AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_tpal_reg_300.orf -o00240_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 TP0002 242 DNA polymerase III, subunit beta (dnaN) #2 TP0053 170 ribonucleoside-diphosphate reductase, subunit beta (nrdB) #3 TP0103 64 ATP-dependent DNA helicase, putative #4 TP0104 246 5'-nucleotidase (ushA) #5 TP0105 166 DNA polymerase I (polA) #6 TP0185 147 signal peptidase I (sip) #7 TP0186 54 oxygen-independent coproporphyrinogen III oxidase, putative #8 TP0187 63 translation elongation factor TU (tuf) #9 TP0188 71 ribosomal protein S10 (rpsJ) #10 TP0189 46 ribosomal protein L3 (rplC) #11 TP0192 55 ribosomal protein L2 (rplB) #12 TP0207 187 ribosomal protein L15 (rplO) #13 TP0231 100 conserved hypothetical protein #14 TP0232 99 T. pallidum predicted coding region TP0232 #15 TP0233 30 anti-sigma F factor antagonist, putative #16 TP0234 234 ribosomal protein L33 (rpmG) #17 TP0235 149 preprotein translocase subunit (secE) #18 TP0237 106 ribosomal protein L11 (rplK) #19 TP0240 108 ribosomal protein L7/L12 (rplL) #20 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #21 TP0274 88 deoxycytidylate deaminase, putative #22 TP0276 172 conserved hypothetical protein #23 TP0277 127 carboxyl-terminal protease (ctp) #24 TP0342 120 cytidylate kinase (cmk) #25 TP0354 262 thymidylate kinase (tmk) #26 TP0438 29 conserved hypothetical protein #27 TP0439 86 purine-binding chemotaxis protein (cheW-2) #28 TP0440 89 spore coat polysaccharide biosynthesis protein, putative #29 TP0445 135 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (thiJ) #30 TP0446 41 gcpE protein (gcpE) #31 TP0448 57 uracil phosphoribosyltransferase, putative #32 TP0524 135 ATP-dependent protease LA (lon-2) #33 TP0642 140 phosphomannomutase (manB) #34 TP0667 230 uridine kinase (udk) #35 TP0669 153 DNA polymerase III, subunit alpha (dnaE) #36 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #37 TP0672 134 glycyl-tRNA synthetase (glyS) #38 TP0673 177 glutamyl-tRNA synthetase (gltX) #39 TP0734 81 purine nucleoside phosphorylase (deoD) #40 TP0736 233 hydrogenase, gamma chain (hydG) #41 TP0814 222 thioredoxin reductase (trxB) #42 TP0824 300 transketolase B (tktB) #43 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) #44 TP0891 175 translation initiation factor 2 (infB) #45 TP0892 49 N utilization substance protein A (nusA) #46 TP0893 174 conserved hypothetical protein #47 TP0895 21 T. pallidum predicted coding region TP0895 #48 TP0900 38 T. pallidum predicted coding region TP0900 #49 TP0901 40 conserved hypothetical integral membrane protein #50 TP1005 58 DNA polymerase III, subunits gamma and tau (dnaH) #51 TP1006 108 DNA gyrase, subunit B (gyrB) #52 TP1007 42 thymidylate synthase-complementing protein (thy1) #53 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #54 TP1009 96 glycerol-3-phosphate dehydrogenase (gpsA) #55 TP1010 125 nucleoside-diphosphate kinase (ndk) #56 TP1011 34 peptidyl-tRNA hydrolase (pth) #57 TP1012 204 RNA polymerase sigma-43 factor (sigA) #58 TP1026 300 oligoendopeptidase F, putative #59 TP1027 121 uridine phosphorylase (udp) Motif number 1 ATTCTCAATTGCGGCGGGCGTAAAAATGTCT 2 96 0 GCGGCGGGCT 0.591958 -75 TACCGTGCGGGCACGGAACACATCGAGCGGA 4 203 1 GCACGGAACC 0.82058 -44 AAGGTTATGTGCAGCACCCTTCTTTCCGCTC 5 109 0 GCAGCACCCT 0.729422 -58 GCCCCTCATGGCGCCGGATGCTACCGGATAG 6 62 1 GCGCCGGATC 0.852785 -86 CACCACAAATGCGGCGCCTACACA 7 4 0 GCGGCGCCTC 0.961917 -51 AGCACGATGCGCAGCACGCACCACAAATGCG 7 22 0 GCAGCACGCC 0.982612 -33 AACACACTCCGCGCCGCAAACGC 9 3 0 GCGCCGCAAC 0.926259 -69 ACCGTCCGACGCACCGGCTCCCTCTGACCGA 12 53 0 GCACCGGCTC 0.900023 -135 CCCCAAGACGGCAGGACTCCCGTCTTTCTCC 12 120 0 GCAGGACTCC 0.845413 -68 GAAACAGCTCGCACCATCCCCAAGACGGCAG 12 137 0 GCACCATCCC 0.887335 -51 TCCTCCACCCGCACCAGGTGCGAAACAGCTC 12 158 0 GCACCAGGTC 0.791288 -30 CCTATACCAGGCACCGCATACTACCGGTCAA 13 56 0 GCACCGCATC 0.968802 -45 TTGCCTGTAGCAGGGCATTCTGGTAGGCGG 14 10 1 GCAGGGCATC 0.895581 -90 CACACATCAAGCACGAAACACCTCCCTAAAC 16 52 0 GCACGAAACC 0.674805 -183 CATGCGCATTGCAACACTCTCCACCCTGGAA 18 