AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_hpyl_reg_300.orf -o00510_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 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP0246 188 flagellar basal-body P-ring protein (flgI) #3 HP1154 130 H. pylori predicted coding region HP1154 #4 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #5 HP1361 56 competence locus E (comE3) #6 HP1365 83 response regulator #7 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 ACAAAAATAAGATCAAAAAAATTTTTTATT 1 108 1 GATCAAAAAA 0.694326 -98 CACCAAAAGAGTTAATAAAAAATTTTTTTG 1 121 0 GTTAATAAAA 0.847668 -85 AGGCTTTTATTTTCATAAAAACCTTGATCG 1 159 0 TTTCATAAAA 0.789939 -47 CCTAAAACAATTTTAAAAAAAGGACTTTTG 1 186 1 TTTTAAAAAA 0.755416 -20 TAATTTGAAACTTTATAAAAAGCTAATAAA 2 31 1 CTTTATAAAA 0.797772 -158 TTTATAAAAAGCTAATAAAAGGCTAAAATT 2 42 1 GCTAATAAAA 0.847474 -147 GGTTTAAAGTTTTTATAAAAGGCTTATGCT 2 132 1 TTTTATAAAA 0.498108 -57 ATAAAAGGCTTATGCTAAAATAATTAGAAT 2 146 1 TATGCTAAAA 0.740919 -43 TATTATCCTAAAATAGAGCGTTC 3 4 1 TATCCTAAAA 0.789741 -127 ATAGAGCGTTCCTTAAAAAATGGTTGGATT 3 23 1 CCTTAAAAAA 0.908718 -108 GTTGTATAATTTTGAAAAAATACGCAACAA 3 82 0 TTTGAAAAAA 0.866567 -49 TGATTTGATCCCTAATAAAATGACTTTT 4 9 0 CCTAATAAAA 0.926034 -20 AAAAACACTCCCTTAAAAAAGACACCGCTT 6 18 0 CCTTAAAAAA 0.908718 -66 TAAAAGCGGTTATAAAAAAACACTCCCTTA 6 33 0 TATAAAAAAA 0.851689 -51 TAATTGCCTTTATACTAAAAGCGGTTATAA 6 48 0 TATACTAAAA 0.800647 -36 TATGAAAAGGTTTTCTAAAACTTCATAAAA 7 12 1 TTTTCTAAAA 0.703632 -289 TTTTCTAAAACTTCATAAAATTGCGCTTCG 7 22 1 CTTCATAAAA 0.920133 -279 TTATAACGCTCCTTAAAAAACATAGGAAGT 7 62 1 CCTTAAAAAA 0.908718 -239 ACAATACCCCCATGCAAAAAAAGATTTTTT 7 121 1 CATGCAAAAA 0.655976 -180 GTAATCGTCTTCTAATAAAAAAATCTTTTT 7 138 0 TCTAATAAAA 0.926583 -163 AATGGGGGTATTTTAAAAAAATGAGTCAGT 7 222 0 TTTTAAAAAA 0.755416 -79 CCCATTGAAGTTTAATAAAAGGTAAAAATA 7 278 1 TTTAATAAAA 0.793631 -23 ********** Masking position 3 Map Score: 32.0138 Number of sites scoring better than the average of aligned sites = 1971 Number in coding regions = 1530 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 2 TTATAGTAAAACTCATTTTTAAGGGGGATAG 1 20 0 ACTCATTTTA 0.464555 -186 AATATTATTTAATCTTTTTAAAATTTTGTTT 1 50 0 AATCTTTTAA 0.647911 -156 AGATCAAAAAAATTTTTTATTAACTCTTTTG 1 117 1 AATTTTTTTT 0.73473 -89 TTTTTTATTAACTCTTTTGGTGTAGGATAGC 1 129 1 ACTCTTTTGT 0.747224 -77 