AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_hpyl_reg_300.orf -o00650_hpyl_300.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 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0193_HP0194 214 HP0193: fumarate reductase, cytochrome b subunit (frdC), HP0194: triosephosphate isomerase (tpi) #3 HP0688 143 H. pylori predicted coding region HP0688 #4 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #5 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #6 HP1377 300 H. pylori predicted coding region HP1377 Motif number 1 GAGAGAAAGGTTTGGGTTTAGGGTTTGAATTATAT 1 27 0 TTGGTAGGTT 0.667346 -231 GATTTAAGAGTAATGGGTGTTTGTTTTAAGACGCT 1 87 0 TAGGTTTGTT 0.704221 -171 GGTAGTTTTTTTTAAGTTGTGTTATTATTTTCAAA 1 151 0 TTAGTTTTAT 0.766782 -107 ATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 166 0 TTGGTGTTTT 0.924349 -92 ATTTAAGAATTTTAGATTGATTTTTTTAAGGGTAG 1 181 0 TTGATATTTT 0.900035 -77 TTTTAGTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 TTAGTTTTTT 0.964893 -51 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATTT 2 86 1 TTAATATTTT 0.776618 -129 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAAT 2 108 1 TTGGTTTTTA 0.821136 -107 TTCTACTACATTTGAAATAATTTTTCTTATAAACA 2 127 0 TTAATATTTT 0.776618 -88 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGC 2 152 1 TTGGATTTTT 0.914815 -63 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 179 1 TTAGTATTTT 0.95767 -36 ATTTTGAGTTTTTAGGAGCAGTTTTT 2 199 1 TTGGGATTTT 0.963183 -16 CAAAGACTGCTTAGAAAGAAATTTTTTAAAGCGTT 4 37 1 TTAAGATTTT 0.608214 -245 AGATATGCACTTTAGGCTCATGTTTCTCTAACGCT 4 66 0 TTGGTAGTTT 0.915551 -216 TGGATTTTATTTTAGGTTTTGTTTTGGATTGAGGG 4 191 0 TTGGTTTTTT 0.986145 -91 GTCTTTGCCTTTAAGTTGATTTATTATTCATAGT 4 258 0 TTAGTATTAT 0.730198 -24 TATGGTATAATAGCGGTTATTTTTTTAGAATAACC 5 98 1 TAGGTTTTTT 0.927885 -74 TTGGATTCAATTAAAGCGCTATTTTTAGCGTTGGT 5 130 0 TTAGGTTTTT 0.924655 -42 AAATGAGATTTACTGGGATTATTTTTCTTGATTTG 6 91 1 TAGGATTTTT 0.660022 -210 TTTTCTTGATTTGTGGTTTTATTTTGCTCATTCCT 6 113 1 TTGGTTTTTT 0.986145 -188 AGCGCTGGTTTTAAGGCGGTCTTTT 6 286 1 TTGGGTTTTT 0.969495 -15 ** ** * * **** Masking position 1 Map Score: 26.12 Number of sites scoring better than the average of aligned sites = 1725 Number in coding regions = 1488 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 2 AGGGTTTGAATTATATTGATTTAGCGTTACTT 1 11 0 TTTTTGATTT 0.751472 -247 AAGAGTAATGGGTGTTTGTTTTAAGACGCTAT 1 85 0 GGGTTGTTTT 0.955045 -173 AGAGTGTGAATTGGCATGATTTAAGAGTAATG 1 107 0 TTGATGATTT 0.424563 -151 TTTTAAGTTGTGTTATTATTTTCAAATTTCAA 1 145 0 TGTTTATTTT 0.891892 -113 TTTAAGAATTTTAGATTGATTTTTTTAAGGGT 1 183 0 TTGTTGATTT 0.911602 -75 TATTATAGCTATATTTTAATTTAAGAATTTTA 1 202 0 ATTTTAATTT 0.372182 -56 TTTGAAACCTTGAGATTGTTTTAGTGTATTAT 1 228 0 TGGTTGTTTT 0.980487 -30 TCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 2 181 1 TTGTTAATTT 0.852392 -34 AAAGTGCATATCTGCTTGATTTTAGATCCCCA 4 88 1 TCGTTGATTT 0.853793 -194 TTGAGGGCGATCCGTTTATTTTTTTCACAAAA 4 166 0 TCGTTATTTT 0.846312 -116 ATTTTATTTTAGGTTTTGTTTTGGATTGAGGG 4 191 0 AGTTTGTTTT 0.837617 -91 CTAACAGGTTGGATTTTATTTTAGGTTTTGTT 4 203 0 GGTTTATTTT 0.777191 -79 ATGGTATAATAGCGGTTATTTTTTTAGAATAA 