AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_mtub_reg_100.orf -o00290_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 leuS 196 leuS #2 ilvD 147 ilvD #3 ileS 300 ileS #4 ilvG 70 ilvG #5 ilvE 71 ilvE #6 aceE 51 aceE #7 valS 87 valS #8 Rv2449c 89 hypothetical protein Rv2449c #9 Rv2450c 81 hypothetical protein Rv2450c #10 pdhA 258 pdhA #11 leuD 24 leuD #12 leuC 71 leuC #13 serA 29 serA #14 ilvC 37 ilvC #15 ilvB 300 ilvB #16 Rv3510c 300 hypothetical protein Rv3510c #17 leuA 256 leuA Motif number 1 GACGGGCACCGTCGCCCGGCCATTCGGAGG 1 22 0 GTCGCCCGGC 0.838735 -175 GGCCGCGCTACCGGCCACGGGTTGGTCTCG 1 140 0 CCGGCCACGG 0.913886 -57 GGCCGGTAGCGCGGCCCCGGAGGTTCCCGG 1 154 1 GCGGCCCCGG 0.579281 -43 GGGTATAAGGGTGGCCCGGGAACCTCCGGG 1 169 0 GTGGCCCGGG 0.952731 -28 GGGCCCTGCTTTCGGGTTGGCGAGTATCTC 2 27 0 TTCGGGTTGG 0.786525 -121 GGTCCGATACCCCGCTGGGGTACAAGATAT 2 73 0 CCCGCTGGGG 0.845579 -75 CAACCGTGCCGCGGCGAGCGCATCCTTGGG 2 113 1 GCGGCGAGCG 0.984896 -35 GCGGCGCAAGGTCGGCTGCCTGCCC 3 6 0 GTCGGCTGCC 0.535778 -295 CCGACCTTGCGCCGCGATGTGGATTTGCGG 3 21 1 GCCGCGATGT 0.918097 -280 ATGTGGATTTGCGGCGCTGGGCGACAATCC 3 37 1 GCGGCGCTGG 0.942303 -264 CCGGCGATCACCGGGGAGCCTTCGGAAGAA 3 94 1 CCGGGGAGCC 0.74145 -207 CTCAAGTCGAGCGGCCGCGCATCGGCGTGG 3 170 1 GCGGCCGCGC 0.852251 -131 CGGCCGCGCATCGGCGTGGCAAGCGGGGTG 3 181 1 TCGGCGTGGC 0.929643 -120 GGCGTGGCAAGCGGGGTGGTACCGCGGCGT 3 193 1 GCGGGGTGGT 0.806635 -108 GGGTGGTACCGCGGCGTTCGCGCACCGGCG 3 206 1 GCGGCGTTCG 0.967312 -95 CGTTCGCGCACCGGCGTGGCGTCGTCCCCG 3 220 1 CCGGCGTGGC 0.778951 -81 GAACGGTGCTGGGGCCTGGGGAGACGACGC 3 276 1 GGGGCCTGGG 0.91464 -25 TGGCAGCGGAGTGGCCTCCGGGCCGTCAAT 5 23 1 GTGGCCTCCG 0.794007 -49 CCCGAACTCGGTCGGGTTCGCTTGCGCTGT 6 18 0 GTCGGGTTCG 0.824546 -34 GTTCGGGTGATCCGCGAGGGT 6 41 1 TCCGCGAGGG 0.988353 -11 ATCCGGGCGGTTTCGGGCGCT 7 2 1 TCCGGGCGGT 0.626232 -86 ATCGGCGGCAGGGTGAGGGCTGG 7 75 0 GGCGGCAGGG 0.867631 -13 TTTGCGTCTTTTCGCGGTGG 8 1 0 TTCGCGGTGG 0.913406 -89 TGACGCTACTCCGGGGTGCGCGAGCAGACG 8 65 0 CCGGGGTGCG 0.884037 -25 GGTTGGCTTTGGCGCGCGCGCACCGCGAAA 9 53 1 GGCGCGCGCG 0.596832 -29 TCGCAACCGTGTCGCGGGGGATCTGCGCCC 10 11 0 GTCGCGGGGG 0.98677 -248 TTGCGATGCGTTCGCGATCGGTCCGGACTC 10 35 1 TTCGCGATCG 0.862875 -224 CGCCAGTGTTGCGGCGAGCGGAAGCTTTGG 10 93 1 GCGGCGAGCG 0.984896 -166 AAGCTTTGGTGCGGCCGGCGATCAACTTCG 10 114 1 GCGGCCGGCG 0.960465 -145 CACAGCACATCCCGCCTGGGAAACCGCTGC 10 148 0 CCCGCCTGGG 0.89752 -111 ATCCTTAGCGTCGGCGCTGGTGGTGCGGCG 10 180 0 TCGGCGCTGG 0.958643 -79 TGACCAGCGAGTCGCGAACGAATGAATAGA 12 41 1 GTCGCGAACG 0.574304 -31 GTGGGCGTCGAGTTCGCGAG 15 1 1 GTGGGCGTCG 0.581603 -300 GGGCGTCGAGTTCGCGAGCGTAACGCCACC 15 13 1 TTCGCGAGCG 0.932179 -288 CATGCGAATTTTCGCGGTGGCGTTACGCTC 15 28 0 TTCGCGGTGG 0.913406 -273 TCAGTCTTGATCCGCGAGCGTGACGGCACT 15 67 0 TCCGCGAGCG 0.97324 -234 AGCAGTCAAATCCGCGGTGTCAGTCTTGAT 15 86 0 TCCGCGGTGT 0.684492 -215 CCCGGGCTTTCCGGCCTTGTCCATAGTGTC 15 139 0 CCGGCCTTGT 0.49657 -162 GGCCGGAAAGCCCGGGATGCTCGTAGTAAT 15 153 1 CCCGGGATGC 