AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iflhCD_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 HP0174 300 H. pylori predicted coding region HP0174 #2 HP0769 87 molybdopterin-guanine dinucleotide biosynthesis protein A (mobA) #3 HP0811 300 H. pylori predicted coding region HP0811 #4 HP1041 140 flagellar biosynthesis protein (flhA) #5 HP1422 24 isoleucyl-tRNA synthetase (ileS) #6 HP1423 101 conserved hypothetical protein Motif number 1 GTAATAATATTTATTGTCTTTTTTGGTGTTAGTTTTATT 1 46 1 TTTTTTTTTT 0.986247 -255 TTGAATCTTCTTTAACATTTTTTTTCTTTCCAAAAAGAA 1 83 0 TTATTTTTTT 0.979993 -218 CCAGGGTTATTATTCTTTATATTTGGTTTTTTAGCATTG 1 190 1 TATATTTTTT 0.851025 -111 ATTAATAGAGTATAGAAGTTATTTAATATGGGATAACAT 1 230 0 TAATTTTTTT 0.945696 -71 TTTGATGTTGTTAAGTCGTTGTTTATTATGTTACACTAA 2 45 0 TTATTTTTTT 0.979993 -43 AAGTTCTATCCATGTTTGATGTTGTTAAGTCG 2 66 0 TTTATTTTTT 0.941409 -22 GCGTATTATATTCCTTCTTTCTTTACTATAACTTAGCAT 3 69 0 TTCTTTTTTT 0.975967 -232 AATAACATCGTTTTTTTTTTTTTTGGTATAATGCTCGGC 3 125 0 TTTTTTTTTT 0.986247 -176 ATTTTTAACATTCTGTTTTTCTTTTTTATAAAATGAAAC 3 172 1 TTTTTTTTTT 0.986247 -129 CTTTTTAAGTTTATTTATTTATTTAATATTGGTGTTTAA 3 212 1 TTTTTTTTTT 0.986247 -89 TGTTTCAAATTATAGCGATTCTTTCTTTTAAACACCAAT 3 239 0 TAATTTTTTT 0.945696 -62 GCGTTTATTTTACCCTATTCTTTAAGTTTTTATCCATA 6 74 0 TTCTTTTTGT 0.874549 -28 ** * ** *** * * Masking position 10 Map Score: 19.7099 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 240 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 TTTTTTGGTGTTAGTTTTATTCTTTTTGGA 1 64 1 TTAGTTTTAT 0.812831 -237 ATTCTTTATATTTGGTTTTTTAGCATTGCA 1 201 1 TTTGGTTTTT 0.77949 -100 ATCTTACATAGTAAGCTTATCAATATGAGA 1 272 0 GTAAGCTTAT 0.771488 -29 GCCCTTTTATTTAAGCTTTTAGTGTAACAT 2 27 1 TTAAGCTTTT 0.974442 -61 GAAACACTTTTTAAGTTTATTTATTTATTT 3 206 1 TTAAGTTTAT 0.952999 -95 ATAGCGTAAAATAAGCTTTTTTGTATCATA 4 49 1 ATAAGCTTTT 0.746203 -92 AATATAAAGTTTAAGCGTATGATACAAAAA 4 66 0 TTAAGCGTAT 0.90758 -75 GTTTGTCTTTTTAGGCTTATTATAATATAA 4 89 0 TTAGGCTTAT 0.975008 -52 TGATTAATCCTTAGTCTTTTGTCT 5 5 0 TTAGTCTTTT 0.91052 -20 ACCCTATTCTTTAAGTTTTTATCCATAACT 6 71 0 TTAAGTTTTT 0.958485 -31 ********** Masking position 8 Map Score: 11.0007 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 342 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 ATTCAAAGCGGGTAAAAGTGTTCGCCTC 1 9 1 CGGGTAAAAG 0.954154 -292 AAAGAAAAAAAATGTTAAAGAAGATTCAAA 1 93 1 AATGTTAAAG 0.862765 -208 CCTGGTAACCAAGGAAAGAGAATGCATACA 1 165 0 AAGGAAAGAG 0.976047 -136 AAAGGGCATAAGGGATAAAGGGA 2 4 0 AGGGATAAAG 0.970899 -84 TTTCTCAATTAAGGTAAGAGCGTCAGGACA 3 16 1 AAGGTAAGAG 0.98047 -285 AGGACATTTTAATGAAAAAGTTGATTAAAA 3 40 1 AATGAAAAAG 0.906784 -261 ATGCTCGGCGAAGGTAAGAGCGAAAGGCGT 3 104 0 AAGGTAAGAG 0.98047 -197 AATCTATTGATGGGATAAAGGGGGTTTT 3 283 1 TGGGATAAAG 0.85671 -18 CTTAAAGAATAGGGTAAAATAAACGC 6 86 1 AGGGTAAAAT 0.884816 -16 ********** Masking position 7 Map Score: 9.79169 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 244 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TCCCTTAATCTTACATAGTAAGCTTATCAATA 1 277 0 TTCATATAAG 0.781344 -24 CACTAAAAGCTTAAATAAAAGGGCATAAGGGA 2 19 0 TTAATAAAGG 0.952825 -69 AATCAACTTTTTCATTAAAATGTCCTGACGCT 3 34 0 TTATTAAATG 0.928863 -267 AATGAAAAAGTTGATTAAAATGCTAAGTTATA 