AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR9_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 HP0392 56 histidine kinase (cheA) #7 HP0395 22 conserved hypothetical protein #8 HP0398 28 H. pylori predicted coding region HP0398 #9 HP0399 120 ribosomal protein S1 (rps1) #10 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #11 HP0813 132 conserved hypothetical protein #12 HP0977 128 conserved hypothetical secreted protein #13 HP1010 300 polyphosphate kinase (ppk) #14 HP1011 36 dihydroorotate dehydrogenase (pyrD) #15 HP1015 111 H. pylori predicted coding region HP1015 #16 HP1017 97 amino acid permease (rocE) #17 HP1018 47 H. pylori predicted coding region HP1018 #18 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 TTTTTAATGTTTTTAAACAATTCCTTTGAT 1 17 0 TTTTAAACAA 0.873864 -219 AAAGTCTTATTTTTTAATGTTTTTAAACAA 1 27 0 TTTTTAATGT 0.846927 -209 AAGACTTTATTTTTCAATATTCCATGAAAA 1 49 1 TTTTCAATAT 0.547408 -187 TGAATTTTTATTTTTAAGATATTTTCAAGG 1 118 1 TTTTTAAGAT 0.869415 -118 TTTTAAGATATTTTCAAGGTATCTTTAATA 1 129 1 TTTTCAAGGT 0.793759 -107 AAGTTAATCGTTTTTAAAGTTGCAGAAATC 1 195 1 TTTTTAAAGT 0.939492 -41 TATAAAACGCTTTTTAAAACCAATTGGCAA 3 46 1 TTTTTAAAAC 0.634281 -29 AATGGCTTTTAACAATGCTATAATG 4 6 1 CTTTTAACAA 0.816219 -55 TATATTTGGTTTTTTAGCATTGCATGTTAT 5 207 1 TTTTTAGCAT 0.888322 -94 TTAAAACCCCTTTTTAGCGTTTGAGATAAG 6 37 0 TTTTTAGCGT 0.927974 -20 CATTCTCATGCTTTTAAAATCACTCT 8 7 0 CTTTTAAAAT 0.749912 -22 TTAAAGAAAATTTTCAAAATGTG 9 4 0 TTTTCAAAAT 0.77469 -117 ATTAGCGGTTTTTTTAAAGAAAATTTTCAA 9 17 0 TTTTTAAAGA 0.866693 -104 AATTGTTAGTTTTTAAACGATTTTGTAAGC 9 44 1 TTTTAAACGA 0.918696 -77 TTTTTGCTCCCTTTTAAGGTTTTTCTTTTA 10 14 1 CTTTTAAGGT 0.771207 -67 GTATTATAGCTTTTTAAAAATAAAATATAA 10 52 1 TTTTTAAAAA 0.49568 -29 TGCGCTATGATTTTCAATAATAATGACTTT 11 84 1 TTTTCAATAA 0.546924 -49 TAATAATGACTTTTTAAAACTAGTTTGAAG 11 101 1 TTTTTAAAAC 0.634281 -32 ACTCTAATCCCTTTAAAAAATCAAAAATAT 12 105 0 CTTTAAAAAA 0.592168 -24 GCTTAAAATTTTTTTAGCGTTT 13 3 0 TTTTTAGCGT 0.927974 -298 GCTAAAAAAATTTTAAGCGATCTTTTAGGG 13 15 1 TTTTAAGCGA 0.861337 -286 TTTAAGCGATCTTTTAGGGTTAAATGAAGT 13 26 1 CTTTTAGGGT 0.649471 -275 AAAAAAGAGTTTTTAAACAACAACTAAGCA 13 80 1 TTTTAAACAA 0.873864 -221 CGACCATGACTTTTTAAAAAAGCTTCAATG 13 212 1 TTTTTAAAAA 0.49568 -89 ACAAACTGATTTTTAAACATGATGATTTAA 13 271 1 TTTTAAACAT 