AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_hpyl_reg_300.orf -o00350_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -x5 -e 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP1067 290 chemotaxis protein (cheY) #4 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #5 HP1377 300 H. pylori predicted coding region HP1377 #6 HP1483 26 gerC2 protein (gerC2) #7 HP1490 103 hemolysin #8 HP1491 138 phosphate permease Motif number 1 ATGCGAGATATATGAGAGAAAGGTTTGGGTTTAGGG 1 39 0 TATGAGATTT 0.753819 -219 ATTTAAGAGTAATGGGTGTTTGTTTTAAGACGCTAT 1 85 0 AATGGGTTTT 0.835572 -173 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 1 167 0 TTTTAGTTTT 0.942589 -91 TTAATTTAAGAATTTTAGATTGATTTTTTTAAGGGT 1 183 0 AATTTGTTTT 0.950195 -75 TGTTTTAGTGTATTATAGCTATATTTTAATTTAAGA 1 208 0 TATTAGTTTT 0.941381 -50 TAATTTTGAGTTTTTAGGAGCAGTTTTT 2 3 0 TTTTTGGTTT 0.841141 -212 GCGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 22 0 ATTTTGTTTT 0.950214 -193 AATGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAG 2 50 0 AATTAGATTT 0.894874 -165 ATTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 AATTTGTTTT 0.950213 -121 AAGAACGCTCATTGAACGCTCCATTTAGCCAATGAT 3 134 1 ATTGAGTTTT 0.945798 -157 AAACATGCTATTATTTGGAACGATTTATTATTATAA 3 197 1 TTATTGATTT 0.44002 -94 GATTGCATTTAAATTAGGCTCTTTTTAAACAGCCAA 3 248 0 AAATTGTTTT 0.81571 -43 TCTTATGGTATAATAGCGGTTATTTTTTTAGAATAA 4 95 1 TAATAGTTTT 0.794435 -77 TTTTGGATTCAATTAAAGCGCTATTTTTAGCGTTGG 4 131 0 AATTAGGTTT 0.858823 -41 CCCACCAAATAATGTCAGCACCATTTCTCCAAATCA 5 19 1 AATGTGATTT 0.760934 -282 ATTTTTCTTGATTTGTGGTTTTATTTTGCTCATTCC 5 111 1 ATTTGGTTTT 0.891382 -190 TGGTAAAATCAATTTTCGCTAGTTTTGGATATAATC 5 208 0 AATTTGTTTT 0.950194 -93 CTTAGAAATCATTGAGCGCTGGTTTTAAGGCGGTCT 5 272 1 ATTGAGTTTT 0.945966 -29 GGTTTTTGAAGGCTTGATTTTTAAAGTTAG 7 5 1 TTTGAGTTTT 0.910447 -99 TATATTTTATATTTATCGTTAGGTTTTAGGTTTAAA 7 75 1 ATTTAGTTTT 0.965839 -29 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 8 6 0 TTTTAGGTTT 0.886923 -133 TTAAGATACCATATAATGAGCCATTTTTATCAAACA 8 39 1 ATATAGGTTT 0.760677 -100 ***** * * *** Masking position 14 Map Score: 26.9571 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 822 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 AAGTAACGCTAAATCAATATAAT 1 3 1 GAACGCTAAA 0.932578 -255 CAATATAATTCAAACCCTAAACCCAAACCTT 1 25 1 CAACCCTAAA 0.979806 -233 TTAAAAAAAACTACCCTTAAAAAAATCAATC 1 171 1 CACCCTTAAA 0.965929 -87 TTCTTATAAACAAAACCTAAATTGAGAAAAA 