AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoN_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 HP0049 51 H. pylori predicted coding region HP0049 #2 HP0051 174 cytosine specific DNA methyltransferase (DDEM) #3 HP0052 194 H. pylori predicted coding region HP0052 #4 HP0054 37 adenine/cytosine DNA methyltransferase #5 HP0055 26 proline permease (putP) #6 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #7 HP0512 290 glutamine synthetase (glnA) #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 HP0900 108 hydrogenase expression/formation protein (hypB) #12 HP0902 300 H. pylori predicted coding region HP0902 #13 HP1169 212 glutamine ABC transporter, permease protein (glnP) Motif number 1 GATTGTGTTATAGTTATTTAAAAGGATATTTTGA 1 28 1 TGTTTTATTT 0.902722 -24 TAGCGCTCATTAGTTTTTGTTTAAAGGTTTTAGAATGCTAT 3 83 0 TGTTTGTTTT 0.64424 -112 AACAATAACCTTTTATTTTTTAAAAGGATTATAAGATAGCG 3 119 0 TTTTTTATTA 0.928085 -76 AAAAGGTTATTGTTGCTTGTTTCTTGCTTTTTAACGCTATT 3 146 1 TTTTTGTTTT 0.841947 -49 CTTCATTTACTTTTCGTTTAATAATAAATTATAACATTCGC 6 72 0 TTTTTTATTA 0.928733 -229 TGATAATTTGTATTGTTTTTAGCTTCATTTACTTTTCGTTT 6 94 0 TTTTTTTTTA 0.928742 -207 TACACAATGATAAGAATTTGAGTGATAATTTGTATTGTTTT 6 116 0 TAGTTTATTT 0.613341 -185 TTCCAACCTTTTTGAGTTTATCACGCATTTTTACACAATGA 6 147 0 TTGTTTTTTT 0.849278 -154 TTATTGGTAATGTTTTTTAATTTTAAATTTTGTTCTAGCGG 6 201 0 TTTTTATTTT 0.774969 -100 GAGCTTACCTTTTATTTAAGAATTTGACTTGATTG 6 276 0 TACTTTATTT 0.697937 -25 GAATTTCGCCTTTTGATTTAATATCAGTTTAATATTTTTCT 8 65 1 TTTTTTTTTA 0.928742 -236 TCTTCCTATATGATATTTATATGATATTTTTGGGTAATTTA 8 103 1 TATTTATTTT 0.492255 -198 AGCTTAAATTTTTTAATTTGCAGCCAAATTTGTTAGGATTG 9 95 0 TTTTTTATTT 0.964661 -93 AATTTAAGCTTTTTTCTTTTTTTTTGATTTAATACTAGGTA 9 126 1 TTTTTTTTTA 0.928742 -62 CGACTTTTTTTATCTTTTTGGCTGATTTTTTAGATCAGAAA 11 16 0 TTCTTTTTTT 0.891395 -93 GTTGTTCCTTTCTTTTAAAATTTTCGTATCGTA 11 86 0 TTTTTTATTT 0.964661 -23 TCCAAAACCTTTTTGGTTTGCAAAGCGATTTCTAATTCTTC 12 160 0 TTTTTTATTT 0.964661 -141 TTAAGAAAGCTAATTTTTTACCCAAAAATTTCTTATAGATT 12 228 0 TATTTTATTT 0.876233 -73 TGTGATATTTTCTTAATTTAGAACTTAATTTAAGAAAGCTA 12 257 0 TTTTTTATTT 0.964661 -44 GTCCTCTCCATTTAATGATTGTTTAATCATTGTTG 13 5 1 TTCTTTTTTA 0.796702 -208 TAATCATTGTTGTTAATTTCAGCCAGTTTTTTTATTATAAT 13 34 1 TTTTTTTTTT 0.964661 -179 TTTTTAAACATGGTGCTTTAAAGCGTCATTAATTTTTAAGG 13 173 1 TGTTTTATTA 0.815866 -40 * ** *** **** Masking position 8 Map Score: 22.2864 Number of sites scoring better than