AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_mtub_reg_100.orf -o00680_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 glyA2 300 glyA2 #2 Rv0079 300 hypothetical protein Rv0079 #3 Rv0081 94 hypothetical protein Rv0081 #4 adhB 98 adhB #5 Rv0767c 201 hypothetical protein Rv0767c #6 glyA 300 glyA #7 katG 37 katG #8 furA 104 furA #9 adhE2 300 adhE2 Motif number 1 AGGGACGGTCGCACCGACCGTGCCTGACCGAAGG 1 18 1 GACGACCGCC 0.894694 -283 TCGCATCATGGCGCCGCTCTACACCTTCGGTCAG 1 41 0 GGCGCTCCAC 0.980561 -260 GCGCCATGATGCGACGCCGCAGACTCTCAGGTTT 1 61 1 GGCGCCGGAC 0.990286 -240 GAGCGGGGAGGGCGCAACCAGCCCGGCGCGATCC 1 102 1 GCCAACCCCC 0.540122 -199 CAACCAGCCCGGCGCGATCCGGGCTCGTCGAAAC 1 116 1 GCCGATCGGC 0.818269 -185 CGCCGTGGCCGAAACGATGTCGCGGCCGCCGGAT 1 197 1 GACGATGGCG 0.98459 -104 GGCGTACTCGGGGGCGGTCAAGGGTGTTCCCGGA 1 257 0 GGCGGTCGGG 0.951182 -44 TTGGGCCGTTCACGACCCAGCCTCAT 2 3 1 GGCGTTCGAC 0.872585 -298 CGAGGTTGGCGAGCAGATGCAGCGCATGAGGCTG 2 28 0 GGAGATGGCG 0.708382 -273 CAGAAGCTGAGGCTCGCTCTGGACATGTACGAGG 2 57 0 GCCGCTCGAC 0.979621 -244 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTGAGGC 2 78 0 CGCGCTGCAG 0.951763 -223 GTGTGGCAACGAGTCGATCCACACGAAATGCCGC 2 134 1 GGCGATCCAC 0.975221 -167 CCGCCGTTGGGCCGCGGACTAGCCGAATTTTCCG 2 164 1 GCCGGACGCC 0.901942 -137 TTTCCGGGTGGTGACACAGCCCACATTTGGCATG 2 192 1 GGCACAGCAC 0.691464 -109 GGCCGACACGGACGCGGACAGGGCCGAAAGTCCC 2 225 0 GCCGGACGGC 0.798339 -76 TTGGGCATTGGCCACAATCGGGCCACAATCGAAA 2 268 1 GCCAATCGCC 0.712813 -33 GGATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 8 0 GGCGCCCGGC 0.843375 -87 GTCAACCGATGTAACGCTGAAGCTCTCAGGAGAC 3 68 1 GACGCTGGCT 0.811682 -27 ACGCCCTAGCGCCGTTGACCTACACTCAG 4 6 1 CACGCCGGAC 0.882025 -93 TACACTCAGCCAGTCGGCGTTCCGGCCGAGGCTA 4 31 1 CGCGGCGCCG 0.831668 -68 GACAAGTGTCCAATCGATGATGAGAGTCGGAGAA 5 25 0 CACGATGGAG 0.926001 -177 TGCGGATACGGTCTCGATGAGGCAATATCGGACA 5 55 0 GCCGATGGCA 0.746564 -147 TCAGGACGGTGTAGCGGCCTTGCGGATACGGTCT 5 75 0 GACGGCCGCG 0.938314 -127 GGCCCCTGGTGCATCGGTCAGGACGGTGTAGCGG 5 92 0 GACGGTCGAC 0.958159 -110 GACTGTCCGCGACGCGACGTGGCCCCTGGTGCAT 5 112 0 GCCGACGGCC 0.978702 -90 CTTGCCTCCTGCCGCGACCATCCGATAGCTTGGA 5 175 1 GCCGACCCCG 0.936558 -27 CCGCGCCCTGGCCCCAGTGCCCAGCTAAGCCCAG 6 24 0 GCCAGTGCAG 0.736761 -277 GAATTCCATCGAAACACCGCGCCCTGGCCCCAGT 6 40 0 GACACCGCCC 0.597741 -261 CTGTGAATTTCGCACGCTGACGCCGGTTGATGCT 