AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_hpyl_reg_300.orf -o00710_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 Purged sequences: HP1350 209 protease Input sequences: #1 HP0175 300 cell binding factor 2 #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP1085 66 H. pylori predicted coding region HP1085 #4 HP1088 46 transketolase A (tktA) #5 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #6 HP1352 300 adenine specific DNA methyltransferase (HINFIM) #7 HP1385_HP1386 70 HP1385: fructose-1,6-bisphosphatase, HP1386: D-ribulose-5-phosphate 3 epimerase (rpe) Motif number 1 AATTTTTGAATCTTCTTTAACATTTTTTTTCTTTCCAAAA 1 65 1 TTTAATTTTT 0.989258 -236 TATTGTCTTTTTTGGTGTTAGTTTTATTCTTTTTGGAAAG 1 95 0 TTTTATTTTT 0.970364 -206 CGCCTCAGATGTTGTAATAATATTTATTGTCTTTTTTGGT 1 119 0 GTTAATTTTT 0.980947 -182 TGATAGCTGATTTTGTTTTAAATTTGCTATAATGTGAATT 1 235 1 TTTTATTTTT 0.970364 -66 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAG 2 16 0 TTTAATTGTT 0.940511 -199 TTCTACTACATTTGAAATAATTTTTCTTATAAACAAAACC 2 74 1 TTTAATTTTT 0.989258 -141 TTGAATTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 TTTTATTTTT 0.970364 -121 TCAAAGGGGCTATTGTTTAAAATTTACATTTTTTAAACGC 2 135 1 TTTAATTTAT 0.953777 -80 CCCTTTTAGTTATAATATAGATTTTATTTTAGCTAAAAAT 3 17 1 TTTAGTTTTT 0.945484 -50 GTTATGCGTTTTTGTTGTATCGTTTAAAATAGGTGGGGAT 6 136 1 TTTATTTTAT 0.723896 -165 GCGTTTTAAGGTTATCTTAATGTTTAATCTTTAGCTTTGT 6 225 0 GTTAATTTTT 0.980947 -76 GATTAACTAACCTTTTATATCTGCTACTCT 6 281 0 GTTAATTTTT 0.980947 -20 * * *** *** * * Masking position 8 Map Score: 16.6628 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 81 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 TTAAATTCACATTATAGCAAATTTAAAACAAA 1 246 0 ATTTACAAAT 0.957066 -55 CACTGCCTTAATTCTACTACATTTGAAATAAT 2 63 1 ATTTATACAT 0.812978 -152 TTTGAATTGAATTTTTTCTCAATTTAGGTTTT 2 108 0 ATTTTCTCAA 0.915351 -107 ACTATCCCTTATTATATCTAATAGCGTTTAAA 2 166 0 ATTTACTAAT 0.935198 -49 TAAAATCTATATTATAACTAAAAGGGGGTTTT 3 11 0 ATTTACTAAA 0.97209 -56 TATAGATTTTATTTTAGCTAAAAATGGCATGG 3 32 1 ATTTACTAAA 0.972141 -35 TTTGAGAGTCATTTTAACACAAA 4 2 0 ATTTACACAA 0.988305 -45 AAAAATCACCATTCTATCACAAATGCTCTTAA 5 52 0 ATTTACACAA 0.988307 -37 TACTCTAGCCATTTTAACACAAGCGTTTTAAG 6 255 0 ATTTACACAA 0.988305 -46 *** ** ***** Masking position 5 Map Score: 12.4475 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 66 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 TTATTGTTGTATGCATTCTCTTT 1 1 0 ATGCTTTTTT 0.84514 -300 TGAATATAATATTCGTAATTATTGTTGTATGCA 1 19 0 ATTCTATATT 0.742059 -282 CTTCTTTAACATTTTTTTTCTTTCCAAAAAGAA 1 76 1 ATTTTTTTTT 0.959225 -225 TTGGTGTTAGTTTTATTCTTTTTGGAAAGAAAA 1 91 0 TTTTTTTTTT 0.883077 -210 TTGTAATAATATTTATTGTCTTTTTTGGTGTTA 1 115 0 ATTTTTTTTT 0.959224 -186 ACTTTAAGCATTTCTTACTCTTTAATGTGAGTT 1 191 1 TTTCTATTTT 0.896685 -110 TTTTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 14 0 ATTTGATTTT 0.884764 -201 ATTGTTTAAAATTTACATTTTTTAAACGCTATT 