AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_tpal_reg_300.orf -o00500_tpal_300.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 TP0060 105 ribosomal protein L9 (rplI) #2 TP0061 116 ribosomal protein S18 (rpsR) #3 TP0063 141 ribosomal protein S6 (rpsF) #4 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #5 TP0102_TP0103 64 TP0102: rep helicase, single-stranded DNA-dependent ATPase (rep), TP0103: ATP-dependent DNA helicase, putative #6 TP0413 102 phosphoglucomutase #7 TP0475 63 glucose-6-phosphate isomerase (gpi) #8 TP0476 66 acetate kinase (ack) #9 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #10 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #11 TP0479 111 T. pallidum predicted coding region TP0479 #12 TP0505 300 hexokinase (hxk) #13 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #14 TP0757 40 polypeptide deformylase (def) #15 TP0758 118 ribosomal protein S21 (rpsU) #16 TP0900 38 T. pallidum predicted coding region TP0900 #17 TP0901 40 conserved hypothetical integral membrane protein #18 TP1028 82 DNA helicase II (uvrD) #19 TP1030 27 T. pallidum predicted coding region TP1030 #20 TP1036 152 cation-transporting ATPase, P-type Motif number 1 ACGTTTTGTCCCCTCCTACGCAGGAATAAAA 1 85 0 CCCTCCACGC 0.936443 -21 TGACCGAACCTGGCGTTCGCCTGGACCTCAG 2 52 1 TGGCGTCGCC 0.500642 -65 TAGCGTAAATCTGTGTGCCGCATCAAGTCTT 3 26 0 CTGTGTCCGC 0.825336 -116 GCACACAGATTTACGCTACGCTGGCGTCTCG 3 39 1 TTACGCACGC 0.517571 -103 GCTGGCGTCTCGCCGCGCGTTCTGCGCACGC 3 58 1 CGCCGCCGTT 0.61369 -84 GCCGCGCGTTCTGCGCACGCTACTCCTCCTT 3 69 1 CTGCGCCGCT 0.916129 -73 AATAACTCCTATGGACGGCTCACCTTATC 3 123 0 CTATGGCGGC 0.541271 -19 TTTGGAAAAGCTCCCCACGCTCTTTCCGCTC 4 21 0 CTCCCCCGCT 0.928341 -60 TCCCCCAAGCTAAAAACTCTC 4 70 0 TCCCCCAGCT 0.402741 -11 TCCTACCTCTCCCCCGCCCCTACACCC 6 7 1 CTCTCCCCGC 0.971437 -96 TGCACTTCCTTCACCCGCGCCCTATCCTCCG 6 79 1 TCACCCCGCC 0.727393 -24 CACCCGCGCCCTATCCTCCGCGC 6 90 1 CTATCCCCGC 0.914303 -13 GAACATCCTCCTCTCTCCCGCTACGTTCTAG 9 36 0 CTCTCTCCGC 0.848583 -25 CAGGCAGACTCTCCGCTCCCTAAGGCA 10 7 0 CTCCGCCCCT 0.971355 -66 AGCGGAGAGTCTGCCTGCGGCACATCCGGTG 10 21 1 CTGCCTCGGC 0.792816 -52 CTTCTTTCAACGGTGCGACCTACACCGGATG 10 43 0 CGGTGCACCT 0.782819 -30 AAAAACTTGACGGCGCGCGCTAAACGCCTAA 11 47 0 CGGCGCCGCT 0.933048 -65 GCCCTCCCCCCTTCCTTGCGAA 11 100 0 CCCTCCCCCT 0.946092 -12 TCGTCGCGTCCCACGCACCTCCTCTTTTCGC 12 13 1 CCACGCCCTC 0.803016 -288 TAGGTATAAACTCCCTGCCCCATACGCCGGC 12 206 1 CTCCCTCCCC 0.936768 -95 CTGCCCCATACGCCGGCACCCCTTTTTTGCA 