AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR6_hpyl_opreg_300.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 HP0166 235 response regulator (ompR) #2 HP0168 46 H. pylori predicted coding region HP0168 #3 HP0170 74 H. pylori predicted coding region HP0170 #4 HP0171 60 peptide chain release factor RF-2 (prfB) #5 HP0174 300 H. pylori predicted coding region HP0174 #6 HP0977 128 conserved hypothetical secreted protein #7 HP1010 300 polyphosphate kinase (ppk) #8 HP1011 36 dihydroorotate dehydrogenase (pyrD) #9 HP1015 111 H. pylori predicted coding region HP1015 #10 HP1017 97 amino acid permease (rocE) #11 HP1018 47 H. pylori predicted coding region HP1018 #12 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 AAACGATCAAAGGAATTGTTTAAAAACATTAAAA 1 12 1 AGGTTTTAAA 0.87915 -224 AGATACCTTGAAAATATCTTAAAAATAAAAATTC 1 119 0 AAATTTAAAA 0.950412 -117 AGATATTTTCAAGGTATCTTTAATAATAAAATGC 1 134 1 AAGTTTTAAT 0.907311 -102 TTAACAAAGTTAATCGTTTTTAAAGTTGCAGAAA 1 189 1 TAATTTTAAA 0.897967 -47 GCGTTTCTCTTAATCATTTTCAATACCTAATCTC 2 23 0 TAATTTCAAT 0.592335 -24 GGTTACTATAAAACGCTTTTTAAAACCAATTGGC 3 40 1 AAATTTTAAA 0.964327 -35 CTTATCATTATAGCATTGTTAAAAGCCATT 4 7 0 TAGTTTAAAA 0.900744 -54 AAAAGACAATAAATATTATTACAACATCTGAGGC 5 34 0 AAATTTACAA 0.646924 -267 AAAAAATGTTAAAGAAGATTCAAAAATTCTCGAT 5 99 1 AAAGTTCAAA 0.835934 -202 AATAGAGTATAGAAGTTATTTAATATGGGATAAC 5 232 0 AGATTTTAAT 0.554658 -69 TATTTTAACCAAAGGTTATTAAAATTATCCTTAT 6 28 0 AAATTTAAAA 0.950412 -101 GATTTTACTATAAGGTTGTTTAAACCTGAATTTC 6 71 1 TAATTTTAAA 0.897967 -58 TTAACCCTAAAAGATCGCTTAAAATTTTTTTAGC 7 15 0 AAGGTTAAAA 0.887936 -286 GGGTTAAATGAAGTTTTATTCAAAAAATGAAGTT 7 42 1 AAGTTTCAAA 0.963056 -259 GTTTTACAAAAAAGAGTTTTTAAACAACAACTAA 7 73 1 AAATTTTAAA 0.964327 -228 ATGGTCGGAGTAGCGGGATTCAAACCCACGACCT 7 185 0 TAGGTTCAAA 0.706956 -116 ATAATCATTGAAGCTTTTTTAAAAAGTCATGGTC 7 213 0 AAGTTTAAAA 0.965367 -88 ACACCAAACAAACTGATTTTTAAACATGATGATT 7 264 1 AACTTTTAAA 0.903555 -37 ATAGCCCAACAAGCATTTTTTAATGAATTGCAAC 9 55 0 AAGTTTTAAT 0.907311 -57 GAACGCTAAAAACTTCTTTTAAAATA 10 3 0 AACTTTAAAA 0.869153 -95 TAAGCGTTTTAAGGTTTTTTTAAAGAACGCTAAA 10 27 0 AAGTTTTAAA 0.975195 -71 *** * ****** Masking position 9 Map Score: 25.3398 Number of sites scoring better than the average of aligned sites = 1400 Number in coding regions = 1156 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 AAAACGATCAAAGGAATTGTTT 1 2 1 AAAGATCAAA 0.745513 -234 GAATTGTTTAAAAACATTAAAAAATAAGACT 1 24 1 AAACATTAAA 0.967147 -212 CCATGAAAACAAAGCCTTAAATTTCCATTAA 1 70 1 AAACCTTAAA 0.970729 -166 ATAAAAATTCAAAACATTATCATAGTTATTA 1 98 0 AAACATTATC 0.880996 -138 TTTAATAATAAAATGCTAGAATTAGTCCCCT 1 152 1 AAAGCTAGAA 0.637855 -84 TTAGTCCCCTAAAACATTAACAAAGTTAATC 1 173 1 AAACATTAAC 0.960212 -63 GCAACTTTAAAAACGATTAACTTTGTTAATG 