AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_mtub_reg_300.orf -o00440_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 Rv0072 300 hypothetical protein Rv0072 #2 Rv0074 79 hypothetical protein Rv0074 #3 Rv0187 300 hypothetical protein Rv0187 #4 Rv0552 77 hypothetical protein Rv0552 #5 menD 42 menD #6 Rv0557 61 hypothetical protein Rv0557 #7 Rv1008 85 hypothetical protein Rv1008 #8 Rv1009 207 hypothetical protein Rv1009 #9 cobG 224 cobG #10 cobL 67 cobL #11 Rv2073c 29 hypothetical protein Rv2073c #12 Rv2294 294 hypothetical protein Rv2294 #13 Rv2689c 173 hypothetical protein Rv2689c #14 Rv2690c 134 hypothetical protein Rv2690c #15 Rv3329 59 hypothetical protein Rv3329 Motif number 1 ATGGTGGACTTCGCACCGGTCACCGGGTG 1 10 0 TCGCACCGGT 0.953848 -291 ATATCGGTTGAGCCGCCGGTTGCCCACTGG 1 45 0 AGCCGCCGGT 0.573792 -256 CATTCCGTTTGGCCGTCGGACCGTTTCCTT 1 135 0 GGCCGTCGGA 0.869013 -166 GCGGTCGAGGTGGGGTGGCGGGATCCATTC 1 160 0 TGGGGTGGCG 0.796398 -141 TCGTTGGTGTGGGCACCGCGGTCGAGGTGG 1 177 0 GGGCACCGCG 0.989305 -124 TCGACCACTAGCGGGCCGCGCCCTGACCAC 1 230 1 GCGGGCCGCG 0.984537 -71 CGGTGTGAACCGCCACCGCTGCCCCGGCAG 2 34 0 CGCCACCGCT 0.650226 -46 CGGTGGCGGTTCACACCGCGTGCGCGTTTG 2 46 1 TCACACCGCG 0.803912 -34 CAATTCGTCGCCGCAGGTGCAGCGGTAG 3 9 1 CGCCGCAGGT 0.776953 -292 GCCACTGTGCTGGCGCCGGTGACGCCTACC 3 34 0 TGGCGCCGGT 0.984628 -267 GCCAGCACAGTGGCATGGGACTTCGATGCG 3 50 1 TGGCATGGGA 0.455027 -251 TGGTAAACCCCCAGGCCGGTGGGCGGTTGC 3 245 1 CCAGGCCGGT 0.814807 -56 CGCGACCACCGACCGTCGCGCGCCAGCAGG 3 274 0 GACCGTCGCG 0.881137 -27 GAGATTACGAGGGCACGGCAGATCCAAATT 4 34 0 GGGCACGGCA 0.876162 -44 GACCGTATGGCCGGGCCGCGC 5 2 0 CCGGGCCGCG 0.848205 -41 CCATTTCGACAGCCGGCGCTGACAGT 6 46 1 AGCCGGCGCT 0.800586 -16 CGTCTGGCTGGGCGGTCGGAGCTCACCCGC 7 32 0 GGCGGTCGGA 0.698136 -54 GCCAGGGGTTCCGGAGCGGGCGGTGGATCT 7 62 0 CCGGAGCGGG 0.837266 -24 CGGCGCCAGGGGTTCCGGAGCGG 7 73 0 CGCCAGGGGT 0.76119 -13 GCGCGCCGAGCGGCCCATAA 8 1 1 GCGCGCCGAG 0.90753 -207 AGCAACTCCGGCGCGCGGGTGTTATGGGCC 8 22 0 GCGCGCGGGT 0.976426 -186 TTGTGATCGAACGGGTGGGGCCTCTAGGTT 8 77 1 ACGGGTGGGG 0.445598 -131 TGAGTGTTGCCGAGGTCGGGGATATAGCGC 8 148 1 CGAGGTCGGG 0.681705 -60 CTACACCTTCTGAGGGCGCGACAGGTGGCC 9 19 0 TGAGGGCGCG 0.537924 -206 TAGCTGCCGATAGCGTCGCGGTGTGCCGCG 9 46 1 TAGCGTCGCG 0.845949 -179 CGTCGCGGTGTGCCGCGGCGTCCGCGCGGT 9 59 1 TGCCGCGGCG 0.507949 -166 GCGGCGTCCGCGCGGTCGCTCGTGCCCGAC 