AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mtub_reg_100.orf -o02010_mtub_100.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 Rv0818 129 hypothetical protein Rv0818 #2 phoT 42 phoT #3 phoS2 271 phoS2 #4 pstS_pstB 215 pstS: pstS, pstB: pstB #5 pstC 59 pstC #6 Rv1234 149 hypothetical protein Rv1234 #7 oppB 206 oppB #8 modA 161 modA #9 Rv1964 300 hypothetical protein Rv1964 #10 Rv2041c 37 hypothetical protein Rv2041c #11 pncA 40 pncA #12 Rv2044c 85 hypothetical protein Rv2044c #13 lipT 48 lipT #14 Rv2059 112 hypothetical protein Rv2059 #15 uspA 33 uspA #16 subI 124 subI #17 ugpA 86 ugpA #18 infB 85 infB #19 Rv2840c 126 hypothetical protein Rv2840c #20 dppC 55 dppC #21 dppA 300 dppA #22 proX 164 proX Motif number 1 GGACGGGCTCGAGCGCTGGGCGACAAT 1 8 0 GAGCGCTGGG 0.804768 -122 AGGCGCTCCGGGACGGGCTCGAGCGCTGGG 1 18 0 GGACGGGCTC 0.616237 -112 TAACGATAACGTGCCGCCTGACGAGGCGCT 1 41 0 GTGCCGCCTG 0.684919 -89 GCCCCTCCAGCGTCGTGGGAAAGGCGT 1 113 0 CAGCGTCGTG 0.47729 -17 GTTACCGTTTCGGCCGACAGCCGGAAAAGA 3 18 0 CGGCCGACAG 0.422596 -254 AAGGATGTCCGTATGCCGTGCATACACAGC 3 98 0 GTATGCCGTG 0.595373 -174 GTGGCTGGTTCGACCGCGGGTCTCAGGGGA 3 127 0 CGACCGCGGG 0.978394 -145 GCGGTCGAACCAGCCACGTGTCCATCATCA 3 140 1 CAGCCACGTG 0.776553 -132 CATCAGGGGTCAACCCCGGCCAAGGGCGAC 3 165 1 CAACCCCGGC 0.817327 -107 CCCCGGCCAAGGGCGACGGCACGCCAAGTT 3 178 1 GGGCGACGGC 0.932883 -94 TCCTAACGGCCGACCAGCTGTTTTGCTCGC 3 246 0 CGACCAGCTG 0.63786 -26 CGGCGCAGGGTACTACATGC 4 1 1 CGGCGCAGGG 0.971957 -215 TACTGAGGGTCGACGGCGCGCTTTGTCCAA 4 46 0 CGACGGCGCG 0.955718 -170 CCCTCAGTATCAGCGGCCCCTCCTGAACGC 4 67 1 CAGCGGCCCC 0.585748 -149 CGATGCACAACGGTGACGGCTCGAATACCG 4 123 1 CGGTGACGGC 0.906399 -93 GCTCGAATACCGACCCCGGGTCGGTGGCTC 4 141 1 CGACCCCGGG 0.985656 -75 GTCGGTGGCTCGGCGACCACCGGTGGCGAG 4 160 1 CGGCGACCAC 0.680615 -56 CGGCGACCACCGGTGGCGAGTGGATCCGCC 4 170 1 CGGTGGCGAG 0.912239 -46 TCCGCCACCACGACCCCCTCGAGAGGAGTT 4 194 1 CGACCCCCTC 0.880818 -22 ACGGAGGTTGCTGTCGCGTGGTGGTCAACG 5 14 0 CTGTCGCGTG 0.789142 -46 CAAAGCAGCCCGATGGCCCGACGGAGGTTG 5 34 0 CGATGGCCCG 0.738204 -26 CGGCGAGCATCGTTGCCGGGATAGGTTGAT 6 15 0 CGTTGCCGGG 0.616315 -135 GAGGCCCACCGAACGGCGAGCATCGTTGCC 6 28 0 GAACGGCGAG 0.437838 -122 AACCCGCGAGCGACCGAGGCCCACCGAACG 6 43 0 CGACCGAGGC 0.72147 -107 TGAGTGGATAGTGTGCCGGGAGTAGCTGGA 6 72 1 GTGTGCCGGG 0.873859 -78 CTACTCAGATCGACGCCGCGGTGAATTTTA 7 45 1 CGACGCCGCG 0.970369 -162 GGAACCATCCGGATCACGGGTGACCCCATC 7 118 1 GGATCACGGG 0.703204 -89 CCCCATCAACCGGCGCGCTGGCGGCACGCC 7 141 1 CGGCGCGCTG 0.573106 -66 GCGAGCCCGGCGATGGCGTGCCGCCAGCGC 7 155 0 CGATGGCGTG 0.926763 -52 GCCGGGCTCGCTACCCTGTCCCAATGCGAC 7 174 1 CTACCCTGTC 0.404978 -33 TGTCCCAATGCGACGCGGTGGTTGGGC 7 190 1 CGACGCGGTG 0.965823 -17 TTCCAGGCAACGGTCCAGGGTCTGGGTTCA 8 31 0 CGGTCCAGGG 