AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_hpyl_reg_100.orf -o00380_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: HP1253 31 tryptophanyl-tRNA synthetase (trpS) Input sequences: #1 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #3 HP0830 58 amidase #4 HP0832 91 spermidine synthase (speE) #5 HP0833 76 H. pylori predicted coding region HP0833 #6 HP0875 300 catalase #7 HP1067 290 chemotaxis protein (cheY) #8 HP1254 116 biotin synthesis protein (bioC) #9 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #10 HP1483 26 gerC2 protein (gerC2) #11 HP1490 103 hemolysin Motif number 1 CTTTTTAAAATTTTGTTTTATAGTAAAACTCA 1 36 0 TTTTTTTATA 0.792134 -170 ACCCCATTCAATTTAATATTATTTAATCTTTT 1 63 0 ATTTATATAT 0.597843 -143 TTGATCTTATTTTTGTCAAATATTGATAAACC 1 92 0 TTTTTCAATA 0.698951 -114 GATCAAAAAAATTTTTTATTAACTCTTTTGGT 1 118 1 ATTTTTATAA 0.692339 -88 TAGGCTTTTATTTTCATAAAAACCTTGATCGC 1 158 0 TTTTATAAAA 0.789379 -48 CAAAAGTCCTTTTTTTAAAATTGTTTTAGGC 1 185 0 TTTTTTAAAT 0.903128 -21 AGTTTCAGGGTTTTAATAGAATT 2 2 0 TTTTATAAAT 0.872771 -280 GCTTTAAAAAATTTCTTTCTAAGCAGTCTTTG 2 37 0 ATTTTTTTAA 0.615441 -245 ATCCGTTTATTTTTTTCACAAAAATATTATTC 2 157 0 TTTTTCAAAA 0.835093 -125 GCTCGTTTTATCTCTAAGCATGTTAAA 3 6 1 TTTTTCTTAA 0.719218 -53 GCTTTTGTTACAATAATTTAGATT 4 3 1 TTTTTTAAAT 0.925959 -89 TTAGCTTACTTTTTAACAATATCCATGCCTTA 4 61 0 TTTTACATAT 0.703889 -31 TGTAATCTAATTTTGATTAAATTGAAGCGATA 5 17 0 TTTTATTAAT 0.818497 -60 TTTGATTTTTATTTTTTAAATTT 6 2 0 ATTTTTAATT 0.607963 -299 TGTTTTTTTTTTTTTTTTGATTTTTATTTTTT 6 17 0 TTTTTTTATT 0.803034 -284 CATTGACGGATTTTGTTTTTTTTTTTTTTTTG 6 30 0 TTTTTTTTTT 0.743552 -271 TTTAATCTGGTTTTAATAATAATTATTATACT 6 76 0 TTTTATATAA 0.796386 -225 AAAAACAAAATTTTATTTTTAATCTGGTTTTA 6 93 0 TTTTTTTTAA 0.855318 -208 AAAAATAAAATTTTGTTTTTAATCTTTCTTAT 6 105 1 TTTTTTTTAA 0.855324 -196 ATCTTTCTTATTTTCATTAATTGTTACGAATA 6 126 1 TTTTATTATT 0.715515 -175 TTAAGGGGGTTTTTCATTCTTAAAAAAAGGAT 6 165 1 TTTTATTTTA 0.626025 -136 CAAAGAGTTATTTTATTACTTTTAAACGATTA 7 70 1 TTTTTTATTT 0.803037 -221 ACAAACTGAATTTTTTTACAAATAAGAACGCT 7 111 1 TTTTTTAAAA 0.920264 -180 TAATAGCATGTTTTGATTAAAATTACCTTGAC 7 178 0 TTTTATTAAA 0.752694 -113 ATTTGGAACGATTTATTATTATAAGGCGTTAG 7 209 1 ATTTTTATAT 0.706543 -82 TCAAGCGTGATTTTTTCTAAATTTTAGGCATT 8 21 0 TTTTTCTAAT 0.793403 -96 ATAGCGGTTATTTTTTTAGAATAACCAACGCT 9 107 1 TTTTTTAAAT 0.925709 -65 AATCTCAGAATTTTAACATAAAAGATTAAGCC 11 40 0 TTTTACAAAA 0.756661 -64 AAATTCTGAGATTTTATATATTTTATATTTAT 11 59 1 ATTTATAATT 0.489324 -45 **** *** *** Masking position 4 Map Score: 29.4901 Number of sites scoring better than the average of aligned sites = 1544 Number in coding