9 73 1 CGCGGTCGCT 0.537428 -152 GCGGGTTTGAGGGCGCCGAGTCGCTCCACG 9 104 0 GGGCGCCGAG 0.926432 -121 CGCGCTCAGGTCCCGTCGGGAGGCCGAGGA 9 169 0 TCCCGTCGGG 0.617346 -56 GACGGGACCTGAGCGCGGCGAGGCGGCGAC 9 182 1 GAGCGCGGCG 0.932063 -43 CGACGATGCAGAGCGCAGCGATGCGGTGGG 10 15 1 GAGCGCAGCG 0.57791 -53 CGGGCGGTACCCCCACCGCATCGCTGCGCT 10 26 0 CCCCACCGCA 0.543864 -42 CTCCCCCGCAAGCGGGCGGTACCCCCACCG 10 38 0 AGCGGGCGGT 0.532361 -30 CGGCGCCGCTCTCCCCCGCA 10 58 0 CGGCGCCGCT 0.982771 -10 GCCCCAAATCGGCCACGGCTAAATGACAGA 12 58 0 GGCCACGGCT 0.921435 -237 CGTTATTTCATCGCGGCGGAACGAGCCGCC 12 163 1 TCGCGGCGGA 0.787169 -132 CAGTTGGTCATAGGGCGGCTCGTTCCGCCG 12 176 0 TAGGGCGGCT 0.63337 -119 GGGAACATAGCCCGACCGGGGCTATCGACC 12 219 0 CCCGACCGGG 0.501488 -76 ACTGGTCTAGCCACACCGGGGAACATAGCC 12 237 0 CCACACCGGG 0.865168 -58 TATCCGCGTCCCGCACCGGTCAACTGGTCT 12 259 0 CCGCACCGGT 0.976345 -36 GCATCGTCGCCGGCGCGGGTCAATCGAAGA 13 18 0 CGGCGCGGGT 0.957471 -156 CGCCGCTCCTCCCCATCGCTTTGCTCTGCA 13 45 0 CCCCATCGCT 0.7489 -129 CGCGGGTCACTGGCGCCGCTCCTCCCCATC 13 58 0 TGGCGCCGCT 0.986795 -116 GCATCGTCGCCGGCGCGGGTCACTGGCGCC 13 71 0 CGGCGCGGGT 0.957471 -103 CGCCGCTCCTCCCCATCGCTTTGCTCTGCA 13 98 0 CCCCATCGCT 0.7489 -76 CGCGGGTCACTGGCGCCGCTCCTCCCCATC 13 111 0 TGGCGCCGCT 0.986795 -63 GCATCGTCGCCGGCGCGGGTCACTGGCGCC 13 124 0 CGGCGCGGGT 0.957471 -50 CGCCGCTCCTCCCCATCGCTTTGCTCTGCA 13 151 0 CCCCATCGCT 0.7489 -23 TGGCGCCGCTCCTCCCCATC 13 164 0 TGGCGCCGCT 0.986795 -10 ATCGCGTACGGCGCACCGGACACAGCCGAG 14 21 0 GCGCACCGGA 0.921923 -114 ACCGCGGGTTGCCGATCGCGTACGGCGCAC 14 35 0 GCCGATCGCG 0.801266 -100 TAAATCGGCTGGCCACCGCGGGTTGCCGAT 14 49 0 GGCCACCGCG 0.927832 -86 AGGCCTATCCGAGCGTGGCGGTAGCGTTCC 14 102 0 GAGCGTGGCG 0.800003 -33 GTGTTGGCGAGCGCAGCGCTAGGCTCGGGC 15 21 0 GCGCAGCGCT 0.920025 -39 ********** Masking position 8 Map Score: 90.3669 Number of sites scoring better than the average of aligned sites = 94325 Number in coding regions = 88221 Number in noncoding regions = 6104 Number of orfs with sites within 600 bp upstream = 1576 Fraction of orfs with sites within 600 bp upstream = 0.253132 Motif number 2 TGGTGGACTTCGCACCGGTCACCGGGTG 1 9 0 CGCACCGGTC 0.870253 -292 CGACCAGTGGGCAACCGGCGGCTCAACCGA 1 42 1 GCAACCGGCG 0.716978 -259 CAGGGCGCGGCCCGCTAGTGGTCGAAGAGG 1 225 0 CCCGCTAGTG 0.931954 -76 AAGACCAGGCCCCACAAGTGCGCCACGTTG 1 268 1 CCCACAAGTG 0.618608 -33 CCACCGCTGCCCCGGCAGTGGCTAGTTCCG 