19 0 GCAACACTCC 0.547595 -88 ACACAACGACGCGCCGGACGCATGCAAAAAA 20 20 0 GCGCCGGACC 0.95027 -243 CTACTCAAAAGCGCGACGCCCTCCCACACGA 20 66 0 GCGCGACGCC 0.968143 -197 GCTGCGGTGCGCAGCACACTCTGGCGGGTGA 21 24 0 GCAGCACACC 0.970726 -65 CATAGCCTGGGCAGCGGGACCGACCTGATAA 22 75 0 GCAGCGGGAC 0.773371 -98 AAGTAGTGCGGCGCCGAGCACGCACAGTCTG 22 111 0 GCGCCGAGCC 0.944701 -62 TGTCTGATCACCAGCGCACTCCCTTCCCCAC 23 61 1 CCAGCGCACC 0.875002 -67 TCCACAGCCGGCACCACCACCATGTTGGCGA 24 26 0 GCACCACCAC 0.895265 -95 AGGAGAAAGTGCAACGCGCACGTGTACACCG 25 188 0 GCAACGCGCC 0.919511 -75 TAAAAACAGTGCAGCATGTACACCCGAGGAG 25 214 0 GCAGCATGTC 0.653952 -49 CGAACGGAGTGCAGGACACGCGCTTGACTGC 27 31 1 GCAGGACACC 0.930017 -56 GATGGACCCCGCACGGCGCTTGGAGCTGCAG 28 36 0 GCACGGCGCT 0.822634 -54 CCCCGCGAGCGCAGCACTACCTTAGGATAGA 29 15 0 GCAGCACTAC 0.627647 -121 TGCTGCGCTCGCGGGGCGCACGGCTAGTACG 29 30 1 GCGGGGCGCC 0.978028 -106 CGCAACACCCCCGTACCTGTTC 29 124 0 GCAACACCCC 0.804057 -12 TGGCTGCCGCGCAGCACGCTCGTCCCTCTGA 30 12 0 GCAGCACGCC 0.982612 -30 TATAGCACACGCGCGAGGAACGTGAATTGGG 31 22 1 GCGCGAGGAC 0.463333 -36 TAAACGTCTTGCACGACCTGCGGGGGCGCAG 32 34 1 GCACGACCTC 0.825732 -102 AAATATACCTGCGCGGTATACTGCGCCCCCG 32 54 0 GCGCGGTATC 0.57596 -82 ATTGCACAGAGCAGCACCTTCCCATTACAAT 33 61 1 GCAGCACCTC 0.927237 -80 CGGAGCTACAGCACAGCATTCTAGGATTGTT 35 101 0 GCACAGCATC 0.676718 -53 GTCAGCACCCGCGGCGACCTCACAGAGATCG 37 75 0 GCGGCGACCC 0.90041 -60 GGTGACGCGCCGCTCACCTTCCCCCCT 37 118 0 GCGCCGCTCC 0.975224 -17 CACTCCTCATGCACCGTGACCGCCTCCCTGT 38 80 0 GCACCGTGAC 0.736303 -98 GGCAACTAACGCGCCGACCGCTGCTTTTCTC 40 115 0 GCGCCGACCC 0.930539 -119 CGTGGGTAAAGCGTCACCCACCTGTACGCAT 42 40 1 GCGTCACCCC 0.594378 -261 TTTTCTTTCCGCAGGGCACGTAGAAACTCCT 42 166 0 GCAGGGCACT 0.644555 -135 CAACCCCTCGGCGGCACGCACTGCGAAACTT 43 26 0 GCGGCACGCC 0.980627 -122 CCAAGCCCTGGCACAGCCACCTGCGAAGCTA 43 92 0 GCACAGCCAC 0.559451 -56 ATCGCAGGCCGCACCAAGCCCTGGCACAGCC 43 105 0 GCACCAAGCC 0.895716 -43 ACCGGTGAACGCACAGCCTGCTCACTAGCAA 44 58 0 GCACAGCCTC 0.732221 -118 ACGCACTCGGGCGGCACCTCCGCACCACGCC 46 37 0 GCGGCACCTC 0.919903 -138 CGCACCCCTCGCGGGGCTCACTCTAGCATGT 46 151 0 GCGGGGCTCC 0.915762 -24 CCGTGCACCGCACTCCCTTTTGGGT 49 26 0 GCACCGCACC 0.990934 -15 CTGTCAGACGGCACCACTCACATGGAAATAC 50 26 0 GCACCACTCC 0.951925 -33 AAAAGAACACGCACCGCAGACCCTAAACTTT 54 11 0 GCACCGCAGC 0.787092 -86 ACGTGGCGCGCCAGCGTACCCACCATTCTTT 55 80 0 CCAGCGTACC 0.450921 -46 GTACGCTGGCGCGCCACGTGTATTAGCTAGG 55 92 1 GCGCCACGTT 0.566146 -34 CTTCACGTTTGCGCCGTATGCCTACACGCAC 57 37 1 GCGCCGTATC 0.766508 -168 TACACGCACCGCGCGGGGCGCATTCTATACA 57 59 1 GCGCGGGGCC 0.638175 -146 CCTCCCTTTCCCACGGCGCGCTACAGTTCTC 57 109 0 CCACGGCGCC 0.880562 -96 TCGGGTGGGCGCAGGATGCACTGCG 58 5 0 GCAGGATGCC 0.733181 -296 AGAGCGAAAACCGCCGCTCCCATCAGCAGCA 58 65 1 CCGCCGCTCC 0.790459 -236 ACCGCGCCCACCACCGCCTCCCGCGCAAAAT 58 107 1 CCACCGCCTC 0.801029 -194 AGCGTAAGGTGCACAGCACTCCCCAGTCACG 59 87 0 GCACAGCACC 0.880509 -35 ********* * Masking position 2 Map Score: 68.1938 Number of sites scoring better than the average of aligned sites = 3458 Number in coding regions = 3160 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 2 GTTAGGAGCGGAAAGAAGGGTGCTGCACATAA 5 104 1 GAAGAAGGTG 0.901927 -63 GCGTTTGCGGCGCGGAGTGTGTTTGGAGTTA 9 10 1 GCGGGAGGTG 0.97238 -62 GAGTTATTTTGCAAGGTGGGTGCGGTTTTAGG 9 36 1 GCAGGTGGTG 0.909301 -36 TAAGGTGCCAGAGCGGTGACCGAAGGAGACGG 11 32 1 GAGGGTGCCG 0.550986 -24 CAATGGTGGAGAAAGACGGGAGTCCTGCCGTC 12 113 1 GAAGACGGAG 0.799591 -75 GCCGTCTTGGGGATGGTGCGAGCTGTTTCGCA 12 139 1 GGAGGTGGAG 0.897224 -49 GTGCGGGACGGAAAGGAGAGAGGAT 13 86 1 GAAGGAGGAG 0.967003 -15 GCATTCTGGTAGGCGGTGTGTGGTTTTGAGTT 14 25 1 AGGGGTGGTG 0.409615 -75 GTAACAGAAAGAGTGTCGTGTGAATTTCAATA 14 63 1 GAGGTCGGTG 0.545192 -37 GCCTGCCCCAGAAAGAAAGGCGCGTCAC 16 7 0 GAAGAAAGCG 0.715716 -228 TCTTCTTCCAGGGTGGAGAGTGTTGCAATGCG 18 14 1 GGGGGAGGTG 0.976469 -93 TCGCGCTTTTGAGTAGAGCGTGGGCTTCTATT 20 81 1 GAGAGAGGTG 0.81618 -182 CCACTCAAGTGAGGAGAACGCGACCCAACCCG 20 146 0 GAGAGAAGCG 0.548638 -117 CACTTGAGTGGAGGGGACGGCGTCTCCCCTGT 20 167 1 GAGGGACGCG 0.786732 -96 GGTGCAGCTTGAGGGGGGAGTGC 20 250 1 GAGGGGGGTG 0.864926 -13 CATCTTTAAGGGAAAAAGGGAGCATACGATA 