AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mtub_reg_100.orf -o00051_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 gca 281 gca #2 fba 95 fba #3 Rv0728c 30 hypothetical protein Rv0728c #4 rpmE 150 rpmE #5 prfA 89 prfA #6 rfe 83 rfe #7 gap 300 gap #8 gmdA 300 gmdA #9 Rv1895 300 hypothetical protein Rv1895 #10 hspX 196 hspX #11 murE 22 murE #12 hypothetical 267 hypothetical protein Rv2160c #13 pfkA 95 pfkA #14 gatC 84 gatC #15 pmmA 101 pmmA #16 deoD 64 deoD #17 mrsA 124 mrsA Motif number 1 GTAACCGTTTGACGAGCCGCGGCCTCGCTG 1 102 1 GACGAGCCGC 0.933245 -180 TACAAACCCAGACGTGCGGGCTTCAATGTT 1 134 0 GACGTGCGGG 0.629181 -148 GCGCCAGATCGGGGAGCGCCCTCGTTGTGT 1 167 0 GGGGAGCGCC 0.701316 -115 CACCTCGTTGCGCGCGCCAGATCGGGGAGC 1 180 0 CGCGCGCCAG 0.709165 -102 TTGATGCTCAGGCCGGTGCGGTTTGTCGAG 1 241 1 GGCCGGTGCG 0.455547 -41 TGCTGGCGTACGGTGGCGCCC 3 2 0 CGGTGGCGCC 0.885221 -29 CCGGCGAGCCGTCTCGCCGGA 4 2 0 GTCTCGCCGG 0.709809 -149 CCGGCGAGACGGCTCGCCGGGAATGTCCGC 4 12 1 GGCTCGCCGG 0.964969 -139 CGCCCGTCGTGGCGTGCCGAGAACCTGGTC 4 109 0 GGCGTGCCGA 0.882296 -42 CCTCTGTGATCGGTGGCCGCCCGTCGTGGC 4 126 0 CGGTGGCCGC 0.985476 -25 GTGCACAGTTCGGGCGTCGGTAAGCCAG 5 9 0 CGGGCGTCGG 0.882784 -81 CGGTACAGGACGGGCGTCGGTTCGCGTTAG 5 42 1 CGGGCGTCGG 0.882784 -48 TTAGGGTCCGCGCTCGCGGGAAGAAGGTTG 5 68 1 CGCTCGCGGG 0.948414 -22 GAGAGCTGAACACTCGCCGAACGTGCAACA 6 58 0 CACTCGCCGA 0.876499 -26 GGGAACATGAGCCCCGCCGCACCGGGCCGT 7 64 1 GCCCCGCCGC 0.891265 -237 CCACCGATCCCAGCCGCCGCGTCCCTACCG 7 142 0 CAGCCGCCGC 0.938268 -159 CTCAAAGCGAGGGGAGCCCCGGGACTCTTA 7 188 1 GGGGAGCCCC 0.800395 -113 AGATCAGTGACACCCGCCGCCTTCGGCCGG 7 218 0 CACCCGCCGC 0.958691 -83 CCGCGCGAAACGGCCGCAGGCGCAATGGTC 8 121 1 CGGCCGCAGG 0.942783 -180 AGGCTAGACTCCACCGCGGCCAAGTTGGTG 8 150 0 CCACCGCGGC 0.543497 -151 TCCTGGTTGTCGGGGGCGACCAGGAAAATG 8 182 0 CGGGGGCGAC 0.853988 -119 CCATCACAGCGGGGCGCCGCTGTCGCTTCA 8 251 0 GGGGCGCCGC 0.514599 -50 TGGTGGAACAGAGTGGTCGCCTGGTCGTGG 9 29 0 GAGTGGTCGC 0.50119 -272 GTCCATCGCCCCGGGGCCGATTGAGGGTTG 9 107 0 CCGGGGCCGA 0.923332 -194 ATCCGCTGGGGCCCCGCCGGTAGCCTAGTG 9 141 1 GCCCCGCCGG 0.878238 -160 CGTGGTGAACGGCGGGCCGGCAATTCCGAG 9 194 0 GGCGGGCCGG 0.97205 -107 TCGCGTACCTGCCTGGCACCGGTCTCGGGC 9 231 0 GCCTGGCACC 0.547844 -70 GGATCACCGACGGGCGCGGACAAATGGCCC 10 90 1 CGGGCGCGGA 0.862262 -107 AGAAGTCCCCGAAGCGCGGGCCATTTGTCC 10 107 0 GAAGCGCGGG 0.649807 -90 CTGTCCCTAGCCCTGGCCACGATGGGCTGG 10 135 1 CCCTGGCCAC 0.659346 -62 GGCCACGATGGGCTGGTCGGATCAAAGGCA 10 149 1 GGCTGGTCGG 0.890424 -48 CTACCGACAGGGCGCGCACAC 11 2 0 GGCGCGCACA 0.841816 -21 CGCCGACGTCGGCCGCCAAACCCGGG 12 7 1 CGTCGGCCGC 0.702506 -261 CCGCCAAACCCGGGCGCAGATCCTGCGCGC 12 23 1 CGGGCGCAGA 0.937359 -245 TATCCATCGCGGCGCGCAGGATCTGCGCCC 12 34 0 GGCGCGCAGG 0.806803 -234 TGGACAGCCCCGAGAGCCCCTTCACCGAGG 12 67 0 CGAGAGCCCC 0.678886 -201 CGGCGAGCTTGCCGGGCGGCTGGGCATGAG 12 98 1 GCCGGGCGGC 0.867327 -170 GCGGCCTCGACGGTCGCCAGCTGCAGCTGC 12 164 0 CGGTCGCCAG 0.870126 -104 GCTGCCATCGCGGGAGCCACGACCTCGGCT 12 209 0 CGGGAGCCAC 0.828707 -59 GTGGCTCCCGCGATGGCAGCGCCGCCCGGG 12 