AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_hpyl_reg_300.orf -o00600_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 HP0428 300 phage/colicin/tellurite resistance cluster terY protein #2 HP0429 124 H. pylori predicted coding region HP0429 #3 HP0430 85 H. pylori predicted coding region HP0430 #4 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #5 HP0966 220 conserved hypothetical protein #6 HP0967 285 virulence associated protein D (vapD) #7 HP0971 49 H. pylori predicted coding region HP0971 #8 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #9 HP1154 130 H. pylori predicted coding region HP1154 Motif number 1 GCTTTATTTTTTTGATTGGGTTTTTTGGCG 1 173 1 TTTGATTGGG 0.818413 -128 CGAAAAATTATTTATAAGGAGATGTTATGG 1 203 1 TTTATAAGGA 0.855599 -98 CATGCTTTCTCTTTAAAGGGTTTAAAATAT 2 78 0 CTTTAAAGGG 0.939175 -47 CAAAAGTGGGATTTAAAGGGTTTAAAAGGG 3 51 1 ATTTAAAGGG 0.907576 -35 ATTTAAAGGGTTTAAAAGGGGAGTTTGAAG 3 61 1 TTTAAAAGGG 0.966301 -25 TGGGTATGGGTTTATATGGGGGTGAAAAGA 5 115 0 TTTATATGGG 0.972795 -106 TTTATATGGGTTTATATGGGTATGGGTTTA 5 131 0 TTTATATGGG 0.972795 -90 CAAAAAAGGGTTTATATGGGTTTATATGGG 5 141 0 TTTATATGGG 0.972795 -80 CATATAAACCCTTTTTTGGGGATTTTTTGG 5 153 1 CTTTTTTGGG 0.884818 -68 TTTTTTGGGGATTTTTTGGGGATTTTTGCG 5 164 1 ATTTTTTGGG 0.830088 -57 TAGTTTTTAATTTTAAAGGATTG 5 208 1 TTTTAAAGGA 0.829857 -13 TTGATGATTTTTTTTATGTGGAATGCTATA 6 19 1 TTTTTATGTG 0.819624 -267 ATTCAAGCTTTTTTTAAGCGAGGAAGTCGC 6 115 1 TTTTTAAGCG 0.897123 -171 GTCTGGCGTTTTTGTTTGGGGGTAACTTTT 7 27 1 TTTGTTTGGG 0.87458 -23 ATGATTTAGTCTTAAAAGTGATTTTGTTTT 8 74 1 CTTAAAAGTG 0.547437 -38 AGTGATTTTGTTTTTTAGGGAGAATTGAGA 8 90 1 TTTTTTAGGG 0.957522 -22 ATCCAACCATTTTTTAAGGAACGCTCTATT 9 22 0 TTTTTAAGGA 0.88299 -109 ATACGCAACAATTAAAAGCGTAAAAGCAAA 9 63 0 ATTAAAAGCG 0.543367 -68 ********** Masking position 3 Map Score: 21.6993 Number of sites scoring better than the average of aligned sites = 1798 Number in coding regions = 1523 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 AATCAGATTGTGCTTTATTTTTTTGATTGG 1 162 1 TGCTTTATTT 0.940447 -139 TATGGAAGAACGCTTTATTCCAGTATTTTT 1 255 1 CGCTTTATTC 0.916278 -46 GCCACAAAAACGCTTTATTTATGGATTTAA 2 32 1 CGCTTTATTT 0.984556 -93 ATGATCTTCATGCTTTCTCTTTAAAGGGTT 2 86 0 TGCTTTCTCT 0.951967 -39 ACATTCAAAACGCTGTCTTTGATTGAAACA 4 47 0 CGCTGTCTTT 0.941649 -85 CTTAAAAATTCGCTTTCTCTCTCTCTCTCT 5 67 1 CGCTTTCTCT 0.987656 -154 TTCTCTCTCTCTCTCTCTCTAGTCAGCCGC 5 81 1 CTCTCTCTCT 0.782402 -140 TCTAGTCAGCCGCTTTATCTTTTCACCCCC 5 98 1 CGCTTTATCT 0.98664 -123 CCCGCTCACCTGCTCTTTTTGGCTTAAAAG 6 69 0 TGCTCTTTTT 0.783589 -217 GCTAAATTCAAGCTTTTTTTAAGCGAGGAA 6 110 1 AGCTTTTTTT 0.695863 -176 GCGAGGAAGTCGCTTTACCTCTAGCAAAAG 6 132 1 CGCTTTACCT 0.926889 -154 TTTTAAGGAACGCTCTATTTTAGGATAATA 9 11 0 CGCTCTATTT 0.975568 -120 ********** Masking position 6 Map Score: 16.6795 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 574 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TGGTGTTGCTTTTTATTTCTTTGCCTTAAGAC 1 16 1 TTTTATCTTT 0.91982 -285 TTTTGATGATTTTATAAGCTTTTGAGTATAGT 1 108 0 TTTATACTTT 0.920512 -193 TGGATGATTTAAAATCTTTACGCCACAAA 2 8 1 TTTAAACTTT 0.989147 -117 TGATAGATATTTTAAACCCTTTAAAGAGAAAG 2 72 1 TTTAAACTTT 0.989147 -53 AAACTCCCCTTTTAAACCCTTTAAATCCCACT 3 55 0 TTTAAACTTT 0.989147 -31 CCTAGCACCATTTAATGGCTCTCATTATACTC 5 15 0 TTTAATCTCT 0.885999 -206 TATAAACCCATATAAACCCTTTTTTGGGGATT 5 145 1 TATAAACTTT 0.920512 -76 CGAACTGATTTTTTAAAGCTTTTGCTAGAGGT 6 148 0 TTTTAACTTT 0.962028 -138 AATAAAACAATTTCATTTCTTTAGAAGCGAAC 6 175 0 TTTCATCTTT 0.906036 -111 TTTAACTCCTTTATTGGTTTGT 6 274 0 TTTAACCTTT 0.96033 -12 TCCTTTTTAATTTAAATGCTTTGTTGTATAAT 9 102 0 TTTAAACTTT 0.989147 -29 ****** **** Masking position 3 Map Score: 18.2231 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 291 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AAGAGTGCTGAAATGAATGTTTTAATCAGATTG 1 139 1 AAAGATGTTT 0.919686 -162 AAAATTATTTATAAGGAGATGTTATGGCATTAG 1 206 1 ATAGAGAGTT 0.807592 -95 TACGCCACAAAAACGCTTTATTTATGGATTTAA 2 29 1 AAAGTTTTTT 0.748323 -96 TTATGGATTTAAACGATGAAGTTGATAGATATT 2 50 1 AAAGTGAGTT 0.94645 -75 ACAGATATACAAAAGTGGGATTTAAAGGGTTTA 3 42 1 AAAGGGGTTT 0.903635 -44 TAAAGGGTTTAAAAGGGGAGTTTGAAGACGCT 3 64 1 AAAGGGATTT 0.749678 -22 ATATTATTTAATATGTATATGTTTCAATCAAAG 4 28 1 ATAGATAGTT 0.722694 -104 CTTACATTCAAAACGCTGTCTTTGATTGAAACA 4 47 0 AAAGTGTTTT 0.82623 -85 TATTATTGTAAAATGGTGAGTTTTACAATCAAT 4 94 1 AAAGTGATTT 0.886105 -38 ATGGGTTTATATGGGTATGGGTTTATATGGGGG 5 123 0 ATGGATGGTT 0.670781 -98 CTCGCTTAAAAAAAGCTTGAATTTAGCGTATCT 6 104 0 AAAGTTGATT 0.730626 -182 TTTTATTCTCAAACGCATGGGTTGTAAAACGCA 6 200 1 AAAGATGGTT 0.964298 -86 ATGGGTTGTAAAACGCATGGGTTATCAAACGAA 6 216 1 AAAGATGGTT 0.964298 -70 TAACTCCTTTATTGGTTTGTGTTATAGCATGTT 6 261 0 ATTGTTGGTT 0.626531 -25 CTTCAAACGCAAAGTCTGGCGTTTTTGTTTGGG 7 14 1 AAATTGGGTT 0.720828 -36 TCTTAATACAAAAGGTAGGCGTT 8 1 0 AAAGAGGGTT 0.977593 -111 TTAGTCTTAAAAGTGATTTTGTTTTTTAGGGAG 8 79 1 AAGGTTTGTT 0.631713 -33 TTCCTTAAAAAATGGTTGGATTTGGAACGCCTT 9 31 1 AATGTGGTTT 0.797731 -100 *** * *** *** Masking