AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00562_hpyl_reg_300.orf -o00562_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 HP0428 300 phage/colicin/tellurite resistance cluster terY protein #2 HP0429 124 H. pylori predicted coding region HP0429 #3 HP0430 85 H. pylori predicted coding region HP0430 Motif number 1 CAAAATTCAGGAACTCTTAAGCTAAGTCTA 1 73 1 GAACTCTTAA 0.94084 -228 TACTATACTCAAAAGCTTATAAAATCATCA 1 107 1 AAAAGCTTAT 0.68415 -194 CACTATGGAAGAACGCTTTATTCCAGTATT 1 252 1 GAACGCTTTA 0.982964 -49 TGGATGATTTAAAATCTTTACGCCACAAAA 2 11 1 AAAATCTTTA 0.936413 -114 TACGCCACAAAAACGCTTTATTTATGGATT 2 29 1 AAACGCTTTA 0.97613 -96 TAGATATTTTAAACCCTTTAAAGAGAAAGC 2 75 1 AAACCCTTTA 0.985463 -50 CCAATTGCTCAAAAGCTAAAAG 3 3 0 AAAAGCTAAA 0.852881 -83 CTCCCCTTTTAAACCCTTTAAATCCCACTT 3 54 0 AAACCCTTTA 0.985463 -32 ********** Masking position 3 Map Score: 12.6382 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 748 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 TGGTGGTGTTGCTTTTTATTTCTTTGCCTTA 1 13 1 GCTTTTTTTT 0.954517 -288 ATTCATTTCAGCACTCTTTTTGATGATTTTA 1 126 0 GCACTCTTTT 0.934625 -175 ATCAGATTGTGCTTTATTTTTTTGATTGGGT 1 163 1 GCTTTATTTT 0.990204 -138 AGATGTTATGGCATTAGATTTAAGTAAATAC 1 222 1 GCATTAGTTT 0.950422 -79 ACGCTTTATTCCAGTATTTTTATTGTTAGAT 1 264 1 CCAGTATTTT 0.884923 -37 CCACAAAAACGCTTTATTTATGGATTTAAAC 2 33 1 GCTTTATTAT 0.969645 -92 TGATCTTCATGCTTTCTCTTTAAAGGGTTTA 2 84 0 GCTTTCTTTT 0.98283 -41 AGATCCTGAATTATCTATAATGATCTTC 2 107 0 GAATTATTAT 0.717661 -18 CTTTTGTATATCTGTATTTTTTAGCCAATTG 3 26 0 TCTGTATTTT 0.864722 -60 ******* *** Masking position 5 Map Score: 7.55696 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 634 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 AAAGCTTATAAAATCATCAAAAAGAGTGCT 1 118 1 AAATCATCAA 0.915836 -183 CAATCTGATTAAAACATTCATTTCAGCACT 1 142 0 AAAACATTCA 0.916875 -159 TTGGCGCGAAAAATTATTTATAAGGAGATG 1 197 1 AAATTATTTA 0.933963 -104 TAAAGATTTTAAATCATCCA 2 1 0 AAATCATCCA 0.967406 -124 TGGATGATTTAAAATCTTTACGCCACAAAA 2 11 1 AAAATCTTTA 0.771044 -114 TAAAGGGTTTAAAATATCTATCAACTTCAT 2 65 0 AAAATATCTA 0.956996 -60 AGATCCTGAATTATCTATAATGATCTT 2 108 0 GAATTATCTA 0.901171 -17 ********** Masking position 3 Map Score: 4.05046 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 317 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TTTGTCTTAAGGCAAAGAAATAAAAAGCAA 1 21 0 GGCAAAGAAA 0.964762 -280 TAATTTTTCGCGCCAAAAAACCCAATCAAA 1 183 0 CGCCAAAAAA 0.992206 -118 AAAATCTTTACGCCACAAAAACGCTTTATT 2 21 1 CGCCACAAAA 0.986786 -104 TTGAGCAATTGGCTAAAAAATACAGATATA 3 21 1 GGCTAAAAAA 0.979024 -65 ********** Masking position 5 Map Score: 1.91698 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 64 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CATAACATCTCCTTATAAATAATTTTTCGC 1 202 0 CCTTATAAAT 0.915404 -99 ATCAACTTCATCGTTTAAATCCATAAATAA 2 46 0 TCGTTTAAAT 0.910599 -79 ATATTTTAAACCCTTTAAAGAGAAAGCATG 2 78 1 CCCTTTAAAG 0.988131 -47 CCCTTTTAAACCCTTTAAATCCCACTTTTG 3 51 0 CCCTTTAAAT 0.993029 -35 CTTCAAACTCCCCTTTTAAACCCTTTAAAT 3 61 0 CCCTTTTAAA 0.944874 -25 ********** Masking position 6 Map Score: 2.42134 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 309 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 ACAAACCATAGAGTCGGCTTGCTACCCCAA 1 46 1 GAGTCGGCTT 0.983697 -255 GTTTTAATCAGATTGTGCTTTATTTTTTTG 1 157 1 GATTGTGCTT 0.974665 -144 TTATTTTTTTGATTGGGTTTTTTGGCGCGA 1 176 1 GATTGGGTTT 0.98247 -125 AGATATACAAAAGTGGGATTTAAAGGGTTT 3 44 1 AAGTGGGATT 0.95355 -42 ********** Masking position 4 Map Score: 0.362112 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 157 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ********** No masking Map Score: 8.55083e-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 8 ********** No masking Map Score: 8.55083e-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 9 ********** No masking Map Score: 8.55083e-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