AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ilexA_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0102 64 rep helicase, single-stranded DNA-dependent ATPase (rep) #2 TP0116 150 excinuclease ABC, subunit B (uvrB) #3 TP0162 174 Holliday junction DNA helicase (ruvB) #4 TP0438 29 conserved hypothetical protein #5 TP0439 86 purine-binding chemotaxis protein (cheW-2) #6 TP0440 89 spore coat polysaccharide biosynthesis protein, putative #7 TP0511 42 transcription factor (carD) #8 TP0512 44 conserved hypothetical protein #9 TP0513 73 K+ transport protein (trkA) #10 TP0514 113 excinuclease ABC, subunit A (uvrA) #11 TP0543 41 Holliday junction DNA helicase (ruvA) #12 TP0544 24 T. pallidum predicted coding region TP0544 #13 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #14 TP0547 143 penicillin tolerance protein (lytB) #15 TP0692 260 recA protein (recA) #16 TP0693 159 T. pallidum predicted coding region TP0693 #17 TP0944 170 conserved hypothetical protein #18 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) #19 TP0999 71 cell division protein, putative #20 TP1028 82 DNA helicase II (uvrD) #21 TP1030 27 T. pallidum predicted coding region TP1030 Motif number 1 GCTCCTTGCAGGTAACTGCGC 4 2 1 CTCCTTGCAG 0.943328 -28 TTTTCACGGCGCAGTTACCTGCAA 4 16 0 CACGGCGCAG 0.974026 -14 TTCGCTCACGCACCTTGCAGAGCA 5 5 0 CACCTTGCAG 0.911235 -82 GTGTCCTGCACTCCGTTCGCTCACGCACCT 5 20 0 CTCCGTTCGC 0.7808 -67 CGTACAATCCCTCCTCTCAGCTGCAGTCAA 5 54 0 CTCCTCTCAG 0.725061 -33 TGTCTGTCTCCTGCCTGCAGCTCCAAGCGC 6 22 1 CTGCCTGCAG 0.885413 -68 CAGCTCCAAGCGCCGTGCGGGGTCCATCCC 6 39 1 CGCCGTGCGG 0.991988 -51 TGACAAGCAACGCGGCGCGGG 8 2 0 CGCGGCGCGG 0.992909 -43 GCGTGCAGAGCTGCCTGCAGCGGTGACAAG 8 25 0 CTGCCTGCAG 0.885413 -20 GCGCGCAGAACACGGCGCACAACGCCTGCC 9 13 0 CACGGCGCAC 0.956315 -61 TTTGCATGGCCAGCGCGCAGAACACGGCGC 9 25 0 CAGCGCGCAG 0.68707 -49 TGCAATTCCACTCCCTTCGCGGCAGACCGC 10 12 0 CTCCCTTCGC 0.780802 -102 AAAGGGAGAACGTGTCGCAGGACGTTCGC 10 95 1 CGTGTCGCAG 0.806872 -19 AGGACACTCCTCACGCGCAGTGTA 12 7 0 CCTCACGCGC 0.636786 -18 TTTCTATATTCCTCGCGCGGGTATCAGGGT 13 11 1 CCTCGCGCGG 0.807084 -74 AACTCACCACCACGCCGCGCCCTTGCATGA 14 60 1 CACGCCGCGC 0.968823 -84 CTTTGGTACACTCGGCGCGCCAGTTTTCTT 14 99 1 CTCGGCGCGC 