AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_hpyl_reg_300.orf -o00950_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 HP1067 290 chemotaxis protein (cheY) #2 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #3 HP1377 300 H. pylori predicted coding region HP1377 #4 HP1483 26 gerC2 protein (gerC2) #5 HP1490 103 hemolysin #6 HP1491 138 phosphate permease Motif number 1 CTTGTCTTTCTTTTTTCAAACCATCCAATGACC 1 25 1 TTTTCAAACA 0.939844 -266 TAAACGATTATCATAGCAAACAAACTGAATTTT 1 92 1 TCTACAAAAA 0.973482 -199 AAACTGAATTTTTTTACAAATAAGAACGCTCAT 1 113 1 TTTTCAAAAA 0.958781 -178 TCAAGGTAATTTTAATCAAAACATGCTATTATT 1 179 1 TTAACAAACA 0.83827 -112 TAATAATAAATCGTTCCAAATAATAGCATGTTT 1 197 0 TCTTCAAAAA 0.972675 -94 TGCATCGGTGTTTTTGCAAATACAAGCGAGCGG 2 59 1 TTTTCAAAAC 0.918173 -113 TTAGCGTTGGTTATTCTAAAAAAATAACCGCTA 2 108 0 TTTTTAAAAA 0.803601 -64 TTCTTATTCCCACCAAATAATGTCAGCACC 3 8 1 TCCACAAAAA 0.933978 -293 GTCAGCACCATTTCTCCAAATCAAGCCCAGCCG 3 32 1 TTCTCAAACA 0.933958 -269 AAACTCTGTATTATATCAAACAATTTTGGTAAA 3 237 0 TTTACAAAAA 0.883789 -64 AATCTCAGAATTTTAACATAAAAGATTAAGCCT 5 39 0 TTTACATAAA 0.881352 -65 AATGAGCCATTTTTATCAAACAACGCTTTTTAA 6 53 1 TTTACAAAAA 0.883789 -86 ** ** **** ** Masking position 8 Map Score: 15.8159 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 290 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 TTGAAAAAAGAAAGACAAGGATTTTACAAGTA 1 12 0 AAAGAAGGAT 0.695711 -279 TTTTTTTACAAATAAGAACGCTCATTGAACGC 1 121 1 AATAAACGCT 0.914474 -170 AACGCTTTGCATAGAAACCGCTTATGCA 2 7 0 ATAGAACGCT 0.878828 -165 TTGTATTTGCAAAAACACCGATGCATTGCGCC 2 52 0 AAAAAACGAT 0.943571 -120 ATTATACCATAAGAAAACCGCTCGCTTGTATT 2 77 0 AAGAAACGCT 0.966848 -95 TTATTCTAAAAAAATAACCGCTATTATACCAT 2 99 0 AAAATACGCT 0.981172 -73 TTTTTTTAGAATAACCAACGCTAAAAATAGCG 2 117 1 ATAACACGCT 0.9442 -55 AACCAACGCTAAAAATAGCGCTTTAATTGAAT 2 129 1 AAAAAACGCT 0.990145 -43 CAGCCGCACCAAAAAGACGCCACCTACCGCTA 3 59 1 AAAAAAGCCA 0.837461 -242 CAAATCAAGAAAAATAATCCCAGTAAATCTCA 3 94 0 AAAATACCCA 0.839916 -207 GATTATATCCAAAACTAGCGAAAATTGATTTT 3 208 1 AAAACACGAA 0.73795 -93 AGACCGCCTTAAAACCAGCGCTCAATGATTTC 3 276 0 AAAACACGCT 0.984358 -25 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 5 10 0 AAAATAGCCT 0.908578 -94 TTTAACATAAAAGATTAAGCCTAACTTTAAAA 5 29 0 AAGATAGCCT 0.742582 -75 GCGTTGTTTGATAAAAATGGCTCATTATATGG 6 47 0 ATAAAAGGCT 0.93225 -92 ***** * **** Masking position 7 Map Score: 17.3251 Number of sites scoring better than the average of aligned sites = 2292 Number in coding regions = 2087 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 CGCCTTATAATAATAAATCGTTCCAAATAA 1 207 0 TAATAAATCG 0.73686 -84 CGATTTATTATTATAAGGCGTTAGAGACGC 1 217 1 TTATAAGGCG 0.980709 -74 CTTTGGCTGTTTAAAAAGAGCCTAATTTAA 1 246 1 TTAAAAAGAG 0.930187 -45 AAATGCAATCTTAAAAGGAGAAGCACT 1 274 1 TTAAAAGGAG 0.935213 -17 TTTTGGATTCAATTAAAGCGCTATTTTTAG 2 137 0 AATTAAAGCG 0.671283 -35 TTATAAAATATAATAAGGAGTTGAGGAATG 3 141 0 TAATAAGGAG 0.956093 -160 TTGTTTGATATAATACAGAGTTTAGCTTAG 3 247 1 TAATACAGAG 0.80738 -54 TGAGCGCTGGTTTTAAGGCGGTCTTTT 3 284 1 TTTTAAGGCG 0.958368 -17 TAAAGTAAAATTTTAAAGAGAGTTTTAAAA 6 12 0 TTTTAAAGAG 0.930187 -127 TGAGCCACTCTTAAAAAGCGTTGTTTGATA 6 66 0 TTAAAAAGCG 0.955052 -73 ********** Masking position 5 Map Score: 10.0287 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 882 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TTTCAAACCATCCAATGACCCTTTATCGCAC 1 38 1 TCAATGACCC 0.981623 -253 AAATGGAGCGTTCAATGAGCGTTCTTATTTG 1 129 0 TCAATGAGCG 0.989339 -162 