AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_mtub_reg_300.orf -o00220_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/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 Rv0496 79 hypothetical protein Rv0496 #2 proC 24 proC #3 argC 193 argC #4 argH 79 argH #5 Rv1847 277 hypothetical protein Rv1847 #6 ureA 48 ureA #7 Rv2323c 64 hypothetical protein Rv2323c #8 proA 300 proA #9 obg 85 obg #10 rplU 300 rplU #11 Rv2595 108 hypothetical protein Rv2595 #12 Rv2597 216 hypothetical protein Rv2597 #13 Rv2600 81 hypothetical protein Rv2600 #14 amiB 64 amiB Motif number 1 ACAAACTAGCCGGGCGAAGATACGGGC 1 8 0 CGGGCGAAGA 0.871733 -72 CGTGCGATTGGGCGTGCTGGACGTGGGTAG 1 41 1 GGCGTGCTGG 0.527769 -39 CACGGATCGGCCGAGCTGTCTGCG 2 8 1 CGGCCGAGCT 0.960745 -17 CCGCCGGGCGGCGCCGATGGGACTCGAAGT 3 118 0 GCGCCGATGG 0.906242 -76 ACTTGACACACCGCCGGGCGGCGCCGATGG 3 128 0 CCGCCGGGCG 0.549814 -66 GTGTCAAGTCCCGGCGCAGTCACCGCGGAA 3 149 1 CCGGCGCAGT 0.950827 -45 CGGTTCTCCCGCGAGCAGACGCAGAAT 4 8 1 CCCGCGAGCA 0.812751 -72 GAATCGCACGCCGACGGGCGTGGCGGTGCG 4 38 0 CCGACGGGCG 0.589678 -42 TGGTTTCAACCCGCAGGAGATGAACGAACA 5 11 0 CCGCAGGAGA 0.696225 -267 GAGTAGTAAGCCGGAGTACGCTGGTTTCAA 5 32 0 CCGGAGTACG 0.511694 -246 CGTATCCAAACCGGCGGGCGGCCGTACCGG 5 67 1 CCGGCGGGCG 0.523558 -211 GCCTATGCACCCGGCTCGCAAACATTACAC 5 97 1 CCGGCTCGCA 0.733381 -181 CCTCAGGACTCGGCCGCGGTCGTTGTGGCT 5 175 0 CGGCCGCGGT 0.953664 -103 CGAGTCCTGAGGGCTGCAGTGACCCCCGGT 5 193 1 GGGCTGCAGT 0.519404 -85 GCTGCAGTGACCCCCGGTCGACTCGATCGG 5 205 1 CCCCCGGTCG 0.747179 -73 GGCACGGGGCTCGCCGATCGAGTCGACCGG 5 218 0 TCGCCGATCG 0.799707 -60 CAACGGGCGAGCCCCGTGCACCAAGGCACG 5 242 0 GCCCCGTGCA 0.489413 -36 GCACGGGGCTCGCCCGTTGGTGTAGACACA 5 253 1 CGCCCGTTGG 0.601991 -25 TCCTGCCACGCCGCGGCAGGTTCAACGGTT 6 20 0 CCGCGGCAGG 0.868926 -29 ACCGGCGGGCTGGGGGTGACA 8 2 1 CCGGCGGGCT 0.935766 -299 GTCTCGACGGCGGCCGCGGTCTGCGGAATC 8 34 0 CGGCCGCGGT 0.953664 -267 GAGTTCCAGCCGGCTTCGCGTGGTCTCGAC 8 56 0 CGGCTTCGCG 0.630155 -245 GCGCCGGGCAGGGGCGACGAATCGGGCGAG 8 83 0 GGGGCGACGA 0.540826 -218 CCGATTCGTCGCGCCGGGCAGGGGCGACGA 8 93 0 GCGCCGGGCA 0.952485 -208 GGACTTCTCGCGGCCGCCGAAAGAGCTAAA 8 130 0 CGGCCGCCGA 0.562025 -171 AAGCTGATCAGGGGCGACCGTCAAGTACGC 8 187 1 GGGGCGACCG 0.795166 -114 CCGTCAAGTACGCCTGATCGCATAGCAACC 8 204 1 CGCCTGATCG 0.627301 -97 GCGCAGCGATCCGGCTGGGTGGTTGCTATG 8 224 0 CCGGCTGGGT 0.505847 -77 CGCTCCGGACGGGCCGCGCAGCGATCCGGC 8 239 0 GGGCCGCGCA 0.970281 -62 