AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ipurR_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0252 300 outer membrane protein (omp7) #3 HP0255 99 adenylosuccinate synthetase (purA) #4 HP0408 165 H. pylori predicted coding region HP0408 #5 HP0417 168 methionyl-tRNA synthetase (metS) #6 HP0584 81 flagellar switch protein (fliN) #7 HP0585 228 endonuclease III (nth) #8 HP0737 146 conserved hypothetical integral membrane protein #9 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #10 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #11 HP0830 58 amidase #12 HP0832 91 spermidine synthase (speE) #13 HP0833 76 H. pylori predicted coding region HP0833 #14 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #15 HP0920 143 conserved hypothetical integral membrane protein #16 HP1010 300 polyphosphate kinase (ppk) #17 HP1011 36 dihydroorotate dehydrogenase (pyrD) #18 HP1112 109 adenylosuccinate lyase (purB) #19 HP1218 119 glycinamide ribonucleotide synthetase (purD) #20 HP1234 300 conserved hypothetical integral membrane protein #21 HP1236 78 H. pylori predicted coding region HP1236 #22 HP1483 26 gerC2 protein (gerC2) #23 HP1490 103 hemolysin Motif number 1 AGATTGATTTTTTTAAGGGTAGTTTTTTTTA 1 76 1 TTTTAAGGTA 0.941246 -182 GGGTAGTTTTTTTTAAGTTGTGTTATTATTT 1 92 1 TTTTAAGTGT 0.585214 -166 AAAGGTTTGGGTTTAGGGTTTGAATTATATT 1 222 1 GTTTAGGGTT 0.739458 -36 AAGATGTCAATTTGATGCTTTTTTGAAACGC 2 190 1 TTTGATGCTT 0.612218 -111 AGAAAGTTTCTTTTATGGATTAAGTAAAATC 2 255 1 TTTTATGGTT 0.961131 -46 GCTCTTTTTAGGGCTTATAAAGAGGC 3 6 1 TTTTAGGGTT 0.980994 -94 GATTGGATTATTTAAAAGCTTGTTAGAATAC 3 54 0 TTTAAAAGTT 0.467514 -46 ATCTACTTTGTTTTAAGGATAATATTTT 3 82 1 TTTTAAGGTA 0.941246 -18 GCGCTCAAGTCTTTAGCGCTTAAGTCTTTCT 4 43 0 CTTTAGCGTT 0.737107 -123 CTTTTATCCTTATAAGCGTCAA 4 154 0 TTTTATCCTA 0.405764 -12 TTTTCAATTTTTTGAGCGTTAATTATAATGA 5 31 1 TTTGAGCGTA 0.583136 -138 AAACTTTGTCTTTAATGGCTTCATTGAGCGT 7 15 0 TTTAATGGTT 0.882688 -214 GAAAGCGTTTTTTAAGGGCTTCATCGCAGTT 7 66 0 TTTAAGGGTT 0.94014 -163 TTGCAATCGTTTTTAGGGAGTTTGATC 9 61 1 TTTTAGGGGT 0.938247 -17 TTTTAATTCATTTTAGGGAGTGTAAGCG 10 47 1 TTTTAGGGGT 0.938247 -18 GTTTTTAGCCTTACAAAAAATTT 11 46 0 TTTTAGCCTA 0.587681 -13 CTTTTTTATCGCTTCAATTTAATC 13 4 1 TTTTATCGTT 0.874023 -73 ATTATAGTTATTTAAAGCTTAAATAAGGGTC 13 51 1 TTTAAAGCTA 0.554232 -26 TTATCAATATTTTAAAGTATTTTTTATTAGG 