0.880844 -131 CGCGTCGTGGCGGTGCGGAGTTTCCCCGAA 8 110 0 CGGTGCGGAG 0.879539 -52 CGCACCGCCACGACGCGCAGACGATCTTGG 8 123 1 CGACGCGCAG 0.759164 -39 ACGGCTTGACCGGTGATGCGCCTGTCGGCC 9 37 1 CGGTGATGCG 0.59797 -264 GCTGCCTTGGCGGCCGACAGGCGCATCACC 9 48 0 CGGCCGACAG 0.422596 -253 CTATAGCGCGGGGCGATGTGCTCTGCTGCC 9 72 0 GGGCGATGTG 0.795436 -229 CCGGACAGGTCGACGATCGGTGACATTGGT 9 219 0 CGACGATCGG 0.688194 -82 GATCGTCGACCTGTCCGGGGGGCCAGCGTG 9 231 1 CTGTCCGGGG 0.824673 -70 CTGGGCCGTTGGGTGAGGTGGCGCACGCTG 9 254 0 GGGTGAGGTG 0.725089 -47 CAGCTGGATTCGATGCTGGGCCGTTGGGTG 9 269 0 CGATGCTGGG 0.88302 -32 AATCCAGCTGGTGCGCCGCGCC 9 289 1 GTGCGCCGCG 0.871327 -12 TCCCGATTTTGGGTCCTGTGGTACAACGAC 10 13 0 GGGTCCTGTG 0.781019 -25 GCAAACTGCCCGGGCAGTCGCCCGA 11 6 1 CTGCCCGGGC 0.870966 -35 TTCCAGGTCGCGGCGCTCCGGCCACTGACA 12 19 0 CGGCGCTCCG 0.837657 -67 GCAGGAATGGGGGCGGGGCGGCTAGCCTGT 13 15 0 GGGCGGGGCG 0.908062 -34 CTGGTCGTTACGGTGGAGTC 15 1 0 CGGTGGAGTC 0.66133 -33 GACCGCGCACGGGTGGGGAGTCAGCGACAA 16 13 0 GGGTGGGGAG 0.694604 -112 CTCCCCACCCGTGCGCGGTCTGATGTGGAG 16 23 1 GTGCGCGGTC 0.729469 -102 ATTGGTTCATCGACCGTGGCGGCAAACTCG 17 38 1 CGACCGTGGC 0.825064 -49 CGGCGCAGTGTAGCTCCGTA 17 77 0 CGGCGCAGTG 0.949163 -10 CGACAGTCGTGGGCCGCGCCTCGGGTTTAG 18 46 0 GGGCCGCGCC 0.891483 -40 CGGCCCACGACTGTCGCCTCATGGACAGGA 18 60 1 CTGTCGCCTC 0.412377 -26 GCCCGGCTATCTGCCGTGGGATAACGCACG 19 14 0 CTGCCGTGGG 0.820477 -113 GGCTCGCGCTGGATCACGGCTAAGTGTAGC 19 64 0 GGATCACGGC 0.522611 -63 CGCGAGCCTTCGGCCTCGGCGCATCGACGC 19 86 1 CGGCCTCGGC 0.775216 -41 CTCGGCGCATCGACGCCCGGATAATCCCCG 19 100 1 CGACGCCCGG 0.976869 -27 CGGTCCGCGGGGATTATCCG 19 117 0 CGGTCCGCGG 0.909941 -10 CATCGAGCCAGAACCCCGTGTGC 20 4 0 GAACCCCGTG 0.719548 -52 GACGCCGGCGCAACCCGCGCCAGGCATCGA 20 28 0 CAACCCGCGC 0.463047 -28 GAATTTAGGACGCCGGCGCAACCCGCG 20 39 0 GGACGCCGGC 0.956912 -17 GCGAGGAAGGCAGCCCGCGCGA 21 3 0 CAGCCCGCGC 0.676189 -298 CCGGTGGTGTCGGCGCTGTGGCGAGGAAGG 21 23 0 CGGCGCTGTG 0.973154 -278 CGCACGCCAACAGCGCCCGGTCGGGCGAGG 21 69 1 CAGCGCCCGG 0.940971 -232 GCGCCCGGTCGGGCGAGGTCTTCCCTTGGG 21 81 1 GGGCGAGGTC 0.791044 -220 CCGTCGTTCGCGATCCGGTGTTGGCTACCC 21 126 0 CGATCCGGTG 0.857637 -175 GGATCGCGAACGACGGTGTGAGCGTTCCCA 21 140 1 CGACGGTGTG 0.898592 -161 ACGCCACCCAGAGTGCCGGCGAACCGGTGG 21 180 0 GAGTGCCGGC 0.731175 -121 CCGGCACTCTGGGTGGCGTGGTAGCTAACG 21 191 1 GGGTGGCGTG 0.940421 -110 TGGTAGCTAACGGTCACCGGCGAGTGTGTC 21 209 1 CGGTCACCGG 0.848965 -92 AGTGTGTCGGCTGCGCTGGCCAGGCCGCAC 21 231 1 CTGCGCTGGC 0.829091 -70 AGCCGGTGAAGTGCGGCCTGGCCAGCGCAG 21 241 0 GTGCGGCCTG 0.766318 -60 TCGTCAGCGGCGGCGCCGTGCTTCCACAAC 22 132 0 CGGCGCCGTG 0.993789 -33 ********** Masking position 8 Map Score: 87.7317 Number of sites scoring better than the average of aligned sites = 145196 Number in coding regions = 136160 Number in