219 1 CGATGGCAGC 0.641222 -49 CCCGGTCCACCCCGGGCGGCGCTGCCATCG 12 229 0 CCCGGGCGGC 0.880822 -39 CATGCATGAGGGCGCGCACCCGGTCCACCC 12 247 0 GGCGCGCACC 0.637041 -21 CGGCGAGCAGACACAGACTCG 13 2 1 GGCGAGCAGA 0.830004 -94 GCACGGGCGAGGGGCGCCGGATGCGAGTCT 13 25 0 GGGGCGCCGG 0.512494 -71 CGGCGCCCCTCGCCCGTGCGATTCTGTGTC 13 36 1 CGCCCGTGCG 0.588684 -60 GCCGACCTGGCGCGAGCAGACACAGAATCG 13 54 0 CGCGAGCAGA 0.848502 -42 CAGGTCGGCGGCCGCGCGGCAAGATGAGGG 13 75 1 GCCGCGCGGC 0.499665 -21 CACGGCGTTTCGGCAGCCGGCGTCGGCCGT 14 39 1 CGGCAGCCGG 0.950002 -46 AAAGCCTAATGGGTGGCCGGACGGCCGACG 14 59 0 GGGTGGCCGG 0.981169 -26 CCGCGAACGACGCGGGCCGAATCGGTCTCG 15 26 0 CGCGGGCCGA 0.987081 -76 CCGCGTCGTTCGCGGGCCGATAGGCTGGCG 15 41 1 CGCGGGCCGA 0.987081 -61 CGGGCCGATAGGCTGGCGGCCAAGAGTCGC 15 53 1 GGCTGGCGGC 0.974795 -49 TGGCGGCCAAGAGTCGCAGAAAATCTAGGT 15 66 1 GAGTCGCAGA 0.459644 -36 TCTAGGTTGTCAGGAGCCCGCGC 15 89 1 CAGGAGCCCG 0.710116 -13 GTATCTCATCGACGAGCACCCGCTCCCCGG 16 18 1 GACGAGCACC 0.437755 -47 TTAACTGAGCCGCTCGCCGGGGAGCGGGTG 16 34 0 CGCTCGCCGG 0.96903 -31 CAAACATGCACGCTTGTCGCCCGAAAGTGA 17 13 0 CGCTTGTCGC 0.541323 -112 TGTTTGTGTGCGCTCGTCGGCGTGTCGGTG 17 37 1 CGCTCGTCGG 0.93289 -88 ********** Masking position 6 Map Score: 95.853 Number of sites scoring better than the average of aligned sites = 75787 Number in coding regions = 70605 Number in noncoding regions = 5182 Number of orfs with sites within 600 bp upstream = 1560 Fraction of orfs with sites within 600 bp upstream = 0.250562 Motif number 2 TCCAGGGTTACCGTCGCGCTCATCCGGAGCAC 1 19 0 CCGCGCGCCA 0.969082 -263 TGACGAGCCGCGGCCTCGCTGCAAACATTGAA 1 111 1 CGGCTCGCGC 0.796305 -171 ATTTACACAACGAGGGCGCTCCCCGATCTGGC 1 163 1 CGAGGCGCCC 0.756827 -119 TCCCAACATACCGGCCATCACGCACAGGCCGA 2 15 1 CCGCCATCCG 0.758669 -81 CACGCACAGGCCGACAAGCTCGGTTGCGGTGT 2 33 1 CCGCAAGCCG 0.950873 -63 CCACCGTACGCCAGCATTGGCAAAC 3 16 1 CCACATTGCA 0.371206 -15 TCCCGGCGAGCCGTCTCGCCGGA 4 2 0 CCGCTCGCGG 0.737878 -149 AGACGGCTCGCCGGGAATGTCCGCACGCATCT 4 18 1 CCGGAATGCC 0.839609 -133 GCACGCATCTCGGTGTTTGGGGTGATAGCGGT 4 40 1 CGGGTTTGGG 0.435817 -111 TCGTGGCGTGCCGAGAACCTGGTCCGGTTCCA 4 101 0 CCGGAACCGG 0.836358 -50 TCTCGGCACGCCACGACGGGCGGCCACCGATC 4 117 1 CCAGACGGCG 0.806183 -34 CGACGGGCGGCCACCGATCACAGAGGGCAGC 4 130 1 CCACGATCCA 0.671433 -21 AACCTTCTTCCCGCGAGCGCGGACCCTAACGC 5 65 0 CCGGAGCGGG 0.462083 -25 CCGCCGAACGTGCACGCACTGCGAAG 6 5 1 CGACGTGCCG 0.839805 -79 AACATGAGCCCCGCCGCACCGGGCCGTTTCCA 7 67 1 CCGCGCACGG 0.583097 -234 GTCCCTACCGCGGACATTGCGCTGGCTTGTGA 7 120 0 CGGCATTGGC 0.65297 -181 CCGATCCCAGCCGCCGCGTCCCTACCGCGGAC 7 137 0 CCGCGCGTCC 0.686509 -164 GGCGCTCACCCCACCGATCCCAGCCGCCGCGT 7 150 0 CCACGATCCA 0.671368 -151 TTTGAGAAGCCGGGCGCTCACCCCACCGATCC 7 162 0 CGGCGCTCCC 0.927075 -139 GGTAAGAGTCCCGGGGCTCCCCTCGCTTTGAG 7 188 0 CCGGGCTCCC 0.955024 -113 GTGACACCCGCCGCCTTCGGCCGGTAAGAGTC 7 210 0 CCGCTTCGCC 0.866033 -91 GGTTTTGTTCCCAAGTTGGTCGTGGCTGTGCG 8 39 1 CCAGTTGGCG 0.650718 -262 TCGCGCGGAACCGAGGAGGAGAATCCATACGA 8 97 0 CCGGGAGGGA 0.876701 -204 GCAATGGTCACCAACTTGGCCGCGGTGGAGTC 8 142 