AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_hpyl_reg_100.orf -o00670_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 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #3 HP0584 81 flagellar switch protein (fliN) #4 HP0585 228 endonuclease III (nth) #5 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #6 HP1141 23 methionyl-tRNA formyltransferase (fmt) #7 HP1142 39 H. pylori predicted coding region HP1142 #8 HP1143 243 H. pylori predicted coding region HP1143 #9 HP1435 70 protease IV (PspA) Motif number 1 TAAAATTCTTAAATTAAAATATAGCTATAATACACTAAAA 1 37 0 AAAAATAAAA 0.910696 -221 ACAACTTAAAAAAAACTACCCTTAAAAAAATCAATCTAAA 1 73 0 AAAACTTAAA 0.984364 -185 ATTGTAGCAAAAATCATGCGTTTAATGGAATAAAAACCTA 2 16 0 AAAGCTTGAA 0.923763 -58 TATATAATTAAAATCCTATTATTGTAGCAAAAATCATGCG 2 36 0 AAAATTTGAA 0.919275 -38 TTTGATTATAAAATCTTAATTTTACTATAAATTTTATAAC 3 22 0 AAAAATTAAA 0.98169 -60 AAAACTCTACTCTTTCAAGAATGATTTGACT 3 61 0 AAAACTTAAA 0.984364 -21 TGAAGCCATTAAAGACAAAGTTTATGAAATCGTAGAAATC 4 23 1 AAAAATTAAT 0.842489 -206 ATTCCATGAAAAAAGCCACGCTTTCGGTTAAAATCAACCG 4 142 1 AAAACTTGTA 0.804247 -87 AGTTGTCCCAAAAGCACAAGTTTTAGAGAACCATACG 8 8 0 AAAAATTAAA 0.981932 -236 TAAATAAAAAAAATGAAGAAATTGAGATAACGATCGATCA 8 54 0 AAAGATTAAA 0.940382 -190 CTTCGCATAAAAACTACATTATAAATAAAAAAAATGAAGA 8 75 0 AAAATTAAAA 0.763189 -169 TAAAAAAGGCAAAAAATACCCTTCGCATAAAAACTACATT 8 95 0 AAAACTTAAA 0.984364 -149 TAAAATATAAAAAATCAAATCTTAAAGGAAAATC 8 220 1 AAAAATTGAA 0.973 -24 TCTTATGGTCAAATATTAAGTTTAGGAAAAGCTGC 9 46 1 AAAAATTAAA 0.981927 -25 *** ** ** * ** Masking position 3 Map Score: 19.7718 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 253 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 CTTGAGATTGTTTTAGTGTATTATAGCTATAT 1 27 1 TTTATGTATT 0.79762 -231 AGACTTGAAATTTGAAAATAATAACACAACTT 1 106 0 TTTAAATAAT 0.87872 -152 ATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 1 119 1 TTCATCTAAA 0.716952 -139 ATTGGCATGATTTAAGAGTAATGGGTGTTTGT 1 149 1 TTTAAGTAAT 0.678804 -109 GGTTTAGGGTTTGAATTATATTGATTTAGCGT 1 231 1 TTGATATATT 0.784719 -27 CAAACTAGGTTTTTATTCCATTAAACGCATGA 2 11 1 TTTATCCATT 0.797941 -63 AACGCATGATTTTTGCTACAATAATAGGATTT 2 34 1 TTTGTACAAT 0.733041 -40 ATAATAGGATTTTAATTATATAAAGGACAA 2 54 1 TTTATATATA 0.90572 -20 TTACTATAAATTTTATAACAAATAAAGCCA 3 9 0 TTTAAACAAA 0.780054 -73 AAAATCTTAATTTTACTATAAATTTTATAACA 3 21 0 TTTATATAAA 0.95709 -61 ATGATTTGACTTTGATTATAAAATCTTAATTT 3 40 0 TTTATATAAA 0.949904 -42 ATTTTAATTATTTTAGTATAATTGAAAGAAAC 5 43 0 TTTATATAAT 0.969209 -106 TGGGTAAAAATTTTACTCCATTTTAACCGGTC 5 75 0 TTTATCCATT 0.797941 -74 