AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_hpyl_reg_100.orf -o00760_hpyl_100.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 HP0429 124 H. pylori predicted coding region HP0429 #3 HP0430 85 H. pylori predicted coding region HP0430 #4 HP1054 63 H. pylori predicted coding region HP1054 #5 HP1057 148 H. pylori predicted coding region HP1057 #6 HP1180 300 pyrimidine nucleoside transport protein (nupC) #7 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #8 HP1361 56 competence locus E (comE3) #9 HP1365 83 response regulator #10 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 TGCTCGGAGGGATTCAAACCCCCGACCTACAGGA 1 103 1 GTCAACCCCG 0.992325 -146 CTTTTAAACCCTTTAAATCCCACTTTTGTATATC 3 45 0 CTAAACCACT 0.916045 -41 AGCGTCTTCAAACTCCCCTTTTAAACCCT 3 67 0 CTAAACCCCT 0.984404 -19 ATAAAGTCATGCTACAATGCCACTATATTTAACA 5 24 0 GTCAACCACT 0.980242 -125 GGAGGTCGGGGGTTCAAGTCCCCCTCTTGACACC 6 171 1 GTCAACCCCC 0.998229 -130 GTCGTAAGAAGTTCAAACGCCCCCTGAAAAGTTT 8 17 0 GTAAACCCCC 0.995861 -40 GGCAATTAGCGCTACAATACCCCC 9 70 1 GTCAACCCCC 0.99823 -14 CTCATTAAGCGCTACAATACCCCCATGCAAAAAA 10 108 1 GTCAACCCCC 0.99823 -193 GACTCATTTTTTTAAAATACCCCCATTTCATTGT 10 225 1 TTAAACCCCC 0.968956 -76 AAAATTCTTTCATGCAAAACCCATTGAAGTTTAA 10 259 1 CTCAACCCAT 0.92817 -42 * * *** ***** Masking position 7 Map Score: 21.4597 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 TATCGCTCCCATTATGGTAAAATAAATACTTGCTTAAA 1 30 0 AGTAAAAAAA 0.931383 -219 AAGAAGTGAAACGATGATTATAGCAAGAAAAGCTAATT 1 180 1 AGTTATAAAA 0.931384 -69 TAGATATTTTAAACCCTTTAAAGAGAAAGCATGAAGAT 2 75 1 ACTTAAAGAA 0.977002 -50 GCTTTTGAGCAATTGGCTAAAAAATACAGATATACAAA 3 17 1 AGTAAAATAA 0.810941 -69 AGTGGGATTTAAAGGGTTTAAAAGGGGAGTTTGAAGAC 3 55 1 AGTTAAAGGA 0.869741 -31 ATAACCCCCTAAAATTAAAACGACTAACGC 4 44 0 ACTAAAAAAA 0.922579 -20 TATAATTGAAAGAAACTTTTAACAAACAATTCAAGGGA 5 111 1 ACTTTAAAAA 0.844376 -38 CCTTTCTTAAAAATCCATTAAAATTACATTAAACTTTT 6 59 0 ACTTAAATAA 0.908101 -242 AAAATAAAAGAATGAGATTATACAAAAACCTTTCTTAA 6 87 0 AGTTATAAAA 0.931383 -214 CGGATATTAAATGAAGTTTAAATCAAAATCATGGTGTC 6 199 0 AGTTAAAAAA 0.97269 -102 TTTTGCTAAAAAAAAGATTAAACGGATATTAAATGAAG 6 221 0 AGTTAAAGAA 0.980082 -80 ATAAAAAAACACTCCCTTAAAAAAGACACCGCTTTATT 9 14 0 ACTAAAAGAA 0.942662 -70 CTTTATACTAAAAGCGGTTATAAAAAAACACTCCCTTA 9 33 0 AGTTATAAAA 0.931384 -51 ATGTTTTTTAAGGAGCGTTATAATGAAAACGAACGAAG 10 47 0 ACTTATAGAA 0.942738 -254 TTAGAAGACGATTACCTTTTAAGCGAGAGCGTTAAGGA 10 153 1 ACTTTAAGAA 0.880968 -148 * * ***** ** * Masking position 12 Map Score: 17.0637 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 224 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 ATCATCGTTTCACTTCTTTAAAAGTGCTCGT 1 167 0 CACTTCTTAA 0.831673 -82 TTCATCGTTTAAATCCATAAATAAAGCGTTT 2 39 0 AAATCCTAAA 0.956694 -86 TAGATATTTTAAACCCTTTAAAGAGAAAGCA 2 75 1 AAACCCTTAA 0.979619 -50 CTCCCCTTTTAAACCCTTTAAATCCCACTTT 3 53 0 AAACCCTTAA 0.979619 -33 ATAACCCCCTAAAATTAAAACGA 4 51 0 AACCCCTAAA 0.948122 -13 AATCGCCAAATCCCTTGAATTGTTTGTT 5 131 0 AAATCCTTGA 0.948226 -18 CCTTTCTTAAAAATCCATTAAAATTACATTA 6 66 0 AAATCCTTAA 0.981428 -235 TTTTGATTTAAACTTCATTTAATATCCGTTT 6 209 1 AACTTCTTTA 0.683824 -92 CGTCAAATCCCTAATGCAAGAAATT 6 286 0 AAATCCTAAT 0.684969 -15 TATAAAAAAACACTCCCTTAAAAAAGACACC 9 22 0 CACTCCTTAA 0.933118 -62 GGTTTTCTAAAACTTCATAAAATTGCGCTTC 10 20 1 AACTTCTAAA 0.876783 -281 TCAATGAGTCAAACTCCTTAACGCTCTCGCT 10 174 0 AAACTCTTAA 0.944511 -127 TTTCATTGTAAAATTCTTTCATGCAAAACCC 10 250 1 AAATTCTTCA 0.778972 -51 CTTTCATGCAAAACCCATTGAAGTTTAATAA 10 265 1 AAACCCTTGA 0.943369 -36 ****** **** Masking position 2 Map Score: 17.2368 Number of sites scoring better than the average of aligned sites = 1202 Number in coding regions = 1009 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 AAGTGAAAAATTAGCTTTTCTTGCTATAATCA 1 194 0 TTACTTTTTT 0.867711 -55 ATCCATAAATAAAGCGTTTTTGTGGCGTAAAG 2 26 0 AAACGTTTTG 0.761976 -99 TAGATATTTTAAACCCTTTAAAGAGAAAGCAT 2 75 1 AAACCTTTAA 0.714533 -50 CTTTTAGCTTTTGAGCAATTGGCTA 3 4 1 TTACTTTTAG 0.841144 -82 CTCCCCTTTTAAACCCTTTAAATCCCACTTTT 3 52 0 AAACCTTTAA 0.714533 -34 AAAATTACATTAAACTTTTATTATCAATCCTA 6 46 0 TAACTTTTTT 0.934074 -255 AGATTATACAAAAACCTTTCTTAAAAATCCAT 6 79 0 AAACCTTTTT 0.901731 -222 AATATCCGTTTAATCTTTTTTTTAGCAAAACT 6 229 1 TAACTTTTTT 0.934074 -72 AAGACAAAACTTTTCAGGGGGCGTTTG 8 6 1 AAACTTTTAG 0.929826 -51 AAGTTTTAGAAAACCTTTTCATAG 10 3 0 AAACTTTTAT 0.934074 -298 TCTAATAAAAAAATCTTTTTTTGCATGGGGGT 10 126 0 AAACTTTTTT 0.942574 -175 TAGAAGACGATTACCTTTTAAGCGAGAGCGTT 10 154 1 TTACTTTTAG 0.841144 -147 TCTTATTTTTACCTTTTATTAAACTTCAAT 10 281 0 TTACTTTTTT 0.867711 -20 *** ***** ** Masking position 3 Map Score: 11.9814 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 477 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 5 TCCGAGCACACCATTTCTTAATATTCTGCA 1 81 0 CCATTTCTTA 0.850515 -168 ATTACATTAAACTTTTATTATCAATCCTAC 6 45 0 ACTTTTATTA 0.60494 -256 ATAATCTCATTCTTTTATTTTTTTGTCAAG 6 104 1 TCTTTTATTT 0.910345 -197 