AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_hpyl_reg_100.orf -o00010_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 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 HP1350 209 protease #10 HP1385 70 fructose-1,6-bisphosphatase Motif number 1 ATTCTATCAAATCCTAGCCTAAAATCTATTATAATAAAAGGACT 1 36 0 AAAAATATAA 0.987327 -63 CTAGGATTTGATAGAATAAACAAATCAAATTCAATAAGGTAATT 1 63 1 AACAATATAA 0.944651 -36 TTGGAAAGAAAAAAAATGTTAAAGAAGATTCAAAAATTCTCGAT 2 59 0 AAAAAAATAA 0.971102 -242 CTAACACCAAAAAAGACAATAAATATTATTACAACATCTGAGGC 2 114 1 AAAAAAATAA 0.971103 -187 TCAGCTATCATGATCACAGAAAACTCACATTAAAGAGTAAGAAA 2 201 0 TAAAATCTAA 0.895928 -100 CATTAAATTCACATTATAGCAAATTTAAAACAAAATCAGCTATC 2 236 0 AAAAATAAAA 0.854984 -65 AAACTGCTCCTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 3 13 1 TAAAATCTAA 0.895928 -202 ATTTAGGTTTTGTTTATAAGAAAAATTATTTCAAATGTAGTAGA 3 75 0 TAAAAAATAA 0.886015 -140 ACAAAACCTAAATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 3 106 1 AAAAATATAA 0.987327 -109 TACTCCTTGAATTCAACTCAATAAATAATTTTAATTAACCCTAC 4 15 1 AAATAAATAA 0.717762 -129 TAGGTCCAATATAATAGCGCAAAATGTAGTAAAATACCAAACAA 4 62 1 AAAAATATAA 0.987327 -82 ATACCAAACAAAACCCCCTAAAATTGAAATTGAAGTCTGAAAAT 4 95 1 ACAAATATAA 0.944652 -49 CTCAATTCTCCCTAAAAAACAAAATCACTTTTAAGACTAAATCA 5 14 1 CAAAATCTAA 0.834703 -98 AAATAAACTAAACTGAGTGTAAATTCAAGTATAATTCTAACATG 5 56 0 AAAAATATAA 0.987327 -56 TTGAGTTATTATTATATATTAAATCTTAATTAAAGGGGTATTC 6 10 0 AAAAACATAA 0.924741 -56 TTGAAAATTGTAATTAAAACTAGCTTATAATACAGCATTA 7 7 1 AAAAATCTAA 0.973834 -57 ATCGCAAAGCATGCCCGTTACAAAAACATTAGAAATGGGGCTTA 9 22 0 ACCAAAATAA 0.61728 -188 TTTTAGATAGAATAAACGCAAAAATTGAATAAAACCTTAAAGGT 9 152 1 AAAAATATAA 0.987327 -58 * * *** * * * ** Masking position 13 Map Score: 25.9778 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 200 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 ATTTTGAGTTTTTAGGAGCAGTTTTT 3 4 0 TTTAGGGATT 0.954822 -211 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 3 23 0 TTTAGGTATT 0.807977 -192 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAA 3 51 0 TTAAGGATTT 0.918945 -164 AGGTTTTGTTTATAAGAAAAATTATTTCAAATG 3 82 0 TATAAGAATT 0.628818 -133 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 3 95 0 TTTAGGTTTT 0.907016 -120 AAATTCAATTCAAAGGGGCTATTGTTTAAAATT 3 126 1 CAAAGGGTTT 0.743888 -89 ATTTACATTTTTTAAACGCTATTAGATATAATA 3 156 1 TTTAAAGTTT 0.573862 -59 CAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 4 94 0 TTTAGGGTTT 0.979999 -50 GATTTTGTTTTTTAGGGAGAATTGAGATT 5 7 0 TTTAGGAATT 0.845653 -105 GATTTAGTCTTAAAAGTGATTTTGTTTTTTAGG 5 24 0 TAAAAGGTTT 0.931142 -88 TAAATCTTAATTAAAGGGGTATTC 6 2 0 TTAAAGGTTT 0.960377 -64 AAAAACACTCTAAAAGGGTTATTG 6 52 1 TAAAAGGTTT 0.931141 -14 ATATCTTTTATTTAAGGGGTATTG 7 50 1 TTTAAGGTTT 0.964482 -14 TGCTCTTAAATAAAGGCATTCTTAAGGGGTTCT 8 28 0 TAAAGGATTT 0.863485 -61 AATGCCTTTATTTAAGAGCATTTGTGATAGAAT 8 41 1 TTTAAGGATT 0.921342 -48 AGAATCACCTTTAAGGTTTTATTCAATTTTTGC 9 169 0 TTAAGGTTTT 0.89698 -41 AATCAAATCATAAAAGGGTTTTT 10 58 1 TAAAAGGTTT 0.931141 -13 ****** * * ** Masking position 4 Map Score: 24.5064 Number of sites scoring better than the average of aligned sites = 1214 Number in coding regions = 1004 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 3 GAATTAAGGCAGTGTTTTTGCGTCAAGCGA 3 47 0 AGTGTTTTTG 0.971824 -168 TCAATTCAAAGGGGCTATTGTTTAAAATTT 3 130 1 GGGGCTATTG 0.914479 -85 TTCAATTTTAGGGGGTTTTGTTTGGTATTT 4 93 0 GGGGGTTTTG 0.982181 -51 TAGTCTTAAAAGTGATTTTGTTTTTTAGGG 5 23 0 AGTGATTTTG 0.912917 -89 TCTTAATTAAAGGGGTATTC 6 1 0 AGGGGTATTC 0.918952 -65 ACCCTTTTAGAGTGTTTTTGAGTTATTATT 6 41 0 AGTGTTTTTG 0.971824 -25 ACACTCTAAAAGGGTTATTG 6 56 1 AGGGTTATTG 0.982208 -10 CTTTTATTTAAGGGGTATTG 7 54 1 AGGGGTATTG 0.988709 -10 GGCATTCTTAAGGGGTTCTGTCTCATTAAG 8 17 0 AGGGGTTCTG 0.963944 -72 CCCCATTTCTAATGTTTTTGTAACGGGCAT 9 26 1 AATGTTTTTG 0.750832 -184 ********** Masking position 6 Map Score: 14.1235 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 4 CCTAAAATCTATTATAATAAAAGGACTTACCC 1 31 0 ATTTATAAAA 0.8857 -68 TGATTTGTTTATTCTATCAAATCCTAGCCTAA 1 58 0 ATTTACAAAT 0.916582 -41 AAGACAATAAATATTATTACAACATCTGAGGC 2 126 1 ATATATACAA 0.533889 -175 TTCTGTGATCATGATAGCTGATTTTGTTTTAA 2 224 1 ATGTACTGAT 0.685863 -77 TTAAATTCACATTATAGCAAATTTAAAACAAA 2 246 0 ATTTACAAAT 0.916148 -55 CACTGCCTTAATTCTACTACATTTGAAATAAT 3 63 1 ATTTATACAT 0.830697 -152 TTTGAATTGAATTTTTTCTCAATTTAGGTTTT 3 108 0 ATTTTCTCAA 0.799106 -107 ACTATCCCTTATTATATCTAATAGCGTTTAAA 3 166 0 ATTTACTAAT 0.944058 -49 TCAATAAATAATTTTAATTAACCCTACAGCTA 4 32 1 ATTTATTAAC 0.691388 -112 TTTGTTTGGTATTTTACTACATTTTGCGCTAT 4 75 0 ATTTATACAT 0.830686 -69 AATCTCAATTCTCCCTAAAAAACAAAATC 5 8 1 ATTTCCTAAA 0.773408 -104 TCATGTTAGAATTATACTTGAATTTACACTCA 5 55 1 ATTTATTGAA 0.868216 -57 TTAATATATAATAATAACTCAAAAACACTCTA 6 32 1 ATATACTCAA 0.80908 -34 TTGAAAATTGTAATTAAAACTAGCTTAT 7 7 1 ATTTATTAAA 0.928828 -57 AAAAATCACCATTCTATCACAAATGCTCTTAA 8 52 0 ATTTACACAA 0.943434 -37 ATGAATGGGCATGTTATCTAAATTTTAGATAG 9 130 1 ATGTACTAAA 0.86995 -80 TTTTGCGTTTATTCTATCTAAAATTTAGATAA 9 143 0 ATTTACTAAA 0.966297 -67 CTTAAAGGTGATTCTTTCTAATCTCAAAAATG 9 187 1 ATTTTCTAAT 0.724021 -23 AGATGCTAATATTTTACTTGAAAACATTGAAA 10 24 0 ATTTATTGAA 0.868216 -47 *** ** ***** Masking position 5 Map Score: 17.5081 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 204 