AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iarcA_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 HP0026_HP0027 198 HP0026: citrate synthase (gltA), HP0027: isocitrate dehydrogenase (icd) #2 HP0140 230 L-lactate permease (lctP) #3 HP0141 56 L-lactate permease (lctP) #4 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #5 HP0497 228 sodium- and chloride-dependent transporter #6 HP0500 57 DNA polymerase III beta-subunit (dnaN) #7 HP0502 45 H. pylori predicted coding region HP0502 #8 HP0503 88 H. pylori predicted coding region HP0503 #9 HP0505 140 H. pylori predicted coding region HP0505 #10 HP0506 203 conserved hypothetical secreted protein Motif number 1 TCAAAAAAAGATTTTTAAGGGTTATATAGT 1 58 0 ATTTTTAAGG 0.895522 -141 TTTTGAATGCGTGTTTAAAAGTAGCGGTTG 1 82 1 GTGTTTAAAA 0.802484 -117 AAACATTGCGTTTTTTCAAGTTATTTCCAA 1 109 0 TTTTTTCAAG 0.780647 -90 AAAACGCAATGTTTTTAAAAGAAATCATTT 1 125 1 GTTTTTAAAA 0.842606 -74 AATTAGTTTTTTCTTTTAAGTAAGATAAAA 2 182 1 TTCTTTTAAG 0.846733 -49 AATACTTTTAATTATTCAAGGAAAATTT 2 213 1 ATTATTCAAG 0.694803 -18 GGGGGTTTTTAAAGAGAACTAGCA 3 5 1 GTTTTTAAAG 0.938241 -52 CTAAGAGAATATTTTTAAAAAGGGATTTTT 3 35 1 ATTTTTAAAA 0.918061 -22 TAAAATTTACATTTTTTAAACGCTATTAGA 4 54 0 ATTTTTTAAA 0.833972 -161 AAAGGGGCTATTGTTTAAAATTTACATTTT 4 69 0 TTGTTTAAAA 0.81288 -146 AGAAAATTTCATTATTTAAGTAAGGGGAAT 5 13 0 ATTATTTAAG 0.823241 -216 GTTGCTCTGTATTTTTTAGGTATTTTTAAA 5 88 1 ATTTTTTAGG 0.793458 -141 TTTTTTAGGTATTTTTAAAGTGGGTTTTTT 5 99 1 ATTTTTAAAG 0.969512 -130 AAATCTTAAGATCTTTAAAGATTTTAAAAA 5 132 1 ATCTTTAAAG 0.960207 -97 TGCTGTATTAGTTTTTAAAATCTTTAAAGA 5 143 0 GTTTTTAAAA 0.842606 -86 CTCCTTGTCAATGATTAAAATTAAAGAGCG 5 195 0 ATGATTAAAA 0.735384 -34 AAAAGCGTTCTTTTAYGCTATAATTAA 6 8 1 TTCTTTTAYG 0.846733 -50 TAAAGCGTTTATTATTAAAGCATCACACTT 8 15 0 ATTATTAAAG 0.912216 -74 GATGATTAAAGGCTCATCTTG 8 78 0 ATGATTAAAG 0.887451 -11 ATTTTTCTTTATCTTTAATGGGGACATCAT 9 38 0 ATCTTTAATG 0.805304 -103 GATATTTTTCATCTTTTAAAGTAGTGAGTT 9 71 0 ATCTTTTAAA 0.792172 -70 GAAAAATATCATTTTTTAGGGGCTAATGAT 9 91 1 ATTTTTTAGG 0.793458 -50 ATGATACGGATTGATTAAAAAGAAAATACC 10 13 1 TTGATTAAAA 0.586712 -191 TGTATCGTTTTTCTTTAATGGCTTATGTTA 10 141 1 TTCTTTAATG 0.678757 -63 GCAGTTGTTTAATGCCTTCAATCA 10 190 0 TTGTTTAATG 0.678757 -14 ********** Masking position 5 Map Score: 28.6837 Number of sites scoring better than the average of aligned sites = 2114 Number in coding regions = 1737 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 2 ATATAACCCTTAAAAATCTTTTTTTGAATGCGTGT 1 61 1 