AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_hpyl_reg_300.orf -o00271_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: HP1141 23 methionyl-tRNA formyltransferase (fmt) Input sequences: #1 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #2 HP0106 24 cystathionine gamma-synthase (metB) #3 HP0107 38 cysteine synthetase (cysK) #4 HP0194 214 triosephosphate isomerase (tpi) #5 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #6 HP0417 168 methionyl-tRNA synthetase (metS) #7 HP0795 111 trigger factor (tig) #8 HP0796 28 H. pylori predicted coding region HP0796 #9 HP0797 118 flagellar sheath adhesin hpaA #10 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #11 HP0802 88 GTP cyclohydrolase II (ribA) #12 HP0803 88 H. pylori predicted coding region HP0803 #13 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #14 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #15 HP1142 39 H. pylori predicted coding region HP1142 #16 HP1143 243 H. pylori predicted coding region HP1143 Motif number 1 TTAACTTATTTTTACTATAATTCTACTTTGTG 1 184 0 TTACTTAATT 0.872529 -117 AGTTTAAGGTTTATTTTAACTTATTTTTACTA 1 199 0 TTTTTAACTT 0.903187 -102 TTTTTCCTTTTTTATTGAATTT 2 1 0 TTATTAATTT 0.940131 -24 GAATTGAATTTTTTCTCAATTTAGGTTTTGTT 4 105 0 TTTCTAATTT 0.959923 -110 AAAGGGGCTATTGTTTAAAATTTACATTTTTT 4 137 1 TTTTTAAATT 0.943463 -78 TAGCTTAAAATTCATTATAATTAACGCTCAAA 6 41 0 TTATTTAATT 0.8528 -128 GCAACCTCTATTCTCTAAATTTTTAAAAGCAT 6 99 1 TTTCTAATTT 0.959923 -70 TACCTTAAATTTGTTTAAATCTCTTAATTTTA 6 133 0 TTTTTAATCT 0.922045 -36 TTTTTTAAATTTTTGAAAACTA 7 1 1 TTTTTAATTT 0.95299 -111 CTCTTTATAATTTTCTTAAATTTTAAGCTC 11 9 0 TTTCTAAATT 0.951729 -80 TTACAACACATTCAATAAAACTTAACGAGCCT 12 12 0 TTAATAAACT 0.741871 -77 TTAAAAAGAGTTTATTATACCTTAAAAACATT 12 42 0 TTATTTACCT 0.653941 -47 GGGAGTTTCATTCAATTAATTTAGAGGCTTTA 13 43 1 TTAATAATTT 0.856819 -128 TATTTCTTTTTTCTATAAAACTCAATATTATT 13 128 1 TTTATAAACT 0.7877 -43 CTCAATATTATTGAATAAAACTAGGGAGTTAG 13 148 1 TTAATAAACT 0.741871 -23 GATGCGTATTTTACTAAAATTTGCGCTAGAA 14 10 1 TTACTAAATT 0.938546 -72 CTGTTTGATATTGATTTTATTTGCATTAAGAA 14 49 1 TTATTTATTT 0.875591 -33 CGTATGGTTCTCTAAAACTTGTGCTTTTG 16 8 1 TTTCTAAACT 0.920022 -236 TGATCGATCGTTATCTCAATTTCTTCATTTTT 16 54 1 TTTCTAATTT 0.959923 -190 AATTTCTTCATTTTTTTTATTTATAATGTAGT 16 71 1 TTTTTTATTT 0.900852 -173 TTATTTTTTGTTGTTTGTATTTAAAATCCCTA 16 132 1 TTTTTTATTT 0.900852 -112 AAATCCCTATTTTACTGAACTTATTGGATAAA 16 155 1 TTACTAACTT 0.895155 -89 TAAGATTTGATTTTTTATATTTTATAATAGAA 