AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -igalR_hpyl_opreg_300.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 HP0359 300 H. pylori predicted coding region HP0359 #2 HP0360 216 UDP-glucose 4-epimerase Motif number 1 TTTAAGCTCCTTAGAACAAATATAAGCCGAT 1 65 1 TTAGAAAAAT 0.892696 -236 TGCGCAATATAAAGAACAAAGCAAATAAAAA 1 144 1 AAAGAAAAAG 0.971691 -157 AGAACAAAGCAAATAAAAAATCTCAATCCAA 1 156 1 AAATAAAAAT 0.966559 -145 CTCCTTGATGGAAGATTAAATTGGATTGAGA 1 176 0 GAAGATAAAT 0.953418 -125 CGACTGATAAAAAGAAAAAATTTAAGGAGAA 1 276 1 AAAGAAAAAT 0.993238 -25 AAAAGCCAATAAAGATGAAATTATAGATTAA 2 115 1 AAAGATAAAT 0.987188 -102 AGATGAAATTATAGATTAAATTTTCTTAAAA 2 127 1 ATAGATAAAT 0.959026 -90 AAAAATCCTTAAATAATAAATGGGATTAAGA 2 155 1 AAATAAAAAT 0.965778 -62 CCCCTTTTAAAATGAAAAAATAACAACTATT 2 192 0 AATGAAAAAT 0.95858 -25 ****** **** Masking position 5 Map Score: 14.8037 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 314 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 ATGTTATACCAAAAACCCTAAAAATTTAAG 1 41 1 AAAAACCCTA 0.876394 -260 CCTAAAAATTTAAGCTCCTTAGAACAAATA 1 57 1 TAAGCTCCTT 0.976292 -244 ATATTGCGCAAAATCTCTTTTGCTTTATAA 1 124 0 AAATCTCTTT 0.902833 -177 CTTTTAACTCAAAGCTCCTTGATGGAAGAT 1 191 0 AAAGCTCCTT 0.974716 -110 ACCTGAGCTATAAGCCCTTAAAAGCCAATA 2 96 1 TAAGCCCTTA 0.882555 -121 AATTTTCTTAAAAAATCCTTAAATAATAAA 2 145 1 AAAAATCCTT 0.920353 -72 TATAACATCTTAATCCCATTTATTATTTAA 2 163 0 TAATCCCATT 0.851094 -54 AAAACCCCTTTTAAAATGAA 2 207 0 AAAACCCCTT 0.98832 -10 ********** Masking position 3 Map Score: 8.0165 Number of sites scoring better than the average of aligned sites = 1304 Number in coding regions = 1116 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 GATGCCAGTGAGAAATGTTATACCAAAAACCCTAA 1 27 1 AAAATATCCA 0.96367 -274 GCTCCTTAGAACAAATATAAGCCGATAAAGCCGCC 1 70 1 AAAATAGCGA 0.985241 -231 TAAAGCCGCCAAAGATAGAAAGCGAAAAGTTATAA 1 95 1 AAGATAACGA 0.958641 -206 GCGAAAAGTTATAAAGCAAAAGAGATTTTGCGCAA 1 116 1 AAAAGAAAGA 0.94928 -185 TTTGCGCAATATAAAGAACAAAGCAAATAAAAAAT 1 142 1 AAAAGAAGCA 0.90627 -159 AAAGCAAATAAAAAATCTCAATCCAATTTAATCTT 1 161 1 AAAATAACCA 0.983864 -140 GCGGCGTTAAACAAAGACGATCCAATCGTTTAGGA 1 225 1 AAAAGATCAA 0.846318 -76 GTCTTGGTTGAGAAATCCTAAACGATTGGATCGTC 1 240 0 AAAATAACGA 0.99002 -61 GATAAAAAGAAAAAATTTAAGGAGAAAACG 1 281 1 AAAATAGAGA 0.938532 -20 * **** ** *** Masking position 10 Map Score: 6.77403 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 217 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 TTCTCACTGGCATCAAGGGTCAAAATATAG 1 11 0 CATCAAGGGT 0.970267 -290 TTTTTCTTTTTATCAGTCGTGTCTTGGTTG 1 265 0 TATCAGTCGT 0.953647 -36 CCAAAGATTGTAAAAATGGTGGGCTTAGGA 2 20 1 TAAAAATGGT 0.908745 -197 ACCTCACCCTTATCAGGGGTGCGCTCTAAC 2 65 1 TATCAGGGGT 0.99391 -152 TTTTTCATTTTAAAAGGGGTTTT 2 204 1 TAAAAGGGGT 0.980603 -13 ********** Masking position 5 Map Score: 2.31096 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 100 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GCCGATAAAGCCGCCAAAGATAGAAAGCGAA 1 90 1 CCCCAAAGAT 0.991362 -211 GCTAATTCCCCAAAGATTGTAAAAATG 2 7 1 TCCCAAAGAT 0.956509 -210 AGGTTCAACTCCTCCTAAGCCCACCATTTTT 2 31 0 CCCCTAAGCC 0.994893 -186 TGCGCTCTAACCACCTGAGCTATAAGCCCTT 2 84 1 CCCCTGAGCT 0.987849 -133 AGCTATAAGCCCTTAAAAGCCAATAAAGATG 2 101 1 CCTAAAAGCC 0.911116 -116 ** ******** Masking position 8 Map Score: 1.47133 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 166 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: -1.63892e-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: -1.63892e-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: -1.63892e-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