AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_hpyl_reg_300.orf -o00760_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 HP0329 248 NH(3)-dependent NAD+ synthetase (nadE) #2 HP0428 300 phage/colicin/tellurite resistance cluster terY protein #3 HP0429 124 H. pylori predicted coding region HP0429 #4 HP0430 85 H. pylori predicted coding region HP0430 #5 HP1054 63 H. pylori predicted coding region HP1054 #6 HP1057 148 H. pylori predicted coding region HP1057 #7 HP1180 300 pyrimidine nucleoside transport protein (nupC) #8 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #9 HP1361 56 competence locus E (comE3) #10 HP1365 83 response regulator #11 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 TCCTGTAGGTCGGGGGTTTGAATCCCTCCGAGCA 1 103 0 CGGGGTTGAC 0.990191 -146 GATATACAAAAGTGGGATTTAAAGGGTTTAAAAG 4 45 1 AGTGGTTTAG 0.894952 -41 AGGGTTTAAAAGGGGAGTTTGAAGACGCT 4 67 1 AGGGGTTTAG 0.980112 -19 TGTTAAATATAGTGGCATTGTAGCATGACTTTAT 6 24 1 AGTGGTTGAC 0.974835 -125 GGTGTCAAGAGGGGGACTTGAACCCCCGACCTCC 7 171 0 GGGGGTTGAC 0.997733 -130 AAACTTTTCAGGGGGCGTTTGAACTTCTTACGAC 9 17 1 GGGGGTTTAC 0.994706 -40 GGGGGTATTGTAGCGCTAATTGCC 10 70 0 GGGGGTTGAC 0.997734 -14 TTTTTTGCATGGGGGTATTGTAGCGCTTAATGAG 11 108 0 GGGGGTTGAC 0.997734 -193 ACAATGAAATGGGGGTATTTTAAAAAAATGAGTC 11 225 0 GGGGGTTTAA 0.960584 -76 TTAAACTTCAATGGGTTTTGCATGAAAGAATTTT 11 259 0 ATGGGTTGAG 0.909823 -42 ***** *** * * Masking position 8 Map Score: 19.4591 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 175 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 CAAGTATTTATTTTACCATAATGGGAGCGAT 1 36 1 TTTTACCATA 0.730837 -213 AACGATGCGTTTTTTCTATTATAATTTAAGG 1 227 1 TTTTTCTATA 0.89943 -22 ATTCCAGTATTTTTATTGTTAGATACGAGTG 2 271 1 TTTTATTGTA 0.941218 -30 AGGTTTAAAATTTTAGCGTTAGTCGTTTTAA 5 29 1 TTTTAGCGTA 0.759435 -35 ATTTTAATTATTTTAGTATAATTGAAAGAAA 6 95 1 TTTTAGTATA 0.932607 -54 TACATTAAACTTTTATTATCAATCCTACTTC 7 42 0 TTTTATTATA 0.963595 -259 TTAAGAAAGGTTTTTGTATAATCTCATTCTT 7 87 1 TTTTTGTATA 0.944348 -214 CATTCTTTTATTTTTTTGTCAAGGTAGCTCA 7 111 1 TTTTTTTGTA 0.93372 -190 CGTTTAATCTTTTTTTTAGCAAAACTAAACT 7 235 1 TTTTTTTAGA 0.772716 -66 TAAGGGAGTGTTTTTTTATAACCGCTTTTAG 10 33 1 TTTTTTTATA 0.958819 -51 TTATAACCGCTTTTAGTATAAAGGCAATTAG 10 48 1 TTTTAGTATA 0.932607 -36 CTTCGTTCGTTTTCATTATAACGCTCCTTAA 11 47 1 TTTCATTATA 0.875807 -254 CAAAAAAAGATTTTTTTATTAGAAGACGATT 11 135 1 TTTTTTTATA 0.958858 -166 GACTGACTCATTTTTTTAAAATACCCCCATT 11 221 1 TTTTTTTAAA 0.695004 -80 AATACCCCCATTTCATTGTAAAATTCTTTCA 11 240 1 TTTCATTGTA 