AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_hpyl_reg_300.orf -o00310_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 HP0170 74 H. pylori predicted coding region HP0170 #2 HP0171 60 peptide chain release factor RF-2 (prfB) #3 HP0174 300 H. pylori predicted coding region HP0174 #4 HP0180_HP0181 257 HP0180: apolipoprotein N-acyltransferase (cute), HP0181: H. pylori predicted coding region HP0181 #5 HP0194 214 triosephosphate isomerase (tpi) #6 HP0654 296 conserved hypothetical protein #7 HP0655 82 protective surface antigen D15 #8 HP0688 143 H. pylori predicted coding region HP0688 #9 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #10 HP1010 300 polyphosphate kinase (ppk) #11 HP1011 36 dihydroorotate dehydrogenase (pyrD) #12 HP1435 70 protease IV (PspA) Motif number 1 TTATTGTCTTTTTTGGTGTTAGTTTTATTCT 3 56 1 TTTTGGGTTA 0.945747 -245 TATTCTTTATATTTGGTTTTTTAGCATTGCA 3 200 1 ATTTGGTTTT 0.700606 -101 AATTATATTGATTTAGCGTTACTT 4 4 0 ATTTAGGTTA 0.899916 -254 AAAGGTTTGGGTTTAGGGTTTGAATTATATT 4 26 0 GTTTAGGTTT 0.888765 -232 AATTTAAGAATTTTAGATTGATTTTTTTAAG 4 186 0 TTTTAGTTGA 0.941564 -72 CTTGAGATTGTTTTAGTGTATTATAGCTATA 4 221 0 TTTTAGGTAT 0.894889 -37 TTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 5 14 0 TTTGAGTTTT 0.732497 -201 CGTCAAGCGATTTTAGGTTAATTTTGAGTTT 5 26 0 TTTTAGTTAA 0.886382 -189 TTTTTTCTCAATTTAGGTTTTGTTTATAAGA 5 98 0 ATTTAGTTTT 0.848092 -117 ATTGTAGCATTTTTAGATTTAAGAATGCTTT 6 244 0 TTTTAGTTTA 0.969108 -53 TAATTTTTAGCGTTTTTAAGAATGA 7 5 1 TTTTAGGTTT 0.971619 -78 CCTTAATAGATTTTAGCTTGAGTGTTGTTAG 7 54 0 TTTTAGTTGA 0.941564 -29 TTTTTCTAATTTTTAGTTATATCGTTTTTAG 8 36 1 TTTTAGTATA 0.680327 -108 GTTATATCGTTTTTAGATTAAAAGTCAGCAC 8 51 1 TTTTAGTTAA 0.886382 -93 CTTTGCCTAGTTTCAGGGTTTTAATAGAATT 9 11 0 TTTCAGGTTT 0.784029 -271 TTAGGTTTTGTTTTGGATTGAGGGCGATCCG 9 184 0 TTTTGGTTGA 0.871027 -98 TTGGATTTTATTTTAGGTTTTGTTTTGGATT 9 196 0 TTTTAGTTTT 0.962719 -86 CTTAAAATTTTTTTAGCGTTT 10 1 0 TTTTAGGTTT 0.971619 -300 TTAAGCGATCTTTTAGGGTTAAATGAAGTTT 10 27 1 TTTTAGGTTA 0.97652 -274 AAATCAGTTTGTTTGGTGTGATTATATAATG 10 252 0 GTTTGGGTGA 0.676338 -49 ****** **** Masking position 3 Map Score: 25.3006 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 668 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 CCAATTGGTTTTAAAAAGCGTTTTATAGTAACCATAATTTA 1 32 0 TTAAGTTTAA 0.97499 -43 