AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_mtub_reg_100.orf -o00720_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 Rv0248c 30 hypothetical protein Rv0248c #2 Rv0249c 79 hypothetical protein Rv0249c #3 Rv0250c 144 hypothetical protein Rv0250c #4 sucC 300 sucC #5 fum 30 fum #6 Rv1099c 100 hypothetical protein Rv1099c #7 mdh 170 mdh #8 acn 157 acn #9 frdA 300 frdA #10 pks12 300 pks12 #11 scoA 82 scoA #12 fadD35 115 fadD35 #13 ald 89 ald #14 sdhC 236 sdhC #15 sdhA 128 sdhA #16 icd1 282 icd1 #17 acs 300 acs Motif number 1 TCTCTGTGTACCCTTCGACGAGATAACACG 2 42 1 CCCTTCGACG 0.5929 -38 ACGGCATGATCCGGCCGGGCCGATGGGTCC 3 19 1 CCGGCCGGGC 0.879433 -126 CCGGGCCGATGGGTCCGCCGGATCATGCCA 3 33 1 GGGTCCGCCG 0.963747 -112 CCCAACGACTCCGTCCGTCGATAGCTAGTA 3 77 1 CCGTCCGTCG 0.968224 -68 GTAACACCGCCAGCCCAGGGAGCACCCA 3 127 1 CAGCCCAGGG 0.735947 -18 TCAGATTTGTCCCAGCACCGTATCGCCCGT 4 11 0 CCCAGCACCG 0.86724 -290 GTTATGGTCACGATCCGAGGACATTTCAGA 4 36 0 CGATCCGAGG 0.4124 -265 CGGTGTGGCACAGCTCACCGATATGTTTGT 4 164 0 CAGCTCACCG 0.570683 -137 CCGGGTGGATGCGGCCGCGGAGTTAATCGG 4 191 1 GCGGCCGCGG 0.992573 -110 GAACTGTATCGAGACCGCCGATTAACTCCG 4 208 0 GAGACCGCCG 0.955052 -93 GTTCTCCGTGCGAGTCGCCGATTTCGGCAC 4 234 1 CGAGTCGCCG 0.730388 -67 GAGCAGTAAGCCGAGCGAAGACGGTGAGCC 4 280 1 CCGAGCGAAG 0.615799 -21 GGGCTCACCGTCTTCGCTCG 4 291 0 GGGCTCACCG 0.660271 -10 GCTGGCCACCGCGGCCGTCGACGAACCGGA 6 24 0 GCGGCCGTCG 0.988488 -77 TGGCCAGCCACGACCCGTCGCACACCAGGC 6 46 1 CGACCCGTCG 0.794654 -55 CGTCGCACACCAGGCCATCGCGCCGGGAAG 6 61 1 CAGGCCATCG 0.820375 -40 GGCCAGGTTGCGGTCCGGGGCTTCCCGGCG 6 81 0 CGGTCCGGGG 0.87965 -20 GTCAACCTCCGATCGCGGTGGATCTGAT 7 9 1 CCGATCGCGG 0.906248 -162 CGCATCCTTCCTGCCGACGTGCTACTGGC 8 10 1 CCTGCCGACG 0.865925 -148 GCGCCGAAGTGCGAGCAGCGCGTAACGTGC 8 38 0 GCGAGCAGCG 0.898069 -120 TCGCACTTCGGCGCGCACCCACACGGCAAC 8 54 1 GCGCGCACCC 0.488055 -104 AGGCTGACACCACGCCGTCGACACGGCCCG 8 106 1 CACGCCGTCG 0.898021 -52 ATTTGGTTCGCCCGCCGACGGGCCGTGTCG 8 124 0 CCCGCCGACG 0.964321 -34 CCGGGCATAGTCTGAATGTG 9 1 1 CCGGGCATAG 0.600274 -300 TAGGTCACGTGCCAGCACCGGAGGAGGCGG 9 34 1 GCCAGCACCG 0.875065 -267 CGTAGTGGTCGCGACCATAGTCCCGCCTCC 9 56 0 GCGACCATAG 0.509697 -245 TCAACCATGTGCCCGCAGGGCGCTTTTTGC 9 97 0 GCCCGCAGGG 0.568388 -204 TCACCACATCGAGCGCGACGACGAAGGCCT 9 133 1 GAGCGCGACG 0.79309 -168 AGGAAAACTTGAGGTCGTCGTAGGCAAGGC 9 159 0 GAGGTCGTCG 0.722994 -142 GGATTTCGCGGCAGCCGCAGGAAAACTTGA 9 177 0 GCAGCCGCAG 0.852262 -124 GTACCCGCATGGATCCGTCGTGGTAGAAAT 9 210 0 GGATCCGTCG 0.662267 -91 GAAGGACGAGCACAGCGGCGATCACGAAGC 9 268 1 CACAGCGGCG 0.788521 -33 GAAGACCACCGCTAGCACCGCATTGACATG 10 31 1 GCTAGCACCG 0.62897 -270 TGACATGCGCCCATCCGGCGTTGACGGGCG 10 54 1 CCATCCGGCG 0.918519 -247 GCGACTGTACCCGCCCGCCCGTCAACGCCG 10 69 0 CCGCCCGCCC 0.898048 -232 GCAAAGCCTGCCGTCCATGGCGCGACTGTA 10 90 0 CCGTCCATGG 0.810991 -211 GGGCACCAGTGCGCCCGTGCAAAGCCTGCC 10 108 0 GCGCCCGTGC 0.715696 -193 