AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_mtub_reg_300.orf -o00520_mtub_300.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 Purged sequences: rmlB2 22 rmlB2 Input sequences: #1 Rv0331 113 hypothetical protein Rv0331 #2 Rv0332 74 hypothetical protein Rv0332 #3 Rv0333 26 hypothetical protein Rv0333 #4 rmlA 29 rmlA #5 galE1 300 galE1 #6 Rv0617 155 hypothetical protein Rv0617 #7 galT' 128 galT' #8 galU 100 galU #9 glgX 38 glgX #10 Rv1565c 98 hypothetical protein Rv1565c #11 Rv1566c 239 hypothetical protein Rv1566c #12 Rv1567c 247 hypothetical protein Rv1567c #13 rmlD 75 rmlD #14 Rv3463 253 hypothetical protein Rv3463 #15 rmlB 72 rmlB #16 mhpE 60 mhpE #17 Rv3779 89 hypothetical protein Rv3779 #18 epiB 155 epiB Motif number 1 ********** No masking Map Score: -3.3087e-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 2 CTTGCGCAAGACTGCGGCGGAATCTAATAT 1 54 1 ACTGCGGCGG 0.797681 -60 CACGCCGGTGGGCGCGGCCCC 2 2 1 ACGCCGGTGG 0.957175 -73 ACGCCGGTGGGCGCGGCCCCCTACCACGGC 2 12 1 GCGCGGCCCC 0.986194 -63 TGTTTCAGGGGCGCCGGTAGGAGCCGTGGT 2 34 0 GCGCCGGTAG 0.865777 -41 GCCGCACGCGGCCGGAGTCCGCCTG 5 6 1 ACGCGGCCGG 0.992813 -295 ATCTGGCAATGCTCGGGCGCTGCCGGTTTG 5 40 1 GCTCGGGCGC 0.966762 -261 CGGACACTCTACCCGGGCGGTCGCACGGAA 5 73 0 ACCCGGGCGG 0.986055 -228 CGGCTATCTGACCCGGACACTCTACCCGGG 5 86 0 ACCCGGACAC 0.653476 -215 TGAACCCATGACCCCGCCATCTATACGGCT 5 111 0 ACCCCGCCAT 0.77366 -190 ACATGCGCTTGCGCCGCTTCTTGATTACTG 5 139 0 GCGCCGCTTC 0.860778 -162 GCTGCGTCGCACCCGGGTGCAGCGCAGGAA 5 191 1 ACCCGGGTGC 0.945425 -110 TTGCGAGCAGACCCCGCCAGCTCGACCGTC 5 235 1 ACCCCGCCAG 0.928235 -66 CGCGCTTGTAACGCCGCCGTTTCGCCTGGC 5 266 1 ACGCCGCCGT 0.544904 -35 CCGCCGTTTCGCCTGGCCGTTAGGCTGTCG 5 279 1 GCCTGGCCGT 0.85037 -22 AGTGAAACGGTCGCCGACCTCATGCGACGA 6 20 1 TCGCCGACCT 0.465884 -136 ATGCGACGAGGCCTGGCCGCCAACCGCCCT 6 41 1 GCCTGGCCGC 0.938166 -115 GGTCACGACGGTCCCGACGCTCACCAAAGG 6 104 0 GTCCCGACGC 0.872914 -52 GCGGCTCGCCGCGCCGCCGGGAGACGATGC 7 14 0 GCGCCGCCGG 0.868099 -115 GCGGCGCGGCGAGCCGCCCCAAAACCAACG 7 27 1 GAGCCGCCCC 0.923057 -102 GCCGGTGAGGGCCGCGACGCCACCTCAGCT 7 80 0 GCCGCGACGC 0.854405 -49 ATCCTCTGTGGTGTCGCCGGTGAGGGCCGC 7 95 0 GTGTCGCCGG 0.750851 -34 CGGATCGGCCCGAGATCCTCTG 7 117 0 GATCGGCCCG 0.858493 -12 CGATGACACAGCCCCGGCCGTCCCGCGCGA 8 19 1 GCCCCGGCCG 0.979589 -82 