AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -iglpR_mtub_opreg_300.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 PE_PGRS 277 PE_PGRS #2 Rv0110 147 hypothetical protein Rv0110 #3 Rv1903 89 hypothetical protein Rv1903 #4 Rv2250c 120 hypothetical protein Rv2250c #5 lpdA 202 lpdA #6 glpK 49 glpK #7 Rv3697c 250 hypothetical protein Rv3697c Motif number 1 GCGTCGAGGTGGCGCACCACGCAGAGTGTT 1 69 0 GGCGCACCAC 0.807753 -209 CTGGTGCCTCCGCGTCGAGGTGGCGCACCA 1 80 0 CGCGTCGAGG 0.9707 -198 CGACGCGGAGGCACCAGCGGGTTGGCCGCG 1 93 1 GCACCAGCGG 0.914333 -185 CAAGAGCGAGCCCGCCGCGGCCAACCCGCT 1 108 0 CCCGCCGCGG 0.997536 -170 AACACGCATTCCCGCTCCGGCAGCTGGTCA 1 156 0 CCCGCTCCGG 0.970932 -122 ATTGGCGCAACGTGCCCCGGAAGCCGCGCT 1 205 1 CGTGCCCCGG 0.984767 -73 TGTTGCCTGCGCCGTTGGGCGGGATGCAAC 2 15 0 GCCGTTGGGC 0.807522 -133 CCAGCTCATCGGAGTCGCCCACCTGCTATC 2 63 1 GGAGTCGCCC 0.94846 -85 ACGTAGGTCCGGCGCCCGGGATGGCGATAG 2 88 0 GGCGCCCGGG 0.990081 -60 GATCACATCGGGTGCAGCGGACGTAGGTCC 2 108 0 GGTGCAGCGG 0.983708 -40 TCTGCATCGTGGCGTACCGGGCGCGGCACC 3 12 1 GGCGTACCGG 0.923515 -78 CCGGACTCGCGGTGCCGCGCCCGGTACGCC 3 22 0 GGTGCCGCGC 0.992496 -68 CGCGGCACCGCGAGTCCGGGGACATGGCGA 3 33 1 CGAGTCCGGG 0.912875 -57 CACGGACATGCGAGCCGCCGCTGTTCGCCA 3 57 0 CGAGCCGCCG 0.991893 -33 TGCCCGATCCTGCCACGGACATGCGAGC 3 72 0 CCTGCCACGG 0.704489 -18 GCCCGTCCGCCCTGTCGGGGGCAGACCACG 4 11 0 CCTGTCGGGG 0.827446 -110 CCGCGCAGGTGCAGCTGCGCCCGTCCGCCC 4 29 0 GCAGCTGCGC 0.970257 -92 AGCCCGAACTCGACCCCGCGCAGGTGCAGC 4 44 0 CGACCCCGCG 0.68887 -77 TAGCGGACTCGGAGCAGCCCGAACTCGACC 4 59 0 GGAGCAGCCC 0.966524 -62 GCAGGTTGTGGGCCTAGCGGACTCGGAGCA 4 73 0 GGCCTAGCGG 0.901152 -48 GGGTACCACCCGAGCCCCCGCCGTCTAAGC 5 19 0 CGAGCCCCCG 0.977236 -184 TGGTACCCATCGCGCCGCGCTGCGGTGCGG 5 41 1 CGCGCCGCGC 0.998562 -162 TTGACGATGACCCGCACCGCAGCGCGGCGC 5 52 0 CCCGCACCGC 0.965282 -151 GGCGTGAGGAGGAGCCGAGCAGTCAAGCAC 5 85 0 GGAGCCGAGC 0.982243 -118 CGATGCACGCCGCGCAGCGGCGTGAGGAGG 5 103 0 CGCGCAGCGG 0.996613 -100 GGCGTGCATCGTCGCCGAGCTGTGTTGGAC 5 122 1 GTCGCCGAGC 0.87216 -81 GGCGTGAGGAGGAGCCGAGCAGTCCAACAC 5 143 0 GGAGCCGAGC 0.982243 -60 CGATGCACGCCGCGCAGCGGCGTGAGGAGG 5 161 0 CGCGCAGCGG 0.996613 -42 GGCGTGCATCGTCGCCGAGCTAGGTTATGG 5 180 1 GTCGCCGAGC 0.87216 -23 CGGCGTCGGACCCGCCGCTGC 6 2 1 GGCGTCGGAC 0.702783 -48 CGTCGGACCCGCCGCTGCGGTGGACCATCA 6 14 1 GCCGCTGCGG 