AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_hpyl_reg_300.orf -o00340_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 HP0194 214 triosephosphate isomerase (tpi) #3 HP1054 63 H. pylori predicted coding region HP1054 #4 HP1057 148 H. pylori predicted coding region HP1057 #5 HP1067 290 chemotaxis protein (cheY) #6 HP1190 61 histidyl-tRNA synthetase (hisS) Motif number 1 AAGTAACGCTAAATCAATATAATT 1 1 1 AATACTAAAT 0.923812 -257 AACAAACACCCATTACTCTTAAATCATGCCAATT 1 97 1 CATCTTAAAT 0.652222 -161 TGAAAATAATAACACAACTTAAAAAAAACTACCC 1 153 1 AAAATTAAAA 0.920998 -105 ACTTAAAAAAAACTACCCTTAAAAAAATCAATCT 1 169 1 AATCTTAAAA 0.96616 -89 ACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 183 1 AATACTAAAA 0.977341 -75 AAATATAGCTATAATACACTAAAACAATCTCAAG 1 218 1 ATAACTAAAA 0.904799 -40 AAAAACTGCTCCTAAAAACTCAAAATT 2 4 1 AATCCTAAAA 0.984308 -211 TAAAAACTCAAAATTAACCTAAAATCGCTTGACG 2 23 1 AATACTAAAA 0.977341 -192 TTTTCTTATAAACAAAACCTAAATTGAGAAAAAA 2 95 1 AAAACTAAAT 0.878203 -120 AATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 2 116 1 AATCTTCAAA 0.75171 -99 TATTATATCTAATAGCGTTTAAAAAATGTAAATT 2 155 0 AAACTTAAAA 0.944303 -60 AAATTAAAACGACTAACGCTAAAATTTTAAACCT 3 29 0 GATACTAAAA 0.909636 -35 ATAACCCCCTAAAATTAAAACGAC 3 50 0 ATACCTAAAA 0.932533 -14 CACCCTAATAAAGTCATGCTACAATGCCACTATA 4 31 0 AATACTACAA 0.820584 -118 AATAATTAAAATGACCGGTTAAAATGGAGTAAAA 4 73 0 ATACTTAAAA 0.86285 -76 AAGTTTCTTTCAATTATACTAAAATAATTAAAAT 4 95 0 CATACTAAAA 0.909636 -54 GTTTGCTATGATAATCGTTTAAAAGTAATAAAAT 5 79 0 ATACTTAAAA 0.86285 -212 CTCCTTTTAAGATTGCATTTAAATTAGGCTCTTT 5 260 0 GATCTTAAAT 0.652279 -31 TTTTTTAAAGATTTTAAGCTAAAATTTTAGCATA 6 20 1 ATTACTAAAA 0.941174 -42 ** * * ****** Masking position 10 Map Score: 24.786 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1164 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.951041 -11 CAAAAACACTGCCTTAATTCTACTACATTTG 2 57 1 GCTTAATTCT 0.698961 -158 AGGGGCTATTGTTTAAAATTTACATTTTTTA 2 139 1 GTTAAAATTT 0.982351 -76 TGGAGTTAAGGTTTAAAATTTTAGCGTTAGT 3 21 1 GTTAAAATTT 0.982351 -43 AGCGTTAGTCGTTTTAATTTTAGGGGGTTAT 3 43 1 GTTTAATTTT 0.926244 -21 TATTAGGGTGGGTAAAAATTTTACTCCATTT 4 55 1 GTAAAAATTT 0.961836 -94 TGAATTGTTTGTTAAAAGTTTCTTTCAATTA 4 113 0 GTAAAAGTTT 0.902107 -36 AGCATGTTTTGATTAAAATTACCTTGACCGA 5 175 0 GTTAAAATTA 0.886772 -116 TAAAATTTTAGCTTAAAATCTTTAAAAAAGG 6 18 0 GTTAAAATCT 0.959892 -44 GTATTTGTATGCTAAAATTTTAGCTTAAAAT 6 30 0 GTAAAATTTT 0.953394 -32 * ********* Masking position 6 