AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_hpyl_reg_300.orf -o00460_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 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0723 128 L-asparaginase II (ansB) #3 HP0830 58 amidase #4 HP0832 91 spermidine synthase (speE) #5 HP0833 76 H. pylori predicted coding region HP0833 #6 HP1118 210 gamma-glutamyltranspeptidase (ggt) #7 HP1120 128 H. pylori predicted coding region HP1120 #8 HP1121 161 cytosine specific DNA methyltransferase (BSP6IM) #9 HP1122 274 H. pylori predicted coding region HP1122 #10 HP1125 66 peptidoglycan associated lipoprotein precursor (omp18) #11 HP1129 52 biopolymer transport protein (exbD) #12 HP1132 22 ATP synthase F1, subunit beta (atpD) #13 HP1137 110 ATP synthase F0, subunit b' (atpF') #14 HP1141 23 methionyl-tRNA formyltransferase (fmt) #15 HP1142 39 H. pylori predicted coding region HP1142 #16 HP1143 243 H. pylori predicted coding region HP1143 #17 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #18 HP1377 300 H. pylori predicted coding region HP1377 Motif number 1 GTTTTAGTGTATTATAGCTATATTTTAATTTAAGAA 1 36 1 ATTTGTTTTT 0.927483 -222 TTTAAGAATTTTAGATTGATTTTTTTAAGGGTAGTT 1 64 1 TTAATTTTTT 0.882339 -194 AAGGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 1 90 1 TTTTATTGTT 0.795892 -168 TAACCCTTTTTAAATTTATTTTAACGATGTTT 2 7 1 TTTTATTTTT 0.849282 -122 AAGGTGGTCCATAATGAGAATATTTTTGAAATTGTT 2 72 1 ATATATTTTT 0.808201 -57 GAAATTGTTGATTCTTTTATTTTGTTTGAAGGGGCA 2 99 1 ATTTTTTGTT 0.887119 -30 TTTTGTTACAATAATTTAGATTTTTTAGCTAGCATG 4 13 1 ATATTTTTTT 0.91351 -79 CAAATAAGCCTTATTTAACTTATTTTTTAAACTCTA 6 35 1 TTATATTTTT 0.839772 -176 TTAAAACTCATTTTTGAGCCTTTTTTATAGCTAGCG 6 77 1 TTTTATTTTT 0.849282 -134 TCAGTTACGCTTAAAATTTCTTTGTTATTATAACAC 6 170 0 TTAATTTGTT 0.838432 -41 TCATTAAATTTTAGTTTCTCTGTGTTTTAAAATGAG 8 64 1 TTATTTTGTT 0.900903 -98 TCTCTGTGTTTTAAAATGAGTTTGTTGCTTTCTTAA 8 80 1 TTAATTTGTT 0.838432 -82 ATAGGGCATGTTTTTAGTCGTGTGTTAGGAATGATT 8 116 1 TTTTGTTGTT 0.916743 -46 TACCATTTGCTTTTTTTTATTTTGTTATATTTTAAT 9 77 1 TTTTTTTGTT 0.907185 -198 TTATTTTGTTATATTTTAATTTTTTTAATGTTCTTT 9 93 1 ATATTTTTTT 0.913518 -182 AAGTTAATGGATTTTTGAAATCTGTTTTTGCAATTC 9 216 0 ATTTGTTGTT 0.898512 -59 TATTCTCAAATTTTAAGCGATTTTTTGTTAAGATAG 13 19 1 TTTAGTTTTT 0.900819 -92 TTTTGTTAAGATAGAGTTAATGTTTTTATAACAAAT 13 41 1 ATAATTTTTT 0.857744 -70 CGTTATCTCAATTTCTTCATTTTTTTTATTTATAAT 16 62 1 ATTCTTTTTT 0.713303 -182 TGCGAAGGGTATTTTTTGCCTTTTTTATTTTTTGTT 