6 84 1 CCCGCTGGCC 0.951958 -217 TAGGTCACGAGTAGCGGTGGGCGGTTTGTGCCCG 6 124 0 GACGGTGCGG 0.875293 -177 TGCCCCAGCTGCCACGTAGGTCACGAGTAGCGGT 6 140 0 GCCGTAGCAC 0.567137 -161 TGTATCCAGCGAGCCGCTCCCGGGCTGATTACCC 6 232 0 GGCGCTCGGG 0.980495 -69 GCTGGATACACTGGCGCCCGTGACTGCTGCACCT 6 256 1 CGCGCCCGAC 0.786491 -45 CTGCACCTGACGCTCGCACTACCGCGGTA 6 282 1 CCCGCACCCG 0.715073 -19 CACCCGCCATCCCACGATCCAGCGGCCCCGGGGC 8 13 1 CCCGATCGCG 0.910557 -92 CGTCTGCTAGGACCCGATCGCCCCGGGGCCGCTG 8 32 0 GCCGATCCCC 0.656262 -73 CCCTTTTCTGGAATCAGTCAAGACTTTGGCTAGC 8 74 0 GACAGTCGAC 0.653515 -31 ATGAGGAGGAGCGGCGCAGATGAGT 9 2 0 GGCGCAGGAG 0.986512 -299 GATGCAGAGCGAAGCGATGAGGAGGAGCGGCGCA 9 18 0 GACGATGGAG 0.985724 -283 AGTCGCGCCGGTGACGATGCAGAGCGAAGCGATG 9 33 0 GGCGATGGAG 0.994101 -268 ATGAGCAGGAGCGGCGCAGATGAGTCGCGCCGGT 9 55 0 GGCGCAGGAG 0.986512 -246 GATGCAGAGCGAAGCGATGAGCAGGAGCGGCGCA 9 71 0 GACGATGCAG 0.970412 -230 AGTCGCGCCGGTGACGATGCAGAGCGAAGCGATG 9 86 0 GGCGATGGAG 0.994101 -215 ATGAGCAGGAGCGGCGCAGATGAGTCGCGCCGGT 9 108 0 GGCGCAGGAG 0.986512 -193 GATGCAGAGCGAAGCGATGAGCAGGAGCGGCGCA 9 124 0 GACGATGCAG 0.970412 -177 AGTCGCGCCGGTGACGATGCAGAGCGAAGCGATG 9 139 0 GGCGATGGAG 0.994101 -162 ATGAGCAGGAGCGGCGCAGATGAGTCGCGCCGGT 9 161 0 GGCGCAGGAG 0.986512 -140 GATGCAGAGCGAAGCGATGAGCAGGAGCGGCGCA 9 177 0 GACGATGCAG 0.970412 -124 AGTCGCGCCGGTGACGATGCAGAGCGAAGCGATG 9 192 0 GGCGATGGAG 0.994101 -109 ATGAGGAGGAGCGGCGCAGATGAGTCGCGCCGGT 9 214 0 GGCGCAGGAG 0.986512 -87 GATGCAGAGCGAAGCGATGAGGAGGAGCGGCGCA 9 230 0 GACGATGGAG 0.985724 -71 ATGCGCGCCGGTGACGATGCAGAGCGAAGCGATG 9 245 0 GGCGATGGAG 0.994101 -56 CTACGGTGTAGCGTCGCTGACCATGCGCGCCGGT 9 267 0 GGCGCTGCAT 0.845389 -34 * * ***** *** Masking position 5 Map Score: 116.702 Number of sites scoring better than the average of aligned sites = 41786 Number in coding regions = 39042 Number in noncoding regions = 2744 Number of orfs with sites within 600 bp upstream = 1165 Fraction of orfs with sites within 600 bp upstream = 0.187119 Motif number 2 CCTGACCGAAGGTGTAGAGCGGCGCCATGATGCG 1 40 1 GGTGTGCGCG 0.914879 -261 AGCCTCAGCTTCTGCGCAGCGACGGAAACTGCCA 2 77 1 TCTGCGCGCG 0.938842 -224 GTGTCCAATCGATGATGAGAGTCGGAGAAGTTGG 5 20 0 GATGAGAGCG 0.989139 -182 CAGGGCCACAGCTGAATTCCATCGAAACACCGCG 6 53 0 GCTGACCACG 0.868729 -248 GACGCCGGTTGATGCTGTGAGTCGGGCACAAACC 6 102 1 GATGCGAGCG 0.989986 -199 CGTTTGCGGTGCAGACGTGCAACGGTGGATGGCG 