AATGGCTTTTAACAATGCTATAATGATAAGTTCAAAAC 2 8 1 TTAAATTATA 0.638159 -53 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGTGTTAT 4 161 0 TTAAGTTTAA 0.958387 -97 TCTAAAATTCTTAAATTAAAATATAGCTATAATACACTAAA 4 200 1 TTAAATTGTA 0.874269 -58 TCTACTACATTTGAAATAATTTTTCTTATAAACAAAACCTA 5 75 1 TTAAATTTAA 0.963816 -140 AATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAGGTTTT 5 108 0 TTAAGTTTAA 0.973767 -107 TCTAATAGCGTTTAAAAAATGTAAATTTTAAACAATAGCCC 5 141 0 TTAAATATAA 0.903379 -74 CTAATTCTCATTAAATAGATTTTTATGATAAAATCTAAGCT 6 142 0 TTAAGTTTAA 0.974994 -155 CAATAGGGGGTTAAAAGGGGATATTTTTATATAATATGTAA 6 203 1 TTAAGTTTTA 0.952128 -94 CATTTTTAGATTTAAGAATGCTTTTTACATATTATATAAAA 6 227 0 TTAAATTTTA 0.950663 -70 GGTTAAATTGCCCTTTCGTTTTAAAGATAAACA 6 274 0 TTAAGTTGTA 0.879052 -23 TTTTAGCGTTTTTAAGAATGATTAGTTATAATAACGCTACT 7 15 1 TTAAATATAA 0.918839 -68 TCTCTAACGCTTTAAAAAATTTCTTTCTAAGCAGTCTTTGC 9 36 0 TTAAATTTAG 0.808151 -246 TCTTTTAGGGTTAAATGAAGTTTTATTCAAAAAATGAAGTT 10 35 1 TTAAATTTAA 0.973128 -266 TTAGTTGTTGTTTAAAAACTCTTTTTTGTAAAACTTCATTT 10 66 0 TTAAATTTAA 0.963816 -235 CCATGACTTTTTAAAAAAGCTTCAATGATTATCATTTCATT 10 215 1 TTAAATATTA 0.853019 -86 TAGAAATCCTTTAAATCATCATGTTTAAAAATCAGTTTGTT 10 270 0 TTAAATTTAA 0.974071 -31 TGTATTATACTTCAAATGTTTTAAGGATTAAATC 12 4 0 TTAAGTAGAA 0.810288 -67 ** ** * * * * ** Masking position 12 Map Score: 27.2187 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 176 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TGCCAATTGGTTTTAAAAAGCGTTTTATAG 1 45 0 TTTTAAAAAG 0.892312 -30 AATGGCTTTTAACAATGCTATAATGA 2 7 1 TTTTAACAAT 0.869401 -54 GAAAAAAAATGTTAAAGAAGATTCAAAAAT 3 96 1 GTTAAAGAAG 0.725192 -205 TGGGTGTTTGTTTTAAGACGCTATGACTAT 4 79 0 TTTTAAGACG 0.695811 -179 CTATATTTTAATTTAAGAATTTTAGATTGA 4 196 0 ATTTAAGAAT 0.79135 -62 AAATGTAAATTTTAAACAATAGCCCCTTTG 5 136 0 TTTAAACAAT 0.811415 -79 TCTAATAGCGTTTAAAAAATGTAAATTTTA 5 152 0 TTTAAAAAAT 0.918104 -63 TTTTGTAAATTTTTAAAAATTTTCATACTC 6 80 0 TTTTAAAAAT 0.945472 -217 GCATTTTTAGATTTAAGAATGCTTTTTACA 6 239 0 ATTTAAGAAT 0.79135 -58 TGCCCTTTCGTTTTAAAGATAAACATTGTA 6 269 0 TTTTAAAGAT 0.855001 -28 TTTTTAGCGTTTTTAAGAATGATTAGTTAT 7 14 1 TTTTAAGAAT 0.956247 -69 AGACAAGAATGTTAAAAAATGAAAGGAGCG 8 120 1 GTTAAAAAAT 0.814258 -24 TCTCTAACGCTTTAAAAAATTTCTTTCTAA 9 47 0 TTTAAAAAAT 0.918104 -235 TTAGTTGTTGTTTAAAAACTCTTTTTTGTA 10 77 0 TTTAAAAACT 