16 108 1 ATTTTTTTTT 0.919072 -136 TTGTTTGTATTTAAAATCCCTATTTTACTGAACTTA 16 142 1 TTAATTTTTT 0.882324 -102 TTATGGTATAATAGCGGTTATTTTTTTAGAATAACC 17 97 1 ATACGTTTTT 0.722758 -75 TTTGGATTCAATTAAAGCGCTATTTTTAGCGTTGGT 17 130 0 ATTAGTTTTT 0.879538 -42 AAAATAAACTCCTTGTTTTGGATTCAATT 17 153 0 ATAATTTTTT 0.857743 -19 AAAATGAGATTTACTGGGATTATTTTTCTTGATTTG 18 90 1 TTATGTTTTT 0.936708 -211 TTTTTCTTGATTTGTGGTTTTATTTTGCTCATTCCT 18 112 1 TTTTGTTTTT 0.940869 -189 GAGCGCTGGTTTTAAGGCGGTCTTTT 18 285 1 TTTAGTTTTT 0.900819 -16 *** * * * **** Masking position 11 Map Score: 30.4822 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 1045 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 TTGATTTTTTTAAGGGTAGTTTTTTTTAAGTT 1 79 1 TAAGGGATTT 0.982634 -179 GATTTAAGAGTAATGGGTGTTTGTTTTAAGAC 1 157 1 TAATGGTTTT 0.97229 -101 ACAAAAAATTTAATGGTAGTTTAACATGCTTA 3 25 0 TAATGGATTT 0.947566 -34 AAAAGTAAGCTAAGGAGTGTTT 4 80 1 TAAGGATTTT 0.869921 -12 ATAAGTTAAATAAGGCTTATTTGATCAAAACG 6 26 0 TAAGGCTTTT 0.948028 -185 TAAGGGAGCTTTAAGGGGAGAA 7 1 1 TAAGGGGTTT 0.953893 -128 CTTAAGGGGATAGGGGGTATTTTGAAATCATT 7 31 0 TAGGGGTTTT 0.983874 -98 GCTTCATTTCTAGGGGGTTTATTCTTGCTGTG 8 22 1 TAGGGGTTAT 0.839242 -140 CTTTCTTAAATAGGGCATGTTTTTAGTCGTGT 8 107 1 TAGGGCTTTT 0.910154 -55 TTGGTGGTGGTGATGGGTTTTTTTCCGGTTTC 9 171 0 TGATGGTTTT 0.897557 -104 GAAAAAAAGTTAATGGATTTTTGAAATCTGTT 9 226 0 TAATGGTTTT 0.97229 -49 AGCTTTTAAGGGGATTTTATAAATATCT 11 7 1 TAAGGGATTT 0.982634 -46 TCTCAAATTTTAAGCGATTTTTTGTTAAGATA 13 22 1 TAAGCGTTTT 0.895907 -89 GTTTTTATGCGAAGGGTATTTTTTGCCTTTTT 16 101 1 GAAGGGATTT 0.877688 -143 TATGGTATAATAGCGGTTATTTTTTTAGAATA 17 98 1 TAGCGGTTTT 0.876924 -74 AACTTAACCATGATGGAAGTTTAACCGAATCA 18 171 0 TGATGGATTT 0.818593 -130 ****** * *** Masking position 10 Map Score: 19.7421 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 612 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 TCATAGCGTCTTAAAACAAACACCCATTACTCT 1 163 0 TTAACAAACC 0.820894 -95 AATTCAAACCCTAAACCCAAACCTTTCTCTCAT 1 215 0 CTAACCAAAC 0.707251 -43 AACCTGCCCCTTCAAACAAAATAAAAGAATCAA 2 106 0 TTAACAAAAA 0.656284 -23 ATCTAAATTATTGTAACAAAAGC 4 1 0 TTTACAAAAC 0.972041 -91 TTAGCTTACTTTTTAACAATATCCATGCCTTAA 4 60 0 TTTACAATAC 0.822683 -32 ATCGCTTCAATTTAATCAAAATTAGATTACAAT 5 18 1 TTAACAAAAT 0.771006 -59 GTTTTCTACCCATAGCGTTTTGATCA 6 4 1 TTTACCATAC 0.733012 -207 TTCTTTGTTATTATAACACAAGCTTTACAAAAC 6 156 0 TTTACACAAC 0.877701 -55 TTCAGCCGTATTCAAGCAAATACTATGCCATTT 7 85 0 TTAACAAATC 