AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_hpyl_reg_100.orf -o00310_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 Input sequences: #1 HP0170 74 H. pylori predicted coding region HP0170 #2 HP0171 60 peptide chain release factor RF-2 (prfB) #3 HP0174 300 H. pylori predicted coding region HP0174 #4 HP0180_HP0181 257 HP0180: apolipoprotein N-acyltransferase (cute), HP0181: H. pylori predicted coding region HP0181 #5 HP0194 214 triosephosphate isomerase (tpi) #6 HP0654 296 conserved hypothetical protein #7 HP0655 82 protective surface antigen D15 #8 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #9 HP1010 300 polyphosphate kinase (ppk) #10 HP1011 36 dihydroorotate dehydrogenase (pyrD) #11 HP1435 70 protease IV (PspA) Motif number 1 TGGTTACTATAAAACGCTTTTTAAAACCAATTGGC 1 39 1 AAAATTTAAA 0.757233 -36 TGATAAGTTCAAAACCCCACTCATAAAGGTTCTGT 2 34 1 AAAACTCATA 0.590094 -27 CAAAAAGAATAAAACTAACACCAAAAAAGACAATA 3 57 0 AAAAACCAAA 0.918944 -244 TTTTGGAAAGAAAAAAAATGTTAAAGAAGATTCAA 3 87 1 AAAAATTAAA 0.947908 -214 TGCAATGCTAAAAAACCAAATATAAAGAATAATAA 3 196 0 AAAAATATAA 0.786912 -105 TTTGAAAATAATAACACAACTTAAAAAAAACTACC 4 151 1 ATAAATTAAA 0.720976 -107 ACAACTTAAAAAAAACTACCCTTAAAAAAATCAAT 4 166 1 AAAAACTTAA 0.940324 -92 CTACCCTTAAAAAAATCAATCTAAAATTCTTAAAT 4 181 1 AAAAACTAAA 0.940342 -77 TTCTTAAATTAAAATATAGCTATAATACACTAAAA 4 207 1 AAAAATATAA 0.786913 -51 AAAAACTGCTCCTAAAAACTCAAAAT 5 2 1 AAAACCTAAA 0.848032 -213 CTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 5 22 1 AAAAATAAAA 0.786913 -193 GCTTGACGCAAAAACACTGCCTTAATTCTACTACA 5 49 1 AAAATCTTAA 0.729866 -166 TGTTTATAAGAAAAATTATTTCAAATGTAGTAGAA 5 74 0 AAAAATCAAA 0.929018 -141 AATTTTTCTTATAAACAAAACCTAAATTGAGAAAA 5 92 1 ATAAACCTAA 0.616838 -123 AAATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 5 115 1 AAAAATCAAA 0.929018 -100 TAGCGTTTAAAAAATGTAAATTTTAAACAATAGCC 5 142 0 AAAAATTTTA 0.8497 -73 TTTTTATGATAAAATCTAAGCTTTATCAAGCCATT 6 129 0 AAAAACTTTA 0.830424 -168 TATAATATGTAAAAAGCATTCTTAAATCTAAAAAT 6 232 1 AAAAACTTAA 0.940324 -65 AACGCTTTAAAAAATTTCTTTCTAAGCAGTCTTTG 8 37 0 AAAACTCTAA 0.822493 -245 TTTTTTCACAAAAATATTATTCTTATCGTTCAATG 8 144 0 AAAATTCTTA 0.41073 -138 CCCTCAATCCAAAACAAAACCTAAAATAAAATCCA 8 191 1 AAAAACTAAA 0.940343 -91 ACTATGAATAATAAATCAACTTAAAGGCAAAGAC 8 258 1 ATAAATTAAA 0.720976 -24 ATTTAACCCTAAAAGATCGCTTAAAATTTTTTTAG 9 16 0 AAAACTTAAA 0.865631 -285 GTTTTATTCAAAAAATGAAGTTTTACAAAAAAGAG 9 54 1 AAAAATTTTA 0.849583 -247 GAAGTTTTACAAAAAAGAGTTTTTAAACAACAACT 9 70 1 AAAAATTTTA 0.849583 -231 TCACACCAAACAAACTGATTTTTAAACATGATGAT 9 262 1 CAAAATTTAA 0.582622 -39 **** * ***** Masking position 4 Map Score: 28.5588 Number of sites scoring better than the average of aligned sites = 1395 Number in coding regions = 1047 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 2 AAGTAACGCTAAATCAATATAAT 4 4 1 TAACGCTAAA 