AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_mtub_reg_100.orf -o00550_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 rpmE 150 rpmE #2 prfA 89 prfA #3 rfe 83 rfe #4 bfrA 300 bfrA #5 Rv1877 84 hypothetical protein Rv1877 #6 glnA3 54 glnA3 #7 Rv2136c 63 hypothetical protein Rv2136c #8 murE 22 murE #9 hypothetical 267 hypothetical protein Rv2160c #10 glnA1 300 glnA1 #11 glnA2 94 glnA2 #12 Rv2223c 61 hypothetical protein Rv2223c #13 Rv2224c 300 hypothetical protein Rv2224c #14 glnA4 159 glnA4 #15 ddlA 77 ddlA #16 gpdA2 118 gpdA2 Motif number 1 ********** No masking Map Score: -1.9652e-13 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 2 GCGGACATTCCCGGCGAGCCGTCTCGCCGG 1 12 0 CCGGCGAGCC 0.609416 -139 CACCGAGATGCGTGCGGACATTCCCGGCGA 1 25 0 CGTGCGGACA 0.921384 -126 CCCGTCGTGGCGTGCCGAGAACCTGGTCCG 1 107 0 CGTGCCGAGA 0.885314 -44 CACGCCACGACGGGCGGCCACCGATCACAG 1 123 1 CGGGCGGCCA 0.976095 -28 GTGCACAGTTCGGGCGTCGGTAAGCCAG 2 9 0 CGGGCGTCGG 0.788025 -81 CGGTACAGGACGGGCGTCGGTTCGCGTTAG 2 42 1 CGGGCGTCGG 0.788025 -48 CTTCTTCCCGCGAGCGCGGACCCTAACGCG 2 64 0 CGAGCGCGGA 0.934896 -26 AGTGCGTGCACGTTCGGCGG 3 1 0 CGTTCGGCGG 0.703719 -83 ACGTGCAACAGCTGCGAACAATTGGCCGAA 3 38 0 GCTGCGAACA 0.65971 -46 AGCTGTTGCACGTTCGGCGAGTGTTCAGCT 3 55 1 CGTTCGGCGA 0.918017 -29 AGCAGATGCTGCGTCGGCGAACGATCAAGC 4 26 1 GCGTCGGCGA 0.946428 -275 CTTGGACTTTGCGCCGGCGAGACGCGCCGA 4 118 1 GCGCCGGCGA 0.834334 -183 GTTTGTTGCGGCGTCGGCGCGTCTCGCCGG 4 131 0 GCGTCGGCGC 0.601397 -170 CGCAACAAACCCTGCGCCGACCCGTACTCG 4 151 1 CCTGCGCCGA 0.908401 -150 GGGCAGGGCTGGAGCGCACCGGTGTCGGGC 4 234 0 GGAGCGCACC 0.753597 -67 GCGCTCCAGCCCTGCCCACCTGGCGCGGTT 4 247 1 CCTGCCCACC 0.806434 -54 TAAGGCTGTCGTGGCGAACCGCGCCAGGTG 4 263 0 GTGGCGAACC 0.51378 -38 GATACCACTCCGGGCGCCGCTGACAAGCTC 5 31 1 CGGGCGCCGC 0.502135 -54 ATCCGCCCTCCCATCGCTGTTC 5 73 0 CCGCCCTCCC 0.480558 -12 CGATGCTTGCCGCGCGTAGCCGCGC 6 6 1 CTTGCCGCGC 0.88261 -49 CTTGCCGCGCGTAGCCGCGCGAGCTGATCC 6 16 1 GTAGCCGCGC 0.826141 -39 CAGTCATTCTGCAGCGCGGATCAGCTCGCG 6 33 0 GCAGCGCGGA 0.906193 -22 TACCCGGTTACCGGCGGCCGGTAGACGGAT 7 15 0 CCGGCGGCCG 0.544684 -49 CGCCGGAGCCGCGGTCACGACGAC 7 50 0 GGAGCCGCGG 0.948272 -14 CTACCGACAGGGCGCGCACAC 8 2 0 GGCGCGCACA 0.590552 -21 CCCGGGTTTGGCGGCCGACGTCGGCG 9 7 0 GCGGCCGACG 0.912023 -261 CCGCCAAACCCGGGCGCAGATCCTGCGCGC 9 23 1 CGGGCGCAGA 0.864719 -245 GGGCGCAGATCCTGCGCGCCGCGATGGATA 9 34 1 CCTGCGCGCC 0.594823 -234 TCGGGGCTGTCCATCGGCGAGCTTGCCGGG 9 84 1 CCATCGGCGA 0.92402 -184 TTGCTCATGCCCAGCCGCCCGGCAAGCTCG 9 101 0 CCAGCCGCCC 0.970767 -167 GCAGCTGCAGCTGGCGACCGTCGAGGCCGC 9 164 1 CTGGCGACCG 0.815173 -104 CACGCTCACGGCGGCCTCGACGGTCGCCAG 9 174 0 GCGGCCTCGA 0.920126 -94 TGCCATCGCGGGAGCCACGACCTCGGCTTC 9 207 0 GGAGCCACGA 0.846604 -61 CGGTCCACCCCGGGCGGCGCTGCCATCGCG 9 227 0 CGGGCGGCGC 0.569467 -41 GGCGCGCACCCGGTCCACCCCGGGCGGCGC 9 237 0 CGGTCCACCC 0.797944 -31 GGGTGGACCGGGTGCGCGCCCTCATGCATG 9 247 1 GGTGCGCGCC 0.568193 -21 GAGCCGCCAGCCGGCGCCCCATCGGAGCCA 10 13 1 CCGGCGCCCC 0.502007 -288 CCCATCGGAGCCAGCGAACCCGGTCCGGTG 10 30 1 CCAGCGAACC 0.736828 -271 ACCCGGTCCGGTGTCCGGCAAGCCCAGCGT 10 47 1 GTGTCCGGCA 0.497186 -254 AGCCCAGCGTCTTGCCGGGATAGTCGGGCG 10 67 1 CTTGCCGGGA 0.758632 -234 