0.874639 -30 CAACAAGCATTTTTTAATGAATTGCAACTC 15 53 0 TTTTTAATGA 0.846176 -59 TATTTTAAAAGAAGTTTTTAGC 16 3 1 TTTTAAAAGA 0.883191 -95 TTAAAAGAAGTTTTTAGCGTTCTTTAAAAA 16 15 1 TTTTTAGCGT 0.927974 -83 TTTTAAGGTTTTTTTAAAGAACGCTAAAAA 16 25 0 TTTTTAAAGA 0.866693 -73 AGCGATAGTTTTTTAAGCGTTTTAAGGTTT 16 44 0 TTTTAAGCGT 0.861337 -54 TTTTTAAAGATTAAATAGTA 16 88 0 TTTTTAAAGA 0.866693 -10 GTTTAGCAAATTTTAAGGAAGTAACCATG 17 29 1 TTTTAAGGAA 0.640138 -19 ********** Masking position 6 Map Score: 39.0013 Number of sites scoring better than the average of aligned sites = 2966 Number in coding regions = 2370 Number in noncoding regions = 596 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 2 AAAAACATTAAAAAATAAGACTTTATTTTT 1 33 1 AAAAATAAGA 0.945494 -203 TGGAATATTGAAAAATAAAGTCTTATTTTT 1 43 0 AAAAATAAAG 0.956266 -193 TTATTAATGGAAATTTAAGGCTTTGTTTTC 1 74 0 AAATTTAAGG 0.886608 -162 AAAATATCTTAAAAATAAAAATTCAAAACA 1 113 0 AAAAATAAAA 0.905782 -123 AGGTATCTTTAATAATAAAATGCTAGAATT 1 145 1 AATAATAAAA 0.625257 -91 TCTTTCCAAAAAGAATAAAACTAACACCAA 5 68 0 AAGAATAAAA 0.720738 -233 CTAAAAAACCAAATATAAAGAATAATAACC 5 194 0 AAATATAAAG 0.930469 -107 CTTACTATGTAAGATTAAGGGACT 5 287 1 AAGATTAAGG 0.774249 -14 ACTATAAAATAAATATAAAATCCTTAAGGG 9 91 0 AAATATAAAA 0.854732 -30 TTTAAAAATAAAATATAAGGATCGTTA 10 64 1 AAATATAAGG 0.960233 -17 ATCATAGCGCAAAAATAAGGCGATTTTGAC 11 65 0 AAAAATAAGG 0.97528 -68 AACCTTTGGTTAAAATAAGGTTATTTGATT 12 45 1 TAAAATAAGG 0.760123 -84 AAAAAATCAAAAATATGAAATTCAGGTTTA 12 91 0 AAATATGAAA 0.578631 -38 GTTTTATTCAAAAAATGAAGTTTTACAAAA 13 54 1 AAAAATGAAG 0.836148 -247 TCAAATCATAAAAGATAAGGATTTAA 14 21 1 AAAGATAAGG 0.881373 -16 GCTAAACTTCAAAATTAAGAAAAGA 17 6 0 AAAATTAAGA 0.848876 -42 AAGTTTAGCAAATTTTAAGGAAGTAACCAT 17 27 1 AATTTTAAGG 0.575733 -21 ********** Masking position 6 Map Score: 16.4944 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 526 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 ATGGAAATTTAAGGCTTTGTTTTCATGGAA 1 68 0 AAGGCTTTGT 0.621054 -168 AATAACTATGATAATGTTTTGAATTTTTAT 1 99 1 ATAATGTTTT 0.773319 -137 TTTTATTTTTAAGATATTTTCAAGGTATCT 1 123 1 AAGATATTTT 0.452754 -113 AAATGGCGTTTAGAGATTAGGT 2 3 1 ATGGCGTTTA 0.642411 -44 TTGGTTTTAAAAAGCGTTTTATAGTAACCA 3 39 0 AAAGCGTTTT 0.786533 -36 AATGGCTTTTAACAATGCTAT 4 2 1 ATGGCTTTTA 0.485635 -59 CGTTTGAGATAAGAGTATTTTACAATTTTA 