12 220 1 CGCCGGACCC 0.8746 -81 AACGAGCTATCCGTGCTACCCTGGCAGCCGA 12 265 1 CCGTGCACCC 0.939363 -36 ACGCGCCCTCCCTGGTCGGCTGCCAGGGTA 12 281 0 CCCTGGCGGC 0.849775 -20 CGTGAGATTTCTACGCAACGCATGATGCGTA 13 26 1 CTACGCACGC 0.899292 -174 TTCGGACAAACCAACCTCCCCTTTCTCTGTA 13 74 0 CCAACCCCCC 0.616434 -126 TTCGCAGGTACCGCGCAACCTCTTCTATCGT 13 114 0 CCGCGCACCT 0.900375 -86 CGCCTCTTCCCGCTCTTACCCAAGAGAAACT 14 20 0 CGCTCTACCC 0.719789 -21 GAAAGCACTCCTGCCTCCCCTGCACGCACAC 15 21 0 CTGCCTCCCT 0.714932 -98 GGGACGTCTTTTGCGCTAGCCTACCCCTGGT 15 70 1 TTGCGCAGCC 0.578739 -49 GCTAGCCTACCCCTGGTAGGCTGTGTTTTTT 15 84 1 CCCTGGAGGC 0.619683 -35 CGACCCTCCCCTGAAAAAAAC 15 108 0 CGACCCCCCC 0.972961 -11 TCCATGCTCCGTGCCTTACCCG 16 27 0 CCATGCCCGT 0.85819 -12 CCGTGCACCGCACTCCCTTTT 17 30 0 CCGTGCCCGC 0.977337 -11 CAGTGCAGGGCGCCGCCCGGGCGCGGTGGCA 18 23 1 CGCCGCCGGG 0.851541 -60 AACCGAAAACTGCCGCACCGCACCGAGTGCC 18 50 0 TGCCGCCCGC 0.938067 -33 GCGCAGCCCTGCAACCGAAAACTGCCG 18 66 0 CCCTGCACCG 0.686046 -17 GCCTGAGCGCGCCCCGCCGCGACGCAG 19 10 1 CGCCCCCCGC 0.989245 -18 CACTGCCAGCCGCTCCTCCCCAGAGCTTTTG 20 92 1 CGCTCCCCCC 0.981856 -61 ****** **** Masking position 1 Map Score: 47.2538 Number of sites scoring better than the average of aligned sites = 6565 Number in coding regions = 5788 Number in noncoding regions = 777 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 2 CGTTTTGTCCCCTCCTACGCAGGAATAAAA 1 85 0 CCTCCTACGC 0.922824 -21 TGCGCACGCTACTCCTCCTTGTCGGGTGAG 3 80 1 ACTCCTCCTT 0.889355 -62 TCCTACCTCTCCCCCGCCCCTACACCC 6 8 1 TCTCCCCCGC 0.911749 -95 CCTGTCAAGACCACCACCTCCCTTGCACTT 6 56 1 CCACCACCTC 0.779205 -47 CACGCAAAATGCGCCACTTTC 8 2 0 GCGCCACTTT 0.758413 -65 AATACACCTCCACCGTTTTGGTAATT 8 51 0 CCTCCACCGT 0.957415 -16 GGGCGAACATCCTCCTCTCTCCCGCTACGT 9 41 0 CCTCCTCTCT 0.949806 -20 AAACCGCCCCTTCTTTCAACGGT 10 60 0 CCGCCCCTTC 0.983178 -13 GAGCTCCTCCTTTTTCTAAAGG 11 3 1 GCTCCTCCTT 0.960823 -109 CGTTTGGCATACTCCTCTTCGCAAGGAAGG 11 83 1 ACTCCTCTTC 0.896285 -29 GCCCTCCCCCCTTCCTTGCGAA 11 100 0 CCTCCCCCCT 0.982739 -12 TATCGTCGCGTCCCACGCACCTCCTCTT 12 9 1 CGTCCCACGC 0.761926 -292 GTCCCACGCACCTCCTCTTTTCGCTCAACA 12 20 1 CCTCCTCTTT 0.979753 -281 ATCCCCTACTACGCCCCTGTTGTGTTCGGC 12 92 0 ACGCCCCTGT 0.870397 -209 CCATACGCCGGCACCCCTTTTTTGCAGGAA 12 225 1 GCACCCCTTT 0.873367 -76 GACAAACCAACCTCCCCTTTCTCTGTAACA 13 71 0 CCTCCCCTTT 0.992084 -129 TTCCCCTTTTGCGCCCACTCATACACGGTA 13 155 0 GCGCCCACTC 0.833987 -45 CTGACGGAATCTTCCCCTTTTGCGCCCACT 13 166 0 CTTCCCCTTT 0.826039 -34 AGCACTCCTGCCTCCCCTGCACGCACACCC 15 