CTTCATTTTTTTTATTTATAATGTAGTTTTTA 8 76 1 TTTTTATAAT 0.723581 -168 AAATAGGGATTTTAAATACAAACAACAAAAAA 8 135 0 TTTATACAAA 0.897776 -109 ATTGATCTCATTCTATTATAAAATATAAAAAA 8 202 1 TTCATATAAA 0.856964 -42 CTTAAAACATTTGAAGTATAATACACTCTTAT 9 20 1 TTGATATAAT 0.894183 -51 *** * ****** Masking position 10 Map Score: 12.639 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 306 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 3 TTAGATTGATTTTTTTAAGGGTAGTTTTTT 1 74 1 TTTTTTAAGG 0.961148 -184 AAGGGTAGTTTTTTTTAAGTTGTGTTATTA 1 90 1 TTTTTTAAGT 0.792856 -168 TGAATTGGCATGATTTAAGAGTAATGGGTG 1 146 1 TGATTTAAGA 0.885573 -112 AATGGGTGTTTGTTTTAAGACGCTATGACT 1 168 1 TGTTTTAAGA 0.977182 -90 AAAACTCTACTCTTTCAAGAATGATTTGAC 3 62 0 TCTTTCAAGA 0.884063 -20 AGAGAAAGCGTTTTTTAAGGGCTTCATCGC 4 70 0 TTTTTTAAGG 0.961148 -159 AAGCGTGGCTTTTTTCATGGAATAATGCAA 4 135 0 TTTTTCATGG 0.756045 -94 GCATTCAAGTGGCTTTAAGATCCCATGAAG 4 181 1 GGCTTTAAGA 0.873992 -48 CAAGGTATTGTGCTTCATGGGATCTTAAAG 4 193 0 TGCTTCATGG 0.871655 -36 TTTTGTGGTGTGCTTTGAGATGATATTGTG 7 12 1 TGCTTTGAGA 0.873992 -28 GATTTTCCTTTAAGATTTGATTTTT 8 229 0 TCCTTTAAGA 0.934257 -15 ATACTTCAAATGTTTTAAGGATTAAATC 9 9 0 TGTTTTAAGG 0.983039 -62 ********** Masking position 5 Map Score: 11.6896 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 467 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 CCTAAACCCAAACCTTTCTCTCATATATCTC 1 208 0 AACCTTTCTT 0.916272 -50 CCCTTAAAAAACGCTTTCTCTCTTTTGGTAT 4 79 1 ACGCTTTCTT 0.99351 -150 AAGGGGTTCAATGCATTCTTTTGCATTATTC 4 115 1 ATGCATTCTT 0.921329 -114 GAAAAAAGCCACGCTTTCGGTTAAAATCAAC 4 149 1 ACGCTTTCGT 0.985703 -80 ACGCTTTCTTTGATGACAAGG 4 218 0 ACGCTTTCTT 0.99351 -11 ********* * Masking position 6 Map Score: 2.92155 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 54 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GTCTAAAGAGTGTGAATTGGCATGATTTAA 1 134 1 TGTGAATTGG 0.800474 -124 GGGTTTAGGGTTTGAATTATATTGATTTAG 1 230 1 TTTGAATTAT 0.980569 -28 AATAATAGGATTTTAATTATATAAAGGACA 2 53 1 TTTTAATTAT 0.942986 -21 AATGCATTCTTTTGCATTATTCCATGAAAA 4 124 1 TTTGCATTAT 0.913228 -105 CGCCAAATCCCTTGAATTGTTTGTTAAAAG 5 14 1 CTTGAATTGT 0.819015 -135 TAAAAGTTTCTTTCAATTATACTAAAATAA 5 38 1 TTTCAATTAT 0.906557 -111 TAACCGGTCATTTTAATTATTTTAGTATAA 5 54 0 TTTTAATTAT 0.942986 -95 GAGATGATATTGTGAATTAGGA 7 28 1 TGTGAATTAG 0.903198 -12 TCTTCATTTTTTTTATTTATAATGTAGTTT 8 75 1 TTTTATTTAT 0.699452 -169 CCTTAAAACATTTGAAGTATAATACACTCT 9 19 1 TTTGAAGTAT 0.913228 -52 ********** Masking position 3 Map Score: 7.19437 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 204 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 