2 97 1 CAAACCTAAA 0.776855 -118 GGGATAGTTACCACCTATAAAATAAGGATCG 2 190 1 CACCTATAAA 0.703602 -25 TTGGCTAAATGGAGCGTTCAATGAGCGTTCT 3 135 0 GAGCGTTCAA 0.739011 -156 TAATTTAAATGCAATCTTAAAAGGAGAAGCA 3 268 1 GAATCTTAAA 0.522311 -23 TTTAGAATAACCAACGCTAAAAATAGCGCTT 4 121 1 CAACGCTAAA 0.979806 -51 AAGACGCCACCTACCGCTAAAATGAGATTTA 5 72 1 CACCGCTAAA 0.978437 -229 CGCCTTAAAACCAGCGCTCAATGATTTCTAA 5 273 0 CAGCGCTCAA 0.940821 -28 CTTTAAAAATCAAGCCTTCAAAAACC 7 6 0 CAGCCTTCAA 0.908531 -98 AAGATTAAGCCTAACTTTAAAAATCAAGCCT 7 20 0 CAACTTTAAA 0.873955 -84 AACCTAAAACCTAACGATAAATATAAAATAT 7 76 0 CAACGATAAA 0.91734 -28 AGCCCTTGAGCCACTCTTAAAAAGCGTTGTT 8 71 0 CACTCTTAAA 0.781992 -68 * ********* Masking position 3 Map Score: 12.8393 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 831 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 CAAACACCCATTACTCTTAAATCATGCCAATTCACACTCTTTAG 1 99 1 TTAAATGTTA 0.944359 -159 TTCACACTCTTTAGACTTGAAATTTGAAAATAATAACACAACTT 1 129 1 TTGAATGTAT 0.860298 -129 CTTAAAAAAATCAATCTAAAATTCTTAAATTAAAATATAGCTAT 1 186 1 TTAAATTTAA 0.55065 -72 GGCTAAATTTTGAAACCTTGAGATTGTTTTAGTGTAT 1 231 0 TTGAATTTTT 0.893305 -27 TTAATTCTACTACATTTGAAATAATTTTTCTTATAAACAAAACC 2 70 1 TTAAATTTTT 0.969276 -145 TTATATCTAATAGCGTTTAAAAAATGTAAATTTTAAACAATAGC 2 143 0 TTAAATGTTT 0.978041 -72 TTACTTGTAAAATCCTTGTCTTTCTTTTTTCAAAC 3 2 1 TTAAATTTTT 0.969279 -289 TGACCCTTTATCGCACTCAAAGAGTTATTTTATTACTTTTAAAC 3 53 1 TTAAATTTAT 0.942028 -238 TGAGCGTTCTTATTTGTAAAAAAATTCAGTTTGTTTGCTATGAT 3 101 0 TTAAATTTTT 0.969226 -190 GTCAAGGTAATTTTAATCAAAACATGCTATTATTTGGAACGATT 3 178 1 TTAAATGTAT 0.958228 -113 CCTTTTAAGATTGCATTTAAATTAGGCTCTTTTTAAACAGCCAA 3 248 0 TTAAAGGTTT 0.866617 -43 TAAACTTCCATCATGGTTAAGTTATTGGGATTATATCCAAAACT 5 180 1 TTAAGTTTTT 0.810634 -121 GCTTAATCTTTTATGTTAAAATTCTGAGATTTTATATATTTTAT 7 41 1 TTAAATGTTA 0.944347 -63 TAATGAGCCATTTTTATCAAACAACGCTTTTTAAGAGTGGCTCA 8 52 1 TTAAACGTTA 0.712308 -87 ATCGTCATAAAAACCTTGTTCTAATAGTGGTCTTA 8 114 0 TTAAATTTAT 0.942028 -25 * * *** ** ** * Masking position 10 Map Score: 15.3248 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 211 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 GACTTGAAATTTGAAAATAATAACACAACTTAA 1 142 1 TTAAAAATAA 0.976928 -116 ATAATTTTTCTTATAAACAAAACCTAAATTGAG 2 90 1 TTAAAAAAAC 0.719271 -125 AAAATGTAAATTTTAAACAATAGCCCCTTTGAA 2 134 0 TTAAAAATAG 0.947941 -81 TTAAACGCTATTAGATATAATAAGGGATAGTTA 2 167 1 TTATAAATAA 0.937639 -48 