noncoding regions = 9036 Number of orfs with sites within 600 bp upstream = 1803 Fraction of orfs with sites within 600 bp upstream = 0.289592 Motif number 2 CTCCGGGACGGGCTCGAGCGCTGGGCGACAAT 1 10 0 GGCTGCGCTG 0.741376 -120 GTCCCGGAGCGCCTCGTCAGGCGGCACGTTATC 1 34 1 GCCTCAGGCG 0.793726 -96 CAAGCTTGTTACCGTTTCGGCCGACAGCCGGAA 3 22 0 ACCGCGGCCG 0.928431 -250 GAAACCTGGGGGTGTGCCTGCTGTGTATGCACG 3 79 1 GGTGCTGCTG 0.937282 -193 ACACGTGGCTGGTTCGACCGCGGGTCTCAGGGG 3 128 0 GGTTCCGCGG 0.873796 -144 GTTAACGGTCGGCGAACTTGGCGTGCCGTCGCC 3 189 0 GGCGTTGGCG 0.97727 -83 AGTGCTGTTAGCTTCATTTGCTGCGAGCAAAAC 3 224 1 GCTTTTGCTG 0.333641 -48 CGAGCAAAACAGCTGGTCGGCCGTTAGGAACTG 3 247 1 AGCTCGGCCG 0.9507 -25 CTAGCGTTCAGGAGGGGCCGCTGATACTGAGGG 4 67 0 GGAGCCGCTG 0.800075 -149 CGGTATTCGAGCCGTCACCGTTGTGCATCGAAA 4 120 0 GCCGCCGTTG 0.781234 -96 CGGGCCATCGGGCTGCTTTGCGGAGC 5 44 1 GGCTTTGCGG 0.920578 -16 CCGAACGGCGAGCATCGTTGCCGGGATAGGTTG 6 17 0 AGCATTGCCG 0.531002 -133 TTCCGCTCGGGCCGATTCTGATGCGTGAAAACT 7 89 0 GCCGCTGATG 0.625164 -118 CCCATCAACCGGCGCGCTGGCGGCACGCCATCG 7 142 1 GGCGTGGCGG 0.976765 -65 GGGACAGGGTAGCGAGCCCGGCGATGGCGTGCC 7 163 0 AGCGCCGGCG 0.96688 -44 TCGAGCCAACGGCTTGACCGGTGATGCGCCTGT 9 29 1 GGCTCCGGTG 0.969602 -272 GTGCTCTGCTGCCTTGGCGGCCGACAGGCGCAT 9 52 0 GCCTCGGCCG 0.968759 -249 TATGGACATCAGCGGTTCTGCCGCGTACGCTCA 9 187 1 AGCGCTGCCG 0.973802 -114 GTCGACGATCGGTGACATTGGTGAGCGTACGCG 9 208 0 GGTGTTGGTG 0.732273 -93 CCGATCGTCGACCTGTCCGGGGGGCCAGCGTGC 9 229 1 ACCTCGGGGG 0.491431 -72 GGCGCGGCGCACCAGCTGGATTCGATGC 9 283 0 GGCGCAGCTG 0.972042 -18 TCCAGGTCGCGGCGCTCCGGCCACTGACAGAAA 12 15 0 GGCGCGGCCA 0.868456 -71 GGGGCGGGGCGGCTAGCCTGTCGGG 13 3 0 GGCTCTGTCG 0.886012 -46 TGGCGACCTTCCGGTGCGGGACTT 16 111 0 GGCGTTCCGG 0.81884 -14 CTGGCCGACATTGCCGTGACGGCGGT 17 4 1 GCCGTTGCCG 0.954152 -83 GTATTCTGTCGGCGAGTTTGCCGCCACGGTCGA 17 47 0 GGCGTTGCCG 0.987922 -40 CTAAACCCGAGGCGCGGCCCACGACTGTCGCCT 18 46 1 GGCGCCCACG 0.759594 -40 CGGGCAATCGGGCTTGCCCGGTGACGCTACACT 19 39 1 GGCTCCGGTG 0.969602 -88 ACGGGGTTCTGGCTCGATGCCTGGCGCGGGTTG 20 15 1 GGCTTGCCTG 0.74096 -41 TTAGGACGCCGGCGCAACCCGCGCCAGGCATCG 20 29 0 GGCGCCCGCG 0.964318 -27 TGGCGAGGAAGGCAGCCCGCGCGA 21 2 0 GGCACGCGCG 0.686081 -299 GAGGAGGACCGGTGGTGTCGGCGCTGTGGCGAG 21 28 0 GGTGTCGGCG 0.899422 -273 CGCCCGACCGGGCGCTGTTGGCGTGCGGCATCC 21 63 0 GGCGTTGGCG 0.977271 -238 TCCCTTGGGAAGCGCAGTCGCGGTGGGTAGCCA 21 102 1 AGCGTCGCGG 0.878728 -199 CCAGAGTGCCGGCGAACCGGTGGGACGATGTTT 21 170 0 GGCGCGGTGG 0.913513 -131 CCGGTTCGCCGGCACTCTGGGTGGCGTGGTAGC 21 183 1 GGCATGGGTG 0.702217 -118 GTCACCGGCGAGTGTGTCGGCTGCGCTGGCCAG 21 221 1 AGTGCGGCTG 0.764343 -80 TGTGCAGTCCGGCTCCCCAGCCGGTGAAGTGCG 21 256 0 GGCTCAGCCG 0.966411 -45 ACCGCTGAGTGGTTGATCAGCCGAGGAAGAGGG 22 17 1 GGTTCAGCCG 0.80018 -148 GTGGAAGCACGGCGCCGCCGCTGACGATAGTGT 