT 15 9 0 TTAAAAATAA 0.453855 -277 ATCAGTTCGCTTCTAAAGAAATGAAATTGTTTTATTCTCAAAC 15 171 1 TTAAAAATTT 0.854935 -115 CTAACATGATTTAGTCTTAAAAGTGATTTTGTTTTTTAGGGAG 17 69 1 TTTTAAATTT 0.930063 -43 TTAAATGAAGTTTTATTCAAAAAATGAAGTTTTACAAAAAAGA 18 45 1 TTATAAATTT 0.957815 -256 AGCGTTCTTATTTGTAAAAAAATTCAGTTTGTTTGCTATGATA 21 100 0 TTTAAAATTT 0.775374 -191 GTCAAGGTAATTTTAATCAAAACATGCTATTATTTGGAACGAT 21 178 1 TTATAAATAT 0.895783 -113 CCTTTTAAGATTGCATTTAAATTAGGCTCTTTTTAAACAGCCA 21 249 0 TTATAAATTT 0.957815 -42 GACTATCCTTTTTAATTTAAATGCTTTGTTGTATAATTTTGAA 22 96 0 TTATAAATTA 0.89426 -35 CTAAAAGCGGTTATAAAAAAACACTCCCTTAAAAAAGACACCG 26 21 0 TTAAAAATAA 0.453854 -63 GGTAATCGTCTTCTAATAAAAAAATCTTTTTTTGCATGGGGGT 27 126 0 TTATAAATTT 0.957815 -175 TGAAAGAATTTTACAATGAAATGGGGGTATTTTAAAAAAATGA 27 228 0 TTATAAATTT 0.957815 -73 ** * * *** * ** Masking position 10 Map Score: 38.4334 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 308 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 TAGTATAATCTAAGGGCGTTGCTCTGTATT 4 71 1 TAAGGGCGTT 0.745064 -158 TTAATCATTGACAAGGAGTTTGGTAGTTAA 4 207 1 ACAAGGAGTT 0.923037 -22 ATTAGGTAAAAAAAGGGGTTGGCATCAATA 5 178 1 AAAAGGGGTT 0.944714 -119 GTTGGCATCAATAGGGGGTTAAAAGGGGAT 5 195 1 ATAGGGGGTT 0.764266 -102 ATAGGGGGTTAAAAGGGGATATTTTTATAT 5 205 1 AAAAGGGGAT 0.767505 -92 AATCAGCTTAAAAAGGATATAAA 7 25 1 AAAAGGATAT 0.632677 -13 TTTCAATAAAATAAGGGGTTTTTT 10 26 1 ATAAGGGGTT 0.890816 -14 TATTTGCATTAAAAAGCGATTTTCTTAAAC 11 84 0 AAAAAGCGAT 0.466956 -63 TTTACCTAAAAAAAGGCTTTTGAATTTTCT 12 16 0 AAAAGGCTTT 0.887088 -62 GCAATCGTTTTTAGGGAGTTTGATC 12 63 1 TTAGGGAGTT 0.612888 -15 AAATCCCCAAAAAAGGGTTTATATGGGTTT 14 148 0 AAAAGGGTTT 0.850125 -73 AAAAGGCTTTGATGATTTTT 15 1 1 AAAAGGCTTT 0.887088 -285 CACAAACCAATAAAGGAGTTAAA 15 273 1 TAAAGGAGTT 0.892987 -13 AAGTTTTACAAAAAAGAGTTTTTAAACAAC 18 71 1 AAAAAGAGTT 0.837263 -230 CCGCAATCAAAAAGGGAGATTGTAGCGCGA 18 113 0 AAAGGGAGAT 0.673402 -188 CATGATGATTTAAAGGATTTCTA 18 288 1 TAAAGGATTT 0.734747 -13 ATCATAAAAGATAAGGATTTAA 19 25 1 ATAAGGATTT 0.809776 -12 ATCCACCAAAACAAAGAGTTGCAATTCATT 20 38 1 ACAAAGAGTT 0.696724 -74 AAAAAGAAAGACAAGGATTTTACAAGTAA 21 10 0 ACAAGGATTT 0.799241 -281 TTTATCGCACTCAAAGAGTTATTTTATTAC 21 59 1 TCAAAGAGTT 0.416482 -232 ATTTATTATTATAAGGCGTTAGAGACGCTT 21 219 1 ATAAGGCGTT 0.918719 -72 TTATCCTAAAATAGAGCGTTCCTTAAAAAA 