5 99 1 AGGTTATTTT 0.907846 -73 TCCAAAACAAGGAGTTTATTTT 5 160 1 GGGTTATTTT 0.922459 -12 TTGGTGCGGCTGGGCTTGATTTGGAGAAATGG 6 39 0 TGGTTGATTT 0.967572 -262 TGAGATTTACTGGGATTATTTTTCTTGATTTG 6 94 1 TGGTTATTTT 0.965679 -207 TCTTGATTTGTGGTTTTATTTTGCTCATTCCT 6 116 1 TGTTTATTTT 0.891892 -185 AAAATCAATTTTCGCTAGTTTTGGATATAATC 6 208 0 TTGTAGTTTT 0.567893 -93 GAAATCATTGAGCGCTGGTTTTAAGGCGGTCT 6 276 1 AGGTGGTTTT 0.66367 -25 ** * ******* Masking position 10 Map Score: 23.309 Number of sites scoring better than the average of aligned sites = 1305 Number in coding regions = 1138 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 AATTATATTGATTTAGCGTTACTT 1 5 0 ATTTAGCGTT 0.840051 -253 ATAAAGATAGTCATAGCGTCTTAAAACAAA 1 73 1 TCATAGCGTC 0.902933 -185 TTATTATATCTAATAGCGTTTAAAAAATGT 2 46 1 TAATAGCGTT 0.94551 -169 TAAGGCAGTGTTTTTGCGTCAAGCGATTTT 2 163 1 TTTTTGCGTC 0.645414 -52 TAATTTTTAGTTATATCGTTTTTAGATTAA 3 42 1 TTATATCGTT 0.896619 -102 ACAATTAGTCTTATAGCGCTATAGTGCTGA 3 75 0 TTATAGCGCT 0.964081 -69 AAGAAATTTTTTAAAGCGTTAGAGAAACAT 4 52 1 TTAAAGCGTT 0.933271 -230 AAAATATTATTCTTATCGTTCAATGATTAT 4 139 0 TCTTATCGTT 0.730379 -143 TCTTATGGTATAATAGCGGTTATTTTTTTA 5 95 1 TAATAGCGGT 0.881811 -77 AAAGCGCTATTTTTAGCGTTGGTTATTCTA 5 123 0 TTTTAGCGTT 0.978422 -49 TTGGATTCAATTAAAGCGCTATTTTTAGCG 5 135 0 TTAAAGCGCT 0.857422 -37 GTAAATCTCATTTTAGCGGTAGGTGGCGTC 6 74 0 TTTTAGCGGT 0.951212 -227 ********** Masking position 7 Map Score: 14.3985 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 915 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 CGCTAAATCAATATAATTCAAACCCTAAACC 1 17 1 ATATAATCAA 0.904009 -241 TGAAATTTGAAAATAATAACACAACTTAAAA 1 146 1 AAATAATACA 0.763191 -112 AACTACCCTTAAAAAAATCAATCTAAAATTC 1 179 1 AAAAAAACAA 0.686774 -79 AATAGCGTTTAAAAAATGTAAATTTTAAACA 2 57 1 AAAAAATTAA 0.840988 -158 CTAAATTGAGAAAAAATTCAATTCAAAGGGG 2 92 0 AAAAAATCAA 0.921162 -123 TTTCTTATAAACAAAACCTAAATTGAGAAAA 2 109 0 ACAAAACTAA 0.558093 -106 TCTAAAAACGATATAACTAAAAATTAGAAAA 3 37 0 ATATAACAAA 0.737754 -107 ACTAATTGTTATATAATAAAAGCGAGACAAG 3 96 1 ATATAATAAA 0.835138 -48 CAAGAATGTTAAAAAATGAAAGGAGCGTGTA 3 123 1 AAAAAATAAA 0.862729 -21 TATTTTTGTGAAAAAAATAAACGGATCGCCC 4 163 1 AAAAAAAAAA 0.541151 -119 TCAATCCAAAACAAAACCTAAAATAAAATCC 4 194 1 ACAAAACTAA 0.558093 -88 AAAACCTAAAATAAAATCCAACCTGTTAGGG 4 206 1 ATAAAATCAA 0.921162 -76 TATTCCCACCAAATAATGTCAGCACCATTTC 6 15 1 AAATAATTCA 0.730608 -286 AAATCAAGAAAAATAATCCCAGTAAATCTCA 6 94 0 AAATAATCCA 0.856971 -207 AATGAGCAAAATAAAACCACAAATCAAGAAA 6 114 0 ATAAAACACA 0.689492 -187 CCGAATCATTATAAAATATAATAAGGAGTTG 6 148 0 ATAAAATTAA 0.84097 -153 CTAGTTTTGGATATAATCCCAATAACTTAAC 6 195 0 ATATAATCCA 0.856971 -106 AAATTGTTTGATATAATACAGAGTTTAGCTT 6 244 1 ATATAATCAG 0.513699 -57 ******* *** Masking position 6 Map Score: 13.725 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 657 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 ATCAATATAATTCAAACCCTAAACCCAAAC 1 23 1 TTCAAACCCT 0.991857 -235 ATCATGCCAATTCACACTCTTTAGACTTGA 1 119 1 TTCACACTCT 0.939839 -139 GGCTAAATTTTGAAACCTTGAGATTGTTT 1 239 0 TTGAAACCTT 0.928246 -19 ATGCGGAGCATTCAAACCCA 3 1 0 TTCAAACCCA 0.967794 -143 AATTCTATTAAAACCCTGAAACTAGGC 