19 0 CCTCCCCTGC 0.993677 -100 GCGCAAAAGACGTCCCCTGTCAATCGTTTC 15 56 0 CGTCCCCTGT 0.928587 -63 CGACCCTCCCCTGAAAAAAACACA 15 105 0 CCTCCCCTGA 0.925278 -14 AATTCGTTGAGCTCCCATTTCACAGCAGAT 20 11 1 GCTCCCATTT 0.90264 -142 ACTGCCAGCCGCTCCTCCCCAGAGCTTTTG 20 93 1 GCTCCTCCCC 0.922956 -60 GAAAGACTACCTCCTATTCAGGACGGGTT 20 134 0 CCTCCTATTC 0.911122 -19 ********** Masking position 5 Map Score: 38.6095 Number of sites scoring better than the average of aligned sites = 1078 Number in coding regions = 913 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TCTCGCCGCGCGTTCTGCGCACGCTACTCCTCCTTGTCGGG 3 65 1 CACGCTACCT 0.805763 -77 TATCAGGCTGCACTAGACTCACCCGACAAGGAGGAGTAGCG 3 86 0 CACCCGACGG 0.99678 -56 AAAAGCTCCCCACGCTCTTTCCGCTCCCAGGATATC 4 6 0 CCCGCTCCGG 0.979629 -75 TACCTCTCCCCCGCCCCTACACCCGACCACACCTGATTTCA 6 14 1 CACCCGACCA 0.924592 -89 GGCGATATGTCTGTAGGTAAACCCTACGGGGTAGAACGATA 7 18 1 CACCCTACGG 0.996089 -46 GAGCTCCTCCTTTTTCTAAAGGCTGCGAGGCAATTATTAG 11 10 1 CAGGCTGCGG 0.917619 -102 TACTACGCCCCTGTTGTGTTCGGCGACTTGGATATCTTCCT 12 75 0 CCGGCGACGG 0.984936 -226 CCAGTGACTGCACAGTCAATCCCCTACTACGCCCCTGTTGT 12 99 0 CCCCCTACCG 0.985083 -202 TCACTGGGTCCGTCGGGTTCACCCTACAAGGAACACTCCGT 12 133 1 CACCCTACGG 0.996083 -168 GCTATCCGTGCTACCCTGGCAGCCGACCAGGGAGGGCGCGT 12 270 1 CAGCCGACGG 0.994305 -31 CCTGCCTCCCCTGCACGCACACCCTACGTGTC 15 2 0 CACCCTACGT 0.97252 -117 CCCTCCCCTGAAAAAAACACAGCCTACCAGGGGTAGGCTAG 15 85 0 AAGCCTACGG 0.897501 -34 AACATGCCGTCAGTGCAGGGCGCCGCCCGGGCGCGGTGGCA 18 13 1 CCGCCGCCGG 0.962296 -70 GCCTGAGCGCGCCCCGCCGCGACGCAG 19 2 1 CCCCCGCCGA 0.951412 -26 * ******* ** Masking position 14 Map Score: 22.8968 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 147 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TTTTGTCCCCTCCTACGCAGGAATAAAAGT 1 83 0 TCCTACGCAG 0.637104 -23 CGTAAATCTGTGTGCCGCATCAAGTCTTTT 3 24 0 TGTGCCGCAT 0.781823 -118 CACAGATTTACGCTACGCTGGCGTCTCGCC 3 42 1 CGCTACGCTG 0.966341 -100 CGCCCTATTTTGCTACGCTTGTGCGTCT 5 47 1 TGCTACGCTT 0.914961 -18 ACACGCAAAATGCGCCACTTTC 8 3 0 TGCGCCACTT 0.457752 -64 TTTGCGTGTATGCTACGGTGTCCGAGAAAT 8 24 1 TGCTACGGTG 0.768581 -43 TCCTCTCTCCCGCTACGTTCTAGTGTCGTT 9 29 0 CGCTACGTTC 0.642331 -32 CGCAGGCAGACTCTCCGCTCCCTAAGGCA 10 10 0 CTCTCCGCTC 0.614744 -63 CTACACCGGATGTGCCGCAGGCAGACTCTC 10 25 0 TGTGCCGCAG 0.869486 -48 CGGTGTAGGTCGCACCGTTGAAAGAAGGGG 10 47 1 CGCACCGTTG 0.78037 -26 TTGCCGTACTCGTTCCGCATAGGCCCTGTC 12 174 1 CGTTCCGCAT 0.862107 -127 GAGCTATCCGTGCTACCCTGGCAGCCGACC 12 268 1 TGCTACCCTG 0.610446 -33 