CGTTGGCGCTGTCCCGGCGCTCGCGCGGGA 8 39 0 GTCCCGGCGC 0.894183 -62 TTATCCAGGTTCTCCGGCGGGTGTAGGCG 9 10 0 TCTCCGGCGG 0.901296 -29 CGGTCCCGCTTGCTTTCTCGCC 10 3 1 GTCCCGCTTG 0.642714 -96 TCGCCTCCCAAACCCGCCTCCTGCTTCCCG 10 28 1 AACCCGCCTC 0.663658 -71 CGCCTCCTGCTTCCCGCTGCTCAGCGCGCG 10 42 1 TTCCCGCTGC 0.692802 -57 CAAAGATTGAGCGCGGCAGTCACCGTCCGG 11 41 1 GCGCGGCAGT 0.678851 -199 GCCGTAACGTGACCGGACGGTGACTGCCGC 11 53 0 GACCGGACGG 0.937912 -187 CCAGCTATGGACGCGGCCGGCATCTGTTGT 11 106 1 ACGCGGCCGG 0.992813 -134 ATAAAGTGACTTCCGGCTGGAATGGCAGAC 11 162 1 TTCCGGCTGG 0.770884 -78 TCCTTGGCACTCTCGGGTGGTGTGTGCCTC 11 208 0 TCTCGGGTGG 0.7697 -32 ATGGGCCGTGGCGTGGCTGCATTACCCTCG 12 17 0 GCGTGGCTGC 0.84398 -231 CCGTTACTGGGATGGGCCGTGGCGTGGCTG 12 28 0 GATGGGCCGT 0.573025 -220 GCATGCATGCTCCCCGATGGCAGAGGTTTT 12 63 0 TCCCCGATGG 0.800494 -185 TCAGGCTGATTCGGCGGTGCCATGCATGCA 12 86 0 TCGGCGGTGC 0.631047 -162 GGCTCGTCTAGAGCCGACCGGGATTCGGTG 12 137 0 GAGCCGACCG 0.797068 -111 GTGTCCGCTCGTCGGGCTCGTCTAGAGCCG 12 151 0 GTCGGGCTCG 0.527696 -97 CGAGCCCGACGAGCGGACACCCCCACGGGT 12 161 1 GAGCGGACAC 0.532721 -87 TACTTGTGTAACGGCGCCCTGTCGGGTAGC 13 18 1 ACGGCGCCCT 0.652955 -58 CGGGTAGCCAACCCCGGCGTGCCCGAGGCG 13 40 1 ACCCCGGCGT 0.873484 -36 GCTGCGCCGGAATCGGGTGCACCGACAAGG 14 34 0 AATCGGGTGC 0.514686 -220 CCGAGCACGTGCTGCGCCGGAATCGGGTGC 14 44 0 GCTGCGCCGG 0.949786 -210 CTACAAACGTGAGCCGGTGGTGGAAATTCC 14 75 1 GAGCCGGTGG 0.931395 -179 TGCGCAGAGCACGGCGATGCGGGTAATGTG 14 173 0 ACGGCGATGC 0.556253 -81 ACCCAACTGGTCGCGGCTCCACTCGGTTAA 15 32 1 TCGCGGCTCC 0.81756 -41 ATTCTTGGACGCGCGGCTGGTGTC 16 5 0 GCGCGGCTGG 0.992493 -56 TCCGGCAAGGGTGCGGGCTGACACTG 16 45 1 GTGCGGGCTG 0.751896 -16 CCACCTTAGAACTCGGGTGTCCTAGACGTC 17 16 1 ACTCGGGTGT 0.649769 -74 GCCCGGGCGGGCTGGGACGTCTAGGACACC 17 31 0 GCTGGGACGT 0.544548 -59 GCTCAGGGAAGCCCGGGCGGGCTGGGACGT 17 41 0 GCCCGGGCGG 0.994816 -49 GAGCCATGTCACCCGGCCAGCCATACTAAT 17 67 1 ACCCGGCCAG 0.932569 -23 CGGTCGGCTATAGCCGCCGGAATAGTCC 18 9 0 TAGCCGCCGG 0.931851 -147 GGCTATAGCCGACCGGCTTCTTTCACGCGG 18 24 1 GACCGGCTTC 0.663087 -132 GGCTTCTTTCACGCGGCTTGCGCGTGACGG 18 38 1 ACGCGGCTTG 0.831233 -118 GCTTGCGCGTGACGGGCCGCCGTTGATCTC 18 53 1 GACGGGCCGC 0.926042 -103 TTGATCTCAAGATCGGCTGGCAACGGCCGC 18 75 1 GATCGGCTGG 0.886054 -81 TGCCGCTGGTACGCGGCCGTTGCCAGCCGA 18 87 0 ACGCGGCCGT 0.962198 -69 CCGTCCCGCCCTCTGAGCCTCA 18 144 0 