0.989654 -36 TTGCGCTCCTCGCGCTGGCGTCGTTTCAAC 7 81 0 CGCGCTGGCG 0.94884 -170 AATTCGGAGGCGAGCTGCCCTAACGTTTTG 7 108 0 CGAGCTGCCC 0.953441 -143 GCAAGCTCTGGCGGCCGAGCCTCCTCCAAA 7 144 1 GCGGCCGAGC 0.772514 -107 AGTCGGCAGTCGACCAGCGGATGTCAACGT 7 173 0 CGACCAGCGG 0.962035 -78 GGTCGACTGCCGACTTGCGGCCCCGTGTGG 7 188 1 CGACTTGCGG 0.790451 -63 ********** Masking position 4 Map Score: 79.5983 Number of sites scoring better than the average of aligned sites = 61986 Number in coding regions = 57683 Number in noncoding regions = 4303 Number of orfs with sites within 600 bp upstream = 1374 Fraction of orfs with sites within 600 bp upstream = 0.220687 Motif number 2 CTAGGGAACACTCTGCGTGGTGCGCCACCTCG 1 63 1 CTCTGGGGTG 0.946558 -215 CTGGTGCCTCCGCGTCGAGGTGGCGCACCACG 1 78 0 CGCGTGGGTG 0.805087 -200 CGCCGCGGCCAACCCGCTGGTGCCTCCGCGTC 1 94 0 AACCCCGGTG 0.57906 -184 CAAGAGCGAGCCCGCCGCGGCCAACCCGCTGG 1 106 0 CCCGCGGGCC 0.837091 -172 GCGGCGGGCTCGCTCTTGGGTGGTCGCCAGTG 1 120 1 CGCTCTGGTG 0.870131 -158 CAGCTGGTCACAATCACTGGCGACCACCCAAG 1 134 0 CAATCCGGCG 0.891008 -144 CGCATTCCCGCTCCGGCAGCTGGTCACAATCA 1 150 0 CTCCGCGCTG 0.850449 -128 GCGCAACGTGCCCCGGAAGCCGCGCTACATTT 1 209 1 CCCCGAGCCG 0.859128 -69 TTTTCGGGCAAGCTGTCTGGTGGCTAGGAGCC 1 241 0 AGCTGCGGTG 0.889997 -37 CAGGGACCTCTGCCGTTTTCGGGCA 1 263 0 GGACCCGCCG 0.70508 -15 TGTTGCATCCCGCCCAACGGCGCAGGCAACAA 2 14 1 CGCCCAGGCG 0.499147 -134 AACAATGGTGCGATGAGTGGCGCCAGCTCATC 2 41 1 CGATGGGGCG 0.982171 -107 GGATGGCGATAGCAGGTGGGCGACTCCGATGA 2 68 0 AGCAGTGGCG 0.763453 -80 CCTGCTATCGCCATCCCGGGCGCCGGACCTAC 2 84 1 CCATCCGGCG 0.949951 -64 GGCGCCGGACCTACGTCCGCTGCACCCGATGT 2 102 1 CTACGCGCTG 0.566446 -46 TGTGATCGGTACATCTGTGGCGAATGT 2 131 1 ACATCGGGCG 0.768121 -17 TGTCCCCGGACTCGCGGTGCCGCGCCCGGTAC 3 25 0 CTCGCGGCCG 0.96855 -65 GGGGACATGGCGAACAGCGGCGGCTCGCATGT 3 50 1 CGAACGGGCG 0.961144 -40 CCCCCGACAGGGCGGACGGGCGCAGCTGCACC 4 20 1 GGCGGCGGCG 0.966121 -101 CGAACTCGACCCCGCGCAGGTGCAGCTGCGCC 4 38 0 CCCGCCGGTG 0.96671 -83 TGACCCGCACCGCAGCGCGGCGCGATGGGTAC 5 43 0 CGCAGGGGCG 0.622445 -160 CTCCTCACGCCGCTGCGCGGCGTGCATCGTCG 5 104 1 CGCTGGGGCG 0.623708 -99 AGCAGTCCAACACAGCTCGGCGACGATGCACG 5 124 0 CACAGTGGCG 0.637879 -79 CTCCTCACGCCGCTGCGCGGCGTGCATCGTCG 5 162 1 CGCTGGGGCG 0.623708 -41 ATGATGGTCCACCGCAGCGGCGGGTCCGACGC 6 13 0 ACCGCGGGCG 0.94924 -37 TTTCAACGCCCGCAGTATGTCGTCATCGAGGT 