0.931264 -254 AATATAATTCAAACCCTAAACCCAAACCTT 4 26 1 AAACCCTAAA 0.976725 -232 AAATAATAACACAACTTAAAAAAAACTACC 4 156 1 ACAACTTAAA 0.847486 -102 CTTAAAAAAATCAATCTAAAATTCTTAAAT 4 186 1 TCAATCTAAA 0.797626 -72 AAACTCAAAATTAACCTAAAATCGCTTGAC 5 26 1 TTAACCTAAA 0.786295 -189 TCTTATAAACAAAACCTAAATTGAGAAAAA 5 98 1 AAAACCTAAA 0.970849 -117 TAATTATGGGACAACTTAAACCAACACAAA 6 20 0 ACAACTTAAA 0.847486 -277 AAAGCATTCTTAAATCTAAAAATGCTACAA 6 244 1 TAAATCTAAA 0.784169 -53 TCATTCTTAAAAACGCTAAAAATTA 7 6 0 AAACGCTAAA 0.945222 -77 CTAACAACACTCAAGCTAAAATCTATTAAG 7 54 1 TCAAGCTAAA 0.921027 -29 AATTCTATTAAAACCCTGAAACTAGGCAAA 8 11 1 AAACCCTGAA 0.841819 -271 AATCCAAAACAAAACCTAAAATAAAATCCA 8 196 1 AAAACCTAAA 0.970849 -86 TAGGTGATTGACACCCTAACAGGTTGGATT 8 220 0 ACACCCTAAC 0.852359 -62 GAATAATAAATCAACTTAAAGGCAAAGAC 8 263 1 TCAACTTAAA 0.813539 -19 AAACGCTAAAAAAATTTTAA 9 1 1 AAACGCTAAA 0.945222 -300 AAACTTCATTTAACCCTAAAAGATCGCTTA 9 28 0 TAACCCTAAA 0.970545 -273 ********** Masking position 7 Map Score: 20.8903 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 651 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 TATAAAACGCTTTTTAAAACCAATTGGCAAGGA 1 46 1 TTTTTAAAAA 0.946918 -29 CATTATAGCATTGTTAAAAGCCATT 2 3 0 TTGTTAAAAA 0.838138 -58 TGGGTGTTTGTTTTAAGACGCTATGACTATCTT 4 76 0 TTTTAAGACA 0.892586 -182 AAAAATGTAAATTTTAAACAATAGCCCCTTTGA 5 135 0 ATTTTAAACA 0.73806 -80 AAATTTACATTTTTTAAACGCTATTAGATATAA 5 154 1 TTTTTAAACA 0.966249 -61 GTATGAAAATTTTTAAAAATTTACAAAAATGAG 6 82 1 TTTTAAAAAA 0.946919 -215 TGCCCTTTCGTTTTAAAGATAAACATTGTAGCA 6 266 0 TTTTAAAGAA 0.92205 -31 ATTTTTAGCGTTTTTAAGAATGATTAGTTATAA 7 13 1 TTTTTAAGAA 0.92205 -70 GAAAGAAATTTTTTAAAGCGTTAGAGAAACATG 8 50 1 TTTTAAAGCA 0.949957 -232 AAACTCTTTTTTGTAAAACTTCATTTTTTGAAT 9 59 0 TTGTAAAACA 0.892586 -242 CAAAAAAGAGTTTTTAAACAACAACTAAGCAAA 9 79 1 TTTTTAAACA 0.966248 -222 ATTGAAGCTTTTTTAAAAAGTCATGGTCGGAGT 9 208 0 TTTTAAAAAA 0.946919 -93 AACAAACTGATTTTTAAACATGATGATTTAAAG 9 270 1 TTTTTAAACA 0.966249 -31 ACTTCAAATGTTTTAAGGATTAAATC 11 4 0 TTTTAAGGAA 0.774444 -67 ********* * Masking position 6 Map Score: 16.0552 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 661 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 ATTCAAAGCGGGTAAAAGTGTTCG 3 5 1 AAAGCGGGTA 0.868015 -296 AAGTTATTTAATATGGGATAACATGCAATG 3 224 0 ATATGGGATA 0.799007 -77 AATTCAATTCAAAGGGGCTATTGTTTAAAA 5 127 1 AAAGGGGCTA 0.941157 -88 ATTAGATATAATAAGGGATAGTTACCACCT 5 176 1 ATAAGGGATA 0.928973 -39 TCCTTATTTTATAGGTGGTAACTATCCCTT 5 188 0 ATAGGTGGTA 0.851632 -27 AAACCAACACAAAGGAGATACT 6 3 0 AAAGGAGATA 0.835954 -294 ATTAGGTAAAAAAAGGGGTTGGCATCAATA 6 178 1 AAAAGGGGTT 0.856386 -119 GTTGGCATCAATAGGGGGTTAAAAGGGGAT 6 195 1 ATAGGGGGTT 0.891758 -102 TAGGGGGTTAAAAGGGGATATTTTTATATA 6 206 1 AAAGGGGATA 0.981125 -91 TCAATCACCTAAAAGTGATACTATGAATAA 8 239 1 AAAAGTGATA 0.793164 -43 TCCGCAATCAAAAAGGGAGATTGTAGCGCG 9 