GTCCCGCCCT 0.78763 -12 ********** Masking position 6 Map Score: 85.2329 Number of sites scoring better than the average of aligned sites = 102794 Number in coding regions = 96225 Number in noncoding regions = 6569 Number of orfs with sites within 600 bp upstream = 1651 Fraction of orfs with sites within 600 bp upstream = 0.265178 Motif number 3 CACGCCGGTGGGCGCGGCCCCCTAC 2 6 1 CGGTGGGCGC 0.910883 -69 CCGGTAGGAGCCGTGGTAGGGGGCCGCGCC 2 21 0 CCGTGGTAGG 0.427852 -54 CTGAAAGTTACCGTGTGCGGCGG 3 4 0 CCGTGTGCGG 0.959234 -23 CTCCTAACTGCCGTTCGCCGACC 4 4 0 CCGTTCGCCG 0.952234 -26 CGGACTCCGGCCGCGTGCGGC 5 2 0 CCGCGTGCGG 0.591124 -299 ATTGCCAGATCGGTCAGGCGGACTCCGGCC 5 20 0 CGGTCAGGCG 0.921285 -281 AATGCTCGGGCGCTGCCGGTTTGGTGTTCC 5 47 1 CGCTGCCGGT 0.770555 -254 GTTTGGTGTTCCGTGCGACCGCCCGGGTAG 5 65 1 CCGTGCGACC 0.90616 -236 CTTGGACATGCGCTTGCGCCGCTTCTTGAT 5 144 0 CGCTTGCGCC 0.677661 -157 GCCAGCTCGACCGTCACGCGCTTGTAACGC 5 250 1 CCGTCACGCG 0.934021 -51 TGTAACGCCGCCGTTTCGCCTGGCCGTTAG 5 272 1 CCGTTTCGCC 0.893128 -29 TTTCGCCTGGCCGTTAGGCTGTCGGA 5 285 1 CCGTTAGGCT 0.794619 -16 AGGTCGGCGACCGTTTCACTCAACGTGCG 6 10 0 CCGTTTCACT 0.392636 -146 CGCGGTAGGGCGGTTGGCGGCCAGGCCTCG 6 47 0 CGGTTGGCGG 0.908548 -109 CCGCCAACCGCCCTACCGCGTTGTCCTCAG 6 57 1 CCCTACCGCG 0.507936 -99 AAAGGCAATCCCGTTCTGGGGTCTGAGGAC 6 79 0 CCGTTCTGGG 0.769063 -77 CGTCTCCCGGCGGCGCGGCGAGCCGCCCCA 7 18 1 CGGCGCGGCG 0.596784 -111 GTGGTGTCGCCGGTGAGGGCCGCGACGCCA 7 88 0 CGGTGAGGGC 0.937533 -41 ACAGCCCCGGCCGTCCCGCGCGAGCGCCGG 8 26 1 CCGTCCCGCG 0.969482 -75 TCTTCGTTGGCGCTGTCCCGGCGCTCGCGC 8 43 0 CGCTGTCCCG 0.803996 -58 GCAATCAGCACGCTGCGGGTTATCGTGTGA 8 78 1 CGCTGCGGGT 0.795182 -23 CGGTCCCGCTTGCTTTCTCG 10 1 1 CGGTCCCGCT 0.81652 -98 GCGGCAGTCACCGTCCGGTCACGTTACGGC 11 53 1 CCGTCCGGTC 0.641384 -187 CTGGGATGGGCCGTGGCGTGGCTGCATTAC 12 22 0 CCGTGGCGTG 0.840535 -226 GTTTTGGCGACCGTTACTGGGATGGGCCGT 12 38 0 CCGTTACTGG 0.394424 -210 GCTGATTCGGCGGTGCCATGCATGCATGCT 12 82 0 CGGTGCCATG 0.576993 -166 GACCGGGATTCGGTGCCAGCATCGGGCTGA 12 122 0 CGGTGCCAGC 0.857759 -126 GCGTGAGTACCCGTGGGGGTGTCCGCTCGT 12 169 0 CCGTGGGGGT 0.915164 -79 GCGGATAGCGCCCTGGGACGTGGTATGTAC 12 200 1 CCCTGGGACG 0.758965 -48 TGTAACGGCGCCCTGTCGGGTAGCCAACCC 13 24 1 CCCTGTCGGG 0.915372 -52 TTTCTCGGAGCCCTTCGCGGAATTTCCACC 14 93 0 CCCTTCGCGG 0.851706 -161 TGTCCCGTGCCGGTTTGGCGTGCCCAGTTT 