AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_hpyl_reg_100.orf -o00061_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: HP0557 22 acetyl-coenzyme A carboxylase (accA) Input sequences: #1 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #4 HP0198 66 nucleoside diphosphate kinase (ndk) #5 HP0199 25 H. pylori predicted coding region HP0199 #6 HP0201 74 fatty acid/phospholipid synthesis protein (plsX) #7 HP0202 24 beta-ketoacyl-acyl carrier protein synthase III (fabH) #8 HP0371 123 biotin carboxyl carrier protein (fabE) #9 HP0558 300 beta ketoacyl-acyl carrier protein synthase II (fabF) #10 HP0561 41 3-ketoacyl-acyl carrier protein reductase (fabG) #11 HP0562 100 ribosomal protein S21 (rps21) #12 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #13 HP0950 77 acetyl-CoA carboxylase beta subunit (accD) Motif number 1 GGTGTCTCGTTAATACATTCTAAACAAAAAGTTT 1 37 1 TAAATCTAAA 0.815947 -264 CATTCTAAACAAAAAGTTTTTAAAGGCAAAAAGG 1 52 1 AAAATTTAAA 0.949649 -249 AAATAAGTTAAAATAAACCTTAAACTTTAATGGT 1 205 1 AAAACTTAAA 0.977577 -96 AATTATGGATTAATAAAACTTAAAGGATAACACC 1 277 1 TAAACTTAAA 0.93043 -24 AAAAACTGCTCCTAAAAACTCAAAAT 2 3 1 AAATCCTAAA 0.941004 -212 CTAAAAACTCAAAATTAACCTAAAATCGCTTGAC 2 22 1 AAATCCTAAA 0.941004 -193 CTTGACGCAAAAACACTGCCTTAATTCTACTACA 2 50 1 AAAACCTTAA 0.915796 -165 TGTTTATAAGAAAAATTATTTCAAATGTAGTAGA 2 75 0 AAAATTTCAA 0.691855 -140 TTTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 94 1 AAAACCTAAA 0.970935 -121 TTATTATATCTAATAGCGTTTAAAAAATGTAAAT 2 156 0 TAAATTTAAA 0.852631 -59 AAAAATATTTTAAGGGTAATATTT 4 1 1 AAAATTTAAG 0.875652 -66 TTGATTATACAAAAATTTTTTAAAATATTACCCT 4 23 0 AAAATTTAAA 0.949649 -44 GCTTACTTAAAAACGCCCTTAAATC 5 4 0 AAAACCTTAA 0.915796 -22 ACATAATTATTAACAAACTTTAAAGGCTTT 8 7 0 TAAATTTAAA 0.852631 -117 TTTTAGTCAAAAATTTGGCTTTAGCTAAAATCTA 9 34 1 AAATCTTTAG 0.716741 -267 TGTTGGGATAAAACTAGATTTTAGCTAAAGCCAA 9 48 0 AAATTTTTAG 0.522594 -253 CCTACCCCAAAAAGACTATTTTAACCTCTTTTAG 9 145 0 AAAATTTTAA 0.859953 -156 CTTAATTTTTAAATTTTTCTTAAAGTCTA 10 6 0 AAATCTTAAA 0.954163 -36 GAAACTAGGCAAAGACTGCTTAGAAAGAAATTTT 12 28 1 AAAACTTAGA 0.798883 -254 CCTCAATCCAAAACAAAACCTAAAATAAAATCCA 12 192 1 AAAACCTAAA 0.970935 -90 CTATGAATAATAAATCAACTTAAAGGCAAAGAC 12 259 1 TAATCTTAAA 0.864601 -23 TATAATAAACAAAATTAGCTTAAGAGTA 13 5 0 AAATCTTAAG 0.886002 -73 *** * ****** Masking position 11 Map Score: 31.4913 Number of sites scoring better than the average of aligned sites = 1398 