AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -irpoN_mtub_opreg_100.orf -g0.656 -x5 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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0072 300 hypothetical protein Rv0072 #2 Rv0079 300 hypothetical protein Rv0079 #3 Rv0081 94 hypothetical protein Rv0081 #4 Rv0196 112 hypothetical protein Rv0196 #5 PE_PGRS 300 PE_PGRS #6 Rv0748 90 hypothetical protein Rv0748 #7 Rv0749 23 hypothetical protein Rv0749 #8 Rv0986 300 hypothetical protein Rv0986 #9 glnA1 300 glnA1 #10 Rv2563 142 hypothetical protein Rv2563 #11 ftsE 43 ftsE #12 prfB 102 prfB Motif number 1 GACTTCGCACCGGTCACCGGGTG 1 4 0 CGGTCACCGG 0.643003 -297 GATATCGGTTGAGCCGCCGGTTGCCCACTG 1 46 0 GAGCCGCCGG 0.794139 -255 AACGGTCCGACGGCCAAACGGAATGGATCC 1 140 1 CGGCCAAACG 0.91914 -161 GGAATGGATCCCGCCACCCCACCTCGACCG 1 159 1 CCGCCACCCC 0.943521 -142 GTCGTTGGTGTGGGCACCGCGGTCGAGGTG 1 178 0 TGGGCACCGC 0.931377 -123 CCAACGACTACCACCACCCCGAACGCCTCT 1 200 1 CCACCACCCC 0.941566 -101 GACCACTAGCGGGCCGCGCCCTGACCACAA 1 232 1 GGGCCGCGCC 0.529238 -69 TCAAGACCAGGCCCCACAAGTGCGCCACGT 1 266 1 GCCCCACAAG 0.538331 -35 CAGCTTCTGCGCAGCGACGGAAACTGCCAC 2 82 1 GCAGCGACGG 0.830802 -219 CAAAGCCTACTGGGCGCACGTGTGGCAACG 2 115 1 TGGGCGCACG 0.919868 -186 GCTAGTCCGCGGCCCAACGGCGGCATTTCG 2 157 0 GGCCCAACGG 0.859545 -144 GTGGGCTGTGTCACCACCCGGAAAATTCGG 2 186 0 TCACCACCCG 0.766299 -115 GACGCGGACAGGGCCGAAAGTCCCATGCCA 2 219 0 GGGCCGAAAG 0.861486 -82 AAAGCTTGTCTGGCCGACACGGACGCGGAC 2 240 0 TGGCCGACAC 0.893059 -61 GGATGCGTGCGGGCCGCCCGCGGCCAATCG 3 12 0 GGGCCGCCCG 0.506524 -83 GCACGTACGTCGGACGCCGGCCATCAA 4 8 0 CGGACGCCGG 0.570944 -105 GGGATCGGCCCGGCCGCACGTACGTCGGAC 4 23 0 CGGCCGCACG 0.878762 -90 ACAAAGCGCTCGAGCGCCGGGGATCTTCGC 5 16 0 CGAGCGCCGG 0.653917 -285 GTCACGACGACCCGCGACGGGCCTCTGACA 5 43 0 CCCGCGACGG 0.611057 -258 CGCGAAACCCGCACCGCCCGGATAGCCGTC 5 73 0 GCACCGCCCG 0.881561 -228 CCGGGCACAGGGCGCGCCGCGAAACCCGCA 5 90 0 GGCGCGCCGC 0.501962 -211 GTGCCCGGCACCGCCGCCCGTTTGTCGGCA 5 112 1 CCGCCGCCCG 0.511248 -189 CGCCCGTTTGTCGGCAACGCCGCCGCGACC 5 126 1 TCGGCAACGC 0.825738 -175 CGGCAACGCCGCCGCGACCCGTGAGCCGTC 5 137 1 GCCGCGACCC 0.61455 -164 ACACGTTTCGCAGGCGCCAGCTGCTGGACG 5 163 0 CAGGCGCCAG 0.792487 -138 ATATCGCGATCCGGCACCGCATGCAGCGCT 5 196 0 CCGGCACCGC 0.785712 -105 TGCCCGACTACCAGCGACACACCCGTACGG 5 252 0 CCAGCGACAC 0.784668 -49 CGCTGGTAGTCGGGCACCAGGCCGTGAGGG 5 266 1 CGGGCACCAG 0.952965 -35 CGCGGTCGCAGGCCCGCCGG 6 1 0 GGCCCGCCGG 0.544673 -90 GGCCTGCGACCGCGCGCGGCGTTGACAGCA 6 17 1 CGCGCGCGGC 0.498253 -74 TGCGGTCGAGCGGCCGAAGCGATGCTGTCA 6 39 0 CGGCCGAAGC 0.954098 -52 CCCCCAATAGGCGCAGAACGGCA 7 11 1 GCGCAGAACG 0.529968 -13 CGGCCGGCAGTCCGCGAGTG 8 1 1 CGGCCGGCAG 0.768179 -300 