AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 fadD30 300 fadD30 #2 fabH 81 fabH #3 accD3 26 accD3 #4 Rv1348 300 hypothetical protein Rv1348 #5 fabG2 128 fabG2 #6 aceE 51 aceE #7 Rv2242 59 hypothetical protein Rv2242 #8 fabD 238 fabD #9 acpM 75 acpM #10 kasB 30 kasB #11 Rv2362c 61 hypothetical protein Rv2362c #12 bex 73 bex #13 Rv2370c 194 hypothetical protein Rv2370c #14 Rv2870c 57 hypothetical protein Rv2870c #15 cdsA 22 cdsA #16 frr 171 frr #17 pyrH 234 pyrH #18 rpsB 283 rpsB #19 Rv2926c 50 hypothetical protein Rv2926c #20 Rv2927c 238 hypothetical protein Rv2927c #21 echA20 54 echA20 #22 Rv3553 97 hypothetical protein Rv3553 Motif number 1 CTTCAACAAGCCGCCGCGTGAGGACGAACC 1 11 1 CCGCCGCGTG 0.990977 -290 ACGAACCCTACCGGGGAGACGCCACTCGTT 1 34 1 CCGGGGAGAC 0.939335 -267 GGAAACATGAGCGGCCCGACGGGAAATTCG 1 217 1 GCGGCCCGAC 0.863339 -84 CCAGACAGCTCGGCGGCCTGGTGGCCAGGA 1 251 1 CGGCGGCCTG 0.871634 -50 CCGACGGAGCCCGCCCTGAGTGCACGTTCG 2 14 0 CCGCCCTGAG 0.885063 -68 TGTGCACCTACGGCGACGACACGCCGACGG 2 37 0 CGGCGACGAC 0.759956 -45 CTTTCGAGCACCGGCACCTAAAACCGGCAT 4 16 0 CCGGCACCTA 0.755019 -285 CATGGAGTGCGGGCGGAGGGACTCGAACCC 4 53 0 GGGCGGAGGG 0.682673 -248 CGTCCGACTGGGGCCGACTGGGTTGTATGC 4 131 1 GGGCCGACTG 0.693187 -170 GATACTCAGCCCGCGCATACAACCCAGTCG 4 145 0 CCGCGCATAC 0.483297 -156 ACCCCGAGCTGCGCCGCGACCGCGCTGATA 4 171 0 GCGCCGCGAC 0.986013 -130 GCGTCGCGCTCCGCCGATACCCCGAGCTGC 4 189 0 CCGCCGATAC 0.93659 -112 TATCGGCGGAGCGCGACGCCGTTGCACGCC 4 200 1 GCGCGACGCC 0.886486 -101 TACCGGCCAACCGGCGTGCAACGGCGTCGC 4 212 0 CCGGCGTGCA 0.933012 -89 CTTCTCAGATCGGGCGACCACGAACGCTGG 4 244 0 CGGGCGACCA 0.780041 -57 GCGGCCTAATCCGCCACGACTTCTCAGATC 4 263 0 CCGCCACGAC 0.974885 -38 GCGGATTAGGCCGCCGCGAGAGAGGACCGC 4 279 1 CCGCCGCGAG 0.994953 -22 AGAAACCACCGCGCCACGCAGATAGCCACT 5 15 1 GCGCCACGCA 0.877273 -114 AAGAGCTTCGCCGCCGACGGTGCAAAATAT 5 100 1 CCGCCGACGG 0.97896 -29 CGCCGGCGAGCCGACCGCCTTT 7 3 1 CCGGCGAGCC 0.984155 -57 CCCCCTCTGACCGGCGAGGGAATCTATGAC 8 31 0 CCGGCGAGGG 0.974283 -208 TGGTATCTTTCCGGGGCCCCTGCTGGACCC 8 58 0 CCGGGGCCCC 0.65055 -181 GATACCAGGGGCGCCGTCGGACGGAAAGTG 8 81 1 GCGCCGTCGG 0.923306 -158 TGAGATCGTCCCGCGACCTGTTGTCTGGAT 8 111 0 CCGCGACCTG 0.857191 -128 AGACGGTTTTGCGCGGTGTAACAGATTATG 8 198 0 GCGCGGTGTA 0.549315 -41 CCGCGGACTCGGCCAGAACA 9 1 1 CCGCGGACTC 0.924054 -75 GCCTCGCGACCCGCGATGTCGTGCT 10 6 0 CCGCGATGTC 0.658381 -25 CTCGGGCCTCGCGACCCGCGAT 10 19 0 CGGGCCTCGC 0.386681 -12 GCGGGTATCCGCGCCGATAGTCTCGTACCC 11 12 0 GCGCCGATAG 0.829535 -50 GTTTTGCACCCCGCCACGACATCGCGGGTA 11 35 0 CCGCCACGAC 0.974885 -27 CCGCTTTTTTCCGCCGTGAATGCACGTTCG 12 14 0 CCGCCGTGAA 0.943729 -60 CGGCGGCAGCGGGCCGTGCGCCTGCCGAGT 13 40 0 GGGCCGTGCG 0.83988 -155 CGGTTACCCACCGCGGCGGCAGCGGGCCGT 13 53 0 CCGCGGCGGC 0.987986 -142 AATCCCGAACGCGCCACACCGGCTAAACGT 13 94 1 GCGCCACACC 0.587941 -101 CGGCCGCTCAGCAACAAAAT 15 1 1 CGGCCGCTCA 0.82217 -22 TGCATCGTCGCCGGCGCGAAGCAGCGCGTA 16 17 0 CCGGCGCGAA 0.974711 -155 CCAACCATCTGCGCCGCTCCTCCTCATCGC 16 54 0 GCGCCGCTCC 0.95494 -118 TGCATCGTCGCCGGCGCCAACCATCTGCGC 16 70 0 CCGGCGCCAA 0.96579 -102 CCAACCATCTGCGCCGCTCCTCCTCATCGC 16 107 0 