6 185 1 GCAGAGCACG 0.883953 -116 CCACGATCCAGCGGCCCCGGGGCGATCGGGTCCT 8 24 1 GCGGCGGGCG 0.947958 -81 AGAGCGAAGCGATGAGGAGGAGCGGCGCAGATGA 9 13 0 GATGAGGACG 0.992108 -288 CGCCGGTGACGATGCAGAGCGAAGCGATGAGGAG 9 28 0 GATGCGCGAG 0.994628 -273 GAGCGGCGCAGATGAGTCGCGCCGGTGACGATGC 9 47 0 GATGAGCGCG 0.998823 -254 AGAGCGAAGCGATGAGCAGGAGCGGCGCAGATGA 9 66 0 GATGAGGACG 0.992108 -235 CGCCGGTGACGATGCAGAGCGAAGCGATGAGCAG 9 81 0 GATGCGCGAG 0.994628 -220 GAGCGGCGCAGATGAGTCGCGCCGGTGACGATGC 9 100 0 GATGAGCGCG 0.998823 -201 AGAGCGAAGCGATGAGCAGGAGCGGCGCAGATGA 9 119 0 GATGAGGACG 0.992108 -182 CGCCGGTGACGATGCAGAGCGAAGCGATGAGCAG 9 134 0 GATGCGCGAG 0.994628 -167 GAGCGGCGCAGATGAGTCGCGCCGGTGACGATGC 9 153 0 GATGAGCGCG 0.998823 -148 AGAGCGAAGCGATGAGCAGGAGCGGCGCAGATGA 9 172 0 GATGAGGACG 0.992108 -129 CGCCGGTGACGATGCAGAGCGAAGCGATGAGCAG 9 187 0 GATGCGCGAG 0.994628 -114 GAGCGGCGCAGATGAGTCGCGCCGGTGACGATGC 9 206 0 GATGAGCGCG 0.998823 -95 AGAGCGAAGCGATGAGGAGGAGCGGCGCAGATGA 9 225 0 GATGAGGACG 0.992108 -76 CGCCGGTGACGATGCAGAGCGAAGCGATGAGGAG 9 240 0 GATGCGCGAG 0.994628 -61 ***** *** ** Masking position 4 Map Score: 68.8765 Number of sites scoring better than the average of aligned sites = 2123 Number in coding regions = 1915 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 GTCGGTGCGACCGTCCCTGTCTCCA 1 6 0 CCGTCCCTGT 0.891223 -295 GTCGCACCGACCGTGCCTGACCGAAGGTGT 1 25 1 CCGTGCCTGA 0.709075 -276 CTGGTTGCGCCCTCCCCGCTCTGTCCTGAA 1 93 0 CCTCCCCGCT 0.813435 -208 CGAGCCCGGATCGCGCCGGGCTGGTTGCGC 1 113 0 TCGCGCCGGG 0.973697 -188 GGCCGCGACATCGTTTCGGCCACGGCGAGG 1 194 0 TCGTTTCGGC 0.843792 -107 GGAGCAATCGGCTGCCCGGCCAAATGGGCA 1 230 0 GCTGCCCGGC 0.7139 -71 ACACCCTTGACCGCCCCCGAGTACGCCGAA 1 264 1 CCGCCCCCGA 0.603503 -37 AAGCTGAGGCTCGCTCTGGACATGTACGAG 2 58 0 TCGCTCTGGA 0.525445 -243 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTG 2 82 0 CCGTCGCTGC 0.449216 -219 CATGGGACTTTCGGCCCTGTCCGCGTCCGT 2 222 1 TCGGCCCTGT 0.817579 -79 CTGTCCGCGTCCGTGTCGGCCAGACAAGCT 2 238 1 CCGTGTCGGC 0.918637 -63 GCGGATGCGTGCGGGCCGCCCGCGGCCAAT 3 14 0 GCGGGCCGCC 0.941682 -81 TAGGTCAACGGCGCTAGGGCGT 4 3 0 GCGCTAGGGC 0.460701 -96 CAGCCAGTCGGCGTTCCGGCCGAGGCTAGG 4 37 1 GCGTTCCGGC 0.969528 -62 GGACGGTGTAGCGGCCTTGCGGATACGGTC 5 76 0 GCGGCCTTGC 0.39159 -126 ATGGGACTGTCCGCGACGCGACGTGGCCCC 5 120 0 CCGCGACGCG 0.666849 -82 TAGCAGACTGGCTTGCCTCCTGCCGCGACC 5 164 1 GCTTGCCTCC 