1 CCACTTGGCG 0.689346 -159 CTGGTCGCCCCCGACAACCAGGAGGTCGCTGC 8 189 1 CCGCAACCGG 0.920531 -112 TGTCTTCCCGCCTCTGTCGGTCATGCTCA 8 282 0 CCGCTCTGCG 0.908157 -19 GCCAAAGTGTCCGACAACCACGACCAGGCGAC 9 12 1 CCGCAACCCG 0.942775 -289 TTCCACCACGCGATCGATCACCCAACCGTGAC 9 51 1 CGACGATCCC 0.666683 -250 GATCACCCAACCGTGACCGTGCAGCAGACCTA 9 66 1 CCGGACCGGC 0.847415 -235 GGATCAAGGTCCATCGCCCCGGGGCCGATTGA 9 113 0 CCACGCCCGG 0.738818 -188 CACTAGGCTACCGGCGGGGCCCCAGCGGATCA 9 139 0 CCGCGGGGCC 0.951918 -162 GCCGGCAATTCCGAGACTCGGCATAGCGTAAT 9 177 0 CCGGACTCGC 0.850279 -124 AATTGCCGGCCCGCCGTTCACCACGTTCAAAC 9 199 1 CCGCGTTCCC 0.964134 -102 TGCCTGGCACCGGTCTCGGGCGTTTGAACGTG 9 220 0 CGGCTCGGCG 0.896759 -81 TGTCTGCCAACCGCCGTTCAGAAAGATCGGGG 10 36 0 CCGCGTTCGA 0.850113 -161 AAGTGGATCACCGACGGGCGCGGACAAATGGC 10 86 1 CCGCGGGCCG 0.970347 -111 GACAAATGGCCCGCGCTTCGGGGACTTCTGTC 10 108 1 CCGGCTTCGG 0.481394 -89 TCCGACCAGCCCATCGTGGCCAGGGCTAGGGA 10 138 0 CCACGTGGCA 0.791518 -59 CCTACCGACAGGGCGCGCACAC 11 7 0 CCGCAGGGGC 0.860162 -16 GGTTTGGCGGCCGACGTCGGCG 12 1 0 CCGCGTCGCG 0.970634 -267 GGATCTGCGCCCGGGTTTGGCGGCCGACGTCG 12 14 0 CCGGTTTGCG 0.789001 -254 GAGGCGATATCCATCGCGGCGCGCAGGATCTG 12 39 0 CCACGCGGGC 0.934103 -229 GATATCGCCTCGGTGAAGGGGCTCTCGGGGCT 12 60 1 CGGGAAGGGC 0.723702 -208 GCCCAGCCGCCCGGCAAGCTCGCCGATGGACA 12 91 0 CCGCAAGCCG 0.660722 -177 CGGAACAGGCCCGACTTGCTCATGCCCAGCCG 12 114 0 CCGCTTGCCA 0.826753 -154 CATTTCGGCGCCAAGGAGCAGCTGCAGCTGGC 12 147 1 CCAGGAGCGC 0.851894 -121 CAGCTGGCGACCGTCGAGGCCGCCGTGAGCGT 12 171 1 CCGCGAGGCG 0.949439 -97 ACCTCGGCTTCGAACACGCTCACGGCGGCCTC 12 186 0 CGACACGCCA 0.428723 -82 GTGTTCGAAGCCGAGGTCGTGGCTCCCGCGAT 12 201 1 CCGGGTCGGG 0.882739 -67 GCAGCGCCGCCCGGGGTGGACCGGGTGCGCGC 12 234 1 CCGGGTGGCC 0.966291 -34 CAGAATCGCACGGGCGAGGGGCGCCGGATGCG 13 30 0 CGGCGAGGGC 0.933821 -66 TGCCGCGCGGCCGCCGACCTGGCGCGAGCAGA 13 64 0 CCGCGACCGG 0.577422 -32 GGCCAACACTGTGGCACAACGATG 14 3 1 CCACACTGGG 0.743147 -82 GATGTATCCACGGCGTTTCGGCAGCCGGCGTC 14 31 1 CGGGTTTCGC 0.400637 -54 GGTGGCCGGACGGCCGACGCCGGCTGCCGAAA 14 46 0 CGGCGACGCG 0.523626 -39 GCCTATCGGCCCGCGAACGACGCGGGCCGAAT 15 34 0 CCGGAACGCG 0.876247 -68 CACCCGCTCCCCGGCGAGCGGCTCAGTTAAGC 16 34 1 CCGCGAGCGC 0.981509 -31 CACCGACACGCCGACGAGCGCACACAAACATG 17 35 0 CCGCGAGCCA 0.957961 -90 *** ***** ** Masking position 1 Map Score: 92.6215 Number of sites scoring better than the average of aligned sites = 90542 Number in coding regions = 85562 Number in noncoding regions = 4980 Number of orfs with sites within 600 bp upstream = 1546 Fraction of orfs with sites within 600 bp upstream = 0.248314 Motif number 3 GTTTGACGAGCCGCGGCCTCGCTGCAAACAT 1 108 1 CCGCGGCCCG 0.868537 -174 GATCTGGCGCGCGCAACGAGGTGCGCACTAT 1 187 1 GCGCAACGGG 0.493773 -95 TGCGGTTTGTCGAGAAAGGCGAATAGGAACA 1 257 1 CGAGAAAGCG 0.824647 -25 ACGCACAGGCCGACAAGCTCGGTTGCGGTGT 2 34 1 CGACAAGCCG 0.973529 -62 CGTGGCGTGCCGAGAACCTGGTCCGGTTCCA 4 101 0 CGAGAACCGG 0.916277 -50 ACCTTCTTCCCGCGAGCGCGGACCCTAACGC 5 65 0 CGCGAGCGGG 0.919176 -25 CCGCCGAACGTGCACGCACTGC 6 2 1 CGCCGAACTG 0.704323 -82 GCTGAACACTCGCCGAACGTGCAACAGCTGC 6 53 0 CGCCGAACTG 0.704323 -31 CTCAAAGCGAGGGGAGCCCCGGGACTCTTAC 7 188 1 GGGGAGCCCG 0.931976 -113 GACTCTTACCGGCCGAAGGCGGCGGGTGTCA 7 210 1 GGCCGAAGCG 0.864234 -91 CTCCAATCCCGCACAGCCACGACCAACTTGG 8 49 0 GCACAGCCCG 0.856397 -252 TTGGAGGTGGCGTGGGGGTCGCGTCGTATGG 8 74 1 CGTGGGGGCG 0.676878 -227 TGGTTGTCGGGGGCGACCAGGAAAATGTGAG 8 178 0 GGGCGACCGG 0.896873 -123 TGGTCGCCCCCGACAACCAGGAGGTCGCTGC 8 190 1 CGACAACCGG 0.953223 -111 TACTATGAAGCGACAGCGGCGCCCCGCTGTG 8 246 1 CGACAGCGCG 0.966981 -55 TGAGCATGACCGACAGAGGCGGGAAGACA 8 282 1 CGACAGAGCG 0.895463 -19 CCAAAGTGTCCGACAACCACGACCAGGCGAC 9 13 1 CGACAACCCG 0.98655 -288 AGGTCCATCGCCCCGGGGCCGATTGAGGGTT 9 108 0 CCCCGGGGCG 0.909831 -193 GTTTGAACGTGGTGAACGGCGGGCCGGCAAT 9 200 0 GGTGAACGCG 0.593414 -101 CAGGCAGGTACGCGAACCTCATGGGTCTCAA 9 246 1 CGCGAACCCA 0.746874 -55 AGTGGATCACCGACGGGCGCGGACAAATGGC 10 87 1 CGACGGGCCG 0.92949 -110 GACAGAAGTCCCCGAAGCGCGGGCCATTTGT 10 109 0 CCCGAAGCCG 0.893427 -88 CGCCGACGTCGGCCGCCAAAC 12 1 1 CGCCGACGCG 0.684114 -267 CGACGTCGGCCGCCAAACCCGGGCGCAGATC 12 14 1 CGCCAAACCG 0.960819 -254 GCTCGCCGATGGACAGCCCCGAGAGCCCCTT 12 75 0 GGACAGCCCG 0.961578 -193 CCCAGCCGCCCGGCAAGCTCGCCGATGGACA 12 91 0 CGGCAAGCCG 0.973629 -177 AACACGCTCACGGCGGCCTCGACGGTCGCCA 12 175 0 CGGCGGCCCG 0.757188 -93 ATCGCGGGAGCCACGACCTCGGCTTCGAACA 12 202 0 CCACGACCCG 0.868635 -66 CCCGGTCCACCCCGGGCGGCGCTGCCATCGC 12 228 0 CCCGGGCGCG 0.680293 -40 TGCATGAGGGCGCGCACCCGGTCCACCCCGG 12 244 0 CGCGCACCGG 0.604728 -24 GAATCGCACGGGCGAGGGGCGCCGGATGCGA 13 29 0 GGCGAGGGCG 0.874816 -67 CGCGCCAGGTCGGCGGCCGCGCGGCAAGATG 13 70 1 CGGCGGCCCG 0.689914 -26 GTGGCCGGACGGCCGACGCCGGCTGCCGAAA 14 46 0 GGCCGACGCG 0.967871 -39 CCTATCGGCCCGCGAACGACGCGGGCCGAAT 15 34 0 CGCGAACGCG 0.976178 -68 AGCCGCTCGCCGGGGAGCGGGTGCTCGTCGA 16 26 0 CGGGGAGCGG 0.856478 -39 CACTTTCGGGCGACAAGCGTGCATGTTTGTG 17 14 1 CGACAAGCTG 0.735084 -111 ACCGACACGCCGACGAGCGCACACAAACATG 17 35 0 CGACGAGCCA 0.660308 -90 ******** ** Masking position 11 Map Score: 65.9327 Number of sites scoring better than the average of aligned sites = 68397 Number in coding regions = 65106 Number in noncoding regions = 3291 Number of orfs with sites within 600 bp upstream = 1239 Fraction of orfs with sites within 600 bp upstream = 0.199004 Motif number 4 TTGAAGCCCGCACGTCTGGGTTTGTATTTA 1 138 1 CACGTCTGGG 0.643982 -144 TTTGTATTTACACAACGAGGGCGCTCCCCG 1 158 1 CACAACGAGG 0.422966 -124 TTGCGCGCGCCAGATCGGGGAGCGCCCTCG 1 173 0 CAGATCGGGG 0.963507 -109 CCTTGATGCTCAGGCCGGTGCGGTTTGTCG 1 239 1 CAGGCCGGTG 0.668553 -43 GCGGTTTGTCGAGAAAGGCGAATAGGAACA 1 258 1 GAGAAAGGCG 0.135725 -24 CGCAACCGAGCTTGTCGGCCTGTGCGTGAT 2 31 0 CTTGTCGGCC 0.412558 -65 CTCGGCACGCCACGACGGGCGGCCACCGAT 4 118 1 CACGACGGGC 0.974663 -33 GGCCACCGATCACAGAGGGCAGC 4 138 1 CACAGAGGGC 0.631532 -13 CGCTGGTGCACAGTTCGGGCGTCGGTAAGC 5 14 0 CAGTTCGGGC 0.892465 -76 ACCAGCGGTACAGGACGGGCGTCGGTTCGC 5 37 1 CAGGACGGGC 0.974667 -53 CGAATCTTCGCAGTGCGTGCACGTTCGGCG 6 12 0 CAGTGCGTGC 0.467684 -72 GGAAACGGCCCGGTGCGGCGGGGCTCATGT 7 68 0 