CATTGAACGCTCCATTTAGCCAATGATTATT 1 143 1 TCATTTAGCC 0.971857 -148 TGATTAAAATTACCTTGACCGACAATAATCA 1 166 0 TCCTTGACCG 0.897124 -125 AAAACACCGATGCATTGCGCCATAAGCTTCA 2 42 0 TCATTGCGCC 0.97567 -130 TAGCTTAGAAATCATTGAGCGCTGGTTTTAA 3 269 1 ACATTGAGCG 0.94328 -32 TAAGATACCATATAATGAGCCATTTTTATCA 6 40 1 TTAATGAGCC 0.944009 -99 TCTTATTCTATCCAATTAGCCCTTGAGCCAC 6 88 0 TCAATTAGCC 0.971857 -51 * ********* Masking position 6 Map Score: 8.48949 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 189 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 CCTTTTAAGATTGCATTTAAATTAGGCTCT 1 262 0 TTGCATTTAA 0.903608 -29 AAGAAACGCTTTGCATAGAAACCGCTTATG 2 13 0 TTGCATAGAA 0.957469 -159 ACTCCTTGTTTTGGATTCAATTAAAGCGCT 2 145 0 TTGGATTCAA 0.876619 -27 TTCGCTAGTTTTGGATATAATCCCAATAAC 3 200 0 TTGGATATAA 0.978915 -101 ACCAAAATTGTTTGATATAATACAGAGTTT 3 240 1 TTTGATATAA 0.933067 -61 AAAAGCGTTGTTTGATAAAAATGGCTCATT 6 53 0 TTTGATAAAA 0.839704 -86 CAAGGGCTAATTGGATAGAATAAGACCACT 6 94 1 TTGGATAGAA 0.980268 -45 ********** Masking position 5 Map Score: 6.35903 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 145 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TTACTTGTAAAATCCTTGTCTTTCTTTT 1 7 1 GAAAACCTTG 0.895283 -284 CAAACCATCCAATGACCCTTTATCGCACTCAA 1 41 1 ATGACCTTTA 0.762056 -250 AAAGTAATAAAATAACTCTTTGAGTGCGATAA 1 60 0 ATAACCTTTG 0.973468 -231 ATAAGGCGTTAGAGACGCTTTGGCTGTTTAAA 1 229 1 AAGACCTTTG 0.982679 -62 ATAAGCTTCAAGAAACGCTTTGCATAGAAACC 2 20 0 AAAACCTTTG 0.988277 -152 AAAATAAACTCCTTGTTTTGGATTC 2 157 0 AAAACCCTTG 0.990277 -15 ATCGTCATAAAAACCTTGTTCTAATAGT 6 121 0 AAAAACCTTG 0.965261 -18 * **** ***** Masking position 5 Map Score: 4.57341 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 163 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AGACAAGGATTTTACAAGTAA 1 2 0 TTTACAAGTA 0.786491 -289 ATGATAATCGTTTAAAAGTAATAAAATAAC 1 76 0 TTTAAAAGTA 0.905641 -215 ACTGAATTTTTTTACAAATAAGAACGCTCA 1 115 1 TTTACAAATA 0.773363 -176 GCATGTTTTGATTAAAATTACCTTGACCGA 1 175 0 ATTAAAATTA 0.646021 -116 TTAGGCTCTTTTTAAACAGCCAAAGCGTCT 1 241 0 TTTAAACAGC 0.625796 -50 TAATGATTCGGTTAAACTTCCATCATGGTT 3 168 1 GTTAAACTTC 0.832551 -133 TAAGCCTAACTTTAAAAATCAAGCCTTCAA 5 16 0 TTTAAAAATC 0.934117 -88 AATCTTTTATGTTAAAATTCTGAGATTTTA 5 45 1 GTTAAAATTC 0.888123 -59 AACTTTAAACCTAAAACCTAACG 5 91 0 TTTAAACCTA 0.857374 -13 TTTTTAAAACTCTCTTTAAAAT 6 3 1 TTTAAAACTC 0.938672 -136 TAAAACTCTCTTTAAAATTTTACTTTAAGA 6 15 1 TTTAAAATTT 0.740672 -124 ********** Masking position 6 Map Score: 3.53255 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 461 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 8 TTACTTGTAAAATCCTTGTCTTT 1 2 1 TATTGTAAAT 0.671823 -289 AGCGGTTTTCTTATGGTATAATAGCGGTTATT 2 87 1 TTTGGTTAAT 0.967115 -85 AAATGAGATTTACTGGGATTATTTTTCTTGAT 3 91 1 TATGGGTTAT 0.943353 -210 TTTTCTTGATTTGTGGTTTTATTTTGCTCATT 3 113 1 TTTGGTTTAT 0.967115 -188 ATGGTTAAGTTATTGGGATTATATCCAAAACT 3 192 1 TATGGGTTAT 0.943353 -109 TATCAAACAATTTTGGTAAAATCAATTTTCGC 3 225 0 TTTGGTAAAT 0.948269 -76 GCTTAATCTTTTATGTTAAAATTCTGAGATTT 5 41 1 TTTGTTAAAT 0.67182 -63 CTTGTTCTAATAGTGGTCTTATTCTATCCAAT 6 103 0 TATGGTTTAT 0.967115 -36 ** **** **** Masking position 11 Map Score: 4.6879 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 158 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 ********** No masking Map Score: -1.39023e-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: -1.39023e-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: -1.39023e-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