22 135 1 GGCGCCGCTG 0.993806 -30 **** ****** Masking position 13 Map Score: 63.0531 Number of sites scoring better than the average of aligned sites = 54157 Number in coding regions = 51517 Number in noncoding regions = 2640 Number of orfs with sites within 600 bp upstream = 1137 Fraction of orfs with sites within 600 bp upstream = 0.182621 Motif number 3 TCCGGGACGGGCTCGAGCGCTGGGCGACAAT 1 11 0 GCCGAGCGCT 0.470584 -119 TCGAGCCCGTCCCGGAGCGCCTCGTCAGGCG 1 26 1 CCGGAGCGCC 0.972846 -104 GCCCCTCCAGCGTCGTGGGAAAGG 1 116 0 CCCCAGCGTC 0.481056 -14 ACAGCCGGAAAAGAGGGCGCC 3 1 0 AAAGGGCGCC 0.487426 -271 CCCGAAACCTGGGGGTGTGCCTGCTGTGTAT 3 76 1 GGGGTGTGCC 0.876698 -196 TGGACACGTGGCTGGTTCGACCGCGGGTCTC 3 133 0 GCGGTTCGAC 0.740641 -139 TCGCCCTTGGCCGGGGTTGACCCCTGATGAT 3 163 0 CCGGGTTGAC 0.571136 -109 TCAACCCCGGCCAAGGGCGACGGCACGCCAA 3 174 1 CCAGGGCGAC 0.889511 -98 CGACGGCACGCCAAGTTCGCCGACCGTTAAC 3 191 1 CCAGTTCGCC 0.900224 -81 GCTCCTTGGACAAAGCGCGCCGTCGACCCTC 4 41 1 CAAGCGCGCC 0.82845 -175 CACTCGCCACCGGTGGTCGCCGAGCCACCGA 4 161 0 CGTGGTCGCC 0.415296 -55 CCGCAAAGCAGCCCGATGGCCCGACGGAGGT 5 36 0 GCCGATGGCC 0.525155 -24 TCCACTCAACCCGCGAGCGACCGAGGCCCAC 6 49 0 CCCGAGCGAC 0.797908 -101 GGGTTGAGTGGATAGTGTGCCGGGAGTAGCT 6 68 1 GAAGTGTGCC 0.72618 -82 ATGGCGTGCCGCCAGCGCGCCGGTTGATGGG 7 142 0 GCAGCGCGCC 0.979911 -65 CGAGCCCGGCGATGGCGTGCCGCCAGCGCGC 7 153 0 GAGGCGTGCC 0.776144 -54 ATTGGGACAGGGTAGCGAGCCCGGCGATGGC 7 168 0 GGAGCGAGCC 0.815523 -39 CCCAGACCCTGGACCGTTGCCTGGAATCGCA 8 35 1 GGCCGTTGCC 0.658545 -127 CTAATGGTTACCAAGATCGTCTGCGCGTCGT 8 132 0 CCAGATCGTC 0.648111 -30 GTGCCTCGCCAGCGTGACTCGAGCCAAC 9 8 1 GCAGCGTGAC 0.725047 -293 TGGCCCCCCGGACAGGTCGACGATCGGTGAC 9 225 0 GAAGGTCGAC 0.587558 -76 TCCGGGGGGCCAGCGTGCGCCACCTCACCCA 9 244 1 CACGTGCGCC 0.74067 -57 ATCGAATCCAGCTGGTGCGCCGCGCC 9 285 1 GCGGTGCGCC 0.975987 -16 TCTGTCAGTGGCCGGAGCGCCGCGACCTGGA 12 17 1 GCGGAGCGCC 0.985902 -69 ATGGGGGCGGGGCGGCTAGCCTGTCGGG 13 8 0 GGGGCTAGCC 0.677383 -41 GAGCTTCGAAGGAAGGGTGCCCC 14 3 0 GGAGGGTGCC 0.948072 -110 CGACGTCGACGGTACAGTGCCACCTAGCTGT 14 59 0 GGACAGTGCC 0.781545 -54 TTTCATTATTGCGACGTCGACGGTACAGTGC 14 70 0 GCACGTCGAC 0.693724 -43 ACCGCGCACGGGTGGGGAGTCAGCGACAACA 16 11 0 GGGGGGAGTC 0.530382 -114 CTGCAATGTTCAGCGATCGCCTTTCCGCCGC 16 63 1 CACGATCGCC 0.696114 -62 CGCCGCTACGGGAACGTTGTCCAAAGTCCCG 16 88 1 GGACGTTGTC 0.231691 -37 GTCCCGCACCGGAAGGTCGCCA 16 113 1 GGAGGTCGCC 0.960064 -12 CTGGCCGACATTGCCGTGACGGCGG 17 5 1 CCACATTGCC 0.629858 -82 TATTCTGTCGGCGAGTTTGCCGCCACGGTCG 17 48 0 GCAGTTTGCC 0.861947 -39 GTTATCCCACGGCAGATAGCCGGGCAATCGG 19 19 1 GGAGATAGCC 0.737797 -108 CACCGGGCAAGCCCGATTGCCCGGCTATCTG 19 31 0 GCCGATTGCC 0.890724 -96 AGCCGTGATCCAGCGCGAGCCTTCGGCCTCG 19 73 1 CACGCGAGCC 0.390277 -54 CTTCGGCCTCGGCGCATCGACGCCCGGATAA 19 