GTGGTGTCAATGGCCACGACGCTGGGATCG 8 55 1 TGGCCACGAC 0.547218 -246 CGGCCGGTTACGCGCACACCACGGTCAGCG 8 154 0 CGCGCACACC 0.856058 -147 GCCGCGTTCCCGACCGGCCGGTTACGCGCA 8 168 0 CGACCGGCCG 0.744621 -133 GGTCGGGAACGCGGCGACGGATGGCGCGGT 8 183 1 GCGGCGACGG 0.521103 -118 ATCACTGTCCTGGCCACCGCGCCATCCGTC 8 198 0 TGGCCACCGC 0.949518 -103 CAGAGCCGCCAGCCGGCGCCCC 9 3 1 GAGCCGCCAG 0.798865 -298 GAGCCGCCAGCCGGCGCCCCATCGGAGCCA 9 13 1 CCGGCGCCCC 0.500883 -288 CCCATCGGAGCCAGCGAACCCGGTCCGGTG 9 30 1 CCAGCGAACC 0.769912 -271 GGTCCGGTGTCCGGCAAGCCCAGCGTCTTG 9 51 1 CCGGCAAGCC 0.829196 -250 CCCGACTATCCCGGCAAGACGCTGGGCTTG 9 65 0 CCGGCAAGAC 0.574105 -236 GACGGCGAAATCGCCGCCCGACTATCCCGG 9 81 0 TCGCCGCCCG 0.879258 -220 CGCCGTCATCGGGCAGACCCGATAACCAGG 9 104 1 GGGCAGACCC 0.856645 -197 CAATAGGGCCGGGGAGACCCGGCGTCAGTG 9 182 1 GGGGAGACCC 0.783474 -119 CTGACCGTGCCGCCCACCACTGACGCCGGG 9 199 0 CGCCCACCAC 0.896296 -102 AGTAACGTCTGCGCAACACGGGGTTGACTG 9 227 1 GCGCAACACG 0.501572 -74 ACTGTATCCGCGGCCGACGCTATGGAGCCG 9 268 0 CGGCCGACGC 0.657669 -33 TCGACCGCCACGACCGACCCCCTCACCTCG 10 42 1 CGACCGACCC 0.951369 -101 CCCCTCACCTCGGTCGAACCTCGGCGAACC 10 60 1 CGGTCGAACC 0.589297 -83 CGGTCGAACCTCGGCGAACCAACGCGGCAA 10 70 1 TCGGCGAACC 0.822987 -73 GCGAACCAACGCGGCAACGCCAGCCCATGA 10 83 1 GCGGCAACGC 0.921429 -60 GTGAGATTAGCGGGCAGGCGAAA 11 4 0 CGGGCAGGCG 0.530674 -40 GCGCCGCAGCCGGGCACAACACAGAGGCTC 12 15 0 CGGGCACAAC 0.859967 -88 GCAGCCCCTTGCGCCGCAGCCGGGCACAAC 12 25 0 GCGCCGCAGC 0.916459 -78 CCCAGCCCATTCGCAGCCCCTTGCGCCGCA 12 37 0 TCGCAGCCCC 0.785708 -66 GCACGACTGCGGCCCAGCCCATTCGCAGCC 12 49 0 GGCCCAGCCC 0.740909 -54 ACCGTCATGTGCACCGCACGACTGCGGCCC 12 64 0 GCACCGCACG 0.879749 -39 ********** Masking position 5 Map Score: 95.3396 Number of sites scoring better than the average of aligned sites = 110923 Number in coding regions = 103861 Number in noncoding regions = 7062 Number of orfs with sites within 600 bp upstream = 1674 Fraction of orfs with sites within 600 bp upstream = 0.268872 Motif number 2 ACTTCGCACCGGTCACCGGGTG 1 3 0 GGTCACCGGG 0.8987 -298 TCGACCAGTGGGCAACCGGCGGCTCAACCG 1 41 1 GGCAACCGGC 0.861005 -260 CCAACCACAAGCTAGTCGGGAAAGGCTGGC 1 101 1 GCTAGTCGGG 0.796316 -200 GGTCGAGGTGGGGTGGCGGGATCCATTCCG 1 158 0 GGGTGGCGGG 0.883684 -143 GTGTGGGCACCGCGGTCGAGGTGGGGTGGC 1 171 0 CGCGGTCGAG 0.921137 -130 TGGTCGAAGAGGCGTTCGGGGTGGTGGTAG 1 207 0 GGCGTTCGGG 0.932144 -94 CCTCTTCGACCACTAGCGGGCCGCGCCCTG 1 225 1 CACTAGCGGG 0.826625 -76 GAGGCTGGGTCGTGAACGGCCCAA 2 5 0 CGTGAACGGC 0.666817 -296 ACATGTACGAGGTTGGCGAGCAGATGCAGC 2 39 0 GGTTGGCGAG 0.801689 -262 CTAGTCCGCGGCCCAACGGCGGCATTTCGT 2 156 0 GCCCAACGGC 0.373661 -145 TGGGCTGTGTCACCACCCGGAAAATTCGGC 2 185 0 CACCACCCGG 0.302215 -116 TTTGGCATGGGACTTTCGGCCCTGTCCGCG 2 