AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00430_hpyl_reg_300.orf -o00430_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 TAAGCCTTATTTAACTTATTTTTTAAACTCTAT 1 39 1 TTCTATTTTT 0.904009 -172 CGCTTAAAATTTCTTTGTTATTATAACACAAGC 1 166 0 TTTTTTATTA 0.684144 -45 AACAAATCCTTTAGCTCTTGTTTCAGCCGTATT 2 106 0 TTCTTTGTTT 0.837086 -23 GATTTTGCTTTTCATTAAATTTTAGTTTCTCTG 3 53 1 TTTTAATTTT 0.87952 -109 AAATTTTAGTTTCTCTGTGTTTTAAAATGAGTT 3 69 1 TTCTTGTTTT 0.942141 -93 TTCCCTACCATTTGCTTTTTTTTATTTTGTTAT 4 72 1 TTCTTTTTTT 0.974273 -203 TTTTTTTTATTTTGTTATATTTTAATTTTTTTA 4 87 1 TTTTTATTTT 0.967057 -188 TTTTTTAATGTTCTTTATGTTTAAAAGTTTGCA 4 113 1 TTTTTGTTTA 0.910504 -162 TCCATTAACTTTTTTTCTTTTTTGCCGATACTT 4 241 1 TTTTTTTTTT 0.974785 -34 TTAACTCACATTCGCTTAATTTAACC 5 4 0 TTCTAATTTA 0.814011 -63 TATAAAAACATTAACTCTATCTTAACAAAAAAT 8 38 0 TTCTTATCTT 0.784795 -73 GTTATTCCTTGTTTTTAATTCAA 9 7 0 TTTTTTTTTA 0.95945 -17 TCTCAATTTCTTCATTTTTTTTATTTATAATGT 11 67 1 TTTTTTTTTA 0.95945 -177 ATTTTTTGCCTTTTTTATTTTTTGTTGTTTGTA 11 118 1 TTTTTTTTTT 0.974785 -126 TTATTTTTTGTTGTTTGTATTTAAAATCCCTAT 11 132 1 TTTTTATTTA 0.947274 -112 TAAGATTTGATTTTTTATATTTTATAATAGAAT 11 211 0 TTTTTATTTT 0.967057 -33 ** ** ****** Masking position 6 Map Score: 19.8886 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 487 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 AATGATTTCAAAATACCCCCTATCCCCTTAA 2 31 1 AAATACCCCT 0.956275 -98 TTTTTATTGTAAAAACCCAATTTCTTAAGGG 2 55 0 AAAAACCCAT 0.971341 -74 CACAGCAAGAATAAACCCCCTAGAAATGAAG 3 23 0 ATAAACCCCT 0.956275 -139 AAAAGTTAAAATCCCCAATCAATCATTC 3 144 0 AAAATCCCCA 0.92803 -18 AGAAACCGGAAAAAAACCCATCACCACCACC 4 170 1 AAAAAACCCT 0.971341 -105 AACAGATTTCAAAAATCCATTAACTTTTTTT 4 226 1 AAAAATCCAT 0.86969 -49 AGATATTTATAAAATCCCCTTAAAAGCT 6 8 0 AAAATCCCCT 0.990242 -45 AAAAACCTTCTAACTCCCTAT 6 42 0 AAAAACCTTT 0.747547 -11 TATCTTAACAAAAAATCGCTTAAAATTTGAG 8 23 0 AAAAATCGCT 0.81443 -88 AAAAAGGCAAAAAATACCCTTCGCATAAAAA 11 102 0 AAAATACCCT 0.952343 -142 GTTTGTATTTAAAATCCCTATTTTACTGAAC 11 144 1 AAAATCCCTT 0.952344 -100 ********* * Masking position 3 Map Score: 13.1161 Number of sites scoring better than the average of aligned sites = 1268 Number in coding regions = 1069 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 TTATAGCTAGCGCTCAAACCATTAATAGCATC 1 101 1 CGCTCAAACT 0.909542 -110 AACACTCTCTCGCTTATAACTTACATGATGCT 1 127 0 CGCTTATAAT 0.932784 -84 CAATCAGTTACGCTTAAAATTTCTTTGTTATT 1 177 0 CGCTTAAAAT 0.989963 -34 AATCATTCTCCCCTTAAAGCTCCCTTA 2 6 0 CCCTTAAAGC 0.918466 -123 ACCCCCTATCCCCTTAAGAAATTGGGTTTTTA 2 45 1 CCCTTAAGAT 0.976965 -84 AGAAATGAAGCCCTTAAACCCC 3 1 0 CCCTTAAACC 0.953983 -161 TTATAAAATCCCCTTAAAAGCT 6 1 0 CCCTTAAAAT 0.989676 -52 AACAAAAAATCGCTTAAAATTTGAGAATATTC 8 16 0 CGCTTAAAAT 0.989963 -95 AAATACCCTTCGCATAAAAACTACATTATAAA 11 90 0 CGCATAAAAT 0.93279 -154 GATTTTCCTTTAAGATTTGATTTTTTAT 11 