CGGTGCGGCG 0.649664 -233 ATGGTGACGTCACAACGGTGTCACAAGCCA 7 100 1 CACAACGGTG 0.610846 -201 CTTACCGGCCGAAGGCGGCGGGTGTCACTG 7 214 1 GAAGGCGGCG 0.660064 -87 GGCTAGACTCCACCGCGGCCAAGTTGGTGA 8 149 0 CACCGCGGCC 0.766407 -152 GAGGTCGCTGCAGAACGGGCGTTCCCTACC 8 210 1 CAGAACGGGC 0.920003 -91 ACTATGAAGCGACAGCGGCGCCCCGCTGTG 8 247 1 GACAGCGGCG 0.880669 -54 GCTCAGCCATCACAGCGGGGCGCCGCTGTC 8 257 0 CACAGCGGGG 0.975156 -44 GAGCATGACCGACAGAGGCGGGAAGACA 8 283 1 GACAGAGGCG 0.294594 -18 GAGTGGTCGCCTGGTCGTGGTTGTCGGACA 9 19 0 CTGGTCGTGG 0.546236 -282 GCACTAGGCTACCGGCGGGGCCCCAGCGGA 9 142 0 ACCGGCGGGG 0.712857 -159 GAACGTGGTGAACGGCGGGCCGGCAATTCC 9 197 0 AACGGCGGGC 0.873134 -104 GCCGTTCAGAAAGATCGGGGTGATATCGAA 10 26 0 AAGATCGGGG 0.639618 -171 CCCGATCTTTCTGAACGGCGGTTGGCAGAC 10 37 1 CTGAACGGCG 0.723895 -160 TTTGTCCGCGCCCGTCGGTGATCCACTTGG 10 84 0 CCCGTCGGTG 0.659695 -113 AAATGGCCCGCGCTTCGGGGACTTCTGTCC 10 111 1 CGCTTCGGGG 0.609939 -86 TAGCCCTGGCCACGATGGGCTGGTCGGATC 10 142 1 CACGATGGGC 0.460502 -55 CCTACCGACAGGGCGCGCACAC 11 5 0 CAGGGCGCGC 0.87109 -18 TTTGGCGGCCGACGTCGGCG 12 1 0 GACGTCGGCG 0.935071 -267 TGGGCATGAGCAAGTCGGGCCTGTTCCGGC 12 118 1 CAAGTCGGGC 0.82152 -150 CCTGTTCCGGCATTTCGGCGCCAAGGAGCA 12 137 1 CATTTCGGCG 0.397844 -131 CGAACACGCTCACGGCGGCCTCGACGGTCG 12 178 0 CACGGCGGCC 0.985834 -90 GTTCGAAGCCGAGGTCGTGGCTCCCGCGAT 12 203 1 GAGGTCGTGG 0.562603 -65 CCGGTCCACCCCGGGCGGCGCTGCCATCGC 12 228 0 CCGGGCGGCG 0.961667 -40 GCATGCATGAGGGCGCGCACCCGGTCCA 12 250 0 GAGGGCGCGC 0.616778 -18 CTGCTCGCGCCAGGTCGGCGGCCGCGCGGC 13 65 1 CAGGTCGGCG 0.983734 -31 TAATGGGTGGCCGGACGGCCGACGCCGGCT 14 53 0 CCGGACGGCC 0.864127 -32 AACTGAGCCGCTCGCCGGGGAGCGGGTGCT 16 32 0 CTCGCCGGGG 0.831011 -33 ACTGGGCGAGCTTAACTGAGC 16 54 0 CTGGGCGAGC 0.493364 -11 TTTGTGTGCGCTCGTCGGCGTGTCGGTGAA 17 39 1 CTCGTCGGCG 0.930944 -86 ********** Masking position 7 Map Score: 42.1293 Number of sites scoring better than the average of aligned sites = 30607 Number in coding regions = 28685 Number in noncoding regions = 1922 Number of orfs with sites within 600 bp upstream = 1053 Fraction of orfs with sites within 600 bp upstream = 0.169129 Motif number 5 CCGCCGTGTGCTCCGGATGAGCGCGACGGTAAC 1 12 1 CTCGGAGACG 0.947986 -270 CCGCACCGGCCTGAGCATCAAGGAGTCCAGTTC 1 229 0 CTGGCACAGG 0.963926 -53 GCTTGTCGGCCTGTGCGTGATGGCCGGTATGTT 2 19 0 CTGGCGGAGG 0.980431 -77 GATCGGAGTCGTCAGGAGGAACGTTTC 2 79 1 GTCGGAGACG 0.572582 -17 GACGCCCGAACTGTGCACCAGCGGTACAGGACG 5 21 1 CTGGCACACG 0.982801 -69 CGAATCTTCGCAGTGCGTGCACGTTCGGCGG 6 9 0 CAGGCGGCCG 0.701381 -75 GGAACATGAGCCCCGCCGCACCGGGCCGTTTCC 7 65 1 CCCGCCCACG 0.711058 -236 CTGATCTAGGCTGACGGCCAGTGGTTGTTTAGC 7 241 1 CTGCGGCATG 0.655107 -60 TTGGTCGTGGCTGTGCGGGATTGGAGGTGGCGT 8 54 1 CTGGCGGATG 0.962037 -247 GCTGTGATGGCTGAGCATGACCGACAGAGGCGG 8 271 1 CTGGCAGACG 0.988473 -30 GTCCATCGCCCCGGGGCCGATTGAGGGTTGATC 9 104 0 CCGGGCGATG 0.739493 -197 GGCGGGGCCCCAGCGGATCAAGGTCCATCGCCC 9 126 0 CAGGGACAGG 0.825919 -175 CTCACTTTCTTTGTGGCAGAACGAATTGAGACC 9 269 0 TTGGGCGACG 0.866307 -32 GGTGATCCACTTGGGGACCATTGACCCTGTTGT 10 65 