14 44 0 TTTAAAGTTT 0.59324 -55 TACATTCTTTCTTTAAGGATTAGTT 14 84 1 CTTTAAGGTT 0.889356 -15 TCAATTTCAATTTTAGGGGGTTTTGTTTGGT 15 37 1 TTTTAGGGGT 0.938247 -107 CTTAAAATTTTTTTAGCGTTT 16 1 0 TTTTAGCGTT 0.935409 -300 TTAAGCGATCTTTTAGGGTTAAATGAAGTTT 16 27 1 TTTTAGGGTA 0.952192 -274 AACATGATGATTTAAAGGATTTCTA 16 286 1 TTTAAAGGTT 0.926648 -15 TCTTTTATGATTTGAACGATAACCC 17 5 0 TTTGAACGTA 0.52945 -32 TTTATGTTACTTTAAAGGGGTTTAAAGAATC 18 63 0 TTTAAAGGGT 0.788073 -47 CCCATTTTGATTTTAAGGATTGTCG 18 95 1 TTTTAAGGTT 0.97648 -15 AGAAAACTCTTTTTAAGCTTTTTAAATCCC 20 10 0 TTTTAAGCTT 0.913711 -291 CTAGACCCTTTTTAAAGGGTTTGAATGCCAC 20 45 0 TTTAAAGGTT 0.926648 -256 GGATTCGTGTTTTTATGTTTTCATATTTCTA 20 93 1 TTTTATGTTT 0.740583 -208 TCAATGCAACTTTTATGCGTTTAAAGCTTAA 20 216 1 TTTTATGCTT 0.863143 -85 GACTTAAAGTTTTTAAGCTTTAAACGCATAA 20 228 0 TTTTAAGCTT 0.913711 -73 AGCTTAAAAACTTTAAGTCTTAATTAGAGAT 20 240 1 CTTTAAGTTT 0.481322 -61 ACCCTAAAATCTTTATGGGTAAAATGC 20 284 1 CTTTATGGTA 0.648799 -17 TTAGAGTGTATTTTATCGTTTTTTAGATAAA 21 31 0 TTTTATCGTT 0.874023 -48 TTTTATTTATTTTTAGAGTGTATTTTATCGT 21 43 0 TTTTAGAGGT 0.513606 -36 ACTTTTCTTTTTTCATGGCTTGTCT 22 5 0 TTTCATGGTT 0.637417 -22 GGTTTTTGAAGGCTTGATTTTTAAA 23 5 1 TTTGAAGGTT 0.912223 -99 AAGGCTTGATTTTTAAAGTTAGGCTTAATCT 23 19 1 TTTTAAAGTA 0.526831 -85 TATCGTTAGGTTTTAGGTTTAAAGTT 23 88 1 TTTTAGGTTA 0.696915 -16 ******** ** Masking position 5 Map Score: 46.6945 Number of sites scoring better than the average of aligned sites = 3194 Number in coding regions = 2739 Number in noncoding regions = 455 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 2 TCTAAAATTCTTAAATTAAAATATAGCTATAATAC 1 44 0 TAATTAAATA 0.442984 -214 TCTTTAGACTTGAAATTTGAAAATAATAACACAAC 1 108 0 TAATTTAATA 0.827256 -150 TCTTTAGCGCTTAAGTCTTTCTAAAACACCCTCAT 4 30 0 TAATCTTAAA 0.948156 -136 GGGGTAATTCTCAATTTTTATATTATAATACCCAA 4 91 1 TAATTTATTA 0.694222 -75 GTCTATTCCTTGAACTCTTTTTCAATTTTTTGAGC 5 13 1 TAATCTTCAA 0.830797 -156 TTAATTATAATGAATTTTAAGCTAAAAACACCCCA 5 49 1 TAATTTATAA 0.784143 -120 TCGTGTTACCTTAAATTTGTTTAAATCTCTTAATT 5 136 0 TAATTTTAAA 0.937403 -33 TTATTTGTTATAAAATTTATAGTAAAATTAAGATT 6 16 1 TAATTTTTAA 0.876751 -66 TACGATTTCATAAACTTTGTCTTTAATGGCTTCAT 7 22 0 TAATTTTTTA 0.810486 -207 TGATAACTTTTAAATTCTCTCAAAAATTAAAGGTT 8 18 0 TAATCTTAAA 0.94816 -129 TCATTGCCTTAAATTCTTTTTAAATCATGGCATT 8 123 0 TAATCTTAAA 0.948158 -24 AAAAGGCTTTTGAATTTTCTTAAAA 