AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inagC_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #2 HP1530 152 purine nucleoside phosphorylase (punB) #3 HP1531 42 H. pylori predicted coding region HP1531 Motif number 1 GCCCCGTCATTGATTTTAGTGATGACGAGTT 1 28 0 TATTTTAGTG 0.848779 -273 CGTCAATCTCTCTTTAAACGCTCCTAATGAT 1 116 0 TTTTAAACGC 0.833702 -185 CTATCAGCGCTCATTAAAGGGCATATTAAAG 1 159 1 TATTAAAGGG 0.991988 -142 ATTAAAGGGCATATTAAAGGGCAAATGAGGA 1 171 1 AATTAAAGGG 0.98855 -130 GTTTCATCAAAGATTTAAGGCTAGAATTTTG 1 221 0 AATTTAAGGC 0.983158 -80 ATCCTTAAACTCATTTTAGGGAATTTTAACA 1 276 0 TATTTTAGGG 0.982829 -25 GGCGTTATTATAGCGTGAATAAGTG 2 5 1 TATTATAGCG 0.892692 -148 GAAACACCTTAATTTTAAGGCTTCATTCACA 2 68 0 ATTTTAAGGC 0.963583 -85 TTAAGGTGTTTCTTTTAAGGGTTTGTCTATA 2 87 1 TTTTTAAGGG 0.98267 -66 GGAGCATTCTAAATTAAAGGCGATCAC 3 26 1 AATTAAAGGC 0.983166 -17 * ********* Masking position 5 Map Score: 14.9797 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 844 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 2 AAACAGCTTGTAACCACCCTTAATGTCATC 1 83 0 TAACCACCCT 0.951791 -218 CTAATGATCCTAAACAGCTTGTAACCACCC 1 94 0 TAAACAGCTT 0.956261 -207 TAGGGAATTTTAACATGCCTTATCTTATAA 1 261 0 TAACATGCCT 0.925262 -40 TAAAATCCTTAAACTCATTT 1 291 0 TAAAATCCTT 0.973183 -10 ACCCTTAAAAGAAACACCTTAATTTTAAGG 2 79 0 GAAACACCTT 0.972118 -74 AAGCATTATAGACAAACCCTTAAAAGAAAC 2 94 0 GACAAACCCT 0.914733 -59 AGGGTTTGTCTATAATGCTTGCTTTATAAT 2 104 1 TATAATGCTT 0.8224 -49 GAAAATCCTTTTTTCGCATC 2 143 0 GAAAATCCTT 0.972655 -10 ********** Masking position 2 Map Score: 6.49163 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 470 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 ATATTAAAGGGCAAATGAGGATTAAAAAAA 1 181 1 GCAAATGAGG 0.947061 -120 TTATTATAGCGTGAATAAGTGGTGAATGAA 2 15 1 GTGAATAAGT 0.922258 -138 TGAATAAGTGGTGAATGAAAAAGGAATAAC 2 26 1 GTGAATGAAA 0.986785 -127 GGAATAACATGTGAATGAAATGTGAATGAA 2 48 1 GTGAATGAAA 0.986785 -105 TGAATGAAATGTGAATGAAGCCTTAAAATT 2 59 1 GTGAATGAAG 0.994091 -94 GCTAATGGATGCGAAAAAAGGATTTTC 2 136 1 GCGAAAAAAG 0.920811 -17 ********** Masking position 5 Map Score: 5.86097 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 156 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TGACGAGTTTCACCCGTTTGATCGTG 1 2 0 CACCTTTTCT 0.987989 -299 TCGCCCTGCTCACGCTTTTAGTTTTAGCCCCGTCA 1 50 0 CACCTTTTTT 0.964225 -251 AGCTTGTAACCACCCTTAATGTCATCGCCCTGCTC 1 74 0 CACCTAATCT 0.980214 -227 TGCGTTTTTTCATTTTTTTAATCCTCATTTGCCCT 1 188 0 CATTTTTTCT 0.910805 -113 ACGCAAAATTCTAGCCTTAAATCTTTGATGAAACG 1 218 1 CTACTTATCT 0.825593 -83 GGAATTTTAACATGCCTTATCTTATAATTTGACTT 1 253 0 CATCTTATTT 0.970059 -48 TAAAATCCTTAAACTCATTTTAGGGAAT 1 283 0 AATCTAATCT 0.753848 -18 ACATTTCATTCACATGTTATTCCTTTTTCATTCAC 2 36 0 CACTTTACCT 0.878254 -117 CCTTTTTTCGCATCCATTAGCTTATTATAAAGCAA 2 122 0 CATCTTATTT 0.97006 -31 *** * *** ** * Masking position 7 Map Score: 5.36954 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 307 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ********** No masking Map Score: 5.21128e-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 6 ********** No masking Map Score: 5.21128e-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 7 ********** No masking Map Score: 5.21128e-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