the average of aligned sites = 1124 Number in coding regions = 864 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 TCAAAATATCCTTTTAAATAACTAT 1 37 0 TCATCCTTTT 0.986959 -15 AAACTCCTCTTCGCTAGATCCTTTTTTTAAAGCCC 2 31 0 TCATCCTTTT 0.986959 -144 TGAGAATGTTTCTAATCAAGCGTTTTTGAAACTCC 2 59 0 TCAAGCGTTT 0.872753 -116 CCCGCTTGACTTATCTTATCCTTTTCTTAAGCCAT 3 39 1 TTATCCTTTT 0.972779 -156 TCATTAGTTTTTGTTTAAAGGTTTTAGAATGCTAT 3 83 0 TTAAGGTTTT 0.685904 -112 ATGAGCGCTATCTTATAATCCTTTTAAAAAATAAA 3 114 1 TCATCCTTTT 0.986959 -81 AATTTTTTGTAAATCCGTTTAATTTAAAAT 6 6 1 TTATCCGTTT 0.912074 -295 TAAAATCGTTTCGTTCAATGGTTTTAAATTACACG 6 35 1 TCATGGTTTT 0.858961 -266 TAATTAATTCTCATTCCAACCTTTTTGAGTTTATC 6 166 0 TCAACCTTTT 0.982896 -135 AAAGTGTTGCTCAAGGCAACCTATTAGAAGTATAA 8 260 0 TCAACCTATT 0.849758 -41 GATTGCTCAATCCTTTTTATGAAAGAG 9 3 1 TTATCCTTTT 0.972779 -185 TTGAGTTAAATCAACCCAAGCTTTTAGCACCAAGA 9 48 0 TCAAGCTTTT 0.959398 -140 ATTTAGCGACTTTTTTTATCTTTTTGGCTGATTTT 11 28 0 TTATCTTTTT 0.719432 -81 TATTCTGTTTTTTCCAAAACCTTTTTGGTTTGCAA 12 178 0 TTAACCTTTT 0.964458 -123 ** ******** Masking position 8 Map Score: 18.4203 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 195 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 ATGTTTCTAATCAAGCGTTTTTGAAACTCCTCT 2 56 0 TAAGCTTTTG 0.777665 -119 AGCGGGTTTTTATAGCCAGTTTCAATAAAACTT 3 12 0 TTAGCATTTC 0.933334 -183 ATAAGATAAGTCAAGCGGGTTTTTATAGCCAGT 3 25 0 TAAGCGTTTT 0.956659 -170 AAAAGGTTATTGTTGCTTGTTTCTTGCTTTTTA 3 146 1 TTTGCTTTTC 0.579466 -49 TTGTATTGTTTTTAGCTTCATTTACTTTTCGTT 6 95 0 TTAGCTATTT 0.664638 -206 TTGACTTGATTGTAGCATGTTTTAAGCGGGTGG 6 255 0 TTAGCTTTTT 0.958613 -46 CACTCCTTGATTTAGCGGATTTTACCGCATGCA 7 169 1 TTAGCGTTTT 0.961677 -122 AAGTAGAATCTGTATCAAGTTTTATTAAGATGC 7 199 0 TTATCATTTT 0.550416 -92 ATTAGAAGTATAAGGCTGATTTTTAAATGGAAA 8 240 0 TAGGCGTTTT 0.855604 -61 CCAAGAGGCATAAAGCCTCTTTCATAAAAAGGA 9 21 0 TAAGCTTTTC 0.924068 -167 TTGATTTAACTCAAGCAAATTTTCTTCAATCCT 9 69 1 TAAGCATTTT 0.953216 -119 ATTAAAAAATTTAAGCTTTTTTCTTTTTTTTTG 9 119 1 TAAGCTTTTC 0.924899 -69 TTTTTATCTTTTTGGCTGATTTTTTAGATCAGA 11 18 0 TTGGCGTTTT 0.870745 -91 ACGACTATGATTTAGCGACTTTTTTTATCTTTT 11 39 0 TTAGCATTTT 0.958613 -70 CTTAATTTAAGAAAGCTAATTTTTTACCCAAAA 12 242 0 GAAGCATTTT 0.720851 -59 TGTTGTTAATTTCAGCCAGTTTTTTTATTATAA 13 41 1 TCAGCATTTT 0.844034 -172 * **** * **** Masking position 11 Map Score: 15.4419 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 578 