TAAATTTTTT 0.878292 -138 GCAATGTTTTTAAAAGAAATCATTTAATTTTTTGG 1 130 1 TAAAATATTT 0.885013 -69 ATATTGTGTTTGAAACTCTTAATTTGGAATTTAAG 2 20 0 TAAATTATTT 0.827519 -211 AAATGCTACTTAAAATTAGTTTTTTCTTTTAAGTA 2 169 1 TAAAGTTTTT 0.973163 -62 CCTTGAATAATTAAAAGTATTTTTTTATCTTACTT 2 199 0 TAAAATTTTT 0.922504 -32 AGAATATTTTTAAAAAGGGATTTTTTA 3 40 1 TAAAGATTTT 0.88946 -17 TAATAGCGTTTAAAAAATGTAAATTTTAAACAATA 4 56 1 TAAAGTAATT 0.65935 -159 ATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAG 4 88 1 TAATATTTTT 0.792665 -127 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGC 4 152 1 TAAGGTTTTT 0.968377 -63 CGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGT 4 186 1 TAATGATTTT 0.721288 -29 TCCCCTTACTTAAATAATGAAATTTTCTTAAAATT 5 15 1 TAATGAATTT 0.625837 -214 TAGGTATTTTTAAAGTGGGTTTTTTCTTAAATCTT 5 104 1 TAAGGTTTTT 0.968336 -125 GACCAAAAATTCAAGGGGATTATTTTAACT 6 38 1 TAAGATATTT 0.863416 -20 TAGGATTAACTAAAGCGTTTATTATTAAAGCATCA 8 20 0 TAAGTTTTAT 0.463371 -69 TTTTCATCTTTTAAAGTAGTGAGTTCAAATTTTTC 9 61 0 TAAAGTAGTT 0.741518 -80 CTTTAAAAGATGAAAAATATCATTTTTTAGGGGCT 9 80 1 TAAAATATTT 0.885013 -61 TATAGCTTTATGAAGCGCGTTTTATTGATGCATGG 10 83 0 TAAGGTTTAT 0.812636 -121 ATGCCTTCAATCAAATCTGTATTTTATTAGTATAA 10 168 0 TAAAGTTTTT 0.973866 -36 * *** ** **** Masking position 1 Map Score: 18.3543 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 710 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 AACTCCTAATTATAAGCCAAAAAATTAAATGA 1 149 0 TTAAGCAAAA 0.828074 -50 AGCATTTAATATTAAGTCAAATTTAATGGGTT 2 144 0 ATAAGTAAAT 0.685915 -87 TTATCTTACTTAAAAGAAAAAACTAATTTTAA 2 178 0 TAAAGAAAAA 0.962862 -53 TTTTCTTTTAAGTAAGATAAAAAAATACTTTT 2 190 1 ATAAGAAAAA 0.970605 -41 GAGAACTAGCACTAAGAGAATATTTTTAAAAA 3 24 1 ATAAGAAATA 0.891441 -33 CAAAACCTAAATTGAGAAAAAATTCAATTCAA 4 97 0 ATGAGAAAAA 0.807228 -118 AGGTTTTGTTTATAAGAAAAATTATTTCAAAT 4 121 1 TTAAGAAAAT 0.926379 -94 ATTGTATAATTTTAAGAAAATTTCATTATTTA 5 25 0 TTAAGAAATT 0.757825 -204 GATCTTAAGATTTAAGAAAAAACCCACTTTAA 5 113 0 TTAAGAAAAA 0.970605 -116 TTAYGCTATAATTAAGACCAAAAATTCAAGGG 6 23 1 ATAAGACAAA 0.817522 -35 TAGTTAATCCTAAAAGAGAAAATTATGGCATT 8 43 1 TAAAGAAAAA 0.962862 -46 CCCATTAAAGATAAAGAAAAATTTGAACTCAC 9 46 1 AAAAGAAAAT 0.908088 -95 CTCACTACTTTAAAAGATGAAAAATATCATTT 9 73 1 TAAAGAGAAA 0.778648 -68 GGGGCTAATGATAAAGTAAAAACTCTTTATGA 9 109 1 AAAAGTAAAA 0.81817 -32 CGGATTGATTAAAAAGAAAATACCCAACGCTA 10 19 1 AAAAGAAATA 0.865727 -185 ACATAAGCCATTAAAGAAAAACGATACAAGTT 10 137 0 TAAAGAAAAC 0.81654 -67 * ***** **** Masking position 5 Map Score: 15.9528 