114 0 AAAAGGGAGA 0.806855 -187 ********** Masking position 3 Map Score: 8.35939 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 370 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GGCTTTTAACAATGCTATAATGATAAGTTC 2 14 1 AATGCTATAA 0.950861 -47 GATAACATGCAATGCTAAAAAACCAAATAT 3 208 0 AATGCTAAAA 0.897562 -93 ATAACTTCTATACTCTATTAATCAATCTCA 3 247 1 TACTCTATTA 0.610826 -54 ACACTGCCTTAATTCTACTACATTTGAAAT 5 62 1 AATTCTACTA 0.773681 -153 ACATTTTTTAAACGCTATTAGATATAATAA 5 160 1 AACGCTATTA 0.963944 -55 CATTATCATTTATGCTATAATTATGGGACA 6 37 0 TATGCTATAA 0.798071 -260 TAAATCTAAAAATGCTACAATGTTTATCTT 6 254 1 AATGCTACAA 0.93233 -43 CATTCTTAAAAACGCTAAAAATTA 7 5 0 AACGCTAAAA 0.93344 -78 TAGTTATAATAACGCTACTAACAACACTCA 7 37 1 AACGCTACTA 0.950088 -46 ACTCAAGCTAAAATCTATTAAGGAAATCAG 7 62 1 AAATCTATTA 0.499194 -21 AATTCTATTAAAACCCTGAA 8 1 1 AATTCTATTA 0.827624 -281 ATGTTTCTCTAACGCTTTAAAAAATTTCTT 8 52 0 AACGCTTTAA 0.767221 -230 AAACGCTAAAAAAATTTTAAG 9 2 1 AACGCTAAAA 0.93344 -299 ********** Masking position 2 Map Score: 13.6753 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 393 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 TGTCGTTCCTTGCCAATTGGTTTTAAAA 1 57 0 TCTTCCAATT 0.714553 -18 GTAATAATATTTATTGTCTTTTTTGGTGTTAG 3 46 1 TTTTTCTTTT 0.879974 -255 TTGGTGTTAGTTTTATTCTTTTTGGAAAGAAA 3 68 1 TTTATCTTTT 0.459222 -233 TTTTGAATCTTCTTTAACATTTTTTTTCTTTC 3 92 0 TCTTACATTT 0.878389 -209 TGAATTGAATTTTTTCTCAATTTAGGTTTTGT 5 106 0 TTTTTCAATT 0.621593 -109 ATTTACTTTTTCATTATCATTTATGCTATAAT 6 46 0 TCTTTCATTT 0.962941 -251 TTTCATACTCTCATTTACTTTTTCATTATCAT 6 58 0 TCTTACTTTT 0.878389 -239 TAGCCGGTGTTCTTTCTCATTTTTGTAAATTT 6 98 0 TCTTTCATTT 0.962941 -199 AATGCTACAATGTTTATCTTTAAAACGAAAGG 6 264 1 TGTTTCTTTA 0.639413 -33 GTCTTTGCCTTTAAGTTGATTTA 8 269 0 TCTTCCTTTA 0.714553 -13 AAAGCTTCAATGATTATCATTTCATTATATAA 9 230 1 TGTTTCATTT 0.887822 -71 TTAAATCCTTATCTTTTATGATTTGAA 10 20 0 TCTTTCTTTT 0.962941 -17 ** ** ****** Masking position 4 Map Score: 7.1087 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 477 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 TTTGGGTTTAGGGTTTGAATTATATTGATT 4 22 0 GGGTTTGAAT 0.987638 -236 CAAGTCTAAAGAGTGTGAATTGGCATGATT 4 118 0 GAGTGTGAAT 0.947121 -140 GTAAAAAAAGGGGTTGGCATCAATAGGGGG 6 183 1 GGGTTGGCAT 0.923172 -114 CCTAGTTTCAGGGTTTTAATAGAATT 8 7 0 GGGTTTTAAT 0.911993 -275 CAACCTGTTAGGGTGTCAATCACCTAAAAG 8 224 1 GGGTGTCAAT 0.937712 -58 ATTGTAGCGCGAGTTTGCTTAGTTGTTGTT 9 95 0 GAGTTTGCTT 0.791149 -206 GTGAGGTCGTGGGTTTGAATCCCGCTACTC 9 182 1 GGGTTTGAAT 0.987638 -119 TCAGTTTGTTTGGTGTGATTATATAATGAA 9 250 0 TGGTGTGATT 0.761978 -51 ********** Masking position 4 Map Score: 4.87883 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 147 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 GTGCGCTAAAATGACAGCCGATAA 1 5 1 GCTAAAATGA 0.927823 -70 TTTTAACAATGCTATAATGATAAGTTCAAA 2 17 