AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_hpyl_reg_300.orf -o00670_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 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #3 HP0584 81 flagellar switch protein (fliN) #4 HP0585 228 endonuclease III (nth) #5 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #6 HP1141 23 methionyl-tRNA formyltransferase (fmt) #7 HP1142 39 H. pylori predicted coding region HP1142 #8 HP1143 243 H. pylori predicted coding region HP1143 #9 HP1435 70 protease IV (PspA) Motif number 1 TTTTAGTGTATTATAGCTATATTTTAATTTAAGAATTTTA 1 37 1 TTTTATTTTT 0.818272 -221 TTTAGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 73 1 TTTAATATTT 0.981479 -185 TAGGTTTTTATTCCATTAAACGCATGATTTTTGCTACAAT 2 16 1 TTCAACATTT 0.933293 -58 CGCATGATTTTTGCTACAATAATAGGATTTTAATTATATA 2 36 1 TTCAATATTT 0.979675 -38 GTTATAAAATTTATAGTAAAATTAAGATTTTATAATCAAA 3 22 1 TTTAATATTT 0.981243 -60 AGTCAAATCATTCTTGAAAGAGTAGAGTTTT 3 61 1 TTTAATATTT 0.981479 -21 ATTTCTACGATTTCATAAACTTTGTCTTTAATGGCTTCAT 4 22 0 TTCAATGTTA 0.816058 -207 CGGTTGATTTTAACCGAAAGCGTGGCTTTTTTCATGGAAT 4 142 0 TACAATGTTT 0.816058 -87 CGTATGGTTCTCTAAAACTTGTGCTTTTGGGACAACT 8 8 1 TTTAATGTTT 0.980221 -236 TGATCGATCGTTATCTCAATTTCTTCATTTTTTTTATTTA 8 54 1 TTTAACTTTT 0.874448 -190 TCTTCATTTTTTTTATTTATAATGTAGTTTTTATGCGAAG 8 75 1 TTTTATGTTT 0.902913 -169 AATGTAGTTTTTATGCGAAGGGTATTTTTTGCCTTTTTTA 8 95 1 TTTAATATTT 0.981479 -149 GATTTTCCTTTAAGATTTGATTTTTTATATTTTA 8 220 0 TTCAATTTTT 0.956189 -24 GCAGCTTTTCCTAAACTTAATATTTGACCATAAGA 9 46 0 TTTAATATTT 0.981474 -25 ** * ** ** *** Masking position 9 Map Score: 18.3779 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 328 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 ACTACCCTTAAAAAAATCAATCTAAAATTC 1 69 0 AAAAAATCAA 0.908365 -189 ATTACTCTTAAATCATGCCAATTCACACTC 1 141 0 AATCATGCCA 0.743864 -117 TTTTATAACAAATAAAGCCA 3 1 0 AATAAAGCCA 0.972387 -81 AATGACGCTCAATGAAGCCATTAAAGACAA 4 11 1 AATGAAGCCA 0.945095 -218 GAATAATGCAAAAGAATGCATTGAACCCCT 4 116 0 AAAGAATGCA 0.910465 -113 TTATTCCATGAAAAAAGCCACGCTTTCGGT 4 140 1 AAAAAAGCCA 0.985486 -89 AACTTTTAACAAACAATTCAAGGGATTTGG 5 16 0 AAACAATTCA 0.833473 -133 TACCCACCCTAATAAAGTCATGCTACAATG 5 101 1 AATAAAGTCA 0.889559 -48 TTGAATTAAAAACAAGGAATAAC 6 10 1 AAACAAGGAA 0.913455 -14 TTATAAATAAAAAAAATGAAGAAATTGAGA 8 67 0 AAAAAATGAA 0.870298 -177 AACAAAAAATAAAAAAGGCAAAAAATACCC 8 114 0 AAAAAAGGCA 0.978705 -130 TATAAAATATAAAAAATCAAATCTTAAAGG 8 218 1 AAAAAATCAA 0.908365 -26 ********** Masking position 5 Map Score: 13.1668 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 847 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TATAGCTATATTTTAATTTAAGAATTTTAGA 1 48 1 TTTAATTTAA 0.892498 -210 TATTTTCAAATTTCAAGTCTAAAGAGTGTGA 1 118 1 TTTAAGTCTA 0.864811 -140 