CGCGGCCCGTCCGGAGCGGGTCGTCTTACC 8 251 1 CCGGAGCGGG 0.76788 -50 CGTCTTACCTGGCCAGCGCAAGCCCGTTAC 8 272 1 GGCCAGCGCA 0.63052 -29 GCGTCGCGCGTGTGCGCCCA 9 1 1 GCGTCGCGCG 0.733963 -85 ATCTTCGCAGTGGGCGCACACGCGCGACGC 9 11 0 TGGGCGCACA 0.748858 -75 GCTGCACACTCCGCAGATGAAGGGGAGCTC 9 65 1 CCGCAGATGA 0.651466 -21 CGCAGATGAAGGGGAGCTCG 9 76 1 GGGGAGCTCG 0.830108 -10 CCGGGTTGGACCGCTGATGGCTGCGGC 10 8 0 CCGCTGATGG 0.83375 -293 CCGGCGCACTCCGGGGCCCGGGTGGTGACG 10 42 0 CCGGGGCCCG 0.744346 -259 CTCGACGCTACCGGCGCACTCCGGGGCCCG 10 52 0 CCGGCGCACT 0.964638 -249 ATCGACGCTACCGGCGCACTTTCGTGTGCT 10 82 1 CCGGCGCACT 0.964638 -219 GCGAGATCGACGCCAGCACACGAAAGTGCG 10 96 0 CGCCAGCACA 0.620988 -205 TCTCGCTGAGGCCCCGCTGGTTTGACCCCG 10 120 1 GCCCCGCTGG 0.898203 -181 GCCAGGCTGACGGCTGGAGACGATGCGGGG 10 183 1 CGGCTGGAGA 0.673912 -118 TGCTGGGTCTTGGGCGGGCACCTACAACGG 10 214 0 TGGGCGGGCA 0.617462 -87 AGCGGCGGGACGCGTGCTGGGTCTTGGGCG 10 228 0 CGCGTGCTGG 0.76542 -73 AGCACGCGTCCCGCCGCTGGCCCGCGCGCG 10 240 1 CCGCCGCTGG 0.931612 -61 CCGCCGCTGGCCCGCGCGCGAAGCGCAACG 10 250 1 CCCGCGCGCG 0.502056 -51 TGTTCGGAAATGGCTGAGGGAGCGTGCG 11 9 0 TGGCTGAGGG 0.503505 -100 GTCCCGACATCCCGCGCAGGACACGCCTAT 11 62 1 CCCGCGCAGG 0.6561 -47 CATCCGGGTGTCGGTGAGCGTGCAACTCAA 12 34 0 TCGGTGAGCG 0.604405 -183 GCCGCGGTCACCCCAGCTCACTGGTGCACC 12 63 0 CCCCAGCTCA 0.711685 -154 CGGCAGGTCTCGGCCGCGGTCACCCCAGCT 12 75 0 CGGCCGCGGT 0.953664 -142 GCCGGGAACCCGGCAGGTCTCGGCCGCGGT 12 85 0 CGGCAGGTCT 0.701466 -132 GCCGGGTTCCCGGCCGGACAACTCGCCCGT 12 101 1 CGGCCGGACA 0.935592 -116 TTTCGCGGGACCGGGGGTCACAACGGGCGA 12 123 0 CCGGGGGTCA 0.658309 -94 TCGTACCGCTGCGCCGCGGTTGGTCGATCG 12 187 0 GCGCCGCGGT 0.95902 -30 ACTGGGCGAGCTTAACTGAGCC 14 3 1 TGGGCGAGCT 0.680837 -62 CACCCGCTCCCCGGCGAGCGGCTCAGTTAA 14 22 0 CCGGCGAGCG 0.826832 -43 CGCCGGGGAGCGGGTGCTCGTCGATGAGAT 14 36 1 CGGGTGCTCG 0.940929 -29 ********** Masking position 6 Map Score: 81.2107 Number of sites scoring better than the average of aligned sites = 97642 Number in coding regions = 90938 Number in noncoding regions = 6704 Number of orfs with sites within 600 bp upstream = 1694 Fraction of orfs with sites within 600 bp upstream = 0.272085 Motif number 2 CGTCCAGCACGCCCAATCGCACGAAAACAA 1 34 0 GCCCAATCGC 0.893597 -46 CAGACAGCTCGGCCGATCCGTG 2 3 0 GGCCGATCCG 0.94454 -22 CCGAGTCGAAGGGGGACCGCC 3 2 0 GGGGGACCGC 0.643817 -192 CACTAGCTGCGCCGAGTCGAAGGGGGACCG 3 13 0 GCCGAGTCGA 0.534821 -181 CACACCGCCGGGCGGCGCCGATGGGACTCG 3 122 