AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_hpyl_reg_300.orf -o00010_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 Purged sequences: HP1350 209 protease Input sequences: #1 HP0153 98 recombinase (recA) #2 HP0175 300 cell binding factor 2 #3 HP0194 214 triosephosphate isomerase (tpi) #4 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #5 HP0973 111 H. pylori predicted coding region HP0973 #6 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) #7 HP1166 63 glucose-6-phosphate isomerase (pgi) #8 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #9 HP1352 300 adenine specific DNA methyltransferase (HINFIM) #10 HP1385 70 fructose-1,6-bisphosphatase Motif number 1 ATTTTGAGTTTTTAGGAGCAGTTTTT 3 4 0 TTTAGGGATT 0.961597 -211 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 3 23 0 TTTAGGTATT 0.878012 -192 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAA 3 51 0 TTAAGGATTT 0.935288 -164 AGGTTTTGTTTATAAGAAAAATTATTTCAAATG 3 82 0 TATAAGAATT 0.738784 -133 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 3 95 0 TTTAGGTTTT 0.928062 -120 AAATTCAATTCAAAGGGGCTATTGTTTAAAATT 3 126 1 CAAAGGGTTT 0.809302 -89 CAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 4 94 0 TTTAGGGTTT 0.978204 -50 GATTTTGTTTTTTAGGGAGAATTGAGATT 5 7 0 TTTAGGAATT 0.878012 -105 GATTTAGTCTTAAAAGTGATTTTGTTTTTTAGG 5 24 0 TAAAAGGTTT 0.951826 -88 TAAATCTTAATTAAAGGGGTATTC 6 2 0 TTAAAGGTTT 0.965358 -64 AAAAACACTCTAAAAGGGTTATTG 6 52 1 TAAAAGGTTT 0.951825 -14 ATATCTTTTATTTAAGGGGTATTG 7 50 1 TTTAAGGTTT 0.961351 -14 TGCTCTTAAATAAAGGCATTCTTAAGGGGTTCT 8 28 0 TAAAGGATTT 0.911092 -61 AATGCCTTTATTTAAGAGCATTTGTGATAGAAT 8 41 1 TTTAAGGATT 0.932784 -48 CACAAGCGTTTTAAGGTTATCTTAATGTTTAAT 9 237 0 TTAAGGTTTT 0.935288 -64 GTAGCAGATATAAAAGGTTAGTTAATC 9 284 1 TAAAAGTATT 0.760111 -17 AATCAAATCATAAAAGGGTTTTT 10 58 1 TAAAAGGTTT 0.951825 -13 ****** * * ** Masking position 4 Map Score: 24.9816 Number of sites scoring better than the average of aligned sites = 1137 Number in coding regions = 944 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 TTGATAGAATAAACAAATCAAATTCAATAAGGT 1 70 1 AAAAAAAAAT 0.970594 -29 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGAAG 2 76 0 AAAAAAAAAT 0.970594 -225 TTTCTTTCCAAAAAGAATAAAACTAACACCAAA 2 92 1 AAAGAAAAAC 0.808909 -209 TAACACCAAAAAAGACAATAAATATTATTACAA 2 115 1 AAAACAAAAT 0.964424 -186 AATGTGAATTTAATGATGAAAATTAGTTTAGAG 2 265 1 TAAGATAAAT 0.695415 -36 AACTGCTCCTAAAAACTCAAAATTAACCTAAAA 3 14 1 AAAACTAAAT 0.960314 -201 CTAAATTGAGAAAAAATTCAATTCAAAGGGGCT 3 113 1 AAAAATAATT 0.702828 -102 AATAGCGTTTAAAAAATGTAAATTTTAAACAAT 3 146 0 AAAAATAAAT 0.967167 -69 TCAACTCAATAAATAATTTTAATTAACCCTACA 4 27 1 AAAAATTAAT 0.702891 -117 CAATTCTCCCTAAAAAACAAAATCACTTTTAAG 5 16 1 TAAAAAAAAT 0.832779 -96 TTGTATTAAGAAATAAACTAAACTGAGTGTAAA 5 77 0 AAAAAAAAAC 0.891795 -35 AATAACTCAAAAACACTCTAAAAGGGTTATTG 6 44 1 AAAACTAAAA 0.688972 -22 AATACCCCTTAAATAAAAGATATAATGCTGTAT 7 40 0 AAAAAAATAT 0.726094 -24 TTCGTTACAAAAACATTAGAAATGGGGCTTACT 9 68 0 AAAATTAAAT 0.868438 -233 CATCAAATGCAAATGCATCAAATGATAGAAGCT 9 180 0 AAAGCAAAAT 0.932965 -121 TGTTCTCATCAAATGCATCAAATGCAAATGCAT 9 195 0 AAAGCAAAAT 0.932965 -106 TTTTACTTGAAAACATTGAAAATAGGGAAGTAT 10 12 0 AAAATTAAAT 0.868438 -59 *** *** **** Masking position 3 Map Score: 16.6473 