GGGTTTAGGGTTTGAATTATATTGATTTAGC 1 230 1 TTTAATTATA 0.961527 -28 AATAATAGGATTTTAATTATATAAAGGACAA 2 53 1 TTTAATTATA 0.961527 -21 TTAATTTTACTATAAATTTTATAACAAATAA 3 16 0 TATAATTTTA 0.845353 -66 GATTATAAAATCTTAATTTTACTATAAATTT 3 28 0 TCTAATTTTA 0.829989 -54 TAAAAGTTTCTTTCAATTATACTAAAATAAT 5 38 1 TTTAATTATA 0.961527 -111 TAACCGGTCATTTTAATTATTTTAGTATAAT 5 53 0 TTTAATTATT 0.822565 -96 TATTCCTTGTTTTTAATTCAA 6 1 0 TTTAATTCAA 0.802479 -23 TCTTCATTTTTTTTATTTATAATGTAGTTTT 8 75 1 TTTATTTATA 0.691626 -169 TTTTTTGCCTTTTTTATTTTTTGTTGTTTGT 8 119 1 TTTTATTTTT 0.590916 -125 TTTTTTGTTGTTTGTATTTAAAATCCCTATT 8 135 1 TTTTATTTAA 0.691157 -109 GATTTGATTTTTTATATTTTATAATAGAATG 8 210 0 TTTTATTTTA 0.892682 -34 CCTTAAAACATTTGAAGTATAATACACTCTT 9 19 1 TTTAAGTATA 0.918621 -52 TATGGTCAAATATTAAGTTTAGGAAAAGCTG 9 49 1 TATAAGTTTA 0.710633 -22 *** ******* Masking position 8 Map Score: 15.5746 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 239 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 GGCTAAATTTTGAAACCTTGAGAT 1 4 1 TAAATTTGAA 0.694344 -254 TATTTTAATTTAAGAATTTTAGATTGATTTT 1 56 1 TAAGATTTTA 0.819392 -202 TTTTTAAGGGTAGTTTTTTTTAAGTTGTGTT 1 85 1 TAGTTTTTTT 0.590316 -173 GGTTTGGGTTTAGGGTTTGAATTATATTGAT 1 225 1 TAGGTTTGAA 0.925968 -33 CAAACTAGGTTTTTATTCCATTAAAC 2 6 1 TAGGTTTTAT 0.903409 -68 GCTACAATAATAGGATTTTAATTATATAAAG 2 48 1 TAGGTTTTAA 0.957191 -26 TTATTTGTTATAAAATTTATAGTAAAATTAA 3 16 1 TAAATTTATA 0.475324 -66 ATAGTAAAATTAAGATTTTATAATCAAAGTC 3 34 1 TAAGTTTTAT 0.884986 -48 CCGGTCATTTTAATTATTTTAGTATAATTGA 5 50 0 TAATATTTTA 0.541431 -99 TAAAATGGAGTAAAATTTTTACCCACCCTAA 5 82 1 TAAATTTTTA 0.519416 -67 ATTTAACACTTAGGATTTTTA 5 138 1 TAGGTTTTTA 0.956046 -11 TTCAGTAAAATAGGGATTTTAAATACAAACA 8 143 0 TAGGATTTTA 0.903352 -101 GATTTTCCTTTAAGATTTGATTTTTTATATT 8 223 0 TAAGTTTGAT 0.811402 -21 TCAAATGTTTTAAGGATTAAATC 9 3 0 TAAGATTAAA 0.656294 -68 **** ****** Masking position 2 Map Score: 9.55732 Number of sites scoring better than the average of aligned sites = 1238 Number in coding regions = 1045 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 5 TATAGCTATATTTTAATTTAAGAATTTTAGA 1 48 1 TTTTATTTAA 0.758577 -210 ATTTTAGATTGATTTTTTTAAGGGTAGTTTT 1 71 1 GATTTTTTAA 0.691446 -187 TTTAAGGGTAGTTTTTTTTAAGTTGTGTTAT 1 87 1 GTTTTTTTAA 0.954665 -171 AGTAATGGGTGTTTGTTTTAAGACGCTATGA 1 165 1 GTTTTTTTAA 0.954665 -93 AAAATCTTAATTTTACTATAAATTTTATAAC 3 22 0 TTTTCTATAA 0.557053 -60 TCAAGAATGATTTGACTTTGATTATAAAATC 3 47 0 TTTGCTTTGA 0.826713 -35 TTTCATAAACTTTGTCTTTAATGGCTTCATT 4 21 0 TTTGCTTTAA 0.918591 -208 AAGAGAGAAAGCGTTTTTTAAGGGCTTCATC 4 72 0 GCGTTTTTAA 0.621341 -157 CTTGAATGCGGTTGATTTTAACCGAAAGCGT 4 159 0 GTTGTTTTAA 0.945341 -70 ACGCTTTCTTTGATGACAAGGTA 4 216 0 GCTTCTTTGA 0.781206 -13 TTTGTTAAAAGTTTCTTTCAATTATACTAAA 5 33 1 GTTTTTTCAA 0.740739 -116 GTTATTCCTTGTTTTTAATTCAA 6 6 