AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_hpyl_reg_100.orf -o00220_hpyl_100.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 Purged sequences: HP1157 22 H. pylori predicted coding region HP1157 Input sequences: #1 HP0073 300 urease alpha subunit (ureA) (urea amidohydrolase) #2 HP0832 91 spermidine synthase (speE) #3 HP0833 76 H. pylori predicted coding region HP0833 #4 HP1156 107 H. pylori predicted coding region HP1156 #5 HP1399 201 arginase (rocF) Motif number 1 TAAAGATCAAAAACTCGCAAAAAAATGAGAATT 1 78 0 AACTGAAAAA 0.869299 -223 TATAAATTCTAAAGGGGTATTAAACGCACTTCT 1 109 1 AAGGGATTAA 0.801472 -192 TATATCTTTGAAGCGCTATAAAATCGTTATTAG 1 140 0 AACGTTAAAA 0.850913 -161 AGATTAACAGAAGCGTTCATTAACTAATTATTA 1 191 0 AACGTATTAA 0.979607 -110 TAAGGCATGGATATTGTTAAAAAGTAAGCTAAG 2 61 1 ATTTTAAAAA 0.480671 -31 GATTAAATTGAAGCGATAAAAAAG 3 2 0 AACGTAAAAA 0.984214 -75 ACCCTTATTTAAGCTTTAAATAACTATAATATT 3 48 0 AACTTAATAA 0.965711 -29 TTAGTCGCTTAATTGTTGATTAAAATGGGCTAT 4 12 0 AATGTATTAA 0.869695 -96 CATTAAACTTAAGCGATAAATAAGATAAAATTT 4 46 1 AACGTAATAA 0.986087 -62 GGATAGCTCAAATCTTTTAAAAAGAAAAGGATA 4 80 1 AACTTAAAAA 0.961203 -28 GTTAATCCTTTAAATAATAGTGTCAGT 5 5 1 ATCTTAATAA 0.883355 -197 TTATGATTATATTCGCTCAATAAGACTATTGGG 5 37 1 ATCGTAATAA 0.950143 -165 TTAATAAGCAAATGGATAATAAATAGAACAATT 5 118 0 AAGGTATAAA 0.929718 -84 CAAAATTAACAACCAATTATTAATAAGCAAATG 5 137 0 AACATATTAA 0.892521 -65 AGGGGATTTAAAGGAGTTATAAA 5 189 1 AAGATATAAA 0.695753 -13 ** ** * ***** Masking position 12 Map Score: 17.1355 Number of sites scoring better than the average of aligned sites = 1174 Number in coding regions = 1030 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 TTTATAGCGCTTCAAAGATATAACACTAATTC 1 151 1 TTCAAGAATA 0.91238 -150 AATTATTATTTAAAATGAATTAGTGTTATATC 1 167 0 TAAAAGATTA 0.848232 -134 TCGTTATGTCTTCAAGGAAAAACACTTTAAGA 1 266 1 TTCAAGAAAA 0.938443 -35 TTGATTAAATTGAAGCGATAAAAAAG 3 5 0 TGAAGGAAAA 0.854929 -72 TAATCAACAATTAAGCGACTAACCATTAAACT 4 23 1 TTAAGGATAA 0.971725 -85 ACCATTAAACTTAAGCGATAAATAAGATAAAA 4 44 1 TTAAGGAAAA 0.959533 -64 CCTTTTCTTTTTAAAAGATTTGAGCTATCCTA 4 78 0 TTAAAGATTG 0.880862 -30 ACACTATTATTTAAAGGATTAAC 5 2 0 TTAAAGATAA 0.979891 -200 ATTTCATTGTGTAAAAGAGTAAAACCATTCAA 5 89 0 GTAAAGATAA 0.915433 -113 TAGAGGGGATTTAAAGGAGTTATAAA 5 186 1 TTAAAGATTA 0.972563 -16 ***** ** *** Masking position 8 Map Score: 8.9645 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 179 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 AAAAAATGAGAATTAAAATTGGAGTGATAA 1 62 0 AATTAAAATT 0.628541 -239 ATTTATAAAGATCAAAAACTCGCAAAAAAA 1 86 0 ATCAAAAACT 0.896614 -215 ATTCATTTTAAATAATAATTAGTTAATGAA 1 179 1 AATAATAATT 0.808883 -122 AATCTTAGTAAATCAAAACATTGCTACAAT 1 219 1 AATCAAAACA 0.694232 -82 CTAGCTAAAAAATCTAAATTATTGTAACAA 2 15 0 AATCTAAATT 0.828094 -77 GCTTCAATTTAATCAAAATTAGATTACAAT 3 21 1 AATCAAAATT 0.95315 -56 GCCCATTTTAATCAACAATTAAGCGACTAA 4 15 1 ATCAACAATT 0.711239 -93 GATTTGAGCTATCCTAAATTTTATCTTATT 4 64 0 ATCCTAAATT 0.817918 -44 GAGCGAATATAATCATAACTGACACTATTA 5 25 0 AATCATAACT 0.885305 -177 