22 13 1 ATAGAGCGTT 0.462463 -118 GCGTAAAAGCAAAAGGCGTTCCAAATCCAA 22 46 0 AAAAGGCGTT 0.959469 -85 CTATGAAAAGGTTTTCTAAAACTTC 27 6 1 AAAAGGTTTT 0.467351 -295 CCCCATGCAAAAAAAGATTTTTTTATTAGA 27 128 1 AAAAAGATTT 0.630699 -173 AGCGAGAGCGTTAAGGAGTTTGACTCATTG 27 174 1 TTAAGGAGTT 0.79937 -127 ********** Masking position 10 Map Score: 24.0312 Number of sites scoring better than the average of aligned sites = 1262 Number in coding regions = 1036 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 4 CCCTTAAAAAAATCAATCTAAAATTCTTAAATTA 1 184 1 AAAACTAAAT 0.846974 -74 AAAAACTCAAAATTAACCTAAAATCGCTTGACGC 2 24 1 AAAACTAAAT 0.846974 -191 TTTTCTTATAAACAAAACCTAAATTGAGAAAAAA 2 95 1 AAAACCTAAT 0.896962 -120 TATAGGTGGTAACTATCCCTTATTATATCTAATA 2 175 0 AAATCCTATT 0.618286 -40 TGAACGATCCTTATTTTATAGGTGGT 2 199 0 AAATCTTTTT 0.507388 -16 AATATGTAAAAAGCATTCTTAAATCTAAAAATGC 5 235 1 AAATCTTAAT 0.911693 -62 TCTTAAATCTAAAAATGCTACAATGTTTATCTTT 5 251 1 AAATCTAAAT 0.704834 -46 AAAAAAAAAGAAAAAAGCTTAAATTTTTTAATTT 9 117 0 AAAACTTAAT 0.922139 -71 TAAAATTAACCTTTAATTTTTGAGAGA 11 4 1 AAAACTTAAT 0.957941 -143 ACGTGCTTAAAATTAAGCCTTATTGTTTAAGAAA 11 60 1 AAAACCTATT 0.660505 -87 TCCTCGCTTAAAAAAAGCTTGAATTTAGCGTATC 15 105 0 AAAACTTAAT 0.922139 -181 ATCATGTTAGAATTATACTTGAATTTACACTCAG 17 45 0 AAATCTTAAT 0.911653 -67 TCATTTTTTGAATAAAACTTCATTTAACCCTAAA 18 38 0 AAAACTTATT 0.827745 -263 ATGACTTTTTAAAAAAGCTTCAATGATTATCATT 18 217 1 AAAACTTAAT 0.922139 -84 GATTAACTAACCTTTTATATCTGCTACT 23 283 0 AAAACTTTAT 0.846968 -18 TCTTCTAATAAAAAAATCTTTTTTTGCATGGGGG 27 127 0 AAAACTTTTT 0.687358 -174 TTTTACCTTTTATTAAACTTCAATGGGTTTTGCA 27 271 0 TAAACTTAAT 0.657789 -30 ** ** *** *** Masking position 5 Map Score: 18.1431 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 99 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTAAGAGTAATGGGTGTTTGTTTTAAGACGC 1 88 0 TGGGGTTTGT 0.814375 -170 TCAATTCAAAGGGGCTATTGTTTAAAATTTA 2 130 1 GGGGTATTGT 0.986762 -85 TATTTTTAAAGTGGGTTTTTTCTTAAATCTT 4 108 1 GTGGTTTTTT 0.672339 -121 GGGGTTAAAAGGGGATATTTTTATATAATAT 5 209 1 GGGGTATTTT 0.978883 -88 CAATAAAATAAGGGGTTTTTT 10 29 1 AGGGTTTTTT 0.882371 -11 TTTGAATGTAAGGGCTATTTTAAACTTATTA 13 68 1 AGGGTATTTT 0.893662 -64 ACCCTTTTTTGGGGATTTTTTGGGGATTTTT 14 160 1 GGGGTTTTTT 0.976402 -61 GGGATTTTTTGGGGATTTTTGCGTCTTATTT 14 171 1 GGGGTTTTTG 0.839928 -50 