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 629 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 TTAAGGGTTATATAGTATTTTTGCGCTAGTAT 1 42 0 TATAGTTTTT 0.551275 -157 TAACCCTTAAAAATCTTTTTTTGAATGCGTGT 1 64 1 AAATCTTTTT 0.895998 -135 CCAAAAAATTAAATGATTTCTTTTAAAAACAT 1 133 0 AAATGTTCTT 0.865803 -66 AAGTCAAATTTAATGGGTTTGTGGTTTATTTT 2 131 0 TAATGTTTGT 0.598922 -100 CTTAAAAGAAAAAACTAATTTTAAGTAGCATT 2 170 0 AAAACATTTT 0.625725 -61 TTGAATAATTAAAAGTATTTTTTTATCTTACT 2 200 0 AAAAGTTTTT 0.944992 -31 AACTAGCACTAAGAGAATATTTTTAAAAAGGG 3 27 1 AAGAGTATTT 0.506402 -30 TAAAAAATCCCTTTTTAAAAATATTC 3 41 0 AAATCTTTTT 0.895998 -16 AGCGTTTAAAAAATGTAAATTTTAAACAATAG 4 60 1 AAATGAATTT 0.656548 -155 AGCCCCTTTGAATTGAATTTTTTCTCAATTTA 4 90 1 AATTGTTTTT 0.826506 -125 CTTACTTAAATAATGAAATTTTCTTAAAATTA 5 19 1 TAATGATTTT 0.780035 -210 GGTATTTTTAAAGTGGGTTTTTTCTTAAATCT 5 106 1 AAGTGTTTTT 0.880293 -123 AAAAGCGTTCTTTTAYGCTATA 6 1 1 AAAAGTTCTT 0.80581 -57 TAGGATTAACTAAAGCGTTTATTATTAAAGCA 8 23 0 TAAAGTTTAT 0.534514 -66 AGCCCCTAAAAAATGATATTTTTCATCTTTTA 9 83 0 AAATGATTTT 0.897811 -58 ACTCAATTCATAAAGAGTTTTTACTTTATCAT 9 116 0 TAAAGTTTTT 0.883781 -25 GGTTTCTCATAAATGGTTTTATCTCGTCTTAT 10 50 0 AAATGTTTAT 0.816608 -154 GCCTTCAATCAAATCTGTATTTTATTAGTATA 10 169 0 AAATCTATTT 0.652081 -35 ***** ***** Masking position 12 Map Score: 14.1435 Number of sites scoring better than the average of aligned sites = 2049 Number in coding regions = 1715 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 5 TCATTTAATTTTTTGGCTTATAATTAGGAG 1 149 1 TTTTGGCTTA 0.669076 -50 CCTTAAGTTTTGATAGCATTCAACTCCTAA 1 172 0 TGATAGCATT 0.75992 -27 AAGTCAAATTTAATGGGTTTGTGGTTTATT 2 133 0 TAATGGGTTT 0.769333 -98 TTATTATATCTAATAGCGTTTAAAAAATGT 4 46 1 TAATAGCGTT 0.940587 -169 TAGTATAATCTAAGGGCGTTGCTCTGTATT 5 71 1 TAAGGGCGTT 0.840385 -158 TTGGTCTTAATTATAGCTAAAAGAACGCT 6 14 0 TTATAGCTA 0.796738 -44 AAAGAGAAAATTATGGCATTAGCCAAGATG 8 55 1 TTATGGCATT 0.932455 -34 TTATCTCGTCTTATAGCGTTGGGTATTTTC 10 34 0 TTATAGCGTT 0.951231 -170 GGCCTTGTTTTTATAGCTTTATGAAGCGCG 10 99 0 TTATAGCTTT 0.952151 -105 CGTTTTTCTTTAATGGCTTATGTTATACTA 10 146 1 TAATGGCTTA 0.920998 -58 ********** Masking position 9 Map Score: 5.93793 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 467 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 AGTTATTTCCAACCGCTACTTTTAAACACG 1 91 0 AACCGCTACT 0.954901 -108 ACTTAATATTAAATGCTACTTAAAATTAGT 2 159 1 AAATGCTACT 0.831762 -72 AATTTTAAACAATAGCCCCTTTGAATTGAA 4 77 1 AATAGCCCCT 0.955893 -138 AAAAACTGCTCCTAAAAACTCAA 4 