21 68 1 GGAAAAGGAG 0.327205 -21 ATACATATCTGAAAGTAGTGCGGCGCCGAGCA 22 122 0 GAAGTAGGCG 0.804479 -51 TCCATGTGGGGAAGGGAGTGCGCTGGTGATCA 23 65 0 GAAGGAGGCG 0.990316 -63 AGTCTTCCGAGGAAGACGAGCGC 23 115 1 GGAGACGGCG 0.919279 -13 GGTGGATATAGGGTGAAGTGAGACAGGCTGCG 24 60 1 GGGGAAGGAG 0.876644 -61 GTGATGCAAAGAGCGGAGTGCGGAGGGGTGC 24 100 1 GAGGGAGGCG 0.992412 -21 AGATATTTTCGCAAGGAGGGAGAATGAGGCGC 25 81 1 GCAGGAGGAG 0.953132 -182 ATGTACACCCGAGGAGAAAGTGCAACGCGCAC 25 198 0 GAGAGAAGTG 0.320426 -65 TGCTCTGCAAGGTGCGTGAGCGAACGGA 27 7 1 GCAGGTGGTG 0.909301 -80 CGAACGGAGTGCAGGACACGCGCTTGACTGCA 27 31 1 GCAGACAGCG 0.506417 -56 GACTGCAGCTGAGAGGAGGGATTGTACGAAGA 27 56 1 GAGGGAGGAT 0.617036 -31 TGCTGCGCTCGCGGGGCGCACGGCTAGTACGT 29 30 1 GCGGGCGACG 0.700685 -106 CGTCGCTTTTGAACGGAGGACGATTATCCGTA 29 59 1 GAAGGAGACG 0.817907 -77 ATCAGAGGGACGAGCGTGCTGCGCGG 30 5 1 GAGGACGGCG 0.946824 -37 TAGCACACGCGCGAGGAACGTGAATTGGGGGA 31 24 1 GCGGGAAGTG 0.788968 -34 AAATTATTCGGGACGGAGGGATTTGAACCCTC 34 90 1 GGAGGAGGAT 0.507517 -141 TTTCCCCGCGCGCAGAGAGCGGACAACAAC 36 10 0 GCGAGAGGCG 0.888179 -21 GGGATGTGTTCAAAGGCGGGCGCGATCTCTGT 37 53 1 CAAGGCGGCG 0.812579 -82 TAGACAGGGGGGAAGGTGAGCGGCGCGTCACC 37 113 1 GGAGGTGGCG 0.968218 -22 CGGTCACGGTGCATGAGGAGTGTAATTTTCAG 38 89 1 GCAGAGGGTG 0.446128 -89 GCGCCCCGGAGGGGGATGTGCGATAATCGGCC 38 139 1 GGGGATGGCG 0.900315 -39 CGGCCCCCGGGGAGGGCGAGCG 38 166 1 GGAGGCGGCG 0.98005 -12 TAGGCCCCACGAAGGGAGGGAGTGACG 39 65 1 GAAGGAGGAG 0.967003 -17 TAACCGCTGAGAATGACAGGCGCACGCACGGC 41 83 1 GAAGACAGCG 0.596535 -140 GCACAGGCTCGGAAGGAGCGAGTTTACTGAAT 42 69 0 GGAGGAGGAG 0.959954 -232 GCCTCATGTCGAACAGAAGGCGCACGGGCCGA 42 270 0 GAAAGAAGCG 0.487301 -31 TGAGCCCCGCGAGGGGTGCGTGC 46 162 1 GAGGGTGGTG 0.948655 -13 TTCGGGTAAGGCACGGAGCATGGA 48 25 1 GCAGGAGATG 0.547325 -14 TGTCTACCCAAAAGGGAGTGCGGTGCACGG 49 21 1 AAAGGAGGCG 0.824407 -20 TATGCTGATGAAAAGGAGAGCGGTCAGTT 51 90 1 AAAGGAGGCG 0.824407 -19 GCTTCCCCCACAGAGACGCGCGGAAGAAAACA 53 19 0 CAGGACGGCG 0.562431 -108 ATCCGCGTTCGGACGGAGAGATAT 53 113 1 GGAGGAGGAT 0.507517 -14 AATGCGCCCCGCGCGGTGCGTGTAGGCATACG 57 51 0 GCGGGTGGTG 0.927648 -154 CTCCATAGGGGAAAGAAGAGCGAAAACCGCCG 58 49 1 GAAGAAGGCG 0.959527 -252 GCGCGGGAGGCGGTGGTGGGCGCGGTTTTGGT 58 101 0 CGGGGTGGCG 0.7377 -200 *** **** *** Masking position 12 Map Score: 55.7047 Number of sites scoring better than the average of aligned sites = 1623 Number in coding regions = 1402 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 ACCCTTCTTTCCGCTCCTAACGTGGCATACCC 5 93 0 CCGCTCCACG 0.91832 -74 AAAACGGCGTCCCTCCCAGACACGGCAGCCT 6 127 0 TCCCTCCAAC 0.69155 -21 CAAACACACTCCGCGCCGCAAACGC 9 4 0 CCGCGCCCAA 0.562711 -68 AACCCCTCCATCAGCCTAAAACCG 9 58 0 CCCCTCCTAG 0.942956 -14 TAACCTAACTCCTCCACCCGCACCAGGTGC 12 168 0 CTCCTCCCCG 0.786535 -20 TCTCTCCTTTCCGTCCCGCACCTATACCAGGC 13 75 0 CCGTCCCCCC 0.785491 -26 CAAAACCACACACCGCCTACCAGAATGCCCTG 14 21 0 CACCGCCACA 0.559889 -79 AAGCACGAAACACCTCCCTAAACAGGCAGCCA 16 43 0 CACCTCCTAA 0.570813 -192 ACCACCCCTCCTCACATCCACAGACG 16 219 0 CCCCTCCCCA 0.982938 -16 AAGGTTCGAGTCCTTCCTGGCCTGAGTGCTTT 17 114 1 TCCTTCCGCC 0.494077 -36 AAGCGCGACGCCCTCCCACACGAAAGGGTGTC 20 57 0 CCCTCCCCCG 0.920696 -206 GAGACGCCGTCCCCTCCACTCAAGTGAGGAGA 20 161 0 CCCCTCCCCA 0.982938 -102 GCACTCCCCCCTCAAGCTGCACCGAA 20 247 0 TCCCCCCCAG 0.679894 -16 CCAGCGCACTCCCTTCCCCACATGGACTGCCG 23 71 1 CCCTTCCCCA 0.945308 -57 GCACCCCTCCGCACTCCGCTCTTTG 24 106 0 CCCCTCCCCT 0.879806 -15 GAAAATATCTTCGCTCCATCACCAACTGTCGG 25 59 0 TCGCTCCTAC 0.610029 -204 CGCCTCATTCTCCCTCCTTGCGAAAATATCTT 25 80 0 TCCCTCCTCG 0.964424 -183 CGCACGTGTACACCGCCTTGCAGAATAAGACA 25 171 0 CACCGCCTCA 0.750775 -92 CTTCGTACAATCCCTCCTCTCAGCTGCAGTCA 27 55 0 TCCCTCCCCA 0.945308 -32 CTCCTGCCTGCAGCTCCAAGCGCCGTGCGGGG 28 29 1 CAGCTCCACG 0.670108 -61 CCGTCCACAGCCCCGCCATCCGAAGGTCCGAA 28 68 1 CCCCGCCTCG 0.973986 -22 CGCAACACCCCCGTACCTGTTCTTACA 29 119 0 CACCCCCTCC 0.839413 -17 GAAAAGTCAATGCCTCCATTCGAGGCCTTTTA 32 87 0 TGCCTCCTCG 0.75416 -49 CATTGACTTTTCGTCCCTTGCCTGGATACTAG 32 107 1 TCGTCCCTCC 0.434178 -29 GAGCGCTTCCTCACCTTTAAAAGTA 33 126 0 CGCTTCCCCC 0.824614 -15 AGGGTTCAAATCCCTCCGTCCCGAATAATTTC 34 89 0 