CATTGGATGGTTTGAAAAAAGAAAGACAAGGAT 3 22 0 TTAAAAAGAA 0.942036 -269 TGATAATCGTTTAAAAGTAATAAAATAACTCTT 3 72 0 TTAAGAATAA 0.879005 -219 CTGAATTTTTTTACAAATAAGAACGCTCATTGA 3 116 1 TTAAAAAGAA 0.94196 -175 TAATAAATCGTTCCAAATAATAGCATGTTTTGA 3 194 0 TTAAAAATAG 0.947941 -97 CGTTGGTTATTCTAAAAAAATAACCGCTATTAT 4 104 0 TCAAAAATAA 0.87908 -68 AACCGAATCATTATAAAATATAATAAGGAGTTG 5 148 0 TTAAATATAA 0.794734 -153 ACCAAAATTGTTTGATATAATACAGAGTTTAGC 5 240 1 TTATAAATAC 0.866201 -61 CAAGGGCTAATTGGATAGAATAAGACCACTATT 8 94 1 TTATAAATAA 0.937719 -45 ** *** ***** Masking position 5 Map Score: 10.5389 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 273 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 TAAAGATAGTCATAGCGTCTTAAAACAAAC 1 74 1 CATAGCGTCT 0.972684 -184 AAATTCAATTCAAAGGGGCTATTGTTTAAA 2 126 1 CAAAGGGGCT 0.862094 -89 TATTATATCTAATAGCGTTTAAAAAATGTA 2 159 0 AATAGCGTTT 0.969449 -56 TTTAAACAGCCAAAGCGTCTCTAACGCCTT 3 231 0 CAAAGCGTCT 0.977483 -60 TGCATAAGCGGTTTCTATGCAAA 4 4 1 ATAAGCGGTT 0.864553 -168 GGTTTCTATGCAAAGCGTTTCTTGAAGCTT 4 20 1 CAAAGCGTTT 0.975116 -152 CTTATGGTATAATAGCGGTTATTTTTTTAG 4 96 1 AATAGCGGTT 0.970394 -76 CAACGCTAAAAATAGCGCTTTAATTGAATC 4 132 1 AATAGCGCTT 0.924537 -40 GCCACTCTTAAAAAGCGTTGTTTGATAAAA 8 63 0 AAAAGCGTTG 0.875347 -76 ********** Masking position 4 Map Score: 9.40608 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 482 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CGCTATTAGATATAATAAGGGATAGTTACC 2 172 1 TATAATAAGG 0.980748 -43 TTACCACCTATAAAATAAGGATCGTTCA 2 197 1 TAAAATAAGG 0.972669 -18 AACGATTTATTATTATAAGGCGTTAGAGAC 3 215 1 TATTATAAGG 0.913264 -76 TAATTGAATCCAAAACAAGGAGTTTATTTT 4 152 1 CAAAACAAGG 0.880509 -20 CATTATAAAATATAATAAGGAGTTGAGGAA 5 143 0 TATAATAAGG 0.980748 -158 GCTAATTGGATAGAATAAGACCACTATTAG 8 99 1 TAGAATAAGA 0.877155 -40 AGACCACTATTAGAACAAGGTTTTTATGAC 8 116 1 TAGAACAAGG 0.973714 -23 ********** Masking position 5 Map Score: 6.29612 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 48 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TAGCGTCTTAAAACAAACACCCATTACTCTT 1 86 1 AAAAAACACC 0.838834 -172 ACACAACTTAAAAAAAACTACCCTTAAAAAA 1 164 1 AAAAAACTAC 0.564796 -94 TAATACACTAAAACAATCTCAAGGTTTCAAA 1 229 1 AAAAATCTCA 0.934069 -29 AAAACTGCTCCTAAAAACTCAAAATTAACCT 2 12 1 CTAAAACTCA 0.602346 -203 TGGTTTGAAAAAAGAAAGACAAGGATTTTAC 3 17 0 AAAAAAGACA 0.605713 -274 TTATCATAGCAAACAAACTGAATTTTTTTAC 3 99 1 AAAAAACTGA 0.886054 -192 