CCGGGATAGTCGGGCGGCGATTTCGCCGTC 10 81 1 CGGGCGGCGA 0.9755 -220 CGGTTACGATCTTGCCGACCATGGCCCCAC 10 153 1 CTTGCCGACC 0.601366 -148 CCCCACAATAGGGCCGGGGAGACCCGGCGT 10 177 1 GGGCCGGGGA 0.704751 -124 CGTTACTGACCGTGCCGCCCACCACTGACG 10 204 0 CGTGCCGCCC 0.967501 -97 TCAACCCCGTGTTGCGCAGACGTTACTGAC 10 224 0 GTTGCGCAGA 0.524656 -77 CGGCTCCATAGCGTCGGCCGCGGATACAGT 10 268 1 GCGTCGGCCG 0.565966 -33 GAAGCGTTGCGGGGCGGCCCGCAAGGGGAG 11 23 0 GGGGCGGCCC 0.562457 -72 CGCAACGCTTCTGGCCGGGCATCGGTAACA 11 42 1 CTGGCCGGGC 0.893529 -53 CGGGGCGAAGAAACGAAGGTG 12 2 1 GGGGCGAAGA 0.82767 -60 GATGGGTTCGTCGAAGGGGTGGAC 13 5 1 GGTTCGTCGA 0.553962 -296 ATCCCCGATGCCGTCCACCCCTTCGACGAA 13 17 0 CCGTCCACCC 0.806795 -284 CGCCCGAGGGCGATCCCCGATGCCGTCCAC 13 29 0 CGATCCCCGA 0.806014 -272 TGCACCTTGGCCATCGCCCGAGGGCGATCC 13 43 0 CCATCGCCCG 0.75354 -258 GTGCACCATGCCGGCGTGGACGGGGTGCCA 13 68 1 CCGGCGTGGA 0.923784 -233 GCGTGGACGGGGTGCCAGCGCCAACCTGAT 13 81 1 GGTGCCAGCG 0.62304 -220 GGGCGCGTCGGCCTCGGCGGTGCACAACTG 13 115 0 GCCTCGGCGG 0.492569 -186 GTGCCGGATCCGGTCGACGGGTCGGTGTCT 13 145 1 CGGTCGACGG 0.491415 -156 GGGTCGGTGTCTTGCCCGGATCTGTTACCG 13 163 1 CTTGCCCGGA 0.656589 -138 AACTCGTCGGCCATCCCCCATACGTCCGGT 13 189 0 CCATCCCCCA 0.803265 -112 GACGAGTTCGCCATCGGCGATGGCAGGACT 13 211 1 CCATCGGCGA 0.92402 -90 AGGACTGCTGGCAGCGGCCGGTTAGTCGGC 13 235 1 GCAGCGGCCG 0.945292 -66 CCAGCGGCCACCGTCGGCCGACTAACCGGC 13 251 0 CCGTCGGCCG 0.585879 -50 GAGATCCTGGCCAGCGGCCACCGTCGGCCG 13 261 0 CCAGCGGCCA 0.983094 -40 ATGATGGGCACCAGCGCCCATCATGTTCTT 14 32 1 CCAGCGCCCA 0.971189 -128 GCGAACCGCCGGAGCCGGCGAGTAGACGCG 14 63 0 GGAGCCGGCG 0.870889 -97 GGCGGTTCGCGGTGCCCGCGACAGCCAGCA 14 83 1 GGTGCCCGCG 0.799152 -77 CTATAGGCTCCGGGCCCACATGCTGGCTGT 14 103 0 CGGGCCCACA 0.923757 -57 AGATGGTTGACTAGCGGCCATGGTGTGGGA 14 131 1 CTAGCGGCCA 0.924285 -29 GCCTCGCACGGGCCGGCACGACCGAAAA 15 9 1 CGGGCCGGCA 0.973415 -69 AGTCATCCTGCCAGCGTCGATCCACGCGGC 16 13 1 CCAGCGTCGA 0.915832 -106 GTCGAAGTGTGCCGCGTGGATCGACGCTGG 16 23 0 GCCGCGTGGA 0.492089 -96 CGACGGCATTGCCGCCACGGTCGTGGCCGG 16 49 1 GCCGCCACGG 0.617656 -70 TGCCTGGGCCCCGGCCACGACCGTGGCGGC 16 59 0 CCGGCCACGA 0.962878 -60 CCGTCGGGACCGTGCCTGGGCCCCGGCCAC 16 71 0 CGTGCCTGGG 0.665235 -48 GACGGCAACCGCGGCGCAGATTAGTGTGTG 16 96 1 GCGGCGCAGA 0.829112 -23 ********** Masking position 5 Map Score: 121.591 Number of sites scoring better than the average of aligned sites = 115484 Number in coding regions = 107886 Number in noncoding regions = 7598 Number of orfs with sites within 600 bp upstream = 1697 Fraction of orfs with sites within 600 bp upstream = 0.272567 Motif number 3 TTCCCGGCGAGCCGTCTCGCCGGA 1 5 0 GCCGTCTCGC 0.771097 -146 CACCCCAAACACCGAGATGCGTGCGGACAT 1 34 0 ACCGAGATGC 0.552854 -117 GTCGTGGCGTGCCGAGAACCTGGTCCGGTT 1 104 0 GCCGAGAACC 0.52614 -47 TCGGTGGCCGCCCGTCGTGGCGTGCCGAGA 1 117 0 CCCGTCGTGG 0.941262 -34 CTGGCTTACCGACGCCCGAACTGTGCA 2 8 1 ACCGACGCCC 0.964849 -82 CCTAACGCGAACCGACGCCCGTCCTGTACC 2 43 0 ACCGACGCCC 0.964849 -47 CAACCTTCTTCCCGCGAGCGCGGACCCTAA 2 68 0 CCCGCGAGCG 0.92718 -22 TTGATCGTTCGCCGACGCAGCATCTGCTGG 4 24 0 GCCGACGCAG 0.70508 -277 GTCGGCGCGTCTCGCCGGCGCAAAGTCCAA 4 119 0 CTCGCCGGCG 0.593546 -182 GGCGAGACGCGCCGACGCCGCAACAAACCC 4 133 1 GCCGACGCCG 