1 187 0 AAAGATTAAC 0.952772 -49 AAAGTTGCAGAAATCATTGAAGGAGTTAATT 1 210 1 AAACATTGAA 0.85174 -26 TAGGTATTGAAAATGATTAAGAGAAACGC 2 28 1 AAAGATTAAG 0.769527 -19 TTTCTTTCCAAAAAGAATAAAACTAACACCA 5 69 0 AAAGAATAAA 0.602035 -232 AAACGCTAAAAAAATTTTAAG 7 1 1 AAAGCTAAAA 0.900255 -300 AAACTTCATTTAACCCTAAAAGATCGCTTAA 7 27 0 TAACCTAAAA 0.551171 -274 GACTTTTTAAAAAAGCTTCAATGATTATCAT 7 219 1 AAAGCTTCAA 0.746173 -82 TTATATAATGAAATGATAATCATTGAAGCTT 7 231 0 AAAGATAATC 0.668299 -70 TAGAAATCCTTTAAATCATCATGT 7 287 0 AAACCTTTAA 0.703503 -14 GTTATCGTTCAAATCATAAAAGATAAGGATT 8 13 1 AAACATAAAA 0.90552 -24 TTAAATCCTTATCTTTTATGATT 8 24 0 AAACCTTATC 0.892932 -13 TATTTCTTGCAAAACATTATCCACATCCACC 9 14 1 AAACATTATC 0.880996 -98 AAAGAGTTGCAATTCATTAAAAAATGCTTGT 9 50 1 AATCATTAAA 0.64409 -62 GTTCTTTAAAAAAACCTTAAAACGCTTAAAA 10 33 1 AAACCTTAAA 0.970729 -65 TTTTTAAAGATTAAATAGTAAAAGA 10 83 0 TAAGATTAAA 0.736767 -15 TTTGAATGACAAAAGCTTATCGCAAAGGTTT 12 100 1 AAAGCTTATC 0.874554 -21 *** ******* Masking position 2 Map Score: 22.3216 Number of sites scoring better than the average of aligned sites = 1500 Number in coding regions = 1229 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 3 ATTGTTTAAAAACATTAAAAAATAAGACTTT 1 26 1 AACATTAAAA 0.959813 -210 AAAATATCTTAAAAATAAAAATTCAAAACAT 1 112 0 AAAAATAAAA 0.891215 -124 AGTCCCCTAAAACATTAACAAAGTTAATCGT 1 175 1 AACATTAAAA 0.959813 -61 TGATTTCTGCAACTTTAAAAACGATTAACTT 1 195 0 AACTTTAAAA 0.701554 -41 GAATAAAACTAACACCAAAAAAGACAATAAA 5 55 0 AACACCAAAA 0.948308 -246 TTTTCTTTCCAAAAAGAATAAAACTAACACC 5 70 0 AAAAAGAAAA 0.606734 -231 GAATGCATACAACAATAATTACGAATATTAT 5 145 0 AACAATAATA 0.890655 -156 ACCAAATATAAAGAATAATAACCCTGGTAAC 5 186 0 AAGAATAAAA 0.822668 -115 GCAATGCTAAAAAACCAAATATAAAGAATAA 5 199 0 AAAACCAATA 0.802651 -102 ACCTTATAGTAAAATCAAATAACCTTATTTT 6 56 0 AAAATCAATA 0.813048 -73 ATCCCTTTAAAAAATCAAAAATATGAAATTC 6 98 0 AAAATCAAAA 0.902563 -31 AAACGCTAAAAAAATTTTAAGC 7 2 1 AACGCTAAAA 0.857066 -299 AGAGTTTTTAAACAACAACTAAGCAAACTCG 7 85 1 AACAACAATA 0.869961 -216 TTTTTTAAAGAACGCTAAAAACTTCTTTTAA 10 15 0 AACGCTAAAA 0.857066 -83 TTTTTAAAGATTAAATAGTAAAAGAGC 10 81 0 AAGATTAATA 0.749902 -17 GCTAAACTTCAAAATTAAGAAAAGA 11 5 0 AAAATTAAAA 0.918555 -43 ******** ** Masking position 7 Map Score: 13.8225 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 491 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 GTTATTAATGGAAATTTAAGGCTTTGTTTTC 1 74 0 GAATTTAAGG 0.90448 -162 TTTATCGGCTGTCATTTTAGCGCAC 3 5 0 GTATTTTAGC 0.915127 -70 AATATTTATTGTCTTTTTTGGTGTTAGTTTT 5 51 1 GTTTTTTTGG 0.405785 -250 CTTTATATTTGGTTTTTTAGCATTGCATGTT 5 204 1 GGTTTTTAGC 0.947959 -97 TTATTATAGAGAGTTTTTAAC 6 1 0 GATTTTTAAC 0.846447 -128 AACGCTAAAAAAATTTTAAGCGATCTTTTAG 7 12 1 AATTTTAAGC 0.867263 -289 AATTTTAAGCGATCTTTTAGGGTTAAATGAA 