226 0 CCTTTAAGAT 0.787478 -18 ********* * Masking position 6 Map Score: 10.2862 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 283 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 AAAAAATAAGTTAAATAAGGCTTATTTGATC 1 32 0 TTAAATAGGC 0.986536 -179 AGCGCTAGCTATAAAAAAGGCTCAAAAATGA 1 84 0 ATAAAAAGGC 0.975974 -127 TTTTTACAATAAAAAAATGGCATAGTATTTG 2 71 1 AAAAAAAGGC 0.965213 -58 TAGTATTTGCTTGAATACGGCTGAAACAAGA 2 93 1 TTGAATAGGC 0.938576 -36 TGTTGCTTTCTTAAATAGGGCATGTTTTTAG 3 102 1 TTAAATAGGC 0.986536 -60 TATAACAAAATAAAAAAAAGCAAATGGTAGG 4 75 0 TAAAAAAAGC 0.78017 -200 TATAAATATCTTAAATAGGGAGTTAGAAGGT 6 28 1 TTAAATAGGA 0.953861 -25 TTGAATTAAAAACAAGGAATAAC 9 8 1 AAAAACAGGA 0.779089 -16 ACAACAAAAAATAAAAAAGGCAAAAAATACC 11 115 0 ATAAAAAGGC 0.975974 -129 ATAAGTTCAGTAAAATAGGGATTTTAAATAC 11 148 0 TAAAATAGGA 0.933866 -96 ******* *** Masking position 5 Map Score: 12.4037 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 349 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 TATTTAACTTATTTTTTAAACTCTATCTATTTTA 1 46 1 ATTTTTTATT 0.876037 -165 TTTAAAACTCATTTTTGAGCCTTTTTTATAGCTA 1 76 1 ATTTTTGATT 0.951592 -135 GCTTTTCATTAAATTTTAGTTTCTCTGTGTTTTA 3 59 1 AAATTTTATT 0.847191 -103 GGAATAGCCAATTTTTGAGATTAGAACTATTCAT 4 42 0 ATTTTTGATG 0.963477 -233 TTATTTTGTTATATTTTAATTTTTTTAATGTTCT 4 93 1 ATATTTTATT 0.920705 -182 AAGTTAATGGATTTTTGAAATCTGTTTTTGCAAT 4 218 0 ATTTTTGACG 0.832437 -57 ACACTTATTAAAATTTGATTCTTGGAGAATTTAT 5 42 1 AAATTTGATG 0.952962 -25 AAATCGCTTAAAATTTGAGAATATTCAAGCG 8 8 0 AAATTTGATT 0.929406 -103 ATCCTACAAAATATTTGAAACTCGCATTTGTTAT 8 68 0 ATATTTGATG 0.978073 -43 TTGATTTTTTATATTTTATAATAGAATGAGATCA 11 204 0 ATATTTTATG 0.934142 -40 TTTTCCTTTAAGATTTGATTTTTTATATTTTATA 11 218 0 AGATTTGATT 0.89853 -26 ******** * * Masking position 8 Map Score: 9.76322 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 142 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 AGCCTTATTTAACTTATTTTTTAAACTCTA 1 41 1 AACTTATTTT 0.843558 -170 TTATTTTTTAAACTCTATCTATTTTAAAAC 1 54 1 AACTCTATCT 0.94211 -157 TCTATTTTAAAACTCATTTTTGAGCCTTTT 1 71 1 AACTCATTTT 0.972265 -140 GGGTATTTTGAAATCATTCTCCCCTTAAAG 2 19 0 AAATCATTCT 0.721006 -110 TTATTGTAAAAACCCAATTTCTTAAGGGGA 2 53 0 AACCCAATTT 0.918861 -76 GAAAGCAACAAACTCATTTTAAAACACAGA 3 82 0 AACTCATTTT 0.972265 -80 AAAATCCATTAACTTTTTTTCTTTTTTGCC 4 237 1 AACTTTTTTT 0.761068 -38 TAAAAACATTAACTCTATCTTAACAAAAAA 8 39 0 AACTCTATCT 0.94211 -72 ATCGATCGTTATCTCAATTTCTTCATTTTT 11 56 1 ATCTCAATTT 0.921591 -188 TGTATTTAAAATCCCTATTTTACTGAACTT 11 147 1 ATCCCTATTT 0.7268 -97 AGTTAAATTGATCTCATTCTATTATAAAAT 11 196 1 ATCTCATTCT 0.928902 -48 ********** Masking position 1 Map Score: 12.7787 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 226 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 CTGTTTTCCTTTCAATCAGTTAC 1 198 0 TTTTCCTTTC 0.948296 -13 CTTGCTGTGATTTTGCTTTTCATTAAATTT 3 45 