0.991913 -168 CCGCAACAAACCCTGCGCCGACCCGTACTC 4 150 1 CCCTGCGCCG 0.607917 -151 CCAAGACGAGCCCGACACCGGTGCGCTCCA 4 225 1 CCCGACACCG 0.977437 -76 GGTGGGCAGGGCTGGAGCGCACCGGTGTCG 4 237 0 GCTGGAGCGC 0.546664 -64 GCCCTGCCCACCTGGCGCGGTTCGCCACGA 4 255 1 CCTGGCGCGG 0.929942 -46 GGGATATAAGGCTGTCGTGGCGAACCGCGC 4 269 0 GCTGTCGTGG 0.714633 -32 GTCAGCGGCGCCCGGAGTGGTATCGGAGAA 5 25 0 CCCGGAGTGG 0.795875 -60 GTACCCGGTTACCGGCGGCCGGTAGACGGA 7 16 0 ACCGGCGGCC 0.958957 -48 GTAACCGGGTACCGTCGTCGTCGTGACCGC 7 34 1 ACCGTCGTCG 0.886897 -30 CGCCGGAGCCGCGGTCACGAC 7 53 0 GCCGGAGCCG 0.944047 -11 CCTACCGACAGGGCGCGCACAC 8 10 0 ACCGACAGGG 0.878152 -13 CGCCGACGTCGGCCGCCAAAC 9 2 1 GCCGACGTCG 0.978059 -266 GATCCTGCGCGCCGCGATGGATATCGCCTC 9 41 1 GCCGCGATGG 0.824468 -227 GAGCCCCTTCACCGAGGCGATATCCATCGC 9 54 0 ACCGAGGCGA 0.391697 -214 GATGGACAGCCCCGAGAGCCCCTTCACCGA 9 69 0 CCCGAGAGCC 0.915066 -199 CTCATGCCCAGCCGCCCGGCAAGCTCGCCG 9 98 0 GCCGCCCGGC 0.405346 -170 CCGGAACAGGCCCGACTTGCTCATGCCCAG 9 117 0 CCCGACTTGC 0.667992 -151 GCTCCTTGGCGCCGAAATGCCGGAACAGGC 9 136 0 GCCGAAATGC 0.494646 -132 GCAGCTGGCGACCGTCGAGGCCGCCGTGAG 9 170 1 ACCGTCGAGG 0.506467 -98 CGTCGAGGCCGCCGTGAGCGTGTTCGAAGC 9 182 1 GCCGTGAGCG 0.90114 -86 CGTGTTCGAAGCCGAGGTCGTGGCTCCCGC 9 200 1 GCCGAGGTCG 0.955021 -68 GGTCGTGGCTCCCGCGATGGCAGCGCCGCC 9 215 1 CCCGCGATGG 0.813557 -53 GGCAGCGCCGCCCGGGGTGGACCGGGTGCG 9 233 1 CCCGGGGTGG 0.940571 -35 CCCGGGGTGGACCGGGTGCGCGCCCTCATG 9 243 1 ACCGGGTGCG 0.604238 -25 CAGAGCCGCCAGCCGGCGCCCCAT 10 5 1 GCCGCCAGCC 0.953901 -296 GACCGGGTTCGCTGGCTCCGATGGGGCGCC 10 25 0 GCTGGCTCCG 0.673254 -276 GCTGGGCTTGCCGGACACCGGACCGGGTTC 10 45 0 CCGGACACCG 0.47848 -256 CGGCGATTTCGCCGTCATCGGGCAGACCCG 10 95 1 GCCGTCATCG 0.905502 -206 GCCGCCCACCACTGACGCCGGGTCTCCCCG 10 191 0 ACTGACGCCG 0.847095 -110 GTCAGTCAACCCCGTGTTGCGCAGACGTTA 10 229 0 CCCGTGTTGC 0.351416 -72 CACGGGGTTGACTGACGGGCAATATCGGCT 10 243 1 ACTGACGGGC 0.664411 -58 CTTTACTGTATCCGCGGCCGACGCTATGGA 10 272 0 TCCGCGGCCG 0.713851 -29 TGCGGGGCGGCCCGCAAGGGGAGTGCGCGG 11 16 0 CCCGCAAGGG 0.678616 -79 TGCGGGCCGCCCCGCAACGCTTCTGGCCGG 11 30 1 CCCGCAACGC 0.680162 -65 AAACCGTGTTACCGATGCCCGGCCAGAAGC 11 48 0 ACCGATGCCC 0.763042 -47 CCGGCGAATACCTGTGACGGCGCGAAATGA 12 35 0 CCTGTGACGG 0.536858 -27 GAGGGCGATCCCCGATGCCGTCCACCCCTT 13 24 0 CCCGATGCCG 0.9304 -277 TTGGCCATCGCCCGAGGGCGATCCCCGATG 13 37 0 CCCGAGGGCG 0.975245 -264 GGTGCACCATGCCGGCGTGGACGGGGTGCC 13 67 1 GCCGGCGTGG 0.972794 -234 TCAGGTTGGCGCTGGCACCCCGTCCACGCC 13 80 0 GCTGGCACCC 0.850971 -221 CCAGCGCCAACCTGATGTCGCAGTTGTGCA 13 95 1 CCTGATGTCG 0.413623 -206 CACCGCCGAGGCCGACGCGCCCGTGCCGGA 13 123 1 GCCGACGCGC 0.983697 -178 GTCGACCGGATCCGGCACGGGCGCGTCGGC 13 133 0 TCCGGCACGG 0.652692 -168 AAGACACCGACCCGTCGACCGGATCCGGCA 13 146 0 CCCGTCGACC 0.763075 -155 CGATGGCGAACTCGTCGGCCATCCCCCATA 13 197 0 CTCGTCGGCC 0.411236 -104 TCCTGCCATCGCCGATGGCGAACTCGTCGG 13 209 0 GCCGATGGCG 0.912626 -92 TGGCAGGACTGCTGGCAGCGGCCGGTTAGT 13 231 1 GCTGGCAGCG 0.852125 -70 GCCAGCGGCCACCGTCGGCCGACTAACCGG 13 252 0 ACCGTCGGCC 0.918473 -49 GCCGACGGTGGCCGCTGGCCAGGATCTCGG 13 263 1 GCCGCTGGCC 0.86465 -38 CCAGAGCAGACCCGAGATCCTGGCCAGCGG 13 274 0 CCCGAGATCC 0.843619 -27 CATGATGGGCGCTGGTGCCCATCATGTTCT 14 27 0 GCTGGTGCCC 