0.827211 -148 GTAATTGGTCGGCGCGTTGGTGCCTGACTA 15 178 1 GGCGCGTTGG 0.940673 -123 CGCGTTGGTGCTCGCTTGGGCTAGTCAGGC 15 199 0 CTCGCTTGGG 0.692494 -102 CTGCACGAGGGTCGCGTTGGTGCTCGCTTG 15 211 0 GTCGCGTTGG 0.974447 -90 AGCAGCTGAGCTGGCGAGGGTTTTTTCTTG 15 239 1 CTGGCGAGGG 0.971989 -62 CCCGGCGTTCGTGGCCACGCGGTGCTTCGC 16 94 0 GTGGCCACGC 0.791933 -207 GGCCACGAACGCCGGGAGGGACAATCTCGG 16 108 1 GCCGGGAGGG 0.960085 -193 ACAATCTCGGGCGGCTAGGGCTTCTCGCGG 16 128 1 GCGGCTAGGG 0.943273 -173 GTTTCAACACGTCGCGTCGCCCTCCGACCG 16 177 1 GTCGCGTCGC 0.891648 -124 TCCCCGAATGTTCGCGGTCGGAGGGCGACG 16 191 0 TTCGCGGTCG 0.801892 -110 CCGCGAACATTCGGGGATGGCAGCAACCTG 16 204 1 TCGGGGATGG 0.914204 -97 AGATCATCGCCCGGCCAGGGTGCTACCAGG 16 230 0 CCGGCCAGGG 0.943871 -71 GCGACTACCCGCGGCGACGCTGCAGATCAT 16 253 0 GCGGCGACGC 0.911854 -48 GCGGGTAGTCGCCGCCCGGGCGGCTACAGT 16 271 1 GCCGCCCGGG 0.527888 -30 CAGAATAGGGGGCGCGCCGGCCTGCGCTGA 17 45 1 GGCGCGCCGG 0.511348 -212 CTCCTCGGACGCCGCGACGGGGTCTGATCC 17 162 1 GCCGCGACGG 0.940021 -95 GCGACGGGAAGCCGGTCTGGATCAGACCCC 17 180 0 GCCGGTCTGG 0.697012 -77 TCGCGAACGTCCCGCGACGGGAAGCCGGTC 17 193 0 CCCGCGACGG 0.830209 -64 TCGCGGGACGTTCGCGATGCGCCGGTCTGA 17 206 1 TTCGCGATGC 0.813058 -51 GGTAGTTGCTCCGGGATGGTGAGAAGGAA 17 238 0 TCCGGGATGG 0.933507 -19 ********** Masking position 4 Map Score: 103.645 Number of sites scoring better than the average of aligned sites = 62850 Number in coding regions = 58758 Number in noncoding regions = 4092 Number of orfs with sites within 600 bp upstream = 1464 Fraction of orfs with sites within 600 bp upstream = 0.235143 Motif number 2 TTGCGTCGGTCCCTCCGAATGGCCGG 1 7 1 CGGTCCCTCC 0.870358 -190 GCACCGTCGCCCGGCCATTCGGAGGGACCG 1 17 0 CCGGCCATTC 0.931391 -180 CTGAATGTAACCAGCGCTCCATGGCAGTGC 1 59 1 CCAGCGCTCC 0.934322 -138 GGTCTCGGTTCCGTTGCACCACGATCAGAG 1 117 0 CCGTTGCACC 0.369652 -80 CGGAGGTTCCCGGGCCACCCTTATACCCTG 1 171 1 CGGGCCACCC 0.840239 -26 TTACTCGCCATCTCCAGAGATAC 2 4 1 CTCGCCATCT 0.439633 -144 TCCAGAGATACTCGCCAACCCGAAAGCAGG 2 23 1 CTCGCCAACC 0.805891 -125 CGTGCCGCGGCGAGCGCATCCTTGGGCCGC 2 117 1 CGAGCGCATC 0.729694 -31 CGGCATCGATCCGGCGATCACCGGGGAGCC 3 84 1 CCGGCGATCA 0.95396 -217 CTGGGCCTAACCGGCCGTTCTTCCGAAGGC 3 111 0 CCGGCCGTTC 0.930061 -190 GAGGCTGTGACGGGCCAACCCGTTCGGTTC 3 143 0 CGGGCCAACC 0.965433 -158 AAGTCGAGCGGCCGCGCATCGGCGTGGCAA 3 173 1 GCCGCGCATC 0.664823 -128 GAGTGGCCTCCGGGCCGTCAATAACCGTTC 5 31 1 CGGGCCGTCA 0.928467 -41 CGACCGAGTTCGGGTGATCCGCGAGGGT 6 34 1 CGGGTGATCC 0.929657 -18 ATCCGGGCGGTTTCGGGCGCTTT 7 4 1 CGGGCGGTTT 0.75353 -84 CGGGCGGTTTCGGGCGCTTTCATGCCGGTG 7 14 1 CGGGCGCTTT 0.888843 -74 AGGGTGAGGGCTGGCGGTCACCGATCAATT 7 59 0 CTGGCGGTCA 0.902329 -29 TTTGCGTCTGCTCGCGCACCCCGGAGTAGC 8 61 1 CTCGCGCACC 0.954736 -29 GGCTTTGGCGCGCGCGCACCGCGAAAGGAA 9 57 1 CGCGCGCACC 0.982992 -25 CGCCGCAACACTGGCGCTTCCTCCATTATG 10 79 0 CTGGCGCTTC 0.969129 -180 TTTGGTGCGGCCGGCGATCAACTTCGGCTC 10 118 1 CCGGCGATCA 0.95396 -141 CGCTGGTGGTGCGGCGCTCACAGCACATCC 10 166 0 GCGGCGCTCA 