0.980679 -45 CTTGAACCGGCGACCCGCGGATTATGAGTC 15 159 0 CGACCCGCGG 0.968748 -102 AGACGCGCTACCACCTGCACACAAATAGTA 15 203 0 CCACCTGCAC 0.713232 -58 GCGTCTCTTGCGCCTTGCGCGGGGTTTTTC 15 227 1 CGCCTTGCGC 0.957248 -34 GTGTCGGCGTCGTCCTGCACGTCCCTAACG 16 20 1 CGTCCTGCAC 0.887339 -140 AAGAAGCAGTATCCCCGCAGAAAAACAAGC 17 57 0 ATCCCCGCAG 0.769726 -114 CGCGTGCAAGCACCACGCAGCAAAAACTAA 17 101 0 CACCACGCAG 0.92914 -70 CGGGGTCAGCCTACCCGCGGGAAGGATATT 18 13 1 CTACCCGCGG 0.94908 -139 TTAGCTTGCACGCCCTGCAGGCTACCGACC 19 28 0 CGCCCTGCAG 0.989354 -44 GCCCGGGCGGCGCCCTGCACTGACGGCATG 20 15 0 CGCCCTGCAC 0.981895 -68 AGGGCGCCGCCCGGGCGCGGTGGCACTCGG 20 29 1 CCGGGCGCGG 0.796494 -54 CGCGGTGGCACTCGGTGCGGTGCGGCAGTT 20 44 1 CTCGGTGCGG 0.976192 -39 TGCGTCGCGGCGGGGCGCGCTCAGGC 21 7 0 CGGGGCGCGC 0.958932 -21 CGCGCCCCGCCGCGACGCAG 21 18 1 CGCGACGCAG 0.94717 -10 ********** Masking position 8 Map Score: 54.374 Number of sites scoring better than the average of aligned sites = 2711 Number in coding regions = 2473 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 AGACGCACAAGCGTAGCAAAATAGGGC 1 48 0 CGCACAAGGC 0.956091 -17 GTCAACCAGAGGTTCTAAGAGAGCAAAATCAAAG 2 62 1 GGTTCTAAGC 0.353835 -89 CAAAGGGAAAGGCACAGCATGTACTACAGATTTT 2 91 1 GGCACAGCAC 0.546904 -60 TCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT 3 91 0 CGCGCCAGCC 0.975006 -84 AAGAGGGCGCAACTGTAGCTGCTTATGCG 3 156 0 GGCGCAACGC 0.982277 -19 GAGCGAACGGAGTGCAGGACACGCGCTTGACTGC 5 28 1 AGTGCAGGGC 0.866684 -59 GCGTGCAGAGCTGCCTGCAGCGGTG 8 30 0 CGTGCAGACC 0.947602 -15 CAGAACACGGCGCACAACGCCTGCCAC 9 4 0 CGCACAACGC 0.91706 -70 CCGTGTTCTGCGCGCTGGCCATGCAAAAAAATTT 9 28 1 CGCGCTGGGC 0.983361 -46 AAAAAAATTTCGTGCTACTATGGCCTTCGGAC 9 52 1 CGTGCTACGC 0.958647 -22 TCGCGCAGGAAAAGCAACGTGTCTT 14 2 1 CGCGCAGGGC 0.994165 -142 AGAAAACTGGCGCGCCGAGTGTACCAAAGGCACC 14 94 0 CGCGCCGAAC 0.770199 -50 TGTGTTGTTTCGTGCTACAAGTCCCGCCGGAAGG 15 97 1 CGTGCTACCC 0.931855 -164 GCGGGTCGCCGGTTCAAGTCCAGCTGGGCCCATA 15 171 1 GGTTCAAGGC 0.855358 -90 CCCCGCGCAAGGCGCAAGAGACGCGCTACCACCT 15 217 0 GGCGCAAGGC 0.991204 -44 TCGTTAGGGACGTGCAGGACGACGCCGACACCAC 16 17 0 CGTGCAGGCG 0.880248 -143 ACCACAGCCGCGTGCTAAAGTACCGTCACGGGCC 16 103 0 CGTGCTAACC 0.877843 -57 GGTGTTCAGGTGTAAGGAGACCCTGTCGCTCA 17 9 1 GGTGTAAGCC 0.618537 -162 ACCACTGTCGCGTGCAAGCACCACGCAGCAAAAA 17 105 0 CGTGCAAGAC 0.966132 -66 AGTGGTTGTTCGTGCAAGTTATGGTAATGTTTGT 17 133 1 CGTGCAAGGG 0.93455 -38 TATCGGTTTAGGCGCAAATAAAACAGGATAAGCA 18 47 1 GGCGCAAAAC 0.867012 -105 GCCTGCAGGGCGTGCAAGCTAACAGATTAACTGT 19 36 1 CGTGCAAGCA 0.755363 -36 GTCAGTGCAGGGCGCCGCCCGGGCGCGGTGGCAC 20 21 1 GGCGCCGCGC 0.944377 -62 ******** ** Masking position 2 Map Score: 30.5134 Number of sites scoring better than the average of aligned sites = 2299 Number in coding regions = 2147 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 AGGTCCGCGCCAGAGTGCCGTTTTCTTTTCC 3 89 0 CGAGTGCCGT 0.75174 -86 GCAGTCAAGCGCGTGTCCTGCACTCCGTTCG 5 31 0 GGTGTCCTGC 0.9436 -56 ACAATCCCTCCTCTCAGCTGCAGTCAAGCGC 5 50 0 CCTCAGCTGC 0.717905 -37 TGCCCCACCGCTGTCTGTCTCCTG 6 4 1 CCACCGCTGT 0.662767 -86 CCACCGCTGTCTGTCTCCTGCCTGCAGCTCC 6 15 1 CGTCTCCTGC 0.937919 -75 GCCTGCAGCTCCAAGCGCCGTGCGGGGTCCA 6 34 1 CAAGCGCCGT 0.412957 -56 CATCCCCGTCCACAGCCCCGCCATCCGAAGG 6 63 1 CCAGCCCCGC 0.958827 -27 CCCGCGCCGCGTTGCTTGTCACCGC 8 5 1 CCCGCGTTGC 0.895287 -40 CGCGTTGCTTGTCACCGCTGCAGGCAGCTCT 8 18 1 GCACCGCTGC 0.908688 -27 CACCGCTGCAGGCAGCTCTGCACGC 8 30 1 GCAGCTCTGC 0.645039 -15 GCGTTGTGCGCCGTGTTCTGCGCGCTGGCCA 9 18 1 CGTGTTCTGC 0.79966 -56 TGCGGTCTGCCGCGAAGGGAGTG 10 3 1 CGTCTGCCGC 0.949546 -111 GCGAACGTCCTGCGACACGTTCT 10 101 0 GACGTCCTGC 0.766835 -13 GTGTTCGCTTCAGTGCGCCACACATAAAGAG 11 15 1 CGTGCGCCAC 0.780678 -27 AAGAACTCACCACCACGCCGCGCCCTTGCAT 14 57 1 CCCACGCCGC 0.738251 -87 AAGAATTGACGCGTGTGTTGTTTCGTGCTAC 15 84 1 GGTGTGTTGT 0.217254 -177 CGCGGATTATGAGTCCGCTGCTCTAACCAAC 15 143 0 GGTCCGCTGC 0.952808 -118 GGACTTGAACCGGCGACCCGCGGATTATGAG 15 161 0 CGCGACCCGC 0.873892 -100 AGGTGGTAGCGCGTCTCTTGCGCCTTGCGCG 15 217 1 GGTCTCTTGC 0.465678 -44 GTGGTGTCGGCGTCGTCCTGCACGTCCCTAA 16 17 1 CTCGTCCTGC 0.710251 -143 CGCGGCTGTGGTGTGCGCTGCAGAATAAAGA 16 125 1 GGTGCGCTGC 0.97683 -35 GGTGTAAGGAGACCCTGTCGCTCATAGGGTA 17 19 1 GCCCTGTCGC 0.518345 -152 TTAGTTTTTGCTGCGTGGTGCTTGCACGCGA 17 101 1 CGCGTGGTGC 0.767479 -70 ACATTCAAGACAGTGTCCTGCTTATCCTGTT 18 68 0 CGTGTCCTGC 0.969276 -84 CTGTTAGCTTGCACGCCCTGCAGGCTACCGA 19 30 0 GACGCCCTGC 0.851149 -42 CGCGCCCGGGCGGCGCCCTGCACTGACGGCA 20 17 0 CGCGCCCTGC 0.987755 -66 CCGCACCGCACCGAGTGCCACCGCGCCCGGG 