AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_hpyl_reg_100.orf -o00510_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 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP1154 130 H. pylori predicted coding region HP1154 #3 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #4 HP1361 56 competence locus E (comE3) #5 HP1365 83 response regulator #6 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 AAATTTTGTTTTATAGTAAAACTCATTTTTAA 1 29 0 TTATTAAAAC 0.922471 -177 TATTATTTAATCTTTTTAAAATTTTGTTTTAT 1 47 0 TCTTTAAAAT 0.945352 -159 AAAGATTAAATAATATTAAATTGAATGGGGTT 1 64 1 TAATTAAATT 0.654724 -142 TTTTGTCAAATATTGATAAACCCCATTCAATT 1 82 0 TATTTAAACC 0.661709 -124 TTTATCAATATTTGACAAAAATAAGATCAAAA 1 94 1 TTTGAAAAAT 0.692874 -112 CCAAAAGAGTTAATAAAAAATTTTTTTGATCT 1 117 0 TAATAAAATT 0.697299 -89 CGATCAAGGTTTTTATGAAAATAAAAGCCTAA 1 159 1 TTTTGAAAAT 0.801947 -47 CAAAAGTCCTTTTTTTAAAATTGTTTTAGGC 1 185 0 TTTTTAAAAT 0.944525 -21 TATTATCCTAAAATAGAGCGTTCC 2 3 1 TTATTAAAAT 0.95558 -128 AATAGAGCGTTCCTTAAAAAATGGTTGGATTT 2 22 1 TCCTAAAAAT 0.889961 -109 TGTTGTATAATTTTGAAAAAATACGCAACAAT 2 81 0 TTTTAAAAAT 0.959268 -50 CTAAAAGCGGTTATAAAAAAACACTCCCTTAA 5 32 0 TTATAAAAAC 0.935293 -52 CTAATTGCCTTTATACTAAAAGCGGTTATAAA 5 47 0 TTATTAAAAG 0.731771 -37 TATGAAAAGGTTTTCTAAAACTTCATAAAATT 6 12 1 TTTTAAAACT 0.918524 -289 ATTATAACGCTCCTTAAAAAACATAGGAAGTA 6 61 1 TCCTAAAAAC 0.817295 -240 AATCGTCTTCTAATAAAAAAATCTTTTTTTGC 6 134 0 TAATAAAAAT 0.908751 -167 GGAGTTTGACTCATTGAAAATTTAGATTGCCT 6 188 1 TCATAAAATT 0.843699 -113 AATGGGGGTATTTTAAAAAAATGAGTCAGTCA 6 220 0 TTTTAAAAAT 0.959268 -81 TACCCCCATTTCATTGTAAAATTCTTTCATGC 6 242 1 TCATTAAAAT 0.950519 -59 TAAAATTCTTTCATGCAAAACCCATTGAAGTT 6 258 1 TCATAAAACC 0.860457 -43 TATTTTTACCTTTTATTAAACTTCAATGGGTT 6 276 0 TTTTTAAACT 0.902724 -25 **** ****** Masking position 1 Map Score: 26.2191 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 1316 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 2 TAACTATCCCCCTTAAAAATGAGTTTTACT 1 17 1 CCTTAAAAAT 0.880712 -189 TGAGTTTTACTATAAAACAAAATTTTAAAA 1 36 1 TATAAAACAA 0.734985 -170 TAAAACAAAATTTTAAAAAGATTAAATAAT 1 48 1 TTTTAAAAAG 0.788558 -158 CAAAAGAGTTAATAAAAAATTTTTTTGATC 1 118 0 AATAAAAAAT 0.485532 -88 AAAATAAAAGCCTAAAACAATTTTAAAAAA 1 176 1 CCTAAAACAA 0.907686 -30 CCTAAAACAATTTTAAAAAAAGGACTTTTG 1 186 1 TTTTAAAAAA 0.891495 -20 TATTATCCTAAAATAGAGCGTTCCTT 2 7 1 CCTAAAATAG 0.603828 -124 ATAGAGCGTTCCTTAAAAAATGGTTGGATT 2 23 1 CCTTAAAAAA 0.975013 -108 GTTGTATAATTTTGAAAAAATACGCAACAA 2 82 0 TTTGAAAAAA 0.721454 -49 AAAGCATTTAAATTAAAAAGGATAGTCCA 2 112 1 AATTAAAAAG 0.680034 -19 TGATTTGATCCCTAATAAAATGACTTTT 3 9 0 CCTAATAAAA 0.855744 -20 AAAAACACTCCCTTAAAAAAGACACCGCTT 5 18 0 CCTTAAAAAA 0.975013 -66 TAAAAGCGGTTATAAAAAAACACTCCCTTA 5 33 0 TATAAAAAAA 0.917394 -51 TTATAACGCTCCTTAAAAAACATAGGAAGT 6 62 1 CCTTAAAAAA 0.975013 -239 ATCGTCTTCTAATAAAAAAATCTTTTTTTG 6 135 0 AATAAAAAAA 0.834141 -166 AATGGGGGTATTTTAAAAAAATGAGTCAGT 6 222 0 TTTTAAAAAA 0.891495 -79 CCCATTGAAGTTTAATAAAAGGTAAAAATA 6 278 1 TTTAATAAAA 0.608848 -23 ********** Masking position 5 Map Score: 17.6407 Number of sites scoring better than the average of aligned sites = 2419 Number in coding regions = 1966 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 3 TCATTTTTAAGGGGGATAGTTATCCAAA 1 8 0 GGGGGATGTT 0.954925 -198 TAAATTGAATGGGGTTTATCAATATTTGACA 1 80 1 GGGGTTTTCA 0.967987 -126 ACTTTTCAGGGGGCGTTTGAACTTCTTACGA 4 19 1 GGGCGTTGAA 0.894716 -38 AGGTATTCTTTGGGGGTCGTAAGAAGTTCAA 4 