AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_tpal_reg_100.orf -o00010_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #2 TP0164 147 ABC transporter, ATP-binding protein (troB) #3 TP0168 79 phosphoglycerate mutase (pgm) #4 TP0413 102 phosphoglucomutase #5 TP0475 63 glucose-6-phosphate isomerase (gpi) #6 TP0476 66 acetate kinase (ack) #7 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #8 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #9 TP0479 111 T. pallidum predicted coding region TP0479 #10 TP0505 300 hexokinase (hxk) #11 TP0537 150 triosephosphate isomerase (tpi) #12 TP0662 266 fructose-bisphosphate aldolase (cbbA) #13 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #14 TP0818 26 T. pallidum predicted coding region TP0818 #15 TP0819 27 conserved hypothetical protein #16 TP0820 95 hypothetical protein #17 TP0821 80 lipoprotein (tpn32) #18 TP0822 87 conserved hypothetical protein #19 TP0823 300 desulfoferrodoxin (rbo) #20 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) Motif number 1 GGAAAAGCTCCCCACGCTCTTTCCGCTCCCAGG 1 16 0 CCACCTCTTC 0.757287 -65 CCGACCACCAACGGCTCTTCTACCCACTCAACT 2 23 0 ACGCCTTCTC 0.71559 -125 CGGCTGTACGGCAGCGCCTGTTCACGACGTGGT 2 53 1 GCGCCCTGTC 0.892946 -95 GGTGAGCGCGCCACCTCCTTCACTAATCACCAC 2 81 0 CCCCCCTTCC 0.968655 -67 ATACTGCTCCCTTCTTTTCGCTCAA 2 133 0 ACGCCCCTTT 0.757249 -15 ACGTTTTGCACATCCCCTTTTATCTGACAAAAG 3 37 0 CACCCTTTTT 0.593172 -43 GGCCCTCTCCTCTCAACAATACGTT 3 65 0 CCTCCCTCTA 0.575351 -15 TCCTACCTCTCCCCCGCCCCTACACCCGACCAC 4 11 1 CCCCCCCCTC 0.996486 -92 GTCAAGACCACCACCTCCCTTGCACTTCCTTCA 4 59 1 CCCCCCCTTC 0.988883 -44 CCTTGCACTTCCTTCACCCGCGCCCTATCCTCC 4 76 1 CCTCCCCGCC 0.813797 -27 AATACACCTCCACCGTTTTGGTA 6 54 0 AAACCCTCCC 0.774713 -13 GGGCGAACATCCTCCTCTCTCCCGCTACGT 7 41 0 CACCCCTCTT 0.976574 -20 AAACCGCCCCTTCTTTCAACGGT 8 60 0 AACCCCCCTC 0.969197 -13 GAGCTCCTCCTTTTTCTAAAGGCTG 9 3 1 GCCCCCTTTT 0.817959 -109 CACCGTTTGGCATACTCCTCTTCGCAAGGAAGG 9 80 1 CAACCCTCTC 0.974488 -32 GCCCTCCCCCCTTCCTTGCGAAGAG 9 97 0 CCCCCCCTTC 0.988883 -15 CGTCGCGTCCCACGCACCTCCTCTTTTCGCTCA 10 14 1 CAGCCCTCCC 0.964773 -287 TCAATCCCCTACTACGCCCCTGTTGTGTTCGGC 10 92 0 ACACCCCCTT 0.860804 -209 GCCCCATACGCCGGCACCCCTTTTTTGCAGGAA 10 222 1 CCGCCCCCTT 0.9801 -79 GTTCACACCACAAACACCCCGCCGATAGCTCCA 11 104 0 CAACCCCCGC 0.783451 -47 TCGCAAACTCCTTTTCACCACCCCTA 12 4 1 CAACCCTTTC 0.922973 -263 ATAGCTTGTCAAACCTCCCGCGTGGTACCTGTC 12 81 1 AACCCCCGCT 0.655642 -186 TGCTGCCGTTCCAACGCCTGCGTGTGGACTCAA 12 124 1 CCACCCTGCT 0.807908 -143 