AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_hpyl_reg_100.orf -o00860_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 HP0163 71 delta-aminolevulinic acid dehydratase (hemB) #2 HP0165 25 H. pylori predicted coding region HP0165 #3 HP0166 235 response regulator (ompR) #4 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #5 HP0305 243 H. pylori predicted coding region HP0305 #6 HP0376 55 ferrochelatase (hemH) #7 HP0382 182 zinc-metallo protease (YJR117W) #8 HP0476 117 glutamyl-tRNA synthetase (gltX) #9 HP0602 117 endonuclease III #10 HP0603 44 H. pylori predicted coding region HP0603 #11 HP0604 65 uroporphyrinogen decarboxylase (hemE) #12 HP0643 164 glutamyl-tRNA synthetase (gltX) #13 HP1223 65 H. pylori predicted coding region HP1223 Motif number 1 TTTTTAATGTTTTTAAACAATTCCTTTGATCGTTTT 3 10 0 TTTTATTCTT 0.860854 -226 TAAGGCTTTGTTTTCATGGAATATTGAAAAATAAAGT 3 52 0 TTTTAATTTA 0.932335 -184 TATGATAATGTTTTGAATTTTTATTTTTAAGATATTT 3 105 1 TTTTATTTTT 0.984783 -131 TTTTAAGATATTTTCAAGGTATCTTTAATAATAAAAT 3 129 1 TTTTAATTTA 0.932335 -107 AGGGGACTAATTCTAGCATTTTATTATTAAAGATACC 3 146 0 TTCTGTTTTT 0.861445 -90 TATTTAATCTTTTTAAAATTTTGTTTTATAGTAAAAC 4 39 0 TTTTATTTTT 0.984783 -167 TTTGATCTTATTTTTGTCAAATATTGATAAACCCCAT 4 88 0 TTTTGATTTA 0.877356 -118 TCAAAAAAATTTTTTATTAACTCTTTTGGTGTAGGAT 4 120 1 TTTTACTTTT 0.937904 -86 TTTAAAATTGTTTTAGGCTTTTATTTTCATAAAAACC 4 166 0 TTTTGTTTTT 0.971098 -40 CGCTTTAACCTTTTGATGAATGGTTCAGAAAGTTTGT 5 50 1 TTTTATGTTA 0.950812 -194 ATTGCGTTTATTTTAAACTCTTTTTGTAAATAATGCT 5 94 0 TTTTATTTTT 0.984783 -150 TAACTTCTTTCTAACGATTTATTTTTTATTAATCG 6 9 1 TTCTATTTTT 0.92293 -47 AAAGAGACTATTTTTGAGCGTTTTTAATCCTAAAAAG 7 49 0 TTTTGTTTTA 0.962137 -134 TATGGTAAATTTTTGAAAAATTGTTATAATTCCTACA 7 117 1 TTTTATTTTT 0.984783 -66 GTGAAACCATTTTTAAGCCATTTTTGAATACAATAAG 8 65 1 TTTTATTTTA 0.979978 -53 TTTGCTTTAATTTTTACTTCTTTTTTAATAAAATACT 9 58 1 TTTTATTTTA 0.979978 -60 AAAATACTCTTTTTGATTCCTTTTTATTATAGGCGGT 9 87 1 TTTTATTTTT 0.984783 -31 TTTTTAGATTTTTCTTAATCTTAAGCCT 10 2 1 TTTTGTTTTA 0.962137 -43 ATCTTAAGCCTTTTAAAAGGCGTTTTA 10 28 1 TTTTACGTTA 0.818557 -17 AACGCCAAGCTTTTTATGGTTGGTTATCAAAAAGCTA 12 20 0 TTTTATGTTT 0.962348 -145 TATCCTTAGTTTTTAAAATAAGGTTATGTTACAATGA 13 36 0 TTTTAAGTTT 0.877977 -30 **** * ** ** * Masking position 4 Map Score: 40.4492 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 556 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 2 