9 1 0 TAATTTTAAA 0.937562 -77 ACGATTGCAATAAAGTCTATCTATATTTACCTAAA 9 36 0 TAATCTTATA 0.9194 -42 TAAACTACCATTAAATTTTTTGTAAGGCTAAAAAC 11 34 1 TAATTTTTAA 0.876824 -25 TTTTATCGCTTCAATTTAATCAAAATTAGATTACA 13 14 1 TAATTATAAA 0.730783 -63 AAATTGAAATTGAAGTCTGAAAATAGGATAATAGT 15 15 0 TAATCTAATA 0.853654 -129 CTCCTTGAATTCAACTCAATAAATAATTTTAATTA 15 113 0 TAATCATATA 0.673662 -31 TAGGGTTAAATGAAGTTTTATTCAAAAAATGAAGT 16 40 1 TAATTTACAA 0.673114 -261 ATTCAAAAAATGAAGTTTTACAAAAAAGAGTTTTT 16 59 1 TAATTTAAAA 0.884667 -242 TAGTTTAACCTAAAATCTCTAATTAAGACTTAAAG 20 250 0 TAATCTTTTA 0.84408 -51 ATTAATTCTTTAAAAAGCGTTTTATC 21 2 1 TAATCTTAAA 0.94816 -77 * ** *** * *** Masking position 6 Map Score: 21.638 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 347 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 GGCTAAATTTTGAAACCTTGA 1 2 1 GCTAAATTTT 0.929108 -256 GTGTATTATAGCTATATTTTAATTTAAGAA 1 42 1 GCTATATTTT 0.793201 -216 TATAATGCTCGCTTAATTTTATTTGGGGTG 2 147 0 GCTTAATTTT 0.979896 -154 AGATAATCATTCTTAATTTGCTATTAAGCG 2 218 0 TCTTAATTTG 0.847174 -83 GTGGGGTAATTCTCAATTTTTATATTATAA 4 89 1 TCTCAATTTT 0.690967 -77 ACCTCTATTCTCTAAATTTTTAAAAGCATG 5 102 1 TCTAAATTTT 0.792176 -67 TGTTTAAATCTCTTAATTTTAACATGCTTT 5 124 0 TCTTAATTTT 0.934107 -45 TGGCTTTATTTGTTATAAAATT 6 3 1 GCTTTATTTG 0.84798 -79 GATTATAAAATCTTAATTTTACTATAAATT 6 29 0 TCTTAATTTT 0.934107 -53 ACTTGAATGCGGTTGATTTTAACCGAAAGC 7 161 0 GGTTGATTTT 0.703841 -68 ACGCTTTCTTTGATGACAAGGT 7 217 0 GCTTTCTTTG 0.582084 -12 AAAAATTAAAGGTTAATTTTA 8 2 0 GGTTAATTTT 0.882663 -145 AAACAATAAGGCTTAATTTTAAGCACGTTT 8 58 0 GCTTAATTTT 0.979896 -89 ACACTCCTTAGCTTACTTTTTAACAATATC 12 70 0 GCTTACTTTT 0.924073 -22 GTTTTTGAAGGCTTGATTTTTAAAGTTAGG 23 12 1 GCTTGATTTT 0.93902 -92 TTAAAGTTAGGCTTAATCTTTTATGTTAAA 23 31 1 GCTTAATCTT 0.860749 -73 ********** Masking position 7 Map Score: 18.1034 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 296 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TACTAGCAAGAAAACGGGTTTGATCCATAAA 2 25 1 AAAACGGTTT 0.941005 -276 AAAAAAAAGTAAAAAGCCTCTTTATAAGCCC 3 21 0 AAAAAGCTCT 0.911112 -79 CAAAAAATTGAAAAAGAGTTCAAGGAATAGA 5 14 0 AAAAAGGTTC 0.889758 -155 ACCAAAAGAGAGAAAGCGTTTTTTAAGGGCT 7 77 0 AGAAAGGTTT 0.889755 -152 TTATCATACTAAAACGTGCTTAAAATTAAGC 8 47 1 AAAACGGCTT 0.822543 -100 TATTTGCATTAAAAAGCGATTTTCTTAAACA 8 83 0 AAAAAGGATT 0.86358 -64 