0 GGCGGCGCCG 0.949454 -72 GCGAGCAGACGCAGAATCGCACCGCCACGC 4 21 1 GCAGAATCGC 0.739618 -59 AGAATCGCACGCCGACGGGCGTGGCGGTGC 4 39 0 GCCGACGGGC 0.713824 -41 GCGAGCAGACGCAGAATCGCACGCCGACGG 4 51 0 GCAGAATCGC 0.739618 -29 GGCCCGGTACGGCCGCCCGCCGGTTTGGAT 5 70 0 GGCCGCCCGC 0.464849 -208 ATGTTTGCGAGCCGGGTGCATAGGCCCGGT 5 92 0 GCCGGGTGCA 0.648524 -186 CTAAATTAGGGCAGCCTTGCCTATCATTAC 5 138 1 GCAGCCTTGC 0.536522 -140 CAACGACCGCGGCCGAGTCCTGAGGGCTGC 5 180 1 GGCCGAGTCC 0.718723 -98 CGATCGGCGAGCCCCGTGCCTTGGTGCACG 5 228 1 GCCCCGTGCC 0.798708 -50 CTACACCAACGGGCGAGCCCCGTGCACCAA 5 248 0 GGGCGAGCCC 0.820683 -30 CCGCGGCGTGGCAGGATCGCAGAGC 6 34 1 GCAGGATCGC 0.924298 -15 TGCTTAGAACGGAGGAGGGCCG 7 3 0 GGAGGAGGGC 0.50156 -62 ACCGGCGGGCTGGGGGTGACACTG 8 5 1 GCGGGCTGGG 0.888949 -296 TCCGCAGACCGCGGCCGCCGTCGAGACCAC 8 37 1 GCGGCCGCCG 0.929042 -264 GCGAGTTCCAGCCGGCTTCGCGTGGTCTCG 8 58 0 GCCGGCTTCG 0.936047 -243 GCTGGAACTCGCCCGATTCGTCGCCCCTGC 8 76 1 GCCCGATTCG 0.924048 -225 CGTCGCCCCTGCCCGGCGCGACGAATCGGT 8 94 1 GCCCGGCGCG 0.812117 -207 AGGACTTCTCGCGGCCGCCGAAAGAGCTAA 8 131 0 GCGGCCGCCG 0.929042 -170 CGTCAAGTACGCCTGATCGCATAGCAACCA 8 205 1 GCCTGATCGC 0.566643 -96 CAACCACCCAGCCGGATCGCTGCGCGGCCC 8 229 1 GCCGGATCGC 0.976979 -72 ATCGCTGCGCGGCCCGTCCGGAGCGGGTCG 8 244 1 GGCCCGTCCG 0.839265 -57 TACCTGGCCAGCGCAAGCCCGTTACCCTGG 8 277 1 GCGCAAGCCC 0.821225 -24 CGCAGTGGGCGCACACGCGCGACGC 9 6 0 GCACACGCGC 0.676056 -80 GCGCGTGTGCGCCCACTGCGAAGATTCACG 9 16 1 GCCCACTGCG 0.807402 -70 CGCAGTAGCTGCACACTCCGCAGATGAAGG 9 58 1 GCACACTCCG 0.797835 -28 GCCGCAGCCATCAGCGGTCC 10 1 1 GCCGCAGCCA 0.793531 -300 GCACTCCGGGGCCCGGGTGGTGACGTCATC 10 37 0 GCCCGGGTGG 0.863246 -264 GACGCTACCGGCGCACTCCGGGGCCCGGGT 10 49 0 GCGCACTCCG 0.864325 -252 ACTTTCGTGTGCTGGCGTCGATCTCGCTGA 10 99 1 GCTGGCGTCG 0.54284 -202 TCTCGCTGAGGCCCCGCTGGTTTGACCCCG 10 120 1 GCCCCGCTGG 0.527364 -181 TGGAGACGATGCGGGGTCCGTTGTAGGTGC 10 197 1 GCGGGGTCCG 0.955928 -104 CGGGCCAGCGGCGGGACGCGTGCTGGGTCT 10 234 0 GCGGGACGCG 0.7812 -67 CCCGCCGCTGGCCCGCGCGCGAAGCGCAAC 10 249 1 GCCCGCGCGC 0.535995 -52 TCATACTTCCGCTGCATGCGTTGCGCTTCG 10 268 0 GCTGCATGCG 0.439836 -33 CGCACGCTCCCTCAGCCATTT 11 2 1 GCACGCTCCC 0.920352 -107 CGGGATGTCGGGACGATCCGCTAGCGTATC 11 46 0 GGACGATCCG 0.829946 -63 GCTCACTGGTGCACCATCCGGGTGTCGGTG 12 48 0 GCACCATCCG 0.881902 -169 GCAGGTCTCGGCCGCGGTCACCCCAGCTCA 12 73 0 GCCGCGGTCA 0.354776 -144 GCCGAGACCTGCCGGGTTCCCGGCCGGACA 12 91 1 GCCGGGTTCC 0.880917 -126 