ATTGTGGGGTTAAAGAAAAACAATAAAGAG 1 47 1 TAAAGAAAAA 0.905871 -25 TTTCATGGAATATTGAAAAATAAAGTCTTA 3 48 0 TATTGAAAAA 0.791905 -188 GAAAATATCTTAAAAATAAAAATTCAAAAC 3 114 0 TAAAAATAAA 0.887373 -122 AAGGTATCTTTAATAATAAAATGCTAGAAT 3 144 1 TAATAATAAA 0.853775 -92 AGTTTTACTATAAAACAAAATTTTAAAAAG 4 38 1 TAAAACAAAA 0.849521 -168 AAAGATTAAATAATATTAAATTGAATGGGG 4 64 1 TAATATTAAA 0.570797 -142 TTTTGTCAAATATTGATAAACCCCATTCAA 4 84 0 TATTGATAAA 0.658633 -122 CCAAAAGAGTTAATAAAAAATTTTTTTGAT 4 119 0 TAATAAAAAA 0.920111 -87 ATCGCTATCCTACACCAAAAGAGTTAATAA 4 133 0 TACACCAAAA 0.691118 -73 TAGGCTTTTATTTTCATAAAAACCTTGATC 4 160 0 TTTTCATAAA 0.533597 -46 CTAAAACAATTTTAAAAAAAGGACTTTTG 4 187 1 TTTAAAAAAA 0.7283 -19 TAACCTTGGATACAGAAAAAT 5 2 0 TACAGAAAAA 0.773094 -242 GTCAGCATTATTTACAAAAAGAGTTTAAAA 5 91 1 TTTACAAAAA 0.75288 -153 CAAAAAGAGTTTAAAATAAACGCAATTGTA 5 105 1 TTAAAATAAA 0.721164 -139 TAAGCACGCTTACAACTAAAACGATTCATT 5 172 0 TACAACTAAA 0.503295 -72 CGTGCTTATTTACACTAAAATAATAAGCGT 5 194 1 TACACTAAAA 0.583865 -50 ATAAAACGATTAATAAAAAATAAATCGTTA 6 22 0 TAATAAAAAA 0.920111 -34 TGGTGCATGCTAAAATAAAACGATTAATAA 6 36 0 TAAAATAAAA 0.77974 -20 CAACCCGCTATAAACAAAAAGGTTTGTC 7 9 0 TAAACAAAAA 0.945645 -174 TGAGCGTTTTTAATCCTAAAAAGCTGTGTT 7 42 0 TAATCCTAAA 0.703643 -141 CATAAAACCATAAAATTAAATAAATATGGT 7 91 0 TAAAATTAAA 0.642176 -92 TTATAACAATTTTTCAAAAATTTACCATAA 7 116 0 TTTTCAAAAA 0.692909 -67 GGTTGATCCTAATCAAAAATAATCTCAAT 8 10 1 TAATCAAAAA 0.92802 -108 ACTCTTATTGTATTCAAAAATGGCTTAAAA 8 75 0 TATTCAAAAA 0.873152 -43 GTTCTAACCTTAAAAATAAAATACTCTTAT 8 97 0 TAAAAATAAA 0.887373 -21 AAGTAAAAATTAAAGCAAAAAGCCAACGCT 9 47 0 TAAAGCAAAA 0.777568 -71 AAGAGTATTTTATTAAAAAAGAAGTAAAAA 9 68 0 TATTAAAAAA 0.860059 -50 AATAACCGCCTATAATAAAAAGGAATCAAA 9 98 0 TATAATAAAA 0.652604 -20 AGGCTTAAGATTAAGAAAAATCTAAAAA 10 9 0 TTAAGAAAAA 0.759551 -36 ATATTCATTTTAAAAAACAACTATGGAGTA 11 12 1 TAAAAAACAA 0.482922 -54 TTATGGTTGGTTATCAAAAAGCTAACAGCG 12 14 0 TTATCAAAAA 0.808903 -151 TCTTTAGGTATAATCAAAAACTATTTTTAA 12 132 1 TAATCAAAAA 0.92802 -33 AAAAACTATTTTTAAATAAAGGGTTTTT 12 147 1 TTTAAATAAA 0.576628 -18 ********** Masking position 9 Map Score: 37.7441 Number of sites scoring better than the average of aligned sites = 1593 Number in coding regions = 1242 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 3 GTTTAAAAACATTAAAAAATAAGACTTTAT 3 29 1 ATTAAAAAAT 0.741747 -207 CTTGAAAATATCTTAAAAATAAAAATTCAA 3 117 0 TCTTAAAAAT 0.738868 -119 ATTAAAGATACCTTGAAAATATCTTAAAAA 