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 554 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 GGGTAAGTCCTTTTATTATAATAGATTTTAGG 1 31 1 TTTTATAAAT 0.918369 -68 TTAGGCTAGGATTTGATAGAATAAACAAATCA 1 58 1 ATTTGTAAAT 0.902944 -41 GCCTCAGATGTTGTAATAATATTTATTGTCTT 2 126 0 TTGTATATAT 0.744551 -175 TTTGTTTTAAATTTGCTATAATGTGAATTTAA 2 246 1 ATTTGTAAAT 0.90258 -55 ATTATTTCAAATGTAGTAGAATTAAGGCAGTG 3 63 0 ATGTATAAAT 0.902907 -152 AAAACCTAAATTGAGAAAAAATTCAATTCAAA 3 108 1 TTGAGAAAAT 0.726618 -107 TTTAAACGCTATTAGATATAATAAGGGATAGT 3 166 1 ATTAGTAAAT 0.899404 -49 TAGCTGTAGGGTTAATTAAAATTATTTATTGA 4 32 0 GTTAATAAAT 0.679361 -112 ATAGCGCAAAATGTAGTAAAATACCAAACAAA 4 75 1 ATGTATAAAT 0.902905 -69 GATTTTGTTTTTTAGGGAGAATTGAGATT 5 8 0 TTTAGGAAAT 0.710542 -104 TGAGTGTAAATTCAAGTATAATTCTAACATGA 5 55 0 TTCAATAAAT 0.846145 -57 TAGAGTGTTTTTGAGTTATTATTATATATTAA 6 32 0 TTGAGTATAT 0.824156 -34 ATAAGCTAGTTTTAATTACAATTTTCAA 7 7 0 TTTAATAAAT 0.918375 -57 TTAAGAGCATTTGTGATAGAATGGTGATTTTT 8 52 1 TTGTGTAAAT 0.966704 -37 CTTAAAACGCTTGTGTTAAAATGGCTAGAGTA 9 255 1 TTGTGTAAAT 0.966704 -46 TTTCAATGTTTTCAAGTAAAATATTAGCATCT 10 24 1 TTCAATAAAT 0.846145 -47 ***** ** *** Masking position 8 Map Score: 13.5999 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 166 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 TCGCTTGACGCAAAAACACTGCCTTAATTC 3 47 1 CAAAAACACT 0.968117 -168 AAATTTTAAACAATAGCCCCTTTGAATTGA 3 130 0 CAATAGCCCC 0.903975 -85 AAATACCAAACAAAACCCCCTAAAATTGAA 4 93 1 CAAAACCCCC 0.979809 -51 CCCTAAAAAACAAAATCACTTTTAAGACTA 5 23 1 CAAAATCACT 0.902241 -89 GAATACCCCTTTAATTAAGA 6 1 1 GAATACCCCT 0.908942 -65 AATAATAACTCAAAAACACTCTAAAAGGGT 6 41 1 CAAAAACACT 0.968117 -25 CAATAACCCTTTTAGAGTGT 6 56 0 CAATAACCCT 0.979839 -10 CAATACCCCTTAAATAAAAG 7 54 0 CAATACCCCT 0.987194 -10 CTTAATGAGACAGAACCCCTTAAGAATGCC 8 17 1 CAGAACCCCT 0.959245 -72 ATGTTCGTTACAAAAACATTAGAAATGGGG 9 74 0 CAAAAACATT 0.726245 -227 ********** Masking position 5 Map Score: 13.4272 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 403 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 GTTTATTCTATCAAATCCTAGCCTAAAATC 1 54 0 TCAAATCCTA 0.951423 -45 AATAAACAAATCAAATTCAATAAGGTAATT 1 77 1 TCAAATTCAA 0.954412 -22 CACAGAAAACTCACATTAAAGAGTAAGAAA 2 201 0 TCACATTAAA 0.935798 -100 ATCATTAAATTCACATTATAGCAAATTTAA 2 252 0 TCACATTATA 0.895815 -49 GAGAAAAAATTCAATTCAAAGGGGCTATTG 3 120 1 TCAATTCAAA 0.859982 -95 TTTTCAGACTTCAATTTCAATTTTAGGGGG 4 108 0 TCAATTTCAA 0.838617 -36 CCCGATCCATTCACATGCAAATCGCAAAGC 9 104 0 TCACATGCAA 0.959418 -197 TGCAAATGCATCAAATGATAGAAGCTATCT 9 176 0 TCAAATGATA 0.917375 -125 ATCAAATGCATCAAATGCAAATGCATCAAA 9 191 0 TCAAATGCAA 0.961949 -110 TTAGCTTTGTTCTCATCAAATGCATCAAAT 9 205 0 TCTCATCAAA 0.746232 -96 GCATCTTTAATCAAATCATAAAAGGGTTTT 10 50 1 TCAAATCATA 0.935874 -21 ********** Masking position 10 Map Score: 11.5882 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 297 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AATCTATTATAATAAAAGGACTTACCCTAT 1 28 0 AATAAAAGGA 0.962746 -71 TACCACCTATAAAATAAGGATCGTTCA 3 198 1 AAAATAAGGA 0.881285 -17 AATGCTCTTAAATAAAGGCATTCTTAAGGG 8 33 0 AATAAAGGCA 0.946051 -56 GTGATTTTTAAATAAAGGGAAAAC 8 75 1 AATAAAGGGA 0.987094 -14 GGCAATACAGAATAAAGGGAAGGC 9 5 0 AATAAAGGGA 0.987094 -296 GAAAACATTGAAAATAGGGAAGTATT 10 7 0 AAAATAGGGA 