CTTTGTCTTTAATGGCTTCATTGAGCGTCA 4 13 0 AATGGCTTCA 0.97974 -216 AGCGTTTTTTAAGGGCTTCATCGCAGTTAG 4 64 0 AAGGGCTTCA 0.981204 -165 GGTATCCATGAAGGGGTTCAATGCATTCTT 4 105 1 AAGGGGTTCA 0.98702 -124 GGTTTTATCCAATAAGTTCAGTAAAATAGG 8 160 0 AATAAGTTCA 0.856956 -84 TTTATAATAGAATGAGATCAATTTAACTTA 8 194 0 AATGAGATCA 0.904783 -50 ********** Masking position 8 Map Score: 1.9049 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 69 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 CTCATATATCTCGCATAAAGATAGTCATAG 1 190 0 TCGCATAAAG 0.911543 -68 AGCCACGCTTTCGGTTAAAATCAACCGCAT 4 155 1 TCGGTTAAAA 0.981792 -74 CCTTGAATTGTTTGTTAAAAGTTTCTTTCA 5 23 1 TTTGTTAAAA 0.737912 -126 ATTAAAATGACCGGTTAAAATGGAGTAAAA 5 67 1 CCGGTTAAAA 0.951731 -82 AAAATACCCTTCGCATAAAAACTACATTAT 8 93 0 TCGCATAAAA 0.965721 -151 ACTGAACTTATTGGATAAAACCTGCTTAAG 8 168 1 TTGGATAAAA 0.947681 -76 ********** Masking position 6 Map Score: 1.80894 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 250 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TATTTTAATTTAAGAATTTTAGATTGATTTTT 1 56 1 TAAATTTTAG 0.967481 -202 TTAATTTTACTATAAATTTTATAACAAATAAA 3 15 0 TAAATTTTAT 0.882208 -67 GATTATAAAATCTTAATTTTACTATAAATTTT 3 27 0 TCAATTTTAC 0.952437 -55 CCGGTCATTTTAATTATTTTAGTATAATTGAA 5 49 0 TATATTTTAG 0.928294 -100 TTAGGGTGGGTAAAAATTTTACTCCATTTTAA 5 81 0 TAAATTTTAC 0.967309 -68 GTATTTAAAATCCCTATTTTACTGAACTTATT 8 148 1 TCTATTTTAC 0.897028 -96 TATGGTCAAATATTAAGTTTAGGAAAAGCTGC 9 49 1 TAAAGTTTAG 0.901543 -22 ** ******** Masking position 6 Map Score: 3.12161 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 46 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TGAAACCTTGAGATTGTTTTAGTGTATTAT 1 21 1 AGATTGTTTT 0.887194 -237 TAAGAATTTTAGATTGATTTTTTTAAGGGT 1 66 1 AGATTGATTT 0.955516 -192 AGTGTGAATTGGCATGATTTAAGAGTAATG 1 142 1 GGCATGATTT 0.943901 -116 GGTTTGAATTATATTGATTTAGCGTTACTT 1 238 1 ATATTGATTT 0.705847 -20 TTCCATTAAACGCATGATTTTTGCTACAAT 2 26 1 CGCATGATTT 0.943901 -48 TACTCTTTCAAGAATGATTTGACTTTGATT 3 55 0 AGAATGATTT 0.971803 -27 GTGGCATTGTAGCATGACTTTATTAGGGTG 5 105 0 AGCATGACTT 0.935583 -44 ATTTAACTTAAGCAGGTTTTATCCAATAAG 8 174 0 AGCAGGTTTT 0.841696 -70 ********** Masking position 9 Map Score: 5.40984 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 461 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 ********** No masking Map Score: -1.40444e-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 11 ********** No masking Map Score: -1.40444e-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: -1.40444e-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