AACAGCTTTCGCGGGACCGGGGGTCACAAC 12 129 0 GCGGGACCGG 0.90528 -88 ACGTTAAACGGCGCCATCGATATGCGACCG 12 159 1 GCGCCATCGA 0.559673 -58 CGCCGCGGTTGGTCGATCGGTCGCATATCG 12 176 0 GGTCGATCGG 0.538251 -41 GACCAACCGCGGCGCAGCGGTACGAGAGGG 12 192 1 GGCGCAGCGG 0.876716 -25 CATGTATTAGGCCGGAGTCGATTTCGGGAC 13 34 1 GCCGGAGTCG 0.932827 -48 CCCATGCAGGATCGGGGTAAGGCTG 13 67 0 GCAGGATCGG 0.941328 -15 ********** Masking position 1 Map Score: 69.0509 Number of sites scoring better than the average of aligned sites = 92172 Number in coding regions = 86463 Number in noncoding regions = 5709 Number of orfs with sites within 600 bp upstream = 1630 Fraction of orfs with sites within 600 bp upstream = 0.261805 Motif number 3 CACGAAAACAAACTAGCCGGGCGAAGATACG 1 14 0 AACTACCGGG 0.75566 -66 GGAAAACGCACGTTTTCGCGGACGCAACTTC 3 92 1 CGTTTCGCGG 0.704041 -102 GTCCCGGCGCAGTCACCGCGGAATGAGTTTG 3 156 1 AGTCACGCGG 0.89147 -38 AGAATCGCACCGCCACGCCCGTCGGCGTGCG 4 33 1 CGCCAGCCCG 0.812944 -47 TGCATAGGCCCGGTACGGCCGCCCGCCGGTT 5 75 0 CGGTAGGCCG 0.574171 -203 GTGTAATGTTTGCGAGCCGGGTGCATAGGCC 5 96 0 TGCGACCGGG 0.838166 -182 ATTTAGCAAGCGTTAGCGTGTAATGTTTGCG 5 113 0 CGTTACGTGT 0.280063 -165 GTCGAGCCACAACGACCGCGGCCGAGTCCTG 5 171 1 AACGACGCGG 0.729527 -107 TGAGGGCTGCAGTGACCCCCGGTCGACTCGA 5 200 1 AGTGACCCCG 0.732426 -78 CCCCGGTCGACTCGATCGGCGAGCCCCGTGC 5 216 1 CTCGACGGCG 0.744918 -62 CTTGTGTCTACACCAACGGGCGAGCCCCGTG 5 254 0 CACCACGGGC 0.676616 -24 TGATACATTGCGTTAACCTCGAATCTGTGGT 7 44 0 CGTTACCTCG 0.781161 -21 GTGGTCTCGACGGCGGCCGCGGTCTGCGGAA 8 36 0 CGGCGCCGCG 0.501493 -265 GAGTTCCAGCCGGCTTCGCGTGGTCTCGACG 8 55 0 CGGCTCGCGT 0.257136 -246 TTAGCTCTTTCGGCGGCCGCGAGAAGTCCTA 8 131 1 CGGCGCCGCG 0.501493 -170 AGCGCAAGCCCGTTACCCTGGGGCA 8 286 1 CGTTACCTGG 0.870505 -15 CGGGTGGTGACGTCATCCGGGTTGGACCGCT 10 23 0 CGTCACCGGG 0.988758 -278 CGGATGACGTCACCACCCGGGCCCCGGAGTG 10 35 1 CACCACCGGG 0.977268 -266 TCGATCTCGACGCTACCGGCGCACTCCGGGG 10 56 0 CGCTACGGCG 0.980408 -245 TCGAGATCGACGCTACCGGCGCACTTTCGTG 10 77 1 CGCTACGGCG 0.980408 -224 TACGGGGTCAAACCAGCGGGGCCTCAGCGAG 10 121 0 AACCACGGGG 0.876121 -180 CGTCTCCAGCCGTCAGCCTGGCGACAACTGG 10 174 0 CGTCACCTGG 0.934899 -127 TTCGCGCGCGGGCCAGCGGCGGGACGCGTGC 10 241 0 GGCCACGGCG 0.917868 -60 CTCACTGGTGCACCATCCGGGTGTCGGTGAG 12 46 0 CACCACCGGG 0.977268 -171 AGTGAGCTGGGGTGACCGCGGCCGAGACCTG 12 71 1 GGTGACGCGG 0.787848 -146 GTTGTCCGGCCGGGAACCCGGCAGGTCTCGG 12 92 0 CGGGACCCGG 0.976701 -125 ACAGCTTTCGCGGGACCGGGGGTCACAACGG 