AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_hpyl_reg_100.orf -o00252_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 HP0031 108 H. pylori predicted coding region HP0031 #2 HP0032 30 conserved hypothetical protein #3 HP0252 300 outer membrane protein (omp7) #4 HP0255 99 adenylosuccinate synthetase (purA) #5 HP0616 77 chemotaxis protein (cheV) #6 HP0617 34 aspartyl-tRNA synthetase (aspS) #7 HP0643 164 glutamyl-tRNA synthetase (gltX) #8 HP0649 57 aspartate ammonia-lyase (aspA) #9 HP0723 128 L-asparaginase II (ansB) #10 HP0942 40 D-alanine glycine permease (dagA) #11 HP0943 21 D-amino acid dehydrogenase (dadA) #12 HP0944 300 translation initiation inhibitor, putative #13 HP1084 66 aspartate transcarbamoylase (pyrB) #14 HP1112 109 adenylosuccinate lyase (purB) #15 HP1241 119 alanyl-tRNA synthetase (alaS) Motif number 1 GAACCAACCTTAAATGAAGTTTTGGTATTATA 1 85 0 TAAAGAATTT 0.804699 -24 TACTAGCAAGAAAACGGGTTTGATCCATAAAG 3 25 1 AAAAGGGTTG 0.916194 -276 TATCAAAGCAAAAAGGATATTT 3 289 1 AAAAGATTTT 0.822656 -12 TTAGGGCTTATAAAGAGGCTTTTTACTTTTTT 4 18 1 TAAAAGGTTT 0.931315 -82 TAATTTAGTTTAAAAGGTTTTTACAAAC 5 7 0 TAAAGGTTTT 0.972307 -71 TTGTTTTAATTTAAAGGGATAAAAC 6 20 1 TTAAGGGTAA 0.607375 -15 CCTTTATTTAAAAATAGTTTTTGATTATACCT 7 137 0 AAAAAGTTTT 0.620541 -28 TATTTTTAAATAAAGGGTTTTT 7 153 1 TAAAGGTTTT 0.972693 -12 CAATTATTACATAAGGAGCTTTT 8 45 1 ATAAGAGTTT 0.845849 -13 AAAATAAATTTAAAAAGGGTTA 9 1 0 TAAAAGGTTA 0.733447 -128 TAAATTTATTTTAACGATGTTTTACTATACTA 9 21 1 TTAAGATTTT 0.796067 -108 CTTTTGAAATTAAAAGATTTTATAGTATAGTA 9 43 0 TAAAGATTTA 0.694805 -86 CCCTAGTTTATTAAGGAGTTTTT 10 28 1 TTAAGAGTTT 0.930133 -13 TTTATTAAAGGGACTATCAGC 11 6 1 TAAAGGATAT 0.702301 -16 TAAGCCATAATAAAAGGGCTTGCAAGCGAGTG 12 82 1 TAAAGGGTTG 0.963813 -219 TAGAAATTCTTAAACGGGTTTTGTTTGAGTTT 12 145 0 TAAAGGGTTT 0.990435 -156 TATTATAACTAAAAGGGGGTTTT 13 54 1 AAAAGGGTTT 0.980432 -13 TTTAATTAAATCAAGGGGCTTTTTTGCGCCTT 14 14 1 TCAAGGGTTT 0.939091 -96 TTATGTTACTTTAAAGGGGTTTAAAGAATCAA 14 61 0 TTAAGGGTTT 0.976833 -49 CCTTAAAATCAAAATGGGATTTATGTTACTTT 14 81 0 AAAAGGGTTT 0.980423 -29 AAAAATAACTTAAAAGAGCTATAAAATAGCCT 15 63 1 TAAAGAGTAT 0.874042 -57 **** *** *** Masking position 10 Map Score: 30.1923 Number of sites scoring better than the average of aligned sites = 1893 Number in coding regions = 1589 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 TAACATTTTGCTTAAAAGATGTCAATTTGA 3 175 1 CTTAAAAGAT 0.53121 -126 CTTAATAGCAAATTAAGAATGATTATCTTA 3 220 1 AATTAAGAAT 0.341622 -81 TTTTAGGGCTTATAAAGAGGCTTTTTACTT 4 16 1 TATAAAGAGG 0.8078 -84 ATCTACTTTGTTTTAAGGATAATATTTT 4 82 1 TTTTAAGGAT 0.73542 -18 CCTAATTTAGTTTAAAAGGTTTTTACAAAC 5 11 0 TTTAAAAGGT 0.86448 -67 