AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR_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 HP0166 235 response regulator (ompR) #2 HP0392 56 histidine kinase (cheA) #3 HP0395 22 conserved hypothetical protein #4 HP0398 28 H. pylori predicted coding region HP0398 #5 HP0399 120 ribosomal protein S1 (rps1) #6 HP0600 163 multidrug resistance protein (spaB) #7 HP0813 132 conserved hypothetical protein #8 HP0977 128 conserved hypothetical secreted protein #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 HP1206 300 multidrug resistance protein (hetA) #13 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 TTTTTTAATGTTTTTAAACAATTCCTTTGAT 1 17 0 TTTTTAAACA 0.955667 -219 TGAATTTTTATTTTTAAGATATTTTCAAGGT 1 118 1 TTTTTAAGAA 0.779107 -118 TTTTAAGATATTTTCAAGGTATCTTTAATAA 1 129 1 TTTTCAAGGA 0.908687 -107 AAGTTAATCGTTTTTAAAGTTGCAGAAATCA 1 195 1 TTTTTAAAGT 0.923563 -41 AGAGTGATTTTAAAAGCATGAGAATGGC 4 8 1 TTTTAAAAGA 0.973062 -21 ATTAGCGGTTTTTTTAAAGAAAATTTTCAAA 5 16 0 TTTTTAAAGA 0.981562 -105 TAATTGTTAGTTTTTAAACGATTTTGTAAGC 5 43 1 TTTTTAAACA 0.956491 -78 TTTAAACGATTTTGTAAGCCAAAAAAGGATA 5 55 1 TTTGTAAGCA 0.718976 -66 AAGTTTGAAATTTTAAAGGGCTTTGTTTTAA 6 78 1 TTTTAAAGGC 0.826131 -86 AAGGGCTTTGTTTTAAAAGCAAAATTTAAAG 6 93 1 TTTTAAAAGA 0.973062 -71 AATAATGACTTTTTAAAACTAGTTTGAAGGG 7 102 1 TTTTAAAACA 0.934268 -31 ATTTTTGATTTTTTAAAGGGATTAGAGTTCT 8 107 1 TTTTAAAGGA 0.974003 -22 CAACAAGCATTTTTTAATGAATTGCAACTCT 9 52 0 TTTTTAATGA 0.866177 -60 TATTTTAAAAGAAGTTTTTAGCG 10 3 1 TTTTAAAAGA 0.973048 -95 TTTTAAGGTTTTTTTAAAGAACGCTAAAAAC 10 24 0 TTTTTAAAGA 0.981562 -74 AAGCGATAGTTTTTTAAGCGTTTTAAGGTTT 10 44 0 TTTTTAAGCT 0.831404 -54 TTTTTAAAGATTAAATAGTAA 10 87 0 TTTTTAAAGT 0.923506 -11 AGTTTAGCAAATTTTAAGGAAGTAACCATG 11 28 1 ATTTTAAGGA 0.805709 -20 ACCGCTTAAATTTCAAAAGTATCCTACAACA 13 21 1 TTTCAAAAGA 0.802044 -100 ********* * Masking position 3 Map Score: 31.7958 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 522 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 AAACAAAGCCTTAAATTTCCATTAATAACTATGATAATG 1 76 1 TAAATTATAC 0.904965 -160 ATCTTAAAAATAAAAATTCAAAACATTATCATAGTTATT 1 99 0 TAAATTATAT 0.982291 -137 TAAGATATTTTCAAGGTATCTTTAATAATAAAATGCTAG 1 132 1 TAAGTAATAT 0.690083 -104 TTAATCGTTTTTAAAGTTGCAGAAATCATTGAAGGAGTT 1 198 1 TAAATTATAT 0.982291 -38 CTTTAAAATTTCAAACTTTAACCGATTATAGTTCCAACC 6 57 0 TAAATTATAT 0.982291 -107 TAAGATTTGGTATAAATTTTCTTTATTATAGCCCATTTT 6 131 0 TTAATTATAT 0.966408 -33 ATTTTTGCGCTATGATTTTCAATAATAATGACTTTTTAA 