AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -intrC_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 HP0512 290 glutamine synthetase (glnA) #2 HP0695 300 hydantoin utilization protein A (hyuA) #3 HP0698 187 H. pylori predicted coding region HP0698 #4 HP0699 39 H. pylori predicted coding region HP0699 #5 HP1169 212 glutamine ABC transporter, permease protein (glnP) Motif number 1 ATATTATAAAAATTGGTGGGAATGATAAG 1 5 0 AATTGTGTGA 0.993263 -286 ATCATCCCATAATTGTTCGCATTATTCCTTTTTCC 1 38 1 AATTGTGTAT 0.910428 -253 TACAACCTCTGATAGATAGGAATGACAAATTGATT 1 78 1 GATAGTGTGA 0.976114 -213 AGGAATGACAAATTGATTGTTTTGATTTTCTTCAA 1 95 1 AATTGTGTGA 0.993263 -196 AATTGAGTTTGATTGATAGGGGTGATTATAGCATT 1 245 0 GATTGTGTGA 0.989874 -46 CTTAGGCTGGGATTGAAAGGTTTTACTA 2 4 0 GATTGAGTTA 0.730801 -297 TAAAGTGCCGATTTGATGGTGCTTAGGCTGGGATT 2 25 0 ATTTGTGTTA 0.950635 -276 TTTATTTCAAAGTTGTTTGTAATAAGGGAAAATTT 2 202 0 AGTTGTGTAA 0.918672 -99 TTATACTTCTAATAGGTTGCCTTGAGCAACACTTT 2 260 1 AATAGTGTGA 0.984033 -41 TCTTGGTGCTAAAAGCTTGGGTTGATTTAACTCAA 3 48 1 AAAAGTGTGA 0.858473 -140 ATTGAAGAAAATTTGCTTGAGTTAAATCAACCCAA 3 64 0 ATTTGTGTAA 0.961649 -124 TTGCAGCCAAATTTGTTAGGATTGAAGAAAATTTG 3 84 0 ATTTGTGTGA 0.98556 -104 GCTTTTCCTTGTTAGGTGGAATTAAAATTATACCT 3 162 0 GTTAGTGTAA 0.874225 -26 TATTCACCCCAATTGTTAGAAGTTTGGAAAACCCA 5 131 0 AATTGTGTTT 0.88644 -82 ***** * * *** Masking position 13 Map Score: 20.8896 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 158 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 TATGGGATGATATTATAAAAATTGGTGGGAATGATAAG 1 9 0 TTAAATTGGA 0.987752 -282 TTTTATAATATCATCCCATAATTGTTCGCATTATTCCTTT 1 29 1 TTATATTTGA 0.966964 -262 GCAACCACACTATTAGGATTTTTTGAAGAAAATCAAAACA 1 112 0 TTATTTTGGA 0.848864 -179 ACCGCATGCATCTTAATAAAACTTGATACAGATTCTACTT 1 192 1 TTAAACTGAA 0.88395 -99 TATATGATATTTATATGATATTTTTGGGTAATTTAAGATG 2 109 1 TTATATTTGA 0.967237 -192 AAGTGAAAAGTAGTAACAAATTTATTCAAAACGCTACCGA 2 153 0 TTAAATTTAA 0.880468 -148 TGGAAATCATTTATTTCAAAGTTGTTTGTAATAAGGGAAA 2 206 0 TTAAATTTGA 0.984852 -95 TTTTCTTCAATCCTAACAAATTTGGCTGCAAATTAAAAAA 3 88 1 TTAAATTGGA 0.597157 -100 TTTTGGATTATAATAAAAAAACTGGCTGAAATTAACAACA 5 41 0 TTAAACTGGA 0.97792 -172 TTTTTTATTATAATCCAAAATTTCTTTGAATAGTGGCAAA 5 61 1 TTAAATTTGA 0.92245 -152 * * *** ** * * * Masking position 8 Map Score: 11.1081 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTATTAGGATTTTTTGAAGAAAATCAAAACAAT 1 110 0 TTTTGAGAAA 0.958134 -181 ATTAAACTGATATTAAATCAAAAGGCGAAATTC 2 65 0 TATTAACAAA 0.884854 -236 ATAAATATCATATAGGAAGAAAAATATTAAACT 2 90 0 TATAGAGAAA 0.899401 -211 TTTTGGGTAATTTAAGATGAATATCGGTAGCGT 2 130 1 TTTAGAGATA 0.798529 -171 TAAGGCTGATTTTTAAATGGAAATCATTTATTT 2 230 0 TTTTAAGAAA 0.955025 -71 CAAGGCAACCTATTAGAAGTATAAGGCTGATTT 2 251 0 TATTGAGATA 0.958644 -50 TTATACCTAGTATTAAATCAAAAAAAAAGAAAA 3 137 0 TATTAACAAA 0.884854 -51 CCCCTTATTTTATTGAAAGTATAGTGATAGAAC 4 11 0 TATTAAGATA 0.953314 -29 GTTTTGCCACTATTCAAAGAAATTTTGGATTAT 5 70 0 TATTAAGAAT 0.815288 -143 GCGTCATTAATTTTTAAGGTATAGCGTT 5 195 1 TTTTAAGATA 0.935971 -18 **** ** * *** Masking position 7 Map Score: 