0.637941 -133 ACCGCGAACCGCCGGAGCCGGCGAGTAGAC 14 66 0 GCCGGAGCCG 0.944047 -94 CCACATGCTGGCTGTCGCGGGCACCGCGAA 14 88 0 GCTGTCGCGG 0.873258 -72 CCTCGCACGGGCCGGCACGACCGAAAACTG 15 12 1 GCCGGCACGA 0.65952 -66 CTCGTGGGAGCCCGTCTGCCTGACCCGGTA 15 45 1 CCCGTCTGCC 0.768507 -33 GTCTGCCTGACCCGGTAGCCTCTGCAGGTT 15 58 1 CCCGGTAGCC 0.75676 -20 GAAGTCATCCTGCCAGCGTCGATCCACG 16 9 1 CCTGCCAGCG 0.79517 -110 CGACGGCATTGCCGCCACGGTCGTGGCCGG 16 49 1 GCCGCCACGG 0.964293 -70 CACGGTCGTGGCCGGGGCCCAGGCACGGTC 16 64 1 GCCGGGGCCC 0.980109 -55 CAGGCACGGTCCCGACGGCAACCGCGGCGC 16 83 1 CCCGACGGCA 0.810677 -36 CCCGACGGCAACCGCGGCGCAGATTAGTGT 16 93 1 ACCGCGGCGC 0.883828 -26 ********** Masking position 4 Map Score: 109.822 Number of sites scoring better than the average of aligned sites = 90318 Number in coding regions = 85023 Number in noncoding regions = 5295 Number of orfs with sites within 600 bp upstream = 1596 Fraction of orfs with sites within 600 bp upstream = 0.256344 Motif number 4 ACCCTAACGCGAACCGACGCCCGTCCTGTA 2 45 0 GAACCGACGC 0.809592 -45 GCCGAACGTGCAACAGCTGCGAACAATTGG 3 43 0 CAACAGCTGC 0.48665 -41 CATCAGCAAACCCCCAGCAGATG 4 4 1 CAGCAAACCC 0.923765 -297 AGCAAACCCCCAGCAGATGCTGCGTCGGCG 4 15 1 CAGCAGATGC 0.892851 -286 ACTTTGCGCCGGCGAGACGCGCCGACGCCG 4 123 1 GGCGAGACGC 0.590865 -178 GCCGACGCCGCAACAAACCCTGCGCCGACC 4 143 1 CAACAAACCC 0.661397 -158 CAGCGAGTACGGGTCGGCGCAGGGTTTGTT 4 154 0 GGGTCGGCGC 0.46248 -147 TGCTTGCCGCGCGTAGCCGCGCGAGCTGAT 6 14 1 GCGTAGCCGC 0.597346 -41 GTAGCCGCGCGAGCTGATCCGCGCTGCAGA 6 26 1 GAGCTGATCC 0.433293 -29 CGACGTCGGCCGCCAAACCCGGGCGCAGAT 9 14 1 CGCCAAACCC 0.626444 -254 CCAAACCCGGGCGCAGATCCTGCGCGCCGC 9 26 1 GCGCAGATCC 0.746195 -242 GCTCGCCGATGGACAGCCCCGAGAGCCCCT 9 76 0 GGACAGCCCC 0.898233 -192 CCCAGCCGCCCGGCAAGCTCGCCGATGGAC 9 92 0 CGGCAAGCTC 0.435401 -176 CGAAATGCCGGAACAGGCCCGACTTGCTCA 9 124 0 GAACAGGCCC 0.894391 -144 CGGCGCCAAGGAGCAGCTGCAGCTGGCGAC 9 152 1 GAGCAGCTGC 0.894757 -116 CAGAGCCGCCAGCCGGCGCCCCATCGGAG 10 10 1 CAGCCGGCGC 0.937535 -291 CCATCGGAGCCAGCGAACCCGGTCCGGTGT 10 31 1 CAGCGAACCC 0.536697 -270 GTCCGGTGTCCGGCAAGCCCAGCGTCTTGC 10 52 1 CGGCAAGCCC 0.926583 -249 CGCCGTCATCGGGCAGACCCGATAACCAGG 10 104 1 GGGCAGACCC 0.953971 -197 CAATAGGGCCGGGGAGACCCGGCGTCAGTG 10 182 1 GGGGAGACCC 0.902134 -119 ACTGTATCCGCGGCCGACGCTATGGAGCCG 10 268 0 CGGCCGACGC 0.955554 -33 CTCCCCTTGCGGGCCGCCCCGCAACGCTTC 11 23 1 GGGCCGCCCC 0.53592 -72 AATGCTGCCAGAGCAGACCCGAGATCCTGG 13 281 0 GAGCAGACCC 0.98286 -20 CGCGAGTAGGCGCAAAAGAACAT 14 4 1 GAGTAGGCGC 0.872717 -156 CGGAGCCGGCGAGTAGACGCGAAAGAACAT 14 54 0 GAGTAGACGC 0.89581 -106 CATGGTGTGGGAGGAAGTGCG 14 149 1 GAGGAAGTGC 0.292994 -11 ACGGTCCCGACGGCAACCGCGGCGCAGATT 16 88 1 CGGCAACCGC 0.916038 -31 ********** Masking position 10 Map Score: 33.6612 Number of sites scoring better than the average of aligned sites = 19589 Number in coding regions = 18149 Number in noncoding regions = 1440 Number of orfs with sites within 600 bp upstream = 839 Fraction of orfs with sites within 600 bp upstream = 0.134757 Motif number 5 AACCGGACCAGGTTCTCGGCACGCCACGAC 1 104 1 GGTTCTCGGC 0.818799 -47 CTGTACCGCTGGTGCACAGTTCGGGCGTCG 2 20 0 GGTGCACAGT 0.917539 -70 GACGGGCGTCGGTTCGCGTTAGGGTCCGCG 2 50 