AACGCTTTGCATAGAAACCGCTTATGCA 4 8 0 ATAAAACCGC 0.714033 -164 TTGTATTTGCAAAAACACCGATGCATTGCGC 4 53 0 AAAACACCGA 0.567849 -119 AAAATAAACTCCTTGTTTTGGA 4 160 0 AAAAAACTCC 0.942761 -12 TATTCCCACCAAATAATGTCAGCACCATTTC 5 15 1 AAAAATGTCA 0.734939 -286 AAATCAAGAAAAATAATCCCAGTAAATCTCA 5 94 0 AAAAATCCCA 0.942567 -207 GGAATGAGCAAAATAAAACCACAAATCAAGA 5 116 0 AAAAAAACCA 0.673694 -185 CTAGTTTTGGATATAATCCCAATAACTTAAC 5 195 0 ATAAATCCCA 0.872785 -106 TATAAAATATATAAAATCTCAGAATTTTAAC 7 55 0 ATAAATCTCA 0.855545 -49 *** ******* Masking position 5 Map Score: 5.80307 Number of sites scoring better than the average of aligned sites = 1313 Number in coding regions = 1158 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 GAATTATATTGATTTAGCGTTACTT 1 6 0 GATTTAGCGT 0.939729 -252 GAAAGGTTTGGGTTTAGGGTTTGAATTATA 1 28 0 GGTTTAGGGT 0.95115 -230 TAATTTAAGAATTTTAGATTGATTTTTTTA 1 188 0 ATTTTAGATT 0.715617 -70 CCTTGAGATTGTTTTAGTGTATTATAGCTA 1 223 0 GTTTTAGTGT 0.884165 -35 GCGTCAAGCGATTTTAGGTTAATTTTGAGT 2 28 0 ATTTTAGGTT 0.929243 -187 TTAAGGCAGTGTTTTTGCGTCAAGCGATTT 2 44 0 GTTTTTGCGT 0.862433 -171 ATTTTTTCTCAATTTAGGTTTTGTTTATAA 2 100 0 AATTTAGGTT 0.80582 -115 TAAAGCGCTATTTTTAGCGTTGGTTATTCT 4 124 0 TTTTTAGCGT 0.884165 -48 AGTAAATCTCATTTTAGCGGTAGGTGGCGT 5 75 0 ATTTTAGCGG 0.853514 -226 TATAATACAGAGTTTAGCTTAGAAATCATT 5 255 1 AGTTTAGCTT 0.888286 -46 TTATCGTTAGGTTTTAGGTTTAAAGTT 7 87 1 GTTTTAGGTT 0.954428 -17 ********** Masking position 5 Map Score: 8.29355 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 595 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 GTGCGATAAAGGGTCATTGGATGGTTTGAAA 3 38 0 GGGTCATTGA 0.960107 -253 CAAATAAGAACGCTCATTGAACGCTCCATTT 3 129 1 CGCTCATTGA 0.976642 -162 AATAATCATTGGCTAAATGGAGCGTTCAATG 3 143 0 GGCTAAATGA 0.924164 -148 TGATTATTGTCGGTCAAGGTAATTTTAATCA 3 166 1 CGGTCAAGGA 0.930739 -125 TGAAGCTTATGGCGCAATGCATCGGTGTTTT 4 42 1 GGCGCAATGA 0.96665 -130 TTAAAACCAGCGCTCAATGATTTCTAAGCTA 5 269 0 CGCTCAATGT 0.933 -32 TGATAAAAATGGCTCATTATATGGTATCTTA 8 40 0 GGCTCATTAA 0.883672 -99 TTTTAAGAGTGGCTCAAGGGCTAATTGGATA 8 80 1 GGCTCAAGGC 0.950036 -59 ********* * Masking position 6 Map Score: 3.52062 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 183 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: 2.8375e-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: 2.8375e-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: 2.8375e-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