0 TTGGGACATG 0.583267 -132 GTCCCTAGCCCTGGCCACGATGGGCTGGTCGGA 10 137 1 CTGCCAGAGG 0.843254 -60 TGCCGGGCGGCTGGGCATGAGCAAGTCGGGCCT 12 107 1 CTGGCAGACA 0.782027 -161 GTTCCGGCATTTCGGCGCCAAGGAGCAGCTGCA 12 140 1 TTCGCGCAGG 0.521959 -128 GGAGCAGCTGCAGCTGGCGACCGTCGAGGCCGC 12 161 1 CAGTGGGACG 0.62654 -107 GGCCAACACTGTGGCACAACGATGTATCCAC 14 9 1 CTGGGCCACG 0.972018 -76 TCTTCCCATGCTGTTCGAGACCGATTCGGCCCG 15 11 1 CTGTCGGACG 0.904294 -91 *** *** ** ** Masking position 10 Map Score: 15.8208 Number of sites scoring better than the average of aligned sites = 8632 Number in coding regions = 8041 Number in noncoding regions = 591 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 6 TTCGCCTTTCTCGACAAACCGCACCGGCCT 1 250 0 TCGACAAACC 0.583379 -32 CACGCACAGGCCGACAAGCTCGGTTGCGGT 2 33 1 CCGACAAGCT 0.448006 -63 CCACCCAGTATCGCAACACCGCAACCGAGC 2 50 0 TCGCAACACC 0.748488 -46 CCTGACGACTCCGATCCACCCAGTATCGCA 2 65 0 CCGATCCACC 0.905196 -31 TCCCGGCGAGCCGTCTCGCCGGA 4 4 0 CCGTCTCGCC 0.760781 -147 CCGCTATCACCCCAAACACCGAGATGCGTG 4 41 0 CCCAAACACC 0.891882 -110 GACCAGGTTCTCGGCACGCCACGACGGGCG 4 109 1 TCGGCACGCC 0.886444 -42 AACATGAGCCCCGCCGCACCGGGCCGTTTC 7 67 1 CCGCCGCACC 0.898811 -234 CCCCACCGATCCCAGCCGCCGCGTCCCTAC 7 144 0 CCCAGCCGCC 0.926111 -157 AGCCGGGCGCTCACCCCACCGATCCCAGCC 7 157 0 TCACCCCACC 0.341779 -144 ACCTCCAATCCCGCACAGCCACGACCAACT 8 52 0 CCGCACAGCC 0.952178 -249 TACGACGCGACCCCCACGCCACCTCCAATC 8 72 0 CCCCCACGCC 0.984355 -229 CCTGGTCGCCCCCGACAACCAGGAGGTCGC 8 188 1 CCCGACAACC 0.656403 -113 CTCGGAATTGCCGGCCCGCCGTTCACCACG 9 194 1 CCGGCCCGCC 0.988146 -107 CCTGTTGTCTGCCAACCGCCGTTCAGAAAG 10 43 0 GCCAACCGCC 0.768873 -154 TGCCTTTGATCCGACCAGCCCATCGTGGCC 10 149 0 CCGACCAGCC 0.972933 -48 CCGACGTCGGCCGCCAAACCCGGGCGCAGA 12 13 1 CCGCCAAACC 0.930967 -255 GCCCCGAGAGCCCCTTCACCGAGGCGATAT 12 61 0 CCCCTTCACC 0.560412 -207 CTTGCTCATGCCCAGCCGCCCGGCAAGCTC 12 102 0 CCCAGCCGCC 0.926111 -166 CTCCTTGGCGCCGAAATGCCGGAACAGGCC 12 135 0 CCGAAATGCC 0.646756 -133 GGGCGCGCACCCGGTCCACCCCGGGCGGCG 12 238 0 CCGGTCCACC 0.852319 -30 CGCATCCGGCGCCCCTCGCCCGTGCGATTC 13 30 1 GCCCCTCGCC 0.677571 -66 ACGCCGGCTGCCGAAACGCCGTGGATACAT 14 32 0 CCGAAACGCC 0.975124 -53 GACCGCAAAGCCTAATGGGTGG 14 73 0 CCGCAAAGCC 0.931247 -12 TGTTGGTTCACCGACACGCCGACGAGCGCA 17 45 0 CCGACACGCC 0.989454 -80 ********** Masking position 2 Map Score: 36.1984 Number of sites scoring better than the average of aligned sites = 13522 Number in coding regions = 12441 Number in noncoding regions = 1081 Number of orfs with sites within 600 bp upstream = 748 Fraction of orfs with sites within 600 bp upstream = 0.120141 Motif number 7 GCGCTCATCCGGAGCACACGGCGGA 1 4 0 GGCACACGGC 0.95807 -278 GGTGCGGTTTGTCGAGAAAGGCGAATAGGAAC 1 255 1 GGAGAAAGGC 0.608003 -27 TGCTCAACGAGTTGGAACCGGACCAGGTTCTC 4 89 1 GGGAACCGGA 0.924835 -62 TTGAGCCGATGGTCGAAAAGGAACTCGATACG 7 16 0 GCGAAAAGGA 0.741376 -285 GACGTCACCATTTGGAAACGGCCCGGTGCGGC 7 79 0 TGGAAACGGC 0.926259 -222 ATGTCCGCGGTAGGGACGCGGCGGCTGGGATC 7 135 1 TGGACGCGGC 0.754432 -166 ATCGGTGGGGTGAGCGCCCGGCTTCTCAAAGC 7 