TCCCTCCTCC 0.966688 -142 TTGAACACATCCCCTGCATACCTCTTTTCCCT 37 34 0 CCCCTGCTCC 0.745999 -101 CCCTGTCTTCCCCTTCCTACCACGCAGGATGC 38 54 0 CCCTTCCACA 0.836013 -124 CGTCACTCCCTCCCTTCGTGGGGCCTAG 39 64 0 TCCCTCCTCG 0.964424 -18 CTATCATCCATCCCTCCGAGAGTTTGGTCGAA 40 200 1 TCCCTCCAAG 0.676837 -34 AGCGGTTAGGCCCTTCCTTTCCCTTGGTTTGT 41 59 0 CCCTTCCTCC 0.966688 -164 AATTGATTATTCCTGCCGTGCGTGCGCCTGTC 41 97 0 TCCTGCCTCG 0.771185 -126 TTCAGTAAACTCGCTCCTTCCGAGCCTGTGCT 42 70 1 TCGCTCCTCG 0.888736 -231 ACTCGGGCGGCACCTCCGCACCACGCCGGTGC 46 32 0 CACCTCCCCC 0.961569 -143 TCCATGCTCCGTGCCTTACCCGAAGGACGT 48 19 0 CCGTGCCTCC 0.779888 -20 TCGTTCTTTACGCTTCCCCCACAGAGACGCGC 53 30 0 CGCTTCCCAC 0.462414 -97 TAAGAGTTCTCACTTCCACTCCTAGACTCGTT 53 57 0 CACTTCCCCC 0.882448 -70 TCTCTTTTTACCCTTCCTTCACCGTATGGTGA 55 23 0 CCCTTCCTAC 0.841498 -103 GCGAAAACCGCCGCTCCCATCAGCAGCACACC 58 68 1 CCGCTCCACA 0.833517 -233 CCGCGCCCACCACCGCCTCCCGCGCAAAATCT 58 108 1 CACCGCCCCG 0.906415 -193 ******* * ** Masking position 7 Map Score: 40.8171 Number of sites scoring better than the average of aligned sites = 1243 Number in coding regions = 1014 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 4 TCTCAATTGCGGCGGGCGTAAAAATGTCTGTCT 2 92 0 GGGGGCGTAA 0.923555 -79 TCCGTATGTGGAAGGGCATAGACT 3 51 1 GAGGGCATAC 0.643525 -14 CCGGCGCCATGAGGGGCACAGGAACCCATCTCA 6 46 0 GAGGGCACAA 0.861885 -102 AGCTCAGTTGGCAGAGCGCAACCATGGTAAGGT 16 152 1 GCGAGCGCAC 0.956871 -83 ACAACGACGCGCCGGACGCATGCAAAAAAAACC 20 16 0 GCGGACGCAC 0.894232 -247 CCCTTGTGCTGCGGTGCGCAGCACACTCTGGCG 21 29 0 GCGTGCGCAA 0.771961 -60 AGGGGTATAACAAGGGCGCACGCGTAGCGAACT 22 17 0 CAGGGCGCAC 0.98643 -156 TCAGAACACTCATGGGCGGATGATGGA 23 5 0 CAGGGCGGAA 0.911943 -123 GACAACAGACGAGGAGCGCAAACAGTCTCAGAA 23 32 0 GAGAGCGCAC 0.956708 -96 CCGTGCGCCCCGCGAGCGCAGCACTACCTTAGG 29 20 0 CGGAGCGCAA 0.839734 -116 GCACGACCTGCGGGGGCGCAGTATACCGCGCAG 32 44 1 CGGGGCGCAA 0.971522 -92 TGTGTTCAAAGGCGGGCGCGATCTCTGTGAGGT 37 57 1 GGGGGCGCGC 0.889587 -78 ACATCCCCCTCCGGGGCGCAAGCATCCCTGTGA 38 125 0 CCGGGCGCAC 0.986483 -53 TCGCCCTCCCCGGGGGCCGATTATCGCACATCC 38 152 0 CGGGGCCGAA 0.619889 -26 TGCTGCATGCGCTGAGCGTACACGCGCGAGGTT 39 15 1 GCGAGCGTAC 0.798773 -67 CAAGGGAAAGGAAGGGCCTAACCGCTGAGAATG 41 65 1 GAGGGCCTAC 0.842332 -158 CGCTGAGAATGACAGGCGCACGCACGGCAGGAA 41 87 1 GAAGGCGCAC 0.815193 -136 ACAGAAGGCGCACGGGCCGAGACTACCTGTTCT 42 257 0 CAGGGCCGAC 0.776537 -44 AGAATGTATCGCAGGCCGCACCAAGCCCTGGCA 43 110 0 GCGGCCGCAA 0.814645 -38 ACCTCTCGTACACGGGCGGATGTTGACGTAAAG 44 105 1 CAGGGCGGAT 0.504776 -71 AACTCTCACACAAGGGCCCACAAAAATGAGGAT 46 114 0 CAGGGCCCAA 0.903198 -61 CGCACCCCTCGCGGGGCTCACTCTAGCATGTTT 46 149 0 GCGGGCTCAC 0.851731 -26 TGCCTTACCCGAAGGACGTAACACGTA 48 5 0 GAGGACGTAA 0.482371 -34 TGCTCACACAGACGAGCGCACTATAGACTT 51 8 0 GAGAGCGCAA 0.931823 -101 CACGCACCGCGCGGGGCGCATTCTATACATTTC 57 61 1 GCGGGCGCAC 0.993124 -144 TGTGGTCTCGGGTGGGCGCAGGATGCACTGCG 58 10 0 GGGGGCGCAA 0.985407 -291 TCCGCCTGATGATGGGCGCATAACGC 58 285 1 GAGGGCGCAA 0.988888 -16 ** ******* * Masking position 7 Map Score: 34.1506 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 422 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TCCCGGAAAAGCAGATTGGCACAGCCTGTAAAGA 5 51 0 GCAGTCACAG 0.964834 -116 AAGGTGCAAGGAGTATACCACGGTCAATCGCAA 5 144 0 GGAGTCACGG 0.983357 -23 CCCAGACACGGCAGCCTAACACGGCGATAATCGA 6 110 0 GCAGTCACGG 0.981753 -38 AGAGGGAGCCGGTGCGTCGGACGGTTCGGTCTTT 12 59 1 GGTGTGACGG 0.749077 -129 CACGCAAACAGCAGGATAACACGGAGTACATCTA 13 17 0 GCAGTCACGG 0.981753 -84 ATCCCCACTAGCGGTTTCGCACACT 15 2 0 GCGGTCACAC 0.681919 -29 TCCCCTGTGTGGGGAGTATTACGGTAGAGCGTGT 20 191 1 GGGGTTACGG 0.815909 -72 GTCTTTGCAAGGGGTATAACAAGGGCGCACGCGT 22 25 0 GGGGTCAAGG 0.766208 -148 GGAGGGAGAATGAGGCGCGCACGGATTGTGCAGG 25 95 1 TGAGGCACGG 0.793473 -168 ACACCGCCTTGCAGAATAAGACAGCGTACCGCAA 25 160 0 GCAGTGACAG 0.922889 -103 TTCGGATGGCGGGGCTGTGGACGGGGATGGACCC 28 58 0 GGGGGGACGG 0.967862 -32 GTCTGTGTGCGCGGGGTTGCACTGTTGCTGTAAG 29 91 1 GCGGTCACTG 0.83655 -45 GCACTTTTTGTGAGCATTGCACAGAGCAGCACCT 33 46 1 TGAGTCACAG 0.689715 -95 GTTTTTGCTCGCAGCGTACCACGGGATCATAGCT 35 34 0 GCAGTCACGG 0.981753 -120 TGAGGTCGCCGCGGGTGCTGACAGTATGCTAGAC 