202 0 AACTGCTCCT 0.959561 -13 GGGATTTTAATCGCCACTCCCAAACATT 7 9 1 AATCGCCACT 0.965195 -37 ATCATAACCGATCTGCCACTCTACATAATG 9 13 0 ATCTGCCACT 0.946393 -128 TTACTTTATCATTAGCCCCTAAAAAATGAT 9 98 0 ATTAGCCCCT 0.904283 -43 ********** Masking position 1 Map Score: 3.84969 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 162 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CCTTTTTCTAAAGTTTGAGTAACTATACTA 1 18 1 AAGTTTGAGT 0.926554 -181 TTTGGCTTATAATTAGGAGTTGAATGCTAT 1 160 1 AATTAGGAGT 0.934114 -39 TTAAATTCCAAATTAAGAGTTTCAAACACA 2 21 1 AATTAAGAGT 0.943563 -210 ATTTCTTACCAATTTTGAGTATTATATTGT 2 48 0 AATTTTGAGT 0.975979 -183 AGAAAAAACTAATTTTAAGTAGCATTTAAT 2 166 0 AATTTTAAGT 0.913251 -65 TTCCTTGAATAATTAAAAGTATTTTTTTAT 2 206 0 AATTAAAAGT 0.811541 -25 ATTTTAGGTTAATTTTGAGTTTTTAGGAGC 4 188 1 AATTTTGAGT 0.975979 -27 ********** Masking position 8 Map Score: 7.25176 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 31 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 GCATTCAAAAAAAGATTTTTAAGGGTTATA 1 62 0 AAAGATTTTT 0.679205 -137 TCTTTTTTTGAATGCGTGTTTAAAAGTAGC 1 77 1 AATGCGTGTT 0.660864 -122 TTTTAAAAACATTGCGTTTTTTCAAGTTAT 1 115 0 ATTGCGTTTT 0.792226 -84 CAAAAAATTAAATGATTTCTTTTAAAAACA 1 134 0 AATGATTTCT 0.521974 -65 TGTTTGAGCGAGTGGGTTTATCAACTTGTG 2 93 0 AGTGGGTTTA 0.892735 -138 AGTCAAATTTAATGGGTTTGTGGTTTATTT 2 132 0 AATGGGTTTG 0.708487 -99 ATTATATCTAATAGCGTTTAAAAAATGTAA 4 48 1 ATAGCGTTTA 0.718059 -167 TTTTGCGTCAAGCGATTTTAGGTTAATTTT 4 174 1 AGCGATTTTA 0.489972 -41 GTATTTTTAAAGTGGGTTTTTTCTTAAATC 5 107 1 AGTGGGTTTT 0.904408 -122 TAAGATCTTTAAAGATTTTAAAAACTAATA 5 138 1 AAAGATTTTA 0.65098 -91 AAAAGCGTTCTTTTAYGCTAT 6 2 1 AAAGCGTTCT 0.818308 -56 AGGATTAACTAAAGCGTTTATTATTAAAGC 8 24 0 AAAGCGTTTA 0.911181 -65 CTTTTAAAGTAGTGAGTTCAAATTTTTCTT 9 59 0 AGTGAGTTCA 0.750246 -82 CTCAATTCATAAAGAGTTTTTACTTTATCA 9 117 0 AAAGAGTTTT 0.878715 -24 GTTTCTCATAAATGGTTTTATCTCGTCTTA 10 51 0 AATGGTTTTA 0.726873 -153 AGCTTTATGAAGCGCGTTTTATTGATGCAT 10 85 0 AGCGCGTTTT 0.857236 -119 ********** Masking position 7 Map Score: 9.14188 Number of sites scoring better than the average of aligned sites = 2378 Number in coding regions = 2090 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 9 ********** No masking Map Score: -1.90893e-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 10 ********** No masking Map Score: -1.90893e-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 11 ********** No masking Map Score: -1.90893e-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