CCTAAAGCCCTATCAAAGATTAAATGCTAT 5 49 0 TATCAAAGAT 0.697894 -29 TTTTGTTTTAATTTAAAGGGATAAAAC 6 18 1 ATTTAAAGGG 0.901701 -17 TATGGTTGGTTATCAAAAAGCTAACAGCGT 7 13 0 TATCAAAAAG 0.62652 -152 ACTATTTTTAAATAAAGGGTTTTT 7 151 1 AATAAAGGGT 0.832744 -14 TTAAAATAAATTTAAAAAGGGTTA 9 5 0 TTTAAAAAGG 0.822451 -124 ACCTTTTGAAATTAAAAGATTTTATAGTAT 9 47 0 ATTAAAAGAT 0.796079 -82 GAATCAACAATTTCAAAAATATTCTCATTA 9 83 0 TTTCAAAAAT 0.403851 -46 TTTTATTTTGTTTGAAGGGGCAGGTT 9 113 1 TTTGAAGGGG 0.72435 -16 TAAACTAGGGTTTAAAAAAGAAATTCC 10 8 0 TTTAAAAAAG 0.767195 -33 AACCCTAGTTTATTAAGGAGTTTTT 10 26 1 TATTAAGGAG 0.873145 -15 TTTATTAAAGGGACTATCAGC 11 3 1 TATTAAAGGG 0.901701 -19 ACTCATTGCCACTAAAAGAGGGCAAAGCCG 12 19 0 ACTAAAAGAG 0.737257 -282 AATAAGCCATAATAAAAGGGCTTGCAAGCG 12 80 1 AATAAAAGGG 0.931453 -221 TTAATAAAGAAATAAAAAATGAGCGCAAAA 12 229 0 AATAAAAAAT 0.45863 -72 CTATATTATAACTAAAAGGGGGTTTT 13 51 1 ACTAAAAGGG 0.797745 -16 CCCTTGATTTAATTAAAGGG 14 1 0 AATTAAAGGG 0.887527 -109 CCTTTAATTAAATCAAGGGGCTTTTTTGCG 14 12 1 AATCAAGGGG 0.894526 -98 GGGTTTAAAGAATCAAGGGGAAAAATCGCA 14 47 0 AATCAAGGGG 0.894526 -63 TTTATGTTACTTTAAAGGGGTTTAAAGAAT 14 64 0 TTTAAAGGGG 0.950902 -46 CCCATTTTGATTTTAAGGATTGTCG 14 95 1 TTTTAAGGAT 0.73542 -15 AACATCCAAAATTAAAGGAGAAAACC 15 7 0 ATTAAAGGAG 0.922195 -113 TAAGTTATTTTTTTAAAAAGATAGTTTATT 15 45 0 TTTTAAAAAG 0.656794 -75 AAAAAAATAACTTAAAAGAGCTATAAAATA 15 61 1 CTTAAAAGAG 0.765363 -59 ********** Masking position 5 Map Score: 25.3197 Number of sites scoring better than the average of aligned sites = 2993 Number in coding regions = 2554 Number in noncoding regions = 439 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 3 TCAGCGGGTCATTAGGGTTTATTTGGTATAATA 1 59 1 ATTAGGGTTT 0.970997 -50 TTAAATGAAGTTTTGGTATTATACCAAATAAAC 1 75 0 TTTTGGTTTA 0.474961 -34 CAAAACTTCATTTAAGGTTGGTTCTT 1 93 1 TTTAAGGTTT 0.961006 -16 TTATCCATGCTATTTGGCTACTTGG 2 3 0 TATTTGGTTT 0.536121 -28 TTAATTATGGGTAATACTAGCAAGAA 3 4 1 ATTATGGTTA 0.904416 -297 AAAGAAAGAGAATAAGCGTAATAATGGTGGAGT 3 53 1 AATAAGCTTA 0.467308 -248 GCTTAATTTTATTTGGGGTGTTAGCTCAGCTGG 3 134 0 ATTTGGGTTA 0.889956 -167 TTAATAGCAAATTAAGAATGATTATCTTAAAAT 3 221 1 ATTAAGATTT 0.608665 -80 GCTCTTTTTAGGGCTTATAAAGAGGCTTT 4 7 1 TTTAGGGTTA 0.945823 -93 TTTACTTTTTTTTTGGTATTCTAACAAGCTTTT 4 39 1 TTTTGGTTTA 0.474961 -61 TCTACTTTGTTTTAAGGATAATATTTT 4 83 1 TTTAAGGTTA 0.938943 -17 TTTTAAACTAAATTAGGGTAGTATTATAGCATT 5 24 1 AATTAGGTTA 0.625862 -54 CGCCAAGCTTTTTATGGTTGGTTATCAAAAAGC 7 22 0 TTTATGGTTT 0.92697 -143 ATCAAACATGAATAGGCATCATTTAAGAGATTA 7 67 0 AATAGGCTTT 0.623358 -98 CCACAACACAATTAAGTATTCTTTAGGTATAAT 7 113 1 ATTAAGTTTT 0.797158 -52 CTATTTTTAAATAAAGGGTTTTT 7 152 1 ATAAAGGTTT 0.643982 -13 