regions = 1151 Number in noncoding regions = 393 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 2 ACAAAATTTTAAAAAGATTAAATAATATTAAA 1 52 1 AAAAGTTAAA 0.917237 -154 ATTTGACAAAAATAAGATCAAAAAAATTTTTT 1 103 1 ATAAGTCAAA 0.726395 -103 TTTATGAAAATAAAAGCCTAAAACAATTTTAA 1 170 1 TAAAGCTAAA 0.947095 -36 TCAATCCAAAACAAAACCTAAAATAAAATCCA 2 194 1 AAAAACTAAA 0.958344 -88 AAAACCTAAAATAAAATCCAACCTGTTAGGGT 2 206 1 AAAAACCAAC 0.867764 -76 TTAAATTTTTTGTAAGGCTAAAAAC 3 44 1 TTAAGCTAAA 0.885359 -15 CATGCTAGCTAAAAAATCTAAATTATTGTAAC 4 17 0 AAAAACTAAA 0.958344 -75 TTATAGTTATTTAAAGCTTAAATAAGGGTCTA 5 52 1 TAAAGTTAAA 0.798771 -25 AATTTAAAAAATAAAAATCAAAAAAAAAAAAA 6 12 1 AAAAATCAAA 0.773297 -289 CAAAAAAAAAAAAAAAACAAAATCCGTCAATG 6 30 1 AAAAACAAAA 0.709999 -271 AATGAAAATAAGAAAGATTAAAAACAAAATTT 6 112 0 AAAAGTTAAA 0.917237 -189 AATTTGTTATACAAAGACTAACAAGATTCAAT 6 208 0 AAAAGCTAAC 0.955199 -93 TGATTCCTTAAATGCCTAAAATTTAGAAAA 8 9 1 TAATGCTAAA 0.729855 -108 CACGCTTGAAATTAAAACTAAATTTTAGTGTA 8 76 0 ATAAACTAAA 0.908439 -41 TTATTTTTTTAGAATAACCAACGCTAAAAATA 9 114 1 AAATACCAAC 0.497518 -58 AACATAAAAGATTAAGCCTAACTTTAAAAATC 11 26 0 ATAAGCTAAC 0.901881 -78 AACTTTAAACCTAAAACCTAACGAT 11 89 0 TTAAACTAAA 0.779671 -15 * **** ***** Masking position 4 Map Score: 15.7994 Number of sites scoring better than the average of aligned sites = 1079 Number in coding regions = 889 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TTCATAAAAACCTTGATCGCTATCCTACAC 1 148 0 CCTTGATCGC 0.98854 -58 GGCTCATGTTTCTCTAACGCTTTAAAAAAT 2 57 0 TCTCTAACGC 0.945086 -225 GTGCAATAATCATTGAACGATAAGAATAAT 2 134 1 CATTGAACGA 0.861732 -148 CTTTTTTATCGCTTCAATTTAA 5 3 1 TTTTTATCGC 0.740138 -74 ATCCAATGACCCTTTATCGCACTCAAAGAG 7 47 1 CCTTTATCGC 0.985291 -244 TAAGAACGCTCATTGAACGCTCCATTTAGC 7 133 1 CATTGAACGC 0.969372 -158 ATTAAAATTACCTTGACCGACAATAATCAT 7 165 0 CCTTGACCGA 0.908785 -126 AGCCAAAGCGTCTCTAACGCCTTATAATAA 7 224 0 TCTCTAACGC 0.945086 -67 ACCACCGCCTTTAACGCACCACGCTTG 8 100 0 CCTTTAACGC 0.990722 -17 ********** Masking position 6 Map Score: 9.26494 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 275 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 GTGCATATCTGCTTGATTTTAGATCCCCAC 2 91 1 GCTTGATTTT 0.977186 -191 ACACTCCTTAGCTTACTTTTTAACAATATC 4 70 0 GCTTACTTTT 0.857875 -22 CTTTTTTATCGCTTCAATTTAATCAAAATT 5 11 1 GCTTCAATTT 0.94739 -66 AGACTAACAAGATTCAATTTCCTTAAAAAA 6 196 0 GATTCAATTT 0.816871 -105 AGCATGTTTTGATTAAAATTACCTTGACCG 7 176 0 GATTAAAATT 0.566301 -115 CTCCTTTTAAGATTGCATTTAAATTAGGCT 7 264 0 GATTGCATTT 0.844247 -27 AAAAAATCACGCTTGATCTTATCTAAAATT 8 37 1 GCTTGATCTT 0.954414 -80 AACGCACCACGCTTGAAATTAAAACTAAAT 8 85 0 GCTTGAAATT 