0.882984 -93 GTCTCCTCAGCTCGCGATCACAACGCGGTT 10 236 0 CTCGCGATCA 0.796163 -23 TGCCGTCACGCTCGCGGATCAAGACTGACA 15 69 1 CTCGCGGATC 0.706315 -232 CAGGCACCAACGCGCCGACCAATTACTACG 15 174 0 CGCGCCGACC 0.918902 -127 ACGTATTGGGCGGGTGCTGAATTATGATCC 16 15 0 CGGGTGCTGA 0.445445 -286 TCGTGGCCACGCGGTGCTTCGCCTTTTTGC 16 86 0 GCGGTGCTTC 0.533364 -215 GCCGTACGTTCGGGCCTTCCCGCGAGAAGC 16 147 0 CGGGCCTTCC 0.880024 -154 AACACGTCGCGTCGCCCTCCGACCGCGAAC 16 182 1 GTCGCCCTCC 0.759371 -119 GCACCCTGGCCGGGCGATGATCTGCAGCGT 16 237 1 CGGGCGATGA 0.730861 -64 TCAGCGCAGGCCGGCGCGCCCCCTATTCTG 17 45 0 CCGGCGCGCC 0.953358 -212 TCATGTGCAGCGGGTGCTCCTCCTCGGACG 17 143 1 CGGGTGCTCC 0.971297 -114 GAACCTCAGACCGGCGCATCGCGAACGTCC 17 211 0 CCGGCGCATC 0.970904 -46 ********** Masking position 4 Map Score: 42.5034 Number of sites scoring better than the average of aligned sites = 24158 Number in coding regions = 22372 Number in noncoding regions = 1786 Number of orfs with sites within 600 bp upstream = 1014 Fraction of orfs with sites within 600 bp upstream = 0.162865 Motif number 3 ACGACGGGCACCGTCGCCCGGCCATTCGGAGG 1 22 0 CCTCGCCGGC 0.864327 -175 GCGACGGTGCCCGTCGTCGAGGCTGAATGTAA 1 37 1 CCTCGTGAGG 0.546985 -160 AACCAGCGCTCCATGGCAGTGCACAGGCTTGA 1 67 1 CCTGGCGTGC 0.963967 -130 TAAGGGTGGCCCGGGAACCTCCGGGGCCGCGC 1 162 0 CCGGAACTCC 0.59116 -35 GGGTAGCATGCCTGGGCCCTGCTTTCGGGTTG 2 38 0 CCGGGCCTGC 0.72071 -110 CCCAAGGATGCGCTCGCCGCGGCACGGTTGCC 2 111 0 CGTCGCGCGG 0.687859 -37 GATGCCGTTCCCCTGATTCTACGGGGATTGTC 3 59 0 CCTGATCTAC 0.402782 -242 CGGCATCGATCCGGCGATCACCGGGGAGCCTT 3 84 1 CCGCGACACC 0.783121 -217 CACGCCGATGCGCGGCCGCTCGACTTGAGGCT 3 167 0 CGGGCCCTCG 0.795178 -134 GGTACCGCGGCGTTCGCGCACCGGCGTGGCGT 3 210 1 CGTCGCCACC 0.945889 -91 CGTCGTCTCCCCAGGCCCCAGCACCGTTCGGC 3 273 0 CCGGCCCAGC 0.867987 -28 CGTCAATAACCGTTCGCCCACGGATAGAATCG 5 46 1 CGTCGCCACG 0.661773 -26 ACCCTCGCGGATCACCCGAACTC 6 39 0 CCTCGCGATC 0.364302 -13 TGACCGCCAGCCCTCACCCTGCCGCCGAT 7 69 1 CCTCACCTGC 0.942131 -19 TGCGTCTGCTCGCGCACCCCGGAGTAGCGTCA 8 63 1 CGGCACCCGG 0.462138 -27 CAGGTGCATTCGAGGGTGCTGC 9 1 0 CGGGGTCTGC 0.820801 -81 GGCAGCTAACCCATGCCCGTGGGTTGGCTTTG 9 32 1 CCTGCCGTGG 0.637797 -50 TTGGCTTTGGCGCGCGCGCACCGCGAAAGGAA 9 55 1 CGGCGCCACC 0.907871 -27 AACCGTGTCGCGGGGGATCTGCGCCC 10 5 0 CGGGGACTGC 0.895771 -254 GGTTGCGATGCGTTCGCGATCGGTCCGGACTC 10 33 1 CGTCGCATCG 0.438812 -226 TTTGGTGCGGCCGGCGATCAACTTCGGCTCGC 10 118 1 CCGCGACAAC 0.453023 -141 TTAGCGTCGGCGCTGGTGGTGCGGCGCTCACA 10 174 0 CGTGGTGTGC 0.845216 -85 AGAGATTCAGCGGTGGCACTAGAG 14 24 1 CGTGGCCTAG 0.850194 -14 CGAATTTTCGCGGTGGCGTTACGCTCGCGAAC 15 22 0 CGTGGCTTAC 0.427144 -279 TTTCGCAGTGCCGTCACGCTCGCGGATCAAGA 15 61 1 CCTCACCTCG 0.777682 -240 CCGACGGTAGCCTTCACACAGCTCAGCAGTCA 15 108 0 CCTCACCAGC 0.889731 -193 CTACGAGCATCCCGGGCTTTCCGGCCTTGTCC 15 147 0 CCGGGCTTCC 0.793237 -154 ACGAGGGTCGCGTTGGTGCTCGCTTGGGCTAG 15 205 0 CGTGGTCTCG 0.760494 -96 ACCAACGCGACCCTCGTGCAGCAGCTGAGCTG 15 220 1 CCTCGTCAGC 0.902917 -81 