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TAAAAGGATTATAAGATAGCGCTCATTAGTTTTTG 3 105 0 ATAAGTGGTA 0.784134 -90 GATAAACTCAAAAAGGTTGGAATGAGAATTAATTA 6 166 1 AAAAGTGATA 0.862071 -135 ATATTATAAAAATTGGTGGGAATGATAAG 7 5 0 AATTGTGATA 0.971668 -286 ATCATCCCATAATTGTTCGCATTATTCCTTTTTCC 7 38 1 AATTGTGATT 0.856159 -253 TACAACCTCTGATAGATAGGAATGACAAATTGATT 7 78 1 GATAGTGATA 0.907645 -213 AGGAATGACAAATTGATTGTTTTGATTTTCTTCAA 7 95 1 AATTGTGTTA 0.843906 -196 AATTGAGTTTGATTGATAGGGGTGATTATAGCATT 7 245 0 GATTGTGGTA 0.936612 -46 TAAAGTGCCGATTTGATGGTGCTTAGGCTGGGATT 8 25 0 ATTTGTGGTA 0.952227 -276 TTTATTTCAAAGTTGTTTGTAATAAGGGAAAATTT 8 202 0 AGTTGTGATA 0.877334 -99 TTATACTTCTAATAGGTTGCCTTGAGCAACACTTT 8 260 1 AATAGTGCTA 0.8445 -41 TCTTGGTGCTAAAAGCTTGGGTTGATTTAACTCAA 9 48 1 AAAAGTGGTA 0.864294 -140 ATTGAAGAAAATTTGCTTGAGTTAAATCAACCCAA 9 64 0 ATTTGTGGTA 0.952227 -124 TTGCAGCCAAATTTGTTAGGATTGAAGAAAATTTG 9 84 0 ATTTGTGATA 0.951363 -104 GCTTTTCCTTGTTAGGTGGAATTAAAATTATACCT 9 162 0 GTTAGTGATA 0.848607 -26 TATTCACCCCAATTGTTAGAAGTTTGGAAAACCCA 13 131 0 AATTGTGATT 0.856159 -82 ***** * * * * * Masking position 7 Map Score: 11.8359 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 116 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TGTGTTATAGTTATTTAAAAGGATATTTTG 1 31 1 TTATTTAAAA 0.790692 -21 CCCTAAATTAAAAGGGTCAATAG 3 182 0 TAAATTAAAA 0.922645 -13 TAAATCCGTTTAATTTAAAATCGTTTCGTT 6 20 1 TAATTTAAAA 0.938236 -281 TCGCATCGTGTAATTTAAAACCATTGAACG 6 46 0 TAATTTAAAA 0.938236 -255 CGTTTAATAATAAATTATAACATTCGCATC 6 69 0 TAAATTATAA 0.505091 -232 CGCTAGAACAAAATTTAAAATTAAAAAACA 6 202 1 AAATTTAAAA 0.725004 -99 AGCTTACCTTTTATTTAAGAATTTGACTTG 6 280 0 TTATTTAAGA 0.677205 -21 TTTTTTGAAGAAAATCAAAACAATCAATTT 7 104 0 AAAATCAAAA 0.607823 -187 AAACTGATATTAAATCAAAAGGCGAAATTC 8 65 0 TAAATCAAAA 0.899297 -236 TATTTTTGGGTAATTTAAGATGAATATCGG 8 127 1 TAATTTAAGA 0.894024 -174 AGTAACAAATTTATTCAAAACGCTACCGAT 8 152 0 TTATTCAAAA 0.738793 -149 AATTTGGCTGCAAATTAAAAAATTTAAGCT 9 106 1 CAAATTAAAA 0.635023 -82 TACCTAGTATTAAATCAAAAAAAAAGAAAA 9 137 0 TAAATCAAAA 0.899297 -51 ATTTAGAACTTAATTTAAGAAAGCTAATTT 12 253 0 TAATTTAAGA 0.894024 -48 AATTAAGTTCTAAATTAAGAAAATATCACA 12 268 1 TAAATTAAGA 0.868833 -33 TTTTTTATTATAATCCAAAATTTCTTTGAA 13 61 1 TAATCCAAAA 0.590559 -152 ********** Masking position 7 Map Score: 17.2799 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 112 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 CTTCGCTAGATCCTTTTTTTAAAGCCCTATG 2 27 0 TCCTTTTTTA 