GATAGCGATCAAGGTTTTTATGAAAATAAAA 1 154 1 AAGGTTTTAT 0.699281 -52 AAATTGTTTTAGGCTTTTATTTTCATAAAAA 1 168 0 AGGCTTTTTT 0.923661 -38 CAAAAGTCCTTTTTTTAAAATTGTT 1 191 0 AGTCCTTTTT 0.947019 -15 TTTTAATTTTAGCCTTTTATTAGCTTTTTAT 2 45 0 AGCCTTTTTT 0.947019 -144 CTAAAATTAAAATCTTTGATTTAAAGTTTAT 2 64 1 AATCTTTGTT 0.742503 -125 ATTTTAGCATAAGCCTTTTATAAAAACTTTA 2 136 0 AAGCCTTTAT 0.880549 -53 TCAAACCCTTTCTTATTCCCTAAA 2 175 0 AACCCTTTTT 0.955194 -14 TTCCAAATCCAACCATTTTTTAAGGAACGCT 3 27 0 AACCATTTTT 0.900966 -104 TTTTGCTTTTACGCTTTTAATTGTTGCGTAT 3 62 1 ACGCTTTTAT 0.860739 -69 TTTTAATTTAAATGCTTTGTTGTATAATTTT 3 99 0 AATGCTTTTT 0.87055 -32 AAAAGTCATTTTATTAGGGATCAA 4 4 1 AGTCATTTAT 0.795781 -25 TAAAAAAGACACCGCTTTATTTTA 6 4 0 ACCGCTTTTT 0.791463 -80 TTTTTAAGGGAGTGTTTTTTTATAACCGCTT 6 29 1 AGTGTTTTTT 0.849365 -55 AGTTTTAGAAAACCTTTTCATAG 7 3 0 AACCTTTTAT 0.929942 -298 CTAATAAAAAAATCTTTTTTTGCATGGGGGT 7 126 0 AATCTTTTTT 0.969393 -175 GCCTTGACTGACTCATTTTTTTAAAATACCC 7 216 1 ACTCATTTTT 0.8841 -85 TTCATTGTAAAATTCTTTCATGCAAAACCCA 7 251 1 AATTCTTTAT 0.537209 -50 TCTTATTTTTACCTTTTATTAAACTTCAAT 7 281 0 TACCTTTTTT 0.614998 -20 ******** ** Masking position 6 Map Score: 22.6946 Number of sites scoring better than the average of aligned sites = 1806 Number in coding regions = 1505 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 TCAATATTTGACAAAAATAAGATCAAAAAA 1 98 1 ACAAAAATAA 0.796052 -108 CTAATAAAAGGCTAAAATTAAAATCTTTGA 2 53 1 GCTAAAATTA 0.869406 -136 TGAGTATAGCATAAAAATACGCTCAATTAG 2 103 1 ATAAAAATAC 0.760083 -86 AAAGGCTTATGCTAAAATAATTAGAATTTA 2 149 1 GCTAAAATAA 0.964069 -40 GAAAAAATACGCAACAATTAAAAGCGTAAA 3 69 0 GCAACAATTA 0.799552 -62 GTATAATTTTGAAAAAATACGCAACAATTA 3 79 0 GAAAAAATAC 0.847785 -52 GGCAATTAGCGCTACAATACCCCC 6 70 1 GCTACAATAC 0.973215 -14 AGCGGGCTTTGTTATAATACTTCCTATGTT 7 80 0 GTTATAATAC 0.79598 -221 CTCATTAAGCGCTACAATACCCCCATGCAA 7 108 1 GCTACAATAC 0.973215 -193 GACTCATTTTTTTAAAATACCCCCATTTCA 7 225 1 TTTAAAATAC 0.68102 -76 TTAATAAAAGGTAAAAATAAGA 7 289 1 GTAAAAATAA 0.90597 -12 ********** Masking position 6 Map Score: 8.56283 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 572 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TTTTATAGTAAAACTCATTTTTAAGGGGGATAGTTATCC 1 14 0 ATATTAAGGG 0.881116 -192 AAGATTAAATAATATTAAATTGAATGGGGTTTATCAATA 1 65 1 ATAAAAAGGG 0.993324 -141 CTTTTTATAAAGTTTCAAATTAAATTGAGGTATGAATCT 2 14 