AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_hpyl_reg_100.orf -o00710_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 HP0175 300 cell binding factor 2 #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP1085 66 H. pylori predicted coding region HP1085 #4 HP1088 46 transketolase A (tktA) #5 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #6 HP1350 209 protease #7 HP1385_HP1386 70 HP1385: fructose-1,6-bisphosphatase, HP1386: D-ribulose-5-phosphate 3 epimerase (rpe) Motif number 1 GACAATAAATATTATTACAACATCTGAGGCGA 1 128 1 ATTTTCAACA 0.820827 -173 TTAAATTCACATTATAGCAAATTTAAAACAAA 1 246 0 ATTTACAAAT 0.963364 -55 TATAAGAAAAATTATTTCAAATGTAGTAGAAT 2 73 0 ATTTTCAAAT 0.919562 -142 TTTGAATTGAATTTTTTCTCAATTTAGGTTTT 2 108 0 ATTTTCTCAA 0.953528 -107 ACTATCCCTTATTATATCTAATAGCGTTTAAA 2 166 0 ATTTACTAAT 0.959862 -49 TAAAATCTATATTATAACTAAAAGGGGGTTTT 3 11 0 ATTTACTAAA 0.985893 -56 TATAGATTTTATTTTAGCTAAAAATGGCATGG 3 32 1 ATTTACTAAA 0.986069 -35 TTTGAGAGTCATTTTAACACAAA 4 2 0 ATTTACACAA 0.966381 -45 AAAAATCACCATTCTATCACAAATGCTCTTAA 5 52 0 ATTTACACAA 0.966401 -37 ATGAATGGGCATGTTATCTAAATTTTAGATAG 6 130 1 ATGTACTAAA 0.923877 -80 TTTTGCGTTTATTCTATCTAAAATTTAGATAA 6 143 0 ATTTACTAAA 0.986064 -67 CTTAAAGGTGATTCTTTCTAATCTCAAAAATG 6 187 1 ATTTTCTAAT 0.949556 -23 *** ** ***** Masking position 1 Map Score: 20.8258 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 178 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 AACATTTTTTTTCTTTCCAAAAAGAATAAAA 1 83 1 TTTTTCCAAA 0.785143 -218 TATAGCAAATTTAAAACAAAATCAGCTATCA 1 235 0 TTAAACAAAA 0.611384 -66 TAAATTCACATTATAGCAAATTTAAAACAAA 1 246 0 TTTAGCAAAT 0.869681 -55 ATAAGAAAAATTATTTCAAATGTAGTAGAAT 2 73 0 TTTTTCAAAT 0.889489 -142 TTGAATTGAATTTTTTCTCAATTTAGGTTTT 2 108 0 TTTTTCTCAA 0.901 -107 CTATCCCTTATTATATCTAATAGCGTTTAAA 2 166 0 TTTATCTAAT 0.96206 -49 AAAATCTATATTATAACTAAAAGGGGGTTTT 3 11 0 TTTAACTAAA 0.922855 -56 ATAGATTTTATTTTAGCTAAAAATGGCATGG 3 33 1 TTTAGCTAAA 0.92808 -34 TTGAGAGTCATTTTAACACAAA 4 2 0 TTTAACACAA 0.797036 -45 TCTTAAGGGGTTCTGTCTCATTAAGCATCAA 5 11 0 TTTGTCTCAT 0.742584 -78 AAAATCACCATTCTATCACAAATGCTCTTAA 5 52 0 TTTATCACAA 0.944417 -37 TGAATGGGCATGTTATCTAAATTTTAGATAG 6 131 1 TGTATCTAAA 0.83537 -79 TTTGCGTTTATTCTATCTAAAATTTAGATAA 6 143 0 TTTATCTAAA 0.973869 -67 TTAAAGGTGATTCTTTCTAATCTCAAAAATG 6 188 1 TTTTTCTAAT 0.9138 -22 TATTAGCATCTTTAATCAAATCATAAAAGGG 7 45 1 TTAATCAAAT 0.769246 -26 ** ******** Masking position 10 Map Score: 14.2407 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 563 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 3 TGAATCTTCTTTAACATTTTTTTTCTTTCCAAA 1 71 1 TTAACTTTTT 0.891148 -230 TAATAATATTTATTGTCTTTTTTGGTGTTAGTT 1 112 0 TATTGTTTTT 0.94609 -189 ATGAATAACTTTAAGCATTTCTTACTCTTTAAT 1 184 1 TTAAGTTTTT 0.941437 -117 TTTAGGTTAATTTTGAGTTTTTAGGAGCAGTTT 2 13 0 TTTTGTTTTA 0.94609 -202 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 2 95 0 TTTAGTTTTT 0.968956 -120 AGCCCCTTTGAATTGAATTTTTTCTCAATTTAG 2 113 0 AATTGTTTTT 0.616349 -102 TTGTTTAAAATTTACATTTTTTAAACGCTATTA 2 147 1 TTTACTTTTA 0.858216 -68 TTAGTTATAATATAGATTTTATTTTAGCTAAAA 3 22 1 TATAGTTTTT 0.922293 -45 CAAATTTTTCCATTTTTAAGGTTTTTGA 4 29 0 TTTTCTTTTA 0.89938 -18 GTTTTCCCTTTATTTAAAAATCAC 5 75 0 TTTTCTTTTT 0.959109 -14 GCCCCATTTCTAATGTTTTTGTAACGGGCATGC 6 25 1 TAATGTTTTA 0.774998 -185 TTTATTCAATTTTTGCGTTTATTCTATCTAAAA 6 152 0 TTTTGTTTTT 0.978747 -58 AGAATCACCTTTAAGGTTTTATTCAATTTTTGC 6 169 0 TTAAGTTTTT 0.941437 -41 TACTTCCCTATTTTCAATGTTTTCAAGTAAAAT 7 13 1 TTTTCTGTTT 0.760899 -58 AAAAACCCTTTTATGATTTGATTAAAGATGCTA 