AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_hpyl_reg_100.orf -o00340_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 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP1054 63 H. pylori predicted coding region HP1054 #4 HP1057 148 H. pylori predicted coding region HP1057 #5 HP1067 290 chemotaxis protein (cheY) #6 HP1190 61 histidyl-tRNA synthetase (hisS) Motif number 1 AATTATATTGATTTAGCGTTACTT 1 1 0 ATTTAGTATT 0.926774 -257 AATTGGCATGATTTAAGAGTAATGGGTGTTTGTT 1 97 0 ATTTAAGATG 0.661897 -161 GGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 1 153 0 TTTTAATTTT 0.924067 -105 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGT 1 169 0 TTTTAAGATT 0.967537 -89 AATTTAAGAATTTTAGATTGATTTTTTTAAGGGT 1 183 0 TTTTAGTATT 0.978273 -75 CTTGAGATTGTTTTAGTGTATTATAGCTATATTT 1 218 0 TTTTAGTTAT 0.908436 -40 AATTTTGAGTTTTTAGGAGCAGTTTTT 2 4 0 TTTTAGGATT 0.984958 -211 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 2 23 0 TTTTAGTATT 0.978273 -192 TTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 2 95 0 ATTTAGTTTT 0.882724 -120 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATT 2 116 0 TTTGAAGATT 0.759641 -99 AATTTACATTTTTTAAACGCTATTAGATATAATA 2 155 1 TTTTAAGTTT 0.94652 -60 AGGTTTAAAATTTTAGCGTTAGTCGTTTTAATTT 3 29 1 TTTTAGTATC 0.913106 -35 GTCGTTTTAATTTTAGGGGGTTAT 3 50 1 TTTTAGGTAT 0.935186 -14 TATAGTGGCATTGTAGCATGACTTTATTAGGGTG 4 31 1 TTGTAGTATT 0.826822 -118 TTTTACTCCATTTTAACCGGTCATTTTAATTATT 4 73 1 TTTTAAGTAT 0.867855 -76 ATTTTAATTATTTTAGTATAATTGAAAGAAACTT 4 95 1 TTTTAGTATG 0.913106 -54 ATTTTATTACTTTTAAACGATTATCATAGCAAAC 5 79 1 TTTTAAGTAT 0.867855 -212 AAAGAGCCTAATTTAAATGCAATCTTAAAAGGAG 5 260 1 ATTTAAGATC 0.661957 -31 TATGCTAAAATTTTAGCTTAAAATCTTTAAAAAA 6 20 0 TTTTAGTAAT 0.943507 -42 ****** * * ** Masking position 2 Map Score: 24.786 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1164 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 AGAAAGGTTTGGGTTTAGGGTTTGAATTATATTGAT 1 23 0 GGTTGGTTAA 0.965102 -235 TTAAGAGTAATGGGTGTTTGTTTTAAGACGCTATGA 1 83 0 TGGTTGTTAA 0.845994 -175 TTTTTAAGTTGTGTTATTATTTTCAAATTTCAAGTC 1 142 0 GGTTTTTTAA 0.991245 -116 ATTTTTTTAAGGGTAGTTTTTTTTAAGTTGTGTTAT 1 161 0 GGTATTTTAA 0.912035 -97 TAAGAATTTTAGATTGATTTTTTTAAGGGTAGTTTT 1 177 0 AATTTTTTAA 0.723672 -81 TTTCTCAATTTAGGTTTTGTTTATAAGAAAAATTAT 2 90 0 TGGTTTTTAA 0.857945 -125 CAATTCAAAGGGGCTATTGTTTAAAATTTACATTTT 2 131 1 GGCTTTTTAA 0.984452 -84 CTTGATCTTGGAGTTAAGGTTTAAAATTTTAGCGTT 3 13 1 GGTTGTTTAA 0.968158 -51 TAAAATTTTAGCGTTAGTCGTTTTAATTTTAGGGGG 3 34 1 GGTTTGTTAA 0.990386 -30 CAAATCCCTTGAATTGTTTGTTAAAAGTTTCTTTCA 4 117 0 GATTTGTTAA 0.922867 -32 TAAAATCCTTGTCTTTCTTTTTTCAAACCATCCAAT 5 18 1 GCTTTTTTAA 0.917057 -273 TTTGTTTGCTATGATAATCGTTTAAAAGTAATAAAA 5 80 0 AGATTGTTAA 0.742652 -211 CGTTCAATGAGCGTTCTTATTTGTAAAAAAATTCAG 5 116 0 GGTTTTTTAA 0.991248 -175 TAATCAAAACATGCTATTATTTGGAACGATTTATTA 5 191 1 AGCTTTTTAA 0.9265 -100 AGTGCTTCTCCTTTTAAGATTGCATTT 5 274 0 GGCTTCTTAA 0.9296 -17 * *** * *** ** Masking position 15 Map Score: 18.2791 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 391 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 ATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTT 1 168 0 TTAAGAGTTT 0.789735 -90 TTTAAGAATTTTAGATTGATTTTTTTAAGGGTA 1 182 0 TTAGAATTTT 0.875241 -76 TTAGTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 ATAGCATTTT 0.869547 -51 TTTTGAGTTTTTAGGAGCAGTTTTT 2 3 0 TTAGGAGTTT 0.982766 -212 TCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 22 0 TTAGGATTTT 0.972698 -193 GTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAG 2 50 0 TAAGGTGTTT 0.944032 -165 TTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 TTAGGTGTTT 0.973289 -121 TTAGATATAATAAGGGATAGTTACCACCTATAA 2 177 1 TAAGGAGTTA 0.737482 -38 TATCGCACTCAAAGAGTTATTTTATTACTTTTA 5 61 1 AAAGAATTTT 0.510303 -230 AACGCTCCATTTAGCCAATGATTATTGTCGGTC 5 148 1 TTAGCTGATT 0.693221 -143 TGCATTTAAATTAGGCTCTTTTTAAACAGCCAA 5 248 0 TTAGGTTTTT 0.957922 -43 CAATAGCCCTTTTTTAAAGATTTTA 6 3 1 ATAGCTTTTT 0.809856 -59 TTAAAGATTTTAAGCTAAAATTTTAGCATACAA 6 24 1 TAAGCAATTT 0.666159 -38 ***** ***** Masking position 3 Map Score: 8.13817 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 736 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 TTTAAGTTGTGTTATTATTTTCAAATTTCA 1 146 0 GTTATTATTT 0.932828 -112 TTTAAGGGTAGTTTTTTTTAAGTTGTGTTA 1 162 0 GTTTTTTTTA 0.398499 -96 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.934394 -51 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.80651 -11 ATTCAAAGGGGCTATTGTTTAAAATTTACA 2 133 1 GCTATTGTTT 0.900488 -82 AACGACTAACGCTAAAATTTTAAACCTTAA 3 26 0 GCTAAAATTT 0.782515 -38 AATCCTTGTCTTTCTTTTTTCAAACCATCC 5 21 1 TTTCTTTTTT 0.578427 -270 CACTCAAAGAGTTATTTTATTACTTTTAAA 5 66 1 GTTATTTTAT 0.612917 -225 TTCAATGAGCGTTCTTATTTGTAAAAAAAT 5 120 0 GTTCTTATTT 0.910693 -171 ATCAAAACATGCTATTATTTGGAACGATTT 5 193 1 GCTATTATTT 0.967115 -98 TTTGGAACGATTTATTATTATAAGGCGTTA 5 210 1 TTTATTATTA 0.320672 -81 TTTAAATTAGGCTCTTTTTAAACAGCCAAA 5 247 0 GCTCTTTTTA 0.87983 -44 CAATAGCCCTTTTTTAAAGATTTTA 6 6 1 GCCCTTTTTT 0.784916 -56 GTATTTGTATGCTAAAATTTTAGCTTAAAA 6 31 0 GCTAAAATTT 0.782515 -31 ********** Masking position 8 Map Score: 6.86185 Number of sites scoring better than the average of aligned sites = 1781 Number in coding regions = 1531 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 5 TAAATTGAGAAAAAATTCAATTCAAAGGGGCT 2 114 1 AAAAATCAAT 0.965532 -101 ATAGCGTTTAAAAAATGTAAATTTTAAACAAT 2 146 0 AAAAATTAAT 0.795588 -69 TAAAAATCCTAAGTGTTAAATAT 4 2 1 AAAAATCTAG 0.95877 -147 TAGGGTGGGTAAAAATTTTACTCCATTTTAAC 4 58 1 AAAAATTTAT 0.668718 -91 ACTTTTAACAAACAATTCAAGGGATTTGGCGA 4 125 1 AACAATCAAG 0.939536 -24 GTTTGAAAAAAGAAAGACAAGGATTTTACAAG 5 14 0 AGAAAGCAAG 0.825184 -277 TCTTTTTTCAAACCATCCAATGACCCTTTATC 5 33 1 AACCATCAAG 0.906823 -258 TTATTTGTAAAAAAATTCAGTTTGTTTGCTAT 5 104 0 AAAAATCAGT 0.82785 -187 ATTTTAATCAAAACATGCTATTATTTGGAACG 5 187 1 AAACATCTAT 0.900987 -104 GGCTCTTTTTAAACAGCCAAAGCGTCTCTAAC 5 236 0 AAACAGCAAG 0.940116 -55 GGCTGTTTAAAAAGAGCCTAATTTAAATGCAA 5 250 1 AAAGAGCTAT 0.654901 -41 ATTTTAGCATACAAATACAAGGAAATGGA 6 43 1 ACAAATCAAG 0.894106 -19 ****** *** * Masking position 5 Map Score: 5.28099 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 733 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 AAGTAACGCTAAATCAATATAATT 1 5 1 AACGCTAAAT 0.88735 -253 TGAACGATCCTTATTTTATAGG 2 203 0 AACGATCCTT 0.744405 -12 CTCCATTTTAACCGGTCATTTTAATTATTT 4 78 1 ACCGGTCATT 0.959543 -71 GAGTGCGATAAAGGGTCATTGGATGGTTTG 5 41 0 AAGGGTCATT 0.906197 -250 TACAAATAAGAACGCTCATTGAACGCTCCA 5 127 1 AACGCTCATT 0.986542 -164 ACGCTCATTGAACGCTCCATTTAGCCAATG 5 138 1 AACGCTCCAT 0.975757 -153 ********** Masking position 6 Map Score: 3.01271 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 240 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ********** No masking Map Score: 1.63668e-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 8 ********** No masking Map Score: 1.63668e-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: 1.63668e-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