217 1 GACTTTCGGC 0.372241 -84 CGGCCCTGTCCGCGTCCGTGTCGGCCAGAC 2 233 1 CGCGTCCGTG 0.651075 -68 GGGCATTGGCCACAATCGGGCCACAATCGA 2 270 1 CACAATCGGG 0.687198 -31 CCGATTGGCCGCGGGCGGCCCGCACGCAT 3 10 1 CGCGGGCGGC 0.964045 -85 GCGTTACATCGGTTGACGAGTTGAAGAATT 3 55 0 GGTTGACGAG 0.654258 -40 TTGATGGCCGGCGTCCGACGTA 4 3 1 GATGGCCGGC 0.832333 -110 CCGACGTACGTGCGGCCGGGCCGATCCCAA 4 25 1 TGCGGCCGGG 0.9449 -88 CCGGGCCGATCCCAAGCGAGTGGTGTAACG 4 40 1 CCCAAGCGAG 0.238484 -73 TATACATAATGGCTACCGTGCACGTTACAC 4 62 0 GGCTACCGTG 0.87412 -51 CAAAGCGCTCGAGCGCCGGGGATCTTCGCC 5 15 0 GAGCGCCGGG 0.589312 -286 GCCCGTCGCGGGTCGTCGTGACGACGGCTA 5 51 1 GGTCGTCGTG 0.718059 -250 TCGTGACGACGGCTATCCGGGCGGTGCGGG 5 66 1 GGCTATCCGG 0.785411 -235 AAACGGGCGGCGGTGCCGGGCACAGGGCGC 5 105 0 CGGTGCCGGG 0.866909 -196 CGGCGTTGCCGACAAACGGGCGGCGGTGCC 5 118 0 GACAAACGGG 0.638692 -183 GGCGCCAGCTGCTGGACGGCTCACGGGTCG 5 151 0 GCTGGACGGC 0.677505 -150 TCAACGATATCGCGATCCGGCACCGCATGC 5 202 0 CGCGATCCGG 0.809957 -99 TTAATTCCTACCCGTACGGGTGTGTCGCTG 5 241 1 CCCGTACGGG 0.396556 -60 GTGTGTCGCTGGTAGTCGGGCACCAGGCCG 5 260 1 GGTAGTCGGG 0.935734 -41 CCGGCGGGCCTGCGACCGCGCG 6 3 1 GGCGGGCCTG 0.75488 -88 CAGCATCATCTGCGGTCGAGCGGCCGAAGC 6 49 0 TGCGGTCGAG 0.608673 -42 GCTGTTGATGCGTTACCGTGTGCATC 6 75 1 CGTTACCGTG 0.624592 -16 TCCACTCGCGGACTGCCGGCCG 8 3 0 GACTGCCGGC 0.886884 -298 GGGGAGCTGACGCTGCCGGGATCCGGTGCT 8 95 1 CGCTGCCGGG 0.9849 -206 TGCTGTTGTTTGTTGACGGGATGCCCTTGA 8 121 1 TGTTGACGGG 0.536799 -180 CCTTGACTTCGCTGACCGTGGTGTGCGCGT 8 145 1 GCTGACCGTG 0.539448 -156 CGCGTAACCGGCCGGTCGGGAACGCGGCGA 8 170 1 GCCGGTCGGG 0.545459 -131 CGGATGGCGCGGTGGCCAGGACAGTGATCG 8 200 1 GGTGGCCAGG 0.57875 -101 CTGAAGGCGTTGTTGGCGTGATGTCATCTC 8 229 0 TGTTGGCGTG 0.2853 -72 ATGGGGCGCCGGCTGGCGGCTCTG 9 5 0 GGCTGGCGGC 0.959337 -296 AGCCAGCGAACCCGGTCCGGTGTCCGGCAA 9 38 1 CCCGGTCCGG 0.508101 -263 CAAGACGCTGGGCTTGCCGGACACCGGACC 9 51 0 GGCTTGCCGG 0.496381 -250 GTCTTGCCGGGATAGTCGGGCGGCGATTTC 9 75 1 GATAGTCGGG 0.788787 -226 GCGATTTCGCCGTCATCGGGCAGACCCGAT 9 97 1 CGTCATCGGG 0.78794 -204 ACGGGAACCTGGTTATCGGGTCTGCCCGAT 9 111 0 GGTTATCGGG 0.921127 -190 CCGGTGGCATGCCGAACGGGAACCTGGTTA 9 126 0 GCCGAACGGG 0.629186 -175 ATTGTGGGGCCATGGTCGGCAAGATCGTAA 9 156 0 CATGGTCGGC 0.696032 -145 CGGCGTCAGTGGTGGGCGGCACGGTCAGTA 9 201 1 GGTGGGCGGC 0.947888 -100 ACACGGGGTTGACTGACGGGCAATATCGGC 9 242 1 GACTGACGGG 0.904165 -59 TTACTGTATCCGCGGCCGACGCTATGGAGC 9 270 0 CGCGGCCGAC 0.832637 -31 CGAGATCATCGGCGATCGAGCCAAGCGAAC 10 15 0 GGCGATCGAG 0.88289 -128 GGTCGGTCGTGGCGGTCGAGATCATCGGCG 10 31 0 GGCGGTCGAG 0.950929 -112 GTAGCGGTGAGATTAGCGGGCAGGCGAAA 11 10 0 GATTAGCGGG 0.755244 -34 CTCACCGCTACACTGGCGTGCCGTG 11 29 1 CACTGGCGTG 0.665356 -15 CCCCTTGCGCCGCAGCCGGGCACAACACAG 12 21 0 