6 20 0 AAGAGTATTT 0.454717 -37 AAACGCTAAAAAGGGGTTTTAA 6 45 1 AAGGGGTTTT 0.898476 -12 AAGTTGTATTATAGCTTTTTAAAAATAAAA 10 47 1 ATAGCTTTTT 0.767222 -34 GCGCAAAAATAAGGCGATTTTGACTAGAAT 11 59 0 AAGGCGATTT 0.776785 -74 TTCAATAATAATGACTTTTTAAAACTAGTT 11 96 1 ATGACTTTTT 0.877171 -37 TGGTTAAAATAAGGTTATTTGATTTTACTA 12 51 1 AAGGTTATTT 0.585262 -78 TGATTTTACTATAAGGTTGTTTAAACCTGA 12 70 1 ATAAGGTTGT 0.38983 -59 AAGATCGCTTAAAATTTTTTTAGCGTTT 13 9 0 AAAATTTTTT 0.533909 -292 TTAGGGTTAAATGAAGTTTTATTCAAAAAA 13 39 1 ATGAAGTTTT 0.77093 -262 TATTCAAAAAATGAAGTTTTACAAAAAAGA 13 58 1 ATGAAGTTTT 0.77093 -243 TTTTACAAAAAAGAGTTTTTAAACAACAAC 13 74 1 AAGAGTTTTT 0.76983 -227 TACTCCGACCATGACTTTTTAAAAAAGCTT 13 207 1 ATGACTTTTT 0.877171 -94 ATTTTTAAACATGATGATTTAAAGGATTTC 13 279 1 ATGATGATTT 0.723391 -22 ATCATAAAAGATAAGGATTTAA 14 25 1 ATAAGGATTT 0.416224 -12 GTGGATGTGGATAATGTTTTGCAAGAAATA 15 14 0 ATAATGTTTT 0.773319 -98 TATTTTAAAAGAAGTTTTTAGCGTTCTT 16 9 1 AAGAAGTTTT 0.699359 -89 TAAGCGTTTTAAGGTTTTTTTAAAGAACGC 16 31 0 AAGGTTTTTT 0.84991 -67 TGATCAAGCGATAGTTTTTTAAGCGTTTTA 16 50 0 ATAGTTTTTT 0.71788 -48 ATTTTAGCCGATAGTGTTGTAGGATACTTT 18 36 0 ATAGTGTTGT 0.519499 -85 ATTAAAACAAATGGTATTTTAGCCGATAGT 18 51 0 ATGGTATTTT 0.610253 -70 ********** Masking position 8 Map Score: 17.6275 Number of sites scoring better than the average of aligned sites = 3511 Number in coding regions = 3130 Number in noncoding regions = 381 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 4 ATCGGCTGTCATTTTAGCGCAC 3 3 0 ATTTTAGCGC 0.888216 -72 AATATAAAGAATAATAACCCTGGTAACCAA 5 183 0 ATAATAACCC 0.7435 -118 AGAATAGCCATAAAGAAGAA 7 1 1 AGAATAGCCA 0.822142 -22 GATTTTGACTAGAATAGCGCTTCTATTATT 11 44 0 AGAATAGCGC 0.990164 -89 ATTATTGAAAATCATAGCGCAAAAATAAGG 11 75 0 ATCATAGCGC 0.943716 -58 AAAAAGGGAGATTGTAGCGCGAGTTTGCTT 13 105 0 ATTGTAGCGC 0.869768 -196 TTGATTGCGGAGTATGGCGCAGCCTGATTA 13 133 1 AGTATGGCGC 0.895663 -168 TGGCGCAGCCTGATTAGCGCGCACCCTTGG 13 147 1 TGATTAGCGC 0.780494 -154 AAGGGGCGAAAAAATAGCCCAACAAGCATT 15 72 0 AAAATAGCCC 0.900752 -40 TAACAGAATAGCCCCACACAAAGG 15 98 0 AGAATAGCCC 0.98324 -14 ATTTGTTGCTATAATAGAGCATTTGAATGA 18 79 1 ATAATAGAGC 0.832609 -42 ********** Masking position 5 Map Score: 6.68103 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 241 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 