14 129 0 CGGTTTGGCG 0.940015 -125 GTTGGCGGTGCGGTGTCCCGTGCCGGTTTG 14 142 0 CGGTGTCCCG 0.938237 -112 GGTGCTATTCCGGTGAGCGCGTGGCCTACG 14 209 0 CGGTGAGCGC 0.887464 -45 GGAATAGCACCGGTGAGCCGAGCGGTTAGA 14 228 1 CGGTGAGCCG 0.93288 -26 GTGAGCCGAGCGGTTAGAGCAACC 14 240 1 CGGTTAGAGC 0.574138 -14 TCGCAACCCTCCGTTTCGGGA 15 2 0 CCGTTTCGGG 0.949424 -71 GGTTAAGGCTCGGTTAGGGTTTGATCC 15 56 1 CGGTTAGGGT 0.736415 -17 TCAGCCCGCACCCTTGCCGGATCCTTGATG 16 36 0 CCCTTGCCGG 0.769789 -25 TCAGGGAAGCCCGGGCGGGCTGGGACGTCT 17 39 0 CCGGGCGGGC 0.702784 -51 CAACGGCGGCCCGTCACGCGCAAGCCGCGT 18 48 0 CCGTCACGCG 0.934021 -108 ATTAGGTTCACCGTTTGCCGATGAGGCTCA 18 123 1 CCGTTTGCCG 0.919089 -33 CCGTCCCGCCCTCTGAGCCT 18 146 0 CCGTCCCGCC 0.938988 -10 ********** Masking position 1 Map Score: 52.2749 Number of sites scoring better than the average of aligned sites = 33360 Number in coding regions = 30798 Number in noncoding regions = 2562 Number of orfs with sites within 600 bp upstream = 1241 Fraction of orfs with sites within 600 bp upstream = 0.199325 Motif number 4 CCAAGACCTTGCGCAAGACTGCGGCGGAAT 1 47 1 GCGCAAGACT 0.867633 -67 GCCGCACGCGGCCGGAGTCCGCC 5 4 1 GCACGCGGCC 0.837552 -297 CCGGGCGGTCGCACGGAACACCAAACCGGC 5 61 0 GCACGGAACA 0.782211 -240 GGCGTTACAAGCGCGTGACGGTCGAGCTGG 5 251 0 GCGCGTGACG 0.995965 -50 CCCGGCGCTCGCGCGGGACGGCCGGGGCTG 8 27 0 GCGCGGGACG 0.99699 -74 GCAGCGGGAAGCAGGAGGCGGGTTTGGGAG 10 32 0 GCAGGAGGCG 0.813215 -67 GCTGCTCAGCGCGCGAAGCAGGAGGCTGGT 10 57 1 GCGCGAAGCA 0.862957 -42 TCGCGCGTGACTGAAATCACAA 11 3 1 GCGCGTGACT 0.981976 -237 GTGTGCCTCAGCACGTGACTTCACCGTCTG 11 187 0 GCACGTGACT 0.945654 -53 TACTGGGATGGGCCGTGGCGTGGCTGCATT 12 24 0 GGCCGTGGCG 0.871577 -224 ACCCCGGCGTGCCCGAGGCGTGCCAGACTC 13 50 1 GCCCGAGGCG 0.975525 -26 CCCGATTCCGGCGCAGCACGTGCTCGGACT 14 47 1 GCGCAGCACG 0.81032 -207 CGCCAAACCGGCACGGGACACCGCACCGCC 14 139 1 GCACGGGACA 0.958935 -115 GCCGTGCTCTGCGCAAAACGCCGTAGGCCA 14 188 1 GCGCAAAACG 0.820369 -66 ATTCCGGTGAGCGCGTGGCCTACGGCGTTT 14 203 0 GCGCGTGGCC 0.981291 -51 CACGCGGCTTGCGCGTGACGGGCCGCCGTT 18 47 1 GCGCGTGACG 0.995965 -109 GAGGCTCAGAGGGCGGGACGG 18 145 1 GGGCGGGACG 0.979487 -11 ********** Masking position 1 Map Score: 28.2908 Number of sites scoring better than the average of aligned sites = 4933 Number in coding regions = 4535 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 