12 127 0 CGGGACGGGG 0.987061 -90 CCCATGCAGGATCGGGGTAAGGCTGAT 13 65 0 CAGGACGGGG 0.944014 -17 TTAACTGAGCCGCTCGCCGGGGAGCGGGTGC 14 22 1 CGCTCCCGGG 0.883714 -43 ***** ***** Masking position 7 Map Score: 34.067 Number of sites scoring better than the average of aligned sites = 42440 Number in coding regions = 40004 Number in noncoding regions = 2436 Number of orfs with sites within 600 bp upstream = 1154 Fraction of orfs with sites within 600 bp upstream = 0.185352 Motif number 4 CAGATGGACCGTGTTGCTACCCACGTCCAGCAC 1 54 0 GGTTCACCCA 0.821946 -26 TATGTCATGTGAGGGAAAACGCACGTTTTCGCG 3 79 1 GGGGAACGCA 0.379489 -115 GCCCGGCGGTGTGTCAAGTCCCGGCGCAGTCAC 3 139 1 GGTCATCCCG 0.914814 -55 CATCTCCTGCGGGTTGAAACCAGCGTACTCCGG 5 19 1 GGTTAACCAG 0.881137 -259 ACTCGCTGTCGTATCCAAACCGGCGGGCGGCCG 5 58 1 GATCAACCGG 0.784094 -220 AAACCGGCGGGCGGCCGTACCGGGCCTATGCAC 5 74 1 GGGCGACCGG 0.965122 -204 CGCGGTCGTTGTGGCTCGACGAAGTAATGATAG 5 158 0 GGGCCACGAA 0.840388 -120 CCTGAGGGCTGCAGTGACCCCCGGTCGACTCGA 5 198 1 GAGTACCCCG 0.808175 -80 GTCGACTCGATCGGCGAGCCCCGTGCCTTGGTG 5 221 1 TGGCACCCCG 0.738148 -57 TCTACACCAACGGGCGAGCCCCGTGCACCAAGG 5 246 0 CGGCACCCCG 0.805307 -32 GTCCTTGTGTCTACACCAACGGGCGAGCC 5 259 0 GGTCAACCAA 0.78089 -19 TGCGGAATCAGTGTCACCCCCAGCCCGCCGGT 8 10 0 GGTCCCCCAG 0.948796 -291 CGAATCGGGCGAGTTCCAGCCGGCTTCGCGTGG 8 63 0 GGTTCGCCGG 0.592111 -238 GCGGCCGCGAGAAGTCCTACCAGCGTCTTGCCG 8 143 1 GAGTCACCAG 0.845517 -158 GGATCGCTGCGCGGCCCGTCCGGAGCGGGTCGT 8 242 1 GGGCCTCCGG 0.954335 -59 AGATTCACGAGGGGCAAAACCCGCAGTAGCTGC 9 37 1 GGGCAACCCG 0.993301 -49 GCAGCCATCAGCGGTCCAACCCGGATGACGTCA 10 14 1 GGGTCACCCG 0.982976 -287 AACCCGGATGACGTCACCACCCGGGCCCCGGAG 10 31 1 AGTCCACCCG 0.755546 -270 CTGCAACTACGGGGTCAAACCAGCGGGGCCTCA 10 126 0 GGGTAACCAG 0.953952 -175 GCGCGGGCCAGCGGCGGGACGCGTGCTGGGTCT 10 234 0 GGGCGACGCG 0.957038 -67 GCCCGCGCGCGAAGCGCAACGCATGCAGCGGAA 10 259 1 GAGCCACGCA 0.670115 -42 CGATACGCTAGCGGATCGTCCCGACATCCCGCG 11 45 1 GGGACTCCCG 0.722097 -64 GGTCTCGGCCGCGGTCACCCCAGCTCACTGGTG 12 67 0 GGGTACCCAG 0.916047 -150 GCGGGACCGGGGGTCACAACGGGCGAGTTGTCC 12 116 0 GGTCCACGGG 0.921453 -101 CAACCGCGGCGCAGCGGTACGAGAGGGTATGC 12 195 1 GAGCGACGAG 0.600163 -22 * *** * ***** Masking position 10 Map Score: 32.1873 Number of sites scoring better than the average of aligned sites = 13407 Number in coding regions = 12339 Number in noncoding regions = 1068 Number of orfs with sites within 600 bp upstream = 709 