164 1 TGCGCCCGGC 0.835781 -137 CCTCGGTTCCGCGCGAAACGGCCGCAGGCGCA 8 113 1 GCGAAACGGC 0.97524 -188 TGGTTGTCGGGGGCGACCAGGAAAATGTGAGG 8 177 0 GCGACCAGGA 0.664637 -124 GTAGATGTGGGTAGGGAACGCCCGTTCTGCAG 8 217 0 GGGGAACGCC 0.884541 -84 AGCGTAATTCGCAGCACTAGGCTACCGGCGGG 9 153 0 GGCACTAGGC 0.635292 -148 GCGTTTGAACGTGGTGAACGGCGGGCCGGCAA 9 201 0 GGTGAACGGC 0.889515 -100 CACCCCGATCTTTCTGAACGGCGGTTGGCAGA 10 34 1 TCTGAACGGC 0.53684 -163 GTGGATCACCGACGGGCGCGGACAAATGGCCC 10 88 1 GGGGCGCGGA 0.732087 -109 GGATGCCTTTGATCCGACCAGCCCATCGTGGC 10 150 0 GCCGACCAGC 0.492228 -47 CCTCCTAATCGATGGAAACGGATGCCTTTGAT 10 169 0 GGGAAACGGA 0.926259 -28 GCGCCGAAATGCCGGAACAGGCCCGACTTGCT 12 126 0 GGGAACAGGC 0.950773 -142 CGACGCCGGCTGCCGAAACGCCGTGGATACAT 14 32 0 TCGAAACGCC 0.503981 -53 CGTCGTTCGCGGGCCGATAGGCTGGCGGCCAA 15 44 1 GCCGATAGGC 0.642866 -58 GCGTGTCGGTGAACCAACAGGCATATTCGCTG 17 56 1 GCCAACAGGC 0.878789 -69 * ********* Masking position 10 Map Score: 13.0234 Number of sites scoring better than the average of aligned sites = 23761 Number in coding regions = 22326 Number in noncoding regions = 1435 Number of orfs with sites within 600 bp upstream = 879 Fraction of orfs with sites within 600 bp upstream = 0.141182 Motif number 8 TCGTTGCGCGCGCCAGATCGGGGAGCGCCCT 1 175 0 CGCCAGATGG 0.503871 -107 CCGCCGAACGTGCACGCACTG 6 1 1 CCGCCGAAGT 0.744037 -83 TGCGAAGATTCGGCCAATTGTTCGCAGCTGT 6 30 1 CGGCCAATGT 0.898898 -54 CATTTGGAAACGGCCCGGTGCGGCGGGGCTC 7 72 0 CGGCCCGGGC 0.930093 -229 GGACTCTTACCGGCCGAAGGCGGCGGGTGTC 7 209 1 CGGCCGAAGC 0.973714 -92 TCTAGGCTGACGGCCAGTGGTTGTTTAGCCA 7 245 1 CGGCCAGTGT 0.798793 -56 CCGCGCGAAACGGCCGCAGGCGCAATGGTCA 8 121 1 CGGCCGCAGC 0.926434 -180 GACTCCACCGCGGCCAAGTTGGTGACCATTG 8 143 0 CGGCCAAGTG 0.597119 -158 CGCCAAAGTGTCCGACAACCA 9 1 1 CGCCAAAGGT 0.837495 -300 CAAGGTCCATCGCCCCGGGGCCGATTGAGGG 9 110 0 CGCCCCGGGC 0.875671 -191 TTCCGAGACTCGGCATAGCGTAATTCGCAGC 9 170 0 CGGCATAGGT 0.703406 -131 CACGTTCAAACGCCCGAGACCGGTGCCAGGC 9 220 1 CGCCCGAGCC 0.925571 -81 ACCCTGTTGTCTGCCAACCGCCGTTCAGAAA 10 44 0 CTGCCAACGC 0.600013 -153 CATTTGTCCGCGCCCGTCGGTGATCCACTTG 10 85 0 CGCCCGTCGT 0.53527 -112 GGCATTTCGGCGCCAAGGAGCAGCTGCAGCT 12 145 1 CGCCAAGGGC 0.769943 -123 ACCGGGTGCGCGCCCTCATGCATGC 12 253 1 CGCCCTCAGC 0.485437 -15 CAGAATCGCACGGGCGAGGGGCGCCGGATGC 13 31 0 CGGGCGAGGG 0.772208 -65 GCCAGGTCGGCGGCCGCGCGGCAAGATGAGG 13 73 1 CGGCCGCGGG 0.95442 -23 GGTGGCCGGACGGCCGACGCCGGCTGCCGAA 14 47 0 CGGCCGACCC 0.857867 -38 GACCGCAAAGCCTAATGGGTGGC 14 72 0 CCGCAAAGCT 0.153488 -13 GATAGGCTGGCGGCCAAGAGTCGCAGAAAAT 15 59 1 CGGCCAAGGT 0.981626 -43 GCACGCTTGTCGCCCGAAAGTGATG 17 5 0 CGCCCGAAGT 0.932127 -120 GGCATATTCGCTGCCAAGAGTGGATATGTGC 17 75 1 CTGCCAAGGT 0.797633 -50 ******** ** Masking position 1 Map Score: 18.7444 Number of sites scoring better than the average of aligned sites = 15478 Number in coding regions = 14322 Number in noncoding regions = 1156 Number of orfs with sites within 600 bp upstream = 737 Fraction of orfs with sites within 600 bp upstream = 0.118375 Motif number 9 