CGCAGCCGGG 0.969762 -82 TGGGCTGGGCCGCAGTCGTGCGGTGCACAT 12 58 1 CGCAGTCGTG 0.783816 -45 TCTAGCATCAGATGACCGTCATGTGCACCG 12 78 0 GATGACCGTC 0.283319 -25 ********** Masking position 7 Map Score: 75.6875 Number of sites scoring better than the average of aligned sites = 57911 Number in coding regions = 53871 Number in noncoding regions = 4040 Number of orfs with sites within 600 bp upstream = 1513 Fraction of orfs with sites within 600 bp upstream = 0.243013 Motif number 3 TGGTGTGGGCACCGCGGTCGAGGTGGGGTGGCGG 1 169 0 ACCGCGTGGT 0.468641 -132 TCACGACCCAGCCTCATGCGCTGCATCTGCTCGC 2 20 1 GCCTCTGGGC 0.501681 -281 AAGCCTACTGGGCGCACGTGTGGCAACGAGTCGA 2 117 1 GGCGCCGGGC 0.903797 -184 CACACGAAATGCCGCCGTTGGGCCGCGGACTAGC 2 153 1 GCCGCGTGCC 0.814489 -148 GAATTTTCCGGGTGGTGACACAGCCCACATTTGG 2 188 1 GGTGGGAAGC 0.318976 -113 GGCCGACACGGACGCGGACAGGGCCGAAAGTCCC 2 225 0 GACGCGAAGC 0.964721 -76 CCGATTGGCCGCGGGCGGCCCGCACGCATCC 3 8 1 GCCGCGGGCC 0.974864 -87 GATCGGCCCGGCCGCACGTACGTCGGACGCCGGC 4 17 0 GCCGCCGATC 0.703708 -96 ACATACATATGCCTCGGATGGAGCGGCG 4 95 1 GCCTCGAGGC 0.984364 -18 CCCGCGACGGGCCTCTGACAAAGCGCTCGAGCGC 5 29 0 GCCTCGAAGC 0.974078 -272 CGAAACCCGCACCGCCCGGATAGCCGTCGTCACG 5 67 0 ACCGCCGAGC 0.912512 -234 CACAGGGCGCGCCGCGAAACCCGCACCGCCCGGA 5 81 0 GCCGCAACGC 0.752279 -220 GGGCGGCGGTGCCGGGCACAGGGCGCGCCGCGAA 5 97 0 GCCGGCAAGC 0.884008 -204 GCTGCTGGACGGCTCACGGGTCGCGGCGGCGTTG 5 140 0 GGCTCCGGGC 0.921506 -161 TCCAGCAGCTGGCGCCTGCGAAACGTGTGGAAGC 5 165 1 GGCGCTGGAC 0.486096 -136 GCGATCCGGCACCGCATGCAGCGCTTCCACACGT 5 187 0 ACCGCTGAGC 0.841505 -114 CCGGCGGGCCTGCGACCGCGCGCGGCGTTGA 6 8 1 GCCTGGACGC 0.72585 -83 CGGCCGCTCGACCGCAGATGATGCTGTTGATGCG 6 53 1 ACCGCGAGGC 0.9802 -38 CAATGGCCACGACGCTGGGATCGCCGTTGCCATG 8 62 1 GACGCGGAGC 0.972638 -239 GTTGCCATGGGGAGCTGACGCTGCCGGGATCCGG 8 87 1 GGAGCGAGGC 0.937158 -214 GACGCTGCCGGGATCCGGTGCTGTTGTTTGTTGA 8 103 1 GGATCGGGGT 0.333173 -198 CGGATCGCTCACAGCTGAAGGCGTTGTTGGCGTG 8 239 0 ACAGCGAGGT 0.39009 -62 GGGCTAGACTACCGCCGAAATATCCAACAAAGGA 8 272 1 ACCGCGAATC 0.634779 -29 CGGGTTCGCTGGCTCCGATGGGGCGCCGGCTGGC 9 18 0 GGCTCGAGGC 0.966646 -283 ATCCCGGCAAGACGCTGGGCTTGCCGGACACCGG 9 54 0 GACGCGGCGC 0.937599 -247 TCTGCCCGATGACGGCGAAATCGCCGCCCGACTA 9 87 0 GACGGGAAGC 0.819869 -214 CCGACGCTATGGAGCCGATATTGCCCGTCAGTCA 9 251 0 GGAGCGAAGC 0.902576 -50 CATAGCGTCGGCCGCGGATACAGTAAAGGAGCAT 9 274 1 GCCGCGAAGT 0.949132 -27 CCCATTCGCAGCCCCTTGCGCCGCAGCCGGGCAC 12 28 0 GCCCCTGGGC 0.562653 -75 ***** ** * ** Masking position 14 Map Score: 39.2618 Number of sites scoring better than the average of aligned sites = 41234 Number in coding regions = 39143 Number in noncoding regions = 2091 Number of orfs with sites within 600 bp upstream = 977 Fraction of orfs