0.950761 -148 CTCTAAATTGTCTTTATTGCGATTGAGAATG 2 86 0 TCTTTATTCG 0.771566 -89 ACTTATCTTATCCTTTTCTTAAGCCATGCTT 3 47 1 TCCTTTTCTA 0.78431 -148 TTTGATCTCCTTATTTAATACAATAT 5 9 0 TCCTTATTAA 0.80438 -18 TTCGCATTATTCCTTTTTCCAACTATACAAC 7 53 1 TCCTTTTTCA 0.932195 -238 ATACAGATTCTACTTTTTTTGCCCCATAAAT 7 217 1 TACTTTTTTG 0.671238 -74 GCCAAATTTTCCCTTATTACAAACAACTTTG 8 199 1 CCCTTATTCA 0.910971 -102 GATTGCTCAATCCTTTTTATGAAAGAGGCTT 9 11 1 TCCTTTTTTG 0.962842 -177 AAAAAACCCCTTATTTTATTGAAAGTAT 10 22 0 CCCTTATTTA 0.934943 -18 CTTAAACAATTCTTTATTCTGTTTTTTCCAA 12 196 0 TCTTTATTTG 0.8259 -105 AAAACCCAAGCCCTTATTATGGGAAGTTTAT 13 108 0 CCCTTATTTG 0.950705 -105 ******** ** Masking position 5 Map Score: 5.6563 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 227 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TCGCAATAAAGACAATTTAGAGTTTGCGCAATTG 2 95 1 GAATTTGGTT 0.983492 -80 ATATTTATATGATATTTTTGGGTAATTTAAGATG 8 115 1 GAATTTGGTA 0.987274 -186 TGTAATAAGGGAAAATTTGGCGTAATAAAGTGAA 8 186 0 GAATTTGGTA 0.987274 -115 TTATTTTATTGAAAGTATAGTGATAGAAC 10 6 0 GAATATGGAT 0.843282 -34 TGAAGGCTTAGAAAATTTAGGGATCGCTTTATGT 12 39 1 GAATTTGGAT 0.962852 -262 AAATCTATAAGAAATTTTTGGGTAAAAAATTAGC 12 227 1 GAATTTGGTA 0.987274 -74 ACTATTCAAAGAAATTTTGGATTATAATAAAAAA 13 61 0 GAATTTGTTA 0.909609 -152 ** * *** * *** Masking position 4 Map Score: 5.38831 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 41 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 AAATATCCTTTTAAATAACTATAACACAATCTCA 1 25 0 TTAAACATAA 0.698414 -27 GATCCTTTTTTTAAAGCCCTATGACAAGTAGGGC 2 16 0 TTAAACATGA 0.969895 -159 GCAATTGCGTTTTGAAACCGATGATTTTTCAACG 2 122 1 TTTGACATGA 0.919066 -53 TTTAAAGGTTTTAGAATGCTATGAACAAAGCATG 3 71 0 TTAGACATGA 0.937313 -124 TTTCTTGCTTTTTAACGCTATTGACCCTTTTAAT 3 165 1 TTTAATTTGA 0.598963 -30 CATCGTGTAATTTAAAACCATTGAACGAAACGAT 6 39 0 TTTAACTTGA 0.822396 -262 TAACCACCTTTAATTGTTATGAATTGAGTTTG 7 269 0 TTTAATATGA 0.88838 -22 AAGAAAAATATTAAACTGATATTAAATCAAAAGG 8 73 0 TTAAAAATTA 0.415473 -228 TACAAACAACTTTGAAATAAATGATTTCCATTTA 8 216 1 TTTGAAATGA 0.662511 -85 GCGCACTTAATTAAACGACTATGATTTAGCGACT 11 52 0 TTAAACATGA 0.970141 -57 ACAACAATGATTAAACAATCATTAAATGGAGAGG 13 13 0 TTAAATATTA 0.570114 -200 ACTGGCTGAAATTAACAACAATGATTAAACAATC 13 27 0 ATTAACATGA 0.708343 -186 TAATGACGCTTTAAAGCACCATGTTTAAAAACAG 13 170 0 TTAAACATGT 0.761818 -43 ACGCTATACCTTAAAAATTAATGACGCTTTAAAG 13 188 0 TTAAATATGA 0.912904 -25 ***** * **** Masking position 5 Map