7 23 1 GACTTTTAGG 0.820134 -278 ATCAAAAAGGGAGATTGTAGCGCGAGTTTGC 7 107 0 GAATTGTAGC 0.815633 -194 CAAACAAACTGATTTTTAAACATGATGATTT 7 268 1 GATTTTAAAC 0.807161 -33 ATTTTAAAAGAAGTTTTTAGCGTTCTTTAAA 10 12 1 AATTTTTAGC 0.895883 -86 TCAAGCGATAGTTTTTTAAGCGTTTTAAGGT 10 46 0 GTTTTTAAGC 0.927602 -52 GAAGTTTAGCAAATTTTAAGGAAGTAACCAT 11 26 1 AATTTTAAGG 0.728745 -22 GGATACTTTTGAAATTTAAGCGGTAAGTTGG 12 14 0 GAATTTAAGC 0.958382 -107 TAAAACAAATGGTATTTTAGCCGATAGTGTT 12 48 0 GGATTTTAGC 0.920883 -73 ** ******** Masking position 6 Map Score: 12.1868 Number of sites scoring better than the average of aligned sites = 939 Number in coding regions = 863 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 ACAATTCCTTTGATCGTTTT 1 1 0 TGATCGTTTT 0.774119 -235 TTAATAACTATGATAATGTTTTGAATTTTT 1 97 1 TGATAATGTT 0.914327 -139 CGATTAACTTTGTTAATGTTTTAGGGGACT 1 175 0 TGTTAATGTT 0.725877 -61 TCTTTTTTGGTGTTAGTTTTATTCTTTTTG 5 62 1 TGTTAGTTTT 0.818689 -239 ATAATTGCATCGAGAATTTTTGAATCTTCT 5 111 0 CGAGAATTTT 0.840992 -190 TCCTTATTATAGAGAGTTTTTAAC 6 5 0 AGAGAGTTTT 0.679784 -124 TCTATAATAAGGATAATTTTAATAACCTTT 6 22 1 GGATAATTTT 0.932344 -107 TGGTGGATGTGGATAATGTTTTGCAAGAAA 9 16 0 GGATAATGTT 0.927994 -96 CTTGATCAAGCGATAGTTTTTTAAGCGTTT 10 52 0 CGATAGTTTT 0.956477 -46 TAGTGTTGTAGGATACTTTTGAAATTTAAG 12 25 0 GGATACTTTT 0.834406 -96 GTATTTTAGCCGATAGTGTTGTAGGATACT 12 38 0 CGATAGTGTT 0.953601 -83 ********** Masking position 7 Map Score: 7.72995 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 121 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 AAACAGAACCTTTATGAGTGGGGTTTTGAACT 4 39 0 CTATGGTGGG 0.981356 -22 TGTATGCATTCTCTTTCCTTGGTTACCAGGGTT 5 165 1 CTTTCTTGGT 0.916834 -136 GGTTATTATTCTTTATATTTGGTTTTTTAGCAT 5 194 1 CTATATTGGT 0.7314 -107 TACAATCTCCCTTTTTGATTGCGGAGTATGGCG 7 119 1 CTTTGTTGCG 0.960443 -182 TTAGCGCGCACCCTTGGGGTGGGTGAGGTCGTG 7 160 1 CTTGGGTGGG 0.974481 -141 GTTTAAAAATCAGTTTGTTTGGTGTGATTATAT 7 256 0 CTTTGTTGGT 0.98286 -45 TGAATTGCAACTCTTTGTTTTGGTGGATGTGGA 9 33 0 CTTTGTTTGG 0.942469 -79 ATTTTTTCGCCCCTTTGTGTGGGGCTATTCTGT 9 87 1 CTTTGGTGGG 0.993089 -25 * **** ***** Masking position 4 Map Score: 4.60871 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 236 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AAAACGATCAAAGGAATTGTTTAAA 1 6 1 GATCAAAGGA 0.929589 -230 TTATCATAGTTATTAATGGAAATTTAAGGC 1 83 0 TATTAATGGA 0.812883 -153 TATTGAAAATGATTAAGAGAAACGC 2 32 1 GATTAAGAGA 0.965614 -15 ATATGAGATTGATTAATAGAGTATAGAAGT 5 250 0 GATTAATAGA 0.925724 -51 TACTATGTAAGATTAAGGGACT 5 289 1 GATTAAGGGA 0.984441 -12 AAAAGAGCTTGATCAAGCGATAGTTTTTTA 10 59 0 GATCAAGCGA 0.95138 -39 ********** Masking position 5 Map Score: 2.66122 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 51 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 