TCAACACGTCGCGTCGCCCTCCGACCGCGAAC 16 180 1 GCTCGCCTCC 0.666307 -121 CATCGCCCGGCCAGGGTGCTACCAGGTTGCTG 16 224 0 CCGGGTCTAC 0.784892 -77 GCAGCGTCGCCGCGGGTAGTCGCCGCCCGGGC 16 260 1 CGGGGTGTCG 0.650813 -41 TCAGCGCAGGCCGGCGCGCCCCCTATTCTGGA 17 43 0 CCGCGCCCCC 0.786458 -214 CGCCGGCCTGCGCTGACTCTGCGTCCACCACG 17 59 1 CGTGACCTGC 0.93746 -198 GCACTTTACACGTTGACTCTGCGTCCACCGTG 17 110 0 CGTGACCTGC 0.937417 -147 CTTCATGTGCAGCGGGTGCTCCTCCTCGGACG 17 141 1 AGGGGTCTCC 0.243137 -116 CGTCGCGGGACGTTCGCGATGCGCCGGTCTGA 17 204 1 CGTCGCATGC 0.788338 -53 TTCCTTCTCACCATCCCGGAGCAACTACC 17 238 1 CCTCCCGAGC 0.675015 -19 ** **** **** Masking position 1 Map Score: 41.1013 Number of sites scoring better than the average of aligned sites = 34166 Number in coding regions = 31808 Number in noncoding regions = 2358 Number of orfs with sites within 600 bp upstream = 1119 Fraction of orfs with sites within 600 bp upstream = 0.17973 Motif number 4 GTAGCGCGGCCCCGGAGGTTCCCGGGCCACCCT 1 159 1 CCGAGGTTCC 0.945655 -38 GCGCTCGCCGCGGCACGGTTGCCAAATTCTAGG 2 101 0 CGACGGTTCC 0.870208 -47 CGGCCGTTCTTCCGAAGGCTCCCCGGTGATCGC 3 97 0 TCAAGGCTCC 0.697855 -204 TTTGCGCGTCGTCTCCCCAGGCCCCAG 3 284 0 CCTCGTCTCC 0.87607 -17 CCGGAGGCCACTCCGCTGCCACCAAGTGGTGAC 5 11 0 CCGCTGCCCC 0.979272 -61 CGCGAAAAGACGCAAAAGCTCCCAAATCCGGTC 8 15 1 CCAAAGCTCC 0.945879 -75 CGCGAGCAGACGCAAAAGCTCCCAAATCCGACC 8 44 0 CCAAAGCTCC 0.945879 -46 CTCGCCGCAACACTGGCGCTTCCTCCATTATGC 10 78 0 CCGGCGCTCC 0.919048 -181 TCGCCGGCCGCACCAAAGCTTCCGCTCGCCGCA 10 102 0 CCAAAGCTCC 0.945981 -157 AACTTCGGCTCGCAGCGGTTTCCCAGGCGGGAT 10 137 1 CCGCGGTTCC 0.983521 -122 GGATGGAACGCACGGCATCTTCTGACGCGTAAC 10 206 1 CCGCATCTCT 0.626787 -53 CTCTAGTGCCACCGCTGAATCTC 14 25 0 CCAGTGCCCC 0.778232 -13 CCCTCGCCAGCTCAGCTGCTGCACGAGGGTCGC 15 226 0 CCGCTGCTCA 0.901257 -75 TAGTCGCCGCCCGGGCGGCTACAGTCTGAAACG 16 276 1 CGGCGGCTCA 0.924976 -25 CCTGCGCTGACTCTGCGTCCACCACGGGAATGT 17 65 1 CCGCGTCCCC 0.977201 -192 TACACGTTGACTCTGCGTCCACCGTGTGGGCTA 17 103 0 CCGCGTCCCC 0.977201 -154 GGGTCTGATCCAGACCGGCTTCCCGTCGCGGGA 17 181 1 CGCCGGCTCC 0.939202 -76 CTCACCATCCCGGAGCAACTACC 17 244 1 CGGCAACTCC 0.740363 -13 * * ****** ** Masking position 12 Map Score: 19.0469 Number of sites scoring better than the average of aligned sites = 11141 Number in coding regions = 10520 Number in noncoding regions = 621 Number of orfs with sites within 600 bp upstream = 458 Fraction of orfs with sites within 600 bp upstream = 0.0735625 Motif number 5 CCTCCGAATGGCCGGGCGACGGTGCCCGTCG 1 22 1 GCCGGGCGCG 0.909706 -175 GTAGCGCGGCCCCGGAGGTTCCCGGGCCACC 1 159 1 CCCGGAGGTC 0.98804 -38 CGAAAGCAGGGCCCAGGCATGCTACCCATCA 2 43 1 GCCCAGGCTG 0.634972 -105 CAAGTATGCGGCCCAAGGATGCGCTCGCCGC 2 123 0 GCCCAAGGTG 0.855471 -25 GGCGACAATCCCCGTAGAATCAGGGGAACGG 3 56 1 CCCGTAGATC 0.544832 -245 CGGCCGTTCTTCCGAAGGCTCCCCGGTGATC 3 99 0 TCCGAAGGTC 0.860285 -202 GTGGCGTCGTCCCCGAGCCTGGATTGCAGGC 3 235 1 CCCCGAGCTG 0.825844 -66 GGCACGCAGTGCCGAACGGTGCTGGGGCCTG 3 263 1 GCCGAACGTG 0.93964 -38 GGTACCTTCGCCCGAAGGATTTCTGTTTGTG 4 25 0 CCCGAAGGTT 0.736825 -46 GGCGAAGGTACCCGAAGGTTGTCGATAGGCT 4 44 1 CCCGAAGGTG 0.95272 -27 CGGAGTGGCCTCCGGGCCGTCAATAACCGTT 5 29 1 TCCGGGCCTC 0.829417 -43 ATCCGGGCGGTTTCGGGCGCTT 7 2 1 TCCGGGCGTT 0.693793 -86 CTAACCCATGCCCGTGGGTTGGCTTTGGCGC 9 37 1 CCCGTGGGTG 0.938112 -45 GCAACCGTGTCGCGGGGGATCTGCGCCC 10 8 0 CGCGGGGGTC 0.838317 -251 GTCAGAAGATGCCGTGCGTTCCATCCTTAGC 10 201 0 GCCGTGCGTC 0.938112 -58 CTACGAGCATCCCGGGCTTTCCGGCCTTGTC 15 148 0 CCCGGGCTTC 0.79785 -153 CTCAGCTGCTGCACGAGGGTCGCGTTGGTGC 15 218 0 GCACGAGGTC 0.456565 -83 AGATTGTCCCTCCCGGCGTTCGTGGCCACGC 16 104 0 TCCCGGCGTC 0.87194 -197 AGCCCTAGCCGCCCGAGATTGTCCCTCCCGG 16 119 0 GCCCGAGATG 0.593352 -182 GTGTTGAAACGCCGTACGTTCGGGCCTTCCC 16 156 0 GCCGTACGTC 0.922366 -145 TGCTGCCATCCCCGAATGTTCGCGGTCGGAG 16 198 0 CCCGAATGTC 0.613562 -103 TAGCACCCTGGCCGGGCGATGATCTGCAGCG 16 235 1 GCCGGGCGTG 0.984352 -66 ACTGTAGCCGCCCGGGCGGCGACTACCCGCG 16 270 0 CCCGGGCGCG 0.917052 -31 GCTTCCCGTCGCGGGACGTTCGCGATGCGCC 17 198 1 GCGGGACGTC 0.76608 -59 TTCTCACCATCCCGGAGCAACTACC 17 242 1 CCCGGAGCAC 0.52771 -15 ******** ** Masking position 2 Map Score: 29.199 Number of sites scoring better than the average of aligned sites = 9549 Number in coding regions = 8794 Number in noncoding regions = 755 Number of orfs with sites within 600 bp upstream = 569 Fraction of orfs with sites within 600 bp upstream = 0.0913909 Motif number 6 TCCACATCGCGGCGCAAGGTCGGCTGCCTGC 3 13 0 GGCGCAAGTC 0.840097 -288 GTCGCCCAGCGCCGCAAATCCACATCGCGGC 3 31 0 GCCGCAAACC 0.920503 -270 GCTCGGGGACGACGCCACGCCGGTGCGCGAA 3 222 0 GACGCCACCC 0.916087 -79 ACCGCGAAAAGACGCAAAAGCTCCCAAATCC 8 13 1 GACGCAAAGC 0.975625 -77 TGCGCGAGCAGACGCAAAAGCTCCCAAATCC 8 48 0 GACGCAAAGC 0.975625 -42 GGGTTTGACGCTACTCCGGGGTGCGCG 8 73 0 GACGCTACCC 0.961557 -17 GGGCGCAGATCCCCCGCGACAC 10 2 1 GGCGCAGACC 0.973581 -257 CCGCAACACTGGCGCTTCCTCCATTATGCCC 10 76 0 GGCGCTTCTC 0.653209 -183 CACCAGCGCCGACGCTAAGGATGGAACGCAC 10 188 1 GACGCTAAGA 0.724346 -71 TGGGCAAAAAGGCGAAGCACCGCGTGGCCAC 16 83 1 GGCGAAGCCC 0.739619 -218 TACCCGCGGCGACGCTGCAGATCATCGCCCG 16 247 0 GACGCTGCGA 0.777802 -54 TCCCGTGGTGGACGCAGAGTCAGCGCAGGCC 17 63 0 GACGCAGATC 0.805375 -194 CCACACGGTGGACGCAGAGTCAACGTGTAAA 17 107 1 GACGCAGATC 0.805375 -150 ******** ** Masking position 3 Map Score: 12.5049 Number of sites scoring better than the average of aligned sites = 4591 Number in coding regions = 4156 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 7 CAGCGCTCCATGGCAGTGCACAGGCTTGAA 1 70 1 TGGCAGTGCA 0.74448 -127 GAACCTCTGATCGTGGTGCAACGGAACCGA 1 113 1 TCGTGGTGCA 0.756194 -84 AACCCGTGGCCGGTAGCGCGGCCCCGGAGG 1 147 1 CGGTAGCGCG 0.963438 -50 AATTTGGCAACCGTGCCGCGGCGAGCGCAT 2 106 1 CCGTGCCGCG 0.980991 -42 CAAATCCACATCGCGGCGCAAGGTCGGCTG 3 18 0 TCGCGGCGCA 0.916592 -283 TGTGGATTTGCGGCGCTGGGCGACAATCCC 3 38 1 CGGCGCTGGG 0.973262 -263 TCAAGTCGAGCGGCCGCGCATCGGCGTGGC 3 171 1 CGGCCGCGCA 0.846392 -130 GCAAGCGGGGTGGTACCGCGGCGTTCGCGC 3 199 