5 TCTTGCGCAAGGTCTTGGGGTGACTGACCG 1 35 0 GGTCTTGGGG 0.922481 -79 GTAGGAGCCGTGGTAGGGGGCCGCGCCCAC 2 18 0 TGGTAGGGGG 0.600015 -57 TTGCCAGATCGGTCAGGCGGACTCCGGCCG 5 19 0 GGTCAGGCGG 0.968692 -282 GGGCGCTGCCGGTTTGGTGTTCCGTGCGAC 5 54 1 GGTTTGGTGT 0.705958 -247 TAGATGGCGGGGTCATGGGTTCAGTAATCA 5 118 1 GGTCATGGGT 0.671031 -183 CGTGACGGTCGAGCTGGCGGGGTCTGCTCG 5 238 0 GAGCTGGCGG 0.811817 -63 ACAGCCTAACGGCCAGGCGAAACGGCGGCG 5 277 0 GGCCAGGCGA 0.698379 -24 CGCGGTAGGGCGGTTGGCGGCCAGGCCTCG 6 47 0 CGGTTGGCGG 0.852585 -109 AGGCAATCCCGTTCTGGGGTCTGAGGACAA 6 77 0 GTTCTGGGGT 0.703054 -79 CCCAATCGTTGGTTTTGGGGCGGCTCGCCG 7 33 0 GGTTTTGGGG 0.919826 -96 AGCAGGAGGCGGGTTTGGGAGGCGAGAAAG 10 23 0 GGGTTTGGGA 0.838383 -76 GCAGGAGGCTGGTTTGGGTAAATTAACTGT 10 74 1 GGTTTGGGTA 0.820114 -25 GATGGCAGAGGTTTTGGCGACCGTTACTGG 12 48 0 GTTTTGGCGA 0.719207 -200 GGGCACGCCGGGGTTGGCTACCCGACAGGG 13 34 0 GGGTTGGCTA 0.853391 -42 GTCCCGTGCCGGTTTGGCGTGCCCAGTTTT 14 128 0 GGTTTGGCGT 0.964888 -126 CGGGTAATGTGGGTTGGCGGTGCGGTGTCC 14 154 0 GGGTTGGCGG 0.987451 -100 GTTAAGGCTCGGTTAGGGTTTGATCC 15 57 1 GGTTAGGGTT 0.662912 -16 AGGGAAGCCCGGGCGGGCTGGGACGTCTAG 17 37 0 GGGCGGGCTG 0.705569 -53 ********** Masking position 7 Map Score: 14.6629 Number of sites scoring better than the average of aligned sites = 9501 Number in coding regions = 8788 Number in noncoding regions = 713 Number of orfs with sites within 600 bp upstream = 519 Fraction of orfs with sites within 600 bp upstream = 0.0833601 Motif number 6 GCCGATAATAGTTTGACTGACTCGGTCAGT 1 13 1 GTTTGACTGA 0.634385 -101 CAAGGTCTTGGGGTGACTGACCGAGTCAGT 1 28 0 GGGTGACTGA 0.868533 -86 GCTCCTACCGGCGCCCCTGAAACACCAGAC 2 40 1 GCGCCCCTGA 0.944061 -35 AGGTGGCGTCGCGGCCCTCACCGGCGACAC 7 85 1 GCGGCCCTCA 0.869707 -44 TCGCGCGTGACTGAAATCACAACT 11 5 1 GCGTGACTGA 0.980776 -235 CGCGTCCATAGCTGGCCAGATCCACCAGAA 11 91 0 GCTGGCCAGA 0.884926 -149 CTCGGGTGGTGTGTGCCTCAGCACGTGACT 11 197 0 GTGTGCCTCA 0.839675 -43 GCCAACCCCGGCGTGCCCGAGGCGTGCCAG 13 46 1 GCGTGCCCGA 0.975894 -30 CGTGCCCGAGGCGTGCCAGACTCAAACAC 13 57 1 GCGTGCCAGA 0.989199 -19 CACCAGCCGCGCGTCCAAGAATTCATCAAG 16 13 1 GCGTCCAAGA 0.868917 -48 GCCCGCCCGGGCTTCCCTGAGCCATGTCAC 17 49 1 GCTTCCCTGA 0.946989 -41 CGCGCAAGCCGCGTGAAAGAAGCCGGTCGG 18 32 0 GCGTGAAAGA 0.806923 -124 ********** Masking position 10 Map Score: 12.8023 Number of sites