2 22 0 CCCGGCAGTG 0.938616 -58 CTGCCGGGGCAGCGGTGGCGGTTCACACCG 2 34 1 AGCGGTGGCG 0.823051 -46 GACCTCCAAACGCGCACGCGGTGTGAACCG 2 52 0 CGCGCACGCG 0.872524 -28 CAATTCGTCGCCGCAGGTGCAGCGGTAGG 3 10 1 GCCGCAGGTG 0.895649 -291 CCACTGTGCTGGCGCCGGTGACGCCTACCG 3 33 0 GGCGCCGGTG 0.991827 -268 CAGGCAACCGCCCACCGGCCTGGGGGTTTA 3 248 0 CCCACCGGCC 0.898274 -53 CCGACCGTCGCGCGCCAGCAGGCAACCGCC 3 266 0 CGCGCCAGCA 0.98024 -35 GGTCGGTGGTCGCGCTAGCGT 3 290 1 CGCGCTAGCG 0.992845 -11 AACCATTTCGACAGCCGGCGCTGACAGT 6 44 1 ACAGCCGGCG 0.739907 -18 CAGGGGTTCCGGAGCGGGCGGTGGATCTCG 7 60 0 GGAGCGGGCG 0.859385 -26 CGGCGCCAGGGGTTCCGGAGC 7 75 0 GGCGCCAGGG 0.933171 -11 ATAACACCCGCGCGCCGGAGTTGCTCAACA 8 27 1 CGCGCCGGAG 0.987214 -181 GGCCACCTGTCGCGCCCTCAGAAGGTGTAG 9 19 1 CGCGCCCTCA 0.614175 -206 GGCACACCGCGACGCTATCGGCAGCTACAC 9 43 0 GACGCTATCG 0.333594 -182 CCGCGGCGTCCGCGCGGTCGCTCGTGCCCG 9 71 1 CGCGCGGTCG 0.938324 -154 CGCCACGATGCGCGCAATCGAAAACGCCCT 9 131 1 CGCGCAATCG 0.948968 -94 CTGAGCGCGGCGAGGCGGCGACCCATTCTC 9 190 1 CGAGGCGGCG 0.93854 -35 GCCGCTCTCCCCCGCAAGCGGGCGGTACCC 10 44 0 CCCGCAAGCG 0.978668 -24 TCACGCTAGCGCAGGCAATAA 11 2 1 CACGCTAGCG 0.901837 -28 CTGATTTTCGCGCACCATCGGCGACGGACG 12 94 1 CGCACCATCG 0.926625 -201 GAAATAACGCCGAGGAATCGCTAGACGAAA 12 142 0 CGAGGAATCG 0.354493 -153 GTTATTTCATCGCGGCGGAACGAGCCGCCC 12 164 1 CGCGGCGGAA 0.608432 -131 ATCCGCGTCCCGCACCGGTCAACTGGTCTA 12 258 0 CGCACCGGTC 0.870253 -37 TCGATTGACCCGCGCCGGCGACGATGCAGA 13 21 1 CGCGCCGGCG 0.969153 -153 GGGGAGGAGCGGCGCCAGTGACCCGCGCCG 13 61 1 GGCGCCAGTG 0.985361 -113 GCCAGTGACCCGCGCCGGCGACGATGCAGA 13 74 1 CGCGCCGGCG 0.969153 -100 GGGGAGGAGCGGCGCCAGTGACCCGCGCCG 13 114 1 GGCGCCAGTG 0.985361 -60 GCCAGTGACCCGCGCCGGCGACGATGCAGA 13 127 1 CGCGCCGGCG 0.969153 -47 ATCGGCAACCCGCGGTGGCCAGCCGATTTA 14 49 1 CGCGGTGGCC 0.918842 -86 ATCCGAGCGTGGCGGTAGCGTTCCCTAGAC 14 96 0 GGCGGTAGCG 0.941737 -39 ********** Masking position 3 Map Score: 65.877 Number of sites scoring better than the average of aligned sites = 37750 Number in coding regions = 35416 Number in noncoding regions = 2334 Number of orfs with sites within 600 bp upstream = 1057 Fraction of orfs with sites within 600 bp upstream = 0.169772 Motif number 3 CACCCGGTGACCGGTGCGAAGTCCA 1 6 1 GGTGACCGGT 0.851877 -295 TTGAGCCGCCGGTTGCCCACTGGTCGATAT 1 38 0 GGTTGCCCAC 0.631858 -263 GTCTGCCAGCCTTTCCCGACTAGCTTGTGG 1 105 0 CTTTCCCGAC 