2 146 1 ATTTCATTTT 0.953665 -69 AAATTTTTCCATTTTTAAGGTTTTTGAGAGTCA 4 23 0 ATTTTAGTTT 0.853086 -24 GTTTTCCCTTTATTTAAAAATCACC 5 74 0 TTTCCTTTTT 0.756122 -15 AGTAAGCCCCATTTCTAATGTTTTTGTAACGAA 6 68 1 ATTTTATTTT 0.973552 -233 GGTTATCTTAATGTTTAATCTTTAGCTTTGTTC 6 223 0 ATGTTATTTT 0.920831 -78 ATACTTCCCTATTTTCAATGTTTTCAAGTAAAA 7 12 1 ATTTCATTTT 0.953664 -59 **** ** * *** Masking position 2 Map Score: 11.7271 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 358 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 AGAATTTTTGAATCTTCTTTAACATTTTTTTT 1 63 1 AACTTCTTTA 0.748887 -238 CGAACACTTTTACCCGCTTTGAATGGAATGAA 1 157 1 TACCGCTTTA 0.981102 -144 TTTAAAACAAAATCAGCTATCATGATCACAGA 1 225 0 AACAGCTATA 0.91995 -76 TTTTAAACAATAGCCCCTTTGAATTGAATTTT 2 125 0 TACCCCTTTA 0.984689 -90 TTACATTTTTTAAACGCTATTAGATATAATAA 2 158 1 TAACGCTATA 0.869319 -57 AGGTGGTAACTATCCCTTATTATATCTAATAG 2 174 0 TACCCTTATA 0.835188 -41 AAGGGATAGTTACCACCTATAAAATAAGGATC 2 188 1 TACACCTATA 0.964846 -27 AAAACCCCCTTTTAGTTATAATAT 3 3 1 AACCCCTTTA 0.970893 -64 TGGGGATAGATAGCTTCTATCATTTGATGCAT 6 169 1 TACTTCTATA 0.851853 -132 ATGGCTAGAGTAGCAGATATAAAAGGTTAGTT 6 275 1 TACAGATATA 0.635817 -26 AGTAAAATATTAGCATCTTTAATCAAATCATA 7 38 1 TACATCTTTA 0.91473 -33 AAAAACCCTTTTATGATTTGATT 7 58 0 AAACCCTTTA 0.822495 -13 ** ******* * Masking position 2 Map Score: 10.2753 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 493 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 AACTAACACCAAAAAAGACAATAAATATTA 1 112 1 AAAAAAGACA 0.8766 -189 AATGTAGTAGAATTAAGGCAGTGTTTTTGC 2 56 0 AATTAAGGCA 0.948943 -159 CTATTAGATATAATAAGGGATAGTTACCAC 2 174 1 TAATAAGGGA 0.783066 -41 TATTTTAGCTAAAAATGGCATGGGTTTTAG 3 41 1 AAAAATGGCA 0.958156 -26 CAAAAACCTTAAAAATGGAAAAATTTG 4 30 1 AAAAATGGAA 0.814397 -17 AATGCTCTTAAATAAAGGCATTCTTAAGGG 5 33 0 AATAAAGGCA 0.983282 -56 GTGATTTTTAAATAAAGGGAAAAC 5 75 1 AATAAAGGGA 0.983282 -14 GGCAATACAGAATAAAGGGAAGGC 6 5 0 AATAAAGGGA 0.983282 -296 GAAAACATTGAAAATAGGGAAGTATT 7 7 0 AAAATAGGGA 0.919504 -64 ********** Masking position 2 Map Score: 10.6547 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 281 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 AATTACGAATATTATATTCATAATTGCATCGA 1 32 1 ATTAATTCAA 0.936967 -269 GGGTAAAAGTGTTCGCCTCAGATGTTGTAATA 1 140 0 GTTCCCTCAA 0.929527 -161 AAAGTTATTCATTCCATTCAAAGCGGGTAAAA 1 164 0 ATTCATTCAA 0.984843 -137 AATTTTCATCATTAAATTCACATTATAGCAAA 1 257 0 ATTAATTCAA 0.936963 -44 TTGAGAAAAAATTCAATTCAAAGGGGCTATTG 2 118 1 ATTCATTCAA 0.984747 -97 ATAACTCCCCGATCCATTCACATGCAAATCGC 6 109 0 GATCATTCAA 0.958882 -192 CTTTAGCTTTGTTCTCATCAAATGCATCAAAT 6 205 0 GTTCCATCAA 0.940093 -96 TAGCATCTTTAATCAAATCATAAAAGGGTTTT 7 48 1 AATCAATCAA 0.911895 -23 **** ***** * Masking position 10 Map Score: 6.09136 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 56 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AATTAACCTAAAATCGCTTGACGCAAAAAC 2 34 1 AAATCGCTTG 0.981967 -181 