CGCAAAGTCTGGCGTTTTTGTTTGGGGGTAA 16 21 1 GGCGTTTTGT 0.905592 -29 GCAATCAAAAAGGGAGATTGTAGCGCGAGTT 18 110 0 AGGGGATTGT 0.830942 -191 AAATGCTTGTTGGGCTATTTTTTCGCCCCTT 20 71 1 TGGGTATTTT 0.893662 -41 CCCTTTGTGTGGGGCTATTCTGTTA 20 97 1 GGGGTATTCT 0.915473 -15 CGGGGAGTTATGCGTTTTTGTTGTATCGTTT 23 130 1 TGCGTTTTGT 0.634911 -171 AACTTTTCAGGGGGCGTTTGAACTTCTTACG 25 18 1 GGGGGTTTGA 0.674329 -39 GGGGGTATTGTAGCGCTAATT 26 73 0 GGGGTATTGT 0.986762 -11 TTTTTTGCATGGGGGTATTGTAGCGCTTAAT 27 111 0 GGGGTATTGT 0.986762 -190 ACAATGAAATGGGGGTATTTTAAAAAAATGA 27 228 0 GGGGTATTTT 0.978883 -73 **** ****** Masking position 8 Map Score: 23.5364 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 618 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TATATGAGAGAAAGGTTTGGGTTTAGGGTTTGA 1 34 0 AAAGTTGGTT 0.904572 -224 AAGAGTGTGAATTGGCATGATTTAAGAGTAATG 1 107 0 ATTGCTGTTT 0.78145 -151 TTATCAAGCCATTAGCCGGTGTTCTTTCTCATT 5 109 0 ATTGCGGGTT 0.918964 -188 TCTTGGTGCTAAAAGCTTGGGTTGATTTAACTC 9 48 1 AAAGCTGGTT 0.970231 -140 ATTGAAGAAAATTTGCTTGAGTTAAATCAACCC 9 66 0 ATTGCTGGTT 0.938067 -122 ATGGGTTTATATGGGTATGGGTTTATATGGGGG 14 123 0 ATGGTTGGTT 0.713839 -98 CTCGCTTAAAAAAAGCTTGAATTTAGCGTATCT 15 104 0 AAAGCTGATT 0.70046 -182 TTTTATTCTCAAACGCATGGGTTGTAAAACGCA 15 200 1 AAAGCTGGTT 0.970231 -86 ATGGGTTGTAAAACGCATGGGTTATCAAACGAA 15 216 1 AAAGCTGGTT 0.970231 -70 TAACTCCTTTATTGGTTTGTGTTATAGCATGTT 15 261 0 ATTGTTGGTT 0.814994 -25 CTTCAAACGCAAAGTCTGGCGTTTTTGTTTGGG 16 14 1 AAATCGGGTT 0.563267 -36 TCTTAATACAAAAGGTAGGCGTT 17 1 0 AAAGTGGGTT 0.876498 -111 CGTTCCAAATAATAGCATGTTTTGATTAAAATT 21 186 0 AATGCTGTTT 0.853845 -105 TTCCTTAAAAAATGGTTGGATTTGGAACGCCTT 22 31 1 AATGTGGTTT 0.559889 -100 GATAACCTTAAAACGCTTGTGTTAAAATGGCTA 23 249 1 AAAGCTGGTT 0.970231 -52 GTAGCGCTTAATGAGCGGGCTTTGTTATAATAC 27 90 0 ATGGCGGTTT 0.602536 -211 *** ** ** *** Masking position 12 Map Score: 15.5782 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 210 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TTAAGGACATCGCTCTTTAATTTTAATCATTGACA 4 185 1 CGCCTTTTTA 0.722488 -44 ATAAAATCTAAGCTTTATCAAGCCATTAGCCGGTG 5 121 0 AGCTTATAGA 0.500504 -176 AATTGAATTTCGCCTTTTGATTTAATATCAGTTTA 8 61 1 CGCTTTTTTA 0.958696 -240 GAATATCGGTAGCGTTTTGAATAAATTTGTTACTA 8 148 1 AGCTTTTATA 0.886734 -153 TTTAAAAATCAGCCTTATACTTCTAATAGGTTGCC 8 246 1 AGCTTATTTA 0.930186 -55 AAAAAATTTAAGCTTTTTTCTTTTTTTTTGATTTA 9 122 1 AGCTTTTTTT 0.662972 -66 CTTAAAATTAAGCCTTATTGTTTAAGAAAATCGCT 11 65 1 AGCTTATTTA 0.930186 -82 ATGGCATTTTAGCATTTTATTTGCATTAAAAAGCG 11 96 0 AGCTTTTTTA 0.962952 -51 CGCTTTTTAATTTTAAAATATTATT 13 1 1 CGCTTTTTTA 0.958696 -131 AATCAAAGACAGCGTTTTGAATGTAAGGGCTATTT 13 53 1 AGCTTTTATA 0.886734 -79 TCTAGTCAGCCGCTTTATCTTTTCACCCCCATATA 14 98 1 CGCTTATTTA 0.922467 -123 TAGCCCAACAAGCATTTTTTAATGAATTGCAACTC 20 53 0 AGCTTTTAAA 0.558257 -59 GCGTCTCTAACGCCTTATAATAATAAATCGTTCCA 21 212 0 CGCTTATTAA 0.657604 -79 GGATTTGGAACGCCTTTTGCTTTTACGCTTTTAAT 22 48 1 CGCTTTTTTA 0.958696 -83 TATACAACAAAGCATTTAAATTAAAAAGGATAGTC 22 104 1 AGCTTTATTA 0.662972 -27 CAAATCGCAAAGCATGTTCGTTACAAAAACATTAG 23 82 0 AGCTGTTTTA 0.744605 -219 CGGGGAGTTATGCGTTTTTGTTGTATCGTTTAAAA 23 130 1 TGCTTTTTTA 0.750665 -171 TTTTTTAAGGAGCGTTATAATGAAAACGAACGAAG 27 47 0 AGCTTATTGA 0.768887 -254 *** **** ** * Masking position 3 Map Score: 16.8832 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 246 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GTTGTGTTATTATTTTCAAATTTCAAGTCT 1 141 0 TATTTTCAAA 0.802718 -117 ATAAGAAAAATTATTTCAAATGTAGTAGAA 2 74 0 TTATTTCAAA 0.69987 -141 TGGAGGTTAGTAATTTTAAAGGGTAAAATA 3 74 1 TAATTTTAAA 0.717687 -22 AATAATGAAATTTTCTTAAAATTATACAAT 4 27 1 TTTTCTTAAA 0.857685 -202 ATTTTTTAGGTATTTTTAAAGTGGGTTTTT 4 98 1 TATTTTTAAA 0.867917 -131 AAAGTGGGTTTTTTCTTAAATCTTAAGATC 4 115 1 TTTTCTTAAA 0.857685 -114 TTCTTTCTCATTTTTGTAAATTTTTAAAAA 5 91 0 TTTTTGTAAA 0.784196 -206 TGGAAATCATTTATTTCAAAGTTGTTTGTA 8 216 0 TTATTTCAAA 0.69987 -85 TAAAAAGCGATTTTCTTAAACAATAAGGCT 11 75 0 TTTTCTTAAA 0.857685 -72 TGCCTTAAATTCTTTTTAAATCATGGCATT 11 123 0 TCTTTTTAAA 0.73859 -24 GGCTTTTGAATTTTCTTAAAA 12 2 0 TTTTCTTAAA 0.857685 -76 CGCTTTTTAATTTTAAAATATTATTTA 13 8 1 TAATTTTAAA 0.717687 -124 TTTAAACTTATTATTGTAAAATGGTGAGTT 13 86 1 TTATTGTAAA 0.584378 -46 TAATGATGATTATTCTTAAAAATTCGCTTT 14 53 1 TATTCTTAAA 0.802717 -168 TTTTAGTTTTTAATTTTAAAGGATTG 14 205 1 TAATTTTAAA 0.717687 -16 GAAATTGTTTTATTCTCAAACGCATGGGTT 15 193 1 TATTCTCAAA 0.715871 -93 TAAAAACTCTTTTTTGTAAAACTTCATTTT 18 65 0 TTTTTGTAAA 0.784196 -236 CTTGTCTTTCTTTTTTCAAACCATCCAATG 21 25 1 TTTTTTCAAA 0.8577 -266 TGAGCGTTCTTATTTGTAAAAAAATTCAGT 21 115 0 TATTTGTAAA 0.710428 -176 TAAATTAGGCTCTTTTTAAACAGCCAAAGC 21 245 0 TCTTTTTAAA 