0.956464 -64 ********** Masking position 6 Map Score: 6.98827 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 54 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TAAAGTTATTCATTCCATTCAAAGCGGGTAAA 2 165 0 CATTCATCAA 0.926729 -136 CATTATAGCAAATTTAAAACAAAATCAGCTAT 2 237 0 AATTTAACAA 0.961182 -64 AATTCTACTACATTTGAAATAATTTTTCTTAT 3 72 1 CATTTAATAA 0.704433 -143 ATTGAGAAAAAATTCAATTCAAAGGGGCTATT 3 117 1 AATTCATCAA 0.962791 -98 AAAAAATGTAAATTTTAAACAATAGCCCCTTT 3 137 0 AATTTAACAA 0.961182 -78 TTACTCCTTGAATTCAACTCAATAAATAATTT 4 14 1 AATTCATCAA 0.962791 -130 CTCAATAAATAATTTTAATTAACCCTACAGCT 4 31 1 AATTTATTAA 0.79829 -113 AATGTAGTAAAATACCAAACAAAACCCCCTAA 4 84 1 AATACAACAA 0.834037 -60 TACTCTAGCCATTTTAACACAAGCGTTTTAAG 9 255 0 ATTTTAACAA 0.796061 -46 ***** * **** Masking position 7 Map Score: 5.29878 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 113 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ATTTTAGGCTAGGATTTGATAGAATAAACA 1 55 1 AGGATTTGAT 0.969475 -44 ATTACCTTATTGAATTTGATTTGTTTATTC 1 76 0 TGAATTTGAT 0.953624 -23 TGCTATAATGTGAATTTAATGATGAAAATT 2 259 1 TGAATTTAAT 0.760839 -42 GATAGCTTCTATCATTTGATGCATTTGCAT 9 177 1 ATCATTTGAT 0.892369 -124 TTGATGCATTTGCATTTGATGCATTTGATG 9 192 1 TGCATTTGAT 0.96946 -109 AAACCCTTTTATGATTTGATTAAAGATGCT 10 49 0 ATGATTTGAT 0.914014 -22 ********** Masking position 5 Map Score: 2.26987 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 215 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 AGTAAAATCCTTTTGTGATAGGGTAAGTC 1 10 1 CTTTTGTGAT 0.977579 -89 TATTTAAGAGCATTTGTGATAGAATGGTGA 8 49 1 CATTTGTGAT 0.977579 -40 ATCTCGCTCTCATTTGCGATAGAGGCTCTA 9 37 1 CATTTGCGAT 0.979195 -264 TAACGAACATGCTTTGCGATTTGCATGTGA 9 94 1 GCTTTGCGAT 0.91827 -207 AAAAACCCTTTTATGATTTGATTAAAG 10 54 0 CTTTTATGAT 0.893103 -17 ********** Masking position 5 Map Score: 1.52138 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 66 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: 1.70773e-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 AAGTCCTTTTATTATAATAGATTTTAGGCTAGGAT 1 35 1 ATTTAAATTT 0.893406 -64 TTTTGAATCTTCTTTAACATTTTTTTTCTTTCCAA 2 68 1 TCTTAAATTT 0.863114 -233 GACAATAAATATTATTACAACATCTGAGGCGAACA 2 128 1 ATTTTAATCT 0.550732 -173 TGAGGCGAACACTTTTACCCGCTTTGAATGGAATG 2 152 1 ACTTTACTTT 0.926263 -149 GGAATGAATAACTTTAAGCATTTCTTACTCTTTAA 2 181 1 ACTTAACTCT 0.895534 -120 TGTGTTCTCCACTCTAAACTAATTTTCATCATTAA 2 274 0 ACTTAACTTT 0.964456 -27 TCCCTTATTATATCTAATAGCGTTTAAAAAATGTA 3 159 0 TATTAAATTT 0.673896 -56 CGTAACTATTATCCTATTTTCAGACTTCA 4 125 0 ACTTTACTTT 0.926263 -19 TTCAAGTATAATTCTAACATGATTTAGTCTTAAAA 5 42 0 ATTTAAATTT 0.893406 -70 ACTCAAAAACACTCTAAAAGGGTTATTG 6 48 1 ACTTAAATTA 0.676378 -18 ATAATGCTGTATTATAAGCTAGTTTTAATTACAAT 7 17 0 ATTTAACTTT 0.920507 -47 AGAATGCCTTTATTTAAGAGCATTTGTGATAGAAT 8 39 1 TATTAAATTT 0.673896 -50 TTTCAAGTAAAATATTAGCATCTTTAATCAAATCA 10 33 1 AATTTACTTT 0.804571 -38 *** *** * *** Masking position 7 Map Score: 8.13944 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 350 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 12 ********** No masking Map Score: 1.70773e-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: 1.70773e-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: 1.70773e-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