TTTTAAACAATTCCTTTGATCGTTTT 1 1 0 TTCTTATCGT 0.948594 -235 AGCCTTAAATTTCCATTAATAACTATGATAATGTTT 1 82 1 TTCTTATAAT 0.964484 -154 GCGTTTCTCTTAATCATTTTCAATACCTAA 2 27 0 TTCTTATCAT 0.98581 -20 AACTTCTATACTCTATTAATCAATCTCATATTGATA 5 249 1 CTCTTATCAT 0.955312 -52 TTCTTTTTATAAAATTGTAAAATACT 6 1 1 TTCTTATAAT 0.964484 -56 TTTAAGGTTTTTCTTTTATTAAAGTTGTATTATAGC 10 26 1 TTCTTTTAAT 0.829544 -55 GATTTTCCTTTCATCAAACTCATCTCAACC 11 5 1 TTCTTATCAT 0.98581 -128 TTAAAAAACTATCGCTTGATCAAGCTCTTTTACTAT 16 58 1 ATCTTATCAT 0.935163 -40 *** ** **** * Masking position 7 Map Score: 5.15548 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AGTTCAAAACCCCACTCATAAAGGTTCTGTTT 4 39 1 CCCACCATAG 0.971405 -22 AACCCTGGTAACCAAGGAAAGAGAATGCATACA 5 165 0 ACCAAGAAAG 0.876647 -136 CGCCATACTCCGCAATCAAAAAGGGAGATTGTA 13 119 0 CGCAACAAAG 0.963033 -182 CACGACCTCACCCACCCCAAGGGTGCGCGCTAA 13 160 0 CCCACCCAAG 0.980519 -141 ATATAATCACACCAAACAAACTGATTTTTAAAC 13 256 1 ACCAACAAAG 0.973662 -45 TCCACATCCACCAAAACAAAGAGTTGCAATTCA 15 33 1 CCAAACAAAG 0.94617 -79 ACAGAATAGCCCCACACAAAGGGGCGAAAAAAT 15 87 0 CCCACCAAAG 0.993918 -25 ***** **** * Masking position 4 Map Score: 2.76577 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 133 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TTGTTGTATGCATTCTCTTTCCTTGGTTACCA 5 161 1 CATTCTCTCC 0.834069 -140 CTCTATTAATCAATCTCATATTGATAAGCTTA 5 259 1 CAATCTCTTT 0.955644 -42 AAAATTGTAAAATACTCTTATCTCAAACGCTA 6 21 1 AATACTCTTC 0.677102 -36 GCCATTCTCATGCTTTTAAAATCA 8 15 0 CATTCTCTCT 0.843135 -14 TTCCTTTCATCAAACTCATCTCAACCAACAAT 11 15 1 CAAACTCTTC 0.97157 -118 CTATTCTAGTCAAAATCGCCTTATTTTTGCGC 11 57 1 CAAAATCCTT 0.729191 -76 ACTCCAAACTCCCTTCAAACTAGTTT 11 117 0 CAAACTCCTC 0.969659 -16 TTGTTGTTTAAAAACTCTTTTTTGTAAAACTT 13 71 0 AAAACTCTTT 0.848968 -230 AACAACTAAGCAAACTCGCGCTACAATCTCCC 13 98 1 CAAACTCCCT 0.955364 -203 ACTCGCGCTACAATCTCCCTTTTTGATTGCGG 13 111 1 CAATCTCCTT 0.952716 -190 TCACACCAAACAAACTGATTTTTAAACATGAT 13 262 1 CAAACTGTTT 0.810149 -39 ******* * ** Masking position 2 Map Score: 6.20568 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 460 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TAATTCTAGCATTTTATTATTAAAGATACCT 1 145 0 ATTTTATATT 0.758992 -91 CAATTAACTCCTTCAATGATTTCTGCAACTT 1 211 0 CTTCAATATT 0.719604 -25 AATGGCTTTTAACAATGCTATAATGA 4 6 