0.73859 -46 TTGTTGCGTATTTTTTCAAAATTATACAAC 22 82 1 TTTTTTCAAA 0.8577 -49 GACTGACTCATTTTTTTAAAATACCCCCAT 27 221 1 TTTTTTTAAA 0.906836 -80 ********** Masking position 4 Map Score: 27.633 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 541 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 9 TACTCTTAAATCATGCCAATTCACACTCTT 1 110 1 TCATGCCAAT 0.855162 -148 TGTAGTAGAATTAAGGCAGTGTTTTTGCGT 2 54 0 TTAAGGCAGT 0.754208 -161 CTAAGCTTTATCAAGCCATTAGCCGGTGTT 5 119 0 TCAAGCCATT 0.911329 -178 CTAAAATCTATTAAGGAAATCAGT 6 69 1 TTAAGGAAAT 0.671519 -14 AAAGTGTTGCTCAAGGCAACCTATTAGAAG 8 265 0 TCAAGGCAAC 0.877974 -36 TTGATTTAACTCAAGCAAATTTTCTTCAAT 9 69 1 TCAAGCAAAT 0.800657 -119 TCTTTTTAAATCATGGCATTTTAGCATTTT 11 113 0 TCATGGCATT 0.768118 -34 TAAAAAGAATTTAAGGCAATGA 11 135 1 TTAAGGCAAT 0.936361 -12 GAACGCTCCATTTAGCCAATGATTATTGTC 21 147 1 TTTAGCCAAT 0.65569 -144 TTATTGTCGGTCAAGGTAATTTTAATCAAA 21 169 1 TCAAGGTAAT 0.782342 -122 TATCTGCTACTCTAGCCATTTTAACACAAG 23 264 0 TCTAGCCATT 0.677331 -37 GCTTTTAGTATAAAGGCAATTAGCGCTACA 26 56 1 TAAAGGCAAT 0.817255 -28 AATGAGTCAGTCAAGGCAATCTAAATTTTC 27 203 0 TCAAGGCAAT 0.978549 -98 ********** Masking position 8 Map Score: 5.99467 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 240 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 TTTATAAGAAAAATTATTTCAAATGTAGTAG 2 76 0 AAATATTTCA 0.568596 -139 TGCTACAATAAAACTTTTTCAAAACTAAGAT 3 43 0 AAATTTTTCA 0.912073 -53 TTAAATAATGAAATTTTCTTAAAATTATACA 4 24 1 AAATTTCTTA 0.390834 -205 ATTAGTTTTTAAAATCTTTAAAGATCTTAAG 4 136 0 AAATCTTTAA 0.771977 -93 TGAGAGTATGAAAATTTTTAAAAATTTACAA 5 77 1 AAATTTTTAA 0.804764 -220 TTTATCATAAAAATCTATTTAATGAGAATTA 5 151 1 AAACTATTTA 0.384971 -146 ACTCAAGCTAAAATCTATTAAGGAAATCAGT 6 62 1 AAACTATTAA 0.501036 -21 TAGTAAAACCTTTCAATCCCAGCCT 8 5 1 AAACCTTTCA 0.892999 -296 AAGTAGTAACAAATTTATTCAAAACGCTACC 8 155 0 AAATTATTCA 0.720641 -146 AAAAAAGCTTAAATTTTTTAATTTGCAGCCA 9 110 0 AAATTTTTAA 0.804764 -78 GATAACTTTTAAATTCTCTCAAAAATTAAAG 11 21 0 AAATCTCTCA 0.680239 -126 AGATCGCTTAAAATTTTTTTAGCGTTT 18 7 0 AAATTTTTTA 0.719846 -294 TAGAAATCCTTTAAATCATCATGT 18 287 0 AAACCTTTAA 0.768325 -14 AAGACAAAACTTTTCAGGGGGCGTTT 25 6 1 AAACTTTTCA 0.910404 -51 AAGTTTTAGAAAACCTTTTCATAG 27 4 0 AAACTTTTCA 0.910404 -297 TTTCATTGTAAAATTCTTTCATGCAAAACCC 27 250 1 AAATCTTTCA 0.894955 -51 *** ******* Masking