0.941466 -32 AAAACCGCTCGCTTGTATTTGCAAAAACAC 9 66 0 GCTTGTATTT 0.889181 -106 GTTTTTGAAGGCTTGATTTTTAAAGTTAGG 11 12 1 GCTTGATTTT 0.977186 -92 TTAAAGTTAGGCTTAATCTTTTATGTTAAA 11 31 1 GCTTAATCTT 0.872803 -73 ********** Masking position 4 Map Score: 10.2571 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 528 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 GTTTTATAGTAAAACTCATTTTTAAGGGGGA 1 23 0 AAACTCATTT 0.896327 -183 TTTATTTTCATAAAAACCTTGATCGCTATCC 1 153 0 TAAAACCTTG 0.696163 -53 CAAAAGTCCTTTTTTTAAAATT 1 194 0 AAAGTCCTTT 0.884573 -12 TATATTGTGCAATAATCATTGAACGATAAGA 2 128 1 AAAATCATTG 0.959685 -154 AAACACTCCTTAGCTTACTTTT 4 80 0 AAACTCCTTA 0.866829 -12 AATTTCCTTAAAAAATCCTTTTTTTAAGAAT 6 180 0 AAAATCCTTT 0.927202 -121 TTACTTGTAAAATCCTTGTCTTTCTTTT 7 8 1 TAAATCCTTG 0.94746 -283 GAGTGCGATAAAGGGTCATTGGATGGTTTGA 7 40 0 AAGGTCATTG 0.860066 -251 TACAAATAAGAACGCTCATTGAACGCTCCAT 7 127 1 AAGCTCATTG 0.921644 -164 CTTGACCGACAATAATCATTGGCTAAATGGA 7 153 0 AAAATCATTG 0.959685 -138 AAAATAAACTCCTTGTTTTGGATTC 9 157 0 TAACTCCTTG 0.958705 -15 ** ******** Masking position 2 Map Score: 8.43013 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 152 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 TTTTAAAATTGTTTTAGGCTTTTATTTTCA 1 174 0 GTTTTAGGCT 0.940889 -32 GCAGATATGCACTTTAGGCTCATGTTTCTC 2 73 0 ACTTTAGGCT 0.780197 -209 TATCTGCTTGATTTTAGATCCCCACTCAAA 2 96 1 ATTTTAGATC 0.825476 -186 TTTAGGTTTTGTTTTGGATTGAGGGCGATC 2 186 0 GTTTTGGATT 0.879055 -96 GTTGGATTTTATTTTAGGTTTTGTTTTGGA 2 198 0 ATTTTAGGTT 0.964506 -84 TTGTTACAATAATTTAGATTTTTTAGCTAG 4 15 1 AATTTAGATT 0.739141 -77 TTTTTTCTAAATTTTAGGCATTTAAGGAAT 8 13 0 ATTTTAGGCA 0.825518 -104 TTCTTAGCAAATTTTAGATAAGATCAAGCG 8 46 0 ATTTTAGATA 0.849146 -71 TAAACTCCTTGTTTTGGATTCAATTAAAGC 9 148 0 GTTTTGGATT 0.879055 -24 GATTTTATATATTTTATATTTATCGTTAGG 11 68 1 ATTTTATATT 0.614692 -36 TTATCGTTAGGTTTTAGGTTTAAAGTT 11 87 1 GTTTTAGGTT 0.962141 -17 ********** Masking position 5 Map Score: 6.02122 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 194 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 AATTTAATATTATTTAATCTTTTTAAAATT 1 56 0 TATTTAATCT 0.914046 -150 ATAAAAAATTTTTTTGATCTTATTTTTGTC 1 107 0 TTTTTGATCT 0.972283 -99 ATAATTTAGATTTTTTAGCTAGCATGTTAG 4 23 1 TTTTTTAGCT 0.833323 -69 GCTAGACCCTTATTTAAGCTTTAAATAACT 5 56 0 TATTTAAGCT 0.857586 -21 TTTTTTTTTTTTTTTGATTTTTATTTTTTA 6 16 0 TTTTTGATTT 0.796632 -285 CAAAATTTTATTTTTAATCTGGTTTTAATA 6 90 0 TTTTTAATCT 0.96672 -211 TAAAATTTTGTTTTTAATCTTTCTTATTTT 6 110 1 TTTTTAATCT 0.96672 -191 CTTTTTTCCTTTTATGATCTTAAATCTTCG 6 281 0 TTTATGATCT 0.862756 -20 ********** Masking position 7 Map Score: 6.74699 