0.344078 -38 TCGAAACACCGCGCCCTGGCCCCAGTGCCC 6 36 0 GCGCCCTGGC 0.919493 -265 CCAGCGAGCCGCTCCCGGGCTGATTACCCT 6 231 0 GCTCCCGGGC 0.502917 -70 ACACTGGCGCCCGTGACTGCTGCACCTGAC 6 263 1 CCGTGACTGC 0.624524 -38 TAGGACCCGATCGCCCCGGGGCCGCTGGAT 8 29 0 TCGCCCCGGG 0.968841 -76 CTCATCTGCGCCGCTCCTCCTCATCGCTTC 9 12 1 CCGCTCCTCC 0.969089 -289 CTCCTCCTCATCGCTTCGCTCTGCATCGTC 9 25 1 TCGCTTCGCT 0.843955 -276 CGCAGATGAGTCGCGCCGGTGACGATGCAG 9 45 0 TCGCGCCGGT 0.989597 -256 CTCATCTGCGCCGCTCCTGCTCATCGCTTC 9 65 1 CCGCTCCTGC 0.986017 -236 CTCCTGCTCATCGCTTCGCTCTGCATCGTC 9 78 1 TCGCTTCGCT 0.843955 -223 CGCAGATGAGTCGCGCCGGTGACGATGCAG 9 98 0 TCGCGCCGGT 0.989597 -203 CTCATCTGCGCCGCTCCTGCTCATCGCTTC 9 118 1 CCGCTCCTGC 0.986017 -183 CTCCTGCTCATCGCTTCGCTCTGCATCGTC 9 131 1 TCGCTTCGCT 0.843955 -170 CGCAGATGAGTCGCGCCGGTGACGATGCAG 9 151 0 TCGCGCCGGT 0.989597 -150 CTCATCTGCGCCGCTCCTGCTCATCGCTTC 9 171 1 CCGCTCCTGC 0.986017 -130 CTCCTGCTCATCGCTTCGCTCTGCATCGTC 9 184 1 TCGCTTCGCT 0.843955 -117 CGCAGATGAGTCGCGCCGGTGACGATGCAG 9 204 0 TCGCGCCGGT 0.989597 -97 CTCATCTGCGCCGCTCCTCCTCATCGCTTC 9 224 1 CCGCTCCTCC 0.969089 -77 CTCCTCCTCATCGCTTCGCTCTGCATCGTC 9 237 1 TCGCTTCGCT 0.843955 -64 CGCTGACCATGCGCGCCGGTGACGATGCAG 9 257 0 GCGCGCCGGT 0.990053 -44 ********** Masking position 2 Map Score: 61.2712 Number of sites scoring better than the average of aligned sites = 35843 Number in coding regions = 33156 Number in noncoding regions = 2687 Number of orfs with sites within 600 bp upstream = 1265 Fraction of orfs with sites within 600 bp upstream = 0.20318 Motif number 4 AACCTGAGAGTCTGCGGCGTCGCATCATGG 1 64 0 TCTGCGGCGT 0.80552 -237 GCCAAATGGGCATCCGGCGGCCGCGACATC 1 212 0 CATCCGGCGG 0.619797 -89 AGTCCGCGGCCCAACGGCGGCATTTCGTGT 2 154 0 CCAACGGCGG 0.927065 -147 CCGATTGGCCGCGGGCGGCCCGCACGCA 3 9 1 CCGCGGGCGG 0.583084 -86 TGAGTGTAGGTCAACGGCGCTAGGGCGT 4 9 0 TCAACGGCGC 0.99322 -90 CTCACAGCATCAACCGGCGTCAGCGTGCGA 6 93 0 CAACCGGCGT 0.844684 -208 CACACGCCATCCACCGTTGCACGTCTGCAC 6 193 0 CCACCGTTGC 0.565789 -108 GGTGCAGCAGTCACGGGCGCCAGTGTATCC 6 259 0 TCACGGGCGC 0.992235 -42 ATCCCACGATCCAGCGGCCCCGGGGCGATC 8 21 1 CCAGCGGCCC 0.935788 -84 ACTCATCTGCGCCGCTCCTCCT 9 3 1 TCATCTGCGC 0.986447 -298 CTCTGCATCGTCACCGGCGCGACTCATCTG 9 43 1 TCACCGGCGC 0.997713 -258 CCGGCGCGACTCATCTGCGCCGCTCCTGCT 9 56 1 TCATCTGCGC 0.986447 -245 CTCTGCATCGTCACCGGCGCGACTCATCTG 9 96 1 