93 1 GGGCATCGAC 0.437226 -34 GGCGCGGGTTGCGCCGGCGTCCTAAATTC 20 37 1 GCCCGGCGTC 0.73681 -19 TGCCTTCCTCGCCACAGCGCCGACACCACCG 21 21 1 GCACAGCGCC 0.943244 -280 ATGCCGCACGCCAACAGCGCCCGGTCGGGCG 21 65 1 CCACAGCGCC 0.914348 -236 GCGCAGTCGCGGTGGGTAGCCAACACCGGAT 21 113 1 GGGGGTAGCC 0.816088 -188 ACATCGTCCCACCGGTTCGCCGGCACTCTGG 21 172 1 ACGGTTCGCC 0.46601 -129 TACCACGCCACCCAGAGTGCCGGCGAACCGG 21 183 0 CCAGAGTGCC 0.9232 -118 ACGGTCACCGGCGAGTGTGTCGGCTGCGCTG 21 218 1 GCAGTGTGTC 0.613767 -83 CACTTCACCGGCTGGGGAGCCGGACTGCACA 21 258 1 GCGGGGAGCC 0.950606 -43 ACTATCGTCAGCGGCGGCGCCGTGCTTCCAC 22 135 0 GCGCGGCGCC 0.9708 -30 ** ******** Masking position 9 Map Score: 62.6521 Number of sites scoring better than the average of aligned sites = 32338 Number in coding regions = 30043 Number in noncoding regions = 2295 Number of orfs with sites within 600 bp upstream = 1138 Fraction of orfs with sites within 600 bp upstream = 0.182782 Motif number 4 GCGCTCGAGCCCGTCCCGGAGCGCCTCGTCAGG 1 22 1 CCGCCGAGCG 0.762224 -108 GCTCATCTAACGATAACGTGCCGCCTGACGAGG 1 45 0 CGAACGGCCG 0.621688 -85 GCTGCCGCTACCGTCACATGGCGCGATGAACTG 1 76 1 CCGACAGGCG 0.945072 -54 GTGACTGCTCCCGAAACCTGGGGGTGTGCCTGC 3 67 1 CCGACCGGGG 0.877814 -205 GGACATCCTTCCCCTGAGACCCGCGGTCGAACC 3 118 1 CCCGAGCCCG 0.676823 -154 GGGGTCAACCCCGGCCAAGGGCGACGGCACGCC 3 170 1 CCGCAAGGCG 0.889477 -102 TGCTCCTTGGACAAAGCGCGCCGTCGACCCTCA 4 40 1 ACAGCGGCCG 0.577807 -176 GGTCGCCGAGCCACCGACCCGGGGTCGGTATTC 4 145 0 CCAGACCGGG 0.791519 -71 GTCGGTGGCTCGGCGACCACCGGTGGCGAGTGG 4 160 1 CGGACCCCGG 0.38106 -56 AGTGGATCCGCCACCACGACCCCCTCGAGAGGA 4 188 1 CCAACGCCCC 0.848986 -28 GCTCCGCAAAGCAGCCCGATGGCCCGAC 5 42 0 GCAGCACCCG 0.419254 -18 CGACCGAGGCCCACCGAACGGCGAGCATCGTTG 6 30 0 CCAGAAGGCG 0.843729 -120 GGCACACTATCCACTCAACCCGCGAGCGACCGA 6 56 0 CCACAACCGC 0.190591 -94 CCAGTCAGGTCCAGCTACTCCCGGCACACTATC 6 78 0 CCATACCCCG 0.404453 -72 ACCGCGATACCCGAGGAGGCCCGC 7 2 0 CCGGAGCCCG 0.976999 -205 CGCATCAGAATCGGCCCGAGCGGAACCATCCGG 7 97 1 TCGCCGGCGG 0.324343 -110 ACGGGTGACCCCATCAACCGGCGCGCTGGCGGC 7 133 1 CCAAACGGCG 0.837462 -74 GCGAGCCCGGCGATGGCGTGCCGCCAGCGCGCC 7 152 0 CGAGCGGCCG 0.75055 -55 CTACCCTGTCCCAATGCGACGCGGTGGTTGGGC 7 184 1 CCAGCGCGCG 0.986464 -23 GGAGCTTACGCCATCACGATGCGATTCCAGGCA 8 52 0 CCAACGTGCG 0.674477 -110 AAACTCCGCACCGCCACGACGCGCAGACGATCT 8 117 1 CCGACGCGCG 0.986998 -45 GCAGCAGAGCACATCGCCCCGCGCTATAGGATA 9 73 1 ACAGCCCGCG 0.620766 -228 GATCAGTTGTCCAAGCAATCGCGTATTGGCTAT 9 157 1 CCACAACGCG 0.874333 -144 CGATCGTCGACCTGTCCGGGGGGCCAGCGTGCG 9 230 1 CCTCCGGGGG 0.339366 -71 TCGAATCCAGCTGGTGCGCCGCGCC 9 286 1 CTGGCGCGCG 0.728597 -15 GCAAACTGCCCGGGCAGTCGCCCGAACGTATG 11 10 1 CCGCAGCGCC 0.847836 -31 CTGTCAGTGGCCGGAGCGCCGCGACCTGGAAAG 12 18 1 CCGGCGCGCG 0.986553 -68 GACAGGCTAGCCGCCCCGCCCCCATTCCTGCAC 