7 79 1 TTGATTATAT 0.831616 -54 CCAAAGGTTATTAAAATTATCCTTATTATAGAGAGTTTT 8 15 0 TAAATTATAT 0.982291 -114 ATACGAATAATTTAGCTTTCCGTCATCATTTCTTGACAA 12 169 0 TTAGTTATAT 0.908848 -132 CAGAGCATGGTTAAAATTTTAGCTATAATCTAGCTCAAT 12 212 1 TAAATTATAT 0.982291 -89 TTAACACAGCTCAAAACTCATTACATTATTGAAAGAATT 12 256 1 TAAACTATAT 0.904965 -45 TACCATTTGTTTTAATTTGTTGCTATAATAGAGCATTTG 13 65 1 TTAATTATAT 0.966408 -56 * *** ** ** ** Masking position 15 Map Score: 15.245 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 50 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 AATGTTTTTAAACAATTCCTTTGATCGTTTT 1 10 0 AACAACCTTT 0.881186 -226 ATTCCATGAAAACAAAGCCTTAAATTTCCATT 1 67 1 AACAACCTTA 0.881186 -169 ATAAAATTGTAAAATACTCTTATCTCAAACGC 2 19 1 AAAATTCTTA 0.875908 -38 TTAAAACCCCTTTTTAGCGTTTG 2 44 0 TAAAACCTTT 0.922147 -13 CACATTTTGAAAATTTTCTTTAAAAAAACCG 5 10 1 AAAATTCTTT 0.875849 -111 AAAAAAGGATACAATACCCTTAAGGATTTTAT 5 75 1 ACAATCCTTA 0.898495 -46 TGCTTTTAAAACAAAGCCCTTTAAAATTTCAA 6 82 0 ACAAACCTTT 0.887652 -82 AGATTTGGTATAAATTTTCTTTATTATAGCCC 6 136 0 TAAATTCTTT 0.711913 -28 TATTCTAGTCAAAATCGCCTTATTTTTGCGCT 7 58 1 AAAATCCTTA 0.97431 -75 AACTAGTTTTAAAAAGTCATTATTATTGAAAA 7 94 0 AAAAACATTA 0.863038 -39 AAGGATAATTTTAATAACCTTTGGTTAAAATA 8 30 1 TTAATCCTTT 0.531886 -99 ATAGTAAAATCAAATAACCTTATTTTAACCAA 8 50 0 CAAATCCTTA 0.916729 -79 AATTCAGGTTTAAACAACCTTATAGTAAAATC 8 71 0 TAAACCCTTA 0.734701 -58 AAAGAACGCTAAAAACTTCTTTTAAAATA 10 8 0 AAAAATCTTT 0.861825 -90 AGCGTTCTTTAAAAAAACCTTAAAACGCTTAA 10 30 1 AAAAACCTTA 0.97129 -68 AAAACTTCGCAAAATAACATTTCAACTGGAGC 12 20 1 AAAATCATTT 0.875936 -281 TAACACAGCTCAAAACTCATTACATTATTGAA 12 257 1 CAAAACATTA 0.646555 -44 ACTATCGGCTAAAATACCATTTGTTTTAATTT 13 51 1 AAAATCATTT 0.875936 -70 ***** ***** Masking position 10 Map Score: 18.1408 Number of sites scoring better than the average of aligned sites = 1436 Number in coding regions = 1218 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 4 ATTGTTTAAAAACATTAAAAAATAAGACTTTA 1 26 1 AACATTAAAA 0.895007 -210 GTTTTCATGGAATATTGAAAAATAAAGTCTTA 1 48 0 AATATTAAAA 0.757591 -188 CTTAAAAATAAAAATTCAAAACATTATCATAG 1 104 0 AAAATTAAAC 0.947537 -132 AGTCCCCTAAAACATTAACAAAGTTAATCGTT 1 175 1 AACATTAAAA 0.895007 -61 TTCTTTTTATAAAATTGTAAAATACTCTTATC 2 11 1 AAAATTTAAA 0.92731 -46 TTTTTTAAAGAAAATTTTCAAAATGTG 5 6 0 AAAATTTAAA 0.92731 -115 AAAGCCCTTTAAAATTTCAAACTTTAACCGAT 6 70 0 AAAATTCAAC 0.808425 -94 TATAATAAAGAAAATTTATACCAAATCTTATT 6 140 1 AAAATTAACC 0.901164 -24 AATCCCTTTAAAAAATCAAAAATATGAAATTC 