16 212 0 TTTTTTATTT 0.900852 -32 ** *** ***** Masking position 6 Map Score: 29.8941 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 529 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 AAAAAGTTTTTAAAGGCAAAAAGGCTGGCGGA 1 62 1 TAAGCAAAAA 0.81884 -239 ATAAGTTAAAATAAACCTTAAACTTTAATGGT 1 207 1 ATACCTTAAA 0.580035 -94 ACAATTTTAAATTATGGATTAATAAAACTTAA 1 268 1 ATAGGATTAA 0.730695 -33 AAATTCAATAAAAAAGGAAAAACC 2 11 1 AAAGGAAAAA 0.794722 -14 AAAACTCAAAATTAACCTAAAATCGCTTGACG 4 25 1 ATACCTAAAA 0.803443 -190 CTAAAATCGCTTGACGCAAAAACACTGCCTTA 4 41 1 TTAGCAAAAA 0.928698 -174 AGAATGAAATAAGCTATAATAAGCCCATT 5 8 1 AAAGCTATAA 0.848937 -57 TATAATGAATTTTAAGCTAAAAACACCCCACA 6 54 1 TTAGCTAAAA 0.859867 -115 ACACCCCACAAATAAGCATAAATGCAACCTCT 6 76 1 AAAGCATAAA 0.796592 -93 ATTAAAACAAATTAAGCTATAATGATACAAAA 7 61 1 ATAGCTATAA 0.941206 -51 TTTTTTAGCCATTAAGGAAAAAA 7 99 1 ATAGGAAAAA 0.917658 -13 AGACAAATAACGCATAAAAAAAGAACGC 8 7 1 ATAGCATAAA 0.917733 -22 ATCTAAAGATGTTAGGGTAAAATAACATTTTG 9 24 1 GTAGGTAAAA 0.669188 -95 AATATTTAAAATCATGCTTTAAAAGATTTAAT 10 41 1 ATAGCTTTAA 0.839143 -32 TTGTAATGTTTTTAAGGTATAATAAACTCTTT 12 38 1 TTAGGTATAA 0.68253 -51 CTCTTTTTAAGTCAAGCAATAAAGTTTGCAAC 12 64 1 GTAGCAATAA 0.865559 -25 AACTCCCCCTATCATGCAAGAAATGCTCAAAG 13 18 0 ATAGCAAGAA 0.848524 -153 TTGTATCTAAATAAAGCAATAAAGTAATAATC 13 80 1 ATAGCAATAA 0.959506 -91 CAAAAAATAAAAAAGGCAAAAAATACCCTTCG 16 110 0 AAAGCAAAAA 0.918903 -134 TTAAGCAGGTTTTATCCAATAAGTTCAGTAAA 16 165 0 TTACCAATAA 0.625688 -79 ** * ******* Masking position 4 Map Score: 20.5297 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 1006 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 TTCTAAACAAAAAGTTTTTAAAGGCAAAAAGG 1 54 1 AAAGTTTAAA 0.783312 -247 CTTAAACTTTAATGGTTTCTAAACAAAACTAA 1 223 1 AATGTTTTAA 0.868109 -78 TTATAAGAAAAATTATTTCAAATGTAGTAGAA 4 74 0 AATTTTTAAA 0.92321 -141 CTTTGAATTGAATTTTTTCTCAATTTAGGTTT 4 109 0 AATTTTTTCA 0.810316 -106 TTTAAAATTTACATTTTTTAAACGCTATTAGA 4 150 1 ACATTTTAAA 0.701152 -65 CTATTCCTTGAACTCTTTTTCAATTTTTTGAG 6 15 1 AACTTTTTCA 0.778484 -154 TTTAGCTTAAAATTCATTATAATTAACGCTCA 6 43 0 AATTATTTAA 0.651941 -126 TCTATTCTCTAAATTTTTAAAAGCATGTTAAA 6 105 1 AAATTTTAAA 0.92321 -64 TGTTACCTTAAATTTGTTTAAATCTCTTAATT 6 136 0 AATTGTTAAA 0.842975 -33 TTTTTTAAATTTTTGAAAACTAGAATTA 7 7 1 AAATTTTAAA 0.92321 -105 ATTATAGCTTAATTTGTTTTAATTCCAGTTTA 7 52 0 AATTGTTTAA 0.90719 -60 CTAAAAAATTAAATTTTTGTATCATTATAGCT 7 75 0 AAATTTTTAT 0.597597 -37 GCATGATTTTAAATATTTTTAAAACCTCTTTA 10 26 0 AAATTTTTAA 