AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inagC_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 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 AACTCGTCATCACTAAAATCAATGACGGGGC 1 28 1 CACTAAAATA 0.830058 -273 ATCATTAGGAGCGTTTAAAGAGAGATTGACG 1 116 1 GCGTTTAAAA 0.813558 -185 CTTTAATATGCCCTTTAATGAGCGCTGATAG 1 159 0 CCCTTTAATA 0.990849 -142 TCCTCATTTGCCCTTTAATATGCCCTTTAAT 1 171 0 CCCTTTAATT 0.986866 -130 CAAAATTCTAGCCTTAAATCTTTGATGAAAC 1 221 1 GCCTTAAATT 0.980702 -80 TGTTAAAATTCCCTAAAATGAGTTTAAGGAT 1 276 1 CCCTAAAATA 0.98032 -25 CACTTATTCACGCTATAATAACGCC 2 5 0 CGCTATAATA 0.878629 -148 TGTGAATGAAGCCTTAAAATTAAGGTGTTTC 2 68 1 GCCTTAAAAT 0.958382 -85 TATAGACAAACCCTTAAAAGAAACACCTTAA 2 87 0 CCCTTAAAAA 0.980181 -66 GTGATCGCCTTTAATTTAGAATGCTCC 3 26 0 GCCTTTAATT 0.980708 -17 ********* * Masking position 7 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 0.953639 -218 CTAATGATCCTAAACAGCTTGTAACCACCC 1 94 0 TAAACAGCTT 0.957946 -207 TAGGGAATTTTAACATGCCTTATCTTATAA 1 261 0 TAACATGCCT 0.928051 -40 TAAAATCCTTAAACTCATTT 1 291 0 TAAAATCCTT 0.974233 -10 ACCCTTAAAAGAAACACCTTAATTTTAAGG 2 79 0 GAAACACCTT 0.973209 -74 AAGCATTATAGACAAACCCTTAAAAGAAAC 2 94 0 GACAAACCCT 0.91788 -59 AGGGTTTGTCTATAATGCTTGCTTTATAAT 2 104 1 TATAATGCTT 0.828314 -49 GAAAATCCTTTTTTCGCATC 2 143 0 GAAAATCCTT 0.973726 -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 0.949081 -120 TTATTATAGCGTGAATAAGTGGTGAATGAA 2 15 1 GTGAATAAGT 0.92515 -138 TGAATAAGTGGTGAATGAAAAAGGAATAAC 2 26 1 GTGAATGAAA 0.987309 -127 GGAATAACATGTGAATGAAATGTGAATGAA 2 48 1 GTGAATGAAA 0.987309 -105 TGAATGAAATGTGAATGAAGCCTTAAAATT 2 59 1 GTGAATGAAG 0.994327 -94 GCTAATGGATGCGAAAAAAGGATTTTC 2 136 1 GCGAAAAAAG 0.923753 -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 CACGATCAAACGGGTGAAACTCGTCA 1 2 1 AGAAAAGGTG 0.990043 -299 TGACGGGGCTAAAACTAAAAGCGTGAGCAGGGCGA 1 50 1 AAAAAAGGTG 0.970219 -251 GAGCAGGGCGATGACATTAAGGGTGGTTACAAGCT 1 74 1 AGATTAGGTG 0.983574 -227 AGGGCAAATGAGGATTAAAAAAATGAAAAAACGCA 1 188 1 AGAAAAAATG 0.92506 -113 CGTTTCATCAAAGATTTAAGGCTAGAATTTTGCGT 1 218 0 AGATAAGTAG 0.851208 -83 AAGTCAAATTATAAGATAAGGCATGTTAAAATTCC 1 253 1 AAATAAGATG 0.975102 -48 ATTCCCTAAAATGAGTTTAAGGATTTTA 1 283 1 AGATTAGATT 0.787329 -18 GTGAATGAAAAAGGAATAACATGTGAATGAAATGT 2 36 1 AGGTAAAGTG 0.897121 -117 TTGCTTTATAATAAGCTAATGGATGCGAAAAAAGG 2 122 1 AAATAAGATG 0.975103 -31 * ** *** * *** Masking position 9 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