8 98 0 AAAAATAAAA 0.723566 -31 GCTAAACTTCAAAATTAAGAAAAGA 11 4 0 AAAATTAAAA 0.960932 -44 GCCAGCAACTAAAATAATCAAAGACTTGGGAT 12 116 1 AAAATATAAA 0.575835 -185 GATTATAGCTAAAATTTTAACCATGCTCTGTG 12 210 0 AAAATTTACC 0.825447 -91 ATTATAGCAACAAATTAAAACAAATGGTATTT 13 62 0 CAAATTAACA 0.661985 -59 ****** * *** Masking position 4 Map Score: 9.3857 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 328 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 TTTAATAATAAAATGCTAGAATTAGTCCCC 1 152 1 AAATGCTAGA 0.903386 -84 GCAACTTTAAAAACGATTAACTTTGTTAAT 1 188 0 AAACGATTAA 0.73479 -48 CTCTTATCTCAAACGCTAAAAAGGGGTTTT 2 35 1 AAACGCTAAA 0.96731 -22 GAGTGATTTTAAAAGCATGAGAATGGC 4 12 1 AAAAGCATGA 0.863617 -17 GCTTTGTTTTAAAAGCAAAATTTAAAGGAG 6 97 1 AAAAGCAAAA 0.850805 -67 ATTCATTAAAAAATGCTTGTTGGGCTATTT 9 61 1 AAATGCTTGT 0.732405 -51 TTTTTTTAAAGAACGCTAAAAACTTCTTTT 10 17 0 GAACGCTAAA 0.919072 -81 AAAAACCTTAAAACGCTTAAAAAACTATCG 10 42 1 AAACGCTTAA 0.972339 -56 TAAATAGTAAAAGAGCTTGATCAAGCGATA 10 67 0 AAGAGCTTGA 0.827877 -31 AATGATGACGGAAAGCTAAATTATTCGTAT 12 178 1 GAAAGCTAAA 0.898178 -123 TTTGAATGACAAAAGCTTATCGCAAAGGTT 13 100 1 AAAAGCTTAT 0.864661 -21 ********** Masking position 2 Map Score: 6.60811 Number of sites scoring better than the average of aligned sites = 1222 Number in coding regions = 1056 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 6 TTCTTCTTTATGGCTATTCT 3 1 0 TGGCTATTCT 0.929741 -22 AAATTTTAAAGGGCTTTGTTTTAAAAGCAA 6 85 1 GGGCTTTGTT 0.863804 -79 GCATGAAAATGGGCTATAATAAAGAAAATT 6 126 1 GGGCTATAAT 0.948959 -38 AATAATAGAAGCGCTATTCTAGTCAAAATC 7 44 1 GCGCTATTCT 0.986457 -89 CCTTATTTTTGCGCTATGATTTTCAATAAT 7 75 1 GCGCTATGAT 0.968915 -58 AATGCTTGTTGGGCTATTTTTTCGCCCCTT 9 72 1 GGGCTATTTT 0.981341 -40 CCTTTGTGTGGGGCTATTCTGTTA 9 98 1 GGGCTATTCT 0.991632 -14 TCATTCAAATGCTCTATTATAGCAACAAAT 13 79 0 GCTCTATTAT 0.837995 -42 ********** Masking position 5 Map Score: 8.32078 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 146 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TTATAGCCCATTTTCATGCTCCTTTAAATTT 6 114 0 TTTCATGCTC 0.888731 -50 GATTTTCCTTTCATCAAACTCATCTCAACCA 7 11 1 TATCAAACTC 0.919815 -122 AACTATCGCTTGATCAAGCTCTTTTACTATT 10 64 1 TATCAAGCTC 0.988819 -34 TTCAAGTCCCTTAGCCAGCTCCAGTTGAAAT 12 38 0 TAGCCAGCTC 0.970613 -263 GCTAAAATTTTAACCATGCTCTGTGCCATAC 12 204 0 TACCATGCTC 0.9696 -97 ATTTTAGCTATAATCTAGCTCAATTTGGCTT 12 227 1 TATCTAGCTC 0.964132 -74 CAATTTGGCTTAACACAGCTCAAAACTCATT 12 247 1 TACACAGCTC 0.887441 -54 * ********* Masking