13 14 1 CCGCCGCCCC 0.935586 -35 GACTCCACCGTAACGACCAGCTTTAATACA 15 8 1 CCGACGCCAG 0.745975 -26 CCACATCAGACCGCGCACGGGTGGGGAGTCAGC 16 18 0 CCGCACGGTG 0.368202 -107 GATCGCCTTTCCGCCGCTACGGGAACGTTGTCC 16 77 1 CCGGCTCGGG 0.555165 -48 AAGTCCCGCACCGGAAGGTCGCCA 16 111 1 CCGAGGCGCC 0.573993 -14 GGTCGATGAACCAATCACCGCCGTCACGGCAAT 17 20 0 CCACACGCCG 0.869167 -67 GCACACCGTGAAGTCCCGATGACAATGC 18 6 1 CCGAAGCCCG 0.959354 -80 ATAGCTAAACCCGAGGCGCGGCCCACGACTGTC 18 42 1 CCGGCGGGCC 0.928517 -44 TGTAGCGTCACCGGGCAAGCCCGATTGCCCGGC 19 37 0 CCGCAACCCG 0.924703 -90 TGCGCCGAGGCCGAAGGCTCGCGCTGGATCACG 19 76 0 CCGGGCCGCG 0.909267 -51 AGGCATCGAGCCAGAACCCCGTGTGC 20 4 0 CCAACCCGTG 0.518415 -52 GGGTTCTGGCTCGATGCCTGGCGCGGGTTGCGC 20 18 1 TCGGCCGGCG 0.654463 -38 ATTTAGGACGCCGGCGCAACCCGCGCCAGGCAT 20 31 0 CCGGCACCCG 0.971988 -25 CGCCACAGCGCCGACACCACCGGTCCTCCTCGA 21 30 1 CCGACCCCGG 0.910768 -271 ATGCCGCACGCCAACAGCGCCCGGTCGGGCGAG 21 65 1 CCAAGCCCCG 0.729587 -236 CCGTTAGCTACCACGCCACCCAGAGTGCCGGCG 21 189 0 CCACCACCAG 0.442573 -112 GGCTCCCCAGCCGGTGAAGTGCGGCCTGGCCAG 21 246 0 CCGGAATGCG 0.478481 -55 CAGAATGAAACCAAACCACGCCGGAAAAATCCC 22 87 1 CCACCAGCCG 0.919458 -78 CGGAAAAATCCCAGTACATGCCGAGTTGTGGAA 22 108 1 CCAACAGCCG 0.890371 -57 *** *** **** Masking position 2 Map Score: 62.6402 Number of sites scoring better than the average of aligned sites = 41400 Number in coding regions = 38099 Number in noncoding regions = 3301 Number of orfs with sites within 600 bp upstream = 1315 Fraction of orfs with sites within 600 bp upstream = 0.211211 Motif number 5 CATCATCAGGGGTCAACCCCGGCCAAGGGC 3 162 1 GGTCAACCCC 0.807307 -110 TTTGTCCAAGGAGCATCCCAAGGAGCATGT 4 25 0 GAGCATCCCA 0.686319 -191 GCTCCGCAAAGCAGCCCGATGGCCCGAC 5 42 0 AAGCAGCCCG 0.871831 -18 CACACTATCCACTCAACCCGCGAGCGACCG 6 57 0 ACTCAACCCG 0.804232 -93 CGCGATACCCGAGGAGGCCCGC 7 3 0 GAGGAGGCCC 0.656999 -204 GGATGGTTCCGCTCGGGCCGATTCTGATGC 7 98 0 GCTCGGGCCG 0.785991 -109 GGGACAGGGTAGCGAGCCCGGCGATGGCGT 7 166 0 AGCGAGCCCG 0.641519 -41 CGTGTTCAACGCTGAACCCAGACCCTGGAC 8 19 1 GCTGAACCCA 0.598501 -143 GCGCATCACCGGTCAAGCCGTTGGCTCGAG 9 28 0 GGTCAAGCCG 0.905444 -273 CGGCCGACAGGCGCATCACCGGTCAAGCCG 9 38 0 GCGCATCACC 0.279788 -263 CGACCTGGAAAGGCAACCCGAGAGATGTAC 12 39 1 AGGCAACCCG 0.929725 -47 CCCGACAGGCTAGCCGCCCCGCCCCC 13 7 1 AGGCTAGCCG 0.47668 -42 TTCCTGCACTGCGCATGCCGC 13 38 1 GCGCATGCCG 0.9574 -11 ATGCGTCATAGCTAAACCCGAGGCGCGGCC 18 35 1 GCTAAACCCG 0.474372 -51 TAAACCCGAGGCGCGGCCCACGACTGTCGC 18 47 1 GCGCGGCCCA 0.836292 -39 TAGCGTCACCGGGCAAGCCCGATTGCCCGG 19 38 0 GGGCAAGCCC 0.657333 -89 GCGTCGATGCGCCGAGGCCGAAGGCTCGCG 19 86 0 GCCGAGGCCG 0.86112 -41 TAGGACGCCGGCGCAACCCGCGCCAGGCAT 20 31 0 GCGCAACCCG 0.986747 -25 GTGGCGAGGAAGGCAGCCCGCGCGA 21 6 0 AGGCAGCCCG 0.959441 -295 GGTCCTCCTCGAGGATGCCGCACGCCAACA 