7 56 0 CGCAGAGTCG 0.462435 -195 TTTTGCGCTCCTCGCGCTGGCGTCGTTTCAAC 7 81 0 CTCGCCGGCG 0.985283 -170 CAAGCAATTCGGAGGCGAGCTGCCCTAACGTT 7 111 0 GGAGGGGCTG 0.518031 -140 CTTGCGCAAGCTCTGGCGGCCGAGCCTCCTCC 7 139 1 CTCTGCGCCG 0.955626 -112 CGTCAAGATCCACACGGGGCCGCAAGTCGGCA 7 195 0 CACACGGCCG 0.906081 -56 ***** * **** Masking position 9 Map Score: 51.6541 Number of sites scoring better than the average of aligned sites = 32568 Number in coding regions = 30000 Number in noncoding regions = 2568 Number of orfs with sites within 600 bp upstream = 1186 Fraction of orfs with sites within 600 bp upstream = 0.190491 Motif number 3 ATTTCCGTTTGACTCCACGCGAAACACAGT 1 17 1 GACTCCACGC 0.953239 -261 GTCGAGGTGGCGCACCACGCAGAGTGTTCC 1 67 0 CGCACCACGC 0.908247 -211 GGCACCAGCGGGTTGGCCGCGGCGGGCTCG 1 102 1 GGTTGGCCGC 0.56257 -176 GCTCGCTCTTGGGTGGTCGCCAGTGATTGT 1 127 1 GGGTGGTCGC 0.841024 -151 TTGGACAGCCGAATCCCCGCAATTGGCGCA 1 184 1 GAATCCCCGC 0.884233 -94 ACGTGCCCCGGAAGCCGCGCTACATTTGGC 1 214 1 GAAGCCGCGC 0.724816 -64 CGCTACATTTGGCTCCTAGCCACCAGACAG 1 231 1 GGCTCCTAGC 0.788381 -47 TGTTGCATCCCGCCCAACGGCGCAGGCAAC 2 14 1 CGCCCAACGG 0.502636 -134 GAGCTGGCGCCACTCATCGCACCATTGTTG 2 40 0 CACTCATCGC 0.603481 -108 GACGTAGGTCCGGCGCCCGGGATGGCGATA 2 89 0 CGGCGCCCGG 0.857524 -59 GACCTACGTCCGCTGCACCCGATGTGATCG 2 109 1 CGCTGCACCC 0.88082 -39 GCGTACCGGGCGCGGCACCGCGAGTCCGGG 3 23 1 CGCGGCACCG 0.622152 -67 GGCGAACAGCGGCGGCTCGCATGTCCGTGG 3 58 1 GGCGGCTCGC 0.986185 -32 CCGACAGGGCGGACGGGCGCAGCTGCACCT 4 23 1 GGACGGGCGC 0.832863 -98 GCCCGAACTCGACCCCGCGCAGGTGCAGCT 4 43 0 GACCCCGCGC 0.946156 -78 GTCGAGTTCGGGCTGCTCCGAGTCCGCTAG 4 60 1 GGCTGCTCCG 0.83313 -61 CTTCAGCAACGACCGGACGCCATCAGAAA 4 102 1 GACCGGACGC 0.899756 -19 GGTACCACCCGAGCCCCCGCCGTCTAAGCT 5 18 0 GAGCCCCCGC 0.833586 -185 TGGTACCCATCGCGCCGCGCTGCGGTGCGG 5 41 1 CGCGCCGCGC 0.954191 -162 AGCTGTGCTTGACTGCTCGGCTCCTCCTCA 5 81 1 GACTGCTCGG 0.94608 -122 AGCTCGGCGACGATGCACGCCGCGCAGCGG 5 113 0 CGATGCACGC 0.947009 -90 AGCAGTCCAACACAGCTCGGCGACGATGCA 5 126 0 CACAGCTCGG 0.77013 -77 AGCTGTGTTGGACTGCTCGGCTCCTCCTCA 5 139 1 GACTGCTCGG 0.94608 -64 AGCTCGGCGACGATGCACGCCGCGCAGCGG 5 171 0 CGATGCACGC 0.947009 -32 CGGCGTCGGACCCGCCGCTGCGGTGGAC 6 9 1 GACCCGCCGC 0.88949 -41 GGCGTCGTTTCAACGCCCGCAGTATGTCGT 7 65 0 CAACGCCCGC 0.912283 -186 GGCGTTGAAACGACGCCAGCGCGAGGAGCG 7 