AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_hpyl_reg_100.orf -o00271_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: HP1141 23 methionyl-tRNA formyltransferase (fmt) Input sequences: #1 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #2 HP0106 24 cystathionine gamma-synthase (metB) #3 HP0107 38 cysteine synthetase (cysK) #4 HP0194 214 triosephosphate isomerase (tpi) #5 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #6 HP0417 168 methionyl-tRNA synthetase (metS) #7 HP0795 111 trigger factor (tig) #8 HP1142 39 H. pylori predicted coding region HP1142 #9 HP1143 243 H. pylori predicted coding region HP1143 Motif number 1 TTAACTTATTTTTACTATAATTCTACTTTGTG 1 184 0 TTACTTAATT 0.665492 -117 AGTTTAAGGTTTATTTTAACTTATTTTTACTA 1 199 0 TTTTTAACTT 0.942153 -102 TTTTTCCTTTTTTATTGAATTT 2 1 0 TTATTAATTT 0.944688 -24 GAATTGAATTTTTTCTCAATTTAGGTTTTGTT 4 105 0 TTTCTAATTT 0.978739 -110 AAAGGGGCTATTGTTTAAAATTTACATTTTTT 4 137 1 TTTTTAAATT 0.951562 -78 TTATTATAGCTTATTTCATTCT 5 1 0 TTTTTATTCT 0.72095 -64 TCCTTGAACTCTTTTTCAATTTTTTGAGCGTT 6 19 1 CTTTTAATTT 0.865469 -150 TAGCTTAAAATTCATTATAATTAACGCTCAAA 6 41 0 TTATTTAATT 0.723902 -128 GCAACCTCTATTCTCTAAATTTTTAAAAGCAT 6 99 1 TTTCTAATTT 0.978739 -70 TACCTTAAATTTGTTTAAATCTCTTAATTTTA 6 133 0 TTTTTAATCT 0.950883 -36 TTTTTTAAATTTTTGAAAACTA 7 1 1 TTTTTAATTT 0.983783 -111 ATAGCTTAATTTGTTTTAATTCCAGTTTATAA 7 49 0 TTTTTAATTC 0.865469 -63 CGTATGGTTCTCTAAAACTTGTGCTTTTG 9 8 1 TTTCTAAACT 0.826297 -236 TGATCGATCGTTATCTCAATTTCTTCATTTTT 9 54 1 TTTCTAATTT 0.978739 -190 AATTTCTTCATTTTTTTTATTTATAATGTAGT 9 71 1 TTTTTTATTT 0.9664 -173 ATTTTTTGCCTTTTTTATTTTTTGTTGTTTGT 9 118 1 TTTTTTTTTT 0.793312 -126 TTATTTTTTGTTGTTTGTATTTAAAATCCCTA 9 132 1 TTTTTTATTT 0.9664 -112 AAATCCCTATTTTACTGAACTTATTGGATAAA 9 155 1 TTACTAACTT 0.776738 -89 TAAGATTTGATTTTTTATATTTTATAATAGAA 9 212 0 TTTTTTATTT 0.9664 -32 ** *** ***** Masking position 6 Map Score: 27.0864 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 633 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 TTCACAAAGTAGAATTATAGTAAAAATAAGTTAAAA 1 182 1 AGAATATAAA 0.806994 -119 AAAAATAAGTTAAAATAAACCTTAAACTTTAATGGT 1 203 1 TAAATACAAA 0.910745 -98 TCCATAATTTAAAATTGTAATATAAAAGCCCTTAGT 1 250 0 AAAATATAAA 0.963649 -51 TAAATTATGGATTAATAAAACTTAAAGGATAACACC 1 275 1 ATTATACAAA 0.555763 -26 AAAAACTGCTCCTAAAAACTCAAAAT 4 1 1 AAAACCCAAA 0.940898 -214 CCTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 4 21 1 CAAATACAAA 0.940418 -194 AATTTTTCTTATAAACAAAACCTAAATTGAGAAAAA 4 92 1 ATAACACAAA 0.916296 -123 TAAATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 4 114 1 AAAATATAAA 0.963649 -101 AGCGTTTAAAAAATGTAAATTTTAAACAATAGCCCC 4 140 0 AAATTATAAA 0.69403 -75 AAAATTCATTATAATTAACGCTCAAAAAATTGAAAA 6 31 0 ATAATCCAAA 0.851133 -138 ATTTTAAGCTAAAAACACCCCACAAATAAGCATAAA 6 62 1 AAAACCCAAA 0.940898 -107 TAAATTTTTGAAAACTAGAATTAAAACCGCTTTTTA 7 16 1 AAAATATAAA 0.963649 -96 CCGCTTTTTATAAACTGGAATTAAAACAAATTAAGC 7 42 1 TAAATATAAA 0.832624 -70 AATATCATCTCAAAGCACACCACAAAAA 8 3 0 CAAACACAAA 0.92198 -37 CCTTCGCATAAAAACTACATTATAAATAAAAAAAAT 9 80 0 AAAATATAAA 0.963649 -164 TAAAATATAAAAAATCAAATCTTAAAGGAAAATC 9 220 1 AAAACACAAA 0.976026 -24 **** * * * *** Masking position 14 Map Score: 19.1617 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 780 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 3 AAAAAGTTTTTAAAGGCAAAAAGGCTGGCGG 1 62 1 TAAAGGAAAA 0.935509 -239 TATAGTAAAAATAAGTTAAAATAAACCTTAA 1 197 1 ATAAGTAAAA 0.781924 -104 TTAAGTTTTATTAATCCATAATTTAAAATTG 1 269 0 TTAATCATAA 0.573917 -32 TTAATAAAACTTAAAGGATAACACC 1 286 1 TTAAAGATAA 0.775394 -15 AATTCAATAAAAAAGGAAAAACC 2 12 1 AAAAGGAAAA 0.907701 -13 AAACTCAAAATTAACCTAAAATCGCTTGACG 4 26 1 TTAACCAAAA 0.812532 -189 ATTAGATATAATAAGGGATAGTTACCACCTA 4 176 1 ATAAGGATAG 0.718768 -39 AGAATGAAATAAGCTATAATAAGCCCATT 5 9 1 ATAAGCATAA 0.934238 -56 ATAATGAATTTTAAGCTAAAAACACCCCACA 6 55 1 TTAAGCAAAA 0.975939 -114 CACCCCACAAATAAGCATAAATGCAACCTCT 6 77 1 ATAAGCTAAA 0.716701 -92 TTAAACAAATTTAAGGTAACACGATTATAAA 6 147 1 TTAAGGAACA 0.87983 -22 TTAAAACAAATTAAGCTATAATGATACAAAA 7 62 1 TTAAGCATAA 0.948417 -50 TTTTTAGCCATTAAGGAAAAAA 7 100 1 TTAAGGAAAA 0.98175 -12 CAAAAAATAAAAAAGGCAAAAAATACCCTTC 9 111 0 AAAAGGAAAA 0.907701 -133 AAATCAAATCTTAAAGGAAAATC 9 231 1 TTAAAGAAAA 0.872174 -13 ****** **** Masking position 4 Map Score: 15.603 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 495 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 4 TAACAAACAATAAAATTCAATTTTGCGATT 3 9 0 TAAAATAATT 0.903702 -30 ACTGCTCCTAAAAACTCAAAATTAACCTAAAA 4 15 1 AAAACTAAAT 0.961582 -200 TCTTATAAACAAAACCTAAATTGAGAAAAAAT 4 98 1 AAAACCAATT 0.855391 -117 TAAATTGAGAAAAAATTCAATTCAAAGGGGCT 4 114 1 AAAAATAATT 0.976682 -101 ATAGCGTTTAAAAAATGTAAATTTTAAACAAT 4 146 0 AAAAATAAAT 0.968178 -69 TTAACGCTCAAAAAATTGAAAAAGAGTTCAAG 6 21 0 AAAAATAAAA 0.923774 -148 TCTAGTTTTCAAAAATTTAAAAAA 7 3 0 AAAAATAAAA 0.923774 -109 TAAATTTTTGAAAACTAGAATTAAAACCGCTT 7 16 1 AAAACTAATT 0.971783 -96 CCGCTTTTTATAAACTGGAATTAAAACAAATT 7 42 1 TAAACTAATT 0.885323 -70 ATAATGATACAAAAATTTAATTTTTTAGCCAT 7 79 1 AAAAATAATT 0.976681 -33 ACAAACAACAAAAAATAAAAAAGGCAAAAAAT 9 118 0 AAAAATAAAA 0.923774 -126 ATAAAATATAAAAAATCAAATCTTAAAGGAAA 9 219 1 AAAAATAATC 0.907288 -25 ****** **** Masking position 4 Map Score: 16.5999 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 174 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 CGTTAATACATTCTAAACAAAAAGTTTTTAAA 1 44 1 TTCTAAAAAA 0.88994 -257 CACCCACCTGTCCTCATTCACAAAGTAGAATT 1 166 1 TCCTATCACA 0.930132 -135 