0.811063 -61 ********* * Masking position 11 Map Score: 16.366 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 200 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 TCATCGTTTCACTTCTTTAAAAGTGCTCGTAG 1 165 0 ACTTCTAAAA 0.944728 -84 GCGCCAAAAAACCCAATCAAAAAAATAAAGCA 2 172 0 ACCCATAAAA 0.83561 -129 TGCCATAACATCTCCTTATAAATAATTTTTCG 2 203 0 TCTCCTTAAA 0.898563 -98 GTCTTCAAACTCCCCTTTTAAACCCTTTAAAT 4 61 0 TCCCCTTAAA 0.84263 -25 ATAACCCCCTAAAATTAAAACGACT 5 49 0 ACCCCTAAAT 0.943433 -15 TAAAAATTTTACTCCATTTTAACCGGTCATTT 6 67 1 ACTCCTTTAA 0.716384 -82 TATCAATCCTACTTCCTCAAATTGATGACAAA 7 25 0 ACTTCTAAAT 0.866906 -276 CTTTCTTAAAAATCCATTAAAATTACATTAAA 7 64 0 AATCCTAAAA 0.803799 -237 TTTGATTTAAACTTCATTTAATATCCGTTTAA 7 210 1 ACTTCTTAAT 0.712815 -91 AAGTTCAAACGCCCCCTGAAAAGTTTTGTCTT 9 11 0 GCCCCTAAAA 0.938149 -46 ATAAAAAAACACTCCCTTAAAAAAGACACCGC 10 20 0 ACTCCTAAAA 0.986377 -64 GTTTTCTAAAACTTCATAAAATTGCGCTTCGT 11 21 1 ACTTCTAAAT 0.866885 -280 TCATTATAACGCTCCTTAAAAAACATAGGAAG 11 59 1 GCTCCTAAAA 0.961676 -242 TCCTTAACGCTCTCGCTTAAAAGGTAATCGTC 11 159 0 TCTCGTAAAA 0.694119 -142 AAGGAGTTTGACTCATTGAAAATTTAGATTGC 11 186 1 ACTCATAAAA 0.893724 -115 ***** * **** Masking position 11 Map Score: 15.4917 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 575 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 ATGGTAAAATAAATACTTGCTTAAACACGCTAGGA 1 20 0 AAATTTTTAA 0.883837 -229 CAAGAAAAGCTAATTTTTCACTTAAACGATGCGTT 1 203 1 TAATTTCTAA 0.727602 -46 CAATCTGATTAAAACATTCATTTCAGCACTCTTTT 2 137 0 AAAATTTTCA 0.952359 -164 TCCTTATAAATAATTTTTCGCGCCAAAAAACCCAA 2 188 0 TAATTTCGCA 0.762799 -113 TGGATGATTTAAAATCTTTACGCCACAAAAACGCT 3 11 1 AAAATTCGCA 0.95481 -114 GCTAAAATTTTAAACCTTAACTCCAAGATCAAGCC 5 11 0 TAAATTCTCA 0.87528 -53 TAGGGTGGGTAAAAATTTTACTCCATTTTAACCGG 6 58 1 AAAATTCTCA 0.965777 -91 ATTGTTTGTTAAAAGTTTCTTTCAATTATACTAAA 6 106 0 AAAATTTTAA 0.92555 -43 GATTGATAATAAAAGTTTAATGTAATTTTAATGGA 7 49 1 AAAATTTGAA 0.902986 -252 AGATTATACAAAAACCTTTCTTAAAAATCCATTAA 7 76 0 AAAATTTTAA 0.92555 -225 AGTTTAAATCAAAATCATGGTGTCAAGAGGGGGAC 7 188 0 AAAAATTGCA 0.595648 -113 CGTCAAATCCCTAATGCAAGAAATTAAAA 7 282 0 AAATCTTGAA 0.604632 -19 CGGTTATAAAAAAACACTCCCTTAAAAAAGACACC 10 22 0 AAAACTCTAA 0.824909 -62 CTATGAAAAGGTTTTCTAAAACTTCATAAA 11 6 1 AAAATTCTAA 0.946091 -295 TCTAATAAAAAAATCTTTTTTTGCATGGGGGTATT 11 123 0 AAATTTTTCA 0.924441 -178 TTTCATTGTAAAATTCTTTCATGCAAAACCCATTG 11 250 1 AAATTTATCA 0.658551 -51 **** ** ** ** Masking position 8 Map Score: 11.0211 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 