GCTTTGAAATCCTGCCGGAGTTGGCAATAC 10 152 1 CCTGCCGGAG 0.676899 -149 GAACTTGCGCCAGAGCGCCGTACGACGGCG 10 190 1 CAGAGCGCCG 0.929173 -111 TGCACAAAACGACGCCGTCGTACGGCGCTC 10 202 0 GACGCCGTCG 0.889566 -99 GCCGGATGCGGCTCCCGCCGAGTCACCGAA 10 237 0 GCTCCCGCCG 0.947737 -64 TTGGCCGTCGCCGACCGCCGGATGCGGCTC 10 253 0 CCGACCGCCG 0.991351 -48 GAATACCATTGCCCCCGCGGTGCGTCTAGG 11 15 0 GCCCCCGCGG 0.969184 -68 GCGGTAGGCACCAGGCGGAGGAACC 12 101 1 CCAGGCGGAG 0.681372 -15 TCGGCAACCCCGCTCGTCGATGGGCCGAC 14 10 1 CCGCTCGTCG 0.89526 -227 GATCGTGTGTGGATCCGGGGTTAGGCTGGC 14 48 0 GGATCCGGGG 0.64603 -189 CGGACTGTTCGACACCGCGGGCAACCTGGC 14 83 1 GACACCGCGG 0.844727 -154 ACCGTCTCGCGCGGGCGGCGGCCACCTCGG 14 193 1 GCGGGCGGCG 0.985603 -44 CCCCGATACAGGGTCCGAGGTGGCCGCCGC 14 207 0 GGGTCCGAGG 0.760334 -30 GGTACCGCCCGCTTGCGGGGGAGAGGTGGC 15 37 0 GCTTGCGGGG 0.588854 -92 AAGCGACGAGGGGGCCGCAGCGATGAGGTG 15 69 0 GGGGCCGCAG 0.9011 -60 GCCCCCTCGTCGCTTCGCGGCTGGGGGTGC 15 84 1 CGCTTCGCGG 0.525781 -45 ACGATGCAGTGGGGGCACCCCCAGCCGCGA 15 98 0 GGGGGCACCC 0.479563 -31 CGCCGCCGCCGACGATGCAGT 15 118 0 GCCGCCGCCG 0.991577 -11 TGGTCAGGGGCCCGTCATGGCGGACCCGCG 16 25 1 CCCGTCATGG 0.475298 -258 CGGCTGCGCGGCAAGCGCGGGTCCGCCATG 16 40 0 GCAAGCGCGG 0.864797 -243 CGCTTGCCGCGCAGCCGGCGATGGCTACTC 16 53 1 GCAGCCGGCG 0.967787 -230 CCCGGGGCACCCCACCGCGGTTGGAGGGTT 16 96 1 CCCACCGCGG 0.96742 -187 TGCCGGCCAGCAAGCCGGGGCTTGACGCTG 16 125 1 CAAGCCGGGG 0.778632 -158 AGGGCCAGTTGAGACCGCCGGAGTTGTGCT 16 210 0 GAGACCGCCG 0.955052 -73 ATTACTAGCAGCCCGCGCGGGCCCCTAGCG 16 248 0 GCCCGCGCGG 0.561219 -35 TTAGCTTTATCGGCGCGGCGGATCGCGTTG 17 22 0 CGGCGCGGCG 0.501634 -279 ATCTCCGTTGCCGGCCACCGTAACCGTCAG 17 101 1 CCGGCCACCG 0.985151 -200 CGTTGGTCGGCCTTGCAGCGTGCGGCTGGC 17 147 0 CCTTGCAGCG 0.410582 -154 CGCTGCAAGGCCGACCAACGTGTGATGTGT 17 157 1 CCGACCAACG 0.858042 -144 CGACGATACAGCCGGCATGGCAGAGGTTGA 17 262 0 GCCGGCATGG 0.753861 -39 GTGAGCCTAACCGCGCGACGATACAGCCGG 17 277 0 CCGCGCGACG 0.580561 -24 ********** Masking position 6 Map Score: 84.875 Number of sites scoring better than the average of aligned sites = 109299 Number in coding regions = 102602 Number in noncoding regions = 6697 Number of orfs with sites within 600 bp upstream = 1698 Fraction of orfs with sites within 600 bp upstream = 0.272727 Motif number 2 ACAACCGAGCCCCCCAGAAAAAGGG 2 4 1 ACCGAGCCCC 0.928356 -76 CATCGGCCCGGCCGGATCATGCCGTATCGCGA 3 12 0 GCCGGACAGC 0.788971 -133 CGATGGGTCCGCCGGATCATGCCATTGGGCCG 3 39 1 GCCGGACAGC 0.788971 -106 ATGCCATTGGGCCGAGTAGACCCAACGACTCC 3 57 1 GCCGAGAGCC 0.922709 -88 TTGTCCCAGCACCGTATCGCCCGT 4 3 0 ACCGTACGCC 0.581674 -298 CACAATCACAGCCGAATTCCGCGCTGAAGTTG 4 110 0 GCCGAATCGC 0.524259 -191 TGTTTGTCCAGCCGAAACGTGATCCAACTCAC 4 139 0 GCCGAACGGA 0.657589 -162 TAACTCCGCGGCCGCATCCACCCGGTGTGGCA 4 184 0 GCCGCACCCC 0.975386 -117 GGTAGGCGGTGCCGAAATCGGCGACTCGCACG 4 240 0 GCCGAATCGC 0.764586 -61 TTCGTCGACGGCCGCGGTGGCCAGCCACGACC 6 29 1 GCCGCGTGCC 0.989784 -72 AGGCCATCGCGCCGGGAAGCCCCGGACCGCAA 6 72 1 GCCGGGAGCC 0.95071 -29 GAAGCCCCGGACCGCAACCTGGCC 6 87 1 ACCGCACCGG 0.783705 -14 GATCAGATCCACCGCGATCGGAGGTTGAC 7 8 0 ACCGCGTCGA 0.708982 -163 CAAGTTCCATACCGGGACGCGTAACCTGGAGC 7 47 0 ACCGGGCGGT 0.502282 -124 GTGGGTGCGCGCCGAAGTGCGAGCAGCGCGTA 8 44 0 GCCGAATGGA 0.505932 -114 CCGCCGACGGGCCGTGTCGACGGCGTGGTGTC 8 111 0 GCCGTGCGCG 0.869099 -47 CGACCATAGTCCCGCCTCCTCCGGTGCTGGCA 9 43 0 CCCGCCCCCC 0.80311 -258 CACATGGTTGACGGCGATCACCACATCGAGCG 9 116 1 ACGGCGTCCC 0.898148 -185 TCCTGCGGCTGCCGCGAAATCCGGCATTTCTA 9 185 1 GCCGCGAACC 0.871732 -116 GACGAGCACAGCGGCGATCACGAAGCGTGAAC 9 272 1 GCGGCGTCCG 0.924664 -29 CACCGCTAGCACCGCATTGACATGCGCCCATC 10 37 1 ACCGCATGCA 0.565441 -264 ATGCGCCCATCCGGCGTTGACGGGCGGGCGGG 10 58 1 CCGGCGTGCG 0.830984 -243 TTGAAATCCTGCCGGAGTTGGCAATACTCACC 10 155 1 GCCGGATTGC 0.260538 -146 ACGCCGTCGTACGGCGCTCTGGCGCAAGTTCG 10 189 0 ACGGCGTCGG 0.727581 -112 TGCGGCTCCCGCCGAGTCACCGAAGTTGCTGC 10 229 0 GCCGAGCACG 0.820562 -72 CTCGGCGGGAGCCGCATCCGGCGGTCGGCGAC 10 245 1 GCCGCACCGC 0.608734 -56 CATCCGGCGGTCGGCGACGGCCAATATTAGCG 10 259 1 TCGGCGCGCC 0.792355 -42 TACCATTGCCCCCGCGGTGCGTCTAGGGACC 11 10 0 CCCGCGTGGT 0.506875 -73 GTGACGATTAACCGAAGTGTCCAGCATGAGTC 12 27 0 ACCGAATGCC 0.733909 -89 CCATCGACGAGCGGGGTTGCCGA 14 2 0 GCGGGGTGCG 0.895602 -235 CCAGCCTAACCCCGGATCCACACACGATCCCG 14 49 1 CCCGGACCCA 0.49189 -188 GGCCAGGTTGCCCGCGGTGTCGAACAGTCCGA 14 82 0 CCCGCGTGCG 0.924201 -155 AACAGCTAGAGCCGGGCAATCGAGCTTAACTT 14 114 0 GCCGGGAACG 0.598699 -123 GGTGAATACAACGGCGACAACCGTCTCGCGCG 14 174 1 ACGGCGCACC 0.80285 -63 TCTCGCGCGGGCGGCGGCCACCTCGGACCCTG 14 197 1 GCGGCGCCCC 0.982133 -40 ACCGGGATCTCCCCGATACAGG 14 225 0 ACCGGGTCCC 0.919969 -12 CCGCCCGCTTGCGGGGGAGAGGTGGCGTGATC 15 31 0 GCGGGGAGGG 0.702179 -98 CCACCTCATCGCTGCGGCCCCCTCGTCGCTTC 15 68 1 GCTGCGCCCC 0.756577 -61 GGCACCCCCAGCCGCGAAGCGACGAGGGGGCC 15 83 0 GCCGCGAGGA 0.803478 -46 CACTGCATCGTCGGCGGCGGCG 15 117 1 TCGGCGCGCG 0.614429 -12 GCCCGTCATGGCGGACCCGCGCTTGCCGCGCA 16 34 1 GCGGACCGGC 0.607535 -249 ACCCGCGCTTGCCGCGCAGCCGGCGATGGCTA 16 48 1 GCCGCGAGCG 0.938738 -235 CTGGTCATCACCCGGGGCACCCCACCGCGGTT 16 86 1 CCCGGGCACC 0.842 -197 GTTGAGACCGCCGGAGTTGTGCTTTGAGTTGG 16 201 0 CCGGAGTGGC 0.735461 -82 TTACTAGCAGCCCGCGCGGGCCCCTAGCGGCC 16 245 0 CCCGCGGGCC 0.843764 -38 GTGGCCGGCAACGGAGATCGGCTGGCGTGAGC 17 87 0 ACGGAGTCGC 0.672318 -214 GCTGACGGTTACGGTGGCCGGCAACGGAGATC 17 100 0 ACGGTGCCGC 0.489636 -201 CTGGCATTGTGCCGAGTCGTGCTGACGGTTAC 17 120 0 GCCGAGCGGC 0.977071 -181 CACAATGCCAGCCGCACGCTGCAAGGCCGACC 17 141 1 GCCGCAGCGC 0.705714 -160 CGACGATACAGCCGGCATGGCAGAGGTTGAGC 17 260 0 GCCGGCTGCA 0.436621 -41 ****** ** ** Masking position 4 Map Score: 65.2281 Number of sites scoring better than the average of aligned sites = 69438 Number in coding regions = 65306 Number in noncoding regions = 4132 Number of orfs with sites within 600 bp upstream = 1414 Fraction of