0.845033 -44 GAAACTAAAATTTAATGAAAAGCAAAATCACAG 8 49 0 TTAAGAAAAC 0.89643 -113 GTTAATGTTTTTATAACAAATGCGAGTTTCAAA 13 56 1 TTTACAAATC 0.831198 -55 TTGAATTAAAAACAAGGAATAAC 14 1 1 TTAATAAAAC 0.793451 -23 CAGCTGCAAGTTGTCCCAAAAGCACAAGTTTTA 16 23 0 TTTCCAAAAC 0.786629 -221 AAATAGGGATTTTAAATACAAACAACAAAAAAT 16 134 0 TTAATACAAC 0.442264 -110 AAATCAAATCTTAAAGGAAAATC 16 231 1 TTAAGAAAAC 0.896431 -13 CATAAGCGGTTTCTATGCAAAGCGTTTCTTGAA 17 13 1 TTTAGCAAAC 0.822222 -159 AGCGCTTTAATTGAATCCAAAACAAGGAGTTTA 17 145 1 TTAACCAAAC 0.957953 -27 GTTATTGGGATTATATCCAAAACTAGCGAAAAT 18 200 1 TTTACCAAAC 0.953646 -101 CGAAAATTGATTTTACCAAAATTGTTTGATATA 18 226 1 TTTACAAAAT 0.752497 -75 ** ** ***** * Masking position 2 Map Score: 17.0114 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 593 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 AATTTAAGAATTTTAGATTGATTTTTTTAAG 1 62 1 TTTTAATTGA 0.854264 -196 AGACTTGAAATTTGAAAATAATAACACAACT 1 107 0 TTTGAAATAA 0.95434 -151 TGGACCACCTTTTGAAATTAAAAGATTTTAT 2 52 0 TTTGAATTAA 0.888455 -77 TGAGAATATTTTTGAAATTGTTGATTCTTTT 2 86 1 TTTGAATTGT 0.518928 -43 GCTTTTGTTACAATAATTTAGATTTT 4 6 1 TGTTAAATAA 0.872313 -86 CAAAAATGAGTTTTAAAATAGATAGAGTTTA 6 62 0 TTTTAAATAG 0.927781 -149 GTAAAGCTTGTGTTATAATAACAAAGAAATT 6 161 1 TGTTAAATAA 0.872313 -50 GAAATTGGGTTTTTACAATAAAAAAATGGCA 7 62 1 TTTTAAATAA 0.962185 -67 TTTCTCTGTGTTTTAAAATGAGTTTGTTGCT 8 78 1 TTTTAAATGA 0.938957 -84 ATAGCCAATTTTTGAGATTAGAACTATTCAT 9 42 0 TTTGAATTAG 0.800833 -233 TCGCTTAAAATTTGAGAATATTCAAGCG 13 8 0 TTTGAAATAT 0.824036 -103 GAGTTAATGTTTTTATAACAAATGCGAGTTT 13 54 1 TTTTAAACAA 0.775417 -57 ATTTTTTATATTTTATAATAGAATGAGATCA 16 204 0 TTTTAAATAG 0.927781 -40 GCGGTTATTTTTTTAGAATAACCAACGCTAA 17 110 1 TTTTAAATAA 0.962185 -62 CCTTATTATATTTTATAATGATTCGGTTAAA 18 153 1 TTTTAAATGA 0.938957 -148 ***** ***** Masking position 5 Map Score: 14.834 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 187 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 AAAAAAAACTACCCTTAAAAAAATCAATCT 1 76 0 ACCCTTAAAA 0.932559 -182 ATAGTCATAGCGTCTTAAAACAAACACCCA 1 170 0 CGTCTTAAAA 0.705861 -88 AACCTGCCCCTTCAAACAAAATAAAA 2 113 0 CCCCTTCAAA 0.803406 -16 ATTTTTTGTAAGGCTAAAAAC 3 48 1 AGGCTAAAAA 0.88195 -11 GCTATAAAAAAGGCTCAAAAATGAGTTTTA 6 78 0 AGGCTCAAAA 0.664918 -133 AAACACTCTCTCGCTTATAACTTACATGAT 6 130 0 TCGCTTATAA 0.423796 -81 TCAATCAGTTACGCTTAAAATTTCTTTGTT 6 180 0 ACGCTTAAAA 0.95145 -31 AAATCATTCTCCCCTTAAAGCTCCCTTA 7 9 0 CCCCTTAAAG 0.803406 -120 