position 10 Map Score: 2.86189 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 107 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TTTTCAATATTCCATGAAAACAAAGCCTTAA 1 59 1 TCCATAAAAC 0.962045 -177 CTAGAATTAGTCCCCTAAAACATTAACAAAG 1 167 1 TCCCCAAAAC 0.992289 -69 ACTCCAAACTCCCTTCAAACTAGTTTTAAA 7 113 0 TCCCTCAAAC 0.962585 -20 ATTATCCACATCCACCAAAACAAAGAGTTGC 9 29 1 TCCACAAAAC 0.982791 -83 ATCTCACCAAAAACTTCGCAAAAT 12 4 1 TCACCAAAAC 0.961025 -297 ***** ***** Masking position 8 Map Score: 2.81818 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 72 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TTTGAGATAAGAGTATTTTACAATTTTATA 2 18 0 GAGTATTTTA 0.930532 -39 ACGCTAAAAAGGGGTTTTAA 2 47 1 GGGGTTTTAA 0.80115 -10 AACAATTAGCGGTTTTTTTAAAGAAAATTT 5 21 0 GGTTTTTTTA 0.928026 -100 CGCTAATTGTTAGTTTTTAAACGATTTTGT 5 40 1 TAGTTTTTAA 0.786366 -81 AAATCCTTAAGGGTATTGTATCCTTTTTTG 5 74 0 GGGTATTGTA 0.744827 -47 GGATGCCTTTGGGTTTTTTATAACAAGGAG 6 19 0 GGGTTTTTTA 0.975595 -145 CAATAATAATGACTTTTTAAAACTAGTTTG 7 98 1 GACTTTTTAA 0.728733 -35 TTATTATAGAGAGTTTTTAAC 8 2 0 GAGTTTTTAA 0.948689 -127 TCATATTTTTGATTTTTTAAAGGGATTAGA 8 103 1 GATTTTTTAA 0.856392 -26 AGCGTTTTAAGGTTTTTTTAAAGAACGCTA 10 29 0 GGTTTTTTTA 0.928026 -69 GATCAAGCGATAGTTTTTTAAGCGTTTTAA 10 49 0 TAGTTTTTTA 0.852082 -49 CCAAGTCTTTGATTATTTTAGTTGCTGGCT 12 115 0 GATTATTTTA 0.812046 -186 TTAAAACAAATGGTATTTTAGCCGATAGTG 13 50 0 TGGTATTTTA 0.786527 -71 ********** Masking position 10 Map Score: 14.5739 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 1162 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 10 ACATTTTGAAAATTTTCTTTAAAAAAACCG 5 12 1 AATTTTCTTT 0.92557 -109 TGCTCCTTTAAATTTTGCTTTTAAAACAAA 6 99 0 AATTTTGCTT 0.971989 -65 ATTTGGTATAAATTTTCTTTATTATAGCCC 6 136 0 AATTTTCTTT 0.92557 -28 GATTTTCCTTTCATCAAACT 7 1 1 GATTTTCCTT 0.933457 -132 AGGTTATTAAAATTATCCTTATTATAGAGA 8 20 0 AATTATCCTT 0.904416 -109 CCATACGAATAATTTAGCTTTCCGTCATCA 12 180 0 AATTTAGCTT 0.895399 -121 AATCTAGCTCAATTTGGCTTAACACAGCTC 12 238 1 AATTTGGCTT 0.926959 -63 ********** Masking position 2 Map Score: 4.49474 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 37 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ********** No masking Map Score: 6.98764e-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 12 ********** No masking Map Score: 6.98764e-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 13 ********** No masking Map Score: 6.98764e-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