3 128 0 CCTTGAAAAT 0.824387 -108 TTCAAGGTATCTTTAATAATAAAATGCTAG 3 141 1 CTTTAATAAT 0.875241 -95 GAATTAGTCCCCTAAAACATTAACAAAGTT 3 170 1 CCTAAAACAT 0.874225 -66 ATTTCTGCAACTTTAAAAACGATTAACTTT 3 194 0 CTTTAAAAAC 0.72234 -42 TAACTATCCCCCTTAAAAATGAGTTTTACT 4 17 1 CCTTAAAAAT 0.975268 -189 TTTTAAAAAGATTAAATAATATTAAATTGA 4 58 1 ATTAAATAAT 0.48013 -148 CCAAGGTTAGCCTTAAGGATGGCCATGCGC 5 23 1 CCTTAAGGAT 0.940494 -221 ATAAGACCACATTAAAGGATAATGA 5 229 1 ATTAAAGGAT 0.535675 -15 TTCAAAAATGGCTTAAAAATGGTTTCACTT 8 63 0 GCTTAAAAAT 0.807454 -55 TGTTCTAACCTTAAAAATAAAATACTCT 8 100 0 CCTTAAAAAT 0.975268 -18 TTAGACAAACCTTTAAGGATTT 11 54 1 CTTTAAGGAT 0.897535 -12 GTGCTAATCTCTTAAATGATGCCTATTCAT 12 63 1 CTTAAATGAT 0.702927 -102 TTTGATTATACCTAAAGAATACTTAATTGT 12 120 0 CCTAAAGAAT 0.935849 -45 AAAACCCTTTATTTAAAAATAGTTTTTGAT 12 144 0 ATTTAAAAAT 0.836178 -21 TCCTTAAACATTCCTATTTAT 13 2 1 CCTTAAACAT 0.925697 -64 ********** Masking position 6 Map Score: 13.6239 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 687 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 TTAAGGGGGATAGTTATCCAAA 4 2 0 TGTTATCCAA 0.965234 -204 AATTGAATGGGGTTTATCAATATTTGACAAA 4 82 1 GTTTATCAAT 0.685603 -124 TTTGATCTTATTTTTGTCAAATATTGATAAA 4 94 0 TTTTGTCAAA 0.83767 -112 GCGATCAAGGTTTTTATGAAAATAAAAGCCT 4 158 1 TTTTATGAAA 0.761907 -48 ATTTTTCTGTATCCAAGGTTAGCCTT 5 6 1 TTGTATCCAA 0.828352 -238 AGAGTGCAAATGATTATCAAAATGAATCGTT 5 152 1 TATTATCAAA 0.850498 -92 CTAAAAAGCTGTGTTATCCAACCCGCTATAA 7 26 0 GGTTATCCAA 0.94562 -157 TTTTTATGGTTGGTTATCAAAAAGCTAACAG 12 16 0 TGTTATCAAA 0.967414 -149 AAAAAGCTTGGCGTTAGCCAAGTGCTAATCT 12 42 1 GGTTAGCCAA 0.766067 -123 GGTAGTTCTGTTTTTATCAAACATGAATAGG 12 84 0 TTTTATCAAA 0.964789 -81 TAAACATTCCTATTTATCAAATCATTGTAAC 13 15 1 TTTTATCAAA 0.964791 -51 * ********* Masking position 10 Map Score: 8.59811 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 221 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TATTCTAATAAGGAGTTAAGGGGTT 2 9 1 TAAGGAGTTA 0.917841 -17 AGAAATCATTGAAGGAGTTAATTGAAGT 3 218 1 GAAGGAGTTA 0.943153 -18 TCCCCCTTAAAAATGAGTTTTACTATAAAA 4 23 1 AAATGAGTTT 0.920458 -183 ATCCTACACCAAAAGAGTTAATAAAAAATT 4 127 0 AAAAGAGTTA 0.933231 -79 AATTTTAAAAAAAGGACTTTTG 4 194 1 AAAGGACTTT 0.877519 -12 ATTATTTACAAAAAGAGTTTAAAATAAACG 5 97 1 AAAAGAGTTT 0.953175 -147 AAATCGTTAGAAAGAAGTTA 6 1 0 AAAGAAGTTA 0.861057 -55 TTTAATGGAGAAAGGAGTTTGGAAT 7 168 1 AAAGGAGTTT 0.988778 -15 TTTTAAGAAAGGTGTTTGTATGGGGCT 