37 84 1 GCGGGGACAG 0.933265 -51 GGGAAGACAGGGAGGCGGTCACGGTGCATGAGGA 38 74 1 GGAGGCACGG 0.981159 -104 GTGCCGCCGAGGGGTTGTGCATAGGACGGTTGTC 43 40 1 GGGGGCATAG 0.595625 -108 CACGCAGCGGAGGTAGGCGGG 47 7 1 GCGGGGGCGG 0.723888 -15 CGTGGGAAAGGGAGGTATGCACAGAGGGTCCAGT 57 125 1 GGAGACACAG 0.747814 -80 TTGTGCTAGCGCAGCTTGACACAGAATGATTTTT 58 154 0 GCAGTCACAG 0.964834 -147 CCCGACCACGGGGGACGGTGACAGGTAGTTCTCT 59 47 0 GGGGGGACAG 0.938864 -75 **** * ***** Masking position 4 Map Score: 24.4725 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 218 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GAAAGCAAGAAGGATGGCGAGAACATACAGT 4 39 1 AGGATGGGAG 0.75574 -208 CGTTAGGAGCGGAAAGAAGGGTGCTGCACAT 5 103 1 GGAAAGAGGG 0.954744 -64 TCAATGGTGGAGAAAGACGGGAGTCCTGCCG 12 112 1 AGAAAGAGGG 0.84182 -76 TGCCGTCTTGGGGATGGTGCGAGCTGTTTCG 12 138 1 GGGATGGGCG 0.659222 -50 CACCTGGTGCGGGTGGAGGAGTTAGGTTA 12 169 1 GGGTGGAGAG 0.544547 -19 GGTGCGGGACGGAAAGGAGAGAGGAT 13 85 1 GGAAAGGGAG 0.951045 -16 AGCCTGCCCCAGAAAGAAAGGCGCGTCAC 16 9 0 AGAAAGAAGG 0.517964 -226 GCATCTTTAAGGGAAAAAGGGAGCATACGAT 21 67 1 GGGAAAAGGG 0.738919 -22 GTCCATGTGGGGAAGGGAGTGCGCTGGTGAT 23 67 0 GGAAGGGGTG 0.640721 -61 CAGTCTTCCGAGGAAGACGAGCGC 23 114 1 AGGAAGAGAG 0.83053 -14 TTCGCAAGGAGGGAGAATGAGGCGCGCACGG 25 88 1 GGGAGAAGAG 0.424014 -175 TTCGGACCTTCGGATGGCGGGGCTGTGGACG 28 69 0 CGGATGGGGG 0.576197 -21 CGTGAATTGGGGGATGAGGAGTTTAT 31 42 1 GGGATGAGAG 0.876264 -16 CGGCACCACAGGATAGAGGGGCATTGTAATG 33 83 0 GGATAGAGGG 0.726336 -58 GAAATTATTCGGGACGGAGGGATTTGAACCC 34 89 1 GGGACGGGGG 0.876509 -142 GCGGGCTATAGGGAAAAGAGGTATGCAGGGG 37 25 1 GGGAAAAAGG 0.363643 -110 CTAGACAGGGGGGAAGGTGAGCGGCGCGTCA 37 112 1 GGGAAGGGAG 0.971137 -23 TGGTAGGAAGGGGAAGACAGGGAGGCGGTCA 38 64 1 GGGAAGAAGG 0.880628 -114 TCGGCCCCCGGGGAGGGCGAGCG 38 165 1 GGGAGGGGAG 0.942724 -13 GCCCCACGAAGGGAGGGAGTGACG 39 68 1 GGGAGGGGTG 0.755419 -14 ACAAACCAAGGGAAAGGAAGGGCCTAACCGC 41 59 1 GGAAAGGAGG 0.880628 -164 CTAACCGCTGAGAATGACAGGCGCACGCACG 41 82 1 AGAATGAAGG 0.281454 -141 CGTGCCCTGCGGAAAGAAAAGAAAAAAGCAA 42 177 1 GGAAAGAAAG 0.693703 -124 CACGCAGCGGAGGTAGGCGGG 47 11 1 AGGTAGGGGG 0.667586 -11 GTATGCTGATGAAAAGGAGAGCGGTCAGTT 51 89 1 GAAAAGGGAG 0.356216 -20 CTCTTGCTGAAGAAAGGTGAGGATCAGGGGA 54 63 1 AGAAAGGGAG 0.83053 -34 GCATAAAGAAAGAATGGTGGGTACGCTGGCG 55 72 1 AGAATGGGGG 0.770637 -54 GCGCGCCGTGGGAAAGGGAGGTATGCACAGA 57 119 1 GGAAAGGAGG 0.880628 -86 ACTCCATAGGGGAAAGAAGAGCGAAAACCGC 58 48 1 GGAAAGAGAG 0.918147 -253 ******* *** Masking position 11 Map Score: 27.2834 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 483 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 TTTCCTACGTCTCTGTTAGGTTTCCCCAAA 2 17 1 CTCTGTTAGG 0.217154 -154 AAGTATACTACCCTGTGCCCGCACTCAGGA 2 139 1 CCCTGTGCCC 0.901848 -32 AAAAGAATATCCGTATGTGGAAGGGCATAG 3 42 1 CCGTATGTGG 0.523811 -23 AGGTTCCGTACCGTGCGGGCACGGAACACA 4 195 1 CCGTGCGGGC 0.884419 -52 TCGATTATCGCCGTGTTAGGCTGCCGTGTC 6 110 1 CCGTGTTAGG 0.641146 -38 TGTTAGGCTGCCGTGTCTGGGAGGGACGCC 6 123 1 CCGTGTCTGG 0.535017 -25 CGCACCGGCTCCCTCTGACCGATCGTACTC 12 45 0 CCCTCTGACC 0.802625 -143 AAAGACCGAACCGTCCGACGCACCGGCTCC 12 63 0 CCGTCCGACG 0.775275 -125 TTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 14 28 1 CGGTGTGTGG 0.58505 -72 TCGGAAGCTTCCGTCTGTGGATGTGAGGAG 16 208 1 CCGTCTGTGG 0.943505 -27 ACGGCGTCTCCCCTGTGTGGGGAGTATTAC 20 183 1 CCCTGTGTGG 0.940736 -80 TCAGGTCGGTCCCGCTGCCCAGGCTATGGG 22 78 1 CCCGCTGCCC 0.644095 -95 GGGAGCCAGACTGTGCGTGCTCGGCGCCGC 22 105 1 CTGTGCGTGC 0.879952 -68 GGTGGTGGTGCCGGCTGTGGATCTGGTGGA 24 36 1 CCGGCTGTGG 0.838144 -85 GCCTCATTCTCCCTCCTTGCGAAAATATCT 25 81 0 CCCTCCTTGC 0.515064 -182 CCTGCACAATCCGTGCGCGCCTCATTCTCC 25 99 0 CCGTGCGCGC 0.966227 -164 TGTGCCCTCTCCGTGTTAGCTTTCCTCTAA 25 242 0 CCGTGTTAGC 0.722174 -21 GCTCCAAGCGCCGTGCGGGGTCCATCCCCG 28 41 1 CCGTGCGGGG 0.839459 -49 GACGTACTAGCCGTGCGCCCCGCGAGCGCA 29 33 0 CCGTGCGCCC 0.918968 -103 TATCCGTAGTCTGTGTGCGCGGGGTTGCAC 29 83 1 CTGTGTGCGC 0.908046 -53 CTTTTCCTCTGGCTGCCGCGCAGCACGC 30 24 0 CTGGCTGCCG 0.346315 -18 GGGTTCAAATCCCTCCGTCCCGAATAATTT 34 90 0 CCCTCCGTCC 0.812468 -141 CGGTCCCAAACCGGGTGCCCTAGCCCCTAG 34 129 1 