GCGCCGCTCC 0.95494 -65 TGCATCGTCGCCGGCGCCAACCATCTGCGC 16 123 0 CCGGCGCCAA 0.96579 -49 CTGCGCCGCTCCTCCTCATCGC 16 160 0 GCGCCGCTCC 0.95494 -12 AACGAGGGGCCGGCCGAGGCCAGGCCCGTC 17 109 0 CGGCCGAGGC 0.944946 -126 TAGCCGCGCTCCGGCGTGGGCGGGGTGCGT 17 151 0 CCGGCGTGGG 0.961395 -84 CAGTGCCATCCCGGCACCACCAGGACGGCA 17 199 0 CCGGCACCAC 0.939036 -36 TCGCCGCCGCCCGTTTTGTGGAC 18 4 1 CCGCCGCCCG 0.90704 -280 GCTGTGGATTCCGCTGCCGGGAAAATCACC 18 43 1 CCGCTGCCGG 0.680951 -241 GATGCGAGCTGCGCCGAGTAGTTTACACCG 18 81 0 GCGCCGAGTA 0.834058 -203 CGAAGTCAGCCCGCCGATGCGAGCTGCGCC 18 96 0 CCGCCGATGC 0.939939 -188 CGTGTCTGCACCGCGGCCCGCCTTTCCGGG 18 126 1 CCGCGGCCCG 0.971546 -158 GCCCGCCTTTCCGGGATCCGCAACAGCATG 18 141 1 CCGGGATCCG 0.67692 -143 CGCCGCGGGACCGCCCCGGCATGCTGTTGC 18 160 0 CCGCCCCGGC 0.972962 -124 CCGAAGGGAACCGCCGCGGGACCGCCCCGG 18 171 0 CCGCCGCGGG 0.993733 -113 CTGGCGTCTGCCGCGATGCCGGACCCGGGA 18 209 0 CCGCGATGCC 0.842153 -75 TCGGCTGAAGCCGGGCCCTGGCGTCTGCCG 18 226 0 CCGGGCCCTG 0.7263 -58 GGTTGTTCGCCCGGCATCGGCTGAAGCCGG 18 242 0 CCGGCATCGG 0.781275 -42 CACCATTCACCCGGCGCAAGGATCAAGCGC 19 11 1 CCGGCGCAAG 0.879974 -40 TGGGCGTTGGCCGGCGCTTGATCCTTGCGC 19 24 0 CCGGCGCTTG 0.919607 -27 CACCCGTCAGCCGCCGAACGGTCTACGACA 20 64 1 CCGCCGAACG 0.886027 -175 TCTACGACACGCGCCCAGCAGGCCGCGTGA 20 85 1 GCGCCCAGCA 0.698465 -154 TCGACGAGCCCGGGCGACCACTCAGATCAC 20 111 0 CGGGCGACCA 0.780041 -128 TCCCGACACACCGGCGCCACCAGTGCAGTC 20 154 1 CCGGCGCCAC 0.90127 -85 CTCCCGCTTGCGGGGGAGAGGAGGCGGAAC 22 13 0 CGGGGGAGAG 0.761229 -85 AGCCACCGCCGACAATGCAGTGGGG 22 83 0 CCGCCGACAA 0.952379 -15 ********** Masking position 3 Map Score: 111.954 Number of sites scoring better than the average of aligned sites = 77699 Number in coding regions = 72739 Number in noncoding regions = 4960 Number of orfs with sites within 600 bp upstream = 1546 Fraction of orfs with sites within 600 bp upstream = 0.248314 Motif number 2 GAGACGCCACTCGTTGGGGCAGTTTTGTACAC 1 49 1 TCGTGGGGCG 0.939122 -252 TTTCGGTTAATCGTACAGGCTGCCGCTCGGTC 1 114 1 TCGTCAGGCG 0.895349 -187 CAGAGCCGCTTCGACCAGCCTGTGGTCGAAGC 1 163 1 TCGACAGCCG 0.864352 -138 CACCAGGCCGCCGAGCTGTCTGGGCATCGAAT 1 242 0 CCGACTGTCG 0.515197 -59 AACGATCCTGGCCACCAGGCCGCCGAGCTGTC 1 254 0 GCCACAGGCG 0.965155 -47 CTATCTGTTCTCGTCGAGTGTGCACCTACGGC 2 53 0 TCGTGAGTGG 0.298408 -29 GCGATGAGGCTATATAGGCTGA 3 15 0 GCGAGAGGCA 0.890359 -12 GGGGACCATGGAGTGCGGGCGGAGGGACTCGA 4 57 0 GAGTCGGGCG 0.644217 -244 GAGCTGCGCCGCGACCGCGCTGATACTCAGCC 4 164 0 GCGACGCGCG 0.988278 -137 TCGGCGGAGCGCGACGCCGTTGCACGCCGGTT 4 202 1 GCGAGCCGTG 0.718194 -99 GAACTAGCTGGCAAGGTGGCCGACCTCGCGAT 5 61 0 GCAAGTGGCG 0.83017 -68 ATATTTTGCACCGTCGGCGGCGAAGCTCTTCT 5 98 0 CCGTGGCGGG 0.760868 -31 CGCCGGCGAGCCGACCGCCTTTGGCCG 7 6 1 GCGACCGACG 0.621488 -54 ATCGCGGGTCGCGAGGCCCGAG 10 19 1 GCGAGCCCGG 0.77265 -12 GCGGATACCCGCGATGTCGTGGCGGGGTGCAA 11 30 1 GCGAGTCGTG 0.615109 -32 CGCCGAACGTGCATTCACGGCGGAAAAAAGCG 12 11 1 GCATCACGGG 0.348365 -63 TCGACATTTAGCGTTCAGGAGGTCTCG 13 6 0 GCGTCAGGAG 0.8864 -189 ACGCTAAATGTCGACGACTCGGCAGGCGCACG 13 24 1 TCGAGACTCG 0.688342 -171 GACTCGGCAGGCGCACGGCCCGCTGCCGCCGC 13 39 1 GCGCCGGCCG 0.7009 -156 