orfs with sites within 600 bp upstream = 0.227112 Motif number 3 CCGGCCGGATCATGCCGTATCGCGAA 3 4 0 CAGCCGACGC 0.78929 -141 GATTTGTCCCAGCACCGTATCGCCCGT 4 5 0 AGACCGACGC 0.721588 -296 CACCCGGTGTGGCACAGCTCACCGATATGTTTG 4 165 0 GGACAGTACC 0.274935 -136 CGCCGATTTCGGCACCGCCTACCTATTGGTCGA 4 249 1 GGACCGCACC 0.908497 -52 CGGCCGTCGACGAACCGGATCCCTCAGCTGTC 6 10 0 CGACCGACCC 0.910134 -91 GGCCGCGGTGGCCAGCCACGACCCGTCGCACAC 6 38 1 GCAGCCCACC 0.698097 -63 CGTCGCACACCAGGCCATCGCGCCGGGAAGCCC 6 61 1 CAGCCACCGC 0.780252 -40 GGACGCGTAACCTGGAGCACCGCCCGATCAGAT 7 32 0 CCGGAGACGC 0.627173 -139 CGGACATCTGGGGTCCAACCCCCACAGCTACGA 7 90 0 GGTCCACCCC 0.715265 -81 ATGTCCGTCCGGTGCCGGTGCGCTAGTTTCAAC 7 116 1 GGGCCGTCGC 0.973825 -55 CGCATCCTTCCTGCCGACGTGCTACTGGCACG 8 10 1 CCGCCGCTGC 0.721944 -148 CGTGTGGGTGCGCGCCGAAGTGCGAGCAGCGCG 8 46 0 CGGCCGATGC 0.629769 -112 GTGGTGTCAGCCTAGCAGTACGCTTGTCCTGCT 8 86 0 CCAGCATCGC 0.756604 -72 ATTTGGTTCGCCCGCCGACGGGCCGTGTCGACG 8 121 0 CCGCCGCGGC 0.685762 -37 CGTCGGCGGGCGAACCAAATCCCTGGGAGTTGA 8 134 1 CGACCAACCC 0.811511 -24 GACTATGGTCGCGACCACTACGCACTTCCCGAA 9 64 1 GCACCATCGC 0.869761 -237 ACGCACTTCCCGAAGCAAAAAGCGCCCTGCGGG 9 83 1 CGAGCAAAGC 0.628093 -218 GCACATGGTTGACGGCGATCACCACATCGAGCG 9 115 1 GAGGCGTACC 0.321235 -186 CGGGCGGGCGGGTACAGTCGCGCCATGGACGGC 10 78 1 GGACAGCCGC 0.8789 -223 ATACTCCCTGGGCACCAGTGCGCCCGTGCAAAG 10 114 0 GGACCATCGC 0.907026 -187 ACGGCGCTCTGGCGCAAGTTCGCTGGTGAGTAT 10 178 0 GGGCAATCGC 0.634829 -123 GCCGACCGCCGGATGCGGCTCCCGCCGAGTCAC 10 241 0 GGTGCGCCCC 0.595952 -60 ACTAAGAAAAGCCAGCCTAACCCCGGATCCACA 14 38 1 GCAGCCACCC 0.782353 -199 CAGCTAGAGCCGGGCAATCGAGCTTAACTTGGC 14 111 0 CGGCAACAGC 0.485679 -126 TGTATTCACCGCTGGCAAACCCCTTAAAAGCAC 14 151 0 GCGGCAACCC 0.83829 -86 TACAACGGCGACAACCGTCTCGCGCGGGCGGCG 14 180 1 ACACCGCCGC 0.798224 -57 GTCTCGCGCGGGCGGCGGCCACCTCGGACCCTG 14 196 1 GGGGCGCACC 0.636173 -41 TCCCCCGCAAGCGGGCGGTACCCCCACCTCATC 15 45 1 GCGGCGTCCC 0.868929 -84 CCCACCTCATCGCTGCGGCCCCCTCGTCGCTTC 15 67 1 CGTGCGCCCC 0.730494 -62 TCCGCCATGACGGGCCCCTGACCAGACGGGGAA 16 16 0 CGGCCCTACC 0.637009 -267 GGCCCGTCATGGCGGACCCGCGCTTGCCGCGCA 16 33 1 GGGGACCCGC 0.800193 -250 CATCACCCGGGGCACCCCACCGCGGTTGGAGGG 16 91 1 GGACCCACGC 0.934158 -192 TGGAGGGTTGCCGGCCAGCAAGCCGGGGCTTGA 16 117 1 CCGCCACAGC 0.854688 -166 GGTCATGAGCGCCAGCGTCAAGCCCCGGCTTGC 16 134 0 GCAGCGCAGC 0.890944 -149 ATGACCGACTCGAAGCCTAGCGCATGGCAGCTA 16 161 1 CGAGCCACGC 0.868494 -122 AGCAGCCCGCGCGGGCCCCTAGCGGCCGGTAAA 16 239 0 GCGGCCCAGC 0.76679 -44 ACATCAGATTACTAGCAGCCCGCGCGGGCCCCT 16 252 0 ACAGCACCGC 0.544065 -31 CAGCGGTGCCCCAACGCGATCCGCCGC 17 5 1 GGGCCCACGC 0.958342 -296 GTCGTTCGTTGGCACCGGTTAGCTTTATCGGCG 17 37 0 GGACCGTAGC 0.868577 -264 GCCAACGAACGACGCCACATCGCACATGTCGCT 17 57 1 GAGCCAACGC 0.708542 -244 TCGGCACAATGCCAGCCGCACGCTGCAAGGCCG 17 137 1 GCAGCCCCGC 0.784046 -164 ** **** * *** Masking position 13 Map Score: 49.0783 Number of sites scoring better