20 38 0 CGAGTGCCAC 0.600549 -45 GCGCAGCCCTGCAACCGAAAAC 20 71 0 CCAGCCCTGC 0.964347 -12 GCCTGAGCGCGCCCCGCCGCGACGCAG 21 10 1 CCCCCGCCGC 0.969954 -18 * ********* Masking position 10 Map Score: 35.2578 Number of sites scoring better than the average of aligned sites = 3892 Number in coding regions = 3565 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 AGTCTATGCCCTTCCACATACGGATATTCTT 1 10 1 CTCCACATAC 0.947545 -55 CTCTGGTTGACAAACCACACCCATGGTGAATA 2 41 0 CACCACACCC 0.983572 -110 CCACCGCTGTCTGTCTCCTGCCTGCAGCTCCA 6 15 1 CTCTCCTGCC 0.876943 -75 GGGTCCATCCCCGTCCACAGCCCCGCCATCCG 6 58 1 CTCCACAGCC 0.990164 -32 TGCTTTATGCAATTCCACTCCCTTCGCGGCAG 10 17 0 ATCCACTCCC 0.839509 -97 CCTTTCTACGCGATCCCCATCCATAAGAGGGC 10 68 0 CTCCCCATCC 0.9903 -46 TTTGACACTTCTTTCCCCTCACACCCTGATAC 13 31 0 CTCCCCTCAC 0.964209 -54 CCCTCTCATCCTATCCCCATACCCCGATCTAC 15 24 0 CTCCCCATAC 0.966451 -237 CAGGACGACGCCGACACCACCCATAC 16 5 0 CACACCACCC 0.903477 -155 TTCTGCAGCGCACACCACAGCCGCGTGCTAAA 16 118 0 CACCACAGCC 0.978533 -42 * ********* Masking position 5 Map Score: 11.0313 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 264 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 GGAGTGCAGGACACGCGCTTGACTGCAGCT 5 36 1 ACACGCGCTT 0.946803 -51 GAACGTGTAGACTGGCGCACCCTTTTGTAC 7 15 0 ACTGGCGCAC 0.968591 -28 GCGCCAGTCTACACGTTCTTTGTGTT 7 27 1 ACACGTTCTT 0.722325 -16 ACGTCCTGCGACACGTTCTCCCTTTCTACG 10 90 0 ACACGTTCTC 0.900496 -24 CCGGAAGAAAACTGGCGCGCCGAGTGTACC 14 103 0 ACTGGCGCGC 0.970835 -41 ATCACTCACTGGGGCACTAAACCGGAA 14 127 0 ACTGGGGCAC 0.903782 -17 ACCCCGGGGAACACCCTCTCATCCTATCCC 15 39 0 ACACCCTCTC 0.918238 -222 AGCGCACACCACAGCCGCGTGCTAAAGTAC 16 114 0 ACAGCCGCGT 0.872223 -46 CCTATGAGCGACAGGGTCTCCTTACACCTG 17 17 0 ACAGGGTCTC 0.936164 -154 CCGCAGAAAAACAAGCGCTCTAGTACCCTA 17 43 0 ACAAGCGCTC 0.922349 -128 CTGCGGGGATACTGCTTCTTGCTATGCATA 17 67 1 ACTGCTTCTT 0.596994 -104 ATCCATATTTACAGGTGCTCGATTTGTTTG 18 119 1 ACAGGTGCTC 0.978029 -33 GCAACCGAAAACTGCCGCACCGCACCGAGT 20 53 0 ACTGCCGCAC 0.9336 -30 ********** Masking position 1 Map Score: 12.9591 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 580 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TGGTGAATAGAGTGGACCCCGCTTAAGAGGA 2 19 0 AGTGACCCCG 0.847346 -132 