1 TGGTACCGCG 0.891519 -102 GACGACGCCACGCCGGTGCGCGAACGCCGC 3 216 0 CGCCGGTGCG 0.918923 -85 CAGCACCGTTCGGCACTGCGTGCCTGCAAT 3 257 0 CGGCACTGCG 0.968051 -44 CAGTGCCGAACGGTGCTGGGGCCTGGGGAG 3 269 1 CGGTGCTGGG 0.943189 -32 CACCACTTGGTGGCAGCGGAGTGGCCTCCG 5 13 1 TGGCAGCGGA 0.626534 -59 ATCGGCGGCAGGGTGAGGGCTG 7 76 0 CGGCGGCAGG 0.688704 -12 TGACGCTACTCCGGGGTGCGCGAGCAGACG 8 65 0 CCGGGGTGCG 0.867093 -25 GTTGTTCCTTTCGCGGTGCGCGCGCGCCAA 9 61 0 TCGCGGTGCG 0.968382 -21 CGCATCGCAACCGTGTCGCGGGGGATCTGC 10 15 0 CCGTGTCGCG 0.789084 -244 GCGTCGGCGCTGGTGGTGCGGCGCTCACAG 10 173 0 TGGTGGTGCG 0.952878 -86 GCGAGCGTAACGCCACCGCGAAAATTCGCA 15 26 1 CGCCACCGCG 0.821243 -275 GCGAGCGTGACGGCACTGCGAAATCCCATG 15 54 0 CGGCACTGCG 0.968051 -247 GGATCAAGACTGACACCGCGGATTTGACTG 15 84 1 TGACACCGCG 0.384065 -217 AACGCGACCCTCGTGCAGCAGCTGAGCTGG 15 223 1 TCGTGCAGCA 0.205688 -78 CGTGGCCACGCGGTGCTTCGCCTTTTTGCC 16 85 0 CGGTGCTTCG 0.597983 -216 TGATCTGCAGCGTCGCCGCGGGTAGTCGCC 16 254 1 CGTCGCCGCG 0.850826 -47 TCGCACATTCCCGTGGTGGACGCAGAGTCA 17 72 0 CCGTGGTGGA 0.750296 -185 TCCTCGGACGCCGCGACGGGGTCTGATCCA 17 163 1 CCGCGACGGG 0.837387 -94 GACCGGCTTCCCGTCGCGGGACGTTCGCGA 17 193 1 CCGTCGCGGG 0.736076 -64 CGCGGGACGTTCGCGATGCGCCGGTCTGAG 17 207 1 TCGCGATGCG 0.766769 -50 ********** Masking position 8 Map Score: 38.3605 Number of sites scoring better than the average of aligned sites = 37650 Number in coding regions = 35049 Number in noncoding regions = 2601 Number of orfs with sites within 600 bp upstream = 1148 Fraction of orfs with sites within 600 bp upstream = 0.184388 Motif number 8 CGGCCATTCGGAGGGACCGACGCAA 1 5 0 GAGGGACCGC 0.82625 -192 ACCACGATCAGAGGTTCATTCCAGCTGCATT 1 99 0 GAGGTTCATC 0.920841 -98 AGGTGCATTCGAGGGTGCTGC 9 1 0 GAGGGTGCTC 0.992809 -81 GGTTAGCTGCCAGGTGCATTCGAGGGTGCTG 9 12 0 CAGGTGCATC 0.614287 -70 GACGTATTGGGCGGGTGCTGAATTATGATCC 16 15 0 GCGGGTGCTA 0.87326 -286 AGGGTGCTACCAGGTTGCTGCCATCCCCGAA 16 213 0 CAGGTTGCTC 0.974172 -88 ATCGCCCGGCCAGGGTGCTACCAGGTTGCTG 16 224 0 CAGGGTGCTC 0.986685 -77 TTCATGTGCAGCGGGTGCTCCTCCTCGGACG 17 142 1 GCGGGTGCTC 0.985948 -115 GCGCCGGTCTGAGGTTCCTTCTCACCATCCC 17 224 1 GAGGTTCCTC 0.982643 -33 ********* * Masking position 4 Map Score: 6.92453 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 412 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 CGCTACCGGCCACGGGTTGGTCTCGGTTCC 1 135 0 CACGGGTTGG 0.965943 -62 GGGCCCTGCTTTCGGGTTGGCGAGTATCTC 2 27 0 TTCGGGTTGG 0.238692 -121 CTCGCCGCGGCACGGTTGCCAAATTCTAGG 2 101 0 CACGGTTGCC 0.344155 -47 CCCGTAGAATCAGGGGAACGGCATCGATCC 3 66 1 CAGGGGAACG 0.285249 -235 CCCCGGTGATCGCCGGATCGATGCCGTTCC 3 80 0 CGCCGGATCG 0.812417 -221 AGTAGAACCGAACGGGTTGGCCCGTCACAG 3 139 1 AACGGGTTGG 0.74025 -162 CGGCGTGGCAAGCGGGGTGGTACCGCGGCG 3 192 1 AGCGGGGTGG 0.781549 -109 GACGACGCCACGCCGGTGCGCGAACGCCGC 3 216 0 CGCCGGTGCG 0.957841 -85 GCAATCCAGGCTCGGGGACGACGCCACGCC 3 232 0 CTCGGGGACG 0.727021 -69 ATCCGGGCGGTTTCGGGCGCTTTCA 7 6 1 GGCGGTTTCG 0.631977 -82 CAGGTGCATTCGAGGGTGCTGC 