with sites within 600 bp upstream = 0.156923 Motif number 4 AACCGGCGGCTCAACCGATATCGACAAACTCAC 1 54 1 TCAACGATAG 0.394803 -247 GGTTGGGTGTGCAGGTGAAGGTGAGTTTGTCGA 1 74 0 GCAGGGAAGG 0.882279 -227 TGGTGTGGGCACCGCGGTCGAGGTGGGGTGGCG 1 170 0 ACCGCGTCGG 0.855866 -131 GCGAGCAGATGCAGCGCATGAGGCTGGGTCGTG 2 21 0 GCAGCCATGG 0.723279 -280 TTTCCGTCGCTGCGCAGAAGCTGAGGCTCGCTC 2 72 0 TGCGCGAAGG 0.949435 -229 CTTCTGCGCAGCGACGGAAACTGCCACACTCAA 2 85 1 GCGACGAAAG 0.624546 -216 GGCCGACACGGACGCGGACAGGGCCGAAAGTCC 2 226 0 GACGCGACAG 0.855482 -75 GGCCGCACGTACGTCGGACGCCGGCCATCAA 4 9 0 ACGTCGACGG 0.655966 -104 ACATACATATGCCTCGGATGGAGCGGCG 4 95 1 GCCTCGATGG 0.97206 -18 CCCGCGACGGGCCTCTGACAAAGCGCTCGAGCG 5 30 0 GCCTCGACAG 0.911642 -271 CCGACAAACGGGCGGCGGTGCCGGGCACAGGGC 5 107 0 GGCGGGGTGG 0.696118 -194 CACGGGTCGCGGCGGCGTTGCCGACAAACGGGC 5 127 0 GGCGGGTTGG 0.731575 -174 CGGCCGCTCGACCGCAGATGATGCTGTTGATGC 6 53 1 ACCGCGATGG 0.978671 -38 GTTGCCATGGGGAGCTGACGCTGCCGGGATCCG 8 87 1 GGAGCGACGG 0.970973 -214 CGGGAACGCGGCGACGGATGGCGCGGTGGCCAG 8 186 1 GCGACGATGG 0.900015 -115 CGGATCGCTCACAGCTGAAGGCGTTGTTGGCGT 8 240 0 ACAGCGAAGG 0.892275 -61 CGGGTTCGCTGGCTCCGATGGGGCGCCGGCTGG 9 19 0 GGCTCGATGG 0.952562 -282 TCTGCCCGATGACGGCGAAATCGCCGCCCGACT 9 88 0 GACGGGAAAG 0.433588 -213 CGTGCCGCCCACCACTGACGCCGGGTCTCCCCG 9 191 0 ACCACGACGG 0.917937 -110 AACCCCGTGTTGCGCAGACGTTACTGACCGTGC 9 219 0 TGCGCGACGA 0.510591 -82 CCGACGCTATGGAGCCGATATTGCCCGTCAGTC 9 252 0 GGAGCGATAG 0.884556 -49 CATAGCGTCGGCCGCGGATACAGTAAAGGAGCA 9 274 1 GCCGCGATAG 0.981182 -27 TTTGATTGGGTCCACGGAAGCAGGTAGCTTCCG 10 116 1 TCCACGAAGG 0.874533 -27 CGCAGCCCCTTGCGCCGCAGCCGGGCACAACAC 12 23 0 TGCGCGCAGG 0.642218 -80 ***** **** * Masking position 13 Map Score: 18.9486 Number of sites scoring better than the average of aligned sites = 34529 Number in coding regions = 32875 Number in noncoding regions = 1654 Number of orfs with sites within 600 bp upstream = 873 Fraction of orfs with sites within 600 bp upstream = 0.140218 Motif number 5 CCACGTTGGTAGCCTCTGGGA 1 290 1 AGCCTCTGGG 0.932448 -11 CCTCATGCGCTGCATCTGCTCGCCAACCTC 2 31 1 TGCATCTGCT 0.316553 -270 AGCGAGCCTCAGCTTCTGCGCAGCGACGGA 2 73 1 AGCTTCTGCG 0.970976 -228 GTCTCCTGAGAGCTTCAGCGTTACATCGGT 3 72 0 AGCTTCAGCG 0.938177 -23 AAAGCGCTCGAGCGCCGGGGATCTTCGCCG 5 14 0 AGCGCCGGGG 0.930576 -287 TCCAGCAGCTGGCGCCTGCGAAACGTGTGG 5 165 1 GGCGCCTGCG 0.946591 -136 CATCAACAGCATCATCTGCGGTCGAGCGGC 6 55 0 ATCATCTGCG 0.824214 -36 CGGCGATCCCAGCGTCGTGGCCATTGACAC 8 58 0 AGCGTCGTGG 0.71233 -243 AGCTCCCCATGGCAACGGCGATCCCAGCGT 8 73 0 GGCAACGGCG 0.792887 -228 GGATCCCGGCAGCGTCAGCTCCCCATGGCA 8 89 0 AGCGTCAGCT 0.842858 -212 GGGGAGACCCGGCGTCAGTGGTGGGCGGCA 9 192 1 GGCGTCAGTG 0.77641 -109 CACGGTCAGTAACGTCTGCGCAACACGGGG 