0 ATAAAAATGG 0.986967 -175 CTTTTATAAAAACTTTAAACCTAATTGAGCGTATTTTTA 2 114 0 ATAAAAATGG 0.986967 -75 AACAATTAAAAGCGTAAAAGCAAAAGGCGTTCCAAATCC 3 48 0 ATAAAAAGGG 0.993324 -83 AAGGAGCGTTATAATGAAAACGAACGAAGCGCAATTTTA 7 37 0 ATAAAAAGAG 0.935838 -264 CAGTCAAGGCAATCTAAATTTTCAATGAGTCAAACTCCT 7 187 0 ATAATCATGG 0.921241 -114 GCATGAAAGAATTTTACAATGAAATGGGGGTATTTTAAA 7 235 0 ATCAAAAGGG 0.972037 -66 ATTTTTACCTTTTATTAAACTTCAATGGGTTTTGCATGA 7 268 0 TTAAACATGG 0.853689 -33 * * *** ** ** * Masking position 14 Map Score: 7.47463 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 130 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 CTATAAAACAAAATTTTAAAAAGATTAAAT 1 45 1 AAATTTTAAA 0.955472 -161 AAGATCAAAAAAATTTTTTATTAACTCTTT 1 116 1 AAATTTTTTA 0.80868 -90 AAGCCTAAAACAATTTTAAAAAAAGGACTT 1 183 1 CAATTTTAAA 0.817352 -23 ATTTAATTTGAAACTTTATAAAAAGCTAAT 2 28 1 AAACTTTATA 0.926075 -161 AAAATCTTATAAACTTTAAATCAAAGATTT 2 73 0 AAACTTTAAA 0.966439 -116 CCTTTTATAAAAACTTTAAACCTAATTGAG 2 124 0 AAACTTTAAA 0.966439 -65 TATTTTTTCAAAATTATACAACAAAGCATT 3 90 1 AAATTATACA 0.778279 -41 AAGACAAAACTTTTCAGGGGGCGTTT 5 7 1 AAACTTTTCA 0.943779 -50 AGTTTTAGAAAACCTTTTCATAG 7 4 0 AACCTTTTCA 0.759692 -297 AAGGCAATCTAAATTTTCAATGAGTCAAAC 7 191 0 AAATTTTCAA 0.850732 -110 TTGCATGAAAGAATTTTACAATGAAATGGG 7 246 0 GAATTTTACA 0.8521 -55 ********** Masking position 2 Map Score: 10.0085 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 359 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 TTGGTGTAGGATAGCGATCAAGGTTTTTAT 1 145 1 ATAGCGATCA 0.926887 -61 ATCCTAAAATAGAGCGTTCCTTAAAAAATG 3 15 1 AGAGCGTTCC 0.777028 -116 GGGGGTATTGTAGCGCTAATTGCCTTTAT 6 65 0 GTAGCGCTAA 0.574287 -19 ACTTCATAAAATTGCGCTTCGTTCGTTTTC 7 31 1 ATTGCGCTTC 0.881001 -270 CGTTTTCATTATAACGCTCCTTAAAAAACA 7 54 1 ATAACGCTCC 0.734667 -247 TGGGGGTATTGTAGCGCTTAATGAGCGGGC 7 103 0 GTAGCGCTTA 0.858378 -198 CTTTTAAGCGAGAGCGTTAAGGAGTTTGAC 7 168 1 AGAGCGTTAA 0.843585 -133 ********** Masking position 8 Map Score: 1.48038 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 525 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 ********** No masking Map Score: -1.97998e-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 8 ********** No masking Map Score: -1.97998e-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: -1.97998e-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