ACCCTAGTTTATTAAGGAGTTTTT 10 27 1 ATTAAGGGTT 0.728335 -14 AAGCCCTTTTATTATGGCTTATTATAGAAAATG 12 70 0 ATTATGGTTT 0.937825 -231 TTGTTTGAGTTTTAGGCTTTGTTGTCATCAATT 12 124 0 TTTAGGCTTT 0.85484 -177 CCATTTTGATTTTAAGGATTGTCG 14 96 1 TTTAAGGTTC 0.782374 -14 TTCTCCTTTAATTTTGGATGTTTAAAGTATAAT 15 15 1 ATTTTGGTTT 0.854296 -105 TATCGCGTATTTTAAGGCTATTTTATAGCTCTT 15 76 0 TTTAAGGTTT 0.960718 -44 ******* * ** Masking position 12 Map Score: 18.255 Number of sites scoring better than the average of aligned sites = 1490 Number in coding regions = 1295 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 TTATACCAAATAAACCCTAATGACCCGCTGA 1 59 0 TAACCCTAAT 0.969388 -50 CTTGCTAGTATTACCCATAATTAA 3 4 0 TTACCATAAT 0.959346 -297 AAAACGGGTTTGATCCATAAAGAAAGAGAAT 3 35 1 TGACCATAAA 0.940755 -266 TGATTTTACTTAATCCATAAAAGAAACTTTC 3 256 0 TAACCATAAA 0.959346 -45 AGCCTCTTTATAAGCCCTAAAAAGAGC 4 7 0 TAACCCTAAA 0.969388 -93 AAAATATTATCCTTAAAACAAAGTAGA 4 83 0 TTACCTTAAA 0.83048 -17 CTATTTTCCCCTAAAGCCCTATCAA 5 63 0 TTTCCCTAAA 0.800943 -15 TAGTTTTTGATTATACCTAAAGAATACTTAA 7 124 0 TTAACCTAAA 0.694395 -41 TTTCAAAAGGTGGTCCATAATGAGAATATTT 9 66 1 TGGCCATAAT 0.749395 -63 ATTTCTTTTTTAAACCCTAGTTTATTAAGGA 10 14 1 TAACCCTAGT 0.856396 -27 TTTTCTATAATAAGCCATAATAAAAGGGCTT 12 72 1 TAACCATAAT 0.959346 -229 TGTATATTTTTTACCCATATTTAGAAATTCT 12 167 0 TTACCATATT 0.749896 -134 *** ******* Masking position 9 Map Score: 10.1363 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 357 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TCGCTTAGAAAAAGGACACAAA 1 3 0 AAAGGACACA 0.786616 -106 TGACCCGCTGAAAGCTCAAAGATAAAGCGC 1 40 0 AAAGCTCAAA 0.967051 -69 GCGTTTCAAAAAAGCATCAAATTGACATCT 3 191 0 AAAGCATCAA 0.747748 -110 ATCACTTATCAAAGCAAAAAGGATATTT 3 283 1 AAAGCAAAAA 0.957978 -18 ATACCAAAAAAAAAGTAAAAAGCCTCTTTA 4 28 0 AAAAGTAAAA 0.703426 -72 CCTTTAAATTAAAACAAAAATTAAAT 6 7 0 AAAACAAAAA 0.893341 -28 TGGTTATCAAAAAGCTAACAGCGTTT 7 7 0 AAAGCTAACA 0.944343 -158 TGTCTGTAAAAATGCTCAAAAGCATTTTCT 12 48 1 AATGCTCAAA 0.78855 -253 CATCAATTTTAAAGCTACCACTCGCTTGCA 12 102 0 AAAGCTACCA 0.913993 -199 AACAAAGCCTAAAACTCAAACAAAACCCGT 12 134 1 AAAACTCAAA 0.915134 -167 AATACGCGATAAAACAACAAAAAGGAATAC 15 98 1 AAAACAACAA 0.839895 -22 ********** Masking position 2 Map Score: 6.38838 Number of sites scoring better than the average of aligned sites = 877 Number in coding regions = 741 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 GCTAACACCCCAAATAAAATTAAGCGAGCA 3 142 1 CAAATAAAAT 0.739939 -159 TGGATTAAGTAAAATCACTTATCAAAGCAA 3 270 1 AAAATCACTT 0.650415 -31 AAAACCTTTTAAACTAAATTAGGGTAGTAT 5 18 1 AAACTAAATT 0.726133 -60 AATTAAAACAAAAATTAAAT 6 1 0 AAAATTAAAT 0.807687 -34 AAACATCGTTAAAATAAATTTAAAAAGGGT 9 13 0 