GCCATGATTTAAAAAGAATTTAAGGCAATGA 8 126 1 AAAAAGATTT 0.810177 -21 ATTTACCTAAAAAAAGGCTTTTGAATTTTCT 9 16 0 AAAAAGCTTT 0.944249 -62 GCACCCAAACTAAAAGCGTTTGTTT 10 5 0 TAAAAGGTTT 0.844854 -60 TTAAAGCTTAAATAAGGGTCTAGCG 13 62 1 AATAAGGTCT 0.766984 -15 AAGTTTTACAAAAAAGAGTTTTTAAACAACA 16 71 1 AAAAAGGTTT 0.983461 -230 ACAAGGCGCAAAAAAGCCCCTTGATTTAATT 18 17 0 AAAAAGCCCT 0.748444 -93 TAAAAAGCTTAAAAAGAGTTTTCTAATAGTG 20 17 1 AAAAAGGTTT 0.983461 -284 CAAACCCTTTAAAAAGGGTCTAGGAGTTTAT 20 53 1 AAAAAGGTCT 0.972932 -248 TTAATTCTTTAAAAAGCGTTTTATCTAAAAA 21 12 1 AAAAAGGTTT 0.983461 -67 ****** **** Masking position 4 Map Score: 20.3611 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 386 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ACAACTTAAAAAAAACTACCCTTAAAAAAA 1 83 0 AAAAACTACC 0.91971 -175 TTGAAAATAATAACACAACTTAAAAAAAAC 1 97 0 TAACACAACT 0.443618 -161 GCGTCTTAAAACAAACACCCATTACTCTTA 1 161 0 ACAAACACCC 0.938257 -97 TAAGTCTTTCTAAAACACCCTCATGCTAGT 4 24 0 TAAAACACCC 0.948644 -142 ATTTTAAGCTAAAAACACCCCACAAATAAG 5 62 1 AAAAACACCC 0.948644 -107 GCTTTCGGTTAAAATCAACCGCATTCAAGT 7 161 1 AAAATCAACC 0.530891 -68 GATCAAACTCCCTAAAAACGAT 9 66 0 TCAAACTCCC 0.961284 -12 CGCTTACACTCCCTAAAATGAAT 10 52 0 TTACACTCCC 0.859575 -13 TCTAAGCATGTTAAACTACCATTAAATTTT 11 23 1 TTAAACTACC 0.85593 -36 AAACACTCCTTAGCTTACTT 12 82 0 AAACACTCCT 0.774397 -10 AACTCGCGCTACAATCTCCCTTTTTGATTG 16 110 1 ACAATCTCCC 0.800322 -191 ATCTGGGTTTAAAAACAACCACATTGCAGG 19 94 1 AAAAACAACC 0.875167 -26 CTTTTTGAAAATAAACTCCTAGACCCTTTT 20 64 0 ATAAACTCCT 0.819909 -237 CTTCAGCATTTCAAACTCCTTATAGAAATA 20 116 0 TCAAACTCCT 0.878366 -185 AAACAAAAGGTAAAACTCCTAGAACATTGT 20 167 1 TAAAACTCCT 0.89773 -134 AGATTTTAGGTTAAACTACCCTAAAATCTT 20 267 1 TTAAACTACC 0.85593 -34 ********** Masking position 3 Map Score: 15.2535 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 769 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 AATCAATATAATTCAAACCCTAAACCCAAA 1 227 0 ATTCAAACCC 0.964211 -31 TTTCTTTATGGATCAAACCCGTTTTCTTGC 2 30 0 GATCAAACCC 0.920537 -271 GAGGTCAGGGGTTCGAACCCCCTACACTCC 2 81 0 GTTCGAACCC 0.895534 -220 TGAAAACAGAAATTAAACGCATTGATTGGG 4 121 0 AATTAAACGC 0.721641 -45 CAAAAGAATGCATTGAACCCCTTCATGGAT 7 108 0 CATTGAACCC 0.90095 -121 AATAAAACTTCATTTAACCCTAAAAGATCG 16 32 0 CATTTAACCC 0.769307 -269 GAGTAGCGGGATTCAAACCCACGACCTCAC 16 182 0 ATTCAAACCC 0.964211 -119 CCCCTTGATTCTTTAAACCCCTTTAAAGTA 