TACCCCCTATCCCCTTAAGAAATTGGGTTT 7 44 1 CCCCTTAAGA 0.794384 -85 AAGAATAAACCCCCTAGAAATGAAGCCCTT 8 18 0 CCCCTAGAAA 0.725374 -144 TCCTAACACACGACTAAAAACATGCCCTAT 8 116 0 CGACTAAAAA 0.608002 -46 CAGCAAGTATCGGCAAAAAAGAAAAAAAGT 9 248 0 CGGCAAAAAA 0.799796 -27 TTTATAAAATCCCCTTAAAAGCT 11 4 0 CCCCTTAAAA 0.973286 -49 TAACAAAAAATCGCTTAAAATTTGAGAATA 13 19 0 TCGCTTAAAA 0.911348 -92 AAAATACCCTTCGCATAAAAACTACATTAT 16 93 0 TCGCATAAAA 0.675985 -151 AAAATAAAAAAGGCAAAAAATACCCTTCGC 16 109 0 AGGCAAAAAA 0.602573 -135 AGAATAACCAACGCTAAAAATAGCGCTTTA 17 124 1 ACGCTAAAAA 0.926828 -48 ACGCCACCTACCGCTAAAATGAGATTTACT 18 75 1 CCGCTAAAAT 0.716368 -226 AAAAGACCGCCTTAAAACCAGCGCTCA 18 284 0 CGCCTTAAAA 0.955535 -17 ********** Masking position 4 Map Score: 13.2351 Number of sites scoring better than the average of aligned sites = 1650 Number in coding regions = 1455 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 TAACCCTTTTTAAATTTATTTTA 2 4 1 CCCTTTTTAA 0.972854 -125 CGCTAGACCCTTATTTAAGCTTTAAATA 5 59 0 CCTTATTTAA 0.973152 -18 ATCAAATAAGCCTTATTTAACTTATTTTTT 6 33 1 CCTTATTTAA 0.973152 -178 CATTTTTGAGCCTTTTTTATAGCTAGCGCT 6 85 1 CCTTTTTTAT 0.892143 -126 TAAAAACATGCCCTATTTAAGAAAGCAACA 8 102 0 CCCTATTTAA 0.982904 -60 CCTTCTAACTCCCTATTTAAGATATTTATA 11 28 0 CCCTATTTAA 0.982904 -25 GTATTTTTTGCCTTTTTTATTTTTTGTTGT 16 116 1 CCTTTTTTAT 0.892143 -128 TATTTAAAATCCCTATTTTACTGAACTTAT 16 149 1 CCCTATTTTA 0.911529 -95 ********** Masking position 6 Map Score: 12.4894 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 64 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 7 ATTCTTAAATTAAAATATAGCTATAATACAC 1 42 0 TAAATATAGC 0.441273 -216 GCCTTACAAAAAATTTAATGGTAGTTTAACA 3 31 0 AAATTAATGG 0.616392 -28 ATCCATGCCTTAATGAATTGCTAACATGCTA 4 42 0 TAATAATTGC 0.750237 -50 CCTATCCCCTTAAGAAATTGGGTTTTTACAA 7 49 1 TAAGAATTGG 0.954147 -80 GTTTTTACAATAAAAAAATGGCATAGTATTT 7 70 1 TAAAAAATGG 0.748521 -59 AACTAAAATTTAATGAAAAGCAAAATCACAG 8 49 0 TAATAAAAGC 0.530887 -113 TAAGGTATAGGAGTATTTAAA 9 1 1 TAAGTATAGG 0.886875 -274 AAAATAAAAAAAAGCAAATGGTAGGGAATAG 9 69 0 AAAGAAATGG 0.886875 -206 AGAAATTTGGTAAGGAATTGCAAAAACAGAT 9 202 1 TAAGAATTGC 0.914132 -73 AAAAAGAAAAAAAGTTAATGGATTTTTGAAA 9 232 0 AAAGTAATGG 0.850631 -43 GGATTTTAGGAAAGAAATAGGTT 13 98 1 AAAGAATAGG 0.84843 -13 CCATCATGGTTAAGTTATTGGGATTATATCC 18 187 1 TAAGTATTGG 0.937948 -114 **** ****** Masking position 7 Map Score: 3.68733 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 258 