78 1 CGACGCCAGC 0.561987 -173 TAACGTTTTGCGCTCCTCGCGCTGGCGTCG 7 88 0 CGCTCCTCGC 0.984471 -163 AAAACGTTAGGGCAGCTCGCCTCCGAATTG 7 109 1 GGCAGCTCGC 0.965447 -142 AACGTTTGGAGGAGGCTCGGCCGCCAGAGC 7 148 0 GGAGGCTCGG 0.87512 -103 CGTTGACATCCGCTGGTCGACTGCCGACTT 7 174 1 CGCTGGTCGA 0.490842 -77 ********** Masking position 8 Map Score: 52.3618 Number of sites scoring better than the average of aligned sites = 34692 Number in coding regions = 31837 Number in noncoding regions = 2855 Number of orfs with sites within 600 bp upstream = 1246 Fraction of orfs with sites within 600 bp upstream = 0.200128 Motif number 4 TCTGCGTGGTGCGCCACCTCGACGCGGAGG 1 74 1 GCGCCACCTC 0.657123 -204 GAGCCCGCCGCGGCCAACCCGCTGGTGCCT 1 101 0 CGGCCAACCC 0.649225 -177 TGGCCGCGGCGGGCTCGCTCTTGGGTGGTC 1 115 1 GGGCTCGCTC 0.544222 -163 CATTCCCGCTCCGGCAGCTGGTCACAATCA 1 150 0 CCGGCAGCTG 0.888228 -128 GCGGCTTCCGGGGCACGTTGCGCCAATTGC 1 202 0 GGGCACGTTG 0.79947 -76 TGCCGTTTTCGGGCAAGCTGTCTGGTGGCT 1 248 0 GGGCAAGCTG 0.948401 -30 GCGTGTTGCATCCCGCCCAACGGCGCAG 2 9 1 CATCCCGCCC 0.838421 -139 GCGATGAGTGGCGCCAGCTCATCGGAGTCG 2 50 1 GCGCCAGCTC 0.968385 -98 GCGCCCGGTACGCCACGATGCAGAC 3 6 0 CGCCACGATG 0.536579 -84 GCAGCTGCGCCCGTCCGCCCTGTCGGGGGC 4 19 0 CCGTCCGCCC 0.79579 -102 ACCCCGCGCAGGTGCAGCTGCGCCCGTCCG 4 32 0 GGTGCAGCTG 0.729774 -89 TACCACCCGAGCCCCCGCCGTCTAAGCTTT 5 16 0 GCCCCCGCCG 0.958394 -187 GGGTGGTACCCATCGCGCCGCGCTGCGGTG 5 38 1 CATCGCGCCG 0.460623 -165 TGCGGGTCATCGTCAAGCTGTGCTTGACTG 5 66 1 CGTCAAGCTG 0.946384 -137 CTCGGCTCCTCCTCACGCCGCTGCGCGGCG 5 96 1 CCTCACGCCG 0.977012 -107 CTCGGCTCCTCCTCACGCCGCTGCGCGGCG 5 154 1 CCTCACGCCG 0.977012 -49 CGGCGTCGGACCCGCCGCTGCGGTGGA 6 8 1 GGACCCGCCG 0.861884 -42 GTTTTGCGCTCCTCGCGCTGGCGTCGTTTC 7 84 0 CCTCGCGCTG 0.925638 -167 CGAATTGCTTGCGCAAGCTCTGGCGGCCGA 7 132 1 GCGCAAGCTC 0.950204 -119 CCACACGGGGCCGCAAGTCGGCAGTCGACC 7 188 0 CCGCAAGTCG 0.804167 -63 GCGTCCTTGTCGTCAAGATCCACACGGGGC 7 207 0 CGTCAAGATC 0.485448 -44 ********** Masking position 7 Map Score: 22.4092 Number of sites scoring better than the average of aligned sites = 42820 Number in coding regions = 39843 Number in noncoding regions = 2977 Number of orfs with sites within 600 bp upstream = 1273 Fraction of orfs with sites within 600 bp upstream = 0.204465 Motif number 5 CCGCGTCGAGGTGGCGCACCACGCAGAGTGTTCC 1 67 0 