CCGGGTGCCC 0.825134 -102 GTCGCTCTATCCGGGTGAGCTATGATCCCG 35 17 1 CCGGGTGAGC 0.892426 -137 TTGTTGTCCGCTCTCTGCGCGCGGGGAAA 36 12 1 CTCTCTGCGC 0.791115 -19 CGGGCGCGATCTCTGTGAGGTCGCCGCGGG 37 69 1 CTCTGTGAGG 0.740608 -66 CATAAAAAACCTGTCTGTGCAATCAACCGC 38 16 1 CTGTCTGTGC 0.862034 -162 GCGCAAGCATCCCTGTGAGGCCCTGAAAAT 38 113 0 CCCTGTGAGG 0.917377 -65 ATTATTCCTGCCGTGCGTGCGCCTGTCATT 41 94 0 CCGTGCGTGC 0.966107 -129 GTGCGCTCGTCTGTGTGAGCAGCAAGAGTA 51 20 1 CTGTGTGAGC 0.873098 -89 ATATCTCTCCGTCCGAACGCGGAT 53 113 0 CTCTCCGTCC 0.526981 -14 CGCCACTGGACCCTCTGTGCATACCTCCCT 57 133 0 CCCTCTGTGC 0.936184 -72 ********** Masking position 1 Map Score: 29.8774 Number of sites scoring better than the average of aligned sites = 1364 Number in coding regions = 1244 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 8 CCTGTTTTGTGGGTAGGTTTGGGGAAACCT 2 34 0 GGGTAGGTTT 0.491696 -137 CTGCCGTCTTGGGGATGGTGCGAGCTGTTT 12 137 1 GGGGATGGTG 0.918931 -51 AACCGCTAGTGGGGATGGCCT 15 20 1 GGGGATGGCC 0.874185 -11 CTTTCTTTCTGGGGCAGGCTGGTTGGCTGC 16 20 1 GGGGCAGGCT 0.71133 -215 CTGCCTGTTTAGGGAGGTGTTTCGTGCTTG 16 46 1 AGGGAGGTGT 0.510804 -189 CTGTGGATGTGAGGAGGGGTGGT 16 222 1 GAGGAGGGGT 0.729422 -13 GGTGTTTTCCGGGGATTTGTGGGTCAGTAG 17 45 1 GGGGATTTGT 0.614598 -105 CTTAGTTACGGGGTATGTGTTAGGCGGTCA 19 24 1 GGGTATGTGT 0.614598 -85 CTTGAGTGGAGGGGACGGCGTCTCCCCTGT 20 169 1 GGGGACGGCG 0.857358 -94 TCCCCTGTGTGGGGAGTATTACGGTAGAGC 20 191 1 GGGGAGTATT 0.309305 -72 CAGTCCATGTGGGGAAGGGAGTGCGCTGGT 23 70 0 GGGGAAGGGA 0.745285 -58 AGAGCGGAGTGCGGAGGGGTGC 24 109 1 GCGGAGGGGT 0.799819 -12 GGCTGTGGACGGGGATGGACCCCGCACGGC 28 50 0 GGGGATGGAC 0.613784 -40 TTCGGATGGCGGGGCTGTGGACGGGGATGG 28 62 0 GGGGCTGTGG 0.645698 -28 ACGTGAATTGGGGGATGAGGAGTTTAT 31 41 1 GGGGATGAGG 0.861348 -17 GAGGTATGCAGGGGATGTGTTCAAAGGCGG 37 42 1 GGGGATGTGT 0.951925 -93 GCTAGACAGGGGGGAAGGTGAGCGGCGCGT 37 111 1 GGGGAAGGTG 0.898991 -24 CGCCCCGGAGGGGGATGTGCGATAATCGGC 38 140 1 GGGGATGTGC 0.856191 -38 ATCGGCCCCCGGGGAGGGCGAGCG 38 164 1 GGGGAGGGCG 0.965478 -14 TATACGTGTCGGGGAGGTTTAC 40 3 0 GGGGAGGTTT 0.923142 -231 GGCTTTGCATGGGGAAGTTTCGCAGTGCGT 43 12 1 GGGGAAGTTT 0.84079 -136 CGTCTGACAGGGGGAAGGATCA 50 47 1 GGGGAAGGAT 0.805827 -12 CGTCTCTGTGGGGGAAGCGTAAAGAACGAG 53 33 1 GGGGAAGCGT 0.764281 -94 AATAACATTTGGGTAAGAGTTCTCACTTCC 53 72 0 GGGTAAGAGT 0.366951 -55 GTGAGGATCAGGGGAGGGGTTAGGAATC 54 79 1 GGGGAGGGGT 0.988756 -18 GAGAAAGTGTGGGGAGGACTTGCATAAAGA 55 51 1 GGGGAGGACT 0.884823 -75 CCCGACCACGGGGGACGGTGACAGGTAGTT 59 51 0 GGGGACGGTG 0.813099 -71 CTTCGTGACTGGGGAGTGCTGTGCACCTTA 59 84 1 GGGGAGTGCT 0.768706 -38 ********** Masking position 3 Map Score: 20.5187 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 545 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 GAATTACCAAACAAAAACCGCACACAAGCTTGTGA 1 122 0 ACAAACCCAC 0.821493 -121 AGTATACTACCCTGTGCCCGCACTCAGGAGGAGGT 2 140 1 CCTGCCCCAC 0.959628 -31 ACGGTACGGAACCTAGACCACACCGTATCGGAGAC 4 174 0 ACAGACCCAG 0.653938 -73 CCTCCATCAGCCTAAAACCGCACCCACCTTGCAAA 9 43 0 CCAAACCCAC 0.965759 -29 TTCCTCAAACCCAAAGACCGAACCGTCCGACGCAC 12 70 0 CCAGACCAAG 0.715078 -118 ACCGGCAGAACTCAAAACCACACACCGCCTACCAG 14 30 0 CTAAACCCAC 0.541303 -70 CGGGATTGAACCGCTGACCTCAACCTTACCATGGT 16 172 0 CCTGACCCAC 0.971165 -63 GGAGAACGCGACCCAACCCGCATGCCAAAATGCCG 20 131 0 ACAACCCCAC 0.764592 -132 ACACGGTGCTCCCTATACCACACGCTCTACCGTAA 20 209 0 CCATACCCAC 0.854133 -54 ACTTCTCTCACCGTAAACCCTATACATATCTGAAA 22 140 0 CCAAACCTAC 0.859395 -33 ACAGTGCAACCCCGCGCACACAGACTACGGATAAT 29 81 0 CCCGCACCAC 0.745842 -55 AAAAAGTGTACCAGAGCCACTACACTG 33 3 0 CCAGCCATAC 0.381015 -138 AAACCGGGTGCCCTAGCCCCTAGGCCACGTCCCGT 34 136 1 CCAGCCCTAC 0.936355 -95 ATCGCGCCCGCCTTTGAACACATCCCCTGCATACC 37 44 0 CCTGAACCAC 0.723867 -91 AGCCATGCCTCCTTCGACCAAACTCTCGGAGGGAT 40 209 0 CCCGACCAAC 0.920487 -25 TTGGTCTGCACCTTCGCCCAAAATCGCCTAAGGAG 45 19 1 CCCGCCCAAC 0.890952 -31 CATCAGCATACCTATGACCACATTCACCTTTTTAA 51 65 0 CCTGACCCAC 0.971165 -44 AGAACACGCACCGCAGACCCTAAACTTT 54 4 0 CCAGACCTAC 0.954224 -93 CCTGCGCCCACCCGAGACCACAACCGTACTCCATA 58 21 1 CCAGACCCAC 0.989711 -280 CATCAGCAGCACACCAACCAAAACCGCGCCCACCA 58 85 1 ACCAACCAAC 0.35643 -216 ** ***** ** * Masking position 12 Map Score: 18.9275 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 157 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 10 AGACACAGAGCCCTGCAGACAGACATTTTTA 2 76 1 CCCTGCAGCA 0.813384 -95 TCTTTCTGTTACCGGCAGAACTCAAAACCAC 14 44 0 ACCGGCAGAC 0.662677 -56 ACCTCCCTAAACAGGCAGCCAACCAGCCTGC 16 33 0 ACAGGCAGCA 0.938204 -202 CCAACGCGTAAGCGGCAGGCAATCATGCGCA 18 42 0 AGCGGCAGCA 0.990301 -65 CTATAAACGGACAGGAAGACAGCACCCCAGA 19 58 0 ACAGGAAGCA 0.619723 -51 AAAGGGTGTCAGAGGCACACAACGACGCGCC 20 36 0 AGAGGCACCA 0.687542 -227 GTGGCAAATAAGCGGCAGTCCATGTGGGGAA 23 84 0 AGCGGCAGCC 0.980969 -44 CCCTCCTCTCAGCTGCAGTCAAGCGCGTGTC 27 45 0 AGCTGCAGCA 0.960167 -42 CGGCGCTTGGAGCTGCAGGCAGGAGACAGAC 28 23 0 AGCTGCAGCA 0.960167 -67 GAGCGTGCTGCGCGGCAGCCAGAGGAAAAG 30 22 1 CGCGGCAGCA 0.964803 -20 AACCGCGTGAAGCGGCATCCTGCGTGGTAGG 38 40 1 AGCGGCATCT 0.726561 -138 CGTGGTAGGAAGGGGAAGACAGGGAGGCGGT 38 62 1 AGGGGAAGCA 0.79186 -116 TATATTTTTTACCGGCATACATAGGGCACCT 41 158 1 ACCGGCATCA 0.88874 -65 TTTTGGGCGAAGGTGCAGACCAAAAGCCCTT 45 11 0 AGGTGCAGCC 0.808572 -39 CAGACGGGCAGTCTGTAACGTGCA 46 4 1 ACGGGCAGCT 0.842492 -171 ******** ** Masking position 7 Map Score: 10.4374 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 163 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 CTTTTTTCCGCCCTATTTTGCTACGCTTGTGCGTCT 3 8 0 CCTTTACGCG 0.948724 -57 ACATACAGTTGCCTTGTATATTCCGCGAGTTACGCGCAT 4 61 1 GCTTTCCGCG 0.927853 -186 GTTATGTGCAGCACCCTTCTTTCCGCTCCTAACGTGGCA 5 98 0 GATCTCCGCC 0.750037 -69 GCAAAATAACTCCAAACACACTCCGCGCCGCAAACGC 9 9 0 TCCCTCCGCC 0.590085 -63 TCGGTCACCGCTCTGGCACCTTACGCAGCTACCGCAGCT 11 16 0 CCCCTACGCC 0.969171 -40 TCGTACTCCTCACCAGCGTTATACGCACCCTCTTTGTCA 12 14 0 CCCTTACGCC 0.939817 -174 ATCCTCTCTCCTTTCCGTCCCGCACCTATACCAGGC 13 75 0 CCTCCCCGCC 0.860487 -26 GCTGTCGTCATATCTGTTACGCACGGGGTTTTCTG 17 7 1 GCTTTACGCG 0.936901 -143 CCAGGGTGGAGAGTGTTGCAATGCGCATGATTGCCTGCC 18 21 1 GGTCTGCGCG 0.481583 -86 ATACCACACGCTCTACCGTAATACTCCCCACACAGGGGA 20 191 0 CCCTTACTCC 0.323753 -72 ACGTCCAGTTCGCTACGCGTGCGCCCTTGTT 22 3 1 GCTCTACGCG 0.96763 -170 GCACCCCTCCGCACTCCGCTCTTTGCATCACC 24 99 0 CCCCTCCGCT 0.62375 -22 ATCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAGGA 30 9 1 GCCTTGCGCC 0.720913 -33 ACGTTCCTCGCGCGTGTGCTATACCCTACACCAC 31 6 0 CCTCTACCCC 0.609715 -52 TAGCCCCTAGGCCACGTCCCGTACGCTTGACACTGTGTG 34 149 1 GCTCTACGCG 0.967274 -82 TCCCTGTCTTCCCCTTCCTACCACGCAGGATGCCGCTTC 38 48 0 CCCTCACGCG 0.775524 -130 AAAAAGCGTTGACTAATCAGTTACGCGTGCATACACTCT 41 190 1 GCTATACGCG 0.612418 -33 TCGCTCCTTCCGAGCCTGTGCTACGCACGAGTATACCTT 42 80 1 CATTTACGCG 0.697566 -221 GACCATTTGGGTAGTTTCCGCTACGCTCCTGCCAGCTTG 42 119 1 GATCTACGCC 0.775986 -182 CACTTTGATTGTCTTCTTTATTACGAGTCTTTTCTCCTT 44 135 0 GCTTTACGAC 0.289549 -41 ACTCGGGCGGCACCTCCGCACCACGCCGGTGCACGTTAC 46 25 0 CCCCCACGCG 0.874302 -150 GAGGATACGCCCGCTACACACTACGCGGGCCTCGGTTAC 46 81 0 CGCCTACGCG 0.83585 -94 CACGGGGGTGTTTTCTTCCGCGCGTCTCTGTGGG 53 6 1 GGTTTCCGCG 0.659428 -121 TCCACTCCTAGACTCGTTCTTTACGCTTCCCCCACAGAG 53 36 0 GCTCTACGCC 0.965198 -91 TCCCCTGATCCTCACCTTTCTTCAGCAAGAGGAAACATG 54 55 0 CCTTTCAGCG 0.46421 -42 CGCGTCCTGCTCCTATTTCATACGCCTCTGATGT 56 7 0 CCTTTACGCC 0.94505 -28 GAGCGAAAACCGCCGCTCCCATCAGCAGCACACCAACCA 58 66 1 CCTCTCAGCC 0.618525 -235 CTAACTTGAACAAACGCTCAGTCCGCCTGATGATGGGCG 58 264 1 CACCTCCGCG 0.785061 -37 * * * * ***** * Masking position 16 Map Score: 23.2763 Number of sites scoring better than the average of aligned sites = 879 Number in coding regions = 813 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 12 GCATGACAAAGAGGGTGCGTATAAC 12 5 1 GACAAAGAGG 0.841039 -183 CTTCCTCAAACCCAAAGACCGAACCGTCCGA 12 75 0 CCCAAAGACG 0.613916 -113 TTCAATGGTGGAGAAAGACGGGAGTCCTGCC 12 111 1 GAGAAAGACG 0.965961 -77 CTGCCGGTAACAGAAAGAGTGTCGTGTGAAT 14 57 1 CAGAAAGAGG 0.792489 -43 CAGCCTGCCCCAGAAAGAAAGGCGCGTCAC 16 10 0 CAGAAAGAAG 0.850199 -225 CTACAGAAGCAACACAGACAGGACTCCCCGA 16 123 0 AACACAGACG 0.770148 -112 TATAAACGGACAGGAAGACAGCACCCCAGAA 19 57 0 CAGGAAGACG 0.684985 -52 CAGGCTATGGGAGCCAGACTGTGCGTGCTCG 22 97 1 GAGCCAGACG 0.790397 -76 AGGGTGAAGTGAGACAGGCTGCGAATGGATG 