3 50 1 TTATTAAATG 0.928863 -251 AAACAGAATGTTAAAAATAAAGTTCAAATAAC 3 158 0 TTAAAAAAAG 0.941693 -143 AGTGTTTCATTTTATAAAAAAGAAAAACAGAA 3 182 0 TTATAAAAAG 0.94169 -119 AATATTGGTGTTTAAAAGAAAGAATCGCTATA 3 236 1 TTAAAAAAAG 0.941693 -65 TTAGGCTTATTATAATATAAAGTTTAAGCGTA 4 77 0 TAAATAAAAG 0.908343 -64 ACAAATTCCTTAAAAAGAGTGGTGGCT 6 6 1 TTCTTAAAAG 0.962114 -96 TTTTTATCCATAACTTATAAGGGTTTTAGTTT 6 54 0 TACTTAAAGG 0.799903 -48 ** **** **** Masking position 7 Map Score: 7.41337 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 242 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TTTTAGCATTGCATGTTATCCCATATTAAA 1 218 1 GCATGTTATC 0.970281 -83 CTATAACTTAGCATTTTAATCAACTTTTTC 3 53 0 GCATTTTAAT 0.852845 -248 CCTTCGCCGAGCATTATACCAAAAAAAAAA 3 120 1 GCATTATACC 0.969001 -181 AATAAAGTTCGCATTATAGCGTAAAATAAG 4 34 1 GCATTATAGC 0.982271 -107 TTTAGTTTTAGCATGTTAGCATTCAGCCAC 6 32 0 GCATGTTAGC 0.988887 -70 ********** Masking position 4 Map Score: 2.10717 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 103 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GAAAGAAAAAAAATGTTAAAGAAGATTCAA 1 92 1 AAATGTTAAA 0.862477 -209 CAATAATTACGAATATTATATTCATAATTG 1 134 0 GAATATTATA 0.787131 -167 CAAATATAAAGAATAATAACCCTGGTAACC 1 185 0 GAATAATAAC 0.742438 -116 GGATAACATGCAATGCTAAAAAACCAAATA 1 209 0 CAATGCTAAA 0.943716 -92 GCATGTTATCCCATATTAAATAACTTCTAT 1 228 1 CCATATTAAA 0.806669 -73 AAGAAAAACAGAATGTTAAAAATAAAGTTC 3 165 0 GAATGTTAAA 0.970351 -136 TTTTAAACACCAATATTAAATAAATAAATA 3 223 0 CAATATTAAA 0.940153 -78 AGTGGTGGCTGAATGCTAACATGCTAAAAC 6 28 1 GAATGCTAAC 0.925767 -74 ********** Masking position 3 Map Score: 3.10053 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 93 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 TTACTATGTAAGATTAAGGGACT 1 288 1 AGATTAAGGG 0.98958 -13 AGGGCATAAGGGATAAAGGGA 2 2 0 GGATAAAGGG 0.965288 -86 TCTATTGATGGGATAAAGGGGGTTTT 3 285 1 GGATAAAGGG 0.965288 -16 TATAATATAAAGTTTAAGCGTATGATACAA 4 69 0 AGTTTAAGCG 0.945617 -72 ACCACCTACCAGATTAAGGCATTGATTTTA 4 117 1 AGATTAAGGC 0.964217 -24 AGACAAAAGACTAAGGATTAATCA 5 8 1 AGACTAAGGA 0.908074 -17 TAAGGGTTTTAGTTTTAGCATGTTAGCATT 6 39 0 AGTTTTAGCA 0.550213 -63 ********** Masking position 7 Map Score: 3.76172 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 193 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ATGCAATTATGAATATAATATTCGTAATTA 1 131 1 GAATATAATA 0.944513 -170 AGTATAGAAGTTATTTAATATGGGATAACA 1 231 0 TTATTTAATA 0.914094 -70 GCTTTTAGTGTAACATAATAAACAACGACT 2 41 1 TAACATAATA 0.897309 -47 AAGAAAGAAGGAATATAATACGCCTTTCGC 3 85 1 GAATATAATA 0.944513 -216 GTTTATTTATTTATTTAATATTGGTGTTTA 3 220 1 TTATTTAATA 0.914094 -81 TCCTAATTGGTAATTTAATAAAGTTCGCAT 4 18 1 TAATTTAATA 0.949724 -123 TTAAACTTTATATTATAATAAGCCTAAAAA 4 82 1 TATTATAATA 0.491459 -59 ********** Masking position 7 Map Score: 5.81524 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 25 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ********** No masking Map Score: 2.8375e-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 10 ********** No masking Map Score: 2.8375e-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 11 ********** No masking Map Score: 2.8375e-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