TTTTAGCTAAAAATGGCATGGGTTTTAGCA 3 43 1 AAATGGCATG 0.969856 -24 ATTCACATGCAAATCGCAAAGCATGTTCGT 6 96 0 AAATCGCAAA 0.898514 -205 CGATACAACAAAAACGCATAACTCCCCGAT 6 128 0 AAAACGCATA 0.898484 -173 AGATAACCTTAAAACGCTTGTGTTAAAATG 6 248 1 AAAACGCTTG 0.976107 -53 GCTTGTGTTAAAATGGCTAGAGTAGCAGAT 6 263 1 AAATGGCTAG 0.969856 -38 TAGCAGATATAAAAGGTTAGTTAATC 6 285 1 AAAAGGTTAG 0.762183 -16 ********** Masking position 3 Map Score: 5.57786 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 559 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TAATTATTGTTGTATGCATTCTCTTT 1 7 0 TGTATGCATT 0.90039 -294 TCAAAAATTCTCGATGCAATTATGAATATA 1 44 0 TCGATGCAAT 0.935127 -257 AATGAATAACTTTAAGCATTTCTTACTCTT 1 183 1 TTTAAGCATT 0.859131 -118 CTAAAATCGCTTGACGCAAAAACACTGCCT 2 41 1 TTGACGCAAA 0.862383 -174 TTGATGCTTAATGAGACAGA 5 1 1 TTGATGCTTA 0.89112 -88 CTTCTATCATTTGATGCATTTGCATTTGAT 6 182 1 TTGATGCATT 0.989085 -119 GCATTTGCATTTGATGCATTTGATGAGAAC 6 197 1 TTGATGCATT 0.989085 -104 ********** Masking position 4 Map Score: 3.54857 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 147 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 AAAACTCACATTAAAGAGTAAGAAATGCTTA 1 195 0 TTAAAGATAA 0.612612 -106 GTGTTCTCCACTCTAAACTAATTTTCATCAT 1 277 0 CTCTAAATAA 0.979895 -24 CTCCTAAAAACTCAAAATTAACCTAAAATCG 2 19 1 CTCAAAATAA 0.973977 -196 TAGTTACCACCTATAAAATAAGGATCGTTCA 2 194 1 CTATAAATAA 0.959283 -21 ATCACAAATGCTCTTAAATAAAGGCATTCTT 5 38 0 CTCTTAATAA 0.91 -51 GCGATAGAGGCTCTAAAGTAAGCCCCATTTC 6 52 1 CTCTAAATAA 0.979895 -249 GAGAACAAAGCTAAAGATTAAACATTAAGAT 6 221 1 CTAAAGATAA 0.924168 -80 ******* *** Masking position 7 Map Score: 5.62858 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 43 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 AGAATGCATACAACAATAATTACGAATATT 1 15 1 CAACAATAAT 0.837832 -286 AAAGAAGATTCAAAAATTCTCGATGCAATT 1 53 0 CAAAAATTCT 0.869161 -248 TTTTTCTTTCCAAAAAGAATAAAACTAACA 1 90 1 CAAAAAGAAT 0.922337 -211 TCGCTTGACGCAAAAACACTGCCTTAATTC 2 47 1 CAAAAACACT 0.980097 -168 AAATGACTCTCAAAAACCTTAAAAATGGAA 4 20 1 CAAAAACCTT 0.934818 -27 ATGTTCGTTACAAAAACATTAGAAATGGGG 6 74 0 CAAAAACATT 0.969546 -227 ********** Masking position 5 Map Score: 0.182753 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 262 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 11 CGGGTAAAAGTGTTCGCCTCAGATGTTGTA 1 143 0 TGTTCGCCTC 0.990206 -158 TGTGTGTTCTCCACTCTAAACTAA 1 287 0 TGTTCTCCAC 0.984932 -14 TCGCAAAGCATGTTCGTTACAAAAACATTA 6 83 0 TGTTCGTTAC 0.903193 -218 TCTTTAGCTTTGTTCTCATCAAATGCATCA 6 208 0 TGTTCTCATC 0.959943 -93 ********** Masking position 4 Map Score: 0.0281604 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 25 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 ********** No masking Map Score: 1.08956e-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: 1.08956e-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: 1.08956e-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