1 GGTTCGCGTT 0.977331 -40 TTCGCGTTAGGGTCCGCGCTCGCGGGAAGA 2 62 1 GGTCCGCGCT 0.916554 -28 CTTCGCAGTGCGTGCACGTTCGGCGG 3 7 0 CGTGCACGTT 0.863984 -77 GTTCGCAGCTGTTGCACGTTCGGCGAGTGT 3 49 1 GTTGCACGTT 0.797333 -35 CGACGACGACGGTACCCGGTTACCGGCGGC 7 27 0 GGTACCCGGT 0.915321 -37 GGGTGGACCGGGTGCGCGCCCTCATGCATG 9 247 1 GGTGCGCGCC 0.884671 -21 CCGATAACCAGGTTCCCGTTCGGCATGCCA 10 122 1 GGTTCCCGTT 0.963637 -179 CCGCAAGGGGAGTGCGCGGTGAGT 11 5 0 AGTGCGCGGT 0.918478 -90 ACGCCGGCATGGTGCACCTTGGCCATCGCC 13 55 0 GGTGCACCTT 0.874613 -246 GATGGGCGCTGGTGCCCATCATGTTCTTTT 14 24 0 GGTGCCCATC 0.834092 -136 CGGCTCCGGCGGTTCGCGGTGCCCGCGACA 14 76 1 GGTTCGCGGT 0.983009 -84 ********** Masking position 3 Map Score: 13.0479 Number of sites scoring better than the average of aligned sites = 3005 Number in coding regions = 2806 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 6 CTCGGCACGCCACGACGGGCGGCCACCGAT 1 118 1 CACGACGGGC 0.947124 -33 GCAGTGCGTGCACGTTCGGCGG 3 3 0 CACGTTCGGC 0.796547 -81 GCAGCTGTTGCACGTTCGGCGAGTGTTCAG 3 53 1 CACGTTCGGC 0.796547 -31 GTGTCGGGCTCGTCTTGGGCTGATAACAGC 4 213 0 CGTCTTGGGC 0.780362 -88 CGATGCTTGCCGCGCGTAGCC 6 2 1 GATGCTTGCC 0.439434 -53 CGCCGACGTCGGCCGCCAAACCCG 9 5 1 GACGTCGGCC 0.931297 -263 CCCGGGCGCAGATCCTGCGCGCCGCGATGG 9 31 1 GATCCTGCGC 0.279307 -237 CGAACACGCTCACGGCGGCCTCGACGGTCG 9 178 0 CACGGCGGCC 0.94352 -90 TCGTGGCTCCCGCGATGGCAGCGCCGCCCG 9 217 1 CGCGATGGCA 0.675867 -51 GCACCCGGTCCACCCCGGGCGGCGCTGCCA 9 232 0 CACCCCGGGC 0.942365 -36 ATCCCGGCAAGACGCTGGGCTTGCCGGACA 10 58 0 GACGCTGGGC 0.973637 -243 CGATCTTGCCGACCATGGCCCCACAATAGG 10 159 1 GACCATGGCC 0.83879 -142 CGGCATGGTGCACCTTGGCCATCGCCCGAG 13 51 0 CACCTTGGCC 0.956513 -250 CCGGCACGGGCGCGTCGGCCTCGGCGGTGC 13 122 0 CGCGTCGGCC 0.928375 -179 CGGACGTATGGGGGATGGCCGACGAGTTCG 13 191 1 GGGGATGGCC 0.585127 -110 CCGACGAGTTCGCCATCGGCGATGGCAGGA 13 209 1 CGCCATCGGC 0.648995 -92 TTAGTCGGCCGACGGTGGCCGCTGGCCAGG 13 256 1 GACGGTGGCC 0.944026 -45 GCAGACCCGAGATCCTGGCCAGCGGCCACC 13 269 0 GATCCTGGCC 0.921512 -32 CGCAAAAGAACATGATGGGCACCAGCGCCC 14 21 1 CATGATGGGC 0.927881 -139 CGCGAAAGAACATGATGGGCGCTGGTGCCC 14 37 0 CATGATGGGC 0.927881 -123 TCCGGGCCCACATGCTGGCTGTCGCGGGCA 14 95 0 CATGCTGGCT 0.527388 -65 CTTCCTCCCACACCATGGCCGCTAGTCAAC 14 136 0 CACCATGGCC 0.965359 -24 AGTTTTCGGTCGTGCCGGCCCGTGCGAGGC 15 11 0 CGTGCCGGCC 0.911772 -67 CGCGTGGATCGACGCTGGCAGGATGACTTC 16 11 0 GACGCTGGCA 0.77846 -108 TTGCCGCCACGGTCGTGGCCGGGGCCCAGG 16 57 1 GGTCGTGGCC 0.711517 -62 ********** Masking position 8 Map Score: 39.9785 Number of sites scoring better than the average of aligned sites = 21460 Number in coding regions = 20372 Number in noncoding regions = 1088 Number of orfs with sites within 600 bp upstream = 722 Fraction of orfs with sites within 600 bp upstream = 0.115965 Motif number 7 GAGCATCGATTATGCCAGGTCAACCGCTATC 1 63 0 TATGCCAGGC 0.821255 -88 CAACCTGAGAGCTGAACACTCGCCGAA 3 67 0 GAGAGCTGAC 0.688019 -17 CCACTAATATGCGGCTTGATCGTTCGCCGAC 4 38 0 GCGGCTTGAC 0.860426 -263 ACAATGACCCGCGGCTTGGACTTTGCGCCGG 4 104 1 GCGGCTTGGC 0.929427 -197 CGCACCGGTGTCGGGCTCGTCTTGGGCTGAT 4 219 0 TCGGGCTCGC 0.832956 -82 ACCGCGCCAGGTGGGCAGGGCTGGAGCGCAC 4 245 0 GTGGGCAGGC 0.92294 -56 TGTTCGAGTCGATGCTAGAGCTTGTCAGCGG 