Fraction of orfs with sites within 600 bp upstream = 0.113877 Motif number 5 TGTCCACTAGCTGCGCCGAGTCGAAGGGGG 3 17 0 CTGCGCCGAG 0.93218 -177 TTCGCGGACGCAACTTCGAGTCCCATCGGC 3 106 1 CAACTTCGAG 0.643492 -88 CACCGCCGGGCGGCGCCGATGGGACTCGAA 3 120 0 CGGCGCCGAT 0.974061 -74 CCTATCATTACTTCGTCGAGCCACAACGAC 5 157 1 CTTCGTCGAG 0.788661 -121 GCAGGTTCAACGGTTTCGAGCGGG 6 5 0 CGGTTTCGAG 0.851152 -44 CGAATCACCACAGATTCGAGGTTAACGCAA 7 38 1 CAGATTCGAG 0.805943 -27 AGACCGCGGCCGCCGTCGAGACCACGCGAA 8 42 1 CGCCGTCGAG 0.989706 -259 GAGTTCCAGCCGGCTTCGCGTGGTCTCGAC 8 56 0 CGGCTTCGCG 0.915347 -245 AGTGCGCCGGTAGCGTCGAGATCGACGCTA 10 62 1 TAGCGTCGAG 0.96578 -239 AGTGCGCCGGTAGCGTCGATCTCGACGCTA 10 72 0 TAGCGTCGAT 0.922342 -229 TTTCGTGTGCTGGCGTCGATCTCGCTGAGG 10 101 1 TGGCGTCGAT 0.97637 -200 GGCTGACGGCTGGAGACGATGCGGGGTCCG 10 187 1 TGGAGACGAT 0.443573 -114 GAAACCGTTGCCGTTGAGTGTGTTTGAG 12 9 1 TGCCGTTGAG 0.634926 -208 CGTTAAACGGCGCCATCGATATGCGACCGA 12 160 1 CGCCATCGAT 0.761401 -57 TGTATTAGGCCGGAGTCGATTTCGGGACCA 13 36 1 CGGAGTCGAT 0.959108 -46 ********** Masking position 8 Map Score: 14.1445 Number of sites scoring better than the average of aligned sites = 15174 Number in coding regions = 14296 Number in noncoding regions = 878 Number of orfs with sites within 600 bp upstream = 622 Fraction of orfs with sites within 600 bp upstream = 0.0999036 Motif number 6 GTTTGTTTTCGTGCGATTGGGCGTGCTGGAC 1 32 1 GTGCGATGGG 0.991805 -48 GGGCGTGGCGGTGCGATTCTGCGTCTGCTCG 4 22 0 GTGCGATCTG 0.993504 -58 GCCCGTCGGCGTGCGATTCTGCGTCTGCTCG 4 49 1 GTGCGATCTG 0.993504 -31 GCTCTGCGATCCTGCCACGCCGCG 6 35 0 CTGCGATCTG 0.984741 -14 GGTGGTTGCTATGCGATCAGGCGTACTTGAC 8 206 0 ATGCGATAGG 0.892584 -95 ACGGGCCGCGCAGCGATCCGGCTGGGTGGTT 8 230 0 CAGCGATCGG 0.929065 -71 CCTATGGAACGTGCGATGGTAAATTTCCTAC 11 87 1 GTGCGATGTA 0.902111 -22 TGGTGCACCAGTGAGCTGGGGTGACCGCGGC 12 62 1 GTGAGCTGGG 0.847748 -155 GTGCTCGTCGATGAGATACTGCGAGC 14 49 1 ATGAGATCTG 0.891487 -16 ******* *** Masking position 7 Map Score: 9.01955 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 713 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 CAGCAGATGGACCGTGTTGCTACCCA 1 64 0 ATGGACCGTG 0.884929 -16 CGAGTCGAAGGGGGACCGCC 3 1 0 GGGGACCGCC 0.914107 -193 CGCCGATCGAGTCGACCGGGGGTCACTGCA 5 207 0 GTCGACCGGG 0.787129 -71 CGCGGCCCGTCCGGAGCGGGTCGTCTTACC 8 251 1 CCGGAGCGGG 0.816418 -50 TGCCCCAGGGTAACGGGCTTGCGCTGG 8 284 0 GGGTAACGGG 0.797232 -17 CGCAGATGAAGGGGAGCTCG 9 76 1 GGGGAGCTCG 