0.139309 -196 GTCGAGGTGGGGTGGCGGGATCCATTCCGT 1 157 0 GGTGGCGGGA 0.948962 -144 GTGGTCAGGGCGCGGCCCGCTAGTGGTCGA 1 230 0 CGCGGCCCGC 0.703735 -71 AGGCTACCAACGTGGCGCACTTGTGGGGCC 1 275 0 CGTGGCGCAC 0.753747 -26 CCCGGCTTGGCCGGAACTAGCCACT 2 6 1 CTTGGCCGGA 0.887114 -74 CCGGGGCAGCGGTGGCGGTTCACACCGCGT 2 37 1 GGTGGCGGTT 0.761487 -43 CAATTCGTCGCCGCAGGTGCAGCGG 3 6 1 CGTCGCCGCA 0.919567 -295 CAGCGGTAGGCGTCACCGGCGCCAGCACAG 3 30 1 CGTCACCGGC 0.912973 -271 CATGGGACTTCGATGCGAACCCGACAGCCA 3 63 1 CGATGCGAAC 0.12551 -238 AGGAATCCCAGGTGGTCAGCTGTCGGTAAT 3 176 1 GGTGGTCAGC 0.543998 -125 TGGTAAACCCCCAGGCCGGTGGGCGGTTGC 3 245 1 CCAGGCCGGT 0.488331 -56 GCCGGTGGGCGGTTGCCTGCTGGCGCGCGA 3 259 1 GGTTGCCTGC 0.483651 -42 GACCACCGACCGTCGCGCGCCAGCAGGCAA 3 271 0 CGTCGCGCGC 0.890346 -30 CGCGACGGTCGGTGGTCGCGCTAGCGT 3 284 1 GGTGGTCGCG 0.441556 -17 GTTGCTCAACATTGGCCGGTTCGTTACCGT 8 46 1 ATTGGCCGGT 0.347519 -162 TGAGTGTTGCCGAGGTCGGGGATATAGCGC 8 148 1 CGAGGTCGGG 0.502306 -60 GGGCGCGACAGGTGGCCGGAGTGGG 9 6 0 GGTGGCCGGA 0.982052 -219 CTGCCGATAGCGTCGCGGTGTGCCGCGGCG 9 49 1 CGTCGCGGTG 0.677213 -176 GCGACCGCGCGGACGCCGCGGCACACCGCG 9 62 0 GGACGCCGCG 0.729402 -163 CGCGGTCGCTCGTGCCCGACTCGTGGAGCG 9 83 1 CGTGCCCGAC 0.877389 -142 GCGGGTTTGAGGGCGCCGAGTCGCTCCACG 9 104 0 GGGCGCCGAG 0.801175 -121 TTGCGCGCATCGTGGCGGGTTTGAGGGCGC 9 118 0 CGTGGCGGGT 0.976474 -107 GGTCCCGTCGGGAGGCCGAGGATCAGGGTC 9 161 0 GGAGGCCGAG 0.847122 -64 CGGGAGAATGGGTCGCCGCCTCGCCGCGCT 9 193 0 GGTCGCCGCC 0.829692 -32 CGGCGCCGCTCTCCCCCGCA 10 58 0 CGGCGCCGCT 0.828662 -10 GATTTGACATGGATGCCGGAACTCTCTGTC 12 34 1 GGATGCCGGA 0.702137 -261 GTCATTTAGCCGTGGCCGATTTGGGGCTTG 12 61 1 CGTGGCCGAT 0.976564 -234 AATATTCGTCCGTCGCCGATGGTGCGCGAA 12 100 0 CGTCGCCGAT 0.972233 -195 GTTATTTCATCGCGGCGGAACGAGCCGCCC 12 164 1 CGCGGCGGAA 0.461522 -131 GTCGGGCTATGTTCCCCGGTGTGGCTAGAC 12 233 1 GTTCCCCGGT 0.476018 -62 GGCTAGACCAGTTGACCGGTGCGGGACGCG 12 255 1 GTTGACCGGT 0.415925 -40 GACCGGTGCGGGACGCGGATACGGCTAGTC 12 268 1 GGACGCGGAT 0.708552 -27 TGCTCTGCATCGTCGCCGGCGCGGGTCAAT 13 24 0 CGTCGCCGGC 0.992473 -150 TGGGGAGGAGCGGCGCCAGTGACCCGCGCC 13 60 1 CGGCGCCAGT 0.718987 -114 TGCTCTGCATCGTCGCCGGCGCGGGTCACT 13 77 0 CGTCGCCGGC 0.992473 -97 TGGGGAGGAGCGGCGCCAGTGACCCGCGCC 13 113 1 CGGCGCCAGT 0.718987 -61 TGCTCTGCATCGTCGCCGGCGCGGGTCACT 13 130 0 CGTCGCCGGC 0.992473 -44 GGCCACCGCGGGTTGCCGATCGCGTACGGC 14 39 0 GGTTGCCGAT 0.874243 -96 