18 57 1 CTTTAAACCC 0.978584 -53 ATGTGGTTGTTTTTAAACCCAGATGACCGC 19 88 0 TTTTAAACCC 0.87607 -32 TAATAGTGGCATTCAAACCCTTTAAAAAGG 20 40 1 ATTCAAACCC 0.964211 -261 AGTTTTTAAGCTTTAAACGCATAAAAGTTG 20 222 0 CTTTAAACGC 0.907584 -79 AACTTTAAACCTAAAACCTAAC 23 92 0 CTTTAAACCT 0.766284 -12 ********** Masking position 6 Map Score: 11.5385 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 392 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 AGATAGTCATAGCGTCTTAAAACAAACACCC 1 171 0 AGCGTCTTAA 0.913543 -87 TTTGCTATTAAGCGTTTCAAAAAAGCATCAA 2 201 0 AGCGTTTCAA 0.913543 -100 GTTAAAATTAAGAGATTTAAACAAATTTAAG 5 131 1 AGAGATTTAA 0.75274 -38 CATCGCAGTTAGCGATTTCTACGATTTCATA 7 45 0 AGCGATTTTA 0.909236 -184 AAAGAGAGAAAGCGTTTTTTAAGGGCTTCAT 7 73 0 AGCGTTTTTA 0.978123 -156 ATGTAAACGAAGCGTTATCAATATTTTAAAG 14 58 0 AGCGTTATAA 0.876987 -41 TTTACAAAAAAGAGTTTTTAAACAACAACTA 16 75 1 AGAGTTTTAA 0.931448 -226 TAATCATTGAAGCTTTTTTAAAAAGTCATGG 16 215 0 AGCTTTTTAA 0.895309 -86 ACTCTTTTTAAGCTTTTTAAATCCC 20 5 0 AGCTTTTTAA 0.895309 -296 AAGCTTAAAAAGAGTTTTCTAATAGTGGCAT 20 21 1 AGAGTTTTTA 0.908003 -280 TTCTTTAAAAAGCGTTTTATCTAAAAAACGA 21 16 1 AGCGTTTTTC 0.884732 -63 AGTGTATTTTATCGTTTTTTAGATAAAACGC 21 27 0 ATCGTTTTTA 0.762362 -52 ******** ** Masking position 1 Map Score: 8.81861 Number of sites scoring better than the average of aligned sites = 1575 Number in coding regions = 1398 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 8 ACACTAAAACAATCTCAAGGTTTCAAAATTTAGCC 1 11 0 AATCAGTTTA 0.923995 -247 AAAGAGTGTGAATTGGCATGATTTAAGAGTAATGG 1 138 1 AATTATATTA 0.898867 -120 AGTAACGCTAAATCAATATAATTCAAACCCTAAAC 1 232 0 AATCATATTA 0.913052 -26 AAAAGCATCAAATTGACATCTTTTAAGCAAAATGT 2 177 0 AATTATTTTA 0.915235 -124 AGCGTGGGGTAATTCTCAATTTTTATATTATAATA 4 86 1 AATTAATTTA 0.534673 -80 TGAAAACAGAAATTAAACGCATTGATTGGGTATTA 4 116 0 AATTCGATTA 0.718051 -50 TTAGCTTAAAATTCATTATAATTAACGCTCAAAAA 5 39 0 ATTCATATTA 0.416024 -130 TGCTTTTAAAAATTTAGAGAATAGAGGTTGCATTT 5 95 0 AATTAGATAA 0.516576 -74 AGCATGTTAAAATTAAGAGATTTAAACAAATTTAA 5 126 1 AATTAGTTTA 0.911422 -43 TTTATAGTAAAATTAAGATTTTATAATCAAAGTCA 6 31 1 AATTATTTAA 0.576666 -51 TTTCGGTTAAAATCAACCGCATTCAAGTGGCTTTA 7 163 1 AATCCGATTA 0.750558 -66 TAAAATGCTAAAATGCCATGATTTAAAAAGAATTT 8 112 1 AAATATATTA 0.376157 -35 TTGTTACAATAATTTAGATTTTTTAGCTAGCATGT 12 15 1 AATTATTTTA 0.915235 -77 CTGTAGGGTTAATTAAAATTATTTATTGAGTTGAA 