GATTTAAACTTCATTTAATATCCGTTTAAT 6 213 1 TCATTTAATA 0.818467 -88 ATCCGTTTAATCTTTTTTTTAGCAAAACTA 6 232 1 TCTTTTTTTT 0.891794 -69 TAGCCTTGCATCTTTTAATTTCTTGCATTA 6 270 1 TCTTTTAATT 0.880608 -31 AAAAGTCATTTTATTAGGGATCAAA 7 6 1 TCATTTTATT 0.813042 -23 TTTTAGAAAACCTTTTCATAG 10 2 0 CCTTTTCATA 0.850515 -299 AATAAAAAAATCTTTTTTTGCATGGGGGTA 10 125 0 TCTTTTTTTG 0.71719 -176 CTTGACTGACTCATTTTTTTAAAATACCCC 10 218 1 TCATTTTTTT 0.856872 -83 TAAAATACCCCCATTTCATTGTAAAATTCT 10 237 1 CCATTTCATT 0.830832 -64 CTTATTTTTACCTTTTATTAAACTTCAATG 10 280 0 CCTTTTATTA 0.888777 -21 ********** Masking position 5 Map Score: 6.76968 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 678 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 6 AAAATAAATACTTGCTTAAACACGCTAGGA 1 20 0 CTTGCTTAAA 0.960569 -229 CATCGTTTCACTTCTTTAAAAGTGCTCGTA 1 166 0 CTTCTTTAAA 0.904972 -83 ATTAGCTTTTCTTGCTATAATCATCGTTTC 1 187 0 CTTGCTATAA 0.754388 -62 TTTTTAGCCAATTGCTCAAAAGCTAAAAG 3 10 0 ATTGCTCAAA 0.668226 -76 AGCGTCTTCAAACTCCCCTTTT 3 74 0 CGTCTTCAAA 0.497263 -12 ATAACCCCCTAAAATTAAAACGAC 4 50 0 CCCCCTAAAA 0.789674 -14 ATCAATCCTACTTCCTCAAATTGATGACAA 6 26 0 CTTCCTCAAA 0.968464 -275 TTTCTTAAAAATCCATTAAAATTACATTAA 6 65 0 ATCCATTAAA 0.476016 -236 ATACAAAAACCTTTCTTAAAAATCCATTAA 6 76 0 CTTTCTTAAA 0.790311 -225 TTGATTTAAACTTCATTTAATATCCGTTTA 6 211 1 CTTCATTTAA 0.62304 -90 GTAGTTTAGTTTTGCTAAAAAAAAGATTAA 6 238 0 TTTGCTAAAA 0.537822 -63 TAAAAAAACACTCCCTTAAAAAAGACACCG 9 21 0 CTCCCTTAAA 0.972552 -63 TTTTCTAAAACTTCATAAAATTGCGCTTCG 10 22 1 CTTCATAAAA 0.87366 -279 CATTATAACGCTCCTTAAAAAACATAGGAA 10 60 1 CTCCTTAAAA 0.850338 -241 CCTTAACGCTCTCGCTTAAAAGGTAATCGT 10 160 0 CTCGCTTAAA 0.952404 -141 ********** Masking position 9 Map Score: 10.5043 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1021 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 7 GGTTTGAATCCCTCCGAGCACACCATTTCT 1 93 0 CCTCCGAGCA 0.956214 -156 GGGATTCAAACCCCCGACCTACAGGACCGC 1 111 1 CCCCCGACCT 0.99262 -138 TTGCTCTATTCAGCTGAGCTACGAGCACTT 1 147 1 CAGCTGAGCT 0.97475 -102 CGCTCTAAACCAGCTGAGCTACCTTGACAA 6 126 0 CAGCTGAGCT 0.97475 -175 GGGACTTGAACCCCCGACCTCCGGCTTATG 6 163 0 CCCCCGACCT 0.99262 -138 ********** Masking position 7 Map Score: 3.04083 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 8 TACCATAATGGGAGCGATAATGTTTAAAAA 1 49 1 GGAGCGATAA 0.970601 -200 CTTTTTTAAGGGAGTGTTTTTTTATAACCG 9 27 1 GGAGTGTTTT 0.788567 -57 GGGGGTATTGTAGCGCTAATTGCCTTTAT 9 65 0 GTAGCGCTAA 0.901298 -19 