5 47 0 GATGCTAGAC 0.464313 -38 CTCGAACAGCGATGGGAGGGCGGAT 5 70 1 GATGGGAGGC 0.499261 -15 GCGTAGCCGCGCGAGCTGATCCGCGCTGCAG 6 24 1 GCGAGCTGAC 0.87476 -31 CTGTCCATCGGCGAGCTTGCCGGGCGGCTGG 9 90 1 GCGAGCTTGC 0.384351 -178 CACGCTCACGGCGGCCTCGACGGTCGCCAGC 9 173 0 GCGGCCTCGC 0.951523 -95 TGGCTCCCGCGATGGCAGCGCCGCCCGGGGT 9 220 1 GATGGCAGCC 0.732458 -48 TTCGCCGTCATCGGGCAGACCCGATAACCAG 10 102 1 TCGGGCAGAC 0.939576 -199 GGGGCCATGGTCGGCAAGATCGTAACCGGTG 10 150 0 TCGGCAAGAC 0.427819 -151 CACTCCCCTTGCGGGCCGCCCCGCAACGCTT 11 21 1 GCGGGCCGCC 0.881983 -74 CCGTGTTACCGATGCCCGGCCAGAAGCGTTG 11 44 0 GATGCCCGGC 0.851941 -51 CACGGGCGCGTCGGCCTCGGCGGTGCACAAC 13 117 0 TCGGCCTCGC 0.844529 -184 CACCGACCCGTCGACCGGATCCGGCACGGGC 13 141 0 TCGACCGGAC 0.446944 -160 CGCCATCGGCGATGGCAGGACTGCTGGCAGC 13 219 1 GATGGCAGGC 0.938427 -82 AATGCTGCCAGAGCAGACCCGAGA 13 287 0 GCTGCCAGAC 0.960946 -14 TGGGAGCCCGTCTGCCTGACCCGGTAGCCTC 15 49 1 TCTGCCTGAC 0.86016 -29 GTGGATCGACGCTGGCAGGATGACTTC 16 7 0 GCTGGCAGGT 0.63591 -112 CGCCACGGTCGTGGCCGGGGCCCAGGCACGG 16 61 1 GTGGCCGGGC 0.81889 -58 ********* * Masking position 11 Map Score: 19.9458 Number of sites scoring better than the average of aligned sites = 26349 Number in coding regions = 24744 Number in noncoding regions = 1605 Number of orfs with sites within 600 bp upstream = 914 Fraction of orfs with sites within 600 bp upstream = 0.146804 Motif number 8 GGTGATAGCGGTTGACCTGGCATAATCGAT 1 60 1 GTTGACCTGG 0.402098 -91 CGAGTTGGAACCGGACCAGGTTCTCGGCAC 1 96 1 CCGGACCAGG 0.938547 -55 TCGGTGGCCGCCCGTCGTGGCGTGCCGAGA 1 117 0 CCCGTCGTGG 0.517324 -34 CTTACCGACGCCCGAACTGTGCACCAGCGG 2 15 1 CCCGAACTGT 0.708334 -75 CTGTGCACCAGCGGTACAGGACGGGCGTCG 2 31 1 GCGGTACAGG 0.555229 -59 CCGCCGAACGTGCACGCACTGC 3 3 1 GCCGAACGTG 0.872256 -81 CTGAACACTCGCCGAACGTGCAACAGCTGC 3 53 0 GCCGAACGTG 0.872256 -31 CAAACCCTGCGCCGACCCGTACTCGCTGCA 4 156 1 GCCGACCCGT 0.88849 -145 CTCCAGCCCTGCCCACCTGGCGCGGTTCGC 4 250 1 GCCCACCTGG 0.685771 -51 GTCAGCGGCGCCCGGAGTGGTATCGGAGAA 5 25 0 CCCGGAGTGG 0.343116 -60 CTAGCATCGACTCGAACAGCGATGGGAGGG 5 60 1 CTCGAACAGC 0.374513 -25 CTCATGCCCAGCCGCCCGGCAAGCTCGCCG 9 98 0 GCCGCCCGGC 0.833778 -170 CGCCGAAATGCCGGAACAGGCCCGACTTGC 9 127 0 CCGGAACAGG 0.899603 -141 CGATGGCAGCGCCGCCCGGGGTGGACCGGG 9 229 1 GCCGCCCGGG 0.925266 -39 GCCGCCCGGGGTGGACCGGGTGCGCGCCCT 9 239 1 GTGGACCGGG 0.960358 -29 TTGCCGGACACCGGACCGGGTTCGCTGGCT 10 38 0 CCGGACCGGG 0.956835 -263 CCGGTGGCATGCCGAACGGGAACCTGGTTA 10 126 0 GCCGAACGGG 0.974255 -175 TTACGATCTTGCCGACCATGGCCCCACAAT 10 156 1 GCCGACCATG 0.764822 -145 TCAGTGGTGGGCGGCACGGTCAGTAACGTC 10 206 1 GCGGCACGGT 0.833219 -95 GCGGGGCGGCCCGCAAGGGGAGTGCGCGGT 11 15 0 CCGCAAGGGG 0.520516 -80 CCCCTTGCGGGCCGCCCCGCAACGCTTCTG 11 25 1 GCCGCCCCGC 0.72368 -70 ACCTCGAACAGTATGCACTGTC 11 83 0 CTCGAACAGT 0.456826 -12 GATGGGTTCGTCGAAGGGGTGGACGGCAT 13 10 1 GTCGAAGGGG 0.918467 -291 CCATGCCGGCGTGGACGGGGTGCCAGCGCC 13 73 1 GTGGACGGGG 0.921237 -228 TCGACCGGATCCGGCACGGGCGCGTCGGCC 13 132 0 CCGGCACGGG 0.811711 -169 GCCGGATCCGGTCGACGGGTCGGTGTCTTG 13 147 1 GTCGACGGGT 0.782044 -154 ATGGGGGATGGCCGACGAGTTCGCCATCGG 13 198 1 GCCGACGAGT 0.768614 -103 GGCAGGACTGCTGGCAGCGGCCGGTTAGTC 13 232 1 CTGGCAGCGG 0.467636 -69 