position 3 Map Score: 9.48763 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 408 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 GGTTTGGGTTTAGGGTTTGAATTATATTGA 1 24 0 TAGGGTTTGA 0.910459 -234 TTTACAACCCATGCGTTTGAGAATAAAACA 15 198 0 ATGCGTTTGA 0.790192 -88 TTACTTAGAATTTCGTTTGATAACCCATGC 15 230 0 TTTCGTTTGA 0.915357 -56 ACGCCAGACTTTGCGTTTGAAGCCA 16 6 0 TTGCGTTTGA 0.959825 -44 GGGTGAGGTCGTGGGTTTGAATCCCGCTAC 18 180 1 GTGGGTTTGA 0.915264 -121 AATCAGTTTGTTTGGTGTGATTATATAATG 18 252 0 TTTGGTGTGA 0.730123 -49 CCTTATCTTTTATGATTTGAACGATAACCC 19 11 0 TATGATTTGA 0.597505 -26 AGGGTCATTGGATGGTTTGAAAAAAGAAAG 21 30 0 GATGGTTTGA 0.742445 -261 GCTTTGCGATTTGCATGTGAATGGATCGGG 23 104 1 TTGCATGTGA 0.727569 -197 AGATAGCTTCTATCATTTGATGCATTTGCA 23 176 1 TATCATTTGA 0.672835 -125 TTTGATGCATTTGCATTTGATGCATTTGAT 23 191 1 TTGCATTTGA 0.885136 -110 ACTTTTCAGGGGGCGTTTGAACTTCTTACG 25 19 1 GGGCGTTTGA 0.798972 -38 ********** Masking position 10 Map Score: 3.6554 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 504 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 12 ACAACTTAAACCAACACAAAGGAGATACT 5 9 0 CCAACCAAAG 0.979226 -288 TGGCTTCAAACGCAAAGTCTGGCGTTT 16 7 1 CAAACCAAAG 0.879407 -43 AAAAGTTACCCCCAAACAAAAACGCCAGACT 16 26 0 CCCAACAAAA 0.775022 -24 CACGACCTCACCCACCCCAAGGGTGCGCGCT 18 162 0 CCCACCCAAG 0.967697 -139 TCCACATCCACCAAAACAAAGAGTTGCAATT 20 33 1 CCAAACAAAG 0.927845 -79 ACAGAATAGCCCCACACAAAGGGGCGAAAAA 20 89 0 CCCACCAAAG 0.989833 -23 GACCCTTTATCGCACTCAAAGAGTTATTTTA 21 54 1 CGCACCAAAG 0.957123 -237 ***** ***** Masking position 4 Map Score: 3.40981 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 85 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 AAACCCTAAACCCAAACCTTTCTCTCATATA 1 36 1 CCCAACCTTT 0.967591 -222 CCCTATTGATGCCAACCCCTTTTTTTACCTA 5 180 0 GCCAACCCTT 0.766162 -117 GGTTAAATTGCCCTTTCGTTTTAAAGATAAA 5 276 0 CCCTTCGTTT 0.893379 -21 GATTGCTCAATCCTTTTTATGAAAGA 9 6 1 CTCAACCTTT 0.745344 -182 GTTAAATCAACCCAAGCTTTTAGCACCAAGA 9 48 0 CCCAACTTTT 0.890644 -140 CGTTTTACAACCCATGCGTTTGAGAATAAAA 15 200 0 CCCATCGTTT 0.934259 -86 CGTTTGATAACCCATGCGTTTTACAACCCAT 15 216 0 CCCATCGTTT 0.934259 -70 AACGCCTACCTTTTGTATTAAGAA 17 4 1 GCCTACTTTT 0.73673 -108 TGGACTATCCTTTTTAATTTAAA 22 118 0 GACTACCTTT 0.639423 -13 GCCTTCCCTTTATTCTGTATT 23 1 1 GCCTTCCTTT 0.858121 -300 GCCATTTTAACACAAGCGTTTTAAGGTTATC 23 249 0 CACAACGTTT 0.806453 -52 ***** ***** Masking position 10 Map Score: 4.47435 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 242 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 TATCTCGCATAAAGATAGTCATAGCGTCTTA 1 65 1 AAAGATAGCA 0.820943 -193 TTATAGCATAAATGATAATGAAAAAGTAAAT 5 47 1 AATGATAAGA 0.887959 -250 AATTTACAAAAATGAGAAAGAACACCGGCTA 5 99 1 AATGAGAAGA 0.926679 -198 AAATCTATTTAATGAGAATTAGGTAAAAAAA 5 161 1 AATGAGAATA 0.661615 -136 CTTTCGTTTTAAAGATAAACATTGTAGCATT 5 264 0 AAAGATAACA 0.847866 -33 AATTGAGTATAATGAGAGCCATTAAATGGTG 14 11 1 AATGAGAGCA 0.925377 -210 TATATAATGAAATGATAATCATTGAAGCTTT 18 230 0 AATGATAACA 0.904328 -71 TCAAATCATAAAAGATAAGGATTTAA 19 21 1 AAAGATAAGA 0.82372 -16 TGGTTTGAAAAAAGAAAGACAAGGATTTTAC 21 17 0 AAAGAAAGCA 0.666057 -274 GCAATCTTAAAAGGAGAAGCACT 21 278 1 AAGGAGAACA 0.800147 -13 CTCTATCGCAAATGAGAGCGAGATTAGGCAA 23 30 0 AATGAGAGGA 0.91226 -271 GGAGCGTTATAATGAAAACGAACGAAGCGCA 27 43 0 AATGAAAAGA 0.775167 -258 ******** ** Masking position 5 Map Score: 5.61109 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 98 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 ACTAACAACACTCAAGCTAAAATCTATTAAG 6 53 1 CCAAGCTAAA 0.654688 -30 TAAACTGATATTAAATCAAAAGGCGAAATTC 8 65 0 TAAATCAAAA 0.484017 -236 GTTGATTTAACTCAAGCAAATTTTCTTCAAT 9 68 1 CCAAGCAAAT 0.887544 -120 ATACCTAGTATTAAATCAAAAAAAAAGAAAA 9 137 0 TAAATCAAAA 0.484017 -51 AAATCGCTTTTTAATGCAAATAAAATGCTAA 11 92 1 TAATGCAAAT 0.548125 -55 AAATAGCCCTTACATTCAAAACGCTGTCTTT 13 57 0 TCATTCAAAA 0.720953 -75 GTCGCTTTACCTCTAGCAAAAGCTTTAAAAA 15 140 1 CCTAGCAAAA 0.782344 -146 AAAAGTTACCCCCAAACAAAAACGCCAGACT 16 26 0 CCAAACAAAA 0.62004 -24 CGCCATACTCCGCAATCAAAAAGGGAGATTG 18 121 0 CCAATCAAAA 0.842988 -180 AGATATTTCTTGCAAAACATTATCCAC 20 7 1 TCTTGCAAAA 0.633658 -105 ATTAAAAGCGTAAAAGCAAAAGGCGTTCCAA 22 52 0 TAAAGCAAAA 0.78348 -79 CCGATCCATTCACATGCAAATCGCAAAGCAT 23 102 0 CCATGCAAAT 0.874097 -199 TCAAATGCATCAAATGCAAATGCATCAAATG 23 189 0 CAATGCAAAT 0.689186 -112 CTACAATACCCCCATGCAAAAAAAGATTTTT 27 119 1 CCATGCAAAA 0.947966 -182 GTAAAATTCTTTCATGCAAAACCCATTGAAG 27 257 1 TCATGCAAAA 0.908811 -44 * ********* Masking position 9 Map Score: 7.6718 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 660 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269