TGAACGGTTACCCACCGCGGCGGCAGCGGGCC 13 55 0 CCCACGCGGG 0.540562 -140 CCCAATAATCCCGAACGCGCCACACCGGCTAA 13 88 1 CCGACGCGCA 0.419959 -107 ACTCCTTCAGCCGTGGTGGACGTTTAGCCGGT 13 111 0 CCGTGTGGAG 0.451455 -84 ACGATTGCATTCCACGGGGAAGT 14 45 1 TCCAGGGGAG 0.597886 -13 CTTCGCGCCGGCGACGATGCAGAGCGCAGCGA 16 26 1 GCGAGATGCG 0.959201 -146 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAG 16 44 1 GCGAGAGGAG 0.975535 -128 GTTGGCGCCGGCGACGATGCAGAGCGCAGCGA 16 79 1 GCGAGATGCG 0.959201 -93 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAG 16 97 1 GCGAGAGGAG 0.975535 -75 GTTGGCGCCGGCGACGATGCAGAGCGCAGCGA 16 132 1 GCGAGATGCG 0.959201 -40 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAG 16 150 1 GCGAGAGGAG 0.975535 -22 CTTGAGATAGTCGACGGGCCTGGCCTCGGCCG 17 97 1 TCGAGGGCCG 0.919915 -138 TCACGCAACAACGAGGGGCCGGCCGAGGCCAG 17 116 0 ACGAGGGCCG 0.644255 -119 CCGCGCTCCGGCGTGGGCGGGGTGCGTTAGTC 17 146 0 GCGTGGCGGG 0.925785 -89 GCACTGTCGTGCGAGGAGTCAG 17 223 1 GCGAGAGTCG 0.961905 -12 CCCGGGTCCGGCATCGCGGCAGACGCCAGGGC 18 210 1 GCATGCGGCG 0.706984 -74 CGCGGCAGACGCCAGGGCCCGGCTTCAGCCGA 18 224 1 GCCAGGCCCG 0.84813 -60 GCGATCTTGCCCGAGCGTGCCGACAACGTAGG 20 16 0 CCGACGTGCG 0.811606 -223 ACGACACGCGCCCAGCAGGCCGCGTGATCTGA 20 88 1 CCCACAGGCG 0.876001 -151 ACGAGCCCGGGCGACCACTCAGATCACGCGGC 20 106 0 GCGACACTCG 0.885637 -133 AATTTCATATTCGACGAGCCCGGGCGACCACT 20 119 0 TCGAGAGCCG 0.909738 -120 CTTGCAAGATGCCAGGAGGGTGTGGCC 20 222 1 GCCAGAGGGG 0.929561 -17 TGCTTAGGTAGCGAACCCGCAGGAGTGCA 21 36 1 GCGACCCGCG 0.968694 -19 GCTTGCGGGGGAGAGGAGGCGGAACAA 22 6 0 GAGAGAGGCG 0.890357 -92 CCTCTCCCCCGCAAGCGGGAGGTGCGCCCACA 22 22 1 GCAACGGGAG 0.689472 -76 AGGGGACGAAGCGATGTGGGCGCACCTCCCGC 22 36 0 GCGAGTGGGG 0.950143 -62 **** ***** * Masking position 2 Map Score: 57.2129 Number of sites scoring better than the average of aligned sites = 31758 Number in coding regions = 29720 Number in noncoding regions = 2038 Number of orfs with sites within 600 bp upstream = 1064 Fraction of orfs with sites within 600 bp upstream = 0.170896 Motif number 3 TCCGGTTCAACTGATCCGCTTCGACCACAGGCTGG 1 177 0 CTGATCCTCC 0.727055 -124 TGCACTCAGGGCGGGCTCCGTCGGCGTGTCGTCGC 2 20 1 GCGGGCCTCC 0.964543 -62 CGCCGGCGAGCCGACCGCCTTTGGCCGAATCTTCC 7 11 1 CCGACCCTTC 0.850663 -49 CGCGCCACACCGGCTAAACGTCCACCACGGCTGAA 13 103 1 CGGCTACTCC 0.951799 -92 CCTCATCGCTGCGCTCTGCATCGTCGCCGGCGCGA 16 28 0 GCGCTCCTCC 0.997558 -144 ACCATCTGCGCCGCTCCTCCTCATCGCTGCGCTCT 16 46 0 CCGCTCCTCC 0.996881 -126 ATCGTCGCCGGCGCCAACCATCTGCGCCGCTCCTC 16 62 0 GCGCCACTCC 0.992709 -110 CCTCATCGCTGCGCTCTGCATCGTCGCCGGCGCCA 16 81 0 GCGCTCCTCC 0.997558 -91 ACCATCTGCGCCGCTCCTCCTCATCGCTGCGCTCT 16 99 0 CCGCTCCTCC 0.996881 -73 ATCGTCGCCGGCGCCAACCATCTGCGCCGCTCCTC 16 115 0 GCGCCACTCC 0.992709 -57 CCTCATCGCTGCGCTCTGCATCGTCGCCGGCGCCA 16 134 0 GCGCTCCTCC 0.997558 -38 CTGCGCCGCTCCTCCTCATCGCTGCGCTCT 16 152 0 CCGCTCCTCC 0.996881 -20 CCCAGGGGTACCGGCAGACATCTCCGCGAGGG 17 8 0 CCGGCACTCC 0.968119 -227 GATAGTCGACGGGCCTGGCCTCGGCCGGCCCCTCG 17 102 1 GGGCCTCTCC 0.915464 -133 TGTCTGCACCGCGGCCCGCCTTTCCGGGATCCGCA 18 128 1 GCGGCCCTTC 0.942544 -156 GCAGACGCCAGGGCCCGGCTTCAGCCGATGCCGGG 