GGGCACACGC 0.711069 -211 ACCTCGACGCGGAGGCACCAGCGGGTTGGCCGCG 1 89 1 GGCACAGCGG 0.917091 -189 GCACCAGCGGGTTGGCCGCGGCGGGCTCGCTCTT 1 103 1 GGCCGGGCGG 0.911778 -175 CACAATCACTGGCGACCACCCAAGAGCGAGCCCG 1 124 0 GGCCACCAAG 0.711708 -154 CGGGGATTCGGCTGTCCAACACGCATTCCCGCTC 1 169 0 GGCCACACGC 0.978674 -109 CGGGGCACGTTGCGCCAATTGCGGGGATTCGGCT 1 190 0 TGCAATGCGG 0.500945 -88 CTGGTGGCTAGGAGCCAAATGTAGCGCGGCTTCC 1 223 0 GGCAATGTAG 0.719752 -55 GCCCAACGGCGCAGGCAACAATGGTGCGATGAGT 2 25 1 GGCAAAATGG 0.799705 -123 CCGATGAGCTGGCGCCACTCATCGCACCATTGTT 2 41 0 GGCACCATCG 0.778105 -107 CGGCGCCCGGGATGGCGATAGCAGGTGGGCGACT 2 75 0 GGCGAAGCAG 0.920721 -73 CCGGACTCGCGGTGCCGCGCCCGGTACGCCACGA 3 18 0 GGCGCCCCGG 0.967108 -72 CCCCGACAGGGCGGACGGGCGCAGCTGCACCTGC 4 21 1 GGCGGCGCAG 0.946692 -100 GCACCTGCGCGGGGTCGAGTTCGGGCTGCTCCGA 4 47 1 GGCGATTCGG 0.872751 -74 GGGCTCGGGTGGTACCCATCGCGCCGCGCTGCGG 5 32 1 GACCACGCGC 0.707166 -171 ACAGCTTGACGATGACCCGCACCGCAGCGCGGCG 5 53 0 GGCCCCACCG 0.963492 -150 GAGGAGCCGAGCAGTCAAGCACAGCTTGACGATG 5 73 0 GGCAACACAG 0.972071 -130 GAGGAGCCGAGCAGTCCAACACAGCTCGGCGACG 5 131 0 GGCCACACAG 0.986186 -72 GGCGTGCATCGTCGCCGAGCTAGGTTATGGGCT 5 180 1 GGCGACTAGG 0.786143 -23 CGCCGCTGCGGTGGACCATCATGGACGATTACAT 6 23 1 GGCCACATGG 0.982842 -27 TGTCGTCATCGAGGTCGATCGTAGTGCGCATACA 7 37 0 GGCGACGTAG 0.956784 -214 CCGCAAGTCGGCAGTCGACCAGCGGATGTCAACG 7 174 0 GGCGACAGCG 0.769327 -77 CTGCCGACTTGCGGCCCCGTGTGGATCTTGACGA 7 194 1 GGCCCTGTGG 0.889499 -57 TGTGGATCTTGACGACAAGGACGCTGTTTGGGCG 7 213 1 GGCAAGACGC 0.775428 -38 * * *** ***** Masking position 4 Map Score: 26.3995 Number of sites scoring better than the average of aligned sites = 31398 Number in coding regions = 29802 Number in noncoding regions = 1596 Number of orfs with sites within 600 bp upstream = 875 Fraction of orfs with sites within 600 bp upstream = 0.14054 Motif number 6 CGTCGAGGTGGCGCACCACGCAGAGTGTTC 1 68 0 GCGCACCACG 0.885746 -210 CAACACGCATTCCCGCTCCGGCAGCTGGTC 1 157 0 TCCCGCTCCG 0.700677 -121 GGATTCGGCTGTCCAACACGCATTCCCGCT 1 170 0 GTCCAACACG 0.712158 -108 GTGTTGGACAGCCGAATCCCCGCAATTGGC 1 181 1 GCCGAATCCC 0.761535 -97 CAGACAGCTTGCCCGAAAACGGCAGAGGTC 1 254 1 GCCCGAAAAC 0.862542 -24 GCGGTGCCGCGCCCGGTACGCCACGATGCA 3 14 0 GCCCGGTACG 0.882741 -76 TGCCCGATCCTGCCACGGACA 3 79 0 GCCCGATCCT 0.816821 -11 ACTCGGAGCAGCCCGAACTCGACCCCGCGC 