TCACCGGCGC 0.997713 -205 CCGGCGCGACTCATCTGCGCCGCTCCTGCT 9 109 1 TCATCTGCGC 0.986447 -192 CTCTGCATCGTCACCGGCGCGACTCATCTG 9 149 1 TCACCGGCGC 0.997713 -152 CCGGCGCGACTCATCTGCGCCGCTCCTGCT 9 162 1 TCATCTGCGC 0.986447 -139 CTCTGCATCGTCACCGGCGCGACTCATCTG 9 202 1 TCACCGGCGC 0.997713 -99 CCGGCGCGACTCATCTGCGCCGCTCCTCCT 9 215 1 TCATCTGCGC 0.986447 -86 CTCTGCATCGTCACCGGCGCGCATGGTCAG 9 255 1 TCACCGGCGC 0.997713 -46 GCGCGCATGGTCAGCGACGCTACACCGTAG 9 271 1 TCAGCGACGC 0.936296 -30 ********** Masking position 8 Map Score: 57.1963 Number of sites scoring better than the average of aligned sites = 5997 Number in coding regions = 5637 Number in noncoding regions = 360 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 5 CCGACCGTGCCTGACCGAAGGTGTAGAGCG 1 31 1 CTGACCGAAG 0.971474 -270 GGTTTCAGGACAGAGCGGGGAGGGCGCAAC 1 90 1 CAGAGCGGGG 0.992495 -211 TCGTTTCGGCCACGGCGAGGTCGCCAACAG 1 184 0 CACGGCGAGG 0.950057 -117 GTACGCCGAACAGACCGGACTGAGCTG 1 284 1 CAGACCGGAC 0.911585 -17 CGTACATGTCCAGAGCGAGCCTCAGCTTCT 2 60 1 CAGAGCGAGC 0.986942 -241 AGTCGGCGTTCCGGCCGAGGCTAGGGACCA 4 42 1 CCGGCCGAGG 0.943629 -57 CTACACCGTCCTGACCGATGCACCAGGGGC 5 95 1 CTGACCGATG 0.859217 -107 GCACTGGGGCCAGGGCGCGGTGTTTCGATG 6 38 1 CAGGGCGCGG 0.972595 -263 GGTGACGATGCAGAGCGAAGCGATGAGGAG 9 28 0 CAGAGCGAAG 0.996993 -273 GGTGACGATGCAGAGCGAAGCGATGAGCAG 9 81 0 CAGAGCGAAG 0.996993 -220 GGTGACGATGCAGAGCGAAGCGATGAGCAG 9 134 0 CAGAGCGAAG 0.996993 -167 GGTGACGATGCAGAGCGAAGCGATGAGCAG 9 187 0 CAGAGCGAAG 0.996993 -114 GGTGACGATGCAGAGCGAAGCGATGAGGAG 9 240 0 CAGAGCGAAG 0.996993 -61 ********** Masking position 6 Map Score: 34.86 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 293 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GTCGCATCATGGCGCCGCTCTACACCTTCGGTCAG 1 41 0 GGCCGCTCAC 0.427327 -260 GGCGCCATGATGCGACGCCGCAGACTCTCAGGTTT 1 60 1 TGCCGCCGAC 0.794719 -241 TCGACGAGCCCGGATCGCGCCGGGCTGGTTGCGCC 1 112 0 CGGCGCCGGC 0.964225 -189 CGCGGCCGCCGGATGCCCATTTGGCCGGGCAGCCG 1 217 1 GGACCCTGGC 0.817763 -84 CGATTGCTCCGGGAACACCCTTGACCGCCCCCGAG 1 250 1 GGGCACTGAC 0.860893 -51 CGGTCTGTTCGGCGTACTCGGGGGCGGTCAAGGGT 1 266 0 GGCACTGGGC 0.343616 -35 CGCATGAGGCTGGGTCGTGAACGGCCCAA 2 5 0 TGGCGTAGGC 0.79872 -296 GGCGAGCAGATGCAGCGCATGAGGCTGGGTCGTGA 2 20 0 TGCCGCGGGC 0.995487 -281 CGACGGAAACTGCCACACTCAAAGCCTACTGGGCG 2 96 1 TGCCACAAGC 0.891068 -205 AAAGCCTACTGGGCGCACGTGTGGCAACGAGTCGA 