9 220 1 AACGTCTGCG 0.927336 -81 TCGGCTCCATAGCGTCGGCCGCGGATACAG 9 267 1 AGCGTCGGCC 0.940992 -34 GGCGGTCGAGATCATCGGCGATCGAGCCAA 10 21 0 ATCATCGGCG 0.882689 -122 ACCTCGGTCGAACCTCGGCGAACCAACGCG 10 66 1 AACCTCGGCG 0.900823 -77 ACTCGAGCCTCTGTGTTGTGCCCGG 12 6 1 AGCCTCTGTG 0.859656 -97 TGTTGTGCCCGGCTGCGGCGCAAGGGGCTG 12 24 1 GGCTGCGGCG 0.807589 -79 ********** Masking position 6 Map Score: 15.2905 Number of sites scoring better than the average of aligned sites = 12686 Number in coding regions = 12032 Number in noncoding regions = 654 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 6 GTGGACTTCGCACCGGTCACCGGGTG 1 6 0 CACGGTCACC 0.77214 -295 GGAATGGATCCCGCCACCCCACCTCGACCGC 1 159 1 CCCCACCCCA 0.502274 -142 CCCACCTCGACCGCGGTGCCCACACCAACGA 1 176 1 CCCGGTGCCC 0.904339 -125 GTGCCCACACCAACGACTACCACCACCCCGA 1 191 1 CACGACTACC 0.824665 -110 ACTACCACCACCCCGAACGCCTCTTCGACCA 1 206 1 CCCGAACGCC 0.450238 -95 GCGGGCCGCGCCCTGACCACAAAACGTCAAG 1 240 1 CCTGACCACA 0.739441 -61 TCCCAGAGGCTACCAACGTGGCGC 1 287 0 CAAGGCTACC 0.412 -14 TTCGGCTAGTCCGCGGCCCAACGGCGGCATT 2 160 0 CCCGGCCCAA 0.730621 -141 AAGCTTTGGGCATTGGCCACAATCGGGCCAC 2 263 1 CATGGCCACA 0.846305 -38 TTGCTATACATAATGGCTACCGTGCACGTTA 4 65 0 TATGGCTACC 0.346033 -48 CGGCGAAGATCCCCGGCGCTCGAGCGCTTTG 5 14 1 CCCGGCGCTC 0.938473 -287 ATAGCCGTCGTCACGACGACCCGCGACGGGC 5 51 0 TCCGACGACC 0.67347 -250 ACAGGGCGCGCCGCGAAACCCGCACCGCCCG 5 83 0 CCCGAAACCC 0.569461 -218 CTGTGCCCGGCACCGCCGCCCGTTTGTCGGC 5 110 1 CACGCCGCCC 0.903696 -191 GCGTCGTGGCCATTGACACCACCTGGTCTAG 8 46 0 CATGACACCA 0.311454 -255 CTCCCCATGGCAACGGCGATCCCAGCGTCGT 8 70 0 CACGGCGATC 0.800068 -231 CAAACAACAGCACCGGATCCCGGCAGCGTCA 8 102 0 CACGGATCCC 0.875162 -199 TCGATCACTGTCCTGGCCACCGCGCCATCCG 8 200 0 TCTGGCCACC 0.727005 -101 GCCGGCGCCCCATCGGAGCCAGCGAACCCGG 9 22 1 CACGGAGCCA 0.864064 -279 ATCTTGCCGACCATGGCCCCACAATAGGGCC 9 161 1 CCTGGCCCCA 0.954522 -140 CGCCGGGTCTCCCCGGCCCTATTGTGGGGCC 9 175 0 CCCGGCCCTA 0.899229 -126 ACGTTACTGACCGTGCCGCCCACCACTGACG 9 204 0 CCTGCCGCCC 0.820493 -97 TGACGGGCAATATCGGCTCCATAGCGTCGGC 9 255 1 TACGGCTCCA 0.639365 -46 ATAGCGTCGGCCGCGGATACAGTAAAGGAGC 9 275 1 CCCGGATACA 0.704372 -26 CGGTCGAGATCATCGGCGATCGAGCCAAGCG 10 18 0 CACGGCGATC 0.799819 -125 CGACCGCCACGACCGACCCCCTCACCTCGGT 10 43 1 GACGACCCCC 0.61527 -100 CTACCTGCTTCCGTGGACCCAATCAAATGAT 10 112 0 CCTGGACCCA 0.808791 -31 ** ******** Masking position 5 Map Score: 24.149 Number of sites scoring better than the average of aligned sites = 38227 Number in coding regions = 36075 Number in noncoding regions = 2152 Number of orfs with sites within 600 bp upstream = 1121 Fraction of orfs with sites within 600 bp upstream = 0.180051 Motif number 7 TTCACCTGCACACCCAACCACAAGCTAGTCG 