AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icspA_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 HP0695 300 hydantoin utilization protein A (hyuA) #2 HP0698 187 H. pylori predicted coding region HP0698 #3 HP0699 39 H. pylori predicted coding region HP0699 Motif number 1 AGTAAAACCTTTCAATCCCAGCCTAAGCAC 1 12 1 TTCAATCCCA 0.956657 -289 AAAGGCGAAATTCAATTCTAAAGTGCCGAT 1 48 0 TTCAATTCTA 0.933857 -253 CGCCTTTTGATTTAATATCAGTTTAATATT 1 71 1 TTTAATATCA 0.775055 -230 GTTTAATATTTTTCTTCCTATATGATATTT 1 91 1 TTTCTTCCTA 0.781961 -210 TAGTAACAAATTTATTCAAAACGCTACCGA 1 153 0 TTTATTCAAA 0.762289 -148 CAAATTTTCCCTTATTACAAACAACTTTGA 1 201 1 CTTATTACAA 0.671928 -100 ATGGAAATCATTTATTTCAAAGTTGTTTGT 1 217 0 TTTATTTCAA 0.923052 -84 AATAAATGATTTCCATTTAAAAATCAGCCT 1 231 1 TTCCATTTAA 0.615944 -70 TGAGCAACACTTTAATACAAGGAGTCTAA 1 282 1 TTTAATACAA 0.970525 -19 ATAAAGCCTCTTTCATAAAAAGGATTGAGC 2 15 0 TTTCATAAAA 0.761944 -173 CTTGGGTTGATTTAACTCAAGCAAATTTTC 2 63 1 TTTAACTCAA 0.814507 -125 GCAAATTTTCTTCAATCCTAACAAATTTGG 2 83 1 TTCAATCCTA 0.948128 -105 TTTTTTTTGATTTAATACTAGGTATAATTT 2 143 1 TTTAATACTA 0.953488 -45 TAGGTATAATTTTAATTCCACCTAACAAGG 2 161 1 TTTAATTCCA 0.950468 -27 TCACTATACTTTCAATAAAATAAGGGGTTT 3 17 1 TTCAATAAAA 0.853144 -23 ********** Masking position 10 Map Score: 15.0274 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 830 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 TAGTAAAACCTTTCAATCCCAGCCTAAGC 1 8 1 ACTTCAATCC 0.891218 -293 ATTTCGCCTTTTGATTTAATATCAGTTTAATA 1 67 1 TTTTTAATAT 0.827301 -234 TAGTAACAAATTTATTCAAAACGCTACCGATA 1 151 0 TTTTCAAAAC 0.763062 -150 TTACTACTTTTCACTTTATTACGCCAAATTTT 1 177 1 TCTTTATTAC 0.871731 -124 ACGCCAAATTTTCCCTTATTACAAACAACTTT 1 197 1 TTCTTATTAC 0.793416 -104 TTAAATGGAAATCATTTATTTCAAAGTTGTTT 1 219 0 ATTTTATTTC 0.841417 -82 GCCTTGAGCAACACTTTAATACAAGGAGTCTA 1 278 1 ACTTTAATAC 0.93116 -23 GATTGCTCAATCCTTTTTATGAA 2 2 1 ATCTCAATCC 0.822376 -186 AAAGCTTGGGTTGATTTAACTCAAGCAAATTT 2 59 1 TTTTTAACTC 0.816177 -129 TCAAGCAAATTTTCTTCAATCCTAACAAATTT 2 79 1 TTTTCAATCC 0.958219 -109 AAAAGCTTAAATTTTTTAATTTGCAGCCAAAT 2 107 0 ATTTTAATTT 0.676457 -81 TTCTTTTTTTTTGATTTAATACTAGGTATAAT 2 139 1 TTTTTAATAC 0.974269 -49 ATACTAGGTATAATTTTAATTCCACCTAACAA 2 157 1 TATTTAATTC 0.784447 -31 ** ******** Masking position 8 Map Score: 7.62828 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 709 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 3 AACTGATATTAAATCAAAAGGCGAAATTCA 1 64 0 AAATCAAAAG 0.960944 -237 TGGCGTAATAAAGTGAAAAGTAGTAACAAA 1 173 0 AAGTGAAAAG 0.970604 -128 TGTTTGTAATAAGGGAAAATTTGGCGTAAT 1 194 0 AAGGGAAAAT 0.907929 -107 GCTGATTTTTAAATGGAAATCATTTATTTC 1 229 0 AAATGGAAAT 0.872993 -72 ATTTGGCTGCAAATTAAAAAATTTAAGCTT 2 107 1 AAATTAAAAA 0.851559 -81 AAATCAAAAAAAAAGAAAAAAGCTTAAATT 2 126 0 AAAAGAAAAA 0.901462 -62 ACCTAGTATTAAATCAAAAAAAAAGAAAAA 2 136 0 AAATCAAAAA 0.93993 -52 TTCCACCTAACAAGGAAAAGCT 2 176 1 CAAGGAAAAG 0.912446 -12 ********** Masking position 7 Map Score: 4.76646 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 552 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 CGCCTTTTGATTTAATATCAGTTTAATATT 1 71 1 TTTAATATCA 0.90853 -230 ATATAGGAAGAAAAATATTAAACTGATATT 1 84 0 AAAAATATTA 0.834557 -217 AAAATATCATATAAATATCATATAGGAAGA 1 103 0 ATAAATATCA 0.983854 -198 TAAATTACCCAAAAATATCATATAAATATC 1 114 0 AAAAATATCA 0.970261 -187 GTAATTTAAGATGAATATCGGTAGCGTTTT 1 136 1 ATGAATATCG 0.909455 -165 TGATTTCCATTTAAAAATCAGCCTTATACT 1 237 1 TTAAAAATCA 0.889651 -64 ********** Masking position 5 Map Score: 2.46462 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 194 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 ATTGAATTTCGCCTTTTGATTTAATATCAGTTT 1 62 1 GCCTTTGATA 0.916963 -239 TTAAAAATCAGCCTTATACTTCTAATAGGTTGC 1 247 1 GCCTTTACCT 0.975892 -54 CTAATAGGTTGCCTTGAGCAACACTTTAATACA 1 268 1 GCCTTAGCCA 0.991245 -33 TATGAAAGAGGCTTTATGCCTCTTGGTGCTAAA 2 28 1 GCTTTTGCCT 0.992611 -160 ATCAACCCAAGCTTTTAGCACCAAGAGGCATAA 2 41 0 GCTTTAGCCA 0.986302 -147 AAAAATTTAAGCTTTTTTCTTTTTTTTTGATTT 2 123 1 GCTTTTTCTT 0.896895 -65 ***** *** ** Masking position 5 Map Score: 2.18348 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 190 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ********** No masking Map Score: -1.0847e-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 7 ********** No masking Map Score: -1.0847e-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 8 ********** No masking Map Score: -1.0847e-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