Number in coding regions = 1099 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 CATTCTAAACAAAAAGTTTTTAAAGGCAAA 1 52 1 AAAAAGTTTT 0.71592 -249 TGTTTATAAGAAAAATTATTTCAAATGTAG 2 79 0 AAAAATTATT 0.575261 -136 TTTGAATACGAATGATTATTTTAATAAGGA 3 39 1 AATGATTATT 0.760198 -26 ATTACCCTTAAAATATTTTT 4 1 0 AAATATTTTT 0.708727 -66 TAATATTTTAAAAAATTTTTGTATAATCAA 4 27 1 AAAAATTTTT 0.495411 -40 CTTTAGTGATAGAAAGTATTTTAAAGGATT 6 23 1 AGAAAGTATT 0.781758 -52 GTTTTTAGCAAAAAATTATTGTTATAATAA 8 40 0 AAAAATTATT 0.575261 -84 CCTACCCCAAAAAGACTATTTTAACCTCTT 9 149 0 AAAGACTATT 0.820697 -152 TTTAAAAATTAAGGATTATTGAATA 10 27 1 AAGGATTATT 0.803359 -15 GCTACAAATGAAATAGTATTATATAAGACG 11 34 0 AAATAGTATT 0.855732 -67 CTGCTTAGAAAGAAATTTTTTAAAGCGTTA 12 43 1 AGAAATTTTT 0.640086 -239 CTTATCGTTCAATGATTATTGCACAATATA 12 128 0 AATGATTATT 0.760198 -154 TTTTTCACAAAAATATTATTCTTATCGTTC 12 148 0 AAATATTATT 0.873661 -134 ********** Masking position 5 Map Score: 10.9062 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 300 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TTAAAGTTTAAGGTTTATTTTAACTTATTT 1 205 0 AGGTTTATTT 0.869387 -96 AAAAGCCCTTAGTTTTGTTTAGAAACCATT 1 233 0 AGTTTTGTTT 0.982099 -68 TTATCCTTTAAGTTTTATTAATCCATAATT 1 277 0 AGTTTTATTA 0.875148 -24 TCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 GGTTTTGTTT 0.975039 -121 AAAGCCTTTAAAGTTTGTTAATAATTATGT 8 11 1 AAGTTTGTTA 0.75087 -113 TTTTATTTTAGGTTTTGTTTTGGATTGAGG 12 192 0 GGTTTTGTTT 0.975039 -90 TAACAGGTTGGATTTTATTTTAGGTTTTGT 12 204 0 GATTTTATTT 0.756686 -78 CTCTTAAGCTAATTTTGTTTATTATAAGCA 13 13 1 AATTTTGTTT 0.939321 -65 ATTGTATCCAAGTTTTGCTTATAATAAACA 13 28 0 AGTTTTGCTT 0.919625 -50 TTAATTTTGCAGTTTTGTTAGGATTGTATC 13 50 0 AGTTTTGTTA 0.961304 -28 ********** Masking position 5 Map Score: 11.1314 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 207 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TAGTTTCTAAGCATTCCTTTTACGA 1 6 0 GCATTCCTTT 0.97619 -295 CTCCCTGTCCGCCAGCCTTTTTGCCTTTAA 1 71 0 GCCAGCCTTT 0.958658 -230 GGTGTTATCCTTTAAGTTTTATT 1 288 0 GTTATCCTTT 0.846934 -13 GCAATCCGTTGCAATCCTTTAAAATACTTT 6 35 0 GCAATCCTTT 0.992351 -40 AAGGCTTGTTGCAATCCGTTGCAATCCTTT 6 45 0 GCAATCCGTT 0.986571 -30 ACGGATTGCAACAAGCCTTTTAAGGACGC 6 56 1 ACAAGCCTTT 0.876261 -19 ACGAAAAACTCCTATCCTTTAGGTAGAGAT 9 84 1 CCTATCCTTT 0.903301 -217 CCTAACTAAAGCATTCCATTGAATGCTAAC 9 217 0 GCATTCCATT 0.894865 -84 TGGATTGAGGGCGATCCGTTTATTTTTTTC 12 172 0 GCGATCCGTT 0.96411 -110 ********** Masking position 9 Map Score: 8.12221 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 157 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ATATAAAAGCCCTTAGTTTTGTTTAGAAAC 1 237 0 CCTTAGTTTT 0.76305 -64 TTTTATTAATCCATAATTTAAAATTGTAAT 1 265 0 CCATAATTTA 0.826581 -36 AAAAACACTGCCTTAATTCTACTACATTTG 2 58 1 CCTTAATTCT 0.752343 -157 GGTAACTATCCCTTATTATATCTAATAGCG 2 172 0 CCTTATTATA 0.960805 -43 TGAACGATCCTTATTTTATAGGTGGTAA 2 197 0 CCTTATTTTA 0.973095 -18 GCTTATTATAGCTTATTTCATTCT 3 5 0 GCTTATTTCA 0.797202 -60 TTCAAAATGGGCTTATTATAGCTTATTTCA 3 15 0 GCTTATTATA 0.901758 -50 TGATTGTCCTTATTAAAATAATCATTC 3 48 0 CCTTATTAAA 0.72289 -17 AAAATATTACCCTTAAAATATTTTT 4 6 0 CCTTAAAATA 0.844902 -61 TCAATCCCCTTAACATAGTCATCT 7 8 0 CCTTAACATA 0.761645 -17 TGTGTTTGTGGCATATTTTAAAATAATATA 8 90 1 GCATATTTTA 0.70153 -34 ACGATCTATTCCTTATATTATTTTAAAATA 8 103 0 CCTTATATTA 0.913682 -21 ATTCAATAATCCTTAATTTTTAAATTTTTC 10 21 0 CCTTAATTTT 0.912784 -21 TCCAAGTTTTGCTTATAATAAACAAAATTA 13 22 0 GCTTATAATA 0.728726 -56 GTTTTTCCTTAATTTTGCAGTTTTGT 13 62 0 CCTTAATTTT 0.912784 -16 ********** Masking position 5 Map Score: 12.5362 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 288 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 TTTAACTTATTTTTACTATAATTCTACTTTG 1 186 0 TTTTACTAAA 0.851408 -115 TAATTTAAAATTGTAATATAAAAGCCCTTAG 1 251 0 TTGTAATAAA 0.906628 -50 AAAACCTAAATTGAGAAAAAATTCAATTCAA 2 108 1 TTGAGAAAAA 0.822409 -107 TGATTGTCCTTATTAAAATAATCATTCGTAT 3 44 0 TATTAAAAAA 0.528682 -21 AAGCTATCTTTAGTGATAGAAAGTATTTTAA 6 16 1 TAGTGATAAA 0.869851 -59 AACAATAATTTTTTGCTAAAAACGCTTATGG 8 47 1 TTTTGCTAAA 0.921473 -77 TTGTGGCATATTTTAAAATAATATAAGGAAT 8 95 1 TTTTAAAAAA 0.792715 -29 AAGCCAAATTTTTGACTAAAACCTGGAGACA 9 24 0 TTTGACTAAA 0.697767 -277 AAAATTTGGCTTTAGCTAAAATCTAGTTTTA 9 43 1 TTTAGCTAAA 0.82136 -258 TTTCGTGCTGTTGGGATAAAACTAGATTTTA 9 59 0 TTGGGATAAA 0.897451 -242 ATCCTTTAGGTAGAGATATAAGTGCATAGCT 9 97 1 TAGAGATAAA 0.70382 -204 AGTTTCAGGGTTTTAATAGAATT 12 3 0 TTTTAATAAA 0.862374 -279 CAAAGCTATATTGTGCAATAATCATTGAACG 12 122 1 TTGTGCAAAA 0.922151 -160 AATAATATTTTTGTGAAAAAAATAAACGGAT 12 158 1 TTGTGAAAAA 0.928364 -124 ******** ** Masking position 8 Map Score: 9.50282 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 545 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 7 TGGCGGACAGGGAGGGATTCGAACCCTCGGTAAC 1 87 1 GGAGGATCAC 0.97868 -214 ATATAATAAGGGATAGTTACCACCTATAAAATAA 2 181 1 GGATGTTCAC 0.989694 -34 