7 48 0 TTATGTTGTT 0.762927 -23 ***** *** ** Masking position 8 Map Score: 18.6332 Number of sites scoring better than the average of aligned sites = 1229 Number in coding regions = 1022 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 4 TTTAAATTTGCTATAATGTGAATTTAATGAT 1 251 1 CTATAATTGA 0.696552 -50 GTGTTCTCCACTCTAAACTAATTTTCATCAT 1 277 0 CTCTAAATAA 0.972515 -24 CTCCTAAAAACTCAAAATTAACCTAAAATCG 2 19 1 CTCAAAATAA 0.972462 -196 TAGTTACCACCTATAAAATAAGGATCGTTCA 2 194 1 CTATAAATAA 0.920369 -21 TCTCAAAAACCTTAAAAATGGAAAAATTTG 4 27 1 CTTAAAATGG 0.779763 -20 ATCACAAATGCTCTTAAATAAAGGCATTCTT 5 38 0 CTCTTAATAA 0.832586 -51 AGGCTCTAAAGTAAGCCCCATTTC 6 4 1 CTCTAAATAA 0.972515 -206 ATCGTTTAGGCTCAAAATGAGTGAATGAATG 6 106 1 CTCAAAAGAG 0.88064 -104 TTTATTCTATCTAAAATTTAGATAACATGCC 6 137 0 CTAAAATTAG 0.711587 -73 TCTTTCTAATCTCAAAAATGG 6 199 1 CTCAAAATGG 0.964572 -11 ******* *** Masking position 6 Map Score: 8.22841 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 155 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 TAGTAGAATTAAGGCAGTGTTTTTGCGTCAA 2 51 0 AAGGCAGTTT 0.954759 -164 ATTCAATTCAAAGGGGCTATTGTTTAAAATT 2 128 1 AAGGGGCTTT 0.982426 -87 TAGATATAATAAGGGATAGTTACCACCTATA 2 178 1 AAGGGATATT 0.926175 -37 TTATAACTAAAAGGGGGTTTT 3 1 0 AAGGGGGTTT 0.990249 -66 AGGCATTCTTAAGGGGTTCTGTCTCATTAAG 5 17 0 AAGGGGTTTG 0.974617 -72 CTCTTAAATAAAGGCATTCTTAAGGGGTTCT 5 28 0 AAGGCATTTT 0.96205 -61 TCAAATCATAAAAGGGTTTTT 7 60 1 AAAGGGTTTT 0.94181 -11 ******** ** Masking position 2 Map Score: 6.08881 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 380 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 ATAGCTGATTTTGTTTTAAATTTGCTATAA 1 237 1 TTGTTTTAAA 0.947774 -64 ATAAGAAAAATTATTTCAAATGTAGTAGAA 2 74 0 TTATTTCAAA 0.892002 -141 AATTTAGGTTTTGTTTATAAGAAAAATTAT 2 90 0 TTGTTTATAA 0.900891 -125 AAAGGGGCTATTGTTTAAAATTTACATTTT 2 137 1 TTGTTTAAAA 0.966726 -78 TGAACGATCCTTATTTTATAGGTGGTAACT 2 195 0 TTATTTTATA 0.716406 -20 AAACCCCCTTTTAGTTATAATATAGATTTT 3 12 1 TTAGTTATAA 0.623406 -55 TTTGTGTTAAAATGACTCTCA 4 2 1 TTGTGTTAAA 0.809167 -45 AAGAATGCCTTTATTTAAGAGCATTTGTGA 5 38 1 TTATTTAAGA 0.857258 -51 GTTTTCCCTTTATTTAAAAATCACCATTC 5 70 0 TTATTTAAAA 0.957156 -19 ********** Masking position 6 Map Score: 5.54953 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 391 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 AATTATTGTTGTATGCATTCTCTTT 1 4 0 GATCATTCTC 0.897035 -297 TAAAGTTATTCATTCCATTCAAAGCGGGTAAA 1 165 0 CTTCATTCAA 0.927379 -136 TAATTTTCATCATTAAATTCACATTATAGCAA 1 258 0 CTTAATTCAC 0.927379 -43 TTAAAAATCACCATTCTATCACAAATGCTCTT 5 54 0 CATCTATCAC 0.903604 -35 CGTAACTCCCCGATCCATTCACATGCAAATCG 6 62 0 CATCATTCAC 0.993549 -148 GATAACATGCCCATTCATTCACTCATTTTGAG 6 116 0 CATCATTCAC 0.993549 -94 * ** ******* Masking position 4 Map Score: 1.645 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 72 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ATATTCGTAATTATTGTTGTATGCATTCTC 1 14 0 TTATTGTTGT 0.957755 -287 TTTATTGTCTTTTTTGGTGTTAGTTTTATT 1 107 0 TTTTTGGTGT 0.9711 -194 GTTGTAATAATATTTATTGTCTTTTTTGGT 1 119 0 TATTTATTGT 0.850884 -182 GAGTTACGCGTTTTTGTTGTATCGTTTAGG 6 86 1 TTTTTGTTGT 0.982843 -124 ********** Masking position 5 Map Score: 0.196188 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 51 Number in noncoding regions = 12 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: -2.84684e-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: -2.84684e-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: -2.84684e-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