AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iflhCD_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 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 ACCAAAAAAGACAATAAATATTATTACAACATCTGAGGC 1 34 0 AAAAAATTAA 0.909977 -267 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGAAGATTCAA 1 83 1 AAAAAAAGAA 0.98463 -218 CAATGCTAAAAAACCAAATATAAAGAATAATAACCCTGG 1 190 0 AAAAAATATA 0.919177 -111 ATGTTATCCCATATTAAATAACTTCTATACTCTATTAAT 1 230 1 AAAAAAATTA 0.909977 -71 TTAGTGTAACATAATAAACAACGACTTAACAACATCAAA 2 45 1 AAAAAAAAAA 0.989008 -43 CGACTTAACAACATCAAACATGGATAGAACTT 2 66 1 AAAAAATAAA 0.969686 -22 ATGCTAAGTTATAGTAAAGAAAGAAGGAATATAATACGC 3 69 1 AAAAAAAAAA 0.989008 -232 GCCGAGCATTATACCAAAAAAAAAAAAAACGATGTTATT 3 125 1 AAAAAAAAAA 0.989008 -176 GTTTCATTTTATAAAAAAGAAAAACAGAATGTTAAAAAT 3 172 0 AAAAAAAAAA 0.989008 -129 TTAAACACCAATATTAAATAAATAAATAAACTTAAAAAG 3 212 0 AAAAAAAAAA 0.989007 -89 ATTGGTGTTTAAAAGAAAGAATCGCTATAATTTGAAACA 3 239 1 AAAAAAAGTA 0.95794 -62 TATGGATAAAAACTTAAAGAATAGGGTAAAATAAACGC 6 74 1 ACAAAAAGAA 0.916647 -28 * * *** ** * ** Masking position 10 Map Score: 19.3974 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 214 Number in noncoding regions = 72 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 0.807937 -237 ATTCTTTATATTTGGTTTTTTAGCATTGCA 1 201 1 TTTGGTTTTT 0.773966 -100 ATCTTACATAGTAAGCTTATCAATATGAGA 1 272 0 GTAAGCTTAT 0.772935 -29 GCCCTTTTATTTAAGCTTTTAGTGTAACAT 2 27 1 TTAAGCTTTT 0.974103 -61 GAAACACTTTTTAAGTTTATTTATTTATTT 3 206 1 TTAAGTTTAT 0.951901 -95 ATAGCGTAAAATAAGCTTTTTTGTATCATA 4 49 1 ATAAGCTTTT 0.746828 -92 AATATAAAGTTTAAGCGTATGATACAAAAA 4 66 0 TTAAGCGTAT 0.90555 -75 GTTTGTCTTTTTAGGCTTATTATAATATAA 4 89 0 TTAGGCTTAT 0.974736 -52 TGATTAATCCTTAGTCTTTTGTCT 5 5 0 TTAGTCTTTT 0.907891 -20 ACCCTATTCTTTAAGTTTTTATCCATAACT 6 71 0 TTAAGTTTTT 0.95721 -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 0.951467 -292 AAAGAAAAAAAATGTTAAAGAAGATTCAAA 1 93 1 AATGTTAAAG 0.855533 -208 CCTGGTAACCAAGGAAAGAGAATGCATACA 1 165 0 AAGGAAAGAG 0.974609 -136 AAAGGGCATAAGGGATAAAGGGA 2 4 0 AGGGATAAAG 0.969162 -84 TTTCTCAATTAAGGTAAGAGCGTCAGGACA 3 16 1 AAGGTAAGAG 0.979292 -285 AGGACATTTTAATGAAAAAGTTGATTAAAA 3 40 1 AATGAAAAAG 0.901607 -261 ATGCTCGGCGAAGGTAAGAGCGAAAGGCGT 3 104 0 AAGGTAAGAG 0.979292 -197 AATCTATTGATGGGATAAAGGGGGTTTT 3 283 1 TGGGATAAAG 0.849214 -18 CTTAAAGAATAGGGTAAAATAAACGC 6 86 1 AGGGTAAAAT 0.878582 -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 0.77735 -24 CACTAAAAGCTTAAATAAAAGGGCATAAGGGA 2 19 0 TTAATAAAGG 0.95177 -69 AATCAACTTTTTCATTAAAATGTCCTGACGCT 3 34 0 TTATTAAATG 0.927313 -267 AATGAAAAAGTTGATTAAAATGCTAAGTTATA 3 50 1 TTATTAAATG 0.927313 -251 AAACAGAATGTTAAAAATAAAGTTCAAATAAC 3 158 0 TTAAAAAAAG 0.940405 -143 AGTGTTTCATTTTATAAAAAAGAAAAACAGAA 3 182 0 TTATAAAAAG 0.940402 -119 AATATTGGTGTTTAAAAGAAAGAATCGCTATA 3 236 1 TTAAAAAAAG 0.940405 -65 TTAGGCTTATTATAATATAAAGTTTAAGCGTA 4 77 0 TAAATAAAAG 0.906393 -64 ACAAATTCCTTAAAAAGAGTGGTGGCT 6 6 1 TTCTTAAAAG 0.961259 -96 TTTTTATCCATAACTTATAAGGGTTTTAGTTT 6 54 0 TACTTAAAGG 0.796159 -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 0.966168 -83 CTATAACTTAGCATTTTAATCAACTTTTTC 3 53 0 GCATTTTAAT 0.835239 -248 CCTTCGCCGAGCATTATACCAAAAAAAAAA 3 120 1 GCATTATACC 0.964723 -181 AATAAAGTTCGCATTATAGCGTAAAATAAG 4 34 1 GCATTATAGC 0.979956 -107 TTTAGTTTTAGCATGTTAGCATTCAGCCAC 6 32 0 GCATGTTAGC 0.987318 -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 0.867916 -209 CAATAATTACGAATATTATATTCATAATTG 1 134 0 GAATATTATA 0.794839 -167 CAAATATAAAGAATAATAACCCTGGTAACC 1 185 0 GAATAATAAC 0.751254 -116 GGATAACATGCAATGCTAAAAAACCAAATA 1 209 0 CAATGCTAAA 0.946143 -92 GCATGTTATCCCATATTAAATAACTTCTAT 1 228 1 CCATATTAAA 0.813838 -73 AAGAAAAACAGAATGTTAAAAATAAAGTTC 3 165 0 GAATGTTAAA 0.971664 -136 TTTTAAACACCAATATTAAATAAATAAATA 3 223 0 CAATATTAAA 0.942724 -78 AGTGGTGGCTGAATGCTAACATGCTAAAAC 6 28 1 GAATGCTAAC 0.928909 -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 ATAATATTTATTGTCTTTTTTGGTGTTAGT 1 49 1 TTGTCTTTTT 0.935729 -252 GTCTTTTTTGGTGTTAGTTTTATTCTTTTT 1 61 1 GTGTTAGTTT 0.812349 -240 GTGTTAGTTTTATTCTTTTTGGAAAGAAAA 1 71 1 TATTCTTTTT 0.672116 -230 CTTTAACATTTTTTTTCTTTCCAAAAAGAA 1 83 0 TTTTTTCTTT 0.777912 -218 TTCTTTATATTTGGTTTTTTAGCATTGCAT 1 202 1 TTGGTTTTTT 0.650648 -99 AAATAACATCGTTTTTTTTTTTTTTGGTAT 3 135 0 GTTTTTTTTT 0.915605 -166 AACATTCTGTTTTTCTTTTTTATAAAATGA 3 178 1 TTTTCTTTTT 0.946517 -123 CTTAAAAAGTGTTTCATTTTATAAAAAAGA 3 191 0 GTTTCATTTT 0.883056 -110 ATGAAACACTTTTTAAGTTTATTTATTTAT 3 204 1 TTTTAAGTTT 0.570443 -97 TAAAATAAGCTTTTTTGTATCATACGCTTA 4 55 1 TTTTTTGTAT 0.588224 -86 GGTAGGTGGTTTGTCTTTTTAGGCTTATTA 4 97 0 TTGTCTTTTT 0.935729 -44 ACTTATAAGGGTTTTAGTTTTAGCATGTTA 6 44 0 GTTTTAGTTT 0.840313 -58 ********** Masking position 8 Map Score: 5.90655 Number of sites scoring better than the average of aligned sites = 1213 Number in coding regions = 911 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 8 ATGCAATTATGAATATAATATTCGTAATTA 1 131 1 GAATATAATA 0.940129 -170 AGTATAGAAGTTATTTAATATGGGATAACA 1 231 0 TTATTTAATA 0.903593 -70 GCTTTTAGTGTAACATAATAAACAACGACT 2 41 1 TAACATAATA 0.887382 -47 AAGAAAGAAGGAATATAATACGCCTTTCGC 3 85 1 GAATATAATA 0.940129 -216 GTTTATTTATTTATTTAATATTGGTGTTTA 3 220 1 TTATTTAATA 0.903593 -81 TCCTAATTGGTAATTTAATAAAGTTCGCAT 4 18 1 TAATTTAATA 0.945994 -123 TTAAACTTTATATTATAATAAGCCTAAAAA 4 82 1 TATTATAATA 0.489348 -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 ACAATAAATATTATTACAACATCTGAGGCGAA 1 31 0 TTATCAACAT 0.958576 -270 AGTCCCTTAATCTTACATAGTAAGCTTA 1 283 0 TTATTTACAT 0.92844 -18 ATTTAAGCTTTTAGTGTAACATAATAAACAAC 2 35 1 TTATTAACAT 0.981319 -53 CCTTCTTTCTTTACTATAACTTAGCATTTTAA 3 64 0 TTATTAACTT 0.965736 -237 AAAAACGATGTTATTTGAACTTTATTTTTAAC 3 149 1 TTATGAACTT 0.926992 -152 CTTTTTAGGCTTATTATAATATAAAGTTTAAG 4 81 0 TTATTAATAT 0.873755 -60 *** * ****** Masking position 5 Map Score: 2.03943 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 11 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 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 Motif number 12 ********** 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