AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR9_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0166 235 response regulator (ompR) #2 HP0392 56 histidine kinase (cheA) #3 HP0395 22 conserved hypothetical protein #4 HP0398 28 H. pylori predicted coding region HP0398 #5 HP0399 120 ribosomal protein S1 (rps1) #6 HP0813 132 conserved hypothetical protein #7 HP0977 128 conserved hypothetical secreted protein #8 HP1015 111 H. pylori predicted coding region HP1015 #9 HP1017 97 amino acid permease (rocE) #10 HP1018 47 H. pylori predicted coding region HP1018 #11 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 TTTTTTAATGTTTTTAAACAATTCCTTTGAT 1 17 0 TTTTTAAACA 0.967849 -219 ATTATCATAGTTATTAATGGAAATTTAAGGC 1 83 0 TTATTAATGA 0.800494 -153 TAGCATTTTATTATTAAAGATACCTTGAAAA 1 139 0 TTATTAAAGT 0.88119 -97 AAGTTAATCGTTTTTAAAGTTGCAGAAATCA 1 195 1 TTTTTAAAGT 0.97715 -41 AGAGTGATTTTAAAAGCATGAGAATGGC 4 8 1 TTTTAAAAGA 0.98068 -21 ATTAGCGGTTTTTTTAAAGAAAATTTTCAAA 5 16 0 TTTTTAAAGA 0.988194 -105 TAATTGTTAGTTTTTAAACGATTTTGTAAGC 5 43 1 TTTTTAAACA 0.972027 -78 AATAATGACTTTTTAAAACTAGTTTGAAGGG 6 102 1 TTTTAAAACA 0.929992 -31 TATTTTTGATTTTTTAAAGGGATTAGAGTTC 7 106 1 TTTTTAAAGG 0.978797 -23 CAACAAGCATTTTTTAATGAATTGCAACTCT 8 52 0 TTTTTAATGA 0.958447 -60 TATTTTAAAAGAAGTTTTTAGCG 9 3 1 TTTTAAAAGA 0.980594 -95 TTTTAAGGTTTTTTTAAAGAACGCTAAAAAC 9 24 0 TTTTTAAAGA 0.988194 -74 CAAGCGATAGTTTTTTAAGCGTTTTAAGGTT 9 45 0 TTTTTTAAGG 0.808645 -53 TTTTTAAAGATTAAATAGTAA 9 87 0 TTTTTAAAGT 0.977064 -11 ACCGCTTAAATTTCAAAAGTATCCTACAACA 11 21 1 TTTCAAAAGA 0.873219 -100 ********* * Masking position 7 Map Score: 30.3575 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 627 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 GTCTTATTTTTTAATGTTTTTAAACAATTC 1 24 0 TTAATGTTTT 0.97143 -212 ACATTAAAAAATAAGACTTTATTTTTCAAT 1 37 1 ATAAGACTTT 0.804825 -199 TAATGGAAATTTAAGGCTTTGTTTTCATGG 1 70 0 TTAAGGCTTT 0.975508 -166 AATAACTATGATAATGTTTTGAATTTTTAT 1 99 1 ATAATGTTTT 0.974916 -137 ATTAACTTTGTTAATGTTTTAGGGGACTAA 1 173 0 TTAATGTTTT 0.97143 -63 TACAATACCCTTAAGGATTTTATATTTATT 5 84 1 TTAAGGATTT 0.935909 -37 TTTGGTTAAAATAAGGTTATTTGATTTTAC 7 49 1 ATAAGGTTAT 0.894478 -80 TGATTTTACTATAAGGTTGTTTAAACCTGA 7 70 1 ATAAGGTTGT 0.956871 -59 GTGGATGTGGATAATGTTTTGCAAGAAATA 8 14 0 ATAATGTTTT 0.974916 -98 TTTAAGCGTTTTAAGGTTTTTTTAAAGAAC 9 33 0 TTAAGGTTTT 0.989281 -65 AACCTTTGCGATAAGCTTTTGTCATTCAAA 11 100 0 ATAAGCTTTT 0.888322 -21 ********** Masking position 4 Map Score: 18.5438 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 