ACCTCTGGTTGACAAACCACACCCATGGTGA 2 44 0 GACAACCACA 0.679704 -107 GCAGGCAGGAGACAGACAGCGGTGGGGCA 6 9 0 GACGACAGCG 0.835927 -81 TGTGGACGGGGATGGACCCCGCACGGCGCTT 6 46 0 GATGACCCCG 0.972499 -44 CTCCCTTCGCGGCAGACCGCA 10 1 0 GGCGACCGCA 0.940989 -113 CAAAACGCTGTACAAACCCCGGGGAACACCC 15 53 0 TACAACCCCG 0.944294 -208 GACTTGAACCGGCGACCCGCGGATTATGAGT 15 160 0 GGCACCCGCG 0.859905 -101 AGCCTCCCATGAAAAACCCCGCGCAAGGCGC 15 236 0 GAAAACCCCG 0.964609 -25 GGGACGTGCAGGACGACGCCGACACCACCCA 16 14 0 GGAGACGCCG 0.84594 -146 ACGCAGCAAAAACTAACCCCTATGCATAGCA 17 86 0 AACAACCCCT 0.596935 -85 CCCGCGGGTAGGCTGACCCCGTC 18 3 0 GGCGACCCCG 0.995224 -149 ATACTGGCGTGAACAACCCCAAACATTCAAG 18 90 0 GAAAACCCCA 0.857482 -62 CCCTGCAGGCTACCGACCCCGACAGAAGGAG 19 15 0 TACGACCCCG 0.969244 -57 *** ******* Masking position 7 Map Score: 12.9003 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 153 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AAAAGAAAACGGCACTCTGGCGCGGACCTCT 3 91 1 GGACTCTGGC 0.910871 -84 AAGAGGGCGCAACTGTAGCTGCTTATGCG 3 156 0 GCACTGTAGC 0.928702 -19 ACCCCGCACGGCGCTTGGAGCTGCAGGCAGG 6 31 0 GCCTTGGAGC 0.731685 -59 AAAATTTCGTGCTACTATGGCCTTCGGAC 9 55 1 GCACTATGGC 0.790503 -19 CCTTCCGGCGGGACTTGTAGCACGAAACAAC 15 100 0 GGCTTGTAGC 0.943011 -161 CCCGCCGGAAGGGCCTATAGCTCAGTTGGTT 15 119 1 GGCCTATAGC 0.974332 -142 CGCGTCTCTTGCGCCTTGCGCGGGGTTTTTC 15 226 1 GCCCTTGCGC 0.804616 -35 GGCCCGTGACGGTACTTTAGCACGCGGCTGT 16 103 1 GGACTTTAGC 0.944481 -57 GGTGTAAGGAGACCCTGTCGCTCATAGGGTA 17 19 1 GACCTGTCGC 0.860066 -152 TCGCTCATAGGGTACTAGAGCGCTTGTTTTT 17 36 1 GGACTAGAGC 0.927888 -135 CCTTCTGTCGGGGTCGGTAGCCTGCAGGGCG 19 17 1 GGTCGGTAGC 0.864636 -55 GCGCCGCCCGGGCGCGGTGGCACTCGGTGCG 20 32 1 GGGCGGTGGC 0.870664 -51 ** ******** Masking position 11 Map Score: 5.29389 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 238 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TCAAAATTCACCCAAGGAGTGTCAC 3 4 0 CCCAAGAGGT 0.208221 -171 TAGCGGATCACGCAGGAAACGTCAATTTTTCA 3 46 1 CGCAGGAAGT 0.897686 -129 GCGAACGGAGTGCAGGACACGCGCTTGACTGC 5 30 1 TGCAGGCAGC 0.964676 -57 CAGCTCCAAGCGCCGTGCGGGGTCCATCCCCG 6 39 1 CGCCGTCGGG 0.831279 -51 TTGTCACCGCTGCAGGCAGCTCTGCACGC 8 26 1 TGCAGGAGTC 0.711816 -19 ATGGCCAGCGCGCAGAACACGGCGCACAACGC 9 18 0 CGCAGACAGG 