35 0 TGGGGGTGTA 0.922607 -22 GGGGGTATTGTAGCGCTAATTG 5 72 0 GGGGTATGTA 0.9939 -12 CTTAATGAGCGGGCTTTGTTATAATACTTCC 6 86 0 GGGCTTTTTA 0.942078 -215 TTTTTGCATGGGGGTATTGTAGCGCTTAATG 6 110 0 GGGGTATGTA 0.9939 -191 CAATGAAATGGGGGTATTTTAAAAAAATGAG 6 227 0 GGGGTATTTA 0.981617 -74 TAAACTTCAATGGGTTTTGCATGAAAGAATT 6 261 0 TGGGTTTGCA 0.947828 -40 ******* *** Masking position 7 Map Score: 11.4749 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 272 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TCCCCCTTAAAAATGAGTTTTACTATAAAAC 1 23 1 AAATGATTTT 0.961294 -183 TTTACTATAAAACAAAATTTTAAAAAGATTA 1 41 1 AACAAATTTT 0.930469 -165 AATTTTTTTGATCTTATTTTTGTCAAATATT 1 100 0 ATCTTATTTT 0.455016 -106 AATAAGATCAAAAAAATTTTTTATTAACTCT 1 113 1 AAAAAATTTT 0.693923 -93 ATAAAAGCCTAAAACAATTTTAAAAAAAGGA 1 179 1 AAAACATTTT 0.787222 -27 AATTTTAAAAAAAGGACTTTTG 1 194 1 AAAGGATTTT 0.903457 -12 ATCCCTAATAAAATGACTTTT 3 1 0 AAATGATTTT 0.937859 -28 AAGACAAAACTTTTCAGGGGGCGT 4 4 1 ACAAAATTTT 0.816907 -53 CCCATGCAAAAAAAGATTTTTTTATTAGAAG 6 129 1 AAAAGATTTT 0.706762 -172 AGTCAAGGCAATCTAAATTTTCAATGAGTCA 6 194 0 ATCTAATTTT 0.733117 -107 GGTTTTGCATGAAAGAATTTTACAATGAAAT 6 249 0 GAAAGATTTT 0.890582 -52 ****** **** Masking position 6 Map Score: 10.5788 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 554 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TTGATAAACCCCATTCAATTTAATATTATTTAA 1 69 0 CCTTATTTAA 0.925041 -137 TTTTTAAGGAACGCTCTATTTTAGGATAATA 2 9 0 ACCTATTTTA 0.767155 -122 ATTTGGAACGCCTTTTGCTTTTACGCTTTTAAT 2 50 1 CCTTCTTTTA 0.974168 -81 TGGACTATCCTTTTTAATTTAAATGCTTTGT 2 110 0 CCTTAATTTA 0.940181 -21 AAAAAAGACACCGCTTTATTTTA 5 1 0 CCCTATTTTA 0.974168 -83 TTTTTATAACCGCTTTTAGTATAAAGGCAATTA 5 45 1 CGTTAGTATA 0.857356 -39 GCGCTTCGTTCGTTTTCATTATAACGCTCCTTA 6 44 1 CGTTATTATA 0.924791 -257 TATTAGAAGACGATTACCTTTTAAGCGAGAGCG 6 151 1 CGTTCTTTTA 0.943603 -150 TAAAATACCCCCATTTCATTGTAAAATTCTTTC 6 237 1 CCTTATTGTA 0.958839 -64 CATGCAAAACCCATTGAAGTTTAATAAAAGGTA 6 269 1 CCTTAGTTTA 0.977205 -32 ** ** ****** Masking position 5 Map Score: 9.23128 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 237 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 TGGTGTAGGATAGCGATCAAGGTTTTTATG 1 146 1 TAGCGATCAA 0.988674 -60 GTCATTTTATTAGGGATCAAATCA 3 15 1 TAGGGATCAA 0.970424 -14 GGGGGTATTGTAGCGCTAATTGCCTTTATA 5 64 0 TAGCGCTAAT 0.95199 -20 GGGGGTATTGTAGCGCTTAATGAGCGGGCT 6 102 0 TAGCGCTTAA 0.980301 -199 ********** Masking position 7 Map Score: 0.569897 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 174 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 ATAACTATCCCCCTTAAAAATGAGTTTTAC 1 16 1 CCCTTAAAAA 0.960181 -190 AAATACGCAACAATTAAAAGCGTAAAAGCA 2 65 0 CAATTAAAAG 0.941756 -66 TTCAAACGCCCCCTGAAAAGTTTTGTCTT 4 10 0 CCCTGAAAAG 0.990643 -47 AAAAAACACTCCCTTAAAAAAGACACCGCT 5 19 0 CCCTTAAAAA 0.960181 -65 CTATGAAAAGGTTTTCTAAA 6 1 1 CTATGAAAAG 0.927027 -300 TTAACGCTCTCGCTTAAAAGGTAATCGTCT 6 158 0 CGCTTAAAAG 0.968572 -143 AAGAATTTTACAATGAAATGGGGGTATTTT 6 238 0 CAATGAAATG 0.826109 -63 ********** Masking position 6 Map Score: 7.05744 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 267 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 ********** No masking Map Score: -1.53234e-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 9 ********** No masking Map Score: -1.53234e-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 10 ********** No masking Map Score: -1.53234e-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