AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00590_hpyl_reg_300.orf -o00590_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 HP1118 210 gamma-glutamyltranspeptidase (ggt) #2 HP1120 128 H. pylori predicted coding region HP1120 #3 HP1121 161 cytosine specific DNA methyltransferase (BSP6IM) #4 HP1122 274 H. pylori predicted coding region HP1122 #5 HP1125 66 peptidoglycan associated lipoprotein precursor (omp18) #6 HP1129 52 biopolymer transport protein (exbD) #7 HP1132 22 ATP synthase F1, subunit beta (atpD) #8 HP1137 110 ATP synthase F0, subunit b' (atpF') #9 HP1141 23 methionyl-tRNA formyltransferase (fmt) #10 HP1142 39 H. pylori predicted coding region HP1142 #11 HP1143 243 H. pylori predicted coding region HP1143 Motif number 1 TTATTTAACTTATTTTTTAAACTCTATCTATTTTAAA 1 45 1 TTTTTTTCTT 0.966922 -166 ATTTTAAAACTCATTTTTGAGCCTTTTTTATAGCTAG 1 74 1 TATTTTCTTT 0.865424 -137 GGGGATAGGGGGTATTTTGAAATCATTCTCCCCTTAA 2 21 0 GTTTTTTCAT 0.777605 -108 TGCTTTTCATTAAATTTTAGTTTCTCTGTGTTTTAAA 3 58 1 TATTTTTCTT 0.966922 -104 TGTTTTAAAATGAGTTTGTTGCTTTCTTAAATAGGGC 3 86 1 TATTTGTTTT 0.865424 -76 CCTACCATTTGCTTTTTTTTATTTTGTTATATTTTAA 4 75 1 GTTTTTTTTT 0.981677 -200 TTTATTTTGTTATATTTTAATTTTTTTAATGTTCTTT 4 92 1 TTTTTTTTTT 0.977819 -183 GTGGTGATGGGTTTTTTTCCGGTTTCTGCCACAGAGC 4 160 0 GTTTTTTTTT 0.981677 -115 AAAAGTTAATGGATTTTTGAAATCTGTTTTTGCAATT 4 217 0 GATTTTTCTT 0.972622 -58 AAAAATCCATTAACTTTTTTTCTTTTTTGCCGATACT 4 236 1 TATTTTTTTT 0.977819 -39 CTCAATTTCTTCATTTTTTTTATTTATAATGTAGTTT 11 68 1 TATTTTTTTT 0.977819 -176 TATGCGAAGGGTATTTTTTGCCTTTTTTATTTTTTGT 11 106 1 GATTTTTTTT 0.981677 -138 TTGCCTTTTTTATTTTTTGTTGTTTGTATTTAAAATC 11 123 1 TTTTTTTTTT 0.977819 -121 TTTAAGATTTGATTTTTTATATTTTATAATAGAATGA 11 209 0 GTTTTTTTTT 0.981677 -35 * * **** *** * Masking position 7 Map Score: 22.3461 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 487 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 AAAAAATAAGTTAAATAAGGCTTATTTGATC 1 32 0 TTAAATAGGC 0.981646 -179 AGCGCTAGCTATAAAAAAGGCTCAAAAATGA 1 84 0 ATAAAAAGGC 0.957476 -127 TTTTTACAATAAAAAAATGGCATAGTATTTG 2 71 1 AAAAAAAGGC 0.942382 -58 TAGTATTTGCTTGAATACGGCTGAAACAAGA 2 93 1 TTGAATAGGC 0.901784 -36 AAACTCATTTTAAAACACAGAGAAACTAAAA 3 72 0 TAAAACAAGA 0.705446 -90 TGTTGCTTTCTTAAATAGGGCATGTTTTTAG 3 102 1 TTAAATAGGC 0.981646 -60 TATAACAAAATAAAAAAAAGCAAATGGTAGG 4 75 0 TAAAAAAAGC 0.814177 -200 TATAAATATCTTAAATAGGGAGTTAGAAGGT 6 28 1 TTAAATAGGA 0.960333 -25 AAATTATATTAATCAAGGAGCG 7 9 1 TTAATCAGGA 0.733229 -14 TTGAATTAAAAACAAGGAATAAC 9 8 1 AAAAACAGGA 0.899398 -16 ACAACAAAAAATAAAAAAGGCAAAAAATACC 11 115 0 ATAAAAAGGC 0.957476 -129 ATAAGTTCAGTAAAATAGGGATTTTAAATAC 11 148 0 TAAAATAGGA 0.946196 -96 ******* *** Masking position 7 Map Score: 13.0976 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 623 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 GATGCTATTAATGGTTTGAGCGCTAGCTATAA 1 101 0 ATTTTGAGCG 0.896873 -110 AGCATCATGTAAGTTATAAGCGAGAGAGTGTT 1 127 1 AATATAAGCG 0.930974 -84 AATAACAAAGAAATTTTAAGCGTAACTGATTG 1 177 1 AATTTAAGCG 0.989676 -34 TAAGGGAGCTTTAAGGGGAGAATGATT 2 6 1 