scoring better than the average of aligned sites = 1875 Number in coding regions = 1702 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 7 ATTGCCAGATCGGTCAGGCGGACTCCGGCC 5 20 0 CGGTCAGGCG 0.884127 -281 TCTACCCGGGCGGTCGCACGGAACACCAAA 5 66 0 CGGTCGCACG 0.67797 -235 GTATAGATGGCGGGGTCATGGGTTCAGTAA 5 115 1 CGGGGTCATG 0.542253 -186 GATGCTTTTTCTTGGACATGCGCTTGCGCC 5 154 0 CTTGGACATG 0.417916 -147 GCCAGCTCGACCGTCACGCGCTTGTAACGC 5 250 1 CCGTCACGCG 0.975919 -51 TCGTGACCTCCGAGGACGTGCGTTCATTAG 6 126 1 CGAGGACGTG 0.850639 -30 CGTTCACACGATAACCCGCA 8 91 0 CGTTCACACG 0.775373 -10 GTTGTGATTTCAGTCACGCGCGA 11 4 0 CAGTCACGCG 0.910715 -236 AGTCACCGTCCGGTCACGTTACGGCAAAAA 11 58 1 CGGTCACGTT 0.740866 -182 GTCCGCTCGTCGGGCTCGTCTAGAGCCGAC 12 149 0 CGGGCTCGTC 0.857915 -99 GGATAGCGCCCTGGGACGTGGTATGTACCG 12 202 1 CTGGGACGTG 0.964114 -46 TGGCACGCCTCGGGCACGCCGGGGTTGGCT 13 45 0 CGGGCACGCC 0.991343 -31 GTGTTTGAGTCTGGCACGCCTCGGGCACGC 13 56 0 CTGGCACGCC 0.980531 -20 GTTTGTAGTCCGAGCACGTGCTGCGCCGGA 14 53 0 CGAGCACGTG 0.928835 -201 TTTTCAAAACTGGGCACGCCAAACCGGCAC 14 123 1 TGGGCACGCC 0.819989 -131 GCACGCCAAACCGGCACGGGACACCGCACC 14 136 1 CCGGCACGGG 0.911068 -118 TTGATGAATTCTTGGACGCGCGGCTGGTGT 16 12 0 CTTGGACGCG 0.917904 -49 CCCGGGCGGGCTGGGACGTCTAGGACACCC 17 30 0 CTGGGACGTC 0.901763 -60 CGACCGGCTTCTTTCACGCGGCTTGCGCGT 18 33 1 CTTTCACGCG 0.908244 -123 CAACGGCGGCCCGTCACGCGCAAGCCGCGT 18 48 0 CCGTCACGCG 0.975919 -108 CATGCTGCCGCTGGTACGCGGCCGTTGCCA 18 92 0 CTGGTACGCG 0.892902 -64 ********** Masking position 1 Map Score: 28.894 Number of sites scoring better than the average of aligned sites = 8208 Number in coding regions = 7499 Number in noncoding regions = 709 Number of orfs with sites within 600 bp upstream = 551 Fraction of orfs with sites within 600 bp upstream = 0.0884998 Motif number 8 CACGCCGGTGGGCGCGGCCCCCTACC 2 3 1 CCCGGGGCCG 0.987795 -72 TCGCAAGCTGCTGCGTCGCACCCGGGTGCAGCGC 5 182 1 CGCGTGACCG 0.989503 -119 AACCGCCCTACCGCGTTGTCCTCAGACCCCAGAA 6 62 1 CGCGTGCCCA 0.947345 -94 GAACGCACGTCCTCGGAGGTCACGACGGTCCCGA 6 117 0 CTCGGGTCCG 0.81678 -39 CCCAAAACCAACGATTGGGCCACGATGCGTAGGC 7 44 1 AGATTGCCCG 0.203708 -85 GACGCCACCTCAGCTATGCCTACGCATCGTGGCC 7 61 0 CGCTAGCTCG 0.737623 -68 GTGGTGTCGCCGGTGAGGGCCGCGACGCCACCTC 7 84 0 CGTGAGCCCG 0.82157 -45 CCGGCGACACCACAGAGGATCTCGGGCCGATCCG 7 105 1 