529 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TTTAAGCAAGTATTTATTTTACCATAATGGG 1 30 1 TATTTTTTTA 0.671071 -219 TTAATATTCTGCATGTTTTTAAACATTATCG 1 63 0 GCATGTTTTA 0.922887 -186 CTTGCTATAATCATCGTTTCACTTCTTTAAA 1 176 0 TCATCTTTCA 0.840003 -73 TAGAAAAAACGCATCGTTTAAGTGAAAAATT 1 214 0 GCATCTTTAA 0.913795 -35 GTGCTGAAATGAATGTTTTAATCAGATTGTG 2 143 1 GAATGTTTAA 0.501115 -158 TCTATCAACTTCATCGTTTAAATCCATAAAT 3 48 0 TCATCTTTAA 0.920976 -77 CCGGTCATTTTAATTATTTTAGTATAATTGA 6 89 1 TAATTTTTTA 0.829908 -60 TTGTATAATCTCATTCTTTTATTTTTTTGTC 7 100 1 TCATTTTTTA 0.964181 -201 ATCCGTTTAATCTTTTTTTTAGCAAAACTAA 7 232 1 TCTTTTTTTA 0.918389 -69 CAATAGCCTTGCATCTTTTAATTTCTTGCAT 7 267 1 GCATCTTTAA 0.913795 -34 AAAAGTCATTTTATTAGGGATCAAAT 8 6 1 TCATTTATTA 0.725939 -23 AAAAGACACCGCTTTATTTTA 10 1 0 GCTTTTTTTA 0.910995 -83 CTTGACTGACTCATTTTTTTAAAATACCCCC 11 218 1 TCATTTTTTA 0.964181 -83 TCTTATTTTTACCTTTTATTA 11 290 0 TCTTATTTTA 0.668506 -11 ***** ***** Masking position 11 Map Score: 9.785 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 504 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTTAAGCAAGTATTTATTTTACCATAATGG 1 30 1 TATTTATTTT 0.823566 -219 GCACACCATTTCTTAATATTCTGCATGTTT 1 76 0 TCTTAATATT 0.566679 -173 TGGTGGTGTTGCTTTTTATTTCTTTGCCTT 2 13 1 GCTTTTTATT 0.807533 -288 ATCAGATTGTGCTTTATTTTTTTGATTGGG 2 163 1 GCTTTATTTT 0.893165 -138 TTTATTCCAGTATTTTTATTGTTAGATACG 2 268 1 TATTTTTATT 0.700834 -33 CTTTTGTATATCTGTATTTTTTAGCCAATT 4 27 0 TCTGTATTTT 0.841478 -59 CCGGTCATTTTAATTATTTTAGTATAATTG 6 89 1 TAATTATTTT 0.640135 -60 TTGTATAATCTCATTCTTTTATTTTTTTGT 7 100 1 TCATTCTTTT 0.698664 -201 ATCCGTTTAATCTTTTTTTTAGCAAAACTA 7 232 1 TCTTTTTTTT 0.963018 -69 AAAAGTCATTTTATTAGGGATCAAA 8 6 1 TCATTTTATT 0.790866 -23 AAAAGACACCGCTTTATTTTA 10 2 0 GCTTTATTTT 0.893165 -82 TAATACTTCCTATGTTTTTTAAGGAGCGTT 11 66 0 TATGTTTTTT 0.622684 -235 AATAAAAAAATCTTTTTTTGCATGGGGGTA 11 125 0 TCTTTTTTTG 0.779404 -176 CTTGACTGACTCATTTTTTTAAAATACCCC 11 218 1 TCATTTTTTT 0.908454 -83 TCTTATTTTTACCTTTTATT 11 291 0 TCTTATTTTT 0.818822 -10 ********** Masking position 7 Map Score: 9.85807 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 1210 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 7 ATGCTTTCTCTTTAAAGGGTTTAAAATATC 3 77 0 TTTAAAGGGT 0.92364 -48 AAAAGTGGGATTTAAAGGGTTTAAAAGGGG 4 52 1 TTTAAAGGGT 0.92364 -34 TCGTTTTAATTTTAGGGGGTTAT 5 51 1 TTTAGGGGGT 0.970694 -13 TAACAAACAATTCAAGGGATTTGGCGATT 6 130 1 TTCAAGGGAT 0.898238 -19 TTAATGTAATTTTAATGGATTTTTAAGAAA 7 65 1 TTTAATGGAT 0.727535 -236 