0.852404 -10 GGCGCACTCCGGGGCCCGGGTGGTGACGTC 10 40 0 GGGGCCCGGG 0.986198 -261 CAACTGGTCAAGGGTACGTGACCTGCAACT 10 151 0 AGGGTACGTG 0.709862 -150 GAGACGATGCGGGGTCCGTTGTAGGTGCCC 10 199 1 GGGGTCCGTT 0.654294 -102 GGCCAGCGGCGGGACGCGTGCTGGGTCTTG 10 232 0 GGGACGCGTG 0.715941 -69 GAAATGGCTGAGGGAGCGTGCG 11 3 0 AGGGAGCGTG 0.975479 -106 GGACACGCCTATGGAACGTGCGATGGTAAA 11 80 1 ATGGAACGTG 0.68453 -29 TCCGGGTGTCGGTGAGCGTGCAACTCAAAC 12 32 0 GGTGAGCGTG 0.942766 -185 AGTGAGCTGGGGTGACCGCGGCCGAGACCT 12 71 1 GGTGACCGCG 0.931613 -146 ACAGCTTTCGCGGGACCGGGGGTCACAACG 12 128 0 CGGGACCGGG 0.981455 -89 GCCGCTCGCCGGGGAGCGGGTGCTCGTCGA 14 30 1 GGGGAGCGGG 0.995304 -35 ********** Masking position 7 Map Score: 19.4973 Number of sites scoring better than the average of aligned sites = 3891 Number in coding regions = 3563 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 8 CACGGATCGGCCGAGCTGTCT 2 2 1 ACGGATCGGC 0.962234 -23 CGGTCCCCCTTCGACTCGGCGCAGCTAGTG 3 13 1 TCGACTCGGC 0.952028 -181 CGATTCTGCGTCTGCTCGCCACAGAAAA 4 62 1 TCTGCTCGCC 0.797347 -18 ACTCCGGCTTACTACTCGCTGTCGTATCCA 5 45 1 ACTACTCGCT 0.844768 -233 TGCAGCCCTCAGGACTCGGCCGCGGTCGTT 5 181 0 AGGACTCGGC 0.978273 -97 ACCAAGGCACGGGGCTCGCCGATCGAGTCG 5 223 0 GGGGCTCGCC 0.943872 -55 CTTGGTGCACGGGGCTCGCCCGTTGGTGTA 5 247 1 GGGGCTCGCC 0.943872 -31 CGATCCTGCCACGCCGCGGCAGGTTCAACG 6 23 0 ACGCCGCGGC 0.749525 -26 TAAGCACGCAACGAATCACCACAGATTCGA 7 27 1 ACGAATCACC 0.664924 -38 GGCAGGGGCGACGAATCGGGCGAGTTCCAG 8 77 0 ACGAATCGGG 0.846762 -224 GCCCGGCGCGACGAATCGGTTTGGTGTTTA 8 104 1 ACGAATCGGT 0.869534 -197 CGCTGGTAGGACTTCTCGCGGCCGCCGAAA 8 138 0 ACTTCTCGCG 0.528177 -163 AACCACCCAGCCGGATCGCTGCGCGGCCCG 8 230 1 CCGGATCGCT 0.575194 -71 GCCAGGTAAGACGACCCGCTCCGGACGGGC 8 255 0 ACGACCCGCT 0.827607 -46 CATCCCGCGCAGGACACGCCTATGGAACGT 11 69 1 AGGACACGCC 0.853839 -40 GGAACCCGGCAGGTCTCGGCCGCGGTCACC 12 81 0 AGGTCTCGGC 0.917844 -136 TCCCGGCCGGACAACTCGCCCGTTGTGACC 12 108 1 ACAACTCGCC 0.901221 -109 ********** Masking position 7 Map Score: 13.2969 Number of sites scoring better than the average of aligned sites = 7947 Number in coding regions = 7183 Number in noncoding regions = 764 Number of orfs with sites within 600 bp upstream = 582 Fraction of orfs with sites within 600 bp upstream = 0.093479 Motif number 9 AGTTTGTTTTCGTGCGATTGGGCGTGCTGGACG 1 31 1 CGTGATTGGC 0.928395 -49 ACATGTGTCACGGGAAATTCAGCCTAGTTGGGT 3 44 1 CGGGATTAGC 0.969393 -150 GTTTGCGAGCCGGGTGCATAGGCCCGGTACGGC 