AAGACTTTATTTTTCAATATTCCATGAAAA 1 49 1 TTTTCAATAT 0.915076 -187 CTCTTAATCATTTTCAATACCTAATCTCTA 2 21 0 TTTTCAATAC 0.74107 -26 GGTTTTGAACTTATCATTATAGCATTGTTA 4 20 0 TTATCATTAT 0.915076 -41 CTCGATGCAATTATGAATATAATATTCGTA 5 127 1 TTATGAATAT 0.911651 -174 ACAACAATAATTACGAATATTATATTCATA 5 138 0 TTACGAATAT 0.734437 -163 CATAGTAAGCTTATCAATATGAGATTGATT 5 266 0 TTATCAATAT 0.967075 -35 GTTATTAAAATTATCCTTATTATAGAGAGT 6 18 0 TTATCCTTAT 0.859164 -111 TTGCAAAACATTATCCACATCCACCAAAAC 9 20 1 TTATCCACAT 0.815708 -92 ********** Masking position 9 Map Score: 2.31632 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 137 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 9 TTAAAAAATAAGACTTTATTTTTCAATATTC 1 40 1 AGACTTATTT 0.850031 -196 ATGAAAACAAAGCCTTAAATTTCCATTAATA 1 72 1 AGCCTTAATT 0.454554 -164 GTTTTATAGTAACCATAATTTATCGGCTGTC 3 23 0 AACCATATTT 0.835046 -52 AATCTTCTTTAACATTTTTTTTCTTTCCAAA 5 88 0 AACATTTTTT 0.809451 -213 AAAATCAAATAACCTTATTTTAACCAAAGGT 6 46 0 AACCTTTTTT 0.955229 -83 AGGTTGTTTAAACCTGAATTTCATATTTTTG 6 83 1 AACCTGATTT 0.932624 -46 AAGATCGCTTAAAATTTTTTTAGCGTTT 7 8 0 AAAATTTTTT 0.739999 -293 TTTTTGAATAAAACTTCATTTAACCCTAAAA 7 37 0 AAACTTATTT 0.947193 -264 CTTTTTTGTAAAACTTCATTTTTTGAATAAA 7 56 0 AAACTTATTT 0.947193 -245 TGTTGTTTAAAAACTCTTTTTTGTAAAACTT 7 71 0 AAACTCTTTT 0.750879 -230 CACACCAAACAAACTGATTTTTAAACATGAT 7 263 1 AAACTGTTTT 0.869913 -38 AAAATAGCCCAACAAGCATTTTTTAATGAAT 9 61 0 AACAAGATTT 0.360384 -51 AGAACGCTAAAAACTTCTTTTAAAATA 10 7 0 AAACTTTTTT 0.939216 -91 ****** **** Masking position 1 Map Score: 11.4942 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 349 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 10 ATTAAAGATACCTTGAAAATATCTTAAAAATAA 1 125 0 CCTTAAAATC 0.984573 -111 AACCAAAGGTTATTAAAATTATCCTTATTATAG 6 23 0 TATTAAAATC 0.774176 -106 AACTCTAATCCCTTTAAAAAATCAAAAATATGA 6 103 0 CCTTAAAATC 0.984573 -26 GCTTAGTTGTTGTTTAAAAACTCTTTTTTGTAA 7 76 0 TGTTAAACTC 0.838651 -225 TAGAAATCCTTTAAATCATCATGTTTAAAA 7 281 0 CCTTAAAATC 0.984573 -20 GGGTTATCGTTCAAATCATAAAAGATAAGG 8 8 1 CGTTAAAATA 0.750452 -29 TTTAAAAAAACCTTAAAACGCTTAAAAAACTAT 10 37 1 CCTTAAACTT 0.874773 -61 ATGGTTACTTCCTTAAAATTTGCTAAACTTCAA 11 24 0 CCTTAAATGC 0.786263 -24 AAGCTTTTGTCATTCAAATGCTCTATTATAGCA 12 85 0 CATTAAACTC 0.944644 -36 **** *** *** Masking position 7 Map Score: 4.0673 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 304 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 ********** No masking Map Score: -1.04207e-12 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 12 ********** No masking Map Score: -1.04207e-12 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 13 ********** No masking Map Score: -1.04207e-12 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