GATTTAAGGG 0.965398 -123 TAAAAACCCAATTTCTTAAGGGGATAGGGGGT 2 45 0 ATCTTAAGGG 0.854795 -84 GGGGTTTAAGGGCTTCATTTCT 3 1 1 GGTTTAAGGG 0.964723 -161 AGCTTTTAAGGGGATTTTATAA 6 1 1 AGTTTAAGGG 0.984502 -52 AAAATTTGAGAATATTCAAGCG 8 1 0 AATTCAAGCG 0.952361 -110 GAATATTCTCAAATTTTAAGCGATTTTTTGTT 8 16 1 AATTTAAGCG 0.989676 -95 TTTATAATGTAGTTTTTATGCGAAGGGTATTT 11 90 1 AGTTTATGCG 0.929676 -154 ** ******** Masking position 10 Map Score: 10.4625 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 226 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AAAATAGATAGAGTTTAAAAAATAAGTTAA 1 49 0 GAGTTTAAAA 0.860699 -162 AAACTCTATCTATTTTAAAACTCATTTTTG 1 63 1 TATTTTAAAA 0.878607 -148 AAATTTCTTTGTTATTATAACACAAGCTTT 1 163 0 GTTATTATAA 0.79733 -48 AGGGGAGAATGATTTCAAAATACCCCCTAT 2 24 1 GATTTCAAAA 0.904973 -105 AAGAAATTGGGTTTTTACAATAAAAAAATG 2 60 1 GTTTTTACAA 0.88459 -69 GCAACAAACTCATTTTAAAACACAGAGAAA 3 78 0 CATTTTAAAA 0.886602 -84 AGGTATAGGAGTATTTAAAAGGCAAGGTCA 4 13 1 GTATTTAAAA 0.913246 -262 TGCAAAAACAGATTTCAAAAATCCATTAAC 4 220 1 GATTTCAAAA 0.904973 -55 AATATTTACACTTATTAAAATTTGATTCTT 5 35 1 CTTATTAAAA 0.594679 -32 CTTTTAAGGGGATTTTATAAATATCTTAAA 6 13 1 GATTTTATAA 0.954473 -40 TAGAGTTAATGTTTTTATAACAAATGCGAG 8 52 1 GTTTTTATAA 0.954447 -59 TTCATTTTTTTTATTTATAATGTAGTTTTT 11 77 1 TTATTTATAA 0.597237 -167 TTTGTTGTTTGTATTTAAAATCCCTATTTT 11 138 1 GTATTTAAAA 0.913246 -106 TGATTTTTTATATTTTATAATAGAATGAGA 11 207 0 TATTTTATAA 0.822297 -37 ********** Masking position 7 Map Score: 12.1416 Number of sites scoring better than the average of aligned sites = 1636 Number in coding regions = 1392 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 5 AGTTACGCTTAAAATTTCTTTGTTATTATA 1 174 0 AAAATTTCTT 0.86996 -37 TTGTAAAAACCCAATTTCTTAAGGGGATAG 2 50 0 CCAATTTCTT 0.983752 -79 AACAAATCCTTTAGCTCTTGT 2 118 0 ACAAATCCTT 0.726789 -11 TTTAAATACTCCTATACCTTA 4 2 0 CCTATACCTT 0.832972 -273 AATTCCTTACCAAATTTCTTGGTGGTGGTG 4 191 0 CAAATTTCTT 0.952013 -84 ATCTGTTTTTGCAATTCCTTACCAAATTTC 4 203 0 GCAATTCCTT 0.934139 -72 GGGGATTTTATAAATATCTTAAATAGGGAG 6 20 1 TAAATATCTT 0.679325 -33 AACCTATTTCTTTCCTAAAATC 8 99 0 CCTATTTCTT 0.950329 -12 GATCGTTATCTCAATTTCTTCATTTTTTTT 11 59 1 TCAATTTCTT 0.953398 -185 ********** Masking position 4 Map Score: 5.67824 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 317 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GTTTAAAAAATAAGTTAAATAAGGCTTATT 1 37 0 TAAGTTAAAT 0.916499 -174 CTCTCGCTTATAACTTACATGATGCTATTA 1 123 0 TAACTTACAT 0.945955 -88 AGTTTGTTGCTTTCTTAAATAGGGCATGTT 3 98 1 TTTCTTAAAT 0.805719 -64 GTGTAAATATTAACTCACATTCGCTTAATT 5 16 0 TAACTCACAT 0.921741 -51 ATTTTATAAATATCTTAAATAGGGAGTTAG 6 24 1 TATCTTAAAT 0.952327 -29 GATCGATCGTTATCTCAATTTCTTCATTTT 11 55 1 TATCTCAATT 0.736196 -189 AAAACCTGCTTAAGTTAAATTGATCTCATT 11 184 1 TAAGTTAAAT 0.916499 -60 ********** Masking position 7 Map Score: 1.71778 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 29 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TAGAGTTTAAAAAATAAGTTAAATAAGGCT 1 41 0 AAAATAAGTT 0.890813 -170 GTTTTAAAATAGATAGAGTTTAAAAAATAA 1 54 0 AGATAGAGTT 0.940774 -157 AAAAGGCTCAAAAATGAGTTTTAAAATAGA 1 71 0 AAAATGAGTT 0.979322 -140 CTTTAAGGGGAGAATGATTTCAAAATACCC 2 19 1 AGAATGATTT 0.817741 -110 TCCCCTTAAGAAATTGGGTTTTTACAATAA 2 53 1 AAATTGGGTT 0.87098 -76 TCTGTGTTTTAAAATGAGTTTGTTGCTTTC 3 82 1 AAAATGAGTT 0.979322 -80 GGCAAAAAAGAAAAAAAGTTAATGGATTTT 4 237 0 AAAAAAAGTT 0.787674 -38 TTTTTTGTTAAGATAGAGTTAATGTTTTTA 8 39 1 AGATAGAGTT 0.940774 -72 AAAAATGAAGAAATTGAGATAACGATCGAT 11 56 0 AAATTGAGAT 0.899986 -188 ATTTTATAATAGAATGAGATCAATTTAACT 11 196 0 AGAATGAGAT 0.934544 -48 ********** Masking position 3 Map Score: 11.5487 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 185 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 TAGGGGGTTTATTCTTGCTGTGATTTTGCT 3 32 1 ATTCTTGCTG 0.986713 -130 CCTTACCAAATTTCTTGGTGGTGGTGATGG 4 187 0 TTTCTTGGTG 0.967095 -88 TTTTTTGCCGATACTTGCTGTAATGGA 4 258 1 ATACTTGCTG 0.967095 -17 TTAAAATTTGATTCTTGGAGAATTTATA 5 49 1 ATTCTTGGAG 0.96709 -18 ********** Masking position 5 Map Score: 1.02678 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TATAAGCGAGAGAGTGTTTTGTAAAGCTTG 1 141 1 AGAGTGTTTT 0.936665 -70 TTAAGGGGATAGGGGGTATTTTGAAATCAT 2 32 0 AGGGGGTATT 0.952532 -97 CTTCATTTCTAGGGGGTTTATTCTTGCTGT 3 23 1 AGGGGGTTTA 0.952532 -139 TCTTAAATAGGGCATGTTTTTAGTCGTGTG 3 110 1 GGCATGTTTT 0.70372 -52 AGCTTTTAAGGGGATTTTATAAATATCT 6 9 1 AGGGGATTTT 0.962422 -44 ATAGGGAGTTAGAAGGTTTTT 6 42 1 AGAAGGTTTT 0.936655 -11 TTTTATGCGAAGGGTATTTTTTGCCTTTTT 11 103 1 AGGGTATTTT 0.909183 -141 ATTTAACTTAAGCAGGTTTTATCCAATAAG 11 174 0 AGCAGGTTTT 0.958119 -70 ********** Masking position 7 Map Score: 5.45919 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 749 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 10 GCTAGCGCTCAAACCATTAATAGCATCATG 1 106 1 AAACCATTAA 0.981382 -105 CCTAGAAATGAAGCCCTTAAACCCC 3 6 0 AAGCCCTTAA 0.933014 -156 TTAAACATAAAGAACATTAAAAAAATTAAA 4 107 0 AGAACATTAA 0.913334 -168 AGATTTCAAAAATCCATTAACTTTTTTTCT 4 229 1 AATCCATTAA 0.954257 -46 ATTTGTTATAAAAACATTAACTCTATCTTA 8 47 0 AAAACATTAA 0.959006 -64 ********** Masking position 7 Map Score: 0.477411 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 125 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 CTGTTTTCCTTTCAATCAGTTA 1 199 0 GTTTTCCTTT 0.91894 -12 TCTTGCTGTGATTTTGCTTTTCATTAAATT 3 44 1 ATTTTGCTTT 0.953949 -118 TAAAATGAGTTTGTTGCTTTCTTAAATAGG 3 91 1 TTGTTGCTTT 0.873979 -71 TATTCCCTACCATTTGCTTTTTTTTATTTT 4 70 1 CATTTGCTTT 0.851682 -205 TCCATTAACTTTTTTTCTTTTTTGCCGATA 4 241 1 TTTTTTCTTT 0.793821 -34 TTTTTGTGGTGTGCTTTGAGATGATAT 10 8 1 GGTGTGCTTT 0.806204 -32 TTCTCTAAAACTTGTGCTTTTGGGACAACT 11 18 1 CTTGTGCTTT 0.939985 -226 CGAAGGGTATTTTTTGCCTTTTTTATTTTT 11 110 1 TTTTTGCCTT 0.873979 -134 GATTTTCCTTTAAGATTTGAT 11 233 0 ATTTTCCTTT 0.879937 -11 ********** Masking position 5 Map Score: 3.48771 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 226 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: -2.20025e-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: -2.20025e-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: -2.20025e-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