24 69 1 GAGACAGGCG 0.778989 -52 CTGCAGGCAGGAGACAGACAGCGGTGGGGCA 28 11 0 GAGACAGACG 0.965276 -79 CCTAACCGCTGAGAATGACAGGCGCACGCAC 41 81 1 GAGAATGACG 0.708299 -142 TGCGAAGCTAGACAAAGAAAGCAGAACGGAC 43 71 0 GACAAAGAAG 0.887167 -77 ACCTTTTTAAGACACAGAAAGGCAATACTCT 51 44 0 GACACAGAAG 0.885085 -65 GACTTGCATAAAGAAAGAATGGTGGGTACGC 55 67 1 AAGAAAGAAG 0.607574 -59 AGCGCAGCTTGACACAGAATGATTTTTATGA 58 150 0 GACACAGAAG 0.885085 -151 GCTGCGCTAGCACAAAGACAGTTAGAATGCG 58 173 1 CACAAAGACG 0.926137 -128 ********* * Masking position 7 Map Score: 8.42648 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 80 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 GATACGATTTGCTCGCAGAATCG 4 2 0 GCCGCAGAAC 0.932859 -245 TACATTAGAGGCCTGTAAAGAACTACGTTCTT 5 23 1 GCTGTAAAGA 0.631434 -144 GATTGGCACAGCCTGTAAAGAACGTAGTTCTT 5 40 0 GCTGTAAAGA 0.631434 -127 ACCGCACCCACCTTGCAAAATAACTCCAAACA 9 30 0 CCTGCAAAAA 0.822014 -42 CGCGCCGGACGCATGCAAAAAAAACCAGACA 20 10 0 GCTGCAAAAA 0.893036 -253 TTGTTATACCCCTTGCAAAGACTTGGTGAGTG 22 37 1 CCTGCAAAGC 0.914231 -136 GCGGCGCCGAGCACGCACAGTCTGGCTCCCAT 22 103 0 GCCGCACAGC 0.820546 -70 GTGTACACCGCCTTGCAGAATAAGACAGCGTA 25 166 0 CCTGCAGAAA 0.791373 -97 CGCTCACGCACCTTGCAGAGCA 27 1 0 CCTGCAGAGA 0.844827 -86 GTGGTACGCTGCGAGCAAAAACCCTGCAAGGG 35 46 1 GCAGCAAAAC 0.653867 -108 TTTCCCCGCGCGCAGAGAGCGGACAACAA 36 12 0 GCCGCAGAGG 0.74343 -19 AATGAGGACTGCACGCAAAACCTGCCAGGAAA 40 76 1 GCCGCAAAAC 0.944186 -158 TTTCCGCAGGGCACGTAGAAACTCCTCAGGAA 42 160 0 GCCGTAGAAC 0.665148 -141 CGAAACTTCCCCATGCAAAGCCC 43 2 0 CCTGCAAAGC 0.914231 -146 CAATCAAAGTGCGCGCAAAGAAA 44 163 1 GCCGCAAAGA 0.937886 -13 GAGCGTGCTTGCATAACACTGTCCACTG 52 7 1 GCTGCATAAA 0.514759 -36 CCACCGCCTCCCGCGCAAAATCTCCCGATCGT 58 117 1 CCCGCAAAAC 0.903454 -184 ** ******* * Masking position 7 Map Score: 11.3439 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 317 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 GATAAGTGGTGGATAAAAGAATATAAATTA 1 35 1 GGATAAAAGA 0.900218 -208 AAAATAGGGCGGAAAAAAGAATATCCGTAT 3 28 1 GGAAAAAAGA 0.957717 -37 CGTTAGGAGCGGAAAGAAGGGTGCTGCACA 5 103 1 GGAAAGAAGG 0.936176 -64 GGTGCGGGACGGAAAGGAGAGAGGAT 13 85 1 GGAAAGGAGA 0.900924 -16 GCATCTTTAAGGGAAAAAGGGAGCATACGA 21 67 1 GGGAAAAAGG 0.829346 -22 CACTACCTTAGGATAGAAGAA 29 2 0 GGATAGAAGA 0.91267 -134 CGGGCTATAGGGAAAAGAGGTATGCAGGGG 37 26 1 GGAAAAGAGG 0.814417 -109 CGTGCCCTGCGGAAAGAAAAGAAAAAAGCA 42 177 1 GGAAAGAAAA 0.653091 -124 TTGACGTAAAGGAGAAAAGACTCGTAATAA 44 127 1 GGAGAAAAGA 0.841068 -49 GTGAAGGAAGGGTAAAAAGAGAAAGTGTGG 55 33 1 GGTAAAAAGA 0.761168 -93 ACTCCATAGGGGAAAGAAGAGCGAAAACCG 58 48 1 GGAAAGAAGA 0.963286 -253 TATGAAAAAAGGGTAAAAGATGCCTCGCCA 59 14 1 GGGTAAAAGA 0.775913 -108 ********** Masking position 5 Map Score: 6.83539 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 75 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 AAACAGGGACCACCACACAAGACACAGAGCCC 2 57 1 CACCAAAAGA 0.6807 -114 GCGCAGCACGCACCACAAATGCGGCGCCTACA 7 13 0 CACCAAATGC 0.51674 -42 ACCCCTCCATCAGCCTAAAACCGCACCCACCT 9 49 0 CAGCCAAACC 0.834863 -23 CCCCGGAAAACACCAGAAAACCCCGTGCGTAA 17 27 0 CACCAAAACC 0.845 -123 CAACACTCTCCACCCTGGAAGAAGAAAA 18 7 0 CACCCGAAGA 0.749351 -100 AACAACAAAACACCCGAAACCAACGCGTAAGC 18 60 0 CACCCAACCA 0.962446 -47 AGGAAGACAGCACCCCAGAAGCCTGACCGCCT 19 45 0 CACCCAAAGC 0.958529 -64 CGACACGGTGCTCCCTATACCACACGCTCTAC 20 214 0 CTCCCAACCA 0.673037 -49 GAACTTCTCTCACCGTAAACCCTATACATATC 22 145 0 CACCGAACCC 0.892563 -28 ACCAGATCCACAGCCGGCACCACCACCATGTT 24 31 0 CAGCCGACCA 0.480014 -90 TGTCTCACTTCACCCTATATCCACCAGATCCA 24 53 0 CACCCAATCC 0.901047 -68 GCAGCATGTACACCCGAGGAGAAAGTGCAACG 25 203 0 CACCCAGAGA 0.603945 -60 GCGTGTGCTATACCCTACACCAC 31 2 0 TACCCAACCA 0.559662 -56 AAAAACGGTGCACCCGATAAGCAGTCGGAGCT 35 125 0 CACCCAAAGC 0.958529 -29 CAAAAGATAGCAACCCACAAGCGCAAGAAGAA 42 205 1 CAACCAAAGC 0.566689 -96 AAAGAACACGCACCGCAGACCCTAAACTTT 54 9 0 CACCGAACCC 0.892563 -88 ATCCTGCGCCCACCCGAGACCACAACCGTACT 58 19 1 CACCCAACCA 0.962446 -282 ***** * **** Masking position 4 Map Score: 9.02312 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 181 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419