9 8 1 AAAGGTGTTT 0.935759 -110 AAGCCTTTTAAAAGGCGTTTTA 10 33 1 AAAGGCGTTT 0.892203 -12 ********** Masking position 3 Map Score: 13.7684 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 227 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 GTTTTTCTTTAACCCCACAATTGGCTTTTT 1 38 0 AACCCCACAA 0.344254 -34 GGGTTAAAGAAAAACAATAAAGAGAGAAC 1 53 1 AAAACAATAA 0.69133 -19 AACCCCTTAACTCCTTATTA 2 16 0 AACCCCTTAA 0.874826 -10 AAAACGATCAAAGGAATTGTT 3 2 1 AAACGATCAA 0.758975 -234 GAATTGTTTAAAAACATTAAAAAATAAGAC 3 24 1 AAAACATTAA 0.894465 -212 CCATGAAAACAAAGCCTTAAATTTCCATTA 3 70 1 AAAGCCTTAA 0.933107 -166 TTAGTCCCCTAAAACATTAACAAAGTTAAT 3 173 1 AAAACATTAA 0.894465 -63 GCAACTTTAAAAACGATTAACTTTGTTAAT 3 188 0 AAACGATTAA 0.917204 -48 CAAAATTTTAAAAAGATTAAATAATATTAA 4 53 1 AAAAGATTAA 0.885296 -153 TATTTTCATAAAAACCTTGATCGCTATCCT 4 152 0 AAAACCTTGA 0.715007 -54 TTATGAAAATAAAAGCCTAAAACAATTTTA 4 171 1 AAAAGCCTAA 0.730084 -35 ACCATTCATCAAAAGGTTAAAGCGCATGGC 5 44 0 AAAAGGTTAA 0.672125 -200 TGCTAAAATAAAACGATTAATAAAAAATAA 6 29 0 AAACGATTAA 0.917204 -27 TTAGGATTAAAAACGCTCAAAAATAGTCTC 7 53 1 AAACGCTCAA 0.902633 -130 AATTTACCATAAAACCATAAAATTAAATAA 7 98 0 AAAACCATAA 0.868311 -85 TGTATTCAAAAATGGCTTAAAAATGGTTTC 8 67 0 AATGGCTTAA 0.476117 -51 AGCAAAAAGCCAACGCTTAAAGCGTTAGCC 9 34 0 CAACGCTTAA 0.757146 -84 ACGCCTTTTAAAAGGCTTAAGATTAAGAAA 10 21 0 AAAGGCTTAA 0.927021 -24 ATGGAGTATAAAAACCATAATTAGACAAAC 11 34 1 AAAACCATAA 0.868311 -32 AAATCCTTAAAGGTTTGTCT 11 56 0 AAATCCTTAA 0.778317 -10 AAAAACCCTTTATTTAAAAATA 12 153 0 AAACCCTTTA 0.70842 -12 ********** Masking position 2 Map Score: 24.2389 Number of sites scoring better than the average of aligned sites = 1457 Number in coding regions = 1219 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 7 GATGGCCATGCGCTTTAACCTTTTGATGAA 5 40 1 CGCTTTAACC 0.978877 -204 TTATCCAACCCGCTATAAACAAAAAGGTTT 7 14 0 CGCTATAAAC 0.946636 -169 ATGGGGCTAACGCTTTAAGCGTTGGCTTTT 9 30 1 CGCTTTAAGC 0.988417 -88 AAACGCTGTTAGCTTTTTGATAA 12 4 1 CGCTGTTAGC 0.965971 -161 ********** Masking position 6 Map Score: 0.110549 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 70 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ********** No masking Map Score: -4.66526e-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: -4.66526e-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 10 ********** No masking Map Score: -4.66526e-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