ATCGCCCTACCATGCCCCTCTTGCCGAGGGTGG 12 189 1 CAGCCCTCTG 0.783561 -78 GAGAACCCCCTTTGTTAGGATTGCT 12 252 0 GACCCCTTTT 0.711758 -15 TCGGACAAACCAACCTCCCCTTTCTCTGTAACA 13 71 0 CACCCCCCTT 0.981653 -129 AGGTACCGCGCAACCTCTTCTATCGTGAGAATT 13 107 0 CACCCTTCTT 0.822945 -93 CTCATTCGGCCTCCCCCTGTCCCTCTATCCAT 17 59 0 CCCCCCTGTC 0.988679 -22 CCCCCAATCTCCTGCTCCCCTTCCTAAAAACAG 18 26 0 CCGCCCCCTC 0.993077 -62 GGTAGTTTCCGCTACGCTCCTGCCAGCTTGGAT 19 65 0 GCACCTCCTC 0.652547 -236 GGTAAAGCGTCACCCACCTGTACGCATTCAGTA 19 149 0 CACCCCTGTC 0.979589 -152 TTAGGTAGAATCAGCGCCTCTGCGGGGCTGTGC 19 194 1 TCGCCCTCTC 0.801748 -107 CCGCGTGCGGAAACCGCCCGCGCCAGAGCACAG 19 221 0 AACCCCCGCC 0.84722 -80 TTGCCCAACCTCCTCTAAAAAGAGCACA 20 75 0 CACCCCTCTA 0.894897 -18 ** ** ***** * Masking position 7 Map Score: 52.5954 Number of sites scoring better than the average of aligned sites = 2065 Number in coding regions = 1777 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 2 TTTTTGGAAAAGCTCCCCACGCTCTTTCCGCT 1 22 0 AGCTCCACGC 0.461127 -59 GGCTCTTCTACCCACTCAACTCTACATTCCAC 2 12 0 CCCACCACTC 0.91379 -136 AAGGAGGTGGCGCGCTCACCGCTGACGGCTCT 2 94 1 CGCGCCCCGC 0.992801 -54 TGACAAAAGGCGCATCCTCACCCCATACAAAA 3 14 0 CGCATCCACC 0.803567 -66 TCCTACCTCTCCCCCGCCCCTACACCCGAC 4 9 1 CTCCCCCCCC 0.870054 -94 CGCCCCTACACCCGACCACACCTGATTTCATC 4 25 1 CCCGACCACC 0.844504 -78 TTCCTTCACCCGCGCCCTATCCTCCGCGC 4 84 1 CGCGCCATCC 0.919633 -19 TTCTCCTTTTATCGTTCTACCCCGTAGGGTTT 5 36 0 ATCGTCACCC 0.780265 -28 TGCGCGTTCTCCTTTTATCGTTCT 5 50 0 CGCGTCCCTT 0.795831 -14 CTTGACGGCGCGCGCTAAACGCCTAATAATTG 9 41 0 CGCGCAACGC 0.863009 -71 TATCGTCGCGTCCCACGCACCTCCTCTT 10 7 1 CGCGTCACGC 0.984842 -294 CACAGTCAATCCCCTACTACGCCCCTGTTGTG 10 98 0 CCCCTCACGC 0.899976 -203 GTAGGGTGAACCCGACGGACCCAGTGACTGCA 10 128 0 CCCGAGACCC 0.906584 -173 GTACTCGTTCCGCATAGGCCCTGTCTTTAGGT 10 179 1 CGCATGCCCT 0.578605 -122 AAACGAGCTATCCGTGCTACCCTGGCAGCCGA 10 264 1 TCCGTCACCC 0.857706 -37 ACGCGCCCTCCCTGGTCGGCTGC 10 288 0 CGCGCCCCCT 0.977167 -13 GCCAGGAGATCTCGCCCCAACCCAAGGGAAAA 11 31 0 CTCGCCAACC 0.776963 -120 TCGCAAACTCCTTTTCACCACCC 12 2 1 CGCAACCCTT 0.366431 -265 CTCGCAGGCGCCAGCTCGCCGCATTCTAGCGC 12 41 1 CCAGCCCCGC 0.756789 -226 TCAAACCTCCCGCGTGGTACCTGTCCAAATCG 12 89 1 CGCGTGACCT 0.793753 -178 ACTAGAGCGTCCCGATCGCCCTACCATGCCCC 12 175 1 CCCGACCCCT 0.905214 -92 CGATCGCCCTACCATGCCCCTCTTGCCGAGGG 12 187 1 ACCATCCCTC 0.53578 -80 GAAATAGAGAAGCGTGCCACCCTCGGCAAGAG 12 206 0 AGCGTCACCC 0.956069 -61 CTTCGGACAAACCAACCTCCCCTTTCTCTGTA 13 74 0 ACCAACCCCC 0.763386 -126 ATTCGCAGGTACCGCGCAACCTCTTCTATCGT 13 114 0 ACCGCCACCT 