AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_hpyl_reg_300.orf -o00480_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 HP0027 198 isocitrate dehydrogenase (icd) #2 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) #3 HP1118 210 gamma-glutamyltranspeptidase (ggt) #4 HP1120 128 H. pylori predicted coding region HP1120 #5 HP1121 161 cytosine specific DNA methyltransferase (BSP6IM) #6 HP1122 274 H. pylori predicted coding region HP1122 #7 HP1125 66 peptidoglycan associated lipoprotein precursor (omp18) #8 HP1129 52 biopolymer transport protein (exbD) #9 HP1132 22 ATP synthase F1, subunit beta (atpD) #10 HP1137 110 ATP synthase F0, subunit b' (atpF') #11 HP1141 23 methionyl-tRNA formyltransferase (fmt) #12 HP1142 39 H. pylori predicted coding region HP1142 #13 HP1143 243 H. pylori predicted coding region HP1143 Motif number 1 TTCAACTCCTAATTATAAGCCAAAAAATTAAATGAT 1 36 1 AATAAAAAAA 0.891802 -163 TAGCGGTTGGAAATAACTTGAAAAAACGCAATGTTT 1 81 0 AATACAAAAA 0.917573 -118 GCTACTTTTAAACACGCATTCAAAAAAAGATTTTTA 1 113 1 AAACCAAAAA 0.940407 -86 AAAAATACTATATAACCCTTAAAAATCTTTTTTTGA 1 132 0 TAAACAAAAT 0.82734 -67 TTTGAGTAACTATACTAGCGCAAAAATACTATATAA 1 153 0 TAACAAAAAA 0.847996 -46 TTTAATATATAATAATAACTCAAAAACACTCTAAAA 2 31 1 AAAAAAAAAA 0.978538 -35 ATAGAGTTTAAAAAATAAGTTAAATAAGGCTTATTT 3 36 0 AAAAAAAATA 0.728054 -175 CGCTAGCTATAAAAAAGGCTCAAAAATGAGTTTTAA 3 77 0 AAAAGAAAAA 0.877919 -134 AAGCTTGTGTTATAATAACAAAGAAATTTTAAGCGT 3 164 1 TAAAAAGAAA 0.784957 -47 AATCATTCCTAACACACGACTAAAAACATGCCCTAT 5 116 0 AAACCAAAAA 0.940407 -46 ATTAAAATATAACAAAATAAAAAAAAGCAAATGGTA 6 77 0 AAAAAAAAAA 0.978538 -198 TTTAAACATAAAGAACATTAAAAAAATTAAAATATA 6 102 0 AAAAAAAAAA 0.978538 -173 GGCTCTGTGGCAGAAACCGGAAAAAAACCCATCACC 6 159 1 CAAACAAAAA 0.886484 -116 GGAATTGCAAAAACAGATTTCAAAAATCCATTAACT 6 215 1 AACAAAAAAA 0.898965 -60 CCATTACAGCAAGTATCGGCAAAAAAGAAAAAAAGT 6 248 0 AATACAAAAA 0.917573 -27 AAGATATTTATAAAATCCCCTTAAAAGCT 8 4 0 TAAACTAAAA 0.633219 -49 TATCTTAACAAAAAATCGCTTAAAATTTGAGAATAT 10 18 0 AAAACAAAAT 0.909386 -93 ATTTCTTTCCTAAAATCCTACAAAATATTTGAAACT 10 80 0 TAAACAAAAT 0.82734 -31 TTGAATTAAAAACAAGGAATAAC 11 7 1 TAAACAATAA 0.633219 -17 TATCATCTCAAAGCACACCACAAAAA 12 1 0 AACAAAAAAA 0.898965 -39 CATTATAAATAAAAAAAATGAAGAAATTGAGATAAC 13 63 0 AAAAAAGAAA 0.884326 -181 AAATACAAACAACAAAAAATAAAAAAGGCAAAAAAT 13 118 0 AAAAAAAAAA 0.978538 -126 CTCATTCTATTATAAAATATAAAAAATCAAATCTTA 13 208 1 TAAAAAAAAA 0.956082 -36 ** ** * ***** Masking position 2 Map Score: 28.8653 Number of sites scoring better than the average of aligned sites = 1816 Number in coding regions = 1484 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 2 ATCATTTAATTTTTTGGCTTATAATTAGGAGT 1 40 0 TTTTTCTTAT 0.784703 -159 CAAAAAAAGATTTTTAAGGGTTATATAGTATT 1 133 1 TTTTTGGGTT 0.943468 -66 GTTTATCCTTTTTCTAAAGTTTGAGTAACTAT 1 176 0 TTTCTAGTTT 0.910417 -23 TTTTAGAGTGTTTTTGAGTTATTATTATATAT 2 35 0 TTTTTGTTAT 0.903452 -31 ACGCTTAAAATTTCTTTGTTATTATAACACAA 3 168 0 TTTCTGTTAT 0.884755 -43 TACTATGCCATTTTTTTATTGTAAAAACCCAA 4 66 0 TTTTTATTGT 0.901247 -63 AAGGGCTTCATTTCTAGGGGGTTTATTCTTGC 5 18 1 TTTCTGGGGT 0.892198 -144 TAAATTTTAGTTTCTCTGTGTTTTAAAATGAG 5 68 1 TTTCTGTGTT 0.943468 -94 ACCATTTGCTTTTTTTTATTTTGTTATATTTT 6 78 1 TTTTTATTTT 0.937882 -197 ATATTTTAATTTTTTTAATGTTCTTTATGTTT 6 103 1 TTTTTATGTT 0.905711 -172 GTGATGGGTTTTTTTCCGGTTTCTGCCACAGA 6 162 0 TTTTTGGTTT 0.963279 -113 CCTTACCAAATTTCTTGGTGGTGGTGATGGGT 6 185 0 TTTCTGTGGT 0.90981 -90 ATCCATTAACTTTTTTTCTTTTTTGCCGATAC 6 240 1 TTTTTCTTTT 0.925672 -35 TTTTTGTGGTGTGCTTTGAGAT 12 1 1 TTTTTGGTGT 0.940674 -39 GTTATCTCAATTTCTTCATTTTTTTTATTTAT 13 63 1 TTTCTATTTT 0.925302 -181 CGAAGGGTATTTTTTGCCTTTTTTATTTTTTG 13 110 1 TTTTTCTTTT 0.925672 -134 CCTTTTTTATTTTTTGTTGTTTGTATTTAAAA 13 126 1 TTTTTTGTTT 0.720019 -118 AAGATTTGATTTTTTATATTTTATAATAGAAT 13 211 0 TTTTTATTTT 0.937882 -33 ***** ***** Masking position 5 Map Score: 23.2728 Number of sites scoring better than the average of aligned sites = 1031 Number in coding regions = 861 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 GAATGCTATCAAAACTTAAGGAAGTCAA 1 6 0 AAAATTAAAA 0.974309 -193 TTATAAGCCAAAAAATTAAATGATTTCTTTTAA 1 48 1 AAAATTAAGA 0.971826 -151 ATTATATATTAAATCTTAATTAAAGGGGTATTC 2 11 0 AAATTTAAAA 0.967507 -55 AGTTTAAAAAATAAGTTAAATAAGGCTTATTTG 3 35 0 ATAATTAAAA 0.859584 -176 AATAACAAAGAAATTTTAAGCGTAACTGATTGA 3 177 1 AAATTTAAGT 0.727193 -34 CAGAGAAACTAAAATTTAATGAAAAGCAAAATC 5 53 0 AAAATTAAAA 0.974308 -109 AGAACATTAAAAAAATTAAAATATAACAAAATA 6 94 0 AAAATTAATA 0.842176 -181 AAAAAAGAAAAAAAGTTAATGGATTTTTGAAAT 6 231 0 AAAATTAAGA 0.971826 -44 TAATAAGTGTAAATATTAACTCACATTCGCTTA 7 19 0 AAATTTAACA 0.861301 -48 TCCAAGAATCAAATTTTAATAAGTGTAAATATT 7 35 0 AAATTTAAAG 0.888811 -32 GATTTTATAAATATCTTAAATAGGGAGTTAGAA 8 23 1 ATATTTAAAG 0.563392 -30 GAATATTCTCAAATTTTAAGCGATTTTTTGTTA 10 16 1 AAATTTAAGA 0.964392 -95 TATAAATAAAAAAAATGAAGAAATTGAGATAAC 13 63 0 AAAATGAAAA 0.827864 -181 TACAAACAACAAAAAATAAAAAAGGCAAAAAAT 13 118 0 AAAAATAAAA 0.859587 -126 ATTCTATTATAAAATATAAAAAATCAAATCTTA 13 211 1 AAAAATAAAA 0.859587 -33 ATAAAAAATCAAATCTTAAAGGAAAATC 13 226 1 AAATTTAAGA 0.964392 -18 **** **** ** Masking position 8 Map Score: 19.2287 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 200 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 AAAGATTTTTAAGGGTTATATAGTATTTTT 1 138 1 AAGGGTTATA 0.679965 -61 ATCTTAATTAAAGGGGTATTC 2 2 0 AAGGGGTATT 0.973853 -64 AACACTCTAAAAGGGTTATTG 2 55 1 AAGGGTTATT 0.958693 -11 TAAGTTAAATAAGGCTTATTTGATCAAAAC 3 27 0 AAGGCTTATT 0.711662 -184 TTAAGGGGATAGGGGGTATTTTGAAATCAT 4 32 0 AGGGGGTATT 0.885943 -97 CCTTAAGAAATTGGGTTTTTACAATAAAAA 4 56 1 TTGGGTTTTT 0.910708 -73 GCTTCATTTCTAGGGGGTTTATTCTTGCTG 5 22 1 TAGGGGGTTT 0.843854 -140 GAATGATTGATTGGGGATTTTAACTTTT 5 144 1 TTGGGGATTT 0.872487 -18 TAAGGTATAGGAGTATTTAAAAGGCAA 6 8 1 TAGGAGTATT 0.82068 -267 GGTGGTGGTGATGGGTTTTTTTCCGGTTTC 6 171 0 ATGGGTTTTT 0.937688 -104 AAAAAAGTTAATGGATTTTTGAAATCTGTT 6 226 0 ATGGATTTTT 0.731774 -49 AATTTGATTCTTGGAGAATTTATA 7 53 1 TTGGAGAATT 0.521809 -14 AGCTTTTAAGGGGATTTTATAAATATC 8 8 1 AAGGGGATTT 0.946525 -45 TTTTTATGCGAAGGGTATTTTTTGCCTTTT 13 102 1 AAGGGTATTT 0.916872 -142 TTCAGTAAAATAGGGATTTTAAATACAAAC 13 144 0 TAGGGATTTT 0.762166 -100 ********** Masking position 9 Map Score: 14.4794 Number of sites scoring better than the average of aligned sites = 1868 Number in coding regions = 1603 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 5 GCCAAAAAATTAAATGATTTCTTTTAAAAA 1 54 1 TAAATGATTT 0.567736 -145 ACGCATTCAAAAAAAGATTTTTAAGGGTTA 1 126 1 AAAAAGATTT 0.869352 -73 AAAAACACTCTAAAAGGGTTATTG 2 52 1 TAAAAGGGTT 0.674193 -14 TAGAGTTTAAAAAATAAGTTAAATAAGGCT 3 41 0 AAAATAAGTT 0.774645 -170 GTTTTAAAATAGATAGAGTTTAAAAAATAA 3 54 0 AGATAGAGTT 0.906732 -157 AAAAGGCTCAAAAATGAGTTTTAAAATAGA 3 71 0 AAAATGAGTT 0.969741 -140 CTTTAAGGGGAGAATGATTTCAAAATACCC 4 19 1 AGAATGATTT 0.820598 -110 TCCCCTTAAGAAATTGGGTTTTTACAATAA 4 53 1 AAATTGGGTT 0.885348 -76 TCTGTGTTTTAAAATGAGTTTGTTGCTTTC 5 82 1 AAAATGAGTT 0.969741 -80 GGAATTGCAAAAACAGATTTCAAAAATCCA 6 215 1 AAACAGATTT 0.580729 -60 GGCAAAAAAGAAAAAAAGTTAATGGATTTT 6 237 0 AAAAAAAGTT 0.75165 -38 TTTTTTGTTAAGATAGAGTTAATGTTTTTA 10 39 1 AGATAGAGTT 0.906732 -72 AAAAATGAAGAAATTGAGATAACGATCGAT 13 56 0 AAATTGAGAT 0.83097 -188 AAGTTCAGTAAAATAGGGATTTTAAATACA 13 147 0 AAATAGGGAT 0.64646 -97 ATTTTATAATAGAATGAGATCAATTTAACT 13 196 0 AGAATGAGAT 0.838977 -48 ********** Masking position 3 Map Score: 12.6097 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 760 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 6 AATACTATATAACCCTTAAAAATCTTTTTT 1 135 0 AACCCTTAAA 0.891258 -64 GAATACCCCTTTAATTAAGATTTA 2 5 1 ACCCCTTTAA 0.965267 -61 CAATAACCCTTTTAGAGTGTTTTTG 2 51 0 ACCCTTTTAG 0.882531 -15 GAAATCATTCTCCCCTTAAAGCTCCCTTA 4 10 0 TCCCCTTAAA 0.984911 -119 ATACCCCCTATCCCCTTAAGAAATTGGGTT 4 43 1 TCCCCTTAAG 0.981765 -86 CTAGAAATGAAGCCCTTAAACCCC 5 5 0 AGCCCTTAAA 0.957184 -157 TTCATGACCTTGCCTTTTAAATACTCCTAT 6 17 0 TGCCTTTTAA 0.825636 -258 ATTTATAAAATCCCCTTAAAAGCT 8 5 0 TCCCCTTAAA 0.984911 -48 GATTTTCCTTTAAGATTTGATTTT 13 230 0 TTCCTTTAAG 0.731885 -14 ********** Masking position 6 Map Score: 10.5118 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 310 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 TGACTTCCTTAAGTTTTGATAGCATTCAACT 1 12 1 AATTTTGATA 0.912648 -187 TCCTTTTTCTAAAGTTTGAGTAACTATACTA 1 172 0 AAGTTTGAGT 0.868601 -27 CCCTTTAATTAAGATTTAATATATAATAATA 2 17 1 AAATTTAATA 0.728402 -49 GGGAATAGCCAATTTTTGAGATTAGAACTAT 6 46 0 AATTTTGAGA 0.926561 -229 TACACTTATTAAAATTTGATTCTTGGAGAAT 7 41 1 AAATTTGATT 0.937386 -26 AAAATCGCTTAAAATTTGAGAATATTCAAGC 10 12 0 AAATTTGAGA 0.966669 -99 AATCCTACAAAATATTTGAAACTCGCATTTG 10 72 0 AAATTTGAAA 0.879514 -39 ATTTTCCTTTAAGATTTGATTTTTTATATTT 13 222 0 AAATTTGATT 0.937386 -22 ** ******** Masking position 9 Map Score: 4.46491 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 187 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ATTTCTTTTAAAAACATTGCGTTTTTTCAA 1 70 1 AAAACATTGC 0.852275 -129 TAATAACTCAAAAACACTCTAAAAGGGTTA 2 43 1 AAAACACTCT 0.967749 -23 CAAGCTTTACAAAACACTCTCTCGCTTATA 3 141 0 AAAACACTCT 0.967749 -70 GGGTATTTTGAAATCATTCTCCCCTTAAAG 4 19 0 AAATCATTCT 0.90252 -110 CACACGACTAAAAACATGCCCTATTTAAGA 5 110 0 AAAACATGCC 0.952818 -52 AAAAACCTTCTAACTCCCTAT 8 42 0 AAAACCTTCT 0.967667 -11 CTTATTGGATAAAACCTGCTTAAGTTAAAT 13 174 1 AAAACCTGCT 0.952815 -70 ********** Masking position 3 Map Score: 4.60144 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 230 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 TGTTTATCCTTTTTCTAAAGTTT 1 186 0 TTATCCTTTT 0.855991 -13 CTGTTTTCCTTTCAATCAGTTAC 3 198 0 TTTTCCTTTC 0.94945 -13 CTTGCTGTGATTTTGCTTTTCATTAAATTT 5 45 1 TTTTGCTTTT 0.981806 -117 AAAATGAGTTTGTTGCTTTCTTAAATAGGG 5 92 1 TGTTGCTTTC 0.877145 -70 ATTCCCTACCATTTGCTTTTTTTTATTTTG 6 71 1 ATTTGCTTTT 0.894813 -204 CCATTAACTTTTTTTCTTTTTTGCCGATAC 6 242 1 TTTTTCTTTT 0.893029 -33 TCTCTAAAACTTGTGCTTTTGGGACAACTT 13 19 1 TTGTGCTTTT 0.934782 -225 GAAGGGTATTTTTTGCCTTTTTTATTTTTT 13 111 1 TTTTGCCTTT 0.926515 -133 GATTTTCCTTTAAGATTTGATT 13 232 0 TTTTCCTTTA 0.873193 -12 ********** Masking position 4 Map Score: 6.86871 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 248 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 10 ATAGCATTCAACTCCTAATTATAAGCCAAA 1 30 1 ACTCCTAATT 0.730053 -169 ATTTCAAAATACCCCCTATCCCCTTAAGAA 4 35 1 ACCCCCTATC 0.97181 -94 GACTAAAAACATGCCCTATTTAAGAAAGCA 5 105 0 ATGCCCTATT 0.907232 -57 AAAAGTTAAAATCCCCAATCAATCATTCCT 5 142 0 ATCCCCAATC 0.912669 -20 AAAATTGGCTATTCCCTACCATTTGCTTTT 6 61 1 ATTCCCTACC 0.960037 -214 TGTTTTTGCAATTCCTTACCAAATTTCTTG 6 200 0 ATTCCTTACC 0.846027 -75 AAACCTTCTAACTCCCTATTTAAGATATTT 8 31 0 ACTCCCTATT 0.969968 -22 TTGTATTTAAAATCCCTATTTTACTGAACT 13 146 1 AATCCCTATT 0.890457 -98 ********** Masking position 8 Map Score: 3.19585 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 238 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 ********** No masking Map Score: -1.32571e-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: -1.32571e-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: -1.32571e-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