GACAAAACTTTTCAGGGGGCGTTTGAACTT 9 13 1 TTCAGGGGGC 0.932308 -44 GGTGTCTTTTTTAAGGGAGTGTTTTTTTAT 10 22 1 TTAAGGGAGT 0.716426 -62 TCCTATGTTTTTTAAGGAGCGTTATAATGA 11 59 0 TTTAAGGAGC 0.881756 -242 AAGCGAGAGCGTTAAGGAGTTTGACTCATT 11 173 1 GTTAAGGAGT 0.785362 -128 AATCTAAATTTTCAATGAGTCAAACTCCTT 11 186 0 TTCAATGAGT 0.873402 -115 TTTATTAAACTTCAATGGGTTTTGCATGAA 11 267 0 TTCAATGGGT 0.949439 -34 ********** Masking position 4 Map Score: 9.23764 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 704 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 8 TATAGCAAGAAAAGCTAATTTTTCACTTAA 1 198 1 AAAGCTAATT 0.675197 -51 ACTATACTCAAAAGCTTATAAAATCATCAA 2 108 1 AAAGCTTATA 0.719189 -193 ACTATGGAAGAACGCTTTATTCCAGTATTT 2 253 1 AACGCTTTAT 0.938687 -48 ACGCCACAAAAACGCTTTATTTATGGATTT 3 30 1 AACGCTTTAT 0.938687 -95 CAATTGCTCAAAAGCTAAAAG 4 2 0 AAAGCTAAAA 0.744341 -84 TAAAACGACTAACGCTAAAATTTTAAACCT 5 29 0 AACGCTAAAA 0.900266 -35 ATTGATAATAAAAGTTTAATGTAATTTTAA 7 50 1 AAAGTTTAAT 0.32785 -251 TTATGAGACCAGCGCTCTAAACCAGCTGAG 7 138 0 AGCGCTCTAA 0.677743 -163 TAAAAAAGACACCGCTTTATTTTA 10 5 0 ACCGCTTTAT 0.882123 -79 TTTTTTTATAACCGCTTTTAGTATAAAGGC 10 43 1 ACCGCTTTTA 0.738178 -41 GGGGTATTGTAGCGCTAATTGCCTTTATAC 10 63 0 AGCGCTAATT 0.821073 -21 GGGGTATTGTAGCGCTTAATGAGCGGGCTT 11 101 0 AGCGCTTAAT 0.937524 -200 ********** Masking position 1 Map Score: 4.70035 Number of sites scoring better than the average of aligned sites = 2588 Number in coding regions = 2310 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 9 AGGGATTCAAACCCCCGACCTACAGGACCGCA 1 110 1 ACCCCCGACA 0.990707 -139 TCGGCTTGCTACCCCAAAATTCAGGAACTCTT 2 59 1 ACCCCAAATC 0.879808 -242 GGGGACTTGAACCCCCGACCTCCGGCTTATGA 7 162 0 ACCCCCGACC 0.988812 -139 ACTTCTTACGACCCCCAAAGAATACCTG 9 39 1 ACCCCCAAGA 0.97958 -18 GCGCTACAATACCCCCATGCAAAAAAAGATTT 11 116 1 ACCCCCATCA 0.985698 -185 TTTTTAAAATACCCCCATTTCATTGTAAAATT 11 233 1 ACCCCCATTA 0.968344 -68 ******** * * Masking position 1 Map Score: 2.72243 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 64 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 AGAAATGGTGTGCTCGGAGGGATTCAAACC 1 93 1 TGCTCGGAGG 0.944848 -156 GCGGTCCTGTAGGTCGGGGGTTTGAATCCC 1 111 0 AGGTCGGGGG 0.990612 -138 AAGTGCTCGTAGCTCAGCTGAATAGAGCAA 1 147 0 AGCTCAGCTG 0.968035 -102 TTGTCAAGGTAGCTCAGCTGGTTTAGAGCG 7 126 1 AGCTCAGCTG 0.968035 -175 CATAAGCCGGAGGTCGGGGGTTCAAGTCCC 7 163 1 AGGTCGGGGG 0.990612 -138 ********** Masking position 4 Map Score: 2.0558 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTAAATTATAATAGAAAAAACGCATCGTTTAA 