than the average of aligned sites = 46151 Number in coding regions = 42656 Number in noncoding regions = 3495 Number of orfs with sites within 600 bp upstream = 1397 Fraction of orfs with sites within 600 bp upstream = 0.224382 Motif number 4 ACAACCGAGCCCCCCAGAAAA 2 2 1 CAACCGAGCC 0.833078 -78 TTGCCACTACCATCCGGTTGCGGATAACGT 4 83 0 CATCCGGTTG 0.661648 -218 CGGTCCGGGGCTTCCCGGCGCGATGGCCTG 6 71 0 CTTCCCGGCG 0.79824 -30 CCCCGGACCGCAACCTGGCC 6 91 1 CAACCTGGCC 0.983428 -10 ACGACGGATCCATGCGGGTACGCACGATTC 9 219 1 CATGCGGGTA 0.763441 -82 GTACACGACTCATGCTGGACACTTCGGTTA 12 21 1 CATGCTGGAC 0.920832 -95 GCGAGTCAGACATGCGGTAGGCACCAGGCG 12 88 1 CATGCGGTAG 0.569522 -28 ACACCGCGGGCAACCTGGCCAAGTTAAGCT 14 94 1 CAACCTGGCC 0.983428 -143 TTGCCCGGCTCTAGCTGTTCGATAGTGCTT 14 127 1 CTAGCTGTTC 0.606093 -110 TCATGTGCTCCTTCCGGGCCTT 15 3 0 CTTCCGGGCC 0.978324 -126 CTCTCCCCCGCAAGCGGGCGGTACCCCCAC 15 42 1 CAAGCGGGCG 0.965752 -87 GATGGCTACTCAACCTGGTCATCACCCGGG 16 72 1 CAACCTGGTC 0.964082 -211 CAAGCCCCGGCTTGCTGGCCGGCAACCCTC 16 119 0 CTTGCTGGCC 0.961079 -164 GCTATGACTGCATCCTGGTCAGCGATTGCA 17 212 1 CATCCTGGTC 0.972507 -89 ********** Masking position 5 Map Score: 13.3693 Number of sites scoring better than the average of aligned sites = 6049 Number in coding regions = 5668 Number in noncoding regions = 381 Number of orfs with sites within 600 bp upstream = 324 Fraction of orfs with sites within 600 bp upstream = 0.0520398 Motif number 5 ACAACCGAGCCCCCCAGAAAA 2 2 1 CAACCGAGCC 0.747137 -78 GATCTGTAACACCGCCAGCCCAGGGAGCAC 3 122 1 ACCGCCAGCC 0.992208 -23 TCCAACTCACAATCACAGCCGAATTCCGCG 4 119 0 AATCACAGCC 0.541991 -182 CGATTTCGGCACCGCCTACCTATTGGTCGA 4 252 1 ACCGCCTACC 0.688558 -49 GAACTTGGTAAACGTCAGTCGTAGCTGTGG 7 72 1 AACGTCAGTC 0.688652 -99 GTGGTCTTCACAACACAGCCGCACGAATG 10 10 0 CAACACAGCC 0.689786 -291 CGCGACTGTACCCGCCCGCCCGTCAACGCC 10 70 0 CCCGCCCGCC 0.9325 -231 GCGCCCGTGCAAAGCCTGCCGTCCATGGCG 10 98 0 AAAGCCTGCC 0.954565 -203 GGACGCTTTGAAATCCTGCCGGAGTTGGCA 10 148 1 AAATCCTGCC 0.601192 -153 ATTCGATGTTAACGCGAGTCAGACATGCGG 12 75 1 AACGCGAGTC 0.672251 -41 CCGACTAAGAAAAGCCAGCCTAACCCCGGA 14 35 1 AAAGCCAGCC 0.983608 -202 CAGTGGGGGCACCCCCAGCCGCGAAGCGAC 15 92 0 ACCCCCAGCC 0.983349 -37 GGGTTGCCGGCCAGCAAGCCGGGGCTTGAC 16 121 1 CCAGCAAGCC 0.675914 -162 ACATGTCGCTCACGCCAGCCGATCTCCGTT 17 80 1 CACGCCAGCC 0.989908 -221 GGCCACCGTAACCGTCAGCACGACTCGGCA 17 113 1 ACCGTCAGCA 0.512409 -188 GACTCGGCACAATGCCAGCCGCACGCTGCA 17 134 1 AATGCCAGCC 0.95646 -167 TGCCCAGCTCAACCTCTGCCATGCCGGCTG 17 254 1 AACCTCTGCC 0.793967 -47 ********** Masking position 8 Map Score: 13.4264 Number of sites scoring better than the average of aligned sites = 7201 Number in coding regions = 6683 Number in noncoding regions = 518 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 6 ATGATCCGGCCGGGCCGATGGGTCCGCCGG 3 24 1 CGGGCCGATG 0.831206 -121 TGTAACACCGCCAGCCCAGGGAGCACCCA 3 126 1 CCAGCCCAGG 