5 87 0 CGGGCATGGC 0.995811 -191 AGCGTCTTGCCGGGATTATCGGCAAGCTGATCA 8 164 1 CGGGTATGGC 0.983561 -137 GGGACGCGTGCTGGGTCTTGGGCGGGCACCTAC 10 219 0 CTGGCTTGGC 0.953243 -82 CGCGGGATGTCGGGACGATCCGCTAGCGTATCG 11 45 0 CGGGGATCGC 0.953116 -64 GGGGTCACAACGGGCGAGTTGTCCGGCCGGGAA 12 107 0 CGGGAGTGTC 0.883792 -110 GAGTCGATTTCGGGACCATCAGCCTTACCCCGA 13 48 1 CGGGCATAGC 0.984814 -34 **** *** *** Masking position 9 Map Score: 5.34886 Number of sites scoring better than the average of aligned sites = 1107 Number in coding regions = 1028 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 GCGCCGCCCGGCGGTGTGTCAAGTCCCGGC 3 134 1 GCGGTGTGTC 0.954154 -60 TCAAGTCCCGGCGCAGTCACCGCGGAATGA 3 152 1 GCGCAGTCAC 0.443044 -42 CGCAGTCACCGCGGAATGAGTTTGCAAACT 3 163 1 GCGGAATGAG 0.914426 -31 TTCATCTCCTGCGGGTTGAAACCAGCGTAC 5 17 1 GCGGGTTGAA 0.602432 -261 TGAACCTGCCGCGGCGTGGCAGGATCGCAG 6 26 1 GCGGCGTGGC 0.823979 -23 ACCGGCGGGCTGGGGGTGACACTG 8 5 1 GCGGGCTGGG 0.840184 -296 GCCGCGGTCTGCGGAATCAGTGTCACCCCC 8 22 0 GCGGAATCAG 0.844382 -279 AGCCGGCTTCGCGTGGTCTCGACGGCGGCC 8 49 0 GCGTGGTCTC 0.690987 -252 CCCGTCCGGAGCGGGTCGTCTTACCTGGCC 8 256 1 GCGGGTCGTC 0.947288 -45 TGCAGCTACTGCGGGTTTTGCCCCTCGTGA 9 41 0 GCGGGTTTTG 0.666991 -45 CCCTTCATCTGCGGAGTGTGCAGCTACTGC 9 59 0 GCGGAGTGTG 0.975415 -27 CACCCGGGCCCCGGAGTGCGCCGGTAGCGT 10 48 1 CCGGAGTGCG 0.592015 -253 GGTCAAACCAGCGGGGCCTCAGCGAGATCG 10 117 0 GCGGGGCCTC 0.963957 -184 TGGAGACGATGCGGGGTCCGTTGTAGGTGC 10 197 1 GCGGGGTCCG 0.963981 -104 CGGGCCAGCGGCGGGACGCGTGCTGGGTCT 10 234 0 GCGGGACGCG 0.936417 -67 CGATACGCTAGCGGATCGTCCCGACATCCC 11 45 1 GCGGATCGTC 0.883215 -64 CGTGTCCTGCGCGGGATGTCGGGACGATCC 11 57 0 GCGGGATGTC 0.978031 -52 CCGCGGCGCAGCGGTACGAGAGGGTATGC 12 198 1 GCGGTACGAG 0.76835 -19 GCTCGCAGTATCTCATCGACGAGC 14 51 0 GCAGTATCTC 0.180514 -14 ********** Masking position 2 Map Score: 16.7773 Number of sites scoring better than the average of aligned sites = 8845 Number in coding regions = 8064 Number in noncoding regions = 781 Number of orfs with sites within 600 bp upstream = 564 Fraction of orfs with sites within 600 bp upstream = 0.0905879 Motif number 11 ********** No masking Map Score: 7.34291e-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 12 ********** No masking Map Score: 7.34291e-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 13 ********** No masking Map Score: 7.34291e-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