0.71065 -224 ATTGAAGCTTTTTTAAAAAGTCATGGTCGG 10 211 0 TTTTAAAAAG 0.892312 -90 AAATCATCATGTTTAAAAATCAGTTTGTTT 10 269 0 GTTTAAAAAT 0.871493 -32 AACATGATGATTTAAAGGATTTCTA 10 286 1 TTTAAAGGAT 0.827653 -15 ACTTCAAATGTTTTAAGGATTAAATC 12 7 0 TTTTAAGGAT 0.881376 -64 ********** Masking position 3 Map Score: 20.7939 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 676 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 4 ATAAGTTCAAAACCCCACTCATAAAGGTTC 2 36 1 AACCCCACTC 0.856575 -25 AATCAATATAATTCAAACCCTAAACCCAAA 4 22 1 ATTCAAACCC 0.975568 -236 AATCATGCCAATTCACACTCTTTAGACTTG 4 118 1 ATTCACACTC 0.966588 -140 CCCCCTATTGATGCCAACCCCTTTTTTTAC 6 183 0 ATGCCAACCC 0.916049 -114 TAACGCTACTAACAACACTCAAGCTAAAAT 7 46 1 AACAACACTC 0.622044 -37 AATGCGGAGCATTCAAACCCA 8 2 0 ATTCAAACCC 0.975568 -142 AATTCTATTAAAACCCTGAAACTAGG 9 7 1 ATTAAAACCC 0.860173 -275 TTGATTTTAGATCCCCACTCAAAGCTATAT 9 103 1 ATCCCCACTC 0.920096 -179 CTTTTAGGTGATTGACACCCTAACAGGTTG 9 224 0 ATTGACACCC 0.892192 -58 AACAACAACTAAGCAAACTCGCGCTACAAT 10 95 1 AAGCAAACTC 0.82086 -206 GAGTAGCGGGATTCAAACCCACGACCTCAC 10 182 0 ATTCAAACCC 0.975568 -119 TTCATTATATAATCACACCAAACAAACTGA 10 250 1 AATCACACCA 0.704002 -51 ********** Masking position 7 Map Score: 11.2632 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 329 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GTAATAATATTTATTGTCTTTTTTGGTGTTAG 3 46 1 TATTTCTTTT 0.955824 -255 TTGGTGTTAGTTTTATTCTTTTTGGAAAGAAA 3 68 1 TTTATCTTTT 0.845343 -233 TCTTTAACATTTTTTTTCTTTCCAAAAAGAAT 3 82 0 TTTTTCTTTC 0.832232 -219 TTACCAGGGTTATTATTCTTTATATTTGGTTT 3 187 1 TTTATCTTTA 0.82512 -114 TAAGACGCTATGACTATCTTTATGCGAGATAT 4 64 0 TACTTCTTTA 0.844265 -194 TCATGCCAATTCACACTCTTTAGACTTGAAAT 4 120 1 TACATCTTTA 0.613387 -138 ATTTACTTTTTCATTATCATTTATGCTATAAT 6 46 0 TATTTCATTT 0.900446 -251 TTTCATACTCTCATTTACTTTTTCATTATCAT 6 58 0 TATTACTTTT 0.697199 -239 TAGCCGGTGTTCTTTCTCATTTTTGTAAATTT 6 98 0 TTTTTCATTT 0.886462 -199 TTTTTTTACCTAATTCTCATTAAATAGATTTT 6 160 0 TATTTCATTA 0.886398 -137 AATGCTACAATGTTTATCTTTAAAACGAAAGG 6 264 1 TTTTTCTTTA 0.941595 -33 GTCTTTGCCTTTAAGTTGATTTA 9 269 0 TTTTCCTTTA 0.717735 -13 AAAGCTTCAATGATTATCATTTCATTATATAA 10 230 1 TATTTCATTT 0.900446 -71 TTAAATCCTTATCTTTTATGATTTGAA 11 20 0 TCTTTCTTTT 0.851781 -17 * *** ****** Masking position 10 Map Score: 6.66935 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 