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AACCTTGAGATTGTTTTAGTGTATTATAGCTA 1 24 1 TTTTTTGTGT 0.845845 -234 AGGGTAGTTTTTTTTAAGTTGTGTTATTATTT 1 91 1 TTTTAATTGT 0.670925 -167 AAATTGTTGATTCTTTTATTTTGTTTGAAGGG 2 100 1 TTTTTTTTTT 0.849724 -29 CTTTTTTATCGCTTCAATTTAATC 5 3 1 TTTTATGCTT 0.682599 -74 CGCTAGACCCTTATTTAAGCTTTAAATAACTA 5 55 0 TTTTTAGCTT 0.581588 -22 TACTATGCCATTTTTTTATTGTAAAAACCCAA 7 66 0 TTTTTTTTGT 0.808924 -63 TTTTTTTATTTTGTTATATTTTAATTTTTTTA 9 88 1 TTTTATTTTT 0.829958 -187 TTTTTTAATGTTCTTTATGTTTAAAAGTTTGC 9 113 1 TTTTTAGTTT 0.803487 -162 ATCCATTAACTTTTTTTCTTTTTTGCCGATAC 9 240 1 TTTTTTTTTT 0.849724 -35 TTTTTGTGGTGTGCTTTGAGAT 15 1 1 TTTTGTGTGT 0.864059 -39 TTTCTTCATTTTTTTTATTTATAATGTAGTTT 16 73 1 TTTTTATTAT 0.391847 -171 CGAAGGGTATTTTTTGCCTTTTTTATTTTTTG 16 110 1 TTTTGCTTTT 0.529289 -134 CCTTTTTTATTTTTTGTTGTTTGTATTTAAAA 16 126 1 TTTTGTGTTT 0.89462 -118 AAGATTTGATTTTTTATATTTTATAATAGAAT 16 211 0 TTTTATTTTT 0.829958 -33 TGCAAAGCGTTTCTTGAAGCTTATGGCGCAAT 17 28 1 TTTTGAGCTT 0.616882 -144 GCGAGCGGTTTTCTTATGGTATAATAGCGGTT 17 84 1 TTTTATGTAT 0.563711 -88 GGGATTATTTTTCTTGATTTGTGGTTTTATTT 18 105 1 TTTTGATTGT 0.732338 -196 CCTCAACTCCTTATTATATTTTATAATGATTC 18 145 1 TTTTATTTTT 0.829958 -156 ** **** **** Masking position 5 Map Score: 12.1829 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 605 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 9 TTTTGAAACCTTGAGATTGTTTTAGTGTATTAT 1 18 1 TTGAGAGTTT 0.735748 -240 CGAGATATATGAGAGAAAGGTTTGGGTTTAGGG 1 207 1 GAGAGAGTTT 0.979395 -51 TTAATGGTTTGAGCGCTAGCTATAAAAAAGGCT 6 93 0 GAGCGCGTAT 0.936539 -118 AGTTATAAGCGAGAGAGTGTTTTGTAAAGCTTG 6 138 1 GAGAGAGTTT 0.979395 -73 GAGCTTTAAGGGGAGAATGATTTCAAAATACCC 7 16 1 GGGAGAGTTT 0.936001 -113 TAAATAGGGAGTTAGAAGGTTTTT 11 39 1 GTTAGAGTTT 0.811683 -14 ACTTGCAGCTGATCGATCGTTATCTCAATTTCT 16 45 1 GATCGAGTAT 0.855767 -199 TGTAGTTTTTATGCGAAGGGTATTTTTTGCCTT 16 97 1 ATGCGAGTAT 0.779989 -147 TTGCAAATACAAGCGAGCGGTTTTCTTATGGTA 17 72 1 AAGCGAGTTT 0.937208 -100 AGAAATCATTGAGCGCTGGTTTTAAGGCGGTCT 18 275 1 GAGCGCGTTT 0.970231 -26 ****** * *** Masking position 11 Map Score: 4.55414 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 377 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TAAGAATTTTAGATTGATTTTTTTAAGGGT 1 66 1 AGATTGATTT 0.744744 -192 AAATAAATTTAAAAAGGGTTA 2 2 0 AAAAAGGGTT 0.796433 -127 CAATTTAATCAAAATTAGATTACAATATTA 5 25 1 AAAATTAGAT 0.432228 -52 TAGAGTTTAAAAAATAAGTTAAATAAGGCT 6 41 0 AAAATAAGTT 0.596399 -170 