AAAATAAATT 0.927072 -116 CCCTTCAAACAAAATAAAAGAATCAACAAT 9 102 0 AAAATAAAAG 0.852912 -27 TAGGGTTTAAAAAAGAAATTCC 10 3 0 AAAAGAAATT 0.70539 -38 ATTTTTAGCTAAAATAAAATCTATATTATA 13 31 1 AAAATAAAAT 0.937921 -36 AAACCCCTTTAAAGTAACATAAATCCCATT 14 71 1 AAAGTAACAT 0.663691 -39 TTAAACATCCAAAATTAAAGGAGAAAACC 15 10 0 AAAATTAAAG 0.617137 -110 TCTTTTTAAAAAAATAACTTAAAAGAGCTA 15 54 1 AAAATAACTT 0.888422 -66 ********** Masking position 7 Map Score: 3.63687 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 304 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 TCAAAGATAAAGCGCTACAATCTCGCTTAG 1 25 0 AGCGCTACAA 0.857339 -84 ACCCGCTGAAAGCTCAAAGATAAAGCGCTA 1 38 0 AGCTCAAAGA 0.90146 -71 CGAACCCCTGACCTCAACGCTGCCAGCGTT 3 96 1 ACCTCAACGC 0.929245 -205 CAGCTGGGAGAGCGCAACGCTGGCAGCGTT 3 111 0 AGCGCAACGC 0.992705 -190 AAACAGAACTACCACAACACAATTAAGTAT 7 102 1 ACCACAACAC 0.824426 -63 CCACTAAAAGAGGGCAAAGCCGCAATCTGT 12 11 0 AGGGCAAAGC 0.934207 -290 ATAAAAAATGAGCGCAAAACGCCATGAATT 12 218 0 AGCGCAAAAC 0.981847 -83 AATCGCACAAGGCGCAAAAAAGCCCCTTGA 14 24 0 GGCGCAAAAA 0.84884 -86 ********** Masking position 7 Map Score: 2.82484 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 350 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GCCGCTTATCCATGCTATTTGGCTACTTGG 2 11 0 CCATGCATTT 0.987592 -20 TTGGCTAACGCCAAGCTTTTTATGGTTGGTT 7 32 0 CCAAGCTTTT 0.969237 -133 GCGCAAAACGCCATGAATTTTCATCTTATTA 12 206 0 CCATGATTTT 0.952464 -95 TTGCTAAAACCCATGCCATTTTTAGCTAAAA 13 14 1 CCATGCATTT 0.987545 -53 ****** **** Masking position 3 Map Score: 0.43297 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 69 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TTTAAAAGCTTGTTAGAATACCAAAAAAAA 4 45 0 TGTTAGAATA 0.802449 -55 AAAATATTATCCTTAAAACAAAGTAGATTG 4 80 0 CCTTAAAACA 0.758081 -20 AAAGATTAAATGCTATAATACTACCCTAAT 5 35 0 TGCTATAATA 0.728397 -43 TGGTTACAATAGCTAGAATATTTTTCAATT 8 20 1 AGCTAGAATA 0.80618 -38 AGTAAAACATCGTTAAAATAAATTTAAAAA 9 17 0 CGTTAAAATA 0.956892 -112 ATATACAATACCTTATAATAAGATGAAAAT 12 191 1 CCTTATAATA 0.903464 -110 TGCCATTTTTAGCTAAAATAAAATCTATAT 13 27 1 AGCTAAAATA 0.860748 -40 ACCCCCTTTTAGTTATAATATAGATTTTAT 13 44 0 AGTTATAATA 0.843356 -23 CGACAATCCTTAAAATCAAAATGGGAT 14 93 0 CCTTAAAATC 0.758176 -17 TATAAAATAGCCTTAAAATACGCGATAAAA 15 82 1 CCTTAAAATA 0.937628 -38 ********** Masking position 5 Map Score: 3.74107 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 180 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 ********** No masking Map Score: 9.97192e-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: 9.97192e-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: 9.97192e-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