CGGTTAGTCGGCCGACGGTGGCCGCTGGCC 13 253 1 GCCGACGGTG 0.850087 -48 CCGCGAACCGCCGGAGCCGGCGAGTAGACG 14 65 0 CCGGAGCCGG 0.509592 -95 GCCTCGCACGGGCCGGCACGAC 15 3 1 CTCGCACGGG 0.900253 -75 AGCCCGTCTGCCTGACCCGGTAGCCTCTGC 15 53 1 CCTGACCCGG 0.670163 -25 CGGCAATGCCGTCGAAGTGTGCCGCGTGGA 16 33 0 GTCGAAGTGT 0.332637 -86 CGCCACGGTCGTGGCCGGGGCCCAGGCACG 16 61 1 GTGGCCGGGG 0.870208 -58 ********** Masking position 4 Map Score: 51.4564 Number of sites scoring better than the average of aligned sites = 32700 Number in coding regions = 30539 Number in noncoding regions = 2161 Number of orfs with sites within 600 bp upstream = 1113 Fraction of orfs with sites within 600 bp upstream = 0.178766 Motif number 9 CCGGCGAGCCGTCTCGCCGGA 1 2 0 GTCTCGCCGG 0.786817 -149 GCTGCCCTCTGTGATCGGTGGCCGCCCG 1 133 0 CTGTGATCGG 0.902851 -18 GCGTCGGCGCGTCTCGCCGGCGCAAAGTCC 4 121 0 GTCTCGCCGG 0.786817 -180 CGCAAACGTGCTGTTATCAGCCCAAGACGA 4 204 1 CTGTTATCAG 0.357962 -97 GACCACTCCTATGGGATATAAGGCT 4 286 0 CTCCTATGGG 0.718096 -15 GGCGCCCGGAGTGGTATCGGAGAATCCTCA 5 19 0 GTGGTATCGG 0.398274 -66 ATCCGCCCTCCCATCGCTGTTCGAGTC 5 68 0 CTCCCATCGC 0.900385 -17 CGACGGTACCCGGTTACCGGCGGCCGGTAG 7 21 0 CGGTTACCGG 0.539662 -43 CGCGCAGGATCTGCGCCCGGGTTTGGCGGC 9 22 0 CTGCGCCCGG 0.863685 -246 CCGGGCGGCGCTGCCATCGCGGGAGCCACG 9 218 0 CTGCCATCGC 0.933105 -50 GGTTCGCTGGCTCCGATGGGGCGCCGGCTG 10 20 0 CTCCGATGGG 0.802515 -281 GGCGATTTCGCCGTCATCGGGCAGACCCGA 10 96 1 CCGTCATCGG 0.688531 -205 CCCGTTCGGCATGCCACCGGTTACGATCTT 10 136 1 ATGCCACCGG 0.815786 -165 CTGACGCCGGGTCTCCCCGGCCCTATTGTG 10 180 0 GTCTCCCCGG 0.717079 -121 CGGCGAATACCTGTGACGGCGCGAAATGAT 12 34 0 CTGTGACGGC 0.753552 -28 CGTCTCACCGGCGAATACCTG 12 51 0 GTCTCACCGG 0.931948 -11 CGTGGACGGGGTGCCAGCGCCAACCTGATG 13 82 1 GTGCCAGCGC 0.657958 -219 TTGCCCGGATCTGTTACCGGACGTATGGGG 13 174 1 CTGTTACCGG 0.930426 -127 GCCAGCAGTCCTGCCATCGCCGATGGCGAA 13 217 0 CTGCCATCGC 0.933105 -84 TAACCGGCCGCTGCCAGCAGTCCTGCCATC 13 229 0 CTGCCAGCAG 0.556284 -72 CACATGCTGGCTGTCGCGGGCACCGCGAAC 14 87 0 CTGTCGCGGG 0.868466 -73 GCCTCGCACGGGCCGGCACGAC 15 3 1 CTCGCACGGG 0.831932 -75 GGCAGACGGGCTCCCACGAGCTGCAGTTTT 15 35 0 CTCCCACGAG 0.70744 -43 ACGCGGCACACTTCGACGGCATTGCCGCCA 16 36 1 CTTCGACGGC 0.218327 -83 ********** Masking position 2 Map Score: 19.3404 Number of sites scoring better than the average of aligned sites = 16112 Number in coding regions = 14935 Number in noncoding regions = 1177 Number of orfs with sites within 600 bp upstream = 774 Fraction of orfs with sites within 600 bp upstream = 0.124317 Motif number 10 ACGACGGGCGGCCACCGATCACAGAGGGCAG 1 129 1 GCCACCGTCA 0.956143 -22 GAACGATCAAGCCGCATATTAGTGGAGTCTA 4 44 1 GCCGCATTTA 0.529014 -257 CAAAGTCCAAGCCGCGGGTCATTGTTAGGTT 4 98 0 GCCGCGGTCA 0.995326 -203 TTGCGGCGTCGGCGCGTCTCGCCGGCGCAAA 4 125 0 GGCGCGTTCG 0.661354 -176 ACGTTTGCGTGCCGCGTCTCAATCTAGTGCA 4 182 0 GCCGCGTTCA 0.970344 -119 CTGCCCACCTGGCGCGGTTCGCCACGACAGC 4 258 1 GGCGCGGTCG 0.926989 -43 TACCACTCCGGGCGCCGCTGACAAGCTCTAG 5 33 1 GGCGCCGTGA 0.794253 -52 GTCATTCTGCAGCGCGGATCAGCTCGCGCGG 6 30 0 AGCGCGGTCA 0.807454 -25 CCGTCTACCGGCCGCCGGTAACCGGGTACCG 7 17 1 GCCGCCGTAA 0.935081 -47 CGTCGTCGTGACCGCGGCTCCGGCG 7 49 1 ACCGCGGTCC 0.821316 -15 