0.757185 -19 ATAACGTTATCTGGACCCTGAGACGTTATC 4 61 1 CTGGACCCTG 0.782004 -240 CTGTGGGGGTTGGACCCCAGATGTCCGTCC 7 96 1 TGGACCCCAG 0.516574 -75 AACTAGCGCACCGGCACCGGACGGACATCT 7 114 0 CCGGCACCGG 0.748861 -57 TCCTCCGGTGCTGGCACGTGACCTAGATCA 9 29 0 CTGGCACGTG 0.696723 -272 AAGCGCCCTGCGGGCACATGGTTGACGGCG 9 102 1 CGGGCACATG 0.954793 -199 CAACGCCGGATGGGCGCATGTCAATGCGGT 10 47 0 TGGGCGCATG 0.892518 -254 CAATACTCCCTGGGCACCAGTGCGCCCGTG 10 119 0 TGGGCACCAG 0.932805 -182 GTACGGCGCTCTGGCGCAAGTTCGCTGGTG 10 183 0 CTGGCGCAAG 0.717155 -118 AGACATGCGGTAGGCACCAGGCGGAGGAAC 12 95 1 TAGGCACCAG 0.674231 -21 CCGTCTCGCGCGGGCGGCGGCCACCTCGGA 14 194 1 CGGGCGGCGG 0.909029 -43 GGCGGCCACCTCGGACCCTGTATCGGGGAG 14 209 1 TCGGACCCTG 0.613624 -28 TCCGCCATGACGGGCCCCTGACCAGACGGG 16 19 0 CGGGCCCCTG 0.988069 -264 GCGCCAGCGTCAAGCCCCGGCTTGCTGGCC 16 129 0 CAAGCCCCGG 0.777935 -154 GAGTCGGTCATGAGCGCCAGCGTCAAGCCC 16 142 0 TGAGCGCCAG 0.7249 -141 GACTCGAAGCCTAGCGCATGGCAGCTACTC 16 167 1 CTAGCGCATG 0.585256 -116 GCAGCCCGCGCGGGCCCCTAGCGGCCGGTA 16 241 0 CGGGCCCCTA 0.845241 -42 GCGTCGTTCGTTGGCACCGGTTAGCTTTAT 17 42 0 TTGGCACCGG 0.895531 -259 GTTACGGTGGCCGGCAACGGAGATCGGCTG 17 95 0 CCGGCAACGG 0.622263 -206 ********** Masking position 4 Map Score: 16.8261 Number of sites scoring better than the average of aligned sites = 12776 Number in coding regions = 11909 Number in noncoding regions = 867 Number of orfs with sites within 600 bp upstream = 606 Fraction of orfs with sites within 600 bp upstream = 0.0973338 Motif number 7 CTAATGTGATCCTCTTCGCGTGTTATCTC 2 61 0 TGTGATCCCC 0.992844 -19 GGGAGCGTACTGTGATCTGTAACACCGCCAGCCCA 3 109 1 TGTGATCTCC 0.985332 -36 CCAGCCGAAACGTGATCCAACTCACAATCACAGCC 4 129 0 CGTGATCCCC 0.994067 -172 CAAACATATCGGTGAGCTGTGCCACACCGGGTGGA 4 165 1 GGTGAGCTCC 0.944861 -136 ATAGTCTGAATGTGATCTAGGTCACGTGCCAGCAC 9 17 1 TGTGATCTCC 0.985332 -284 GGAGAGGTGGCGTGATCATGTGCTCCTTCCGGGCC 15 13 0 CGTGATCACC 0.969794 -116 GGTGCCCCAACGCGATCCGCCGCGCCGATAAAGCT 17 15 1 CGCGATCCCC 0.978022 -286 GGATGTGAGCCTAACCGCGCGACGATAC 17 283 0 TGTGAGCCCC 0.987432 -18 ******** * * Masking position 5 Map Score: 9.82914 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 102 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GCATGATCCGGCGGACCCATCGGCCCGGCCGG 3 29 0 GCGGCCCACG 0.791537 -116 ATTGGGCCGAGTAGACCCAACGACTCCGTCCG 3 62 1 GTAGCCCACG 0.902362 -83 ACATTTCAGATTTGTCCCAGCACCGTATCGCC 4 14 0 TTTGCCCACA 0.371359 -287 ATCGGTGAGCTGTGCCACACCGGGTGGATGCG 4 172 1 TGTGCACACG 0.869848 -129 GACGGGTCGTGGCTGGCCACCGCGGCCGTCGA 6 33 0 GGCTGCCACG 0.969685 -68 TGCGGTCCGGGGCTTCCCGGCGCGATGGCCTG 6 71 0 GGCTCCCGCG 0.933628 -30 GTACGCACGATTCGACACGACGGCAAGGTGTT 9 236 1 TTCGCACGCG 0.618126 -65 GCTAGCGGTGGTCTTCACAACACAGCCGCACG 10 15 0 GTCTCACACA 0.476574 -286 GGCGGGTACAGTCGCGCCATGGACGGCAGGCT 10 84 1 GTCGGCCAGG 0.679464 -217 CCAGCGAACTTGCGCCAGAGCGCCGTACGACG 10 185 1 TGCGCAGACG 0.609787 -116 