GAGATTTCTACGCAACGCATGATGCGTACC 13 29 1 CGCAACGCAT 0.917048 -171 CCGTGCACCGCACTCCCTTTTGG 17 28 0 TGCACCGCAC 0.937722 -13 CGAAAACTGCCGCACCGCACCGAGTGCCAC 18 48 0 CGCACCGCAC 0.955774 -35 CGCGCCCCGCCGCGACGCAG 19 18 1 CGCGACGCAG 0.963584 -10 GAAACTTGCATGTACCGGATAAAAAACCGT 20 55 0 TGTACCGGAT 0.31607 -98 ********** Masking position 6 Map Score: 11.8204 Number of sites scoring better than the average of aligned sites = 2420 Number in coding regions = 2255 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 CCTGGACCTCAGAAAGGAATTGGGCGTGCTAATTTTTC 2 71 1 AGAGATGGGG 0.994124 -46 TGTGGTCGGGTGTAGGGGCGGGGGAGAGGTAGGA 6 7 0 TGAGCGGGGG 0.938757 -96 TGGTCTTGACAGGATGAAATCAGGTGTGGTCGGGTGTA 6 31 0 AGAGATGGGG 0.994124 -72 GCGCGGGTGAAGGAAGTGCAAGGGAGGTGGTGGTCTTG 6 61 0 AGAGCAGGGT 0.936766 -42 CCTACGGGGTAGAACGATAAAAGGAGAACGCGCA 7 40 1 AGAGAAGGGA 0.968058 -24 TGCGAAGAGGAGTATGCCAAACGGTGAGAAAAACTTGA 11 68 0 AGAGAAGGGG 0.996329 -44 TTGGACTGATTGAAGGAAATGTTGAGCGAAAAGAGGAG 12 31 0 TGAGATTGGG 0.83977 -270 ATGCGGAACGAGTACGGCAAACGGAGTGTTCCTTGTAG 12 156 0 AGAGAAGGGG 0.996329 -145 CACAGCAGATAGGATGAAAAGTGTACGGTTTTTTATCC 20 31 1 AGAGAAGTCG 0.794488 -122 ** * * ** ** * * Masking position 4 Map Score: 7.66451 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 75 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 GCGTAGGAGGGGACAAAACGT 1 95 1 GGACAAAACG 0.579469 -11 CGGATAAAAGGACAAAAGACT 3 2 1 GGATAAAAGG 0.701414 -140 TCCTGGGAGCGGAAAGAGCGTGGGGAGCTT 4 15 1 GGAAAGAGCG 0.900599 -66 CACAAGCGTAGCAAAATAGGGCGGAAAAAA 5 40 0 GCAAAATAGG 0.810728 -25 TGAAGGAAGTGCAAGGGAGGTGGTGGTCTT 6 62 0 GCAAGGGAGG 0.951645 -41 GCGCGGAGGATAGGGCGCGGGTGAAGG 6 86 0 GGATAGGGCG 0.737635 -17 TAGCATACACGCAAAATGCGCCACTTTC 8 9 0 GCAAAATGCG 0.835005 -58 AGAACGTAGCGGGAGAGAGGAGGATGTTCG 9 38 1 GGGAGAGAGG 0.83073 -23 TCGCACCGTTGAAAGAAGGGGCGGTTT 10 56 1 GAAAGAAGGG 0.643956 -17 ACTCCTCTTCGCAAGGAAGGGGGGAGGGC 11 93 1 GCAAGGAAGG 0.932027 -19 AACCGTTCCTGCAAAAAAGGGGTGCCGGCG 12 230 0 GCAAAAAAGG 0.923359 -71 TCTACGCAACGCATGATGCGTACCCCAAGT 13 35 1 GCATGATGCG 0.638256 -165 ATGAGTGGGCGCAAAAGGGGAAGATTCCGT 13 163 1 GCAAAAGGGG 0.953338 -37 GATTCCGTCAGGAAAAGTGGGCACC 13 185 1 GGAAAAGTGG 0.643666 -15 GGTAAGAGCGGGAAGAGGCG 14 31 1 GGAAGAGGCG 0.967441 -10 GGGTGTGCGTGCAGGGGAGGCAGGAGTGCT 15 19 1 GCAGGGGAGG 0.713945 -100 GAGTGCTTTCGGAAGAAACGATTGACAGGG 15 42 1 GGAAGAAACG 0.946009 -77 GTAGGCTAGCGCAAAAGACGTCCCCTGTCA 15 64 0 GCAAAAGACG 0.945332 -55 GGCAGTGACGGCAAGAAACTTGCATGTACC 20 69 0 GCAAGAAACT 0.448389 -84 AAAAGCTCTGGGGAGGAGCGGCTGGCAGTG 