15 104 1 AATTATATTA 0.898867 -40 CTCGCGCTACAATCTCCCTTTTTGATTGCGGAGTA 16 112 1 AATCCTTTTA 0.793206 -189 TATATAATGAAATGATAATCATTGAAGCTTTTTTA 16 226 0 AATGATATTA 0.604085 -75 AAATCCTTTAAATCATCATGTTTAAAAATCAGTTT 16 273 0 AATCATTTTA 0.927309 -28 TTAAATCCTTATCTTTTATGATTTGAAC 17 19 0 AATCATTTTA 0.927309 -18 TTTATGTTAAAATTCTGAGATTTTATATATTTTAT 23 50 1 AATTAGTTTA 0.911422 -54 ATTTTATATTTATCGTTAGGTTTTAGGTTTAAAGT 23 78 1 TATCAGTTTA 0.451975 -26 **** ** *** * Masking position 12 Map Score: 12.7135 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 193 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ATATAGCTATAATACACTAAAACAATCTCAAGGTT 1 24 0 AACCTAACAA 0.885415 -234 CTTAAAAAAAACTACCCTTAAAAAAATCAATCTAA 1 74 0 AACCTTAAAA 0.660426 -184 AAGTAACGCTAAATCAATATAATTCAA 1 241 0 GACCTAACAA 0.691635 -17 CAGCTGAGCTAACACCCCAAATAAAATTAAGCGAG 2 135 1 AACCCAAAAA 0.976881 -166 AAAGCTTGTTAGAATACCAAAAAAAAAGTAAAAAG 3 36 0 AATCCAAAAA 0.952275 -64 TTTTTATATTATAATACCCAATCAATGCGTTTAAT 4 105 1 AATCCCACAA 0.743653 -61 TTAAGCTAAAAACACCCCACAAATAAGCATAAATG 5 65 1 AACCCAAATA 0.806158 -104 ATTCTTTTGCATTATTCCATGAAAAAAGCCACGCT 7 129 1 AATCCAGAAA 0.852763 -100 AAAATAGGGGGGGACGCCACGCAAAAACCTAATAA 14 17 1 GACCCAGAAA 0.780709 -82 AAAATGTAGTAAAATACCAAACAAAACCCCCTAAA 15 48 0 AATCCAAAAA 0.952275 -96 TCATTATATAATCACACCAAACAAACTGATTTTTA 16 251 1 AACCCAAAAA 0.976881 -50 AGCTTCTAGAATGATTCTAGACAAAACAAAAGGTA 20 144 1 AATCTAAAAA 0.888005 -157 AAAACGATAAAATACACTCTAAAAATAAATAAAAT 21 40 1 AACCTCAAAA 0.841391 -39 AAATAAATAAAATATGCGAGAAAAATC 21 62 1 AATCGAAAAA 0.743538 -17 * ** *** * *** Masking position 4 Map Score: 6.66521 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 434 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 CTCGCTTAATTTTATTTGGGGTGTTAGCTC 2 140 0 TTTATTTGGG 0.909235 -161 CTTTTTACTTTTTTTTTGGTATTCTAACAA 3 36 1 TTTTTTTGGT 0.923924 -64 TCAAAAGCCTTTTTTTAGGTAAATATAGAT 9 23 1 TTTTTTAGGT 0.864327 -55 ACAAACGCTTTTAGTTTGGGTGCGCTACAA 10 13 1 TTAGTTTGGG 0.82374 -52 TAAAGTATTTTTTATTAGGTTTTTGCGTGG 14 33 0 TTTATTAGGT 0.864327 -66 TTTAGGGGGTTTTGTTTGGTATTTTACTAC 15 48 1 TTTGTTTGGT 0.97293 -96 TAAAAATCAGTTTGTTTGGTGTGATTATAT 16 256 0 TTTGTTTGGT 0.97293 -45 CTAGGAGGATTTTCTTAGGGGCAGATTTAA 19 14 0 TTTCTTAGGG 0.815386 -106 AGTTTTACCTTTTGTTTTGTCTAGAATCAT 20 154 0 TTTGTTTTGT 0.778933 -147 ********** Masking position 5 Map Score: 