AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_hpyl_reg_300.orf -o00030_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 HP0175 300 cell binding factor 2 #2 HP0737 146 conserved hypothetical integral membrane protein #3 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #4 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #5 HP1085 66 H. pylori predicted coding region HP1085 #6 HP1088 46 transketolase A (tktA) #7 HP1100_HP1101 65 HP1100: 6-phosphogluconate dehydratase, HP1101: glucose-6-phosphate dehydrogenase (g6pD) #8 HP1166 63 glucose-6-phosphate isomerase (pgi) #9 HP1180 300 pyrimidine nucleoside transport protein (nupC) #10 HP1385_HP1386 70 HP1385: fructose-1,6-bisphosphatase, HP1386: D-ribulose-5-phosphate 3 epimerase (rpe) #11 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 TTTTGGAAAGAAAAAAAATGTTAAAGAAGATTCAA 1 70 0 AAAAATTAAA 0.980962 -231 AACTAACACCAAAAAAGACAATAAATATTATTACA 1 112 1 AAAAAATAAA 0.760063 -189 CATTAAAGAGTAAGAAATGCTTAAAGTTATTCATT 1 183 0 TAAGATTAAA 0.731632 -118 ATGATCACAGAAAACTCACATTAAAGAGTAAGAAA 1 201 0 AAAACTTAAA 0.974253 -100 TTTTCATCATTAAATTCACATTATAGCAAATTTAA 1 252 0 TAAATTTATA 0.772504 -49 TAAAATTAACCTTTAATTTTTGAGAG 2 2 1 AAAATTTTAA 0.903052 -145 GTTATCATACTAAAACGTGCTTAAAATTAAGCCTT 2 46 1 TAAAATTAAA 0.967548 -101 ATTGTTTAAGAAAATCGCTTTTTAATGCAAATAAA 2 81 1 AAAATTTTAA 0.903052 -66 TCATTGCCTTAAATTCTTTTTAAATCATGGCATT 2 123 0 TAAATTTAAA 0.967656 -24 ATTTACCTAAAAAAAGGCTTTTGAATTTTCTTAAA 3 12 0 AAAAATTGAA 0.845303 -66 TTACACTCCCTAAAATGAATTAAAATCAATTGTAG 4 37 0 TAAAATAAAA 0.790588 -28 TAGCTAAAATAAAATCTATATTATAACTAAAAGGG 5 17 0 AAAATTTATA 0.854242 -50 TTTGTGTTAAAATGACTCTCAAAAACCTTAAAA 6 9 1 AAAATTCAAA 0.909552 -38 ATAATAACTCAAAAACACTCTAAAAGGGTTATTG 7 10 0 AAAAATAAAA 0.866687 -56 TATTATATATTAAATCTTAATTAAAGGGGTATTC 7 42 1 TAAATTTAAA 0.967656 -24 TTGAAAATTGTAATTAAAACTAGCTTAT 8 4 1 AAAATTTAAA 0.980963 -60 AAAAATCCATTAAAATTACATTAAACTTTTATTAT 9 54 0 TAAAATTAAA 0.967548 -247 AGATTATACAAAAACCTTTCTTAAAAATCCATTAA 9 76 0 AAAACTTAAA 0.974253 -225 AAACGGATATTAAATGAAGTTTAAATCAAAATCAT 9 205 0 TAAATTTAAA 0.967656 -96 TAGTTTTGCTAAAAAAAAGATTAAACGGATATTAA 9 227 0 AAAAATTAAA 0.980962 -74 ATCGTCATAAAAACCTTGTTCTAATAGTGGTCTT 11 10 1 AAAACTCTAA 0.571713 -129 TTTTTAAAACTCTCTTTAAAATTTTACTTT 11 119 0 AAAACTTAAA 0.974253 -20 ***** ***** Masking position 3 Map Score: 34.5106 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 647 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 AGAGTAAGAAATGCTTAAAGTTATTCATTCCATTC 1 177 0 ACTTAAAGTT 0.893619 -124 ACAGAAAACTCACATTAAAGAGTAAGAAATGCTTA 1 195 0 CATTAAAGGA 0.736176 -106 AATTCTCTCAAAAATTAAAGGTTAATTTTA 2 6 0 AATTAAAGTA 0.851226 -141 GCATTTTATTTGCATTAAAAAGCGATTTTCTTAAA 2 85 0 TATTAAAAGA 0.851217 -62 TAAAATGCCATGATTTAAAAAGAATTTAAGGCAAT 2 120 1 TTTTAAAAGT 0.649658 -27 GATCAAACTCCCTAAAAACGATTGCAATAAAGT 3 55 0 TCTAAAAAGT 0.884493 -23 TAGCGCACCCAAACTAAAAGCGTTTGTTT 4 5 0 ACTAAAAGGT 0.951994 -60 ATCTATATTATAACTAAAAGGGGGTTTT 5 4 0 TCTAAAAGGT 0.951994 -63 GATTTTATTTTAGCTAAAAATGGCATGGGTTTTAG 5 36 1 TCTAAAAAGA 0.893619 -31 