9 3 0 CGAGGGTGCT 0.585009 -79 AACCCACGGGCATGGGTTAGCTGCCAGGTG 9 27 0 CATGGGTTAG 0.114922 -55 AACCCATGCCCGTGGGTTGGCTTTGGCGCG 9 39 1 CGTGGGTTGG 0.851902 -43 TCCCCCGCGACACGGTTGCGATGCGTTCGC 10 20 1 CACGGTTGCG 0.889149 -239 TTAGCGTCGGCGCTGGTGGTGCGGCGCTCA 10 176 0 CGCTGGTGGT 0.564089 -83 GCGATCACAACGCGGTTACGCGTCAGAAGA 10 223 0 CGCGGTTACG 0.925542 -36 TGCGAATTTTCGCGGTGGCGTTACGCTCGC 15 26 0 CGCGGTGGCG 0.909638 -275 AGACTGACACCGCGGATTTGACTGCTGAGC 15 90 1 CGCGGATTTG 0.312063 -211 GGACGTATTGGGCGGGTGCTGAATTATGAT 16 17 0 GGCGGGTGCT 0.808648 -284 TCCCAAATTACACGGGTGGTACTCACGAGA 16 53 0 CACGGGTGGT 0.918374 -248 TGGCCACGAACGCCGGGAGGGACAATCTCG 16 107 1 CGCCGGGAGG 0.800758 -194 TAGGGCTTCTCGCGGGAAGGCCCGAACGTA 16 143 1 CGCGGGAAGG 0.955976 -158 GCAGCGTCGCCGCGGGTAGTCGCCGCCCGG 16 260 1 CGCGGGTAGT 0.945757 -41 CTGCGTCCACCACGGGAATGTGCGAGTAGC 17 77 1 CACGGGAATG 0.463614 -180 CTTCATGTGCAGCGGGTGCTCCTCCTCGGA 17 141 1 AGCGGGTGCT 0.79653 -116 GGCTTCCCGTCGCGGGACGTTCGCGATGCG 17 197 1 CGCGGGACGT 0.58688 -60 ********** Masking position 5 Map Score: 17.0821 Number of sites scoring better than the average of aligned sites = 15827 Number in coding regions = 14530 Number in noncoding regions = 1297 Number of orfs with sites within 600 bp upstream = 843 Fraction of orfs with sites within 600 bp upstream = 0.1354 Motif number 10 CAGCCTCGACGACGGGCACCGTCGCCCGGC 1 32 0 GACGGGCACC 0.802408 -165 GCACAGGCTTGAAATGCAGCTGGAATGAAC 1 87 1 GAAATGCAGC 0.874642 -110 AAATGCAGCTGGAATGAACCTCTGATCGTG 1 98 1 GGAATGAACC 0.791351 -99 GGGCAGGCAGCCGACCTTGCG 3 2 1 GGCAGGCAGC 0.986695 -299 CCCCGAGCCTGGATTGCAGGCACGCAGTGC 3 245 1 GGATTGCAGG 0.876821 -56 GCAGCACCCTCGAATGCACCTGGCAGCTAA 9 11 1 CGAATGCACC 0.848976 -71 GATCAACTTCGGCTCGCAGCGGTTTCCCAG 10 133 1 GGCTCGCAGC 0.934054 -126 CGCTAAGGATGGAACGCACGGCATCTTCTG 10 200 1 GGAACGCACG 0.939527 -59 GCTTGGGCTAGTCAGGCACCAACGCGCCGA 15 186 0 GTCAGGCACC 0.896596 -115 GCTTCTCGCGGGAAGGCCCGAACGTACGGC 16 147 1 GGAAGGCCCG 0.87401 -154 GAACATTCGGGGATGGCAGCAACCTGGTAG 16 208 1 GGATGGCAGC 0.972904 -93 ********** Masking position 6 Map Score: 5.01065 Number of sites scoring better than the average of aligned sites = 3380 Number in coding regions = 3135 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 11 GTCGGTCCCTCCGAATGGCCGGGCGACGGTG 1 15 1 CCGAATGGCG 0.56591 -182 CCGGCGATCACCGGGGAGCCTTCGGAAGAAC 3 94 1 CCGGGGAGCT 0.814186 -207 TCGCGCACCGGCGTGGCGTCGTCCCCGAGCC 3 223 1 GCGTGGCGCG 0.914516 -78 GTGCTGGGGCCTGGGGAGACGACGCGCAAA 3 281 1 CTGGGGAGCG 0.946698 -20 ATTTCTGTTTGTGAGGAGACGTCGACC 4 7 0 GTGAGGAGCG 0.985745 -64 CCACCGCGAAAAGACGCAAAAGCTCC 8 6 1 GCGAAAAGCG 0.879412 -84 TCCGGGGTGCGCGAGCAGACGCAAAAGCTCC 8 55 0 GCGAGCAGCG 0.968542 -35 GCCCCCAAATGTGAAGAGTCCGGACCGATCG 10 49 0 GTGAAGAGCC 0.837534 -210 TGATCGCGAGCTGAGGAGACGGT 10 246 1 CTGAGGAGCG 0.976748 -13 GCGTTGGTGCCTGACTAGCCCAAGCGAGCAC 15 191 1 CTGACTAGCC 0.492825 -110 GGGCCTTCCCGCGAGAAGCCCTAGCCGCCCG 16 135 0 GCGAGAAGCC 0.932047 -166 