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 TGCTTAAAGTTATTCATTCCATTCAAAGCGGGTAAA 2 165 0 TTCTATTCAA 0.982074 -136 AAACTAATTTTCATCATTAAATTCACATTATAGCAA 2 258 0 TTCTATTCAC 0.988623 -43 GTTTTACTCCTTGAATTCAACTCAATAAAT 4 5 1 TTCTATTCAA 0.982074 -139 CATGTTAGAATTATACTTGAATTTACACTCAGTTTA 5 56 1 TTATATTTAC 0.689393 -56 GTTTTCCCTTTATTTAAAAATCACCAT 8 72 0 TTCTATTTAA 0.926094 -17 AACGCGTAACTCCCCGATCCATTCACATGCAAATCG 9 62 0 TCCTATTCAC 0.980083 -148 TTTAGATAACATGCCCATTCATTCACTCATTTTGAG 9 116 0 ACCTATTCAC 0.898149 -94 TACTTCCCTATTTTCAATGTTTTCAAGTAAAATATT 10 13 1 TTCTTTTCAA 0.90756 -58 * ** * ****** Masking position 15 Map Score: 2.94309 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 86 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AGTAAAATCCTTTTGTGATAGGGTAAGTCC 1 11 1 TTTTGTGATA 0.957754 -88 GGGTAAGTCCTTTTATTATAATAGATTTTA 1 31 1 TTTTATTATA 0.646397 -68 TATTCGTAATTATTGTTGTATGCATTCTCT 2 13 0 TATTGTTGTA 0.68792 -288 TATTGTCTTTTTTGGTGTTAGTTTTATTCT 2 105 0 TTTGGTGTTA 0.840257 -196 TGATAGCTGATTTTGTTTTAAATTTGCTAT 2 235 1 TTTTGTTTTA 0.96266 -66 TTGAAATAATTTTTCTTATAAACAAAACCT 3 85 1 TTTTCTTATA 0.730434 -130 TTAAAAGTGATTTTGTTTTTTAGGGAGAAT 5 18 0 TTTTGTTTTT 0.766125 -94 AACGCCTACCTTTTGTATTAAGAAATAAAC 5 92 0 TTTTGTATTA 0.842577 -20 TTTAGAGTGTTTTTGAGTTATTATTATATA 6 36 0 TTTTGAGTTA 0.780172 -30 ATTTAAGAGCATTTGTGATAGAATGGTGAT 8 50 1 ATTTGTGATA 0.742311 -39 AGTTACGCGTTTTTGTTGTATCGTTTAGGC 9 87 1 TTTTGTTGTA 0.945499 -123 ********** Masking position 3 Map Score: 5.54654 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 149 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 AATCTATTATAATAAAAGGACTTACCCTATCA 1 26 0 AATAAAGACT 0.740461 -73 TTGGAAAGAAAAAAAATGTTAAAGAAGATTCA 2 71 0 AAAAAAGTAA 0.901372 -230 AATAGCGTTTAAAAAATGTAAATTTTAAACAA 3 147 0 AAAAAAGAAA 0.930459 -68 TATTAGATATAATAAGGGATAGTTACCACCTA 3 175 1 AATAAGGTAG 0.652498 -40 TTGAAGTCTGAAAATAGGATAATAGTTACG 4 124 1 AAAATAGTAA 0.717553 -20 ATACCCCTTAAATAAAAGATATAATGCTGTAT 7 40 0 AATAAAGTAT 0.892939 -24 AATGCTCTTAAATAAAGGCATTCTTAAGGGGT 8 31 0 AATAAAGATT 0.658111 -58 GTGATTTTTAAATAAAGGGAAAAC 8 75 1 AATAAAGAAA 0.95143 -14 TTTTAGATAGAATAAACGCAAAAATTGAATAA 9 152 1 AATAAAGAAA 0.95143 -58 GAAAACATTGAAAATAGGGAAGTATT 10 5 0 AAAATAGAAG 0.714515 -66 ****** * *** Masking position 4 Map Score: 1.54555 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 320 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 ********** No masking Map Score: 5.28234e-13 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 9 ********** No masking Map Score: 5.28234e-13 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: 5.28234e-13 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