GACTCTCAAAAACCTTAAAAATGGAAAAATTTG 6 24 1 ACTTAAAATA 0.780607 -23 ACTCAAAAACACTCTAAAAGGGTTATTG 7 4 0 ACTAAAAGGA 0.956052 -62 ATATTAAATCTTAATTAAAGGGGTATTC 7 48 1 TATTAAAGGA 0.936778 -18 CAATACCCCTTAAATAAAAGATATAATGCTGTATT 8 39 0 TATAAAAGTA 0.839118 -25 AGTAGGATTGATAATAAAAGTTTAATGTAATTTTA 9 44 1 AATAAAAGTA 0.839118 -257 TACAAAAACCTTTCTTAAAAATCCATTAAAATTAC 9 70 0 TCTTAAAATA 0.780606 -231 CTAATGCAAGAAATTAAAAGATGCAAGGCTATTGT 9 266 0 ATTAAAAGTA 0.649658 -35 CTTTTATGATTTGATTAAAGATGCTAATATTTTAC 10 39 0 TATTAAAGTT 0.839118 -32 CTTTAATCAAATCATAAAAGGGTTTTT 10 54 1 AATAAAAGGT 0.924885 -17 CCCTTGAGCCACTCTTAAAAAGCGTTGTTTGATAA 11 60 1 ACTTAAAAGT 0.893596 -79 AAAGCGTTGTTTGATAAAAATGGCTCATTATATGG 11 78 1 TATAAAAAGT 0.826225 -61 CTTAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 11 116 1 ATTTAAAGGT 0.827653 -23 * ******* * * Masking position 5 Map Score: 22.5069 Number of sites scoring better than the average of aligned sites = 1955 Number in coding regions = 1698 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 3 CTTAAACAATAAGGCTTAATTTTAAGCACG 2 61 0 AAGGCTTAAT 0.692835 -86 GTTTAAGAAAATCGCTTTTTAATGCAAATA 2 84 1 ATCGCTTTTT 0.871169 -63 TTTTTAAATCATGGCATTTTAGCATTTTAT 2 111 0 ATGGCATTTT 0.787088 -36 TACCTAAAAAAAGGCTTTTGAATTTTCTTA 3 14 0 AAGGCTTTTG 0.950762 -64 AAACAAACGCTTTTAGTTTGGGTGC 4 6 1 AACGCTTTTA 0.71676 -59 TATAACTAAAAGGGGGTTTT 5 1 0 AGGGGGTTTT 0.833195 -66 TAAAAATGGCATGGGTTTTAGCAAGGA 5 50 1 ATGGGTTTTA 0.767146 -17 TTCCATTTTTAAGGTTTTTGAGAGTCATTT 6 20 0 AAGGTTTTTG 0.627842 -27 AACACTCTAAAAGGGTTATTG 7 2 0 AAGGGTTATT 0.965631 -64 ATCTTAATTAAAGGGGTATTC 7 55 1 AAGGGGTATT 0.910864 -11 TCTTTTATTTAAGGGGTATTG 8 53 1 AAGGGGTATT 0.910864 -11 TGTAATTTTAATGGATTTTTAAGAAAGGTT 9 69 1 ATGGATTTTT 0.666753 -232 GATTTTTAAGAAAGGTTTTTGTATAATCTC 9 82 1 AAAGGTTTTT 0.728042 -219 AAAAAGATTAAACGGATATTAAATGAAGTT 9 219 0 AACGGATATT 0.572505 -82 TAAAAGATGCAAGGCTATTGTAGTTTAGTT 9 257 0 AAGGCTATTG 0.732251 -44 CAAATCATAAAAGGGTTTTT 10 61 1 AAGGGTTTTT 0.979302 -10 GAGTGGCTCAAGGGCTAATTGGATAGAATA 11 44 0 AGGGCTAATT 0.564473 -95 TTTATCAAACAACGCTTTTTAAGAGTGGCT 11 66 0 AACGCTTTTT 0.940033 -73 TTTGATAAAAATGGCTCATTATATGGTATC 11 87 1 ATGGCTCATT 0.618153 -52 ********** Masking position 1 Map Score: 15.1916 Number of sites scoring better than the average of aligned sites = 2543 Number in coding regions = 2225 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 4 TATAGCAAATTTAAAACAAAATCAGCTATCAT 1 234 0 TTAACAAAAT 0.941242 -67 CGCTTTTTAATGCAAATAAAATGCTAAAATGC 2 96 1 TGAATAAAAT 0.887135 -51 ACTCCCTAAAATGAATTAAAATCAATTGTAGC 4 36 0 ATAATAAAAT 0.882072 -29 CCATTTTTAGCTAAAATAAAATCTATATTATA 5 27 0 CTAATAAAAT 0.967445 -40 GAATACCCCTTTAATTAAGATTTAATATATA 7 45 0 TTAATAAGAT 0.887135 -21 ATAAGCTAGTTTTAATTACAATTTTCAA 8 7 0 TTAATACAAT 0.941242 -57 CAATACCCCTTAAATAAAAGATATAATGCT 8 44 0 CTAATAAAAG 0.848399 -20 TAAATGAAGTTTAAATCAAAATCATGGTGTCA 9 198 0 TTAACAAAAT 0.941242 -103 TTTAGCAAAACTAAACTACAATAGCCTTGCAT 9 249 1 CTAATACAAT 0.919391 -52 TTTCAATGTTTTCAAGTAAAATATTAGCATCT 10 24 1 TTAATAAAAT 0.976602 -47 ATATGGTATCTTAAAGTAAAATTTTAAAGAGA 11 107 1 TTAATAAAAT 