513 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 AGACAATAAATATTATTACAACATCTGAGGCGAA 3 31 0 TATTATACAT 0.687281 -270 TAATTACGAATATTATATTCATAATTGCATCGAG 3 127 0 TATTATATAA 0.726514 -174 TAAGTTGTGTTATTATTTTCAAATTTCAAGTCTA 4 140 0 TATTATAAAT 0.937756 -118 TGTTTTAGTGTATTATAGCTATATTTTAATTTAA 4 210 0 TATTATATAT 0.789328 -48 AAATAATTTTTCTTATAAACAAAACCTAAATTGA 5 88 1 TCTTATAAAA 0.896858 -127 AACTATCCCTTATTATATCTAATAGCGTTTAAAA 5 165 0 TATTATAATA 0.455016 -50 TTAAATAGATTTTTATGATAAAATCTAAGCTTTA 6 139 0 TTTTATAAAT 0.771367 -158 GCTTTTTACATATTATATAAAAATATCCCCTTTT 6 215 0 TATTATAAAT 0.937241 -82 TAACAATTAGTCTTATAGCGCTATAGTGCTGACT 8 73 0 TCTTATCTAT 0.679162 -71 GTCTCGCTTTTATTATATAACAATTAGTCTTATA 8 90 0 TATTATCAAT 0.911992 -54 ATCGTTCAATGATTATTGCACAATATAGCTTTGA 9 121 0 GATTATCAAT 0.552319 -161 AAAATATTATTCTTATCGTTCAATGATTATTGCA 9 135 0 TCTTATCAAT 0.894871 -147 ATAAGAATAATATTTTTGTGAAAAAAATAAACGG 9 153 1 TATTTTAAAA 0.617072 -129 TTAAATGAAGTTTTATTCAAAAAATGAAGTTTTA 10 45 1 TTTTATAAAA 0.569333 -256 GTTTAAAAACTCTTTTTTGTAAAACTTCATTTTT 10 64 0 TCTTTTAAAA 0.569203 -237 CATAAGAGTGTATTATACTTCAAATGTTTTAAGG 12 19 0 TATTATCAAA 0.880159 -52 TATAATACACTCTTATGGTCAAATATTAAGTTTA 12 36 1 TCTTATAAAT 0.925229 -35 ****** **** Masking position 6 Map Score: 10.44 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 136 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 CATTGCATGTTATCCCATATTAAATAACTTC 3 224 1 TATCCATATT 0.918719 -77 TCTATTAATCAATCTCATATTGATAAGCTTA 3 260 1 AATCCATATT 0.737138 -41 CCCAAACCTTTCTCTCATATATCTCGCATAA 4 46 1 TCTCCATATA 0.938149 -212 CTCTCATATATCTCGCATAAAGATAGTCATA 4 57 1 TCTCCATAAA 0.658391 -201 AGGTGGTAACTATCCCTTATTATATCTAATA 5 175 0 TATCCTTATT 0.885326 -40 AAATTTTCATACTCTCATTTACTTTTTCATT 6 63 0 ACTCCATTTA 0.817264 -234 GCCGGTGTTCTTTCTCATTTTTGTAAATTTT 6 97 0 TTTCCATTTT 0.768178 -200 TATATAAAAATATCCCCTTTTAACCCCCTAT 6 205 0 TATCCCTTTT 0.805179 -92 AACATTCTTGTCTCGCTTTTATTATATAACA 8 102 0 TCTCCTTTTA 0.924879 -42 TTATTCATAGTATCACTTTTAGGTGATTGAC 9 238 0 TATCCTTTTA 0.885326 -44 CGCGCTACAATCTCCCTTTTTGATTGCGGAG 10 114 1 TCTCCTTTTT 0.936023 -187 **** ****** Masking position 8 Map Score: 4.78859 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 189 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 CCCACTCATAAAGGTTCTGTTT 2 49 1 AAGGTTTGTT 0.899914 -12 