GTCCTTAAAAGGCTTGTTGCAATCCGTTGCAATC 6 49 0 GGCTGTTCAC 0.988528 -26 CTAAAGGATAGGAGTTTTTCGTGCTGTTGGGATA 9 72 0 GGAGTTTCTC 0.931126 -229 ATAGCTGTTAGGCTATATTCAAGCTAAAAGAGGT 9 122 1 GGCTTATCAC 0.967062 -179 AAGTCTGCATGGATATTTCCTACCCCAAAAAGAC 9 163 0 GGATTTTCAC 0.984992 -138 **** *** * * * Masking position 8 Map Score: 0.951401 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 74 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTAAGGTTTATTTTAACTTATTTTTACTATA 1 197 0 TTTTAACTAT 0.674654 -104 TATATTACAATTTTAAATTATGGATTAATAA 1 262 1 TTTTAAATAT 0.870788 -39 GGTGTTATCCTTTAAGTTTTATTAATCCAT 1 281 0 CTTTAAGTTT 0.520803 -20 AGTGTTTTTGCGTCAAGCGATTTTAGGTTAA 2 36 0 CGTCAAGCAT 0.366022 -179 AAAATGTAAATTTTAAACAATAGCCCCTTTG 2 136 0 TTTTAAACAT 0.926085 -79 AATTTACATTTTTTAAACGCTATTAGATATA 2 155 1 TTTTAAACCT 0.64635 -60 AAGGGTAATATTTTAAAAAATTTTTGTATAA 4 22 1 TTTTAAAAAT 0.711577 -45 TTAAGGGCGTTTTTAAGTAAGC 5 14 1 TTTTAAGTAG 0.799947 -12 ATAGAAAGTATTTTAAAGGATTGCAACGGAT 6 31 1 TTTTAAAGAT 0.674654 -44 CCTTATATTATTTTAAAATATGCCACAAACA 8 92 0 TTTTAAAAAT 0.711577 -32 AGTGCATAGCTGTTAGGCTATATTCAAGCTA 9 117 1 TGTTAGGCAT 0.819902 -184 AAGCTCCTTGCTTTAAGCAAGGGGTGGTTTC 9 247 1 CTTTAAGCAG 0.744049 -54 TTGTAGCCATTGTTAAGCAATGATTTTAAGC 11 57 1 TGTTAAGCAT 0.920899 -44 TAAGCAATGATTTTAAGCTATGGAAAAGAGG 11 70 1 TTTTAAGCAT 0.967503 -31 TTGGATTTTATTTTAGGTTTTGTTTTGGATT 12 196 0 TTTTAGGTTT 0.520803 -86 ATAGTATCACTTTTAGGTGATTGACACCCTA 12 232 0 TTTTAGGTAT 0.8623 -50 ******** ** Masking position 5 Map Score: 4.84196 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 1057 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 9 AAGTTTTTAAAGGCAAAAAGGCTGGCGGAC 1 65 1 AGGCAAAAAG 0.907902 -236 TAAAACTTAAAGGATAACACC 1 290 1 AGGATAACAC 0.846488 -11 AAATCGCTTGACGCAAAAACACTGCCTTAA 2 44 1 ACGCAAAAAC 0.924304 -171 ATTCCATTGAATGCTAACACGAAAGGCTTT 9 205 0 ATGCTAACAC 0.872271 -96 CCCTGAAACTAGGCAAAGACTGCTTAGAAA 12 24 1 AGGCAAAGAC 0.985186 -258 ATCAACTTAAAGGCAAAGAC 12 272 1 AGGCAAAGAC 0.985186 -10 ********** Masking position 6 Map Score: 1.43598 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 76 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ********** No masking Map Score: -1.16996e-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 11 ********** No masking Map Score: -1.16996e-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 12 ********** No masking Map Score: -1.16996e-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