1 88 1 CACCAACCAC 0.782139 -213 TGGATCCCGCCACCCCACCTCGACCGCGGTG 1 163 1 CACCCACCTC 0.581045 -138 ACTACCACCACCCCGAACGCCTCTTCGACCA 1 206 1 CCCGAACGCC 0.963359 -95 GCGCCCTGACCACAAAACGTCAAGACCAGGC 1 247 1 CACAAACGTC 0.556996 -54 GAAACTGCCACACTCAAAGCCTACTGGGCGC 2 101 1 CACCAAAGCC 0.930985 -200 AGTCGATCCACACGAAATGCCGCCGTTGGGC 2 145 1 CACAAATGCC 0.416237 -156 GGGCGGCCCGCACGCATCCGCACTATCTGAT 3 23 1 CACCATCCGC 0.312845 -72 CGACGGGCCTCTGACAAAGCGCTCGAGCGCC 5 28 0 CTGCAAAGCG 0.201389 -273 CGCCGCGAAACCCGCACCGCCCGGATAGCCG 5 75 0 CCCCACCGCC 0.977043 -226 CGCCCTGTGCCCGGCACCGCCGCCCGTTTGT 5 106 1 CCGCACCGCC 0.971597 -195 CGCCCGTTTGTCGGCAACGCCGCCGCGACCC 5 126 1 TCGCAACGCC 0.872546 -175 CGCATGCCTCCCAACCCCTCACGGCCTG 5 283 0 CTCCAACCCC 0.960235 -18 CGAAGCGATGCTGTCAACGCCGCGCGCGGTC 6 24 0 CTGCAACGCC 0.976391 -67 TGACATCACGCCAACAACGCCTTCAGCTGTG 8 233 1 CCACAACGCC 0.934934 -68 CAGAGCCGCCAGCCGGCGCCCCATCGGAGC 9 10 1 CAGCGGCGCC 0.637164 -291 GGTCCGGTGTCCGGCAAGCCCAGCGTCTTGC 9 51 1 CCGCAAGCCC 0.843474 -250 TATTGCCCGTCAGTCAACCCCGTGTTGCGCA 9 236 0 CAGCAACCCC 0.982011 -65 GCGAACCAACGCGGCAACGCCAGCCCATGAT 10 83 1 GCGCAACGCC 0.910286 -60 CACGGCACGCCAGTGTAGCGG 11 33 0 CACGCACGCC 0.820507 -11 *** ******* Masking position 11 Map Score: 13.6196 Number of sites scoring better than the average of aligned sites = 13570 Number in coding regions = 12895 Number in noncoding regions = 675 Number of orfs with sites within 600 bp upstream = 492 Fraction of orfs with sites within 600 bp upstream = 0.0790235 Motif number 8 GTGGTCAGGGCGCGGCCCGCTAGTGGTCGA 1 230 0 CGCGGCCCGC 0.98711 -71 GAAACTGCCACACTCAAAGCCTACTGGGCG 2 101 1 CACTCAAAGC 0.302839 -200 GCCGTTGGGCCGCGGACTAGCCGAATTTTC 2 166 1 CGCGGACTAG 0.520901 -135 CCGACACGGACGCGGACAGGGCCGAAAGTC 2 227 0 CGCGGACAGG 0.95678 -74 CCGATTGGCCGCGGGCGGCCCGCACGCAT 3 10 1 CGCGGGCGGC 0.901489 -85 CGCCGCTCCATCCGAGGCATATG 4 100 0 CGCTCCATCC 0.586646 -13 GGTTTCGCGGCGCGCCCTGTGCCCGGCACC 5 94 1 CGCGCCCTGT 0.890112 -207 CGTGTGGAAGCGCTGCATGCGGTGCCGGAT 5 188 1 CGCTGCATGC 0.923716 -113 CCCAACCCCTCACGGCCTGGTGCCCGACTA 5 272 0 CACGGCCTGG 0.825685 -29 CCGCGCGCGGCGTTGACAGCATCGCTTCGG 6 26 1 CGTTGACAGC 0.535496 -65 GTGTTCCACTCGCGGACTGCCGGCCG 8 7 0 CGCGGACTGC 0.97952 -294 ATGGCAACGGCGATCCCAGCGTCGTGGCCA 8 65 0 CGATCCCAGC 0.8765 -236 GGGGAGCTGACGCTGCCGGGATCCGGTGCT 8 95 1 CGCTGCCGGG 0.935739 -206 CCCTTGACTTCGCTGACCGTGGTGTGCGCG 8 144 1 CGCTGACCGT 0.598048 -157 CGGCCGGTTACGCGCACACCACGGTCAGCG 8 154 0 CGCGCACACC 0.88413 -147 TCCTGGCCACCGCGCCATCCGTCGCCGCGT 8 191 0 CGCGCCATCC 0.760954 -110 GATGTCATCTCGATCACTGTCCTGGCCACC 8 210 0 CGATCACTGT 0.185 -91 TAGCCCGGATCGCTCACAGCTGAAGGCGTT 8 248 0 CGCTCACAGC 0.945008 -53 CAGAGCCGCCAGCCGGCGCCCCA 9 4 1 AGCCGCCAGC 