8.37201 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 210 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 TGTTCGCATTATTCCTTTTTCCAACTATAC 1 51 1 ATTCCTTTTT 0.920226 -240 GGAATGACAAATTGATTGTTTTGATTTTCT 1 96 1 ATTGATTGTT 0.903105 -195 CCATAATAACACTCCTTGATTTAGCGGATT 1 160 1 ACTCCTTGAT 0.884889 -131 TGATACAGATTCTACTTTTTTTGCCCCATA 1 215 1 TCTACTTTTT 0.55414 -76 ATGAATTGAGTTTGATTGATAGGGGTGATT 1 253 0 TTTGATTGAT 0.5808 -38 TAACCACCTTTAATTGTTATGAATTGAG 1 273 0 TTTAATTGTT 0.732889 -18 TTTAAATGGAAATCATTTATTTCAAAGTTG 2 222 0 AATCATTTAT 0.64671 -79 TTAGACTCCTTGTATTAAAGTGTT 2 287 0 ACTCCTTGTA 0.718158 -14 GATTGCTCAATCCTTTTTATGAAAGAGG 3 9 1 AATCCTTTTT 0.887376 -179 AGCTTTTCCTTGTTAGGTGGAATT 3 174 0 TTTCCTTGTT 0.930742 -14 CTCTCCATTTAATGATTGTTTAATCATTGT 5 14 1 AATGATTGTT 0.864222 -199 ATGATTGTTTAATCATTGTTGTTAATTTCA 5 25 1 AATCATTGTT 0.934812 -188 TTAAAGCGTCATTAATTTTTAAGGTATAGC 5 190 1 ATTAATTTTT 0.701519 -23 ********** Masking position 6 Map Score: 7.05255 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 528 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 GCAACCACACTATTAGGATTTTTTGAAGAAAAT 1 119 0 TATAGGTTTT 0.762249 -172 ACACTCCTTGATTTAGCGGATTTTACCGCATGC 1 168 1 ATTAGCGTTT 0.966009 -123 ATAGGGGTGATTATAGCATTTATGGGGCAAAAA 1 232 0 TTAAGCTTAT 0.704356 -59 ATTCAATTCTAAAGTGCCGATTTGATGGTGCTT 2 36 0 AAATGCGTTT 0.71204 -265 TATTAGAAGTATAAGGCTGATTTTTAAATGGAA 2 241 0 ATAGGCGTTT 0.842621 -60 ACCAAGAGGCATAAAGCCTCTTTCATAAAAAGG 3 22 0 ATAAGCTTTT 0.774753 -166 AATTAAAAAATTTAAGCTTTTTTCTTTTTTTTT 3 118 1 TTTAGCTTTT 0.953647 -70 CTTTCAATAAAATAAGGGGTTTTTT 4 25 1 AATAGGGTTT 0.815652 -15 TTGTTGTTAATTTCAGCCAGTTTTTTTATTATA 5 40 1 TTTAGCATTT 0.835361 -173 ATGGGAAGTTTATGAGCCGTTTTGCCACTATTC 5 88 0 TATAGCGTTT 0.965826 -125 TTGGGGTGAATAAGAGCTGTTTTTAAACATGGT 5 154 1 TAAAGCGTTT 0.965997 -59 ACATGGTGCTTTAAAGCGTCATTAATTTTTAAG 5 180 1 TTAAGCTATT 0.704384 -33 *** *** * *** Masking position 13 Map Score: 6.28424 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1178 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 6 TTCCTATCTATCAGAGGTTGTATAGTTGGA 1 70 0 TCAGAGGTTG 0.951136 -221 TTCATAACAATTAAAGGTGGTTA 1 278 1 TTAAAGGTGG 0.801885 -13 AGGCTGGGATTGAAAGGTTTTACTA 2 6 0 TGAAAGGTTT 0.800887 -295 CTTATACTTCTAATAGGTTGCCTTGAGCAA 2 259 1 TAATAGGTTG 0.923798 -42 CTCCTTGTATTAAAGTGTTGCTCAAGGCAA 2 276 0 TAAAGTGTTG 0.763327 -25 CTCTTGGTGCTAAAAGCTTGGGTTGATTTA 3 47 1 TAAAAGCTTG 0.953598 -141 TTCAATAAAATAAGGGGTTTTTT 4 27 1 TAAGGGGTTT 0.944758 -13 CTTCCCATAATAAGGGCTTGGGTTTTCCAA 5 113 1 TAAGGGCTTG 0.964112 -100 TTGGGGTGAATAAGAGCTGTTTTTAAACAT 5 154 1 TAAGAGCTGT 0.839266 -59 ********** Masking position 3 Map Score: 3.13152 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 424 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ********** No masking Map Score: 6.56131e-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 8 ********** No masking Map Score: 6.56131e-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 9 ********** No masking Map Score: 6.56131e-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