TGTTTTTTAAGGAGCGTTATAATGAAAACG 10 54 0 GGAGCGTTAT 0.977518 -247 TGGGGGTATTGTAGCGCTTAATGAGCGGGC 10 103 0 GTAGCGCTTA 0.932581 -198 CTTTTAAGCGAGAGCGTTAAGGAGTTTGAC 10 168 1 AGAGCGTTAA 0.927261 -133 ********** Masking position 3 Map Score: 2.17091 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 297 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTAAAGAAGTGAAACGATGATTATAGCAAG 1 177 1 GAAACGATGA 0.985547 -72 ATTTTTCACTTAAACGATGCGTTTTTTCTA 1 215 1 TAAACGATGC 0.972934 -34 TTTATGGATTTAAACGATGAAGTTGATAGA 2 49 1 TAAACGATGA 0.977505 -76 CCTTTAAAGAGAAAGCATGAAGATCATTAT 2 89 1 GAAAGCATGA 0.91082 -36 TCCCCCTCTTGACACCATGATTTTGATTTA 6 189 1 GACACCATGA 0.929336 -112 TGCAAGAAATTAAAAGATGCAAGGCTATTG 6 267 0 TAAAAGATGC 0.874246 -34 ********** Masking position 4 Map Score: 2.38684 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 49 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 CCCATTATGGTAAAATAAATACTTGCTTAAA 1 30 0 TAAAATAATA 0.672485 -219 TGGATGATTTAAAATCTTTACGCCACAAAA 2 10 1 TAAAATTTTA 0.921728 -115 TTAAAGGGTTTAAAATATCTATCAACTTCAT 2 65 0 TAAAATTCTA 0.932712 -60 CGACTAACGCTAAAATTTTAAACCTTAACTC 4 23 0 TAAAATTTAA 0.902843 -41 TAAAATGGAGTAAAATTTTTACCCACCCTAA 5 57 0 TAAAATTTTA 0.646931 -92 TCAATTATACTAAAATAATTAAAATGACCGG 5 89 0 TAAAATATTA 0.887127 -60 GGATTGATAATAAAAGTTTAATGTAATTTTA 6 48 1 TAAAAGTTAA 0.763922 -253 CAAGGCAATCTAAATTTTCAATGAGTCAAAC 10 191 0 TAAATTTCAA 0.630184 -110 ****** **** Masking position 4 Map Score: 2.37825 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 244 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 GCGTGTTTAAGCAAGTATTTATTTTACCATA 1 25 1 GCAAGTTTTA 0.953425 -224 TTAATATTCTGCATGTTTTTAAACATTATCG 1 63 0 GCATGTTTTA 0.940325 -186 TTTTGTGGCGTAAAGATTTTAAATCATCCA 2 10 0 TAAAGATTTA 0.724219 -115 TGGCATTGTAGCATGACTTTATTAGGGTGGG 5 36 1 GCATGATTTA 0.97203 -113 AAAAATAAAAGAATGAGATTATACAAAAACC 6 95 0 GAATGAATTA 0.883746 -206 AATCCCTAATGCAAGAAATTAAAAGATGCAA 6 275 0 GCAAGAATTA 0.953528 -26 GGTTTTGCATGAAAGAATTTTACAATGAAAT 10 249 0 GAAAGATTTT 0.825658 -52 ****** **** Masking position 3 Map Score: 1.56295 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 302 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: -3.21633e-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 13 ********** No masking Map Score: -3.21633e-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 14 ********** No masking Map Score: -3.21633e-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