TAGTTTTTTTTAAGTTGTGTTATTATTTTCA 4 153 0 TAAGTTTGTT 0.921964 -105 TTAAGAATTTTAGATTGATTTTTTTAAGGGT 4 183 0 TAGATTATTT 0.676258 -75 CAAGCGATTTTAGGTTAATTTTGAGTTTTTA 5 23 0 TAGGTTATTT 0.941535 -192 TTTCTCAATTTAGGTTTTGTTTATAAGAAAA 5 95 0 TAGGTTTGTT 0.977432 -120 GATTTTATTTTAGGTTTTGTTTTGGATTGAG 9 193 0 TAGGTTTGTT 0.977432 -89 TCTTTGCCTTTAAGTTGATTTATTATTCATA 9 260 0 TAAGTTATTT 0.81458 -22 ****** **** Masking position 2 Map Score: 2.21851 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GGCTTTTAACAATGCTATAATGATAAGTTC 2 14 1 AATGCTATAA 0.94482 -47 GATAACATGCAATGCTAAAAAACCAAATAT 3 208 0 AATGCTAAAA 0.907114 -93 ATAACTTCTATACTCTATTAATCAATCTCA 3 247 1 TACTCTATTA 0.451447 -54 AAGTAACGCTAAATCAATATAATT 4 5 1 AACGCTAAAT 0.673919 -253 ACACTGCCTTAATTCTACTACATTTGAAAT 5 62 1 AATTCTACTA 0.536459 -153 ACATTTTTTAAACGCTATTAGATATAATAA 5 160 1 AACGCTATTA 0.961789 -55 CATTATCATTTATGCTATAATTATGGGACA 6 37 0 TATGCTATAA 0.720942 -260 TAAATCTAAAAATGCTACAATGTTTATCTT 6 254 1 AATGCTACAA 0.905413 -43 CATTCTTAAAAACGCTAAAAATTA 7 5 0 AACGCTAAAA 0.962591 -78 TAGTTATAATAACGCTACTAACAACACTCA 7 37 1 AACGCTACTA 0.933649 -46 ACTCAAGCTAAAATCTATTAAGGAAATCAG 7 62 1 AAATCTATTA 0.300588 -21 TTAATCTAAAAACGATATAACTAAAAATTA 8 42 0 AACGATATAA 0.691107 -102 TCAGCACTATAGCGCTATAAGACTAATTGT 8 75 1 AGCGCTATAA 0.843029 -69 AATTCTATTAAAACCCTGAA 9 1 1 AATTCTATTA 0.67428 -281 ATGTTTCTCTAACGCTTTAAAAAATTTCTT 9 52 0 AACGCTTTAA 0.783718 -230 AAACGCTAAAAAAATTTTAAG 10 2 1 AACGCTAAAA 0.962591 -299 AACTTCATTTAACCCTAAAAGATCGCTTAA 10 27 0 AACCCTAAAA 0.715257 -274 ********** Masking position 6 Map Score: 15.3225 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 850 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 10 TTCTTTCCAAAAAGAATAAAACTAACACCA 3 69 0 AAAGAATAAA 0.665602 -232 ATGCAATGCTAAAAAACCAAATATAAAGAA 3 202 0 AAAAAACCAA 0.835853 -99 ACTACCCTTAAAAAAATCAATCTAAAATTC 4 180 1 AAAAAATCAA 0.964336 -78 AACTGCTCCTAAAAACTCAAAATTAACCTA 5 14 1 AAAAACTCAA 0.863344 -201 TAAATTGAGAAAAAATTCAATTCAAAGGGG 5 114 1 AAAAATTCAA 0.809979 -101 AATAGCGTTTAAAAAATGTAAATTTTAAAC 5 149 0 AAAAAATGTA 0.678635 -66 AATGATAATGAAAAAGTAAATGAGAGTATG 6 57 1 AAAAAGTAAA 0.711774 -240 CAAGAATGTTAAAAAATGAAAGGAGCGTGT 8 123 1 AAAAAATGAA 0.943246 -21 ATTTTTGTGAAAAAAATAAACGGATCGCCC 9 164 1 AAAAAATAAA 0.913566 -118 TACTATGAATAATAAATCAACTTAAAGGCA 9 257 1 AATAAATCAA 0.774556 -25 