AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_hpyl_reg_300.orf -o00680_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 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0875 300 catalase Motif number 1 AACCTTGAGATTGTTTTAGTGTATTATAGC 1 24 1 TTGTTTTAGT 0.866115 -234 TAGCTATATTTTAATTTAAGAATTTTAGAT 1 50 1 TTAATTTAAG 0.809595 -208 TTTAGATTGATTTTTTTAAGGGTAGTTTTT 1 73 1 TTTTTTTAAG 0.989265 -185 TAAGGGTAGTTTTTTTTAAGTTGTGTTATT 1 89 1 TTTTTTTAAG 0.989265 -169 GTGAATTGGCATGATTTAAGAGTAATGGGT 1 145 1 ATGATTTAAG 0.889423 -113 TAATGGGTGTTTGTTTTAAGACGCTATGAC 1 167 1 TTGTTTTAAG 0.989464 -91 TTGATTTTTATTTTTTAAATTT 2 3 0 TTTTTTAAAT 0.810703 -298 GTTTTTTTTTTTTTTTTGATTTTTATTTTT 2 18 0 TTTTTTTGAT 0.863917 -283 ATTTTTAATCTGGTTTTAATAATAATTATT 2 81 0 TGGTTTTAAT 0.938911 -220 AACAAAATTTTATTTTTAATCTGGTTTTAA 2 92 0 TATTTTTAAT 0.906984 -209 AATAAAATTTTGTTTTTAATCTTTCTTATT 2 108 1 TGTTTTTAAT 0.937822 -193 TAAAAAATCCTTTTTTTAAGAATGAAAAAC 2 173 0 TTTTTTTAAG 0.989265 -128 TAAAAAAAGGATTTTTTAAGGAAATTGAAT 2 185 1 ATTTTTTAAG 0.964235 -116 TCATATTACGAAGATTTAAGATCATAAAAG 2 273 1 AAGATTTAAG 0.643142 -28 ********** Masking position 5 Map Score: 22.8742 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 796 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 2 TAAAACAATCTCAAGGTTTCAAAATTTAGCC 1 7 0 TCAAGTTAAT 0.742017 -251 ATATTTTAATTTAAGAATTTTAGATTGATTTTTTT 1 55 1 TTAAGTTAAT 0.948014 -203 ATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 78 1 TTAAGTATTT 0.954804 -180 GTAGTTTTTTTTAAGTTGTGTTATTATTTTCAAAT 1 94 1 TTAAGGTTTT 0.912116 -164 ATTCACACTCTTTAGACTTGAAATTTGAAAATAAT 1 116 0 TTTAGTTATT 0.963364 -142 AAGGTTTGGGTTTAGGGTTTGAATTATATTGATTT 1 223 1 TTTAGTTATT 0.963364 -35 TTTTTTGATTTTTATTTTTTAAATTT 2 2 0 TTTATTTATT 0.866908 -299 CATTGACGGATTTTGTTTTTTTTTTTTTTTTGATT 2 27 0 TTTTGTTTTT 0.76425 -274 TAATCTGGTTTTAATAATAATTATTATACTATTCT 2 71 0 TTAATTATTT 0.839563 -230 TAAAACCAGATTAAAAATAAAATTTTGTTTTTAAT 2 93 1 TTAAATAATT 0.759177 -208 AATTTTGTTTTTAATCTTTCTTATTTTCATTAATT 2 113 1 TTAATTTTTT 0.942195 -188 AAAAACCCCCTTAAGTATTTCTATTCGTAACAATT 2 144 0 TTAAGTTTTT 0.985027 -157 TTTTATGATCTTAAATCTTCGTAATATGACACTAA 2 267 0 TTAAATTTAT 0.78504 -34 ***** ** * ** Masking position 1 Map Score: 11.3649 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 630 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 CTACCCTTAAAAAAATCAATCTAAAATTCTTAAA 1 64 0 AAAACACTAA 0.836368 -194 ACAACTTAAAAAAAACTACCCTTAAAAAAATCAA 1 79 0 AAAATACTTA 0.799765 -179 ATTTGAAAATAATAACACAACTTAAAAAAAACTA 1 95 0 AATAACCTTA 0.921578 -163 ATTATTTTCAAATTTCAAGTCTAAAGAGTGTGAA 1 116 1 AATTAACTAA 0.953806 -142 