0 CTTGTTTTAA 0.715343 -18 TTTTTGTGGTGTGCTTTGAGATGATATTG 7 9 1 GTGTCTTTGA 0.767563 -31 TTTTTTGTTGTTTGTATTTAAAATCCCTATT 8 135 1 TTTGATTTAA 0.720736 -109 GATTTTCCTTTAAGATTTGATTT 8 231 0 TTTTCTTTAA 0.932149 -13 **** ****** Masking position 11 Map Score: 11.1915 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 920 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 GAAACCTTGAGATTGTTTTAGTGTATTATA 1 22 1 GATTGTTTTA 0.834637 -236 ATTTTAGATTGATTTTTTTAAGGGTAGTTT 1 71 1 GATTTTTTTA 0.900283 -187 TTTAAGGGTAGTTTTTTTTAAGTTGTGTTA 1 87 1 GTTTTTTTTA 0.97013 -171 AGTAATGGGTGTTTGTTTTAAGACGCTATG 1 165 1 GTTTGTTTTA 0.9478 -93 AAGAGAGAAAGCGTTTTTTAAGGGCTTCAT 4 73 0 GCGTTTTTTA 0.809245 -156 CGAAAGCGTGGCTTTTTTCATGGAATAATG 4 138 0 GCTTTTTTCA 0.762382 -91 CTTGAATGCGGTTGATTTTAACCGAAAGCG 4 160 0 GTTGATTTTA 0.823224 -69 GTTATTCCTTGTTTTTAATTCAA 6 7 0 CTTGTTTTTA 0.778741 -17 CAATTTCTTCATTTTTTTTATTTATAATGT 8 70 1 ATTTTTTTTA 0.699737 -174 TATTTATAATGTAGTTTTTATGCGAAGGGT 8 88 1 GTAGTTTTTA 0.921671 -156 TATGCGAAGGGTATTTTTTGCCTTTTTTAT 8 106 1 GTATTTTTTG 0.64555 -138 TTTATTTTTTGTTGTTTGTATTTAAAATCC 8 131 1 GTTGTTTGTA 0.839228 -113 TTTAACTTAAGCAGGTTTTATCCAATAAGT 8 173 0 GCAGGTTTTA 0.804688 -71 ********** Masking position 6 Map Score: 8.55121 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 951 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 7 GATTGATTTTTTTAAGGGTAGTTTTTTTTA 1 77 1 TTTAAGGGTA 0.850114 -181 AATCATGCGTTTAATGGAATAAAAACCTAG 2 15 0 TTAATGGAAT 0.884149 -59 GAAAGCGTTTTTTAAGGGCTTCATCGCAGT 4 67 0 TTTAAGGGCT 0.863803 -162 ATTGAACCCCTTCATGGATACCAAAAGAGA 4 97 0 TTCATGGATA 0.880743 -132 CGTGGCTTTTTTCATGGAATAATGCAAAAG 4 132 0 TTCATGGAAT 0.957601 -97 GGTATTGTGCTTCATGGGATCTTAAAGCCA 4 190 0 TTCATGGGAT 0.966752 -39 TAACAAACAATTCAAGGGATTTGGCGATT 5 10 0 TTCAAGGGAT 0.972844 -139 AAATCAAATCTTAAAGGAAAATC 8 231 1 TTAAAGGAAA 0.831428 -13 CTTCAAATGTTTTAAGGATTAAATC 9 6 0 TTTAAGGATT 0.893598 -65 ********** Masking position 4 Map Score: 8.21437 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 244 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 AAACCCAAACCTTTCTCTCATATATCTCGC 1 206 0 CTTTCTCTCA 0.988566 -52 TTAAAAAACGCTTTCTCTCTTTTGGTATCC 4 82 1 CTTTCTCTCT 0.955217 -147 ACGCTTTCTTTGATGACAAGGTA 4 216 0 CTTTCTTTGA 0.892442 -13 TTTGTTAAAAGTTTCTTTCAATTATACTAA 5 33 1 GTTTCTTTCA 0.938537 -116 CGTATGGTTCTCTAAAACTTGTGCT 8 6 1 GGTTCTCTAA 0.877737 -238 GCTGATCGATCGTTATCTCAATTTCTTCAT 8 52 1 CGTTATCTCA 0.917279 -192 ********** Masking position 6 Map Score: 1.21229 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: -1.40444e-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: -1.40444e-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 11 ********** No masking Map Score: -1.40444e-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