416 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 AAAAAATAAGACTTTATTTTTCAATATTCC 1 42 1 ACTTTATTTT 0.889568 -194 GAAATTTAAGGCTTTGTTTTCATGGAATAT 1 65 0 GCTTTGTTTT 0.967836 -171 ATGTTTTGAATTTTTATTTTTAAGATATTT 1 112 1 TTTTTATTTT 0.844975 -124 AAGGATTTTATATTTATTTTATAGTAAGGC 5 96 1 TATTTATTTT 0.791834 -25 AGTCAAAATCGCCTTATTTTTGCGCTATGA 6 64 1 GCCTTATTTT 0.903187 -69 TTATTTTTGCGCTATGATTTTCAATAATAA 6 77 1 GCTATGATTT 0.671715 -56 AAATCAAATAACCTTATTTTAACCAAAGGT 7 46 0 ACCTTATTTT 0.717907 -83 AAAATAAGGTTATTTGATTTTACTATAAGG 7 56 1 TATTTGATTT 0.71238 -73 GAATTTCATATTTTTGATTTTTTAAAGGGA 7 98 1 TTTTTGATTT 0.780173 -31 GAATTGCAACTCTTTGTTTTGGTGGATGTG 8 35 0 TCTTTGTTTT 0.957306 -77 TCTTTTCTTAATTTTGAAGTTTAGC 10 6 1 TCTTAATTTT 0.817991 -42 CCAACTTACCGCTTAAATTTCAAAAGTATC 11 14 1 GCTTAAATTT 0.793978 -107 AATACCATTTGTTTTAATTTGTTGCTATAA 11 63 1 GTTTTAATTT 0.823755 -58 ********** Masking position 8 Map Score: 10.3185 Number of sites scoring better than the average of aligned sites = 1283 Number in coding regions = 1056 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 4 CTTATTTTTTAATGTTTTTAAACAATTCCTT 1 21 0 AAGTTTTTAA 0.729012 -215 AACAAAGTTAATCGTTTTTAAAGTTGCAGAA 1 191 1 ATGTTTTTAA 0.871751 -45 GTTTGAGATAAGAGTATTTTACAATTTTATA 2 18 0 AGGTATTTTA 0.965207 -39 AACGCTAAAAAGGGGTTTTAA 2 46 1 AGGGTTTTAA 0.949818 -11 AGAGTGATTTTAAAAGCATGAGA 4 3 1 AGGATTTTAA 0.893622 -26 ACTAACAATTAGCGGTTTTTTTAAAGAAAAT 5 23 0 AGGGTTTTTT 0.770865 -98 AAAATCCTTAAGGGTATTGTATCCTTTTTTG 5 74 0 AGGTATTGTA 0.801853 -47 AATACCCTTAAGGATTTTATATTTATTTTAT 5 87 1 AGATTTTATA 0.65003 -34 CTTATTATAGAGAGTTTTTAAC 7 2 0 AGGTTTTTAA 0.974021 -127 TAGCCCAACAAGCATTTTTTAATGAATTGCA 8 57 0 AGATTTTTTA 0.949677 -55 TATTTTAAAAGAAGTTTTTAGCGTTCTTTA 9 10 1 AGAGTTTTTA 0.905005 -88 AAGCGTTTTAAGGTTTTTTTAAAGAACGCTA 9 29 0 AGTTTTTTTA 0.851542 -69 TGATCAAGCGATAGTTTTTTAAGCGTTTTAA 9 49 0 ATGTTTTTTA 0.929567 -49 TTTGAAGTTTAGCAAATTTTAAGGAAGTAAC 10 23 1 AGAAATTTTA 0.617048 -25 ATTAAAACAAATGGTATTTTAGCCGATAGTG 11 50 0 ATGTATTTTA 0.834147 -71 ** ******** Masking position 1 Map Score: 16.0535 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 1861 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 5 AAAGGAATTGTTTAAAAACATTAAAAAATA 1 20 1 TTTAAAAACA 0.609395 -216 TTTAAAAACATTAAAAAATAAGACTTTATT 1 30 1 TTAAAAAATA 0.733924 -206 TATAAAATTGTAAAATACTCTTATCTCAAA 2 18 1 TAAAATACTC 0.843174 -39 TTAAAACCCCTTTTTAGCGT 2 47 0 TTAAAACCCC 0.797931 -10 AAATTTTCTTTAAAAAAACCGCTAATTGTT 5 21 1 TAAAAAAACC 0.948586 -100 ACAAAATCGTTTAAAAACTAACAATTAGCG 5 40 