GCCAAACCCGGGCGCAGATCCTGCGCGCCGC 9 25 1 GGCGCAGTCC 0.815027 -243 CTCATGCCCAGCCGCCCGGCAAGCTCGCCGA 9 97 0 GCCGCCCGCA 0.940736 -171 GCATTTCGGCGCCAAGGAGCAGCTGCAGCTG 9 146 1 GCCAAGGGCA 0.476614 -122 CGTTCGGCATGCCACCGGTTACGATCTTGCC 10 138 1 GCCACCGTTA 0.804978 -163 CACCACTGACGCCGGGTCTCCCCGGCCCTAT 10 184 0 GCCGGGTTCC 0.646652 -117 TACTGACCGTGCCGCCCACCACTGACGCCGG 10 200 0 GCCGCCCCCA 0.907047 -101 CATAGCGTCGGCCGCGGATACAGTAAAGGAG 10 274 1 GCCGCGGTAC 0.861287 -27 CCCCTTGCGGGCCGCCCCGCAACGCTTCTGG 11 25 1 GCCGCCCGCA 0.939744 -70 TCGGGCGATGGCCAAGGTGCACCATGCCGGC 13 52 1 GCCAAGGGCA 0.476567 -249 ACTGCTGGCAGCGGCCGGTTAGTCGGCCGAC 13 238 1 GCGGCCGTTA 0.619601 -63 GCCGACGGTGGCCGCTGGCCAGGATCTCGGG 13 263 1 GCCGCTGCCA 0.890122 -38 AACCGCCGGAGCCGGCGAGTAGACGCGAAAG 14 59 0 GCCGGCGGTA 0.719033 -101 CCACACCATGGCCGCTAGTCAACCATCTATA 14 128 0 GCCGCTATCA 0.557214 -32 CACGGTCGTGGCCGGGGCCCAGGCACGGTCC 16 64 1 GCCGGGGCCA 0.909996 -55 CGGCAACCGCGGCGCAGATTAGTGTGTGTGG 16 98 1 GGCGCAGTTA 0.702174 -21 ******* *** Masking position 3 Map Score: 32.2636 Number of sites scoring better than the average of aligned sites = 17275 Number in coding regions = 16231 Number in noncoding regions = 1044 Number of orfs with sites within 600 bp upstream = 677 Fraction of orfs with sites within 600 bp upstream = 0.108738 Motif number 11 CGATCAAGCCGCATATTAGTGGAGTCTAGCC 4 47 1 GCTATTAGTG 0.893127 -254 TCTAGCCTAAGCTGATTAGTGGAGTCTAACC 4 71 1 GCGATTAGTG 0.97336 -230 AGTCCAAGCCGCGGGTCATTGTTAGGTTAGA 4 95 0 GCGGTCATTG 0.932553 -206 CGATGCTAGAGCTTGTCAGCGGCGCCCGGAG 5 38 0 GCTGTCAGCG 0.940362 -47 AGCCGCGCGAGCTGATCCGCGCTGCAGAATG 6 28 1 GCGATCCGCG 0.944908 -27 AGCCGATATTGCCCGTCAGTCAACCCCGTGT 10 242 0 GCCGTCAGTC 0.891979 -59 GCTGGCAGCGGCCGGTTAGTCGGCCGACGGT 13 241 1 GCGGTTAGTC 0.956188 -60 TTTCGGTCGTGCCGGCCCGTGCGAGGC 15 7 0 GCGGCCCGTG 0.941531 -71 CAACCGCGGCGCAGATTAGTGTGTGTGG 16 101 1 GCGATTAGTG 0.97336 -18 ** ******** Masking position 2 Map Score: 5.60984 Number of sites scoring better than the average of aligned sites = 2176 Number in coding regions = 2020 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 12 GTCAACCTTCTTCCCGCGAGCGCGGAC 2 73 0 CTCTTCCCGC 0.87724 -17 CCTGCGCCGACCCGTACTCGCTGCACTAGAT 4 161 1 CCGTACTCGC 0.945351 -140 TCAGCTCGCGCGGCTACGCGCGGCAAGCATC 6 12 0 CGCTACGCGC 0.989173 -43 GCGCATCCGTCTACCGGCCGCCGGTAAC 7 8 1 CGCTACCGGC 0.991619 -56 CGACGGTACCCGGTTACCGGCGGCCGGTAGA 7 20 0 CGTTACCGGC 0.938829 -44 GCAAGTCGGGCCTGTTCCGGCATTTCGGCGC 9 127 1 CCGTTCCGGC 0.871782 -141 CGGGGTGGACCGGGTGCGCGCCCTCATGCAT 9 245 1 CGGTGCGCGC 0.96385 -23 TCCGATGGGGCGCCGGCTGGCGGCTCTG 10 8 0 CGCGGCTGGC 0.898058 -293 TGTTCTTTTGCGCCTACTCGCG 14 2 0 CGCTACTCGC 0.991008 -158 TGTTCTTTCGCGTCTACTCGCCGGCTCCGGC 14 55 1 CGCTACTCGC 0.991008 -105 ** ******** Masking position 7 Map Score: 12.648 Number of sites scoring better than the average of aligned sites = 1835 Number in coding regions = 1622 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 13 ********** No masking Map Score: -1.9652e-13 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: -1.9652e-13 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: -1.9652e-13 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