CTTTAATGGTTTCTAAACAAAACTAAGGGCTT 1 229 1 TTCTAAAAAA 0.88994 -72 TTCTCCTATAACAAACAATAAAATT 3 24 0 TCCTTACAAA 0.771427 -15 AAAAACTGCTCCTAAAAACTCAAAATTA 4 7 1 TGCTCTAAAA 0.756693 -208 GAAATAATTTTTCTTATAAACAAAACCTAAAT 4 87 1 TTCTATAACA 0.924525 -128 AAAATAATCATTCGTATTCAAAATGGGCTTAT 5 29 0 TTCGATCAAA 0.881418 -36 TGATTGTCCTTATTAAAATAATCATTCG 5 47 0 TCCTATAAAA 0.961947 -18 AATTTTAACATGCTTTTAAAAATTTAGAGAAT 6 108 0 TGCTTTAAAA 0.839876 -61 TCCTAATTCACAATATCATCTC 8 28 0 TCCTATCACA 0.930132 -12 AAAAATACCCTTCGCATAAAAACTACATTATA 9 92 0 TTCGATAAAA 0.883187 -152 ATTGATCTCATTCTATTATAAAATATAAAAAA 9 202 1 TTCTTTTAAA 0.626678 -42 **** ** **** Masking position 10 Map Score: 6.68542 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 318 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 AAAGGAATGCTTAGAAACTATGGTGTCTCGT 1 16 1 TTAGAAACAT 0.940377 -285 TTAAGGTTTATTTTAACTTATTTTTACTATA 1 197 0 TTTTAACTAT 0.709437 -104 TTAGTTTTGTTTAGAAACCATTAAAGTTTAA 1 224 0 TTAGAAACAT 0.940381 -77 TATATTACAATTTTAAATTATGGATTAATAA 1 262 1 TTTTAAATAT 0.939321 -39 TTCTACTACATTTGAAATAATTTTTCTTATA 4 74 1 TTTGAAATAT 0.940385 -141 ATAATTTTTCTTATAAACAAAACCTAAATTG 4 90 1 TTATAAACAA 0.759674 -125 AAAATGTAAATTTTAAACAATAGCCCCTTTG 4 136 0 TTTTAAACAT 0.947179 -79 AATTTACATTTTTTAAACGCTATTAGATATA 4 155 1 TTTTAAACCT 0.754807 -60 TTAAACGCTATTAGATATAATAAGGGATAGT 4 167 1 TTAGATATAT 0.611973 -48 TTTTTTAAATTTTTGAAAACTAG 7 3 1 TTTTAAATTT 0.641965 -109 TGTGGTGTGCTTTGAGATGATATTGTGAATT 8 15 1 TTTGAGATAT 0.730311 -25 AAAAACTACATTATAAATAAAAAAAATGAAG 9 76 0 TTATAAATAA 0.731846 -168 TCTCATTCTATTATAAAATATAAAAAATCAA 9 207 1 TTATAAAAAT 0.705419 -37 ******** ** Masking position 5 Map Score: 8.26968 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 222 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 GTTTTTAAAGGCAAAAAGGCTGGCGGACAGGGAG 1 67 1 GCAAAAACGC 0.953506 -234 ATCGCTTGACGCAAAAACACTGCCTTAATTCTAC 4 46 1 GCAAAAACCC 0.991995 -169 AATGAAATAAGCTATAATAAGCCCATTTTGAATA 5 13 1 GCTATAAACC 0.946878 -52 TGAATTTTAAGCTAAAAACACCCCACAAATAAGC 6 59 1 GCTAAAAACC 0.979879 -110 CCACAAATAAGCATAAATGCAACCTCTATTCTCT 6 81 1 GCATAAACCC 0.978423 -88 AACAAATTAAGCTATAATGATACAAAAATTTAAT 7 66 1 GCTATAAACA 0.829404 -46 AATACCCTTCGCATAAAAACTACATTATAAATAA 9 87 0 GCATAAACCA 0.925236 -157 AATAAAAAAGGCAAAAAATACCCTTCGCATAAAA 9 103 0 GCAAAAAACT 0.923584 -141 ******* * ** Masking position 7 Map Score: 4.26893 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 273 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 8 ********** No masking Map Score: 1.65089e-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 9 ********** No masking Map Score: 1.65089e-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: 1.65089e-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