1 224 0 ATAAAAAACG 0.931158 -25 CATAGTGTATTTACTTAAATCTAATGCCATAA 2 227 0 TTATTAAACT 0.605134 -74 GTTTAAATCCATAAATAAAGCGTTTTTGTGGC 3 32 0 ATAATAAACG 0.931158 -93 ATAACCCCCTAAAATTAAAACGACTAACGCTA 5 42 0 AAATTAAACG 0.744563 -22 CAATGCCACTATATTTAACACTTAGGATTTTT 6 12 0 ATATTAACCT 0.694181 -137 TTATACTAAAATAATTAAAATGACCGGTTAAA 6 84 0 ATATTAAATG 0.779455 -65 AGTAGGATTGATAATAAAAGTTTAATGTAATT 7 44 1 ATATAAAATT 0.650128 -257 GAATGAGATTATACAAAAACCTTTCTTAAAAA 7 84 0 ATAAAAAACT 0.876719 -217 AATTGCCTTTATACTAAAAGCGGTTATAAAAA 10 45 0 ATATAAAACG 0.95823 -39 AAGGAGCGTTATAATGAAAACGAACGAAGCGC 11 44 0 ATATGAAACG 0.893483 -257 TCGTCTTCTAATAAAAAAATCTTTTTTTGCAT 11 132 0 ATAAAAAACT 0.876719 -169 *** ***** ** Masking position 7 Map Score: 4.36432 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 182 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 TGGATGATTTAAAATCTTTACGCCA 3 6 1 GATTTAAAAT 0.956034 -119 TTTATTTATGGATTTAAACGATGAAGTTGA 3 45 1 GATTTAAACG 0.93265 -80 CTCTTTAAAGGGTTTAAAATATCTATCAAC 3 70 0 GGTTTAAAAT 0.968168 -55 GGATTTAAAGGGTTTAAAAGGGGAGTTTGA 4 59 1 GGTTTAAAAG 0.962568 -27 TTGGAGTTAAGGTTTAAAATTTTAGCGTTA 5 20 1 GGTTTAAAAT 0.968168 -44 CCATGATTTTGATTTAAACTTCATTTAATA 7 203 1 GATTTAAACT 0.942686 -98 ********** Masking position 5 Map Score: 6.95381 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 55 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 ATAATGTTTAAAAACATGCAGAATATTAAG 1 65 1 AAAACATGCA 0.88942 -184 TAAAGAAGTGAAACGATGATTATAGCAAGA 1 178 1 AAACGATGAT 0.772057 -71 TTTTTCACTTAAACGATGCGTTTTTTCTAT 1 216 1 AAACGATGCG 0.939718 -33 CAATCTGATTAAAACATTCATTTCAGCACT 2 142 0 AAAACATTCA 0.721779 -159 TTATGGATTTAAACGATGAAGTTGATAGAT 3 50 1 AAACGATGAA 0.955528 -75 CTTTAAAGAGAAAGCATGAAGATCATTATA 3 90 1 AAAGCATGAA 0.823704 -35 CCTAAAATTAAAACGACTAACGCTAAAATT 5 37 0 AAACGACTAA 0.543312 -27 AACTTTTAACAAACAATTCAAGGGATTTGG 6 124 1 AAACAATTCA 0.724596 -25 CAAAAAAATAAAAGAATGAGATTATACAAA 7 99 0 AAAGAATGAG 0.650477 -202 TTTGCTAAAAAAAAGATTAAACGGATATTA 7 228 0 AAAAGATTAA 0.812933 -73 GCAAGAAATTAAAAGATGCAAGGCTATTGT 7 266 0 AAAAGATGCA 0.939786 -35 GGGTATTTTAAAAAAATGAGTCAGTCAAGG 11 217 0 AAAAAATGAG 0.734442 -84 ********** Masking position 6 Map Score: 4.93138 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 443 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 14 ********** No masking Map Score: 1.38088e-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 15 ********** No masking Map Score: 1.38088e-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