2 116 1 GGGCACGGGC 0.99659 -185 GGCTAGTCCGCGGCCCAACGGCGGCATTTCGTGTG 2 153 0 CGGCAAGGGC 0.916885 -148 CTTTCGATTGTGGCCCGATTGTGGCCAATGCCCAA 2 268 0 TGGCGAGGGC 0.951954 -33 CGGATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 8 0 CGGCGCGGGC 0.993877 -87 GCCGAGGCTAGGGACCACTCGTAGCCGAAGTTCAA 4 55 1 GGGCACGAGC 0.983266 -44 CCGTCCTGACCGATGCACCAGGGGCCACGTCGCGT 5 100 1 CGACACGGGC 0.964428 -102 CAAGCCAGTCTGCTAAACATGCAGCTAACATGGGA 5 144 0 TGCAACGAGC 0.741212 -58 CCGGGGGTACCCCCTGGGCTTAGCTGGGC 6 5 1 GGGCCCTGGC 0.961165 -296 GGGCGGTTTGTGCCCGACTCACAGCATCAACCGGC 6 105 0 TGCGACAAGC 0.325297 -196 AGCTGCCACGTAGGTCACGAGTAGCGGTGGGCGGT 6 133 0 TAGCACGAGC 0.642794 -168 ACGTGGCAGCTGGGGCACTAGTGGCTGCCGTTTGC 6 157 1 TGGCACGGGC 0.995974 -144 GTTGCACGTCTGCACCGCAAACGGCAGCCACTAGT 6 173 0 TGCCGCAGGC 0.977863 -128 GCGGCTCGCTGGATACACTGGCGCCCGTGACTGCT 6 249 1 GGACACGGCC 0.766429 -52 CGCCCGTGACTGCTGCACCTGACGCTCGCACTACC 6 270 1 TGCCACGCGC 0.964893 -31 *** *** * *** Masking position 15 Map Score: 29.3628 Number of sites scoring better than the average of aligned sites = 15253 Number in coding regions = 14295 Number in noncoding regions = 958 Number of orfs with sites within 600 bp upstream = 620 Fraction of orfs with sites within 600 bp upstream = 0.0995824 Motif number 7 GGGGAGGGCGCAACCAGCCCGGCGCGATCCGGG 1 106 1 CACAGCCCGC 0.933967 -195 TGCGCTGCATCTGCTCGCCAACCTCGTACATGT 2 36 1 CGCCGCCACC 0.972736 -265 CGACTCGTTGCCACACGTGCGCCCAGTAGGCTT 2 117 0 CACCGTGCCC 0.991781 -184 GCACGTGTGGCAACGAGTCGATCCACACGAAAT 2 130 1 CACAGTCGTC 0.819471 -171 TGGGCATTGGCCACAATCGGGCCACAATCGAAA 2 269 1 CACATCGGCC 0.826864 -32 ATAAATTCTTCAACTCGTCAACCGATGTAACGC 3 52 1 CACCGTCACC 0.992358 -43 TGAACTTCGGCTACGAGTGGTCCCTAGCCTCGG 4 56 0 CACAGTGGCC 0.976486 -43 GAGTCGGGCACAAACCGCCCACCGCTACTCGTG 6 120 1 CAACGCCCCC 0.950492 -181 CCGCCCACCGCTACTCGTGACCTACGTGGCAGC 6 134 1 CACCGTGACT 0.870556 -167 CAAACGGCAGCCACTAGTGCCCCAGCTGCCACG 6 158 0 CACAGTGCCC 0.982021 -143 CCTTAATGCAGCACACGCCATCCACCGTTGCAC 6 201 0 GACCGCCACC 0.956714 -100 TCCACCCGCCATCCCACGATCCAG 8 2 1 CACCGCCACC 0.995211 -103 * ** ***** ** Masking position 3 Map Score: 14.9533 Number of sites scoring better than the average of aligned sites = 4156 Number in coding regions = 3868 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 8 GACAGAGCGGGGAGGGCGCAACCAGCCCGG 1 98 1 GGAGGGCGCA 0.651295 -203 ACGATCGAACTGTTGGCGACCTCGCCGTGG 1 175 1 TGTTGGCGAC 0.184076 -126 ATGGGCATCCGGCGGCCGCGACATCGTTTC 1 207 0 GGCGGCCGCG 0.922148 -94 CGGAGCAATCGGCTGCCCGGCCAAATGGGC 1 231 0 GGCTGCCCGG 0.893646 -70 ACATGTACGAGGTTGGCGAGCAGATGCAGC 2 39 0 GGTTGGCGAG 0.969453 -262 AAGCCTACTGGGCGCACGTGTGGCAACGAG 2 117 1 GGCGCACGTG 0.791675 -184 GCGTTACATCGGTTGACGAGTTGAAGAATT 3 55 0 GGTTGACGAG 0.845828 -40 CACGAGTAGCGGTGGGCGGTTTGTGCCCGA 6 123 0 GGTGGGCGGT 0.91119 -178 GGGCACTAGTGGCTGCCGTTTGCGGTGCAG 6 169 1 GGCTGCCGTT 0.858887 -132 GTGCAACGGTGGATGGCGTGTGCTGCATTA 6 201 1 GGATGGCGTG 0.969453 -100 GCCCGGGAGCGGCTCGCTGGATACACTGGC 6 241 1 GGCTCGCTGG 0.757762 -60 CTGGATCGTGGGATGGCGGGTGGA 8 5 0 GGATGGCGGG 0.984215 -100 GCGGCCCCGGGGCGATCGGGTCCTAGCAGA 8 34 1 GGCGATCGGG 0.732442 -71 TCAAGACTTTGGCTAGCGTGACAGGCGTCT 8 61 0 GGCTAGCGTG 0.939859 -44 ********** Masking position 7 Map Score: 7.90001 Number of sites scoring better than the average of aligned sites = 12190 Number in coding regions = 11318 Number in noncoding regions = 872 Number of orfs with sites within 600 bp upstream = 648 Fraction of orfs with sites within 600 bp upstream = 0.10408 Motif number 9 TCGACGAGCCCGGATCGCGCCGGGCTGGTTGCG 1 114 0 CGGACCCCGG 0.982865 -187 AGGGCCAACTCCGGTTTCGACGAGCCCGGATCG 1 130 0 CCGGTCACGA 0.885454 -171 CCGCCGGATGCCCATTTGGCCGGGCAGCCGATT 1 222 1 CCCATGCCGG 0.877119 -79 GGCCGGGCAGCCGATTGCTCCGGGAACACCCTT 1 239 1 CCGATCCCGG 0.99528 -62 TTGACCGCCCCCGAGTACGCCGAACAGACCGGA 1 270 1 CCGATCCCGA 0.992649 -31 CGCGGACTAGCCGAATTTTCCGGGTGGTGACAC 2 176 1 CCGATTCCGG 0.942152 -125 GACACGGACGCGGACAGGGCCGAAAGTCCCATG 2 222 0 CGGAAGCCGA 0.72972 -79 CACTCGTAGCCGAAGTTCAACGATGAAAGCAGG 4 70 1 CGAATCACGA 0.800226 -29 CTACCGCTCCCAACTTCTCCGACTCTCATCAT 5 10 1 CCAATCCCGA 0.981729 -192 CGTCAGCGTGCGAAATTCACAGGGCCACAGCTG 6 73 0 CGAATCCAGG 0.714319 -228 CACTAGTGCCCCAGCTGCCACGTAGGTCACGAG 6 147 0 CCAGTCACGT 0.389851 -154 TCACAGCCCGATAACACCAACTCCTGGAAG 7 8 1 CCGAACCCAA 0.671302 -30 CTGCTAGGACCCGATCGCCCCGGGGCCGCTGGA 8 30 0 CCGACCCCGG 0.98436 -75 GCGTCGCTGACCATGCGCGCCGGTGACGATGCA 9 258 0 CCATCCCCGG 0.864939 -43 **** * * **** Masking position 1 Map Score: 14.8378 Number of sites scoring better than the average of aligned sites = 11130 Number in coding regions = 10614 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 406 Fraction of orfs with sites within 600 bp