18 228 1 GGGCCCCTCC 0.993415 -56 ****** * ** * Masking position 11 Map Score: 42.1252 Number of sites scoring better than the average of aligned sites = 2072 Number in coding regions = 1850 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 GCTCATGTTTCCACTCCTCCGGTTCAACTG 1 199 0 CCACTCCTCC 0.964449 -102 CAACGGCGTCGCGCTCCGCCGATACCCCGA 4 194 0 GCGCTCCGCC 0.998164 -107 CGCGAGAAACCACCGCGCCACGCAGATAG 5 10 1 CCACCGCGCC 0.846432 -119 CAATAGTTTTGCACCCCGCCACGACATCGC 11 40 0 GCACCCCGCC 0.992498 -22 GACTCGGCAGGCGCACGGCCCGCTGCCGCC 13 39 1 GCGCACGGCC 0.930271 -156 CCCGAACGCGCCACACCGGCTAAACGTCCA 13 97 1 CCACACCGGC 0.882891 -98 CGGCCGCTCAGCAACAAAATCC 15 4 1 CCGCTCAGCA 0.886456 -19 CCTCATCGCTGCGCTCTGCATCGTCGCCGG 16 33 0 GCGCTCTGCA 0.943345 -139 ACCATCTGCGCCGCTCCTCCTCATCGCTGC 16 51 0 CCGCTCCTCC 0.990053 -121 CCTCATCGCTGCGCTCTGCATCGTCGCCGG 16 86 0 GCGCTCTGCA 0.943345 -86 ACCATCTGCGCCGCTCCTCCTCATCGCTGC 16 104 0 CCGCTCCTCC 0.990053 -68 CCTCATCGCTGCGCTCTGCATCGTCGCCGG 16 139 0 GCGCTCTGCA 0.943345 -33 CTGCGCCGCTCCTCCTCATCGCTGC 16 157 0 CCGCTCCTCC 0.990053 -15 CGTGACTAACGCACCCCGCCCACGCCGGAG 17 143 1 GCACCCCGCC 0.992498 -92 CTCAATAGCCGCGCTCCGGCGTGGGCGGGG 17 156 0 GCGCTCCGGC 0.992942 -79 TGTCTGCACCGCGGCCCGCCTTTCCGGGAT 18 128 1 GCGGCCCGCC 0.967846 -156 CGCCGCGGGACCGCCCCGGCATGCTGTTGC 18 160 0 CCGCCCCGGC 0.988291 -124 TCTACGACACGCGCCCAGCAGGCCGCGTGA 20 85 1 GCGCCCAGCA 0.912099 -154 TGCACTCCTGCGGGTTCGCTA 21 44 0 GCACTCCTGC 0.912649 -11 AGCGATGTGGGCGCACCTCCCGCTTGCGGG 22 29 0 GCGCACCTCC 0.977456 -69 ********** Masking position 2 Map Score: 51.5561 Number of sites scoring better than the average of aligned sites = 5225 Number in coding regions = 4831 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 5 GTAACGATCCTGGCCACCAGGCCGCCGAGCT 1 257 0 TGCCACCAGG 0.754053 -44 CGCACTCCATGGTCCCCGAGTTTGACCTTCG 4 72 1 GGCCCCGAGT 0.57481 -229 CGTCCGACTGGGGCCGACTGGGTTGTATGCG 4 131 1 GGCCGACTGG 0.76058 -170 CCGTGAATCTGCATCGCGAGGTCGGCCACCT 5 49 1 GCTCGCGAGG 0.958733 -80 GAGTTCGGGTGATCCGCGAGGGT 6 39 1 GACCGCGAGG 0.978523 -13 TCCTAAAAGCTACGCCAGATTTCTGGAAG 7 41 0 GCACGCCAGA 0.771419 -19 GACCCCCTCTGACCGGCGAGGGAATCTATGA 8 32 0 GACGGCGAGG 0.683037 -207 GGTCAGAGGGGGTCCAGCAGGGGCCCCGGAA 8 49 1 GGCCAGCAGG 0.974288 -190 TCCGTCCGACGGCGCCCCTGGTATCTTTCCG 8 75 0 GGGCCCCTGG 0.548175 -164 ACGACATCGCGGGTCGCGAGGCCCGAG 10 14 1 GGTCGCGAGG 0.949176 -17 AAATGTCGACGACTCGGCAGGCGCACGGCCC 13 29 1 GATCGGCAGG 0.953143 -166 CCGGCAGACATCTCCGCGAGGG 17 2 0 TCCCGCGAGG 0.846018 -233 GATGTCTGCCGGTACCCCTGGGTACCCGGTT 17 21 1 GGACCCCTGG 0.729233 -214 GACGGGCCTGGCCTCGGCCGGCCCCTCGTTG 17 109 1 GCTCGGCCGG 0.811868 -126 TGCCATCCCGGCACCACCAGGACGGCATCTC 17 195 0 GCCCACCAGG 0.983548 -40 AGTTTACACCGACCCAGCTGGTGATTTTCCC 18 61 0 GACCAGCTGG 0.890363 -223 GGCGCAGCTCGCATCGGCGGGCTGACTTCGC 18 96 1 GCTCGGCGGG 0.811862 -188 CCGCGGGACCGCCCCGGCATGCTGTTGCGGA 18 157 0 GCCCGGCATG 0.835867 -127 CGCGATGCCGGACCCGGGAGGAAATCCCCGA 18 197 0 GACCGGGAGG 0.972895 -87 GGCATCGCGGCAGACGCCAGGGCCCGGCTTC 18 219 1 CAACGCCAGG 0.634887 -65 TGTTCGCCCGGCATCGGCTGAAGCCGGGCCC 18 238 0 GCTCGGCTGA 0.573146 -46 CTTGATCCTTGCGCCGGGTGAATGGTG 