GTTTTAAAATAGATAGAGTTTAAAAAATAA 6 54 0 AGATAGAGTT 0.869882 -157 AAAAGGCTCAAAAATGAGTTTTAAAATAGA 6 71 0 AAAATGAGTT 0.960443 -140 CTTTAAGGGGAGAATGATTTCAAAATACCC 7 19 1 AGAATGATTT 0.768466 -110 TCCCCTTAAGAAATTGGGTTTTTACAATAA 7 53 1 AAATTGGGTT 0.900306 -76 TCTGTGTTTTAAAATGAGTTTGTTGCTTTC 8 82 1 AAAATGAGTT 0.960443 -80 TTTTTTGTTAAGATAGAGTTAATGTTTTTA 13 39 1 AGATAGAGTT 0.869882 -72 AAAAATGAAGAAATTGAGATAACGATCGAT 16 56 0 AAATTGAGAT 0.916671 -188 AAGTTCAGTAAAATAGGGATTTTAAATACA 16 147 0 AAATAGGGAT 0.639318 -97 ATTTTATAATAGAATGAGATCAATTTAACT 16 196 0 AGAATGAGAT 0.911281 -48 ACCTACCGCTAAAATGAGATTTACTGGGAT 18 80 1 AAAATGAGAT 0.925959 -221 AAACTAGCGAAAATTGATTTTACCAAAATT 18 219 1 AAATTGATTT 0.775885 -82 ********** Masking position 3 Map Score: 14.4313 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 330 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 11 CAAGGTTTCAAAATTTAGCC 1 1 0 AAATTTAGCC 0.674028 -257 CATTACTCTTAAATCATGCCAATTCACACT 1 142 0 AAATCATGCC 0.900402 -116 ATTTTGATTAAATTGAAGCGATAAAAAAG 5 10 0 AATTGAAGCG 0.777118 -67 AACCCCCTAGAAATGAAGCCCTTAAACCCC 8 11 0 AAATGAAGCC 0.943694 -151 CACACGACTAAAAACATGCCCTATTTAAGA 8 110 0 AAAACATGCC 0.883824 -52 GGTTAAATTAAGCGAATGTGAGTT 10 5 1 AAATTAAGCG 0.861818 -62 TGTTTTTGCAAATACAAGCGAGCGGTTTTC 17 67 1 AATACAAGCG 0.850601 -105 CCATTTCTCCAAATCAAGCCCAGCCGCACC 18 39 1 AAATCAAGCC 0.970169 -262 AGCCGCACCAAAAAGACGCCACCTACCGCT 18 60 1 AAAAGACGCC 0.767186 -241 GATTATATCCAAAACTAGCGAAAATTGATT 18 208 1 AAAACTAGCG 0.864473 -93 AGACCGCCTTAAAACCAGCGCTCAATGATT 18 278 0 AAAACCAGCG 0.842799 -23 ********** Masking position 2 Map Score: 6.74003 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 553 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 CTCTTTAGACTTGAAATTTGAAAATAATAA 1 114 0 TTGAAATTTG 0.963122 -144 TCAGTTACGCTTAAAATTTCTTTGTTATTA 6 176 0 TTAAAATTTC 0.87839 -35 TAATGGATTTTTGAAATCTGTTTTTGCAAT 9 218 0 TTGAAATCTG 0.905207 -57 TTTACACTTATTAAAATTTGATTCTTGGAG 10 39 1 TTAAAATTTG 0.969232 -28 AAAAAATCGCTTAAAATTTGAGAATATTCA 13 15 0 TTAAAATTTG 0.969232 -96 GATTTTCCTTTAAGATTTGATTTTTTATA 16 225 0 TTAAGATTTG 0.920118 -19 ********** Masking position 6 Map Score: 3.25195 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 32 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: -2.81842e-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: -2.81842e-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: -2.81842e-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