upstream = 0.0652104 Motif number 10 TGGAGACAGGGACGGTCGCACCG 1 4 1 AGACAGGGAC 0.872436 -297 TCAGGTTTCAGGACAGAGCGGGGAGGGCGC 1 87 1 GGACAGAGCG 0.716547 -214 GTGCGGTTCAGACAAGGGCCAACTCCGGTT 1 147 0 GACAAGGGCC 0.944668 -154 ACATCGTTTCGGCCACGGCGAGGTCGCCAA 1 187 0 GGCCACGGCG 0.763958 -114 GCCGCCGTTGGGCCGCGGACTAGCCGAATT 2 163 1 GGCCGCGGAC 0.749881 -138 GCCCACATTTGGCATGGGACTTTCGGCCCT 2 210 1 GGCATGGGAC 0.955038 -91 ACACGGACGCGGACAGGGCCGAAAGTCCCA 2 224 0 GGACAGGGCC 0.943646 -77 ACAAGCTTTGGGCATTGGCCACAATCGGGC 2 261 1 GGCATTGGCC 0.677787 -40 AGGTCAACGGCGCTAGGGCGT 4 2 0 CGCTAGGGCG 0.774123 -97 TTCCGGCCGAGGCTAGGGACCACTCGTAGC 4 50 1 GGCTAGGGAC 0.959949 -49 ACATGCAGCTAACATGGGACTGTCCGCGAC 5 133 0 AACATGGGAC 0.434974 -69 TGGGCACTGGGGCCAGGGCGCGGTGTTTCG 6 35 1 GGCCAGGGCG 0.782223 -266 AAGGGTAATCAGCCCGGGAGCGGCTCGCTG 6 230 1 AGCCCGGGAG 0.804524 -71 ACTGATTCCAGAAAAGGGAGTCATA 8 90 1 GAAAAGGGAG 0.680608 -15 ********** Masking position 8 Map Score: 12.8349 Number of sites scoring better than the average of aligned sites = 10103 Number in coding regions = 9517 Number in noncoding regions = 586 Number of orfs with sites within 600 bp upstream = 431 Fraction of orfs with sites within 600 bp upstream = 0.0692258 Motif number 11 GCTCTACACCTTCGGTCAGGCACGGTCGGTGC 1 28 0 TTGTCAGGCA 0.823752 -273 CGGATGCCCATTTGGCCGGGCAGCCGATTGCT 1 226 1 TTGCCGGGCA 0.974884 -75 CCGCCCCCGAGTACGCCGAACAGACCGGACTG 1 274 1 GTGCCGAACA 0.972127 -27 CCGCGTCCGTGTCGGCCAGACAAGCTTTGGGC 2 242 1 GTGCCAGACA 0.972127 -59 GGCCACAATCGAAAGCCGAGCAG 2 288 1 GAGCCGAGCA 0.939249 -13 AATCGATGATGAGAGTCGGAGAAGTTGGGAGC 5 16 0 GAGTCGGAGA 0.655023 -186 AGGCAAGCCAGTCTGCTAAACATGCAGCTAAC 5 150 0 GTGCTAAACA 0.735214 -52 ACCCCCTGGGCTTAGCTGGGCACTGGGGCCAG 6 19 1 CTGCTGGGCA 0.902011 -282 GGTTGATGCTGTGAGTCGGGCACAAACCGCCC 6 108 1 GTGTCGGGCA 0.988252 -193 ACGCTACACCGTAGGTTGGACACC 9 287 1 GTGTTGGACA 0.937043 -14 ** ******** Masking position 12 Map Score: 6.44464 Number of sites scoring better than the average of aligned sites = 3099 Number in coding regions = 2871 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 12 ********** No masking Map Score: -2.96053e-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 13 ********** No masking Map Score: -2.96053e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: -2.96053e-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