19 7 0 GCCCGGGTGA 0.702819 -44 CTACGACACGCGCCCAGCAGGCCGCGTGATC 20 86 1 CGCCAGCAGG 0.789016 -153 CGACACACCGGCGCCACCAGTGCAGTCACAG 20 157 1 GCCCACCAGT 0.799785 -82 AGTCACAGACGAAACACCAGGCACACTGGTA 20 180 1 GAACACCAGG 0.838626 -59 CTTAGGTAGCGAACCCGCAGGAGTGCA 21 38 1 GACCCGCAGG 0.956541 -17 ** ******** Masking position 10 Map Score: 26.2289 Number of sites scoring better than the average of aligned sites = 15411 Number in coding regions = 14331 Number in noncoding regions = 1080 Number of orfs with sites within 600 bp upstream = 736 Fraction of orfs with sites within 600 bp upstream = 0.118214 Motif number 6 GGAGACGCCACTCGTTGGGGCAGTTTTGTAC 1 48 1 CTCGTTGGGC 0.835747 -253 GCCCTGAGTGCACGTTCGAAG 2 1 0 CACGTTCGAG 0.848485 -81 TCAGGGCGGGCTCCGTCGGCGTGTCGTCGCC 2 25 1 CTCCGTCGGG 0.662398 -57 GGGTTGTATGCGCGGGCTGAGTATCAGCGCG 4 150 1 CGCGGGCTGG 0.838471 -151 TGAGTATCAGCGCGGTCGCGGCGCAGCTCGG 4 167 1 CGCGGTCGCG 0.959922 -134 ATCTGCATCGCGAGGTCGGCCACCTTGCCAG 5 55 1 CGAGGTCGGC 0.89423 -74 ACCTTGCCAGCTAGTTCGGTGTAGAAGAGCT 5 76 1 CTAGTTCGGG 0.932031 -53 TCATATTTTGCACCGTCGGCGGCGAAGCTCT 5 101 0 CACCGTCGGG 0.666135 -28 ATCACCCGAACTCGGTCGGGTTCGCTTGCGC 6 21 0 CTCGGTCGGT 0.913758 -31 GCCGTGAATGCACGTTCGGCG 12 1 0 CACGTTCGGG 0.990489 -73 TCCCTGTGTTCACGTTCGGCGAGGAAACCGG 12 52 1 CACGTTCGGG 0.990489 -22 CCGCTGCCGCCGCGGTGGGTAACCGTTCATC 13 58 1 CGCGGTGGGA 0.918623 -137 GCCGGTGTGGCGCGTTCGGGATTATTGGGAT 13 86 0 CGCGTTCGGA 0.951679 -109 CGTTGTGCACCACGTTCTGGGGAATGTTGGT 13 150 0 CACGTTCTGG 0.938068 -45 TCGACTATCTCAAGGTGTGAGCATCGCTCGA 17 80 0 CAAGGTGTGG 0.571795 -155 AAATCACCAGCTGGGTCGGTGTAAACTACTC 18 65 1 CTGGGTCGGG 0.935027 -219 GCCGCGTTGGGCGTTGGCCGGCG 19 38 0 CGCGTTGGGG 0.981771 -13 ********* * Masking position 1 Map Score: 26.0396 Number of sites scoring better than the average of aligned sites = 6397 Number in coding regions = 5986 Number in noncoding regions = 411 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 7 TCTCCCCGGTAGGGTTCGTCCTCACGCGGC 1 23 0 AGGGTTCGTC 0.923038 -278 GCTTCGACCACAGGCTGGTCGAAGCGGCTC 1 165 0 CAGGCTGGTC 0.776848 -136 GCCTGGTGGCCAGGATCGTTACCGGGTAAG 1 266 1 CAGGATCGTT 0.879536 -35 TTACCGGGTAAGGGATCGCCACTCCCA 1 284 1 AGGGATCGCC 0.946997 -17 TTAGTTTGGACGAGATCGTCCGACTGGGGC 4 115 1 CGAGATCGTC 0.941582 -186 CGAACTCGGTCGGGTTCGCTTGCGCTGTTT 6 16 0 CGGGTTCGCT 0.940875 -36 GCTATGTTTTTGAGATCGTCCCGCGACCTG 8 121 0 TGAGATCGTC 0.536294 -118 ACATAGCTTACAGGCCCGTTTTGTTGGTTA 8 144 1 CAGGCCCGTT 0.889487 -95 CGGCCGAGGCCAGGCCCGTCGACTATCTCA 17 99 0 CAGGCCCGTC 0.971506 -136 GGAACCGCCGCGGGACCGCCCCGGCATGCT 18 165 0 CGGGACCGCC 0.987813 -119 GATTTCCTCCCGGGTCCGGCATCGCGGCAG 18 202 1 CGGGTCCGGC 0.958954 -82 GGCAGACGCCAGGGCCCGGCTTCAGCCGAT 18 227 1 AGGGCCCGGC 0.892724 -57 CACGCTCGGGCAAGATCGCCCAGACGACGT 20 29 1 CAAGATCGCC 0.839889 -210 AGTGGTCGCCCGGGCTCGTCGAATATGAAA 20 119 1 CGGGCTCGTC 0.992365 -120 TGCACTCCTGCGGGTTCGCTACCTAAGCAA 21 35 0 CGGGTTCGCT 0.940875 -20 ********** Masking position 4 Map Score: 20.6833 Number of sites scoring better than the average of aligned sites = 6815 Number in coding regions = 6389 Number in noncoding regions = 426 Number of orfs with sites within 600 bp upstream = 347 Fraction of orfs with sites within 600 bp upstream = 0.055734 Motif number 8 AACAAGCCGCCGCGTGAGGACGAACCCTAC 1 15 1 CGCGTGAGGA 0.733665 -286 GAATCTGCATCGCGAGGTCGGCCACCTTGC 5 53 1 CGCGAGGTCG 0.902945 -76 CGACCGAGTTCGGGTGATCCGCGAGGGT 6 34 1 CGGGTGATCC 0.972776 -18 CATCGCGGGTCGCGAGGCCCGAG 10 18 1 CGCGAGGCCC 0.942397 -13 TTGATGCCTGCGCTTGATGCTAAGATGCCA 14 14 0 CGCTTGATGC 0.867201 -44 CGCGAAGCAGCGCGTAGTCCCC 16 3 0 CGCGTAGTCC 0.959309 -169 AGATGCCGTCCTGGTGGTGCCGGGATGGCA 17 196 1 CTGGTGGTGC 0.717081 -39 GGTGCAGACACGCGAAGTCAGCCCGCCGAT 18 108 0 CGCGAAGTCA 0.562476 -176 TCGCGGCAGACGCCAGGGCCCGGCTTCAGC 18 223 1 CGCCAGGGCC 0.849001 -61 CGTTGGCCGGCGCTTGATCCTTGCGCCGGG 19 20 0 CGCTTGATCC 0.927648 -31 GCCGCGTTGGGCGTTGGCCGGC 19 39 0 CGCGTTGGGC 0.804537 -12 CGGCGGCTGACGGGTGAGCCTACGTCGTCT 20 50 0 CGGGTGAGCC 0.955748 -189 CCCAGCAGGCCGCGTGATCTGAGTGGTCGC 20 98 1 CGCGTGATCT 0.835372 -141 CCCCCGCAAGCGGGAGGTGCGCCCACATCG 22 27 1 CGGGAGGTGC 0.95747 -71 GCGCCCACATCGCTTCGTCCCCTGCAAGCG 22 45 1 CGCTTCGTCC 0.767325 -53 CCCCTGCAAGCGGGTGGTACCCCCACTGCA 22 63 1 CGGGTGGTAC 0.881209 -35 ********** Masking position 1 Map Score: 12.3719 Number of sites scoring better than the average of aligned sites = 5212 Number in coding regions = 4741 Number in noncoding regions = 471 Number of orfs with sites within 600 bp upstream = 394 Fraction of orfs with sites within 600 bp upstream = 0.063283 Motif number 9 CCCGCACTCCATGGTCCCCGAGTTTGACCT 4 70 1 ATGGTCCCCG 0.742066 -231 TCGCGCTCCGCCGATACCCCGAGCTGCGCC 4 186 0 CCGATACCCC 0.93859 -115 CGCCGGTTGGCCGGTAACCCAGCGTTCGTG 4 226 1 CCGGTAACCC 0.928052 -75 CCCAGCGTTCGTGGTCGCCCGATCTGAGAA 4 243 1 GTGGTCGCCC 0.943169 -58 ACCCTCGCGGATCACCCGAACTCGGTC 6 35 0 CGGATCACCC 0.775844 -17 GGGGCCCCTGCTGGACCCCCTCTGACCGGC 8 46 0 CTGGACCCCC 0.935612 -193 CGCCGATAGTCTCGTACCCC 11 1 0 CTCGTACCCC 0.904464 -61 ACTATCGGCGCGGATACCCGCGATGTCGTG 11 21 1 CGGATACCCG 0.623316 -41 GAGATGTCTGCCGGTACCCCTGGGTACCCG 17 19 1 CCGGTACCCC 0.67619 -216 TGTTCTGAACCGGGTACCCAGGGGTACCGG 17 29 0 CGGGTACCCA 0.6778 -206 GCATGCCGGGGCGGTCCCGCGGCGGTTCCC 18 166 1 GCGGTCCCGC 0.788712 -118 CGTGATCTGAGTGGTCGCCCGGGCTCGTCG 20 110 1 GTGGTCGCCC 0.943169 -129 CTGCAAGCGGGTGGTACCCCCACTGCATTG 22 66 1 GTGGTACCCC 0.70476 -32 ********** Masking position 8 Map Score: 13.0188 Number of sites scoring better than the average of aligned sites = 2074 Number in coding regions = 1863 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 10 CTTCGAACGTGCACTCAGGG 2 1 1 CTTCGAACGT 0.584432 -81 GTTCGAGTCCCTCCGCCCGCACTCCATGGT 4 55 1 CTCCGCCCGC 0.917128 -246 CCGAGCTGCGCCGCGACCGCGCTGATACTC 4 168 0 CCGCGACCGC 0.93696 -133 GATCGGGCGACCACGAACGCTGGGTTACCG 4 237 0 CCACGAACGC 0.891908 -64 AGAGCTTCGCCGCCGACGGTGCAAAATATG 5 101 1 CGCCGACGGT 0.916065 -28 GCGCAAGCGAACCCGACCGAGTTCGGGTGA 6 21 1 ACCCGACCGA 0.69639 -31 CGCCGGCGAGCCGACCGCCTTTGGCCGA 7 9 1 AGCCGACCGC 0.960781 -51 CGCCGAACGTGCATTCACGG 12 1 1 CGCCGAACGT 0.990053 -73 CCGGTTTCCTCGCCGAACGTGAACACAGGG 12 53 0 CGCCGAACGT 0.990053 -21 ATCCCAATAATCCCGAACGCGCCACACCGG 13 86 1 TCCCGAACGC 0.891908 -109 ACCAACATTCCCCAGAACGTGGTGCACAAC 13 150 1 CCCAGAACGT 0.813906 -45 TCGCCGCCGCCCGTTTTGTGGACA 18 5 1 CGCCGCCCGT 0.97231 -279 CGCCGGCCAACGCCCAACGCGGC 19 38 1 CGCCCAACGC 0.934952 -13 ACCCGTCAGCCGCCGAACGGTCTACGACAC 20 65 1 CGCCGAACGG 0.968382 -174 ********** Masking position 9 Map Score: 18.6449 Number of sites scoring better than the average of aligned sites = 5050 Number in coding regions = 4700 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 286 Fraction of orfs with sites within 600 bp upstream = 0.0459364 Motif number 11 CCCAGTCGGACGATCTCGTCCAAACTAAGG 4 113 0 CGATCTCGTC 0.593391 -188 CGGCGGAGCGCGACGCCGTTGCACGCCGGT 4 203 1 CGACGCCGTT 0.531956 -98 GCCCGATCTGAGAAGTCGTGGCGGATTAGG 4 259 1 AGAAGTCGTG 0.478301 -42 GCATCGACAGCAATGCCGTGTCATAGATTC 8 12 1 CAATGCCGTG 0.973858 -227 TCGCGACCCGCGATGTCGTGCT 10 3 0 CGATGTCGTG 0.983555 -28 CGGATACCCGCGATGTCGTGGCGGGGTGCA 11 31 1 CGATGTCGTG 0.983555 -31 CCTGAACGCTAAATGTCGACGACTCGGCAG 13 19 1 AAATGTCGAC 0.291626 -176 GCGCACGGCCCGCTGCCGCCGCGGTGGGTA 13 49 1 CGCTGCCGCC 0.781233 -146 CTTGATGCTAAGATGCCATGC 14 2 0 AGATGCCATG 0.745956 -56 GCGCCGGCGACGATGCAGAGCGCAGCGATG 16 30 1 CGATGCAGAG 0.916128 -142 GCGCCGGCGACGATGCAGAGCGCAGCGATG 16 83 1 CGATGCAGAG 0.916128 -89 GCGCCGGCGACGATGCAGAGCGCAGCGATG 16 136 1 CGATGCAGAG 0.916128 -36 GCAGGATGTGAGATGCCGTCCTGGTGGTGC 17 186 1 AGATGCCGTC 0.936885 -49 GCCGGGATGGCACTGTCGTGCGAGGAGTCA 17 214 1 CACTGTCGTG 0.793696 -21 GTTTTGTGGACAATGTCGTCGCTGTGGATT 18 23 1 CAATGTCGTC 0.834497 -261 CTGTGGATTCCGCTGCCGGGAAAATCACCA 18 44 1 CGCTGCCGGG 0.969394 -240 GCGTCTGCCGCGATGCCGGACCCGGGAGGA 18 206 0 CGATGCCGGA 0.866285 -78 CGGCTTCAGCCGATGCCGGGCGAACAACCG 18 243 1 CGATGCCGGG 0.990688 -41 GGATCTTGCAAGATGCCAGGAGGGTGTGGC 20 218 1 AGATGCCAGG 0.639621 -21 CCACCGCCGACAATGCAGTGGGGGTACCAC 22 76 0 CAATGCAGTG 0.844282 -22 ********** Masking position 5 Map Score: 25.0377 Number of sites scoring better than the average of aligned sites = 9859 Number in coding regions = 9272 Number in noncoding regions = 587 Number of orfs with sites within 600 bp upstream = 463 Fraction of orfs with sites within 600 bp upstream = 0.0743656 Motif number 12 CATGAGCGGCCCGACGGGAAATTCGATGCC 1 222 1 CCGACGGGAA 0.993292 -79 GGTTGCCTTACCGAAGGTCAAACTCGGGGA 4 84 0 CCGAAGGTCA 0.702717 -217 ACAAATCGAACTGACGGGTATGTGGTTGTT 9 27 0 CTGACGGGTA 0.961808 -49 ACAACATATTACGAAGGGAAGCATGCT 9 59 1 ACGAAGGGAA 0.866036 -17 CCGCTTTTTTCCGCCGTGAATGCACGTTCG 12 14 0 CCGCCGTGAA 0.903511 -60 GTGGATTCCGCTGCCGGGAAAATCACCAGC 18 46 1 CTGCCGGGAA 0.970262 -238 GAGGAAATCCCCGAAGGGAACCGCCGCGGG 18 181 0 CCGAAGGGAA 0.98302 -103 CGTTCGGCGGCTGACGGGTGAGCCTACGTC 20 54 0 CTGACGGGTG 0.869898 -185 ********** Masking position 6 Map Score: 5.0937 Number of sites scoring better than the average of aligned sites = 1211 Number in coding regions = 1127 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 13 GTACAAAACTGCCCCAACGAGTGGCGTCTC 1 49 0 GCCCCAACGA 0.920655 -252 AGGTGCCGGTGCTCGAAAGAGTTTGAGGGT 4 27 1 GCTCGAAAGA 0.681263 -274 GATTAGGCCGCCGCGAGAGAGGACCGCTG 4 282 1 CCGCGAGAGA 0.610005 -19 AGAAACCACCGCGCCACGCAGATAGCCACT 5 15 1 