4 8 1 TTAAAACCCT 0.968412 -274 TTTTAGGTGATTGACACCCTAACAGGTTGG 4 223 0 TTGACACCCT 0.98578 -59 ********** Masking position 6 Map Score: 5.27409 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 126 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 AACCCAAACCTTTCTCTCATATATCTCGCA 1 44 1 TTTCTCTCAT 0.868392 -214 CAAACACCCATTACTCTTAAATCATGCCAA 1 99 1 TTACTCTTAA 0.738173 -159 TTAAGGGTAGTTTTTTTTAAGTTGTGTTAT 1 161 0 TTTTTTTTAA 0.536491 -97 TGAATTGAATTTTTTCTCAATTTAGGTTTT 2 98 1 TTTTTCTCAA 0.942641 -117 TTTGAAATAATTTTTCTTATAAACAAAACC 2 122 0 TTTTTCTTAT 0.953179 -93 CGCATTAAAGTTTTTCTAATTTTTAGTTAT 3 26 1 TTTTTCTAAT 0.865468 -118 TATATAACAATTAGTCTTATAGCGCTATAG 3 81 0 TTAGTCTTAT 0.639619 -63 CACAAAAATATTATTCTTATCGTTCAATGA 4 143 0 TTATTCTTAT 0.904072 -139 TCCGTTTATTTTTTTCACAAAAATATTATT 4 158 0 TTTTTCACAA 0.636188 -124 CAAGCGAGCGGTTTTCTTATGGTATAATAG 5 81 1 GTTTTCTTAT 0.762523 -91 TTAGCGTTGGTTATTCTAAAAAAATAACCG 5 111 0 TTATTCTAAA 0.719852 -61 ACTGGGATTATTTTTCTTGATTTGTGGTTT 6 102 1 TTTTTCTTGA 0.734866 -199 TGTGGTTTTATTTTGCTCATTCCTCAACTC 6 124 1 TTTTGCTCAT 0.750178 -177 ********** Masking position 2 Map Score: 7.33048 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 685 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 CGTCTTAAAACAAACACCCATTACTCTTAA 1 89 1 CAAACACCCA 0.864957 -169 GCTTGACGCAAAAACACTGCCTTAATTCTA 2 157 0 AAAACACTGC 0.969924 -58 AATTCTATTAAAACCCTGAAACTAGGCAA 4 10 1 AAAACCCTGA 0.843756 -272 TGAAACTAGGCAAAGACTGCTTAGAAAGAA 4 27 1 CAAAGACTGC 0.918197 -255 TGTATTTGCAAAAACACCGATGCATTGCGC 5 53 0 AAAACACCGA 0.96967 -119 AATTGAATCCAAAACAAGGAGTTTATTTT 5 153 1 AAAACAAGGA 0.710225 -19 AGCCGCACCAAAAAGACGCCACCTACCGCT 6 60 1 AAAAGACGCC 0.88332 -241 AAAAGACCGCCTTAAAACCA 6 291 0 AAAAGACCGC 0.968914 -10 ********** Masking position 4 Map Score: 2.96658 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 318 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.971807 -51 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.877434 -11 ATTCAAAGGGGCTATTGTTTAAAATTTACA 2 73 0 GCTATTGTTT 0.946869 -142 GTCTTATAGCGCTATAGTGCTGACTTTTAA 3 68 0 GCTATAGTGC 0.850412 -76 CCCACTCAAAGCTATATTGTGCAATAATCA 4 116 1 GCTATATTGT 0.958301 -166 TATAATAGCGGTTATTTTTTTAGAATAACC 5 103 1 GTTATTTTTT 0.774534 -69 CAATTAAAGCGCTATTTTTAGCGTTGGTTA 5 128 0 GCTATTTTTA 0.867262 -44 ********** Masking position 4 Map Score: 2.56977 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 115 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TGAACGATCCTTATTTTATAGGTGGTAA 2 9 1 CCTTATTTTA 0.932695 -206 GGTAACTATCCCTTATTATATCTAATAGCG 2 34 1 CCTTATTATA 0.978536 -181 AAAAAATAACCGCTATTATACCATAAGAAA 5 93 0 CGCTATTATA 0.908897 -79 TTCCTCAACTCCTTATTATATTTTATAATG 6 143 1 CCTTATTATA 0.978536 -158 AAGCTAAACTCTGTATTATATCAAACAATT 6 245 0 CTGTATTATA 0.870655 -56 ********** Masking position 5 Map Score: 1.33933 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 7 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: -4.73059e-14 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: -4.73059e-14 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: -4.73059e-14 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