1 TTTTGCTTTT 0.984754 -117 AAAATGAGTTTGTTGCTTTCTTAAATAGGG 3 92 1 TGTTGCTTTC 0.920284 -70 ATTCCCTACCATTTGCTTTTTTTTATTTTG 4 71 1 ATTTGCTTTT 0.92048 -204 CCATTAACTTTTTTTCTTTTTTGCCGATAC 4 242 1 TTTTTCTTTT 0.90903 -33 TCTCTAAAACTTGTGCTTTTGGGACAACTT 11 19 1 TTGTGCTTTT 0.944922 -225 GAAGGGTATTTTTTGCCTTTTTTATTTTTT 11 111 1 TTTTGCCTTT 0.944922 -133 GATTTTCCTTTAAGATTTGATT 11 232 0 TTTTCCTTTA 0.870535 -12 ********** Masking position 4 Map Score: 6.93593 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 223 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TATCCCCTTAAGAAATTGGGTTTTTACAAT 2 51 1 AGAAATTGGG 0.988798 -78 TTTTACAATAAAAAAATGGCATAGTATTTG 2 72 1 AAAAAATGGC 0.822698 -57 TTCTAATCTCAAAAATTGGCTATTCCCTAC 4 50 1 AAAAATTGGC 0.957168 -225 ACCACCACCAAGAAATTTGGTAAGGAATTG 4 192 1 AGAAATTTGG 0.919578 -83 ATTTTAGGAAAGAAATAGGTT 8 100 1 AGAAATAGGT 0.880412 -11 AAAAAAATGAAGAAATTGAGATAACGATCG 11 58 0 AGAAATTGAG 0.91971 -186 ATAAGTTCAGTAAAATAGGGATTTTAAATA 11 149 0 TAAAATAGGG 0.794325 -95 ********** Masking position 5 Map Score: 1.92654 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 215 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CTATGCCATTTTTTTATTGTAAAAACCCAA 2 66 0 TTTTTATTGT 0.658634 -63 TTAGCTCTTGTTTCAGCCGTATTCAAGCAA 2 99 0 TTTCAGCCGT 0.809182 -30 AGGGGGTTTATTCTTGCTGTGATTTTGCTT 3 33 1 TTCTTGCTGT 0.951992 -129 TAGGGCATGTTTTTAGTCGTGTGTTAGGAA 3 117 1 TTTTAGTCGT 0.896669 -45 GTGATGGGTTTTTTTCCGGTTTCTGCCACA 4 164 0 TTTTTCCGGT 0.847451 -111 CTTTTTTTCTTTTTTGCCGATACTTGCTGT 4 249 1 TTTTTGCCGA 0.911448 -26 TTTTTGCCGATACTTGCTGTAATGGA 4 259 1 TACTTGCTGT 0.736163 -16 TTTTTGTGGTGTGCTTTGAG 10 1 1 TTTTTGTGGT 0.942251 -39 CGAAGGGTATTTTTTGCCTTTTTTATTTTT 11 110 1 TTTTTGCCTT 0.864698 -134 CCTTTTTTATTTTTTGTTGTTTGTATTTAA 11 126 1 TTTTTGTTGT 0.951646 -118 ********** Masking position 1 Map Score: 3.42047 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 427 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 ACTCTATCTATTTTAAAACTCATTTTTGAGC 1 65 1 TTTAAAACTC 0.736517 -146 ACTCTCTCGCTTATAACTTACATGATGCTAT 1 125 0 TTTAACTTAC 0.79852 -86 AACACAAGCTTTACAAAACACTCTCTCGCTT 1 144 0 TTCAAAACAC 0.787143 -67 TTCTTTGTTATTATAACACAAGCTTTACAAA 1 158 0 TTTAACACAA 0.886754 -53 AACAAACTCATTTTAAAACACAGAGAAACTA 3 75 0 TTTAAAACAC 0.946615 -87 AATCAATCATTCCTAACACACGACTAAAAAC 3 125 0 TCTAACACAC 0.956848 -37 TAAGTGTAAATATTAACTCACATTCGCTTAA 5 18 0 TATAACTCAC 0.890464 -49 AAAAACCTTCTAACTCCCTATTTAAGAT 6 35 0 TTTAACTCCC 0.913785 -18 TATTCCTTGTTTTTAATTCAA 9 1 0 TTTAATTCAA 0.681424 -23 TCCTAATTCACAATATCATCT 10 29 0 TCTAATTCAC 0.858134 -11 ** ******** Masking position 6 Map Score: 2.87082 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 183 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 ********** 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 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