0.976602 -32 ** ** ****** Masking position 5 Map Score: 14.141 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 41 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 CATCGAGAATTTTTGAATCTTCTTTAACATT 1 58 1 TTTGAATCTT 0.929417 -243 TTGAATCTTCTTTAACATTTTTTTTCTTTCC 1 70 1 TTTACATTTT 0.921378 -231 ATCATGGCATTTTAGCATTTTATTTGCATTA 2 103 0 TTTGCATTTT 0.977252 -44 AAAAAAAGGCTTTTGAATTTTCTTAAAA 3 8 0 TTTGAATTTT 0.964207 -70 CAAATTTTTCCATTTTTAAGGTTTTT 6 31 0 TTTCCATTTT 0.96351 -16 GCTAGTTTTAATTACAATTTTCAA 8 4 0 ATTCAATTTT 0.821514 -60 ATGACAAAAGTTGGGCATTTTC 9 2 0 TTGGCATTTT 0.899589 -299 TACTTCCCTATTTTCAATGTTTTCAAGTAAA 10 13 1 TTTCAATGTT 0.814741 -58 CAAGTAAAATATTAGCATCTTTAATCAAATC 10 36 1 ATTGCATCTT 0.853741 -35 TAAAACTCTCTTTAAAATTTTACTTTAAGAT 11 114 0 TTTAAATTTT 0.880222 -25 *** ******* Masking position 7 Map Score: 8.69726 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 274 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 TTATTTGCATTAAAAAGCGATTTTCTTAAA 2 85 0 TAAAAAGCGA 0.943266 -62 AATAAAATGCTAAAATGCCATGATTTAAAA 2 110 1 TAAAATGCCA 0.893859 -37 TTAAGAAAATTCAAAAGCCTTTTTTTAGGT 3 13 1 TCAAAAGCCT 0.972508 -65 AAAATGACTCTCAAAAACCTTAAAAATGGA 6 19 1 TCAAAAACCT 0.821058 -28 AAACCTTTCTTAAAAATCCATTAAAATTAC 9 70 0 TAAAAATCCA 0.859065 -231 AGCGCTGGTCTCATAAGCCGGAGGTCGGGG 9 152 1 TCATAAGCCG 0.88367 -149 GAGCCACTCTTAAAAAGCGTTGTTTGATAA 11 65 1 TAAAAAGCGT 0.92737 -74 AGATACCATATAATGAGCCATTTTTATCAA 11 88 0 TAATGAGCCA 0.820446 -51 ********** Masking position 3 Map Score: 2.07013 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 484 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TTCCATTTTTAAGGTTTTTGAGAGTCATTT 6 20 0 AAGGTTTTTG 0.971573 -27 ACACTCTAAAAGGGTTATTG 7 1 0 AGGGTTATTG 0.989237 -65 ACCCTTTTAGAGTGTTTTTGAGTTATTATT 7 16 1 AGTGTTTTTG 0.901536 -50 TCTTAATTAAAGGGGTATTC 7 56 1 AGGGGTATTC 0.936099 -10 CTTTTATTTAAGGGGTATTG 8 54 1 AGGGGTATTG 0.987047 -10 ATTTTTAAGAAAGGTTTTTGTATAATCTCA 9 83 1 AAGGTTTTTG 0.971573 -218 TAAAAGATGCAAGGCTATTGTAGTTTAGTT 9 257 0 AAGGCTATTG 0.952489 -44 ********** Masking position 1 Map Score: 8.68779 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 241 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AAAGAGAATGCATACAACAAT 1 2 1 AAGAGAATGC 0.891226 -299 TTTCTTTCCAAAAAGAATAAAACTAACACC 1 92 1 AAAAGAATAA 0.908969 -209 AACACCAAAAAAGACAATAAATATTATTAC 1 116 1 AAGACAATAA 0.881114 -185 ACCCGCTTTGAATGGAATGAATAACTTTAA 1 168 1 AATGGAATGA 0.8147 -133 AAAAGAATTTAAGGCAATGA 2 137 1 AAGGCAATGA 0.914798 -10 ACAAAAAAATAAAAGAATGAGATTATACAA 9 100 0 AAAAGAATGA 0.962328 -201 TTTGCTAAAAAAAAGATTAAACGGATATTA 9 228 0 AAAAGATTAA 0.785198 -73 ATTTTACTTGAAAACATTGAAAATAGGGAA 10 16 0 AAAACATTGA 0.851806 -55 ********** Masking position 6 Map Score: 2.58207 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 312 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 ********** No masking Map Score: 3.24961e-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: 3.24961e-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: 3.24961e-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