position 12 Map Score: 14.7817 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 928 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 GGCAAAGAAATAAAAAGCAACACCACCAAT 1 11 0 TAAAAAGCAA 0.581624 -290 TTGCCTTAAGACAAACCATAGAGTCGGCTT 1 36 1 ACAAACCATA 0.781995 -265 TCTACTATACTCAAAAGCTTATAAAATCAT 1 105 1 TCAAAAGCTT 0.781952 -196 TTTCGCGCCAAAAAACCCAATCAAAAAAAT 1 178 0 AAAAACCCAA 0.870802 -123 TTTACGCCACAAAAACGCTTTATTTATGGA 2 27 1 AAAAACGCTT 0.889563 -98 GATAGATATTTTAAACCCTTTAAAGAGAAA 2 73 1 TTAAACCCTT 0.860281 -52 AGCCAATTGCTCAAAAGCTAAAAG 3 5 0 TCAAAAGCTA 0.714971 -81 AACTCCCCTTTTAAACCCTTTAAATCCCAC 3 56 0 TTAAACCCTT 0.860281 -30 TCACCCCCATATAAACCCATACCCATATAA 5 120 1 ATAAACCCAT 0.860281 -101 CCATACCCATATAAACCCATATAAACCCTT 5 136 1 ATAAACCCAT 0.860281 -85 ATAAACCCATATAAACCCTTTTTTGGGGAT 5 146 1 ATAAACCCTT 0.860281 -75 AAAAAAATCATCAAAGCCTTTT 6 3 0 TCAAAGCCTT 0.846699 -283 TCCTCGCTTAAAAAAAGCTTGAATTTAGCG 6 109 0 AAAAAAGCTT 0.665271 -177 TGTTTTATTCTCAAACGCATGGGTTGTAAA 6 198 1 TCAAACGCAT 0.935625 -88 GCATGGGTTGTAAAACGCATGGGTTATCAA 6 214 1 TAAAACGCAT 0.889563 -72 GCATGGGTTATCAAACGAAATTCTAAGTAA 6 230 1 TCAAACGAAA 0.749908 -56 ATGCTATAACACAAACCAATAAAGGAGTTA 6 264 1 ACAAACCAAT 0.83682 -22 TGGCTTCAAACGCAAAGTCTGGCGT 7 6 1 TCAAACGCAA 0.910444 -44 AATTCTCCCTAAAAAACAAAATCACTTTTA 8 86 0 AAAAAACAAA 0.329093 -26 ATTAAAAGCGTAAAAGCAAAAGGCGTTCCA 9 53 0 TAAAAGCAAA 0.387073 -78 AAATTATACAACAAAGCATTTAAATTAAAA 9 100 1 ACAAAGCATT 0.619635 -31 CATTTAAATTAAAAAGGATAGTCCA 9 116 1 AAAAAGGATA 0.345509 -15 ********** Masking position 5 Map Score: 21.2039 Number of sites scoring better than the average of aligned sites = 3629 Number in coding regions = 3217 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 6 GAGTTCCTGAATTTTGGGGTAGCAAGCCGA 1 59 0 ATTTTGGGGT 0.921262 -242 TTTTATAAGCTTTTGAGTATAGTAGACTTA 1 101 0 TTTTGAGTAT 0.709192 -200 GTATGGGTTTATATGGGGGTGAAAAGATAA 5 112 0 ATATGGGGGT 0.968914 -109 ATATGGGTTTATATGGGTATGGGTTTATAT 5 128 0 ATATGGGTAT 0.912444 -93 AAAAGGGTTTATATGGGTTTATATGGGTAT 5 138 0 ATATGGGTTT 0.719976 -83 ATAAACCCTTTTTTGGGGATTTTTTGGGGA 5 156 1 TTTTGGGGAT 0.974219 -65 TTTGGGGATTTTTTGGGGATTTTTGCGTCT 5 167 1 TTTTGGGGAT 0.974219 -54 TGGCGTTTTTGTTTGGGGGTAACTTTTTTA 7 30 1 GTTTGGGGGT 0.955998 -20 GGAACGCTCTATTTTAGGATAATA 9 5 0 ATTTTAGGAT 0.70154 -126 ********** Masking position 4 Map Score: 6.51381 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 417 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TGGGTTTTTTGGCGCGAAAAATTATTTATAA 