0.854066 -86 AAAAGACACACCCACACCATCCCCATCCTTGA 16 66 0 CCCACCATCC 0.758394 -30 AAAACAGGAGAGCACTACACCC 18 1 0 AGCACAACCC 0.397741 -87 TGCCCCCAATCTCCTGCTCCCCTTCCTAAAAA 18 29 0 CTCCTCCCCC 0.782411 -59 GGCATATTTGCGCGCAGTACGCCCTTGCGTAG 18 57 1 CGCGCGACGC 0.958495 -31 GCCTGCATCCTACGCAAGGGCGTAC 18 73 0 TGCATCACGC 0.533355 -15 TCCTTCCGAGCCTGTGCTACGCACGAGTATAC 19 110 0 CCTGTCACGC 0.721061 -191 CGTGCCTCCGCGTGCGGAAACCGCCCGCGCCA 19 229 0 CGTGCGAACC 0.156111 -72 GAGCACACATCCCGCGCAACGCTATCTGAAAA 20 50 0 CCCGCCACGC 0.990658 -43 TTGCCCAACCTCCTCTAAAAAGAGC 20 78 0 CCCAACCCTC 0.754681 -15 ***** * **** Masking position 3 Map Score: 32.5947 Number of sites scoring better than the average of aligned sites = 4264 Number in coding regions = 3849 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 3 GATATCCTGGGAGCGGAAAGAGCGTGGGGA 1 11 1 GAGCGGAAAG 0.947142 -70 TTACCCGATTGAGCGAAAAGAAGGGAGCAG 2 125 1 GAGCGAAAAG 0.910631 -23 ACGTATTGTTGAGAGGAGAGGGCC 3 66 1 GAGAGGAGAG 0.919865 -14 AGGGGCGGGGGAGAGGTAGGA 4 2 0 GAGAGGTAGG 0.684961 -101 TGAAGGAAGTGCAAGGGAGGTGGTGGTCTT 4 62 0 GCAAGGGAGG 0.856802 -41 GCGCGGAGGATAGGGCGCGG 4 93 0 GCGCGGAGGA 0.868205 -10 CGTAGCGGGAGAGAGGAGGATGTTCGCCC 7 42 1 GAGAGGAGGA 0.716373 -19 TGCCTTAGGGAGCGGAGAGTCTGCCTGCG 8 10 1 GAGCGGAGAG 0.952799 -63 TCGCACCGTTGAAAGAAGGGGCGGTTT 8 56 1 GAAAGAAGGG 0.929791 -17 ACTCCTCTTCGCAAGGAAGGGGGGAGGGC 9 93 1 GCAAGGAAGG 0.968415 -19 AGGAAATGTTGAGCGAAAAGAGGAGGTGCG 10 26 0 GAGCGAAAAG 0.910631 -275 AACCGTTCCTGCAAAAAAGGGGTGCCGGCG 10 230 0 GCAAAAAAGG 0.636617 -71 TGCCAGGGTAGCACGGATAGCTCGTTTAGG 10 261 0 GCACGGATAG 0.640201 -40 TTTGTGGTGTGAACGAAAGGATGTGCTAAG 11 123 1 GAACGAAAGG 0.953859 -28 GCAGGCGTTGGAACGGCAGCAAGACGATTT 12 115 0 GAACGGCAGC 0.447398 -152 GTCAACCGAAGCGCGAAGGCTTGAGTCCAC 12 147 0 GCGCGAAGGC 0.852821 -120 GCCACCCTCGGCAAGAGGGGCATGGTAGGG 12 193 0 GCAAGAGGGG 0.793089 -74 AAATTCTCACGATAGAAGAGGTTGCGCGGT 13 106 1 GATAGAAGAG 0.4756 -94 GTATGAGTGGGCGCAAAAGGGGAAGATTCC 13 161 1 GCGCAAAAGG 0.819129 -39 GTGCCCTGCGGAAAGAAAAGAAAAAAGCAA 19 18 0 GAAAGAAAAG 0.797641 -283 CGTAGCACAGGCTCGGAAGGAGCGAGTTTA 19 121 1 GCTCGGAAGG 0.916752 -180 GCACGCGGAGGCACGACAGGCGTCCGCACG 19 246 1 GCACGACAGG 0.856802 -55 GAGCCCTACAGCAAAGAGGGATTGACGTGC 20 13 1 GCAAAGAGGG 0.776318 -80 ********** Masking position 1 Map Score: 23.6108 Number of sites scoring better than the average of aligned sites = 1398 Number in coding regions = 1225 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 CTCCCCACGCTCTTTCCGCTCCCAGGATAT 1 12 0 TCTTTCCGCT 0.9908 -69 GAGGTGGCGCGCTCACCGCTGACGGCTCTT 