21 51 1 GAGGATGCCG 0.689425 -250 CACCGCGACTGCGCTTCCCAAGGGAAGACC 21 97 0 GCGCTTCCCA 0.511372 -204 GGCCTGGCCAGCGCAGCCGACACACTCGCC 21 227 0 GCGCAGCCGA 0.741287 -74 CGGCTGCGCTGGCCAGGCCGCACTTCACCG 21 238 1 GGCCAGGCCG 0.93395 -63 TTCACCGGCTGGGGAGCCGGACTGCACAAG 21 261 1 GGGGAGCCGG 0.797661 -40 ********** Masking position 8 Map Score: 20.8782 Number of sites scoring better than the average of aligned sites = 18876 Number in coding regions = 17557 Number in noncoding regions = 1319 Number of orfs with sites within 600 bp upstream = 812 Fraction of orfs with sites within 600 bp upstream = 0.130421 Motif number 6 CGCCATGTGACGGTAGCGGCAGCTCATCTA 1 69 0 CGGTAGCGGC 0.736138 -61 GCCCCTCCAGCGTCGTGGGAAAGGCGTCT 1 111 0 GCGTCGTGGG 0.829533 -19 CCTCTCGAGGGGGTCGTGGTGGCGGATCCA 4 190 0 GGGTCGTGGT 0.958812 -26 GGTTGCTGTCGCGTGGTGGTCAACGAGG 5 9 0 GCGTGGTGGT 0.784193 -51 CGAACGGCGAGCATCGTTGCCGGGATAGGT 6 19 0 GCATCGTTGC 0.279666 -131 ACCCCATCAACCGGCGCGCTGGCGGCACGC 7 140 1 CCGGCGCGCT 0.77421 -67 CTGTCCCAATGCGACGCGGTGGTTGGGC 7 189 1 GCGACGCGGT 0.871695 -18 GATCGTCTGCGCGTCGTGGCGGTGCGGAGT 8 119 0 GCGTCGTGGC 0.978087 -43 CCTATAGCGCGGGGCGATGTGCTCTGCTGC 9 73 0 GGGGCGATGT 0.71357 -228 CGGTCGTTGTACCACAGGAC 10 1 1 CGGTCGTTGT 0.837139 -37 TTGCCTTTCCAGGTCGCGGCGCTCCGGCCA 12 25 0 AGGTCGCGGC 0.766045 -61 ATGTACGAAACCGTCGTTGTATCAACGGTG 12 63 1 CCGTCGTTGT 0.894681 -23 TGCAGGAATGGGGGCGGGGCGGCTAGCCTG 13 16 0 GGGGCGGGGC 0.861736 -33 GACAACGTTCCCGTAGCGGCGGAAAGGCGA 16 79 0 CCGTAGCGGC 0.821783 -46 CCAATCACCGCCGTCACGGCAATGTCGGCC 17 13 0 CCGTCACGGC 0.70652 -74 GGTTCATCGACCGTGGCGGCAAACTCGCCG 17 41 1 CCGTGGCGGC 0.877006 -46 AGCTAAACCCGAGGCGCGGCCCACGACTGT 18 44 1 GAGGCGCGGC 0.913774 -42 GATTATCCGGGCGTCGATGCGCCGAGGCCG 19 96 0 GCGTCGATGC 0.78257 -31 ACCGGTGGTGTCGGCGCTGTGGCGAGGAAG 21 24 0 TCGGCGCTGT 0.602641 -277 CTCGCCCGACCGGGCGCTGTTGGCGTGCGG 21 68 0 CGGGCGCTGT 0.927452 -233 AGCGCCCGGTCGGGCGAGGTCTTCCCTTGG 21 80 1 CGGGCGAGGT 0.875431 -221 TTGGGAAGCGCAGTCGCGGTGGGTAGCCAA 21 106 1 CAGTCGCGGT 0.855144 -195 GGCACTCTGGGTGGCGTGGTAGCTAACGGT 21 193 1 GTGGCGTGGT 0.708063 -108 CCGGTGAAGTGCGGCCTGGCCAGCGCAGCC 21 239 0 GCGGCCTGGC 0.720796 -62 GAAGGCTTTAGGGTCGCTGTC 21 290 1 GGGTCGCTGT 0.93145 -11 TGGGATTTTTCCGGCGTGGTTTGGTTTCAT 22 91 0 CCGGCGTGGT 0.973085 -74 ATCGTCAGCGGCGGCGCCGTGCTTCCACAA 22 133 0 GCGGCGCCGT 0.671784 -32 ********** Masking position 3 Map Score: 39.3836 Number of sites scoring better than the average of aligned sites = 18340 Number in coding regions = 17131 Number in noncoding regions = 1209 Number of orfs with sites within 600 bp upstream = 776 Fraction of orfs with sites within 600 bp upstream = 0.124639 Motif number 7 CCGAAGATGTTCCCCCCCAAGAAGT 2 6 1 GATGTTCCCC 0.90674 -37 CCGGTGGCGAGTGGATCCGCCACCACGACC 4 179 1 