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 206 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 TGGATAACTATCCCCCTTAAAAATGAGTTT 1 13 1 TCCCCCTTAA 0.971177 -193 TATTGATAAACCCCATTCAATTTAATATTA 1 74 0 CCCCATTCAA 0.935289 -132 GATTTTAGATCCCCACTCAAAGCTATATTG 2 105 1 CCCCACTCAA 0.981476 -177 AATAAACGGATCGCCCTCAATCCAAAACAA 2 178 1 TCGCCCTCAA 0.981475 -104 AGAATGAAAAACCCCCTTAAGTATTTCTAT 6 155 0 ACCCCCTTAA 0.930243 -146 TGACCCTTTATCGCACTCAAAGAGTTATTT 7 53 1 TCGCACTCAA 0.96248 -238 ACCACCGCCTTTAACGCACCACGC 8 103 0 CCGCCTTTAA 0.916694 -14 ********** Masking position 9 Map Score: 6.84239 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 181 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 CCCTGAAACTAGGCAAAGACTGCTTAGAAA 2 24 1 AGGCAAAGAC 0.96722 -258 ATCAACTTAAAGGCAAAGAC 2 272 1 AGGCAAAGAC 0.96722 -10 GTAGTTTAACATGCTTAGAGATAAAACGAG 3 12 0 ATGCTTAGAG 0.682473 -47 AAATCCGTCAATGCATTGAGATAGAATAGT 6 49 1 ATGCATTGAG 0.912538 -252 ATAATTTGTTATACAAAGACTAACAAGATT 6 212 0 ATACAAAGAC 0.779376 -89 TTTTCAAACCATCCAATGACCCTTTATCGC 7 37 1 ATCCAATGAC 0.905538 -254 CGCTCCATTTAGCCAATGATTATTGTCGGT 7 150 1 AGCCAATGAT 0.665507 -141 CTTTTTAAACAGCCAAAGCGTCTCTAACGC 7 234 0 AGCCAAAGCG 0.930603 -57 AGCGGTTTCTATGCAAAGCGTTTCTTGAAG 9 17 1 ATGCAAAGCG 0.96003 -155 AAAAACACCGATGCATTGCGCCATAAGCTT 9 44 0 ATGCATTGCG 0.881357 -128 ********** Masking position 1 Map Score: 5.30186 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 242 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ATATTATTTAATCTTTTTAAAATTTTGTTT 1 50 0 ATCTTTTTAA 0.759353 -156 CAAAAGTCCTTTTTTTAAAATTGTTTTA 1 188 0 CTTTTTTTAA 0.956334 -18 CGATCCGTTTATTTTTTTCACAAAAATATT 2 161 0 ATTTTTTTCA 0.678795 -121 GCTCGTTTTATCTCTAAGCAT 3 2 1 CTCGTTTTAT 0.655902 -57 TTTAATCTTTCTTATTTTCATTAATTGTTA 6 122 1 CTTATTTTCA 0.683786 -179 TTAAAAAATCCTTTTTTTAAGAATGAAAAA 6 174 0 CTTTTTTTAA 0.956334 -127 CTTTTTTCCTTTTATGATCT 6 291 0 CTTTTTTCCT 0.773863 -10 CCTTGTCTTTCTTTTTTCAAACCATCCAAT 7 24 1 CTTTTTTCAA 0.932053 -267 TTAAATTAGGCTCTTTTTAAACAGCCAAAG 7 246 0 CTCTTTTTAA 0.95345 -45 AGTGCTTCTCCTTTTAAGATTGCATTT 7 274 0 CTCCTTTTAA 0.827155 -17 GACTTTTCTTTTTTCATGGCTTGTCT 10 10 0 CTTTTTTCAT 0.845292 -17 ********** Masking position 5 Map Score: 7.63482 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 639 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 11 ********** No masking Map Score: 2.29806e-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 12 ********** No masking Map Score: 2.29806e-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 13 ********** No masking Map Score: 2.29806e-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