Map Score: 10.8931 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 358 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 ATAGCGTCTTAAAACAAACACCCATTACTCT 1 85 1 AAAACAACAC 0.894333 -173 AACACAACTTAAAAAAAACTACCCTTAAAAA 1 163 1 AAAAAAACTA 0.9468 -95 AACTACCCTTAAAAAAATCAATCTAAAATTC 1 179 1 AAAAAAACAA 0.953741 -79 ATAATACACTAAAACAATCTCAAGGTTTCAA 1 228 1 AAAACAACTC 0.879603 -30 AAAAACTGCTCCTAAAAACTC 2 1 1 AAAAACTCTC 0.710636 -214 TTTTCTTATAAACAAAACCTAAATTGAGAAA 2 95 1 AACAAAACTA 0.737328 -120 CTAAATTGAGAAAAAATTCAATTCAAAGGGG 2 113 1 AAAAAATCAA 0.969939 -102 AATAGCGTTTAAAAAATGTAAATTTTAAACA 2 148 0 AAAAAATTAA 0.680022 -67 TAAAAATCCTAAGTGTTAAAT 4 1 1 TAAAAATCTA 0.747724 -148 AACTTTTAACAAACAATTCAAGGGATTTGGC 4 124 1 AAACAATCAA 0.910664 -25 TTCTTTTTTCAAACCATCCAATGACCCTTTA 5 32 1 AAACCATCAA 0.882149 -259 CTTATTTGTAAAAAAATTCAGTTTGTTTGCT 5 106 0 AAAAAATCAG 0.870617 -185 AATTTTAATCAAAACATGCTATTATTTGGAA 5 186 1 AAAACATCTA 0.953384 -105 ******* *** Masking position 2 Map Score: 10.6835 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 850 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 TTAGGGTTTGAATTATATTGATTTAGCGTTACTT 1 11 0 AATATGATTT 0.423084 -247 TTTCAAGTCTAAAGAGTGTGAATTGGCATGATTT 1 117 0 AAATTGAATT 0.838312 -141 AAATCAATCTAAAATTCTTAAATTAAAATATAGC 1 193 1 AAACTAAATT 0.958258 -65 AAAAACTCAAAATTAACCTAAAATCGCTTGACGC 2 24 1 AATCTAAAAT 0.745705 -191 AAATTATTTCAAATGTAGTAGAATTAAGGCAGTG 2 63 0 AAAATAGAAT 0.654699 -152 TTTCTTATAAACAAAACCTAAATTGAGAAAAAAT 2 96 1 ACACTAAATT 0.745861 -119 AATAGCGTTTAAAAAATGTAAATTTTAAACAATA 2 145 0 AAATTAAATT 0.840624 -70 ATAACCCCCTAAAATTAAAACGACT 3 49 0 TAACTAAAAT 0.608579 -15 TGACCGGTTAAAATGGAGTAAAATTTTTACCCAC 4 62 0 AAAATAAAAT 0.937298 -87 CAATTATACTAAAATAATTAAAATGACCGGTTAA 4 85 0 AAAATAAAAT 0.937016 -64 AATCGCCAAATCCCTTGAATTGTTTGTTAAA 4 128 0 AAACTGAATT 0.828193 -21 TTGAAAAAAGAAAGACAAGGATTTTACAAGTAA 5 10 0 AAAAGGATTT 0.536561 -281 ATAATCGTTTAAAAGTAATAAAATAACTCTTTGA 5 69 0 AAAATAAAAT 0.937309 -222 TTATCATAGCAAACAAACTGAATTTTTTTACAAA 5 99 1 AAAATGAATT 0.949014 -192 GGCTGTTTAAAAAGAGCCTAATTTAAATGCAATC 5 250 1 AAACTAATTT 0.851963 -41 TTTAGCATACAAATACAAGGAAATGGA 6 45 1 AAAAGGAAAT 0.785247 -17 *** * ****** Masking position 14 Map Score: 11.596 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 762 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 TTTAAGTTGTGTTATTATTTTCAAATTTCA 1 146 0 GTTATTATTT 0.909398 -112 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.623614 -51 ATTCAAAGGGGCTATTGTTTAAAATTTACA 2 133 1 GCTATTGTTT 0.854528 -82 GTGGTAACTATCCCTTATTATATCTAATAG 2 174 0 TCCCTTATTA 0.718776 -41 TGAACGATCCTTATTTTATAGGTGGT 2 199 0 ATCCTTATTT 0.571775 -16 AATCCTTGTCTTTCTTTTTTCAAACCATCC 5 21 1 TTTCTTTTTT 0.786291 -270 TTCAATGAGCGTTCTTATTTGTAAAAAAAT 5 120 0 GTTCTTATTT 0.950226 -171 ATCAAAACATGCTATTATTTGGAACGATTT 5 193 1 GCTATTATTT 0.950226 -98 TTTGGAACGATTTATTATTATAAGGCGTTA 5 210 1 TTTATTATTA 0.53009 -81 TTTAAATTAGGCTCTTTTTAAACAGCCAAA 5 247 0 GCTCTTTTTA 0.908077 -44 CAATAGCCCTTTTTTAAAGATTTTA 6 6 1 GCCCTTTTTT 0.939517 -56 ********** Masking position 5 Map Score: 4.70754 Number of sites scoring better than the average of aligned sites = 1261 Number in coding regions = 1108 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 GGGTTTAGGGTTTGAATTATATTGATTTAG 1 19 0 TTTGAATTAT 0.771949 -239 GTGTTATTATTTTCAAATTTCAAGTCTAAA 1 138 0 TTTCAAATTT 0.952862 -120 AATCTCAAGGTTTCAAAATTTAGCC 1 243 1 TTTCAAAATT 0.739879 -15 AGAAAAATTATTTCAAATGTAGTAGAATTA 2 71 0 TTTCAAATGT 0.88083 -144 GGGGCTATTGTTTAAAATTTACATTTTTTA 2 140 1 TTTAAAATTT 0.872294 -75 GGAGTTAAGGTTTAAAATTTTAGCGTTAGT 3 22 1 TTTAAAATTT 0.872294 -42 GCGTTAGTCGTTTTAATTTTAGGGGGTTAT 3 44 1 TTTTAATTTT 0.882548 -20 AAATCCTAAGTGTTAAATATAGTGGCATTG 4 14 1 TGTTAAATAT 0.705884 -135 TAACCGGTCATTTTAATTATTTTAGTATAA 4 86 1 TTTTAATTAT 0.882548 -63 TAAAAGTTTCTTTCAATTATACTAAAATAA 4 102 0 TTTCAATTAT 0.922592 -47 AATAGCCCTTTTTTAAAGATTTTAAGCTAA 6 12 1 TTTTAAAGAT 0.726612 -50 ********** Masking position 5 Map Score: 8.05822 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 524 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 7 TAAAGATAGTCATAGCGTCTTAAAACAAAC 1 74 1 CATAGCGTCT 0.925649 -184 GATTTAAGAGTAATGGGTGTTTGTTTTAAG 1 92 0 TAATGGGTGT 0.821086 -166 ATTTCAAGTCTAAAGAGTGTGAATTGGCAT 1 122 0 TAAAGAGTGT 0.907502 -136 AAATTCAATTCAAAGGGGCTATTGTTTAAA 2 126 1 CAAAGGGGCT 0.964129 -89 TTGAGTGCGATAAAGGGTCATTGGATGGTT 5 43 0 TAAAGGGTCA 0.948447 -248 TTATCGCACTCAAAGAGTTATTTTATTACT 5 60 1 CAAAGAGTTA 0.763686 -231 TTTAAACAGCCAAAGCGTCTCTAACGCCTT 5 231 0 CAAAGCGTCT 0.983596 -60 ********** Masking position 2 Map Score: 0.736653 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 272 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ********** No masking Map Score: 1.63668e-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: 1.63668e-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: 1.63668e-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