GGCAACCCGCGGTGGCCAGCCGATTTACGT 14 52 1 GGTGGCCAGC 0.833577 -83 AGACGAGAATGTTCGCCGACGTAAATCGGC 14 70 0 GTTCGCCGAC 0.848738 -65 CCTATCCGAGCGTGGCGGTAGCGTTCCCTA 14 99 0 CGTGGCGGTA 0.652056 -36 GTGTCGTCGTGTTGGCGAGCGCAGCGCTAG 15 29 0 GTTGGCGAGC 0.43815 -31 ********** Masking position 6 Map Score: 54.7245 Number of sites scoring better than the average of aligned sites = 58228 Number in coding regions = 54875 Number in noncoding regions = 3353 Number of orfs with sites within 600 bp upstream = 1404 Fraction of orfs with sites within 600 bp upstream = 0.225506 Motif number 4 ATGGATCCCGCCACCCCACCTCGACCGCGG 1 162 1 CCACCCCACC 0.869274 -139 GTGACGCCTACCGCTGCACCTGCGGCGACG 3 16 0 CCGCTGCACC 0.839138 -285 GCCGTATGCCGCTACGCAACCATTTCGACA 6 27 1 GCTACGCAAC 0.883048 -35 TCCACCGCCCGCTCCGGAACCCCTGGCGCC 7 65 1 GCTCCGGAAC 0.916397 -21 CAAAATGGGCCCTCCGAAACCTAGAGGCCC 8 94 0 CCTCCGAAAC 0.90031 -114 ATATCCCCGACCTCGGCAACACTCAACCAC 8 143 0 CCTCGGCAAC 0.988689 -65 TGACCCTGATCCTCGGCCTCCCGACGGGAC 9 160 1 CCTCGGCCTC 0.938848 -65 GCATCGCTGCGCTCTGCATCGTCGCGGA 10 9 0 GCTCTGCATC 0.988917 -59 GGCGGTACCCCCACCGCATCGCTGCGCTCT 10 24 0 CCACCGCATC 0.976016 -44 CCATCGCTTTGCTCTGCATCGTCGCCGGCG 13 33 0 GCTCTGCATC 0.988917 -141 TGGCGCCGCTCCTCCCCATCGCTTTGCTCT 13 48 0 CCTCCCCATC 0.990767 -126 CCATCGCTTTGCTCTGCATCGTCGCCGGCG 13 86 0 GCTCTGCATC 0.988917 -88 TGGCGCCGCTCCTCCCCATCGCTTTGCTCT 13 101 0 CCTCCCCATC 0.990767 -73 CCATCGCTTTGCTCTGCATCGTCGCCGGCG 13 139 0 GCTCTGCATC 0.988917 -35 TGGCGCCGCTCCTCCCCATCGCTTTGCTCT 13 154 0 CCTCCCCATC 0.990767 -20 CGCCGTACGCGATCGGCAACCCGCGGTGGC 14 38 1 GATCGGCAAC 0.793558 -97 CTAGCGCTGCGCTCGCCAACACGACGACAC 15 29 1 GCTCGCCAAC 0.970715 -31 ********** Masking position 10 Map Score: 36.0612 Number of sites scoring better than the average of aligned sites = 1616 Number in coding regions = 1442 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 TCGACAAACTCACCTTCACCTGCACACCCA 1 74 1 CACCTTCACC 0.905873 -227 CCCGCCACCCCACCTCGACCGCGGTGCCCA 1 168 1 CACCTCGACC 0.914766 -133 TCGACCGCGGTGCCCACACCAACGACTACC 1 182 1 TGCCCACACC 0.937529 -119 CGACTACCACCACCCCGAACGCCTCTTCGA 1 204 1 CACCCCGAAC 0.902538 -97 TAGCGGGCCGCGCCCTGACCACAAAACGTC 1 238 1 CGCCCTGACC 0.981137 -63 CCCGGCTTGGCCGGAACTAGCCACTGC 2 8 1 TGGCCGGAAC 0.497243 -72 GCGAACCCGACAGCCACAGCCCTCGTGGCT 3 77 1 CAGCCACAGC 0.861989 -224 TCATTCGTATCACCCTCATCCGTGTCGGGG 3 139 