CCAGAGTCCG 0.77608 -24 CGCCTACACCCGCCGGAGAACCTGGATAAGGTCG 9 11 1 CCCGGGACTG 0.734791 -28 AACCAGCCTCCTGCTTCGCGCGCTGAGCAGCGGG 10 54 0 CGCTTGGCCT 0.817386 -45 TGGATCTGGCCAGCTATGGACGCGGCCGGCATCT 11 97 1 CGCTAGACCG 0.94722 -143 GGGTTGTAACCTCCTTGGCACTCTCGGGTGGTGT 11 215 0 CCCTTGACCT 0.776621 -25 GGGTAGCCAACCCCGGCGTGCCCGAGGCGTGCCA 13 41 1 CCCGGGGCCG 0.987793 -35 GGTGGAAATTCCGCGAAGGGCTCCGAGAAATTTT 14 93 1 CGCGAGGCCC 0.840559 -161 TTACCCGCATCGCCGTGCTCTGCGCAAAACGCCG 14 177 1 CCCGTCCTCG 0.503838 -77 CTGCGCAAAACGCCGTAGGCCACGCGCTCACCGG 14 196 1 CCCGTGCCCG 0.994482 -58 GCCAGCCACCTTAGAACTCGGGTGTCCTAG 17 7 1 CCCTTGACCG 0.972102 -83 TATAGCCGACCGGCTTCTTTCACGCGGCTTGCGC 18 27 1 CGCTTTTCCG 0.569153 -129 CGTGACGGGCCGCCGTTGATCTCAAGATCGGCTG 18 60 1 CCCGTGTCCA 0.884765 -96 * **** * ** ** Masking position 13 Map Score: 17.4666 Number of sites scoring better than the average of aligned sites = 15666 Number in coding regions = 14865 Number in noncoding regions = 801 Number of orfs with sites within 600 bp upstream = 584 Fraction of orfs with sites within 600 bp upstream = 0.0938002 Motif number 9 TCAGGCGGACTCCGGCCGCGTGCGGC 5 7 0 TCCGGCCGCG 0.908094 -294 GGCGGGGTCTGCTCGCAACCTATTTGCCCA 5 223 0 GCTCGCAACC 0.892673 -78 AGGCCTGGCCGCCAACCGCCCTACCGCGTT 6 49 1 GCCAACCGCC 0.748854 -107 TTTTGGGGCGGCTCGCCGCGCCGCCGGGAG 7 21 0 GCTCGCCGCG 0.987756 -108 CGTGCTGATTGCCCGCCTCTTCGTTGGCGC 8 60 0 GCCCGCCTCT 0.92687 -41 TCACACGATAACCCGCAGCGTGCTGATTGC 8 78 0 ACCCGCAGCG 0.975506 -23 CCGCTTGCTTTCTCGCCTCCCAAACCCGCC 10 16 1 TCTCGCCTCC 0.76093 -83 CGCCTCCCAAACCCGCCTCCTGCTTCCCGC 10 29 1 ACCCGCCTCC 0.974298 -70 ATTTACCCAAACCAGCCTCCTGCTTCGCGC 10 67 0 ACCAGCCTCC 0.923235 -32 GACAACAGATGCCGGCCGCGTCCATAGCTG 11 107 0 GCCGGCCGCG 0.989175 -133 GGGATTCGGTGCCAGCATCGGGCTGAGTGT 12 118 0 GCCAGCATCG 0.959307 -130 CCAGGGCGCTATCCGCAGCGTGAGTACCCG 12 186 0 ATCCGCAGCG 0.746087 -62 TTTGAGTCTGGCACGCCTCGGGCACGCCGG 13 53 0 GCACGCCTCG 0.950495 -23 AACCCACATTACCCGCATCGCCGTGCTCTG 14 169 1 ACCCGCATCG 0.956116 -85 GACCAGTTGGGTTCGCAACCCTCCGTTTCG 15 14 0 GTTCGCAACC 0.380284 -59 GACACCAGCCGCGCGTCCAAGAA 16 4 1 ACCAGCCGCG 0.970346 -57 CAGTGTCAGCCCGCACCCTTGCCGGATC 16 43 0 GCCCGCACCC 0.929874 -18 GCCAGCCACCTTAGAACTCG 17 1 1 GCCAGCCACC 0.96751 -89 CCCGTCACGCGCAAGCCGCGTGAAAGAAGC 18 39 0 GCAAGCCGCG 0.917593 -117 ATCAACGGCGGCCCGTCACGCGCAAGCCGC 