GCTTTTCTTAGTCGGCCCATCGACGAGCGGGG 14 18 0 GTCGCCCACG 0.989319 -219 CCGATCGGACTGTTCGACACCGCGGGCAACCT 14 78 1 TGTTGACACG 0.426033 -159 GCTTTTAAGGGGTTTGCCAGCGGTGAATACAA 14 153 1 GGTTGCCACG 0.88195 -84 AAGCGACGAGGGGGCCGCAGCGATGAGGTGGG 15 67 0 GGGGCGCACG 0.791534 -62 GGCCCGTCATGGCGGACCCGCGCTTGCCGCGC 16 33 1 GGCGACCCCG 0.723286 -250 CATCACCCGGGGCACCCCACCGCGGTTGGAGG 16 91 1 GGCACCCACG 0.94318 -192 GAGTCGGTCATGAGCGCCAGCGTCAAGCCCCG 16 140 0 TGAGGCCACG 0.767339 -143 CAGCGGTGCCCCAACGCGATCCGCCG 17 5 1 GGTGCCCACG 0.985355 -296 GCCAACGAACGACGCCACATCGCACATGTCGC 17 57 1 GACGCACACG 0.856282 -244 CGATCTCCGTTGCCGGCCACCGTAACCGTCAG 17 99 1 TGCCGCCACG 0.835353 -202 CACGCTGCAAGGCCGACCAACGTGTGATGTGT 17 155 1 GGCCACCACG 0.808431 -146 GTGTCTTGCAGGCTACACATCACACGTTGGTC 17 169 0 GGCTCACACA 0.742512 -132 GCTGGGCAAAGTCGTCACAGTGCAATCGCTGA 17 230 0 GTCGCACATG 0.557473 -71 **** **** ** Masking position 8 Map Score: 15.8715 Number of sites scoring better than the average of aligned sites = 11043 Number in coding regions = 10159 Number in noncoding regions = 884 Number of orfs with sites within 600 bp upstream = 596 Fraction of orfs with sites within 600 bp upstream = 0.0957276 Motif number 9 ATCACAGTACGCTCCCGATACTAGCTATCGA 3 94 0 GTCCCGATAC 0.903928 -51 ATATGTTTGTCCAGCCGAAACGTGATCCAAC 4 143 0 CAGCCGAAAC 0.782594 -158 GTTAATCGGCGGTCTCGATACAGTTCTCCGT 4 212 1 GTCTCGATAC 0.777968 -89 TGGCCAGCCACGACCCGTCGCACACCAGGCC 6 46 1 CACCCGTCGC 0.843275 -55 CGGTCCGGGGCTTCCCGGCGCGATGGCCTGG 6 70 0 CTCCCGGCGC 0.90452 -31 GCGCTAGTTTCAACCCGAAGCCAAGTCCGTA 7 135 1 CACCCGAAGC 0.986804 -36 CCACTACGCACTTCCCGAAGCAAAAAGCGCC 9 78 1 CTCCCGAAGC 0.988861 -223 GCACAGCGGCGATCACGAAGCGTGAACCAGC 9 277 1 GTCACGAAGC 0.775007 -24 GATTACCCCTCTCGATACTGTACGCTTC 13 72 0 CTCTCGATAC 0.909862 -18 ACCGGGATCTCCCCGATACAGGGTCCGAG 14 218 0 CCCCCGATAC 0.894224 -19 CGCTCATGACCGACTCGAAGCCTAGCGCATG 16 156 1 CACTCGAAGC 0.964881 -127 TACTCAGTGCCAACTCAAAGCACAACTCCGG 16 192 1 CACTCAAAGC 0.663455 -91 * ********* Masking position 6 Map Score: 6.60926 Number of sites scoring better than the average of aligned sites = 2736 Number in coding regions = 2521 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 10 CTCGGATCGTGACCATAACGTTATCTGGAC 4 47 1 GACCATAACG 0.392124 -254 CCATCCGGTTGCGGATAACGTCTCAGGGTC 4 74 0 GCGGATAACG 0.726062 -227 TATCGAGACCGCCGATTAACTCCGCGGCCG 4 202 0 GCCGATTAAC 0.569953 -99 CGTGCGAGTCGCCGATTTCGGCACCGCCTA 4 240 1 GCCGATTTCG 0.484897 -61 GCCGAGCGAAGACGGTGAGCCC 4 289 1 GACGGTGAGC 0.47308 -12 GGCCACCGCGGCCGTCGACGAACCGGATCC 6 21 0 GCCGTCGACG 0.920122 -80 GGAAGCCCCGGACCGCAACCTGGCC 6 86 1 GACCGCAACC 0.718684 -15 AGCTACGACTGACGTTTACCAAGTTCCATA 7 68 0 GACGTTTACC 0.282969 -103 AGTGCGAGCAGCGCGTAACGTGCCAGTAGC 8 31 0 GCGCGTAACG 0.467076 -127 CGGCCCGTCGGCGGGCGAACCAAATCCCTG 8 129 1 GCGGGCGAAC 0.7566 -29 CTATGGTCGCGACCACTACGCACTTCCCGA 9 66 1 GACCACTACG 0.533822 -235 TGTGGTGATCGCCGTCAACCATGTGCCCGC 9 111 