GTGTTTTTCTATCAAAAACTTGAATGGTTT 5 70 1 ATCAAAAACT 0.896614 -132 CCATTTGCTTATTAATAATTGGTTGTTAAT 5 136 1 ATTAATAATT 0.782874 -66 TTCTATTCTAAACCAAAATTAACAACCAAT 5 153 0 AACCAAAATT 0.96487 -49 ********** Masking position 7 Map Score: 9.33617 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 458 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 CCACCATTATCACTCCAATTTTAATTCTCA 1 56 1 CACTCCAATT 0.890551 -245 GTATTAAACGCACTTCTAATAACGATTTTA 1 125 1 CACTTCTAAT 0.833479 -176 GATTTTATAGCGCTTCAAAGATATAACACT 1 148 1 CGCTTCAAAG 0.965925 -153 AGTTAATGAACGCTTCTGTTAATCTTAGTA 1 199 1 CGCTTCTGTT 0.972184 -102 CTTTTTTATCGCTTCAATTTAATCAAAAT 3 10 1 CGCTTCAATT 0.989783 -67 AATGGTTAGTCGCTTAATTGTTGATTAAAA 4 20 0 CGCTTAATTG 0.838807 -88 TCTTATTTATCGCTTAAGTTTAATGGTTAG 4 41 0 CGCTTAAGTT 0.950518 -67 ********** Masking position 4 Map Score: 4.2893 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 385 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TAAAATGAATTAGTGTTATATCTTTGAAGC 1 159 0 TAGTGTTATA 0.87884 -142 CTTATTCTCCTATTCTTAAAGTGTTTTTCC 1 281 0 TATTCTTAAA 0.894447 -20 AAATCTAAATTATTGTAACAAAAGC 2 6 0 TATTGTAACA 0.920897 -86 AAGGCATGGATATTGTTAAAAAGTAAGCTA 2 62 1 TATTGTTAAA 0.952466 -30 ATAACTATAATATTGTAATCTAATTTTGAT 3 32 0 TATTGTAATC 0.903454 -45 AACAATTTCATTGTGTAAAAGAGTAAAACC 5 95 0 TTGTGTAAAA 0.785114 -107 TCTAATGTTCTATTCTAAACCAAAATTAAC 5 160 0 TATTCTAAAC 0.881326 -42 ********** Masking position 8 Map Score: 1.36707 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 85 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GGCCACCATTATCACTCCAATTTTAATTCT 1 54 1 ATCACTCCAA 0.862256 -247 AAGTGCGTTTAATACCCCTTTAGAATTTAT 1 110 0 AATACCCCTT 0.962074 -191 AAACACTCCTTAGCTTACTTT 2 81 0 AACACTCCTT 0.962082 -11 AATAGCCCATTTTAATCAAC 4 1 1 AATAGCCCAT 0.930724 -107 TTGATAGAAAAACACCCCAATAGTCTTATT 5 55 0 AACACCCCAA 0.986858 -147 AACCAAAATTAACAACCAATTATTAATAAG 5 143 0 AACAACCAAT 0.805928 -59 ********** Masking position 4 Map Score: 0.982991 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 457 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 7 AGCGGCCACTACCATGTCAAGGTAGT 1 4 0 ACATTCAAGT 0.884819 -297 ACTTCTAATAACGATTTTATAGCGCTTCAAAGA 1 136 1 ACATTTATGC 0.946929 -165 AAGATATAACACTAATTCATTTTAAATAATAAT 1 165 1 ACAATCATTT 0.861187 -136 TGAAGACATAACGAAATCAAGGTTGGATGTAAT 1 247 0 ACAATCAAGT 0.969966 -54 AGCTAAAAAATCTAAATTATTGTAACAAAAGC 2 10 0 TCAATTATGT 0.793569 -82 TTACTTTTTAACAATATCCATGCCTTAATGAAT 2 55 0 ACATTCCAGC 0.89309 -37 AAATTAGATTACAATATTATAGTTATTTAAAGC 3 36 1 ACATTTATGT 0.624622 -41 AATAAATAGAACAATTTCATTGTGTAAAAGAGT 5 101 0 ACATTCATGT 0.892151 -101 ** ** **** ** Masking position 4 Map Score: 5.37248 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 98 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 ********** No masking Map Score: -6.37056e-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: -6.37056e-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 10 ********** No masking Map Score: -6.37056e-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