20 92 0 GGGAGGAGCG 0.740341 -61 ********** Masking position 1 Map Score: 20.1772 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 761 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 CTAGAAGTGGAAAAATTAGCACGCCCAATTC 2 87 0 AAAAATTACA 0.83162 -30 CCCCCAAGCTAAAAACTCTCAAAGGAAAAGT 4 59 0 AAAAACTCCA 0.946376 -22 ACGGTGTCCGAGAAATTACCAAAACGGTGGA 8 38 1 AGAAATTACA 0.947656 -29 GTTTGTCCGAAGAAATTCTCACGATAGAAGA 13 94 1 AGAAATTCCA 0.981623 -106 CGGTACGTTCAGAAATTCGCAGGTACCGCGC 13 129 0 AGAAATTCCA 0.981676 -71 CTTACCCAAGAGAAACTCATACCCGC 14 6 0 AGAAACTCTA 0.893534 -35 AGTGACGGCAAGAAACTTGCATGTACCGGAT 20 65 0 AGAAACTTCA 0.925314 -88 ******** ** Masking position 5 Map Score: 4.86381 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 24 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ATGCATGCTCCTTGTGGGGAAAGAGAC 2 7 0 CTGTGGGGAA 0.950251 -110 AAAAGTCAAGCTTTTTGGAAAAGCTCCCCAC 4 34 0 CTTTTGGAAA 0.900166 -47 GTAGGTAAACCCTACGGGGTAGAACGATAAA 7 30 1 CTACGGGGTA 0.85627 -34 ACACCTCCACCGTTTTGGTAATTTCTCGGAC 8 43 0 CTTTTGGTAA 0.900166 -24 TTTTTCTCACCGTTTGGCATACTCCTCTTCG 11 73 1 CTTTGGCATA 0.718232 -39 GGGGTGCCGGCGTATGGGGCAGGGAGTTTAT 12 211 0 CTATGGGGCA 0.874884 -90 ACGGATAGCTCGTTTAGGAAACCGTTCCTGC 12 248 0 CTTTAGGAAA 0.78111 -53 TAACAAGACACACTTGGGGTACGCATCATGC 13 45 0 CCTTGGGGTA 0.95542 -155 GTATGAGTTTCTCTTGGGTAAGAGCGGGAAG 14 15 1 CCTTGGGTAA 0.924612 -26 CGTGTTACGTCCTTCGGGTAAGGCACGGAGC 16 13 1 CTTCGGGTAA 0.924612 -26 CACCGCACTCCCTTTTGGGTAGACATCACGT 17 15 0 CTTTTGGGTA 0.940319 -26 * ********* Masking position 11 Map Score: 3.79785 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 189 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 GTCCAGGCGAACGCCAGGTTCGGTCATACTT 2 47 0 ACGCAGGTTC 0.800019 -70 CTGGCGTCTCGCCGCGCGTTCTGCGCACGCT 3 59 1 GCCGGCGTTC 0.940201 -83 CTCCTCTCTCCCGCTACGTTCTAGTGTCGTT 9 29 0 CCGCACGTTC 0.834459 -32 TGCGACCTACACCGGATGTGCCGCAGGCAGA 10 30 0 ACCGATGTGC 0.945618 -43 AAACCGCCCCTTCTTTCAACGGT 10 60 0 ACCGCCCTTC 0.886601 -13 GAAAAACTTGACGGCGCGCGCTAAACGCCTA 11 48 0 ACGGGCGCGC 0.918336 -64 AGTACGGCAAACGGAGTGTTCCTTGTAGGGT 12 153 0 ACGGGTGTTC 0.967127 -148 CGTTTAGGAAACCGTTCCTGCAAAAAAGGGG 12 238 0 ACCGTCCTGC 0.812719 -63 AAGAGGTTGCGCGGTACCTGCGAATTTCTGA 13 121 1 GCGGACCTGC 0.947502 -79 CCACTCATACACGGTACGTTCAGAAATTCGC 13 140 0 ACGGACGTTC 0.991187 -60 ACTTTTCCTGACGGAATCTTCCCCTTTTGCG 13 172 0 ACGGATCTTC 0.954831 -28 CCCTGCACTGACGGCATGTTCC 18 2 0 ACGGATGTTC 0.976371 -81 **** ****** Masking position 2 Map Score: 