0.738399 -56 GTGTTCTGCGCGCTGGCCATGCAAAAAAATTT 9 30 1 CGCTGGCAGC 0.939203 -44 CGGTCTGCCGCGAAGGGAGTGGAATTGCATAA 10 13 1 CGAAGGAGGG 0.68056 -101 GAGAACGTGTCGCAGGACGTTCGC 10 100 1 CGCAGGCGTC 0.962069 -14 TCGCGCAGGAAAAGCAACGTGTCTT 14 4 1 CGCAGGAAGC 0.988756 -140 ACCAAAGGCACCCAGGTCATGCAAGGGCGCGG 14 74 0 CCCAGGCAGC 0.966818 -70 CTACAAGTCCCGCCGGAAGGGCCTATAGCTCA 15 111 1 CGCCGGAGGC 0.990957 -150 CCGCGCAAGGCGCAAGAGACGCGCTACCACCT 15 217 0 CGCAAGGAGC 0.601663 -44 CCATGAAAAACCCCGCGCAAGGCGCAAGAGAC 15 229 0 CCCCGCCAGG 0.631639 -32 GCAAGCACCACGCAGCAAAAACTAACCCCTAT 17 94 0 CGCAGCAAAC 0.566112 -77 GTCGGTAGCCTGCAGGGCGTGCAAGCTAACAG 19 29 1 TGCAGGCGGC 0.98167 -43 GGAACATGCCGTCAGTGCAGGGCGCCGC 20 7 1 TGCCGTAGGC 0.671914 -76 CAGTGCAGGGCGCCGCCCGGGCGCGGTGGCAC 20 23 1 CGCCGCCGGC 0.975206 -60 ACTGCCGCACCGCACCGAGTGCCACCGCGCCC 20 41 0 CGCACCAGGC 0.79133 -42 CTGCGTCGCGGCGGGGCGCGCTCAGGC 21 7 0 GGCGGGCGGC 0.778725 -21 ****** ** ** Masking position 3 Map Score: 20.1972 Number of sites scoring better than the average of aligned sites = 1694 Number in coding regions = 1564 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 TGCTCTGCAAGGTGCGTGAGCGAACGGAGT 5 11 1 GGTGCGTGAG 0.95915 -76 CACGGCGCTTGGAGCTGCAGGCAGGAGACA 6 26 0 GGAGCTGCAG 0.911127 -64 AGTACAAAAGGGTGCGCCAGTCTACACGTT 7 14 1 GGTGCGCCAG 0.997671 -29 TGTTCGCTTCAGTGCGCCACACATAAAGAG 11 16 1 AGTGCGCCAC 0.949588 -26 TGGTACACTCGGCGCGCCAGTTTTCTTCCG 14 102 1 GGCGCGCCAG 0.992444 -42 CTTCCGGTTTAGTGCCCCAGTGAGTGAT 14 126 1 AGTGCCCCAG 0.957444 -18 CATATTTACAGGTGCTCGATTTGTTTGCTA 18 122 1 GGTGCTCGAT 0.843024 -30 CACTCGGTGCGGTGCGGCAGTTTTCGGTTG 20 52 1 GGTGCGGCAG 0.994506 -31 ********** Masking position 9 Map Score: 8.99624 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 154 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ATAGAGTGGACCCCGCTTAAGAGGAGGCAC 2 14 0 CCCCGCTTAA 0.824258 -137 ATTTGATCTTCCTCGCATAAGCAGCTACAG 3 143 1 CCTCGCATAA 0.971585 -32 TGCGCGCTGGCCATGCAAAAAAATTTCGTG 9 36 1 CCATGCAAAA 0.836089 -38 TACGCGATCCCCATCCATAAGAGGGCAGAC 10 64 0 CCATCCATAA 0.916175 -50 CTTCAGTGCGCCACACATAAAGAGGAGATA 11 22 1 CCACACATAA 0.894238 -20 CACGCCGCGCCCTTGCATGACCTGGGTGCC 14 70 1 CCTTGCATGA 0.856182 -74 CACAAGCCTCCCATGAAAAACCCCGC 15 245 0 CCTCCCATGA 0.942791 -16 