AGTTTTATTCAAAAAATGAAGTTTTACAAA 10 53 1 AAAAAATGAA 0.943246 -248 ********** Masking position 5 Map Score: 8.17899 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 391 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 GCGGGTAAAAGTGTTCGCCTCAGATGTTGT 3 18 1 GTGTTCGCCT 0.966306 -283 TTAAGGCAGTGTTTTTGCGTCAAGCGATTT 5 44 0 GTTTTTGCGT 0.924845 -171 TTTCTAAGCAGTCTTTGCCTAGTTTCAGGG 9 24 0 GTCTTTGCCT 0.989008 -258 GTCTTTGCCTTTAAGTTGAT 9 272 0 GTCTTTGCCT 0.989008 -10 ********** Masking position 5 Map Score: 0.421365 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 ATCGGCTGTCATTTTAGCGCAC 1 3 0 ATTTTAGCGC 0.793694 -72 AATATAAAGAATAATAACCCTGGTAACCAA 3 183 0 ATAATAACCC 0.943422 -118 AAATTTGAAAATAATAACACAACTTAAAAA 4 148 1 ATAATAACAC 0.761637 -110 TAAATTTTAAACAATAGCCCCTTTGAATTG 5 131 0 ACAATAGCCC 0.946546 -84 ATGATTAGTTATAATAACGCTACTAACAAC 7 32 1 ATAATAACGC 0.943422 -51 AAAAGTCAGCACTATAGCGCTATAAGACTA 8 70 1 ACTATAGCGC 0.946545 -74 AATTCTATTAAAACCCTGAAACTAGG 9 7 1 ATTAAAACCC 0.724415 -275 AAAAAGGGAGATTGTAGCGCGAGTTTGCTT 10 105 0 ATTGTAGCGC 0.850791 -196 TATGATTTGAACGATAACCC 11 1 0 ACGATAACCC 0.861031 -36 ********** Masking position 6 Map Score: 2.14238 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 171 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TTGAATCTTCTTTAACATTTTTTTTCTTTC 3 92 0 TTTAACATTT 0.79335 -209 GTGTTATTATTTTCAAATTTCAAGTCTAAA 4 138 0 TTTCAAATTT 0.950063 -120 AATCTCAAGGTTTCAAAATTTAGCC 4 243 1 TTTCAAAATT 0.883423 -15 AGAAAAATTATTTCAAATGTAGTAGAATTA 5 71 0 TTTCAAATGT 0.922576 -144 GGGGCTATTGTTTAAAATTTACATTTTTTA 5 140 1 TTTAAAATTT 0.909115 -75 TTTGTAAATTTTTAAAAATTTTCATACTCT 6 79 0 TTTAAAAATT 0.799371 -218 GCCGGTGTTCTTTCTCATTTTTGTAAATTT 6 98 0 TTTCTCATTT 0.644348 -199 CATTAAAGTTTTTCTAATTTTTAGTTATAT 8 28 1 TTTCTAATTT 0.825192 -116 TAAAAGATCGCTTAAAATTTTTTTAGCGTT 10 12 0 CTTAAAATTT 0.79335 -289 TTGAAGCTTTTTTAAAAAGTCATGGTCGGA 10 210 0 TTTAAAAAGT 0.713915 -91 GTGTATTATACTTCAAATGTTTTAAGGATT 12 16 0 CTTCAAATGT 0.820574 -55 ********** Masking position 7 Map Score: 8.14919 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 269 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 ********** No masking Map Score: -1.20549e-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 15 ********** No masking Map Score: -1.20549e-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