TGAGCCTGTCTAAGTGGTGCGTAACCGTTTGAC 1 82 1 TAAGTGCGTA 0.729638 -200 TCACCTCGAATGGATAGTGCGCACCTCGTTGCG 1 198 0 TGGATGCGCA 0.914532 -84 TGACCTGGCATAATCGATGCTCAACGAGTTGGA 4 72 1 TAAGTGCTCA 0.848468 -79 CAACCTGAGAGCTGAACACTCGCCGAAC 6 66 0 TGAGTGAACA 0.902003 -18 CATAGGATGCTGACAATTGAGCCGATGGTCGAA 7 31 0 TGAATGAGCC 0.919342 -270 GCCAAGTTGGTGACCATTGCGCCTGCGGCCGTT 8 129 0 TGAATGCGCC 0.956803 -172 CGCCCCGCTGTGATGGCTGAGCATGACCGACAG 8 265 1 TGAGTGAGCA 0.986006 -36 CGGGGCCGATTGAGGGTTGATCAGGGAGTAGGT 9 93 0 TGAGTGATCA 0.935417 -208 CTTTCACAGTTGACGGCTGCGCACATATCCACT 17 93 0 TGAGTGCGCA 0.992888 -32 *** * ****** Masking position 8 Map Score: 2.94364 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 533 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 GACAGGCTCATCACAACGACACAGCCAGCA 1 62 0 TCACAACGAC 0.960193 -220 GCTTCAATGTTTGCAGCGAGGCCGCGGCTC 1 115 0 TTGCAGCGAG 0.717157 -167 GTTTGTATTTACACAACGAGGGCGCTCCCC 1 157 1 ACACAACGAG 0.880925 -125 GATCTGGCGCGCGCAACGAGGTGCGCACTA 1 187 1 GCGCAACGAG 0.956259 -95 CATAATCGATGCTCAACGAGTTGGAACCGG 4 80 1 GCTCAACGAG 0.952945 -71 GCCCGGCTTCTCAAAGCGAGGGGAGCCCCG 7 179 1 TCAAAGCGAG 0.817438 -122 GGCTCTCAGCGACAGCTGTCTGA 8 4 1 TCTCAGCGAC 0.952781 -297 CTCCAATCCCGCACAGCCACGACCAACTTG 8 50 0 GCACAGCCAC 0.82955 -251 TGCTCAGCCATCACAGCGGGGCGCCGCTGT 8 258 0 TCACAGCGGG 0.914542 -43 CAACACTGTGGCACAACGATGTATCCACGG 14 14 1 GCACAACGAT 0.833548 -71 GCTCGCAGTATCTCATCGACGAGCACCCGC 16 11 1 TCTCATCGAC 0.757374 -54 ********** Masking position 5 Map Score: 6.46725 Number of sites scoring better than the average of aligned sites = 1595 Number in coding regions = 1456 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 11 ********** No masking Map Score: 5.63704e-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 GCGCGCGCAACGAGGTGCGCACTATCCATT 1 193 1 CGAGGTGCGC 0.922596 -89 ACTATCCATTCGAGGTGAACTGGACTCCTT 1 213 1 CGAGGTGAAC 0.981951 -69 CGATGCTCAACGAGTTGGAACCGGACCAGG 4 86 1 CGAGTTGGAA 0.76663 -65 CTTCTCAAAGCGAGGGGAGCCCCGGGACTC 7 185 1 CGAGGGGAGC 0.900504 -116 ACAAATAAGCCGAGGAGAGACAA 7 288 1 CGAGGAGAGA 0.871007 -13 CGCGCGGAACCGAGGAGGAGAATCCATACG 8 98 0 CGAGGAGGAG 0.895441 -203 CCAACTTGGCCGCGGTGGAGTCTAGCCTCA 8 152 1 CGCGGTGGAG 0.891101 -149 TGATCGATCGCGTGGTGGAACAGAGTGGTC 9 41 0 CGTGGTGGAA 0.93535 -260 GGCGTTTGAACGTGGTGAACGGCGGGCCGG 9 204 0 CGTGGTGAAC 0.945032 -97 TCAGAAAGATCGGGGTGATATCGAACAGCG 10 21 0 CGGGGTGATA 0.840505 -176 GCCCCTTCACCGAGGCGATATCCATCGCGG 12 52 0 CGAGGCGATA 0.71582 -216 CAGCGCCGCCCGGGGTGGACCGGGTGCGCG 12 235 1 CGGGGTGGAC 0.972743 -33 ********** Masking position 1 Map Score: 9.0893 Number of sites scoring better than the average of aligned sites = 2563 Number in coding regions = 2393 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 13 ********** No masking Map Score: 5.63704e-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 14 ********** No masking Map Score: 5.63704e-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 ********** No masking Map Score: 5.63704e-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