9.03869 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 361 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TCTTTCCCCACAAGGAGCATGCATAATGAA 2 14 1 CAAGGAGCAT 0.988572 -103 TTTTCCACTTCTAGGAGCATATC 2 104 1 CTAGGAGCAT 0.978886 -13 ACTCACCCGACAAGGAGGAGTAGCGTGCGC 3 81 0 CAAGGAGGAG 0.960129 -61 GCGCGGAGGATAGGGCGCGGG 6 92 0 CGCGGAGGAT 0.952299 -11 GTCCAAACCTCTAGGAAGATATCCAAGTCG 12 63 1 CTAGGAAGAT 0.905918 -238 GTTCACCCTACAAGGAACACTCCGTTTGCC 12 149 1 CAAGGAACAC 0.896141 -152 TCGGGTAAGGCACGGAGCATGGA 16 26 1 CACGGAGCAT 0.983111 -13 ********** Masking position 6 Map Score: 5.95372 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 36 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 TACTGAACTAGGAAAAACAACCGCTGTATAC 1 16 0 GGAAAACAAC 0.917397 -90 TCCTACGCAGGAATAAAAGTCCACGCAGAGC 1 72 0 GAAAAAAGTC 0.888127 -34 CATGCATAATGAATAAAAGTATGACCGAACC 2 31 1 GAAAAAAGTA 0.756286 -86 CGGATAAAAGGACAAAAGACTTGATGCGGC 3 10 1 GGAAAAAGAC 0.980142 -132 AAAATAGGGCGGAAAAAAGAATATCCGTATG 5 27 0 GGAAAAAGAA 0.950723 -38 GAATTTCTTCGGACAAACCAACCTCCCCTTT 13 81 0 GGAAAACCAA 0.870385 -119 AGTGCTTTCGGAAGAAACGATTGACAGGGGA 15 43 1 GAAAAACGAT 0.762228 -76 ACCCTCCCCTGAAAAAAACACAGCCTACCAG 15 96 0 GAAAAAACAC 0.913798 -23 TGCATGTACCGGATAAAAAACCGTACACTTT 20 48 0 GGAAAAAAAC 0.930866 -105 *** ******* Masking position 6 Map Score: 3.88129 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 102 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 GTCTCTTTCCCCACAAGGAGCATGCATA 2 9 1 CCCCACAAGG 0.824064 -108 CACTAGACTCACCCGACAAGGAGGAGTAGC 3 87 0 ACCCGACAAG 0.891934 -55 CTGTAGGTAAACCCTACGGGGTAGAACGAT 7 28 1 ACCCTACGGG 0.942225 -36 AAGTCGCCGAACACAACAGGGGCGTAGTAG 12 87 1 ACACAACAGG 0.908979 -214 TGTAGGGTGAACCCGACGGACCCAGTGACT 12 131 0 ACCCGACGGA 0.969111 -170 GTGATACACGCCAGGCGTGAGATTT 13 6 1 ACACGCCAGG 0.943378 -194 TCCCGCTCTTACCCAAGAGAAACTCATACC 14 14 0 ACCCAAGAGA 0.65751 -27 GACACGTAGGGTGTGCGTGCA 15 2 1 ACACGTAGGG 0.705997 -117 TCCGTGCCTTACCCGAAGGACGTAACACGT 16 12 0 ACCCGAAGGA 0.930536 -27 CGTGATGTCTACCCAAAAGGGAGTGCGGTG 17 16 1 ACCCAAAAGG 0.945068 -25 CCTGAGCGCGCCCCGCCGCGACGCAG 19 12 1 CCCCGCCGCG 0.816154 -16 ********** Masking position 4 Map Score: 5.04426 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 326 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: 2.28327e-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: 2.28327e-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: 2.28327e-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