1 CACCCTCATC 0.76671 -162 GCGCGGCCCGGCCATACGGTCCG 5 4 1 CGGCCCGGCC 0.847211 -39 CAGAGTGTCACAGCCGGACCGTATGGCCGG 5 18 0 CAGCCGGACC 0.972109 -25 GGTCGGAGCTCACCCGCACACAATAGGGTG 7 19 0 CACCCGCACA 0.916897 -67 TCCGACCGCCCAGCCAGACGAGATCCACCG 7 42 1 CAGCCAGACG 0.690116 -44 CGAGATCCACCGCCCGCTCCGGAACCCCTG 7 60 1 CGCCCGCTCC 0.83915 -26 CGAAACCTAGAGGCCCCACCCGTTCGATCA 8 80 0 AGGCCCCACC 0.805022 -128 AACACTCAACCACCTACACAGCGAACAAAA 8 126 0 CACCTACACA 0.596601 -82 CCACCTGTCGCGCCCTCAGAAGGTGTAGCT 9 21 1 CGCCCTCAGA 0.60813 -204 ACGCTATCGGCAGCTACACCTTCTGAGGGC 9 32 0 CAGCTACACC 0.870221 -193 AGCGACTCGGCGCCCTCAAACCCGCCACGA 9 109 1 CGCCCTCAAA 0.589756 -116 CAATCGAAAACGCCCTGACCCTGATCCTCG 9 145 1 CGCCCTGACC 0.981137 -80 AAGCGGGCGGTACCCCCACCGCATCGCTGC 10 29 0 TACCCCCACC 0.955201 -39 CCGGGGAACATAGCCCGACCGGGGCTATCG 12 222 0 TAGCCCGACC 0.9119 -73 TCAACTGGTCTAGCCACACCGGGGAACATA 12 240 0 TAGCCACACC 0.90274 -55 ********** Masking position 4 Map Score: 27.1217 Number of sites scoring better than the average of aligned sites = 15491 Number in coding regions = 14558 Number in noncoding regions = 933 Number of orfs with sites within 600 bp upstream = 653 Fraction of orfs with sites within 600 bp upstream = 0.104883 Motif number 6 GCGCCGGAGTTGCTCAACATTGGCCGGTTC 8 38 1 TGCTCAACAT 0.77834 -170 CTGACCCTGATCCTCGGCCTCCCGACGGGA 9 159 1 TCCTCGGCCT 0.901573 -66 CGCATCGCTGCGCTCTGCATCGTCGCGGA 10 10 0 CGCTCTGCAT 0.970413 -58 GGGCGGTACCCCCACCGCATCGCTGCGCTC 10 25 0 CCCACCGCAT 0.868599 -43 CCCTGATTTTCGCGCACCATCGGCGACGGA 12 92 1 CGCGCACCAT 0.658611 -203 GTCTAGCGATTCCTCGGCGTTATTTCATCG 12 146 1 TCCTCGGCGT 0.901573 -149 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 13 34 0 TGCTCTGCAT 0.983241 -140 CTGGCGCCGCTCCTCCCCATCGCTTTGCTC 13 49 0 TCCTCCCCAT 0.981894 -125 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 13 87 0 TGCTCTGCAT 0.983241 -87 CTGGCGCCGCTCCTCCCCATCGCTTTGCTC 13 102 0 TCCTCCCCAT 0.981894 -72 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 13 140 0 TGCTCTGCAT 0.983241 -34 TGGCGCCGCTCCTCCCCATCGCTTTGCTC 13 155 0 TCCTCCCCAT 0.981894 -19 ********** Masking position 10 Map Score: 16.2969 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 241 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 CTAGCTTGTGGTTGGGTGTGCAGGTGAAGG 1 86 0 GTTGGGTGTG 0.690623 -215 TGGTGGTAGTCGTTGGTGTGGGCACCGCGG 1 186 0 CGTTGGTGTG 0.768627 -115 TGACGAACTACGAGGCTGGGACCTTGCTGA 3 112 0 CGAGGCTGGG 0.876913 -189 TGCTGGCGCGCGACGGTCGGTGGTCGCGCT 3 276 1 CGACGGTCGG 0.757937 -25 GCGCGGCCCGGCCATACGGTC 5 2 1 CGCGGCCCGG 0.870363 -41 GGGTGTTATGGGCCGCTCGGCGCGC 8 6 0 GGCCGCTCGG 0.83118 -202 TTTGCTTTTTGTTCGCTGTGTAGGTGGTTG 8 120 1 GTTCGCTGTG 0.851054 -88 CGGTGATTGGGTCTGATGAAGTTTG 8 193 0 ATTGGGTCTG 0.525271 -15 CTGCCGATAGCGTCGCGGTGTGCCGCGGCG 9 49 1 CGTCGCGGTG 0.769727 -176 CACCGCATCGCTGCGCTCTGCATCGTCGCG 10 13 0 CTGCGCTCTG 0.904065 -55 CGGCGCCGCTCTCCCCCGCAAGC 10 55 0 CGCCGCTCTC 0.823213 -13 CGATTTGGGGCTTGGCCCTGATTTTCGCGC 12 77 1 CTTGGCCCTG 0.939205 -218 CTCCCCATCGCTTTGCTCTGCATCGTCGCC 13 37 0 CTTTGCTCTG 0.955278 -137 CTCCCCATCGCTTTGCTCTGCATCGTCGCC 13 90 0 CTTTGCTCTG 0.955278 -84 CTCCCCATCGCTTTGCTCTGCATCGTCGCC 13 143 0 CTTTGCTCTG 0.955278 -31 TAGAGGTCCTCTCGGCTGTGTCCGGTGCGC 14 11 1 CTCGGCTGTG 0.957005 -124 TAGGCCTACCCTTGGCTCTC 14 125 1 CTTGGCTCTC 0.899581 -10 GAGCGCAGCGCTAGGCTCGGGCAATGACCT 15 13 0 CTAGGCTCGG 0.931161 -47 ********** Masking position 5 Map Score: 17.1842 Number of sites scoring better than the average of aligned sites = 5340 Number in coding regions = 4910 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 8 GAATGGATCCCGCCACCCCACCTCGACCGC 1 160 1 CGCCACCCCA 0.970953 -141 GCGGTCGGAGCTCACCCGCACACAATAGGG 7 21 0 CTCACCCGCA 0.971517 -65 CGGCGCCGCTCTCCCCCGCAAGCGGGCGGT 10 48 0 CTCCCCCGCA 0.992066 -20 AATCCCTTATCCCCAAAAATCGTGA 12 6 1 CTTATCCCCA 0.926723 -289 ACTGGCGCCGCTCCTCCCCATCGCTTTGCT 13 50 0 CTCCTCCCCA 0.99721 -124 ACTGGCGCCGCTCCTCCCCATCGCTTTGCT 13 103 0 CTCCTCCCCA 0.99721 -71 TGGCGCCGCTCCTCCCCATCGCTTTGCT 13 156 0 CTCCTCCCCA 0.99721 -18 ********** Masking position 10 Map Score: 14.9913 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 38 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 GGATCCATTCCGTTTGGCCGTCGGACCGTTTCC 1 137 0 CGTTGCGTCG 0.881122 -164 CTGGTCTTGACGTTTTGTGGTCAGGGCGCGGCC 1 243 0 CGTTGGGTCA 0.959114 -58 ACCGCGTGCGCGTTTGGAGGTCCCTGAGCG 2 60 1 CGTTGGGTCC 0.983608 -20 CACCCTCATCCGTGTCGGGGATCCCCGAGGAAT 3 149 1 CGTTGGGATC 0.938856 -152 ACCAGATACCCGTATAGGGTATATATTTAAGTA 3 216 0 CGTTGGTATA 0.509224 -85 TGGCGCGCGACGGTCGGTGGTCGCGCTAGCGT 3 279 1 CGGCGGGTCG 0.967293 -22 TCTGGCTGGGCGGTCGGAGCTCACCCGCACACA 7 27 0 CGGCGGCTCA 0.778412 -59 GGTTCCGGAGCGGGCGGTGGATCTCGTCTGGCT 7 53 0 CGGCGGGATC 0.855166 -33 GGTTCGTTACCGTCTTGTGATCGAACGGGTGGG 