5.53732 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 217 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 AAAAAATCAATCTAAAATTCTTAAATTAAA 1 59 0 TCTAAAATTC 0.693436 -199 ATTAAGCGTTTCAAAAAAGCATCAAATTGA 2 196 0 TCAAAAAAGC 0.852076 -105 CCAAAAAAAAAGTAAAAAGCCTCTTTATAA 3 25 0 AGTAAAAAGC 0.630116 -75 TTTTTGGTATTCTAACAAGCTTTTAAATAA 3 48 1 TCTAACAAGC 0.901348 -52 ATCTCTTAATTTTAACATGCTTTTAAAAAT 5 117 0 TTTAACATGC 0.811528 -52 CATTATTCCATGAAAAAAGCCACGCTTTCG 7 138 1 TGAAAAAAGC 0.718758 -91 TTTTATTTGCATTAAAAAGCGATTTTCTTA 8 87 0 ATTAAAAAGC 0.752918 -60 CAAATAAAATGCTAAAATGCCATGATTTAA 8 108 1 GCTAAAATGC 0.893142 -39 TTAATGGTAGTTTAACATGCTTAGAGATAA 11 18 0 TTTAACATGC 0.811528 -41 TTAATGAATTGCTAACATGCTAGCTAAAAA 12 34 0 GCTAACATGC 0.788681 -58 CCATGACTTTTTAAAAAAGCTTCAATGATT 16 215 1 TTAAAAAAGC 0.820513 -86 AATCATCATGTTTAAAAATCAGTTTGTTTG 16 268 0 TTTAAAAATC 0.751429 -33 CGCACAAGGCGCAAAAAAGCCCCTTGATTT 18 21 0 GCAAAAAAGC 0.798484 -89 GGGATTTAAAAAGCTTAAAAAGAG 20 5 1 TTTAAAAAGC 0.941991 -296 AATCTTTATGGGTAAAATGC 20 291 1 GGTAAAATGC 0.78761 -10 ATTAATTCTTTAAAAAGCGTTTTATCTA 21 9 1 TTTAAAAAGC 0.941991 -70 AAGCGTTTTATCTAAAAAACGATAAAATAC 21 25 1 TCTAAAAAAC 0.536557 -54 TAAGCCTAACTTTAAAAATCAAGCCTTCAA 23 16 0 TTTAAAAATC 0.751429 -88 AATCTTTTATGTTAAAATTCTGAGATTTTA 23 45 1 GTTAAAATTC 0.552543 -59 ********** Masking position 5 Map Score: 19.7284 Number of sites scoring better than the average of aligned sites = 1334 Number in coding regions = 1161 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 12 TTATAGCTATATTTTAATTTAAGAATTTTA 1 47 1 ATTTTAATTT 0.754487 -211 GCATTATAACATTTTGCTTAAAAGATGTCA 2 169 1 ATTTTGCTTA 0.913519 -132 TTGATAAGTGATTTTACTTAATCCATAAAA 2 265 0 ATTTTACTTA 0.887278 -36 CTTAAAATTCATTATAATTAACGCTCAAAA 5 40 0 ATTATAATTA 0.584147 -129 GAATGATTTGACTTTGATTATAAAATCTTA 6 44 0 ACTTTGATTA 0.755741 -38 GCTACAATTGATTTTAATTCATTTTAGGGA 10 36 1 ATTTTAATTC 0.720904 -29 TTGTAATCTAATTTTGATTAAATTGAAGCG 13 20 0 ATTTTGATTA 0.936853 -57 TCAATAAATAATTTTAATTAACCCTACAGC 15 103 0 ATTTTAATTA 0.917049 -41 TTGTAGCGCGAGTTTGCTTAGTTGTTGTTT 16 94 0 AGTTTGCTTA 0.687787 -207 CATAAATCCCATTTTGATTTTAAGGATTGT 18 88 1 ATTTTGATTT 0.804843 -22 TTTCTCGCATATTTTATTTATTTTTAGAGT 21 55 0 ATTTTATTTA 0.664562 -24 ********** Masking position 1 Map Score: 3.57961 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 119 