GTGGATCCGC 0.931538 -37 CCTCGTTGACCACCACGCGACAGC 5 5 1 GTTGACCACC 0.870937 -55 GCCGGGATAGGTTGATCACC 6 1 0 GTTGATCACC 0.909464 -149 CGTGATCCGGATGGTTCCGCTCGGGCCGAT 7 106 0 ATGGTTCCGC 0.801989 -101 TGAGTCCTGCAATGTTCAGCGATCGCCTTT 16 57 1 AATGTTCAGC 0.617687 -68 ACACTTAGCCGTGATCCAGCGCGAGCCTTC 19 67 1 GTGATCCAGC 0.553985 -60 TCGACGCCCGGATAATCCCCGCGGACCG 19 109 1 GATAATCCCC 0.6354 -18 CGTTGTACCGCTGAGTGGTTG 22 2 1 GTTGTACCGC 0.852163 -163 CCGCTGAGTGGTTGATCAGCCGAGGAAGAG 22 18 1 GTTGATCAGC 0.929506 -147 ********** Masking position 7 Map Score: 1.34601 Number of sites scoring better than the average of aligned sites = 3298 Number in coding regions = 3098 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 8 GCCCGTCCCGGAGCGCCTCGTCAGGCGGCA 1 30 1 GAGCGCCTCG 0.956064 -100 TTGGCGTGCCGTCGCCCTTGGCCGGGGTTG 3 175 0 GTCGCCCTTG 0.802139 -97 AGGGTACTACATGCTCCTTGGGATGCTCCT 4 17 1 ATGCTCCTTG 0.776962 -199 GCTCCTTGGGATGCTCCTTGGACAAAGCGC 4 29 1 ATGCTCCTTG 0.776962 -187 CCGCCACCACGACCCCCTCGAGAGGAGTTG 4 195 1 GACCCCCTCG 0.959307 -21 TCGCCGTTCGGTGGGCCTCGGTCGCTCGCG 6 39 1 GTGGGCCTCG 0.928666 -111 GCGGGCCTCCTCGGGTATCGCGG 7 4 1 GGCCTCCTCG 0.969843 -203 GACCTCCTCGTGTTCAACGC 8 1 1 GACCTCCTCG 0.982087 -161 AATCCAGCTGGTGCGCCGCGCC 9 289 1 GTGCGCCGCG 0.896013 -12 CGTCCTCCTTATCGATAACAG 14 102 0 GTCCTCCTTA 0.722682 -11 CGCGCGGGCTGCCTTCCTCGCCACAGCGCC 21 12 1 GCCTTCCTCG 0.832059 -289 GACACCACCGGTCCTCCTCGAGGATGCCGC 21 42 1 GTCCTCCTCG 0.992787 -259 CCAGCAATCCCTCTTCCTCGGCTGATCAAC 22 28 0 CTCTTCCTCG 0.712344 -137 ********** Masking position 6 Map Score: 12.362 Number of sites scoring better than the average of aligned sites = 2474 Number in coding regions = 2305 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 9 AGCAAAACAGCTGGTCGGCCGTTAGGAACT 3 249 1 CTGGTCGGCC 0.796602 -23 CCGGGAGTAGCTGGACCTGACTGGACATGA 6 87 1 CTGGACCTGA 0.927832 -63 CTGGACCTGACTGGACATGAAACGATGGCG 6 97 1 CTGGACATGA 0.976626 -53 GTAGATGTTACTGGACAGTAGCTATTCGGG 8 86 1 CTGGACAGTA 0.936202 -76 CGTATTGGCTATGGACATCAGCGGTTCTGC 9 178 1 ATGGACATCA 0.776375 -123 TGTATTAAAGCTGGTCGTTACGGTGGAGTC 15 11 0 CTGGTCGTTA 0.800932 -23 CTGTCGCCTCATGGACAGGAGATGTA 18 70 1 ATGGACAGGA 0.913738 -16 GTCGGCTGCGCTGGCCAGGCCGCACTTCAC 21 236 1 CTGGCCAGGC 0.905789 -65 AGAGGGATTGCTGGTCATGACACCATTTTT 22 44 1 CTGGTCATGA 0.963025 -121 ********** Masking position 2 Map Score: 3.20749 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 743 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 ********** No masking Map Score: 4.87676e-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 11 ********** No masking Map Score: 4.87676e-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 12 ********** No masking Map Score: 4.87676e-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