18 50 0 GCCCGTCACG 0.847533 -106 CTCAAGATCGGCTGGCAACGGCCGCGTACC 18 80 1 GCTGGCAACG 0.764129 -76 ********** Masking position 9 Map Score: 39.5882 Number of sites scoring better than the average of aligned sites = 13374 Number in coding regions = 12479 Number in noncoding regions = 895 Number of orfs with sites within 600 bp upstream = 620 Fraction of orfs with sites within 600 bp upstream = 0.0995824 Motif number 10 TGGCTCCTAACTGCCGTTCGCCGACC 4 7 0 CTGCCGTTCG 0.762787 -23 CCTGACCGATCTGGCAATGCTCGGGCGCTG 5 32 1 CTGGCAATGC 0.791302 -269 TGGCAATGCTCGGGCGCTGCCGGTTTGGTG 5 43 1 CGGGCGCTGC 0.951893 -258 GACGCAGCAGCTTGCGATGCTTTTTCTTGG 5 169 0 CTTGCGATGC 0.831568 -132 TGCCCAGTTTCCTGCGCTGCACCCGGGTGC 5 199 0 CCTGCGCTGC 0.658795 -102 GCTTGTAACGCCGCCGTTTCGCCTGGCCGT 5 269 1 CCGCCGTTTC 0.737088 -32 CCTCCGAGGACGTGCGTTCATTAGAGGACG 6 132 1 CGTGCGTTCA 0.701638 -24 AGAGGATCTCGGGCCGATCCG 7 118 1 GGGCCGATCC 0.827022 -11 GACACAGCCCCGGCCGTCCCGCGCGAGCGC 8 23 1 CGGCCGTCCC 0.860878 -78 AACGAAGAGGCGGGCAATCAGCACGCTGCG 8 65 1 CGGGCAATCA 0.66924 -36 GAAATCACAACTGCCGATCAAAGATTGAGC 11 23 1 CTGCCGATCA 0.921311 -217 CGGCAGTCACCGTCCGGTCACGTTACGGCA 11 54 1 CGTCCGGTCA 0.526138 -186 ACTTCACCGTCTGCCATTCCAGCCGGAAGT 11 170 0 CTGCCATTCC 0.819014 -70 AGCCACGCCACGGCCCATCCCAGTAACGGT 12 29 1 CGGCCCATCC 0.827051 -219 GTAGCCAACCCCGGCGTGCCCGAGGCGTGC 13 43 1 CCGGCGTGCC 0.781544 -33 TACTTTCTGGCGATCCTTCTCTTCCT 14 7 1 CTGGCGATCC 0.975075 -247 GTAATGTGGGTTGGCGGTGCGGTGTCCCGT 14 151 0 TTGGCGGTGC 0.50386 -103 TGCGCAGAGCACGGCGATGCGGGTAATGTG 14 173 0 ACGGCGATGC 0.604606 -81 GCGTGACGGGCCGCCGTTGATCTCAAGATC 18 59 1 CCGCCGTTGA 0.89739 -97 CGCTGGTACGCGGCCGTTGCCAGCCGATCT 18 84 0 CGGCCGTTGC 0.980633 -72 GGTTCACCGTTTGCCGATGAGGCTCAGAGG 18 127 1 TTGCCGATGA 0.441952 -29 ********** Masking position 5 Map Score: 16.2564 Number of sites scoring better than the average of aligned sites = 20809 Number in coding regions = 19517 Number in noncoding regions = 1292 Number of orfs with sites within 600 bp upstream = 869 Fraction of orfs with sites within 600 bp upstream = 0.139576 Motif number 11 ********** No masking Map Score: -3.3087e-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: -3.3087e-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: -3.3087e-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