AAATCAATATAATTCAAACCCTAAACCCAAACCT 1 224 0 AATTAACTAA 0.953806 -34 AAATTTAAAAAATAAAAATCAAAAA 2 2 1 AATTAAATAA 0.836458 -299 AATCAAAAAAAAAAAAAAAACAAAATCCGTCAAT 2 27 1 AAAAAACAAA 0.760104 -274 ATCTGGTTTTAATAATAATTATTATACTATTCTA 2 70 0 AATAAAATTA 0.9486 -231 AGAAAGATTAAAAACAAAATTTTATTTTTAATCT 2 100 0 AAAAAATTTA 0.856341 -201 AATTAATGAAAATAAGAAAGATTAAAAACAAAAT 2 114 0 AATAAAATTA 0.9486 -187 AATTGTTACGAATAGAAATACTTAAGGGGGTTTT 2 144 1 AATAAACTTA 0.986756 -157 CATAATTTGTTATACAAAGACTAACAAGATTCAA 2 209 0 TATAAACTAA 0.872517 -92 TTAGTGTCATATTACGAAGATTTAAGATCATAAA 2 267 1 ATTAAATTTA 0.578175 -34 **** ** **** Masking position 14 Map Score: 8.64353 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 665 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 ACAATCTCAAGGTTTCAAAATTTAGCC 1 8 0 GGTTTCAAAA 0.198551 -250 TGAAACCTTGAGATTGTTTTAGTGTATTAT 1 21 1 AGATTGTTTT 0.82201 -237 TTATAGCTATATTTTAATTTAAGAATTTTA 1 47 1 ATTTTAATTT 0.718741 -211 TAAGAATTTTAGATTGATTTTTTTAAGGGT 1 66 1 AGATTGATTT 0.940381 -192 TTGTGTTATTATTTTCAAATTTCAAGTCTA 1 109 1 ATTTTCAAAT 0.732321 -149 AAGTCTAAAGAGTGTGAATTGGCATGATTT 1 132 1 AGTGTGAATT 0.862056 -126 TTGGGTTTAGGGTTTGAATTATATTGATTT 1 228 1 GGTTTGAATT 0.862056 -30 GGTTTGAATTATATTGATTTAGCGTTACTT 1 238 1 ATATTGATTT 0.907424 -20 TTTTTTTTTGATTTTTATTTTTTAAATTT 2 10 0 ATTTTTATTT 0.724147 -291 GCATTGACGGATTTTGTTTTTTTTTTTTTT 2 33 0 ATTTTGTTTT 0.873158 -268 TAAAAATAAAATTTTGTTTTTAATCTTTCT 2 104 1 ATTTTGTTTT 0.873158 -197 AATCTTTCTTATTTTCATTAATTGTTACGA 2 125 1 ATTTTCATTA 0.761116 -176 AAGACTAACAAGATTCAATTTCCTTAAAAA 2 197 0 AGATTCAATT 0.866553 -104 TAATCGGCTTAGTGTCATATTACGAAGATT 2 259 1 AGTGTCATAT 0.698307 -42 ********** Masking position 5 Map Score: 8.88716 Number of sites scoring better than the average of aligned sites = 1464 Number in coding regions = 1229 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 5 TTGGCATGATTTAAGAGTAATGGGTGTTTG 1 150 1 TTAAGAGTAA 0.886069 -108 ATGACTATCTTTATGCGAGATATATGAGAG 1 192 1 TTATGCGAGA 0.947979 -66 TATGCGAGATATATGAGAGAAAGGTTTGGG 1 203 1 ATATGAGAGA 0.966106 -55 ATTAATGAAAATAAGAAAGATTAAAAACAA 2 117 0 ATAAGAAAGA 0.947719 -184 AATCCTTTTTTTAAGAATGAAAAACCCCCT 2 168 0 TTAAGAATGA 0.947423 -133 ********** Masking position 3 Map Score: 0.249348 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 141 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ********** No masking Map Score: -1.12023e-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 7 ********** No masking Map Score: -1.12023e-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: -1.12023e-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