0.956314 -47 CCCTTATATTAAATCTTTTAAAGCATGATTTT 10 48 0 AAATTTTAAA 0.92321 -25 ATTCTATCAAAACTCTTTATAATTTTCTTAAA 11 21 0 AACTTTTTAA 0.947392 -68 TTGATAGAATACCTTTTTTTAAAAGATGCGTT 11 43 1 ACCTTTTTAA 0.778484 -46 ATACTCCTAAAATTAGTTTTAAAACGCATCTT 11 65 0 AATTGTTTAA 0.90719 -24 AGTTTTATTGAATGTGTTGTAATGTTTTTAAG 12 22 1 AATGGTTTAA 0.746132 -67 AGGTATAATAAACTCTTTTTAAGTCAAGCAAT 12 52 1 AACTTTTTAA 0.947392 -37 ATTCTAGCGCAAATTTTAGTAAAATACGCATC 14 11 0 AAATTTATAA 0.597597 -71 **** *** *** Masking position 7 Map Score: 20.5709 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 490 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 ACCATTAAAGTTTAAGGTTTATTTTAACTT 1 209 0 TTTAAGGTTT 0.718036 -92 ATATTACAATTTTAAATTATGGATTAATAA 1 263 1 TTTAAATTAT 0.612984 -38 GGTGTTATCCTTTAAGTTTTATTAATCCAT 1 281 0 TTTAAGTTTT 0.957812 -20 AATCGCAAAATTGAATTTTATTGTTTGTT 3 10 1 ATTGAATTTT 0.795785 -29 TTAGGTTAATTTTGAGTTTTTAGGAGCAGT 4 15 0 TTTGAGTTTT 0.944439 -200 TTTTTCTCAATTTAGGTTTTGTTTATAAGA 4 98 0 TTTAGGTTTT 0.729926 -117 GCCCCTTTGAATTGAATTTTTTCTCAATTT 4 115 0 ATTGAATTTT 0.795785 -100 TTGTTTAAAATTTACATTTTTTAAACGCTA 4 147 1 TTTACATTTT 0.713584 -68 TTGAACTCTTTTTCAATTTTTTGAGCGTTA 6 22 1 TTTCAATTTT 0.78227 -147 ACCTCTATTCTCTAAATTTTTAAAAGCATG 6 102 1 TCTAAATTTT 0.701269 -67 TTTTTTAAATTTTTGAAAACTAG 7 4 1 TTTAAATTTT 0.954398 -108 GATACAAAAATTTAATTTTTTAGCCATTAA 7 84 1 TTTAATTTTT 0.881529 -28 AAAGCATGATTTTAAATATTTTTAAAACCT 10 31 0 TTTAAATATT 0.612984 -42 TTATAATTTTCTTAAATTTTAAGCTC 11 7 0 CTTAAATTTT 0.753267 -82 GAGGCTCGTTAAGTTTTATTGAATGTG 12 8 1 GTTAAGTTTT 0.768081 -81 ATTCAATAATATTGAGTTTTATAGAAAAAA 13 134 0 ATTGAGTTTT 0.808695 -37 TTTTTGCCTTTTTTATTTTTTGTTGTTTGT 16 120 1 TTTTATTTTT 0.4629 -124 TCCTTTAAGATTTGATTTTTTATATTTTAT 16 219 0 TTTGATTTTT 0.847817 -25 ********** Masking position 3 Map Score: 13.8072 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 643 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 5 GTTTATTTTAACTTATTTTTACTATAATTC 1 193 0 ACTTATTTTT 0.608299 -108 ATATAAAAGCCCTTAGTTTTGTTTAGAAAC 1 237 0 CCTTAGTTTT 0.924563 -64 TTTTATTAATCCATAATTTAAAATTGTAAT 1 265 0 CCATAATTTA 0.718683 -36 AAAAACACTGCCTTAATTCTACTACATTTG 4 58 1 CCTTAATTCT 0.913802 -157 GGTAACTATCCCTTATTATATCTAATAGCG 4 172 0 CCTTATTATA 0.635425 -43 TGAACGATCCTTATTTTATAGGTGGTAA 4 197 0 CCTTATTTTA 0.950097 -18 TGTTTAAATCTCTTAATTTTAACATGCTTT 6 124 0 TCTTAATTTT 0.819682 -45 AATCGTGTTACCTTAAATTTGTTTAAATCT 6 143 0 CCTTAAATTT 0.870834 -26 TTACCCTTATATTAAATCTTTTAA 10 59 0 CCTTATATTA 