0.300114 -297 GGCGCCCCATCGGAGCCAGCGAACCCGGTC 9 25 1 CGGAGCCAGC 0.495165 -276 CGGTGTCCGGCAAGCCCAGCGTCTTGCCGG 9 55 1 CAAGCCCAGC 0.644817 -246 CGGGTCTGCCCGATGACGGCGAAATCGCCG 9 95 0 CGATGACGGC 0.777711 -206 TTACTGTATCCGCGGCCGACGCTATGGAGC 9 270 0 CGCGGCCGAC 0.892529 -31 CATCGGCGATCGAGCCAAGCGAACCCGA 10 9 0 CGAGCCAAGC 0.779571 -134 GGCGAACCAACGCGGCAACGCCAGCCCATG 10 82 1 CGCGGCAACG 0.635286 -61 CACGGCACGCCAGTGTAGCG 11 34 0 CACGGCACGC 0.659886 -10 CCCCTTGCGCCGCAGCCGGGCACAACACAG 12 21 0 CGCAGCCGGG 0.808635 -82 ********** Masking position 1 Map Score: 28.0441 Number of sites scoring better than the average of aligned sites = 36194 Number in coding regions = 33929 Number in noncoding regions = 2265 Number of orfs with sites within 600 bp upstream = 1130 Fraction of orfs with sites within 600 bp upstream = 0.181497 Motif number 9 ACGGCCAAACGGAATGGATCCCGCCACCCC 1 149 1 GGAATGGATC 0.339038 -152 ACCACCACCCCGAACGCCTCTTCGACCACT 1 209 1 CGAACGCCTC 0.444099 -92 ACGTTTTGTGGTCAGGGCGCGGCCCGCTAG 1 237 0 GTCAGGGCGC 0.629212 -64 GCAGATGCAGCGCATGAGGCTGGGTCGTGA 2 20 0 CGCATGAGGC 0.898417 -281 GCCCACATTTGGCATGGGACTTTCGGCCCT 2 210 1 GGCATGGGAC 0.876489 -91 CCGATTGGCCGCGGGCGGCCCGCACGCAT 3 10 1 CGCGGGCGGC 0.901817 -85 GCGGGCGGCCCGCACGCATCCGCACTATCT 3 21 1 CGCACGCATC 0.794001 -74 TTGATGGCCGGCGTCCGACGTACGT 4 6 1 GGCCGGCGTC 0.821843 -107 ACATATGCCTCGGATGGAGCGGCG 4 99 1 CGGATGGAGC 0.744002 -14 CGGTGCCGGGCACAGGGCGCGCCGCGAAAC 5 95 0 CACAGGGCGC 0.732116 -206 CCACACGTTTCGCAGGCGCCAGCTGCTGGA 5 165 0 CGCAGGCGCC 0.894271 -136 GATCCGGCACCGCATGCAGCGCTTCCACAC 5 189 0 CGCATGCAGC 0.961969 -112 CGCATGCCTCCCAACCCCTC 5 291 0 CGCATGCCTC 0.965502 -10 CCGGCGGGCCTGCGACCGCGCGCGGC 6 7 1 GGCCTGCGAC 0.647406 -84 ATGGCCACGACGCTGGGATCGCCGTTGCCA 8 64 1 CGCTGGGATC 0.711597 -237 AACGCGGCGACGGATGGCGCGGTGGCCAGG 8 190 1 CGGATGGCGC 0.879716 -111 ATGGGGCGCCGGCTGGCGGCTCTG 9 5 0 GGCTGGCGGC 0.906739 -296 CGACTATCCCGGCAAGACGCTGGGCTTGCC 9 63 0 GGCAAGACGC 0.55165 -238 GTTCCCGTTCGGCATGCCACCGGTTACGAT 9 133 1 GGCATGCCAC 0.887245 -168 TCGGGTTCGCTTGGCTCGATCGCCGAT 10 8 1 CGCTTGGCTC 0.845129 -135 CCGGCTGCGGCGCAAGGGGCTGCGAATGGG 12 32 1 CGCAAGGGGC 0.927862 -71 ********** Masking position 6 Map Score: 18.4949 Number of sites scoring better than the average of aligned sites = 13465 Number in coding regions = 12463 Number in noncoding regions = 1002 Number of orfs with sites within 600 bp upstream = 681 Fraction of orfs with sites within 600 bp upstream = 0.10938 Motif number 10 ********** No masking Map Score: -5.39059e-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: -5.39059e-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: -5.39059e-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