1 CTTTTAAAAT 0.690303 -55 AGATAAGAGTATTTTACAATTTTATAAAAAG 6 13 0 ATTTTACATT 0.640714 -44 CATTCTCATGCTTTTAAAATCACTCT 8 6 0 CTTTTAAATC 0.782408 -23 TTTTTGCTCCCTTTTAAGGTTTTTCTTTTAT 10 14 1 CTTTTAAGTT 0.76764 -67 TAGAATAGCGCTTCTATTATTGTTGGTTGAG 11 34 0 CTTCTATATT 0.926283 -99 TTTAAAAAAGCTTCAATGATTATCATTTCAT 13 224 1 CTTCAATATT 0.719604 -77 AAATCCTTATCTTTTATGATTTGAACGATAA 14 14 0 CTTTTATATT 0.961375 -23 CTAAAAACTTCTTTTAAAATA 16 1 0 CTTTTAAATA 0.708122 -97 TGATCAAGCTCTTTTACTATTTAATCTTTAA 16 74 1 CTTTTACATT 0.933752 -24 TTGTAGGATACTTTTGAAATTTAAGCGGTAA 18 19 0 CTTTTGAATT 0.868718 -102 TTGCGATAAGCTTTTGTCATTCAAATGCTCT 18 94 0 CTTTTGTATT 0.887179 -27 ******* *** Masking position 3 Map Score: 5.96443 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 296 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 AAACTAACACCAAAAAAGACAATAAATATT 5 51 0 CAAAAAAGAC 0.869894 -250 TTTTTTCTTTCCAAAAAGAATAAAACTAAC 5 73 0 CCAAAAAGAA 0.91193 -228 ATCTCAAACGCTAAAAAGGGGTTTTAA 6 40 1 CTAAAAAGGG 0.87967 -17 AGAATAGCCATAAAGAAGAATT 7 8 1 CCATAAAGAA 0.620105 -15 TTTTGTAAGCCAAAAAAGGATACAATACCC 9 64 1 CAAAAAAGGA 0.972919 -57 AAGTTTTATTCAAAAAATGAAGTTTTACAA 13 52 1 CAAAAAATGA 0.778858 -249 TGAAGTTTTACAAAAAAGAGTTTTTAAACA 13 69 1 CAAAAAAGAG 0.947154 -232 ACTCCGCAATCAAAAAGGGAGATTGTAGCG 13 116 0 CAAAAAGGGA 0.946123 -185 AATAGCCCCACACAAAGGGGCGAAAAAATA 15 86 0 CACAAAGGGG 0.80086 -26 ********** Masking position 5 Map Score: 3.41387 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 489 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 ATAAATTATGGTTACTATAAAACGCTTTTT 3 31 1 GTTACTATAA 0.931129 -44 CTTTTTAGCGTTTGAGATAAGAGTATTTTA 6 28 0 TTTGAGATAA 0.716275 -29 TGACTGCCTTACTATAAAATAAATATA 9 104 0 CTTACTATAA 0.880189 -17 GTTATTTGATTTTACTATAAGGTTGTTTAA 12 64 1 TTTACTATAA 0.926043 -65 GTTTTAATTTGTTGCTATAATAGAGCATTT 18 73 1 GTTGCTATAA 0.955074 -48 AAACCTTTGCGATAAGCTTTTGTCA 18 106 0 TTTGCGATAA 0.942177 -15 ********** Masking position 7 Map Score: 0.602445 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 55 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 ********** No masking Map Score: 3.15724e-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: 3.15724e-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: 3.15724e-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