1 GCTATAATGA 0.972304 -44 AATTCTCGATGCAATTATGAATATAATATT 3 123 1 GCAATTATGA 0.525356 -178 GTGTATTATAGCTATATTTTAATTTAAGAA 4 207 0 GCTATATTTT 0.626445 -51 TATCATTTATGCTATAATTATGGGACAACT 6 34 0 GCTATAATTA 0.889277 -263 ATCTAAAAATGCTACAATGTTTATCTTTAA 6 257 1 GCTACAATGT 0.960589 -40 CAACACTCAAGCTAAAATCTATTAAGGAAA 7 58 1 GCTAAAATCT 0.847906 -25 CCCACTCAAAGCTATATTGTGCAATAATCA 8 116 1 GCTATATTGT 0.879936 -166 GCTATATTGTGCAATAATCATTGAACGATA 8 126 1 GCAATAATCA 0.817849 -156 GCAAACTCGCGCTACAATCTCCCTTTTTGA 9 107 1 GCTACAATCT 0.926259 -194 TTTTAAAAAAGCTTCAATGATTATCATTTC 9 223 1 GCTTCAATGA 0.786333 -78 ********** Masking position 8 Map Score: 7.11425 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 129 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 TCTTTCCAAAAAGAATAAAACTAACACCAA 3 68 0 AAGAATAAAA 0.809763 -233 ATGCAATTATGAATATAATATTCGTAATTA 3 131 1 GAATATAATA 0.769116 -170 ACCAAATATAAAGAATAATAACCCTGGTAA 3 187 0 AAGAATAATA 0.959599 -114 CTTGAAATTTGAAAATAATAACACAACTTA 4 144 1 GAAAATAATA 0.900994 -114 ATTGAACGATAAGAATAATATTTTTGTGAA 8 145 1 AAGAATAATA 0.959599 -137 ATATTTTTGTGAAAAAAATAAACGGATCGC 8 162 1 GAAAAAAATA 0.619897 -120 AAGTGATACTATGAATAATAAATCAACTTA 8 251 1 ATGAATAATA 0.809763 -31 AAAACATTTGAAGTATAATACACTCTTATG 11 23 1 AAGTATAATA 0.896835 -48 ********** Masking position 5 Map Score: 2.88759 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 53 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 AAGTTCAAAACCCCACTCATAAAGGTTCTGT 2 38 1 CCCACTCATA 0.960409 -23 ACGCTACTAACAACACTCAAGCTAAAATCTA 7 48 1 CACACTCAAG 0.923946 -35 GATTTTAGATCCCCACTCAAAGCTATATTGT 8 105 1 CCCACTCAAA 0.989932 -177 AACGGATCGCCCTCAATCCAAAACAAAACCT 8 182 1 CCCAATCCAA 0.958097 -100 GCGCCATACTCCGCAATCAAAAAGGGAGATT 9 122 0 CCCAATCAAA 0.98426 -179 TATATAATCACACCAAACAAACTGATTTTTA 9 255 1 CACAAACAAA 0.839043 -46 ** ******** Masking position 5 Map Score: 1.56732 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 108 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 GGTTATTATTCTTTATATTTGGTTTTTTAGC 3 194 1 CTTATATTTG 0.961469 -107 ACTCTTTAGACTTGAAATTTGAAAATAATAA 4 134 1 CTTAAATTTG 0.961469 -124 TAAAAGATCGCTTAAAATTTTTTTAGCGTTT 9 11 0 CTTAAATTTT 0.94072 -290 TTTTGTAAAACTTCATTTTTTGAATAAAACT 9 53 0 CTTATTTTTT 0.79654 -248 GTGTATTATACTTCAAATGTTTTAAGGATTA 11 15 0 CTTAAATGTT 0.852995 -56 TTTTCCTAAACTTAATATTTGACCATAAGAG 11 45 0 CTTATATTTG 0.961467 -26 *** ******* Masking position 5 Map Score: 1.18628 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 83 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 ********** No masking Map Score: -7.17405e-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 13 ********** No masking Map Score: -7.17405e-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 14 ********** No masking Map Score: -7.17405e-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