0 TTAAAAACTA 0.795663 -81 CAAAAAAGGATACAATACCCTTAAGGATTT 5 74 1 TACAATACCC 0.640776 -47 ATAAAATAAATATAAAATCCTTAAGGGTAT 5 88 0 TATAAAATCC 0.419717 -33 CAAACTAGTTTTAAAAAGTCATTATTATTG 6 98 0 TTAAAAAGTC 0.707079 -35 GTTAAAAACTCTCTATAATAA 7 2 1 TTAAAAACTC 0.935835 -127 TAAGGATAATTTTAATAACCTTTGGTTAAA 7 29 1 TTTAATAACC 0.732873 -100 TATAGTAAAATCAAATAACCTTATTTTAAC 7 53 0 TCAAATAACC 0.697037 -76 AAATTCAGGTTTAAACAACCTTATAGTAAA 7 74 0 TTAAACAACC 0.801345 -55 TCTAATCCCTTTAAAAAATCAAAAATATGA 7 103 0 TTAAAAAATC 0.91175 -26 TAGCGTTCTTTAAAAAAACCTTAAAACGCT 9 29 1 TAAAAAAACC 0.948586 -69 TTAAAACGCTTAAAAAACTATCGCTTGATC 9 49 1 TAAAAAACTA 0.753536 -49 CACTATCGGCTAAAATACCATTTGTTTTAA 11 50 1 TAAAATACCA 0.765518 -71 ********** Masking position 5 Map Score: 15.0406 Number of sites scoring better than the average of aligned sites = 2693 Number in coding regions = 2341 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 6 AGAATAGCCATAAAGAAGAA 3 1 1 AGAATAGCCA 0.957565 -22 GATTTTGACTAGAATAGCGCTTCTATTATT 6 44 0 AGAATAGCGC 0.991076 -89 TATTCTAGTCAAAATCGCCTTATTTTTGCG 6 58 1 AAAATCGCCT 0.755007 -75 ATTATTGAAAATCATAGCGCAAAAATAAGG 6 75 0 ATCATAGCGC 0.938143 -58 AAGGGGCGAAAAAATAGCCCAACAAGCATT 8 72 0 AAAATAGCCC 0.984789 -40 TAACAGAATAGCCCCACACAAAGG 8 98 0 AGAATAGCCC 0.99319 -14 ATTTGTTGCTATAATAGAGCATTTGAATGA 11 79 1 ATAATAGAGC 0.864742 -42 ********** Masking position 4 Map Score: 6.24546 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 112 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 AAAACGATCAAAGGAATTGTTT 1 3 1 AACGATCAAA 0.917287 -233 TTAATAATAAAATGCTAGAATTAGTCCCCT 1 153 1 AATGCTAGAA 0.662141 -83 CAACTTTAAAAACGATTAACTTTGTTAATG 1 187 0 AACGATTAAC 0.851893 -49 TCTTATCTCAAACGCTAAAAAGGGGTTTTA 2 36 1 AACGCTAAAA 0.986862 -21 TGAAAATCATAGCGCAAAAATAAGGCGATT 6 70 0 AGCGCAAAAA 0.758751 -63 TTTTTTAAAGAACGCTAAAAACTTCTTTTA 9 16 0 AACGCTAAAA 0.986862 -82 AAAACCTTAAAACGCTTAAAAAACTATCGC 9 43 1 AACGCTTAAA 0.986862 -55 TTTTTAAAGATTAAATAGTAAAAGA 9 83 0 AAAGATTAAA 0.733269 -15 TATCCAACTTACCGCTTAAATTTCAAAAGT 11 11 1 ACCGCTTAAA 0.95227 -110 ********** Masking position 9 Map Score: 7.63362 Number of sites scoring better than the average of aligned sites = 1457 Number in coding regions = 1310 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 8 ********** No masking Map Score: -1.4826e-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 9 ********** No masking Map Score: -1.4826e-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: -1.4826e-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