8 63 1 CGTTGGATCG 0.957985 -145 AGTCGCTCCACGAGTCGGGCACGAGCGACCGCG 9 83 0 CGATGGCACG 0.77167 -142 TTGCGCGCATCGTGGCGGGTTTGAGGGCGCCGA 9 115 0 CGTGGGTTTG 0.646318 -110 GCTCAGGTCCCGTCGGGAGGCCGAGGATCAGGG 9 163 0 CGTGGGGCCG 0.869852 -62 CCCATTCTCCCGTACGGTGGACGG 9 211 1 CGTCGGGACG 0.871106 -14 TCGTTTTTTTCGTCTAGCGATTCCTCGGCGTTA 12 135 1 CGTTGGATTC 0.812166 -160 TTGCCGATCGCGTACGGCGCACCGGACACAGCC 14 24 0 CGTCGGCACC 0.947542 -111 CGAACATTCTCGTCTAGGGAACGCTACCGCCAC 14 85 1 CGTTGGAACG 0.94341 -50 *** * * ***** Masking position 7 Map Score: 17.0869 Number of sites scoring better than the average of aligned sites = 3198 Number in coding regions = 2965 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 10 GGCAACCGGCGGCTCAACCGATATCGACAAA 1 51 1 GGCTCACCGA 0.893248 -250 CCACCCCGAACGCCTCTTCGACCACTAGCGG 1 213 1 CGCCTCTCGA 0.887996 -88 GGCTAGTTCCGGCCAAGCCGGG 2 2 0 GGCCAACCGG 0.788799 -78 CGCTCAGGGACCTCCAAACGCGCACGC 2 63 0 GGGACCCCAA 0.7564 -17 TGCAGCGGTAGGCGTCACCGGCGCCAGCACA 3 28 1 GGCGTCCCGG 0.926872 -273 ATCCGTGTCGGGGATCCCCGAGGAATCCCAG 3 156 1 GGGATCCCGA 0.957073 -145 ACGCTAGCGCGACCACCGACCGTCGCGCG 3 282 0 GCGACCCCGA 0.821462 -19 GAAACCTAGAGGCCCCACCCGTTCGATCACA 8 78 0 GGCCCCCCCG 0.907271 -130 AAAGCAAAATGGGCCCTCCGAAACCTAGAGG 8 97 0 GGGCCCCCGA 0.992026 -111 CGCCACGATGCGCGCAATCGAAAACGCCCTG 9 131 1 CGCGCATCGA 0.679486 -94 CCCTGATCCTCGGCCTCCCGACGGGACCTGA 9 163 1 CGGCCTCCGA 0.819699 -62 AATGGGTCGCCGCCTCGCCGCGCTCAGGTCC 9 186 0 CGCCTCCCGC 0.861951 -39 CTGATTTTCGCGCACCATCGGCGACGGACGA 12 94 1 CGCACCTCGG 0.845634 -201 CGGGGCATCTTCGATTGACCCGCG 13 4 1 GGCATCTCGA 0.88977 -170 CGGCGCACCGGACACAGCCGAGAGGACCTCT 14 12 0 GACACACCGA 0.680551 -123 CAACCCGCGGTGGCCAGCCGATTTACGTCGG 14 54 1 TGGCCACCGA 0.77208 -81 GCCAAGGGTAGGCCTATCCGAGCGTGGCGGT 14 110 0 GGCCTACCGA 0.970054 -25 ****** **** Masking position 9 Map Score: 13.7499 Number of sites scoring better than the average of aligned sites = 16860 Number in coding regions = 15895 Number in noncoding regions = 965 Number of orfs with sites within 600 bp upstream = 655 Fraction of orfs with sites within 600 bp upstream = 0.105204 Motif number 11 ********** No masking Map Score: -5.51138e-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: -5.51138e-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: -5.51138e-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