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 ATAATGGTGGAGTGTAGGGGGTTCGAACCC 2 73 1 AGTGTAGGGG 0.843623 -228 AATCAACCGCATTCAAGTGGCTTTAAGATC 7 173 1 ATTCAAGTGG 0.717234 -56 TTCAATTTCAATTTTAGGGGGTTTTGTTTG 15 36 1 ATTTTAGGGG 0.787845 -108 ATTGAGTTGAATTCAAGGAGTAAAAC 15 128 1 ATTCAAGGAG 0.941942 -16 CCTTTAATTAAATCAAGGGGCTTTTTTGCG 18 12 1 AATCAAGGGG 0.918405 -98 GGGTTTAAAGAATCAAGGGGAAAAATCGCA 18 47 0 AATCAAGGGG 0.918405 -63 TACACTAATAAGGCTAGGAGGATTTTCTTA 19 27 0 AGGCTAGGAG 0.82922 -93 CTTTAAAAAGGGTCTAGGAGTTTATTTTCA 20 59 1 GGTCTAGGAG 0.90918 -242 GTCTAGAATCATTCTAGAAGCTTCAGCATT 20 136 0 ATTCTAGAAG 0.69845 -165 TTATAACAATGTTCTAGGAGTTTTACCTTT 20 172 0 GTTCTAGGAG 0.910773 -129 ********** Masking position 6 Map Score: 2.93743 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 140 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 GGCTAAATTTTGAAACCTTGAGATT 1 6 1 AATTTTGAAA 0.823878 -252 TTTAGACTTGAAATTTGAAAATAATAACAC 1 111 0 AAATTTGAAA 0.823878 -147 TTATAATATAAAAATTGAGAATTACCCCAC 4 89 0 AAAATTGAGA 0.817174 -77 TATAAGCGTCAATATTGAAAACAGAAATTA 4 136 0 AATATTGAAA 0.943909 -30 TAACGCTCAAAAAATTGAAAAAGAGTTCAA 5 22 0 AAAATTGAAA 0.943909 -147 TTTTAAGAAAATTCAAAAGCCTTTTTT 9 8 1 AAAATTCAAA 0.685442 -70 TTTTTAGGTAAATATAGATAGACTTTATTG 9 34 1 AATATAGATA 0.428004 -44 AAATAACTATAATATTGTAATCTAATTTTG 13 34 0 AATATTGTAA 0.703078 -43 AATACTTTAAAATATTGATAACGCTTCGTT 14 54 1 AATATTGATA 0.841717 -45 AAAACCCCCTAAAATTGAAATTGAAGTCTG 15 31 0 AAAATTGAAA 0.943909 -113 ********** Masking position 5 Map Score: 5.11022 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 177 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 AAATATCCTTTTTGCTTTGATAAG 2 287 0 ATCCTTTTTG 0.894095 -14 AAAAGTAAAAAGCCTCTTTATAAGCCCTAA 3 18 0 AGCCTCTTTA 0.909107 -82 CTTAAAATTAAGCCTTATTGTTTAAGAAAA 8 65 1 AGCCTTATTG 0.950889 -82 AAAATTCAAAAGCCTTTTTTTAGGTAAATA 9 18 1 AGCCTTTTTT 0.90282 -60 AGTATGGCGCAGCCTGATTAGCGCGCACCC 16 143 1 AGCCTGATTA 0.839915 -158 TAATCATTGAAGCTTTTTTAAAAAGTCATG 16 216 0 AGCTTTTTTA 0.786858 -85 AAATCCTCCTAGCCTTATTAGTGTAGGTTT 19 32 1 AGCCTTATTA 0.951816 -88 AAACTCCTAGACCCTTTTTAAAGGGTTTGA 20 52 0 ACCCTTTTTA 0.878633 -249 AAAAACACGAATCCTTTTTGAAAATAAACT 20 77 0 ATCCTTTTTG 0.894095 -224 ********** Masking position 5 Map Score: 4.49581 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 273 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529