0.836584 -14 TTTATAATTTTCTTAAATTTTAAGCTC 11 8 0 TCTTAAATTT 0.550015 -81 TGATAGAATACCTTTTTTTAAAAGATGCGT 11 44 1 CCTTTTTTTA 0.635425 -45 TCTAACTCCCTAGTTTTATTCAATAAT 13 154 0 CCCTAGTTTT 0.8494 -17 GTTAGCCTTAATTCTTAATGCAAAT 14 67 0 CCTTAATTCT 0.913802 -15 TCCTAATTCACAATATCATC 15 30 0 TCCTAATTCA 0.437582 -10 TATTTAAAATCCCTATTTTACTGAACTTAT 16 149 1 CCCTATTTTA 0.897557 -95 ********** Masking position 4 Map Score: 9.07523 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 426 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 CTTTTTGCCTTTAAAAACTTTTTGTTTAGA 1 55 0 TTAAAAACTT 0.684684 -246 GGTGAGTTGGCTGAAACCACATCCCTGCTA 1 140 0 CTGAAACCAC 0.75186 -161 AAAACTGCTCCTAAAAACTCAAAATTAACC 4 12 1 CTAAAAACTC 0.947655 -203 CAAAATTAACCTAAAATCGCTTGACGCAAA 4 31 1 CTAAAATCGC 0.917091 -184 GAATTTTAAGCTAAAAACACCCCACAAATA 6 60 1 CTAAAAACAC 0.918601 -109 CTTAAATTTGTTTAAATCTCTTAATTTTAA 6 132 0 TTTAAATCTC 0.707362 -37 AAAACTAGAATTAAAACCGCTTTTTATAAA 7 26 1 TTAAAACCGC 0.951742 -86 TTAAATATTTTTAAAACCTCTTTAAAGCAC 10 20 0 TTAAAACCTC 0.952653 -53 TAAAATTAGTTTTAAAACGCATCTTTTAAA 11 60 0 TTTAAAACGC 0.791704 -29 TTATTATACCTTAAAAACATTACAACACAT 12 33 0 TTAAAAACAT 0.575112 -56 ATACAAATCGCTAAAGCCTCTAAATTAATT 13 56 0 CTAAAGCCTC 0.800049 -115 TTGTTTGTATTTAAAATCCCTATTTTACTG 16 142 1 TTAAAATCCC 0.780804 -102 ********** Masking position 5 Map Score: 6.70298 Number of sites scoring better than the average of aligned sites = 1509 Number in coding regions = 1368 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 TTTAAAAACTTTTTGTTTAGAATGTATTAA 1 46 0 TTTTGTTTAG 0.880462 -255 AAGCCCTTAGTTTTGTTTAGAAACCATTAA 1 231 0 TTTTGTTTAG 0.880462 -70 GTTTTTCCTTTTTTATTGAATTT 2 4 0 TTTTATTGAA 0.765753 -21 CAAAATTGAATTTTATTGTTTGTTATAGGA 3 16 1 TTTTATTGTT 0.863456 -23 TCAATTTAGGTTTTGTTTATAAGAAAAATT 4 92 0 TTTTGTTTAT 0.882554 -123 ACCAACACGCTTTTGTTGTCAAAATGTTAT 9 45 0 TTTTGTTGTC 0.86289 -74 GTTGCTTCGGGTTTGTTGTTATAGAAGTCT 9 73 1 GTTTGTTGTT 0.764225 -46 GCTCGTTAAGTTTTATTGAATGTGTTGTAA 12 14 1 TTTTATTGAA 0.765753 -75 TTTTTGTGGTGTGCTTTGAGA 15 2 1 TTTTGTGGTG 0.760598 -38 TCTTCATTTTTTTTATTTATAATGTAGTTT 16 75 1 TTTTATTTAT 0.734102 -169 CTTTTTTATTTTTTGTTGTTTGTATTTAAA 16 127 1 TTTTGTTGTT 0.945091 -117 ********** Masking position 6 Map Score: 5.80852 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 234 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 GAGACACCATAGTTTCTAAGCATTCCTTTTA 1 14 0 AGTTTCTAGC 0.895477 -287 CCTGTCCGCCAGCCTTTTTGCCTTTAAAAAC 1 67 0 AGCCTTTTGC 0.756096 -234 GAATTAAGGCAGTGTTTTTGCGTCAAGCGAT 4 46 0 AGTGTTTTGC 0.889833 -169 TAAAATTTACATTTTTTAAACGCTATTAGAT 4 152 1 ATTTTTTAAC 0.622286 -63 CTCTTTTTCAATTTTTTGAGCGTTAATTATA 6 27 1 ATTTTTTAGC 0.954357 -142 ACAAAAATTTAATTTTTTAGCCATTAAGGAA 7 87 1 AATTTTTAGC 0.918077 -25 GCGTTCTTTTTTTATGCGTTATTTGTC 8 12 0 TTTTTTTTGC 0.690949 -17 TAATTTTCTTAAATTTTAAGCTC 11 3 0 AAATTTTAGC 0.611931 -86 AATAAGTCTTTGAGCATTTCTTGCA 13 5 1 AGTCTTTAGC 0.946421 -166 TTTGATATTGATTTTATTTGCATTAAGAATT 14 52 1 ATTTTATTGC 0.712301 -30 TTTATAATGTAGTTTTTATGCGAAGGGTATT 16 90 1 AGTTTTTTGC 0.971887 -154 ******* *** Masking position 5 Map Score: 3.22688 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 651 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 AAACCTTAAACTTTAATGGTTTCTAAACAA 1 219 1 CTTTAATGGT 0.785291 -82 CAAAATTGAATTTTATTGTTTGTTATAGGA 3 16 1 TTTTATTGTT 0.392493 -23 TGCGTCAAGCGATTTTAGGTTAATTTTGAG 4 29 0 GATTTTAGGT 0.577912 -186 ACGATCCTTATTTTATAGGTGGTAACTATC 4 192 0 TTTTATAGGT 0.771249 -23 AAAATGGGCTTATTATAGCTTATTTCATTC 5 12 0 TATTATAGCT 0.807791 -53 TTTGTGGGGTGTTTTTAGCTTAAAATTCAT 6 58 0 GTTTTTAGCT 0.76384 -111 ATAGAGGTTGCATTTATGCTTATTTGTGGG 6 80 0 CATTTATGCT 0.618449 -89 ATTTTTGTATCATTATAGCTTAATTTGTTT 7 65 0 CATTATAGCT 0.927658 -47 AACATCTTTAGATTATTGGTCTTTTT 9 7 0 GATTATTGGT 0.793859 -112 TTTAAAACCTCTTTAAAGCACTCATAATTT 10 11 0 CTTTAAAGCA 0.420945 -62 AGGTTGCAAACTTTATTGCTTGACTTAAAA 12 68 0 CTTTATTGCT 0.946389 -21 ACGATTATTACTTTATTGCTTTATTTAGAT 13 84 0 CTTTATTGCT 0.946389 -87 ********** Masking position 4 Map Score: 2.92975 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 521 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 TCTTAATTTTAACATGCTTTTAAAAATTTA 6 114 0 AACATGCTTT 0.977247 -55 AATTTAAGGTAACACGATTATAAAG 6 154 1 AACACGATTA 0.74543 -15 ACTAGAATTAAAACCGCTTTTTATAAACTG 7 29 1 AAACCGCTTT 0.809537 -83 CGAAGCAACCAACACGCTTTTGTTGTCAAA 9 52 0 AACACGCTTT 0.980594 -67 AATATTTAAAATCATGCTTTAAAAGATTTA 10 41 1 ATCATGCTTT 0.899212 -32 ATCGTTATTAAACATGCTATATTTCTTTTT 13 109 1 AACATGCTAT 0.899212 -62 TATTGGATAAAACCTGCTTAAGTTAAATTG 16 176 1 AACCTGCTTA 0.926365 -68 ********** Masking position 1 Map Score: 3.21115 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 350 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: -5.32664e-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 12 ********** No masking Map Score: -5.32664e-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: -5.32664e-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