2 97 1 GCTCACCGCT 0.911993 -51 ACTGCTCCCTTCTTTTCGCTCAATCGGGTA 2 126 0 TCTTTTCGCT 0.937355 -22 CCGCAGGCAGACTCTCCGCTCCCTAAGGCA 8 11 0 ACTCTCCGCT 0.980272 -62 CCGGTGTAGGTCGCACCGTTGAAAGAAGGG 8 46 1 TCGCACCGTT 0.845928 -27 GTCAAGTTTTTCTCACCGTTTGGCATACTC 9 67 1 TCTCACCGTT 0.934665 -45 ACGCACCTCCTCTTTTCGCTCAACATTTCC 10 25 1 TCTTTTCGCT 0.937355 -276 CCTACAAGGAACACTCCGTTTGCCGTACTC 10 155 1 ACACTCCGTT 0.692796 -146 TTTGCCGTACTCGTTCCGCATAGGCCCTGT 10 173 1 TCGTTCCGCA 0.90254 -128 GGTGCAAGTTCTTTCCGTTTAAAACCTAC 16 10 1 TCTTTCCGTT 0.972016 -86 TTTTTTCTTTTCTTTCCGCAGGGCACGTAG 19 22 1 TCTTTCCGCA 0.960205 -279 CCATTTGGGTAGTTTCCGCTACGCTCCTGC 19 75 0 AGTTTCCGCT 0.8202 -226 ********** Masking position 7 Map Score: 12.9845 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 130 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GAAGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCACG 2 36 1 TGGGTCGGAG 0.970299 -112 TCTTTTTGTATGGGGTGAGGATGCGCCTTTTGTCA 3 3 1 TTGGTAGGTG 0.57138 -77 GAGGATGCGCCTTTTGTCAGATAAAAGGGGATGTGCAAAACGT 3 27 1 CTGGAAGGGG 0.839362 -53 CAGGTGTGGTCGGGTGTAGGGGCGGGGGAGAGGTAGGA 4 6 0 CGGGGGGGGG 0.969268 -97 GTGGTGGTCTTGACAGGATGAAATCAGGTGTGGTCGGGTGTAG 4 30 0 TGGGTAGGGG 0.995056 -73 GCGCGGAGGATAGGGCGCGGGTGAAGGAAGTGCAAG 4 77 0 CGGGGGGGGG 0.969268 -26 GCGATATGTCTGTAGGTAAACCCTACGGGGTAGAACGATAAAA 5 19 1 TGGATCGGGG 0.979995 -45 TGCCGAGCCTTGAACGACACTAGAACGTAGCGGGAGAGAGGAG 7 17 1 TGGCACGTGG 0.385619 -44 GCGGAGAGTCTGCCTGCGGCACATCCGGTGTAGGTCGCACCGT 8 22 1 TGGCTCGGGG 0.975962 -51 TTCTAAAGGCTGCGAGGCAATTATTAGGCGTTTAGCGCGCGCC 9 24 1 TGGATAGGGT 0.653105 -88 AGGTTTGGACTGATTGAAGGAAATGTTGAGCGAAAAGAGGAGG 10 30 0 TGGGTTTGGA 0.17711 -271 ATAGAACAGTTTCTCGTGGAGCTATCGGCGGGGTGTTTGTGGT 11 88 1 TTGAACGGGG 0.682465 -63 GTGGTGTGAACGAAAGGATGTGCTAAGGAGGGGAT 11 126 1 CGGGTAGGGG 0.991674 -25 GGCGAGCTGGCGCCTGCGAGGCGTTAGGGGTGGTGAAAAGGAG 12 18 0 CGGGTAGGGG 0.991673 -249 CTTTGGACATTGACAGGATGGATAGAGGGACAGGGGGAGGCCG 17 42 1 TGGGAAGGAG 0.903952 -39 GGGTGTAGTGCTCTCCTGTTTTTAGGAAGGGGAGCAGGAGA 18 9 1 TGTGTAGGAG 0.542648 -79 GCTACGCTCCTGCCAGCTTGGATTCCTGAGGAGTTTCTACGTG 19 45 0 TGGGTCTGGG 0.952711 -256 GCGAGTTTACTGAATGCGTACAGGTGGGTGACGCTTTACCCAC 19 142 1 TGGAGGGGGG 0.914335 -159 TCAGCGCCTCTGCGGGGCTGTGCTCTGGCGCGGGCGGTTTCCG 19 204 1 TGGGTTGGGG 0.98244 -97 ** * * * *** * * Masking position 6 Map Score: 19.9678 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 547 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 CAGCCGACCACCAACGGCTCTTCTACCCAC 2 29 0 CCAACGGCTC 0.937682 -119 