1 189 1 GGCGGAAAAA 0.903131 -112 GCGTTTTTGTGGCGTAAAGATTTTAAATCAT 2 14 0 GGCGAAAGAT 0.993884 -111 TTGAGCAATTGGCTAAAAAATACAGATATAC 3 21 1 GGCTAAAAAT 0.941139 -65 TTTATATGGGGGTGAAAAGATAAAGCGGCTG 5 104 0 GGTGAAAGAT 0.961747 -117 ATCTAAATAAGACGCAAAAATCCCCAAAAAA 5 175 0 GACGAAAAAT 0.941139 -46 CAGGTGAGCGGGCGTAAAGATACGCTAAATT 6 87 1 GGCGAAAGAT 0.993884 -199 **** ****** Masking position 7 Map Score: 4.24207 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 79 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 AAAAACCCAATCAAAAAAATAAAGCACAATCT 1 166 0 TAAAAAATAA 0.660761 -135 CACTCGTATCTAACAATAAAAATACTGGAATA 1 270 0 TAAATAAAAA 0.930109 -31 AAATAATATTTTAAAATTAAAAAGCG 4 5 0 TAAATTAAAA 0.917036 -127 ACTCACCATTTTACAATAATAAGTTTAAAATA 4 83 0 TAAATAATAA 0.878322 -49 CAATCCTTTAAAATTAAAAACTAAAATCT 5 202 0 TAAATTAAAA 0.917036 -19 CCCATGCGTTTGAGAATAAAACAATTTCATTT 6 189 0 TAAATAAAAC 0.925659 -97 CCTTTTGTATTAAGAAATAAACTAAACTGAGT 8 19 1 TAAAATAAAC 0.839743 -93 CTAAATCATGTTAGAATTATACTTGAATTTAC 8 51 0 TAAATTATAC 0.91573 -61 AAAAAATACGCAACAATTAAAAGCGTAAAAGC 9 66 0 CAAATTAAAA 0.809577 -65 GCGTATTTTTTCAAAATTATACAACAAAGCAT 9 87 1 TAAATTATAC 0.925382 -44 CAACAAAGCATTTAAATTAAAAAGGATAGTCC 9 108 1 TTAATTAAAA 0.692329 -23 * * ******** Masking position 6 Map Score: 9.00766 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 152 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 TCTTTACGCCACAAAAACGCTTTATTTATG 2 25 1 ACAAAAACGC 0.92932 -100 GATTATTCTTAAAAATTCGCTTTCTCTCTC 5 60 1 AAAAATTCGC 0.929416 -161 AAAATCCCCAAAAAATCCCCAAAAAAGGGT 5 160 0 AAAAATCCCC 0.905694 -61 AATAAGACGCAAAAATCCCCAAAAAATCCC 5 171 0 AAAAATCCCC 0.905694 -50 CTAAAATCTAAATAAGACGCAAAAATCCCC 5 181 0 AATAAGACGC 0.760836 -40 GTGGAATGCTATAAATACGCCGCTTCTTCG 6 36 1 ATAAATACGC 0.929416 -250 GAGCGGGCGTAAAGATACGCTAAATTCAAG 6 92 1 AAAGATACGC 0.938738 -194 AATTCTAAGTAAAAACATGCTATAACACAA 6 248 1 AAAAACATGC 0.663894 -38 TTACCCCCAAACAAAAACGCCAGACTTTGC 7 22 0 ACAAAAACGC 0.92932 -28 ATAATTTTGAAAAAATACGCAACAATTAAA 9 77 0 AAAAATACGC 0.986573 -54 ********** Masking position 5 Map Score: 8.6757 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 495 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 ********** No masking Map Score: -4.59421e-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 11 ********** No masking Map Score: -4.59421e-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 12 ********** No masking Map Score: -4.59421e-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