0 GCCGTCAACC 0.869066 -190 CATCGAGCGCGACGACGAAGGCCTTGCCTA 9 139 1 GACGACGAAG 0.791205 -162 CGAAGGCCTTGCCTACGACGACCTCAAGTT 9 154 1 GCCTACGACG 0.558506 -147 GATTCGACACGACGGCAAGGTGTTGAAGGA 9 244 1 GACGGCAAGG 0.812678 -57 AGCGCCGTACGACGGCGTCGTTTTGTGCAG 10 203 1 GACGGCGTCG 0.77714 -98 GCATCCGGCGGTCGGCGACGGCCAATATTA 10 258 1 GTCGGCGACG 0.78521 -43 CTACGTTAGTGACGATTAACCGAAGTGTCC 12 37 0 GACGATTAAC 0.293185 -79 TCGTCGATGGGCCGACTAAGAAAAGCCAGC 14 24 1 GCCGACTAAG 0.870301 -213 GTTCGACACCGCGGGCAACCTGGCCAAGTT 14 89 1 GCGGGCAACC 0.913019 -148 TGTATTCACCGCTGGCAAACCCCTTAAAAG 14 154 0 GCTGGCAAAC 0.314561 -83 TGAATACAACGGCGACAACCGTCTCGCGCG 14 176 1 GGCGACAACC 0.592647 -61 ACCGTCTCGCGCGGGCGGCGGCCACCTCGG 14 193 1 GCGGGCGGCG 0.704444 -44 CGCCGCCGCCGACGATGCAGTGGG 15 115 0 GCCGCCGACG 0.871082 -14 AGTAGCCATCGCCGGCTGCGCGGCAAGCGC 16 52 0 GCCGGCTGCG 0.869551 -231 CGGCTTGCTGGCCGGCAACCCTCCAACCGC 16 112 0 GCCGGCAACC 0.981463 -171 GCCCCTAGCGGCCGGTAAAGGGCCAGTTGA 16 228 0 GCCGGTAAAG 0.890246 -55 GATCCGCCGCGCCGATAAAGCTAACCGGTG 17 28 1 GCCGATAAAG 0.790796 -273 GGTTACGGTGGCCGGCAACGGAGATCGGCT 17 96 0 GCCGGCAACG 0.98873 -205 GAGTCGTGCTGACGGTTACGGTGGCCGGCA 17 109 0 GACGGTTACG 0.839132 -192 ACGCTGCAAGGCCGACCAACGTGTGATGTG 17 156 1 GCCGACCAAC 0.486247 -145 CGACGATACAGCCGGCATGGCAGAGGTTGA 17 262 0 GCCGGCATGG 0.626873 -39 ********** Masking position 1 Map Score: 32.1821 Number of sites scoring better than the average of aligned sites = 43393 Number in coding regions = 41260 Number in noncoding regions = 2133 Number of orfs with sites within 600 bp upstream = 1041 Fraction of orfs with sites within 600 bp upstream = 0.167202 Motif number 11 CGACACACAAGGAACCCGATCA 5 19 1 GGAACCGATC 0.987389 -12 CGGCCGTCGACGAACCGGATCCCTCAGCTGT 6 12 0 CGAACCGATC 0.991308 -89 CGTCGGCGGGCGAACCAAATCCCTGGGAGTT 8 134 1 CGAACCAATC 0.966334 -24 TGACTCGGCGGGAGCCGCATCCGGCGGTCGG 10 242 1 GGAGCCCATC 0.944844 -59 GATCCACACACGATCCCGATCGGACTGTTCG 14 63 1 CGATCCGATC 0.978324 -174 ****** **** Masking position 3 Map Score: 1.09603 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 189 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 GAAGGGTACACAGAGAACGGCCCCCTTTTT 2 28 0 CAGAGAACGG 0.978263 -52 TCTCAGGGTCCAGATAACGTTATGGTCACG 4 54 0 CAGATAACGT 0.90707 -247 CATCCGGTTGCGGATAACGTCTCAGGGTCC 4 73 0 CGGATAACGT 0.966558 -228 GCGACTCGCACGGAGAACTGTATCGAGACC 4 222 0 CGGAGAACTG 0.953795 -79 GAGTCGTGTACGGAGACCGTC 12 2 0 CGGAGACCGT 0.974728 -114 TGGCCGGCAACGGAGATCGGCTGGCGTGAG 17 88 0 CGGAGATCGG 0.975048 -213 ********** Masking position 6 Map Score: 3.58795 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 271 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 ********** No masking Map Score: 6.49026e-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: 6.49026e-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: 6.49026e-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