GCGCTCACCGCTGACGGCTCTTACCCGATT 2 105 1 CTGACGGCTC 0.985684 -43 TCTAGTGTCGTTCAAGGCTCGGCATTACCG 7 11 0 TTCAAGGCTC 0.617585 -50 CCTCCTTTTTCTAAAGGCTGCGAGGCAATT 9 16 1 CTAAAGGCTG 0.925814 -96 AAGGGAAAATCTCACGGCACCACTATATC 11 10 0 CTCACGGCAC 0.900767 -141 TTCACCACCCCTAACGCCTCGCAGGCGCCA 12 24 1 CTAACGCCTC 0.973942 -243 ATGCGGCGAGCTGGCGCCTGCGAGGCGTTA 12 35 0 CTGGCGCCTG 0.877963 -232 TGCTGCCGTTCCAACGCCTGCGTGTGGACT 12 124 1 CCAACGCCTG 0.928322 -143 TGCGTGTGGACTCAAGCCTTCGCGCTTCGG 12 142 1 CTCAAGCCTT 0.732479 -125 GCGTAGAAATCTCACGCCTGGCGTGTATCA 13 12 0 CTCACGCCTG 0.98655 -188 CTACCCAGTCCTGACGGTTCTTCTGCATAC 16 36 1 CTGACGGTTC 0.831682 -60 CTTCTGCATACTCAAGGATGGGGATGGTGT 16 55 1 CTCAAGGATG 0.637587 -41 TGTTCTCGTGCGGACGCCTGTCGTGCCTCC 19 252 0 CGGACGCCTG 0.917597 -49 ********** Masking position 6 Map Score: 11.502 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 210 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 CGTGGAATGTAGAGTTGAGTGGGT 2 5 1 GAATGTAGAG 0.301809 -143 GATTAGTGAAGGAGGTGGCGCGCTCACCGC 2 86 1 GGAGGTGGCG 0.925818 -62 TATGGGGTGAGGATGCGCCTTTTGTCAGAT 3 19 1 GGATGCGCCT 0.704146 -61 GAAAGTGGCGCATTTTGCGT 6 1 1 GAAAGTGGCG 0.859052 -66 AACGACACTAGAACGTAGCGGGAGAGAGGA 7 29 1 GAACGTAGCG 0.956553 -32 GACCTACACCGGATGTGCCGCAGGCAGACT 8 28 0 GGATGTGCCG 0.96986 -45 ATCCGGTGTAGGTCGCACCGTTGAAAGAAG 8 44 1 GGTCGCACCG 0.832342 -29 TAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 9 48 1 GCGCGCGCCG 0.880339 -64 GAGGTGCGTGGGACGCGACGATA 10 4 0 GGACGCGACG 0.931149 -297 CCATGCGCTAGAATGCGGCGAGCTGGCGCC 12 47 0 GAATGCGGCG 0.960584 -220 GCGAATTTCTGAACGTACCGTGTATGAGTG 13 140 1 GAACGTACCG 0.962369 -60 ATATAACGCGCCGTTGCAATACT 14 4 1 TAACGCGCCG 0.910659 -23 AAGCTGGCAGGAGCGTAGCGGAAACTACCC 19 69 1 GAGCGTAGCG 0.874305 -232 AAAGAGGGATTGACGTGCCGATCTTTTTTC 20 25 1 TGACGTGCCG 0.920555 -68 ********** Masking position 5 Map Score: 12.8856 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 746 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 CTTTTCCTTTGAGAGTTTTTAGCTTGGGGG 1 60 1 GAGAGTTTTT 0.722713 -21 TAGTGGTGCCGTGAGATTTTCCCTTGGGTT 11 15 1 GTGAGATTTT 0.911553 -136 TCTCTATTTCGTGACTCTTCTCGAAGCAAT 12 228 1 GTGACTCTTC 0.89658 -39 CACGCCAGGCGTGAGATTTCTACGCAACGC 13 17 1 GTGAGATTTC 0.873979 -183 CGTACCCCAAGTGTGTCTTGTTACAGAGAA 13 53 1 GTGTGTCTTG 0.899943 -147 CTCTTCTATCGTGAGAATTTCTTCGGACAA 13 96 0 GTGAGAATTT 0.803107 -104 GATGGTGTGGGTGTGTCTTTTGAAAGAAG 16 77 1 GTGTGTCTTT 0.930392 -19 AATGCAGGGTGAGTCTTGATGTGCGCTT 17 9 1 GTGAGTCTTG 0.966058 -72 GTACAGGTGGGTGACGCTTTACCCACGGAC 19 159 1 GTGACGCTTT 0.824892 -142 ********** Masking position 8 Map Score: 2.18038 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 78 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AAAAGTCAAGCTTTTTGGAAAAGCTCCCCAC 1 34 0 CTTTTTGGAA 0.856105 -47 CTCAACAATACGTTTTGCACATCCCCTTTTA 3 48 0 CGTTTTGCAA 0.954026 -32 ACACCTCCACCGTTTTGGTAATTTCTCGGAC 6 43 0 CGTTTTGGTA 0.893603 -24 AATTATTAGGCGTTTAGCGCGCGCCGTCAAG 9 42 1 CGTTTAGCGG 0.716757 -70 TTTTTCTCACCGTTTGGCATACTCCTCTTCG 9 73 1 CGTTTGGCAA 0.846432 -39 TCAGTCCAAACCTCTAGGAAGATATCCAAGT 10 60 1 CCTCTAGGAG 0.719635 -241 TTGTGTTCGGCGACTTGGATATCTTCCTAGA 10 72 0 CGACTTGGAA 0.890647 -229 ACGGATAGCTCGTTTAGGAAACCGTTCCTGC 10 248 0 CGTTTAGGAA 0.960198 -53 GGCAGCAAGACGATTTGGACAGGTACCACGC 12 100 0 CGATTTGGAA 0.954998 -167 CCGACGTCAACCTTTTGGAGG 15 1 0 CCTTTTGGAG 0.936703 -27 TATACCTTGACCATTTGGGTAGTTTCCGCTA 19 84 0 CCATTTGGGA 0.801919 -217 ********* * Masking position 5 Map Score: 2.90417 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 140 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 CTGTAGGTAAACCCTACGGGGTAGAACGAT 5 28 1 ACCCTACGGG 0.800376 -36 ATCTCGCCCCAACCCAAGGGAAAATCTCAC 11 25 0 AACCCAAGGG 0.913913 -126 CGTGCCACCCTCGGCAAGAGGGGCATGGTA 12 196 0 TCGGCAAGAG 0.77603 -71 CATGATGCGTACCCCAAGTGTGTCTTGTTA 13 46 1 ACCCCAAGTG 0.799872 -154 GCCTGCATCCTACGCAAGGGCGTACTGCGC 18 68 0 TACGCAAGGG 0.961629 -20 GAGCCTGTGCTACGCACGAGTATACCTTGA 19 105 0 TACGCACGAG 0.959743 -196 GGTGACGCTTTACCCACGGACCTGATTTAG 19 168 1 TACCCACGGA 0.795664 -133 GCGGGCGGTTTCCGCACGCGGAGGCACGAC 19 233 1 TCCGCACGCG 0.964837 -68 ACGACAGGCGTCCGCACGAGAACAAAATCA 19 258 1 TCCGCACGAG 0.979047 -43 ********** Masking position 6 Map Score: 3.81506 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 412 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 GAGAGAGGAGGATGTTCGCCC 7 50 1 GATGTTCGCC 0.95814 -11 ACGAAATAGAGAAGCGTGCCACCCTCGGCA 12 210 0 GAAGCGTGCC 0.969409 -57 CGCAACGCATGATGCGTACCCCAAGTGTGT 13 39 1 GATGCGTACC 0.951378 -161 GGTGAGTCTTGATGTGCGCTTTTTCTTTGG 17 18 1 GATGTGCGCT 0.958142 -63 CAACATAGGAGATGCTTGCC 19 291 1 GATGCTTGCC 0.977484 -10 CGTTGCGCGGGATGTGTGCTCTTTTTAGAG 20 61 1 GATGTGTGCT 0.96505 -32 ********** Masking position 2 Map Score: 3.73053 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 113 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 ********** No masking Map Score: 5.23203e-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: 5.23203e-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: 5.23203e-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