CGGTCGGAGGGCGACGCGACGTGTTGAAACG 16 176 0 GCGACGCGCG 0.955763 -125 CAGCGTCGCCGCGGGTAGTCGCCGCCCGGGC 16 261 1 GCGGGTAGCG 0.966552 -40 ACGGGAATGTGCGAGTAGCCCACACGGTGGA 17 88 1 GCGAGTAGCC 0.962394 -169 GTCGCGGCGTCCGAGGAGGAGCACCCGCTGC 17 149 0 CCGAGGAGAG 0.884185 -108 CGGGACGTTCGCGATGCGCCGGTCTGAGGTT 17 209 1 GCGATGCGCG 0.887906 -48 ******** ** Masking position 8 Map Score: 17.8986 Number of sites scoring better than the average of aligned sites = 5647 Number in coding regions = 5082 Number in noncoding regions = 565 Number of orfs with sites within 600 bp upstream = 448 Fraction of orfs with sites within 600 bp upstream = 0.0719563 Motif number 12 ATCGGCAGCCTATCGACAACCTTCG 4 56 0 CAGCCTATCG 0.933984 -15 AAAGAGATCATAGCGTCTCGTATTTTGAGA 12 11 1 TAGCGTCTCG 0.959015 -61 TTGAGATGACCAGCGAGTCGCGAACGAATG 12 35 1 CAGCGAGTCG 0.942636 -37 GCCGATAGCGTATCGGCTGTAATTG 13 15 0 TAGCGTATCG 0.975544 -15 TCGAGTTCGCGAGCGTAACGCCACCGCGAA 15 18 1 GAGCGTAACG 0.970649 -283 CTTGATCCGCGAGCGTGACGGCACTGCGAA 15 62 0 GAGCGTGACG 0.972752 -239 ********** Masking position 2 Map Score: 2.44313 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 238 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 GCGCCGCGATGTGGATTTGCGGCGCTGGGC 3 29 1 GTGGATTTGC 0.793373 -272 CGTAGAATCAGGGGAACGGCATCGATCCGG 3 68 1 GGGGAACGGC 0.863091 -233 TCGAGCGGCCGCGCATCGGCGTGGCAAGCG 3 176 1 GCGCATCGGC 0.837675 -125 ACCGAGTTCGGGTGATCCGCGAGGGT 6 36 1 GGTGATCCGC 0.727807 -16 CCGGATTTGGGAGCTTTTGCGTCTTTTCGC 8 16 0 GAGCTTTTGC 0.722169 -74 TCGGATTTGGGAGCTTTTGCGTCTGCTCGC 8 46 1 GAGCTTTTGC 0.722169 -44 CCGTGTCGCGGGGGATCTGCGCCC 10 5 0 GGGGATCTGC 0.986636 -254 AGAACAGCTAGGGGATCAGC 11 15 1 GGGGATCAGC 0.954673 -10 CAGGTAAGGAGAGATTCAGCGGTGGCACTA 14 15 1 GAGATTCAGC 0.599146 -23 CTGGCCGGGCGATGATCTGCAGCGTCGCCG 16 242 1 GATGATCTGC 0.871388 -59 CGTCCACCACGGGAATGTGCGAGTAGCCCA 17 80 1 GGGAATGTGC 0.769234 -177 ********** Masking position 10 Map Score: 2.29075 Number of sites scoring better than the average of aligned sites = 2488 Number in coding regions = 2292 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 14 ********** No masking Map Score: -2.42762e-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 15 AGGGTATAAGGGTGGCCCGGGAACCTCCGG 1 170 0 GGTGGCCCGG 0.814781 -27 GCCCAACAGGGTATAAGGGTGGCCCGG 1 180 0 AGGGTATAAG 0.818035 -17 ATACCCCGCTGGGGTACAAGATATGATGGG 2 67 0 GGGGTACAAG 0.896446 -81 GTACCCCAGCGGGGTATCGGACCTAGAATT 2 80 1 GGGGTATCGG 0.97714 -68 CCGTAGAATCAGGGGAACGGCATCGATCCG 3 67 1 AGGGGAACGG 0.913387 -234 ACCGTGTCGCGGGGGATCTGCGCCC 10 6 0 GGGGGATCTG 0.941497 -253 GAGAACAGCTAGGGGATCAGC 11 14 1 AGGGGATCAG 0.964221 -11 GCCGATAGCGTATCGGCTGTAATTGA 13 14 0 AGCGTATCGG 0.80705 -16 AAGTCTCGTTGGTGGACAAGAAAAAACCCT 15 255 0 GGTGGACAAG 0.795518 -46 ********** Masking position 4 Map Score: 2.4245 Number of sites scoring better than the average of aligned sites = 1319 Number in coding regions = 1183 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288