Score: 7.28623 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 349 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 AAGGATAAGATAAGTCAAGCGGGTTTTTAT 3 32 0 TAAGTCAAGC 0.950454 -163 ATCCTTTTCTTAAGCCATGCTTTGTTCATA 3 56 1 TAAGCCATGC 0.945688 -139 AATGAGACTTAAAGCCACCCGCTTAAAACA 6 241 1 AAAGCCACCC 0.873425 -60 TGAGTTAAATCAACCCAAGCTTTTAGCACC 9 52 0 CAACCCAAGC 0.949621 -136 TGGGTTGATTTAACTCAAGCAAATTTTCTT 9 65 1 TAACTCAAGC 0.92182 -123 TCGCTTTATGTAAGCCCACCAACGACAATC 12 62 1 TAAGCCCACC 0.931937 -239 TTAGTGAATTTAAGCCAACCTGACGCTAAA 12 103 1 TAAGCCAACC 0.980971 -198 GAAGTTTGGAAAACCCAAGCCCTTATTATG 13 118 0 AAACCCAAGC 0.957313 -95 ********** Masking position 3 Map Score: 5.62055 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 155 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 AACGCTATTTGAATGAGATTGTGTTATAGTTATT 1 12 1 GATGAATGTT 0.973947 -40 TCTTTATTGCGATTGAGAATGTTTCTAATCAAGC 2 73 0 GATGAATGTT 0.973947 -102 ATAAGAATTTGAGTGATAATTTGTATTGTTTTTA 6 114 0 GATGAATTTT 0.978305 -187 AAAAAGGTTGGAATGAGAATTAATTACCGCTAGA 6 175 1 GATGAATTAT 0.917523 -126 CTTAGGCTGGGATTGAAAGGTTTTACTA 8 5 0 GATGAAGTTT 0.942818 -296 AAAACTCCTAGTGTGATATTTTCTTAATTTAGAA 12 275 0 GTTGAATTTT 0.917523 -26 ** *** * *** * Masking position 8 Map Score: 0.2801 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: -6.81878e-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 TCAAAATATCCTTTTAAATAAC 1 40 0 AAAATATCCT 0.705554 -12 CAAGCGTTTTTGAAACTCCTCTTCGCTAGA 2 48 0 TGAAACTCCT 0.688017 -127 GATTTTCTTCAAAAAATCCTAATAGTGTGG 7 118 1 AAAAAATCCT 0.938279 -173 GCTTCCATAATAACACTCCTTGATTTAGCG 7 156 1 TAACACTCCT 0.923965 -135 TAAATGCTATAATCACCCCTATCAATCAAA 7 243 1 AATCACCCCT 0.747676 -48 AAAAAACCCCTTATTTTATTG 10 29 0 AAAAACCCCT 0.935898 -11 TAGATTTCTTAAACAATTCTTTATTCTGTT 12 204 0 AAACAATTCT 0.657391 -97 CAAAAACTCCTAGTGTGATAT 12 290 0 AAAAACTCCT 0.967604 -11 AACAATGATTAAACAATCATTAAATGGAGA 13 15 0 AAACAATCAT 0.657394 -198 ********** Masking position 10 Map Score: 0.553569 Number of sites scoring better than the average of aligned sites = 637 Number in coding regions = 553 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 13 ********** No masking Map Score: -6.81878e-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 14 ********** No masking Map Score: -6.81878e-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 15 ********** No masking Map Score: -6.81878e-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