GCGCCACGCA 0.937901 -114 AACTCAAACAGCGCAAGCGAACCCGACCGA 6 11 1 GCGCAAGCGA 0.918142 -41 ATCGTCGCCGGCGCGAAGCAGCGCGTAGTC 16 14 0 GCGCGAAGCA 0.970782 -158 ATCGTCGCCGGCGCCAACCATCTGCGCCGC 16 67 0 GCGCCAACCA 0.98961 -105 ATCGTCGCCGGCGCCAACCATCTGCGCCGC 16 120 0 GCGCCAACCA 0.98961 -52 CAACTTTGTTGCTCGAGCGATGCTCACACC 17 68 1 GCTCGAGCGA 0.910047 -167 CAAGGATCAAGCGCCGGCCAACGCCCAACG 19 27 1 GCGCCGGCCA 0.955446 -24 TCTACGACACGCGCCCAGCAGGCCGCGTGA 20 85 1 GCGCCCAGCA 0.911005 -154 ********** Masking position 10 Map Score: 7.68634 Number of sites scoring better than the average of aligned sites = 2774 Number in coding regions = 2563 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 14 CTTCAACAAGCCGCCGCGTGAGGACGAACC 1 10 1 GCCGCGCGTG 0.750311 -291 CGTACAGGCTGCCGCTCGGTCATCTATAGTC 1 125 1 GCCGCCGGTC 0.985626 -176 TCGATCCAGAGCCGCTTCGACCAGCCTGTGG 1 157 1 GCCGCTCGAC 0.93933 -144 GTTCAACTGATCCGCTTCGACCACAGGCTGG 1 177 0 TCCGCTCGAC 0.786313 -124 CCACCAGGCCGCCGAGCTGTCTGGGCATCGA 1 244 0 GCCGACTGTC 0.640907 -57 TTCGAGTCCCTCCGCCCGCACTCCATGGTCC 4 56 1 TCCGCCGCAC 0.52672 -245 GGGCTGAGTATCAGCGCGGTCGCGGCGCAGC 4 163 1 TCAGCCGGTC 0.516965 -138 GTCGCGCTCCGCCGATACCCCGAGCTGCGCC 4 186 0 GCCGAACCCC 0.556286 -115 CAACCGGCGTGCAACGGCGTCGCGCTCCGCC 4 204 0 GCAACGCGTC 0.366136 -97 GGCCTAATCCGCCACGACTTCTCAGATCGGG 4 260 0 GCCACACTTC 0.62865 -41 CACGCAGATAGCCACTTCCTCCGTGAATCTG 5 29 1 GCCACTCCTC 0.924524 -100 ACCGCCTTTGGCCGAATCTTCCAGAAATCTG 7 24 1 GCCGATCTTC 0.860577 -36 GTTACACCGCGCAAAACCGTCTTCACAGTGT 8 206 1 GCAAACCGTC 0.447309 -33 GGTTGTTCTGGCCGAGTCCGCGG 9 3 0 GCCGATCCGC 0.733746 -73 TTTGCACCCCGCCACGACATCGCGGGTATCC 11 32 0 GCCACACATC 0.382617 -30 CCGTGCGCCTGCCGAGTCGTCGACATTTAGC 13 26 0 GCCGATCGTC 0.928248 -169 TCCCGAACGCGCCACACCGGCTAAACGTCCA 13 96 1 GCCACCCGGC 0.897097 -99 ATCGCTGCGCTCTGCATCGTCGCCGGCGCGA 16 28 0 TCTGCTCGTC 0.656193 -144 AACCATCTGCGCCGCTCCTCCTCATCGCTGC 16 51 0 GCCGCCCTCC 0.955998 -121 ATCGCTGCGCTCTGCATCGTCGCCGGCGCCA 16 81 0 TCTGCTCGTC 0.656193 -91 AACCATCTGCGCCGCTCCTCCTCATCGCTGC 16 104 0 GCCGCCCTCC 0.955998 -68 ATCGCTGCGCTCTGCATCGTCGCCGGCGCCA 16 134 0 TCTGCTCGTC 0.656193 -38 CTGCGCCGCTCCTCCTCATCGCTGC 16 157 0 GCCGCCCTCC 0.955998 -15 CCTGGCCTCGGCCGGCCCCTCGTTGTTGCGT 17 115 1 GCCGGCCCTC 0.934377 -120 TCGCCGCCGCCCGTTTTGTGGACAAT 18 6 1 GCCGCCGTTT 0.332793 -278 CCGCCGCGGGACCGCCCCGGCATGCTGTTGC 18 160 0 ACCGCCCGGC 0.677122 -124 ATCGGCTGAAGCCGGGCCCTGGCGTCTGCCG 18 226 0 GCCGGCCCTG 0.526333 -58 CCCGTCAGCCGCCGAACGGTCTACGACACGC 20 66 1 GCCGACGGTC 0.932699 -173 CGCCCAGCAGGCCGCGTGATCTGAGTGGTCG 20 96 1 GCCGCTGATC 0.745261 -143 GGCCACACCCTCCTGGCATCTT 20 227 0 GCCACCCCTC 0.964083 -12 TTGTTCCGCCTCCTCTCCCCCGCAA 22 5 1 TCCGCTCCTC 0.927419 -93 ***** ***** Masking position 2 Map Score: 38.3553 Number of sites scoring better than the average of aligned sites = 22007 Number in coding regions = 20599 Number in noncoding regions = 1408 Number of orfs with sites within 600 bp upstream = 840 Fraction of orfs with sites within 600 bp upstream = 0.134918 Motif number 15 ********** No masking Map Score: -3.16659e-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