4 53 0 GCCCGAACTC 0.918894 -68 AGTCCGCTAGGCCCACAACCTGCTTCAGCA 4 80 1 GCCCACAACC 0.978746 -41 CTTGACGATGACCCGCACCGCAGCGCGGCG 5 53 0 ACCCGCACCG 0.785564 -150 AGCCCATAACCTAGCTCGGCG 5 192 0 GCCCATAACC 0.876906 -11 TCTGATGTATGCGCACTACGATCGACCTCG 7 32 1 GCGCACTACG 0.920132 -219 AGCGCGAGGAGCGCAAAACGTTAGGGCAGC 7 95 1 GCGCAAAACG 0.951975 -156 CGAATTGCTTGCGCAAGCTCTGGCGGCCGA 7 132 1 GCGCAAGCTC 0.481549 -119 GTCCAAAATCGCCCAAACAGCGTCCTTGTC 7 226 0 GCCCAAACAG 0.901904 -25 CCACGGTCCAAAATCGCCCAAACAG 7 236 0 GTCCAAAATC 0.478028 -15 ********** Masking position 4 Map Score: 9.90874 Number of sites scoring better than the average of aligned sites = 14985 Number in coding regions = 13841 Number in noncoding regions = 1144 Number of orfs with sites within 600 bp upstream = 747 Fraction of orfs with sites within 600 bp upstream = 0.119981 Motif number 7 GCGCAGCGGCGTGAGGAGGAGCCGAGCAGT 5 92 0 GTGAGGAGGA 0.992988 -111 GCGCAGCGGCGTGAGGAGGAGCCGAGCAGT 5 150 0 GTGAGGAGGA 0.992988 -53 GGATGTCAACGTTTGGAGGAGGCTCGGCCG 7 155 0 GTTTGGAGGA 0.989195 -96 CAAGGACGCTGTTTGGGCGATTTTGGACCG 7 228 1 GTTTGGGCGA 0.952455 -23 ********** Masking position 2 Map Score: 2.73261 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 13 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GCGAGCCCGCCGCGGCCAACCCGCTGGTGCC 1 102 0 CGGGCCAACC 0.744323 -176 TGGGCGACTCCGATGAGCTGGCGCCACTCAT 2 53 0 CGTGAGCTGG 0.885483 -95 TCATCGGAGTCGCCCACCTGCTATCGCCATC 2 68 1 CGCCACCTGC 0.936485 -80 ACAGATGTACCGATCACATCGGGTGCAGCGG 2 118 0 CGTCACATCG 0.797794 -30 ACCGCGAGTCCGGGGACATGGCGAACAGCGG 3 39 1 CGGGACATGG 0.979111 -51 CCGATCCTGCCACGGACATGCGAGCCGCCGC 3 66 0 CAGGACATGC 0.929959 -24 CACAGCTTGACGATGACCCGCACCGCAGCGC 5 57 0 CGTGACCCGC 0.967401 -146 CCATCATGGACGATTACATGCA 6 38 1 CGTTACATGC 0.94714 -12 CTCCTCCAAACGTTGACATCCGCTGGTCGAC 7 164 1 CGTGACATCC 0.9812 -87 ** ******** Masking position 1 Map Score: 3.27168 Number of sites scoring better than the average of aligned sites = 5098 Number in coding regions = 4791 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 9 ********** No masking Map Score: 2.68828e-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 10 ********** No masking Map Score: 2.68828e-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: 2.68828e-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