GACGCCGACACCACCCATAC 16 1 0 CCACCCATAC 0.892582 -159 CCTACGATATCCACCAAAGACACATCACGT 16 58 0 CCACCAAAGA 0.438909 -102 GAAGCAGTATCCCCGCAGAAAAACAAGCGC 17 55 0 CCCCGCAGAA 0.947487 -116 CGTGCAAGCACCACGCAGCAAAAACTAACC 17 99 0 CCACGCAGCA 0.894324 -72 ********** Masking position 2 Map Score: 4.66617 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 206 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TGCTCTCTTAGAACCTCTGGTTGACAAACC 2 57 0 GAACCTCTGG 0.781934 -94 AAAAGAAAACGGCACTCTGGCGCGGACCTC 3 91 1 GGCACTCTGG 0.968422 -84 ACTCTGGCGCGGACCTCTCGAGCTACATGA 3 104 1 GGACCTCTCG 0.917633 -71 GCGCGTGTCCTGCACTCCGTTCGCTCACGC 5 24 0 TGCACTCCGT 0.835073 -63 TTCGGACCTTCGGATGGCGGGGC 6 77 0 GGACCTTCGG 0.979435 -13 CGTGCTACTATGGCCTTCGGAC 9 62 1 TGGCCTTCGG 0.846181 -12 CTGAGCTATAGGCCCTTCCGGCGGGACTTG 15 114 0 GGCCCTTCCG 0.973762 -147 TACCGTCACGGGCCCTTCGTTACAGCCACC 16 87 0 GGCCCTTCGT 0.97557 -73 CGGGCGCGGTGGCACTCGGTGCGGTGCGGC 20 40 1 GGCACTCGGT 0.854982 -43 ********** Masking position 6 Map Score: 3.89402 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 134 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 ACCCCGCTTAAGAGGAGGCACGTT 2 5 0 AGAGGAGGCA 0.988596 -146 AAGAGGGCGCAACTGTAGCTG 3 164 0 AGAGGGCGCA 0.942783 -11 ACTGCAGCTGAGAGGAGGGATTGTACGAAG 5 57 1 AGAGGAGGGA 0.979212 -30 CCACACATAAAGAGGAGATA 11 32 1 AGAGGAGATA 0.914814 -10 TATCAGGGTGTGAGGGGAAAGAAGTGTCAA 13 32 1 TGAGGGGAAA 0.893778 -53 CTGGTGAACATGAGGAGGAAAT 13 73 1 TGAGGAGGAA 0.96778 -12 ********** Masking position 3 Map Score: 1.82065 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 73 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 CACCATGGGTGTGGTTTGTCAACCAGAGGT 2 45 1 GTGGTTTGTC 0.877753 -106 AAATTCACCCAAGGAGTGTCAC 3 3 0 AAGGAGTGTC 0.971547 -172 CACTGCGCGTGAGGAGTGTCCT 12 13 1 GAGGAGTGTC 0.987122 -12 TGTGAGGGGAAAGAAGTGTCAAATCAGAAT 13 40 1 AAGAAGTGTC 0.938073 -45 AAAAGAAGACGTGATGTGTCTTTGGTGGAT 16 50 1 GTGATGTGTC 0.943272 -110 ********** Masking position 7 Map Score: 0.875641 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 48 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: 5.81467e-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: 5.81467e-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