AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_mtub_reg_300.orf -o00510_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/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 argS 300 argS #2 thrB 217 thrB #3 rho 256 rho #4 rpmE 150 rpmE #5 prfA 89 prfA #6 rfe 83 rfe #7 murE 22 murE #8 hypothetical 267 hypothetical protein Rv2160c #9 Rv2161c 102 hypothetical protein Rv2161c #10 PE_PGRS 209 PE_PGRS #11 Rv2166c 300 hypothetical protein Rv2166c #12 phyA 28 phyA #13 idsA 22 idsA Motif number 1 AGCCAACTATGCGGCCGCCCTCGCGGGTGG 1 48 1 GCGGCCGCCC 0.746341 -253 CAATGTGATCGGCGCCACCCGCGAGGGCGG 1 62 0 GGCGCCACCC 0.943348 -239 ATCAACCCTTGTGCCCCCGGCAGGATTCGA 1 114 1 GTGCCCCCGG 0.477753 -187 CAGGATTCGAACCTGCGGCCTTCTGCTCCG 1 134 1 ACCTGCGGCC 0.719111 -167 ACGTGTCGTCGTGCGCCCCCGTAGCTCAGG 1 182 0 GTGCGCCCCC 0.595613 -119 GCGCTACTCTGGCGGGGCCCCATGGCGCAA 1 211 0 GGCGGGGCCC 0.620317 -90 CGCCGCACCCGGCTCCGCCGCGCTTGCGAT 2 16 0 GGCTCCGCCG 0.886176 -202 CGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 26 0 CGCCGCACCC 0.593292 -192 GGTGCGGCGGGTCGGCACGGTTTGGATTGG 2 37 1 GTCGGCACGG 0.972399 -181 CGCGCTTGCGATCGCCACCCAATCCAAACC 2 55 0 ATCGCCACCC 0.959436 -163 CGCCGCACCCGGCTCCGCCGCGCTTGCGAT 2 73 0 GGCTCCGCCG 0.886176 -145 CGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 83 0 CGCCGCACCC 0.593292 -135 GGTGCGGCGGGTCGGCACGGTTTGGATTGG 2 94 1 GTCGGCACGG 0.972399 -124 CGCGCTTGCGATCGCCACCCAATCCAAACC 2 112 0 ATCGCCACCC 0.959436 -106 CGCCGCACCCGGCTCCGCCGCGCTTGCGAT 2 130 0 GGCTCCGCCG 0.886176 -88 CGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 140 0 CGCCGCACCC 0.593292 -78 GGTGCGGCGGGTCGGCACGGTTTGGATTGG 2 151 1 GTCGGCACGG 0.972399 -67 CGCGCTTGCGATCGCCACCCAATCCAAACC 2 169 0 ATCGCCACCC 0.959436 -49 CGCCGCACCCGGCTCCGCCGCGCTTGCGAT 2 187 0 GGCTCCGCCG 0.886176 -31 CGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 197 0 CGCCGCACCC 0.593292 -21 GGTGCGGCGGGTCGGCACGC 2 208 1 GTCGGCACGC 0.987164 -10 GCAAGCAAACCCCCGCAACCTTGCGGA 3 8 0 CCCCGCAACC 0.748223 -249 CCCGCTTCCTGGCCGGAAGCAAGCAAACCC 3 26 0 GGCCGGAAGC 0.487497 -231 ATTGCTGGACGGCTCCGAGGATAGCCCGCT 3 50 0 GGCTCCGAGG 0.827692 -207 TGGCTGTCCTAGCGGCAAGGCAGTACGTAT 3 92 0 AGCGGCAAGG 0.783804 -165 TGCGGACATTCCCGGCGAGCCGTCTCGCCG 4 13 0 CCCGGCGAGC 0.917699 -138 CGCCGGGAATGTCCGCACGCATCTCGGTGT 4 26 1 GTCCGCACGC 0.964699 -125 GGACCAGGTTCTCGGCACGCCACGACGGGC 4 108 1 CTCGGCACGC 0.97165 -43 TCTGTGATCGGTGGCCGCCCGTCGTGGCGT 4 124 0 GTGGCCGCCC 0.966943 -27 CTGGCTTACCGACGCCCGAACTGTGCA 5 8 1 ACCGACGCCC 0.851227 -82 CCTAACGCGAACCGACGCCCGTCCTGTACC 5 43 0 ACCGACGCCC 0.851227 -47 GTTCGCGTTAGGGTCCGCGCTCGCGGGAAG 5 61 1 GGGTCCGCGC 0.675251 -29 CCGCCGAACGTGCACGCACTGCGAAGA 6 8 1 ACGTGCACGC 0.578202 -76 GTGTGCGCGCCCTGTCGGTAGG 7 3 1 GTGCGCGCCC 0.782841 -20 CGCCGACGTCGGCCGCCAAACCCGGGC 8 8 1 GTCGGCCGCC 0.813398 -260 GGCGCGCAGGATCTGCGCCCGGGTTTGGCG 8 24 0 ATCTGCGCCC 0.942435 -244 CGATATCCATCGCGGCGCGCAGGATCTGCG 8 37 0 CGCGGCGCGC 0.799566 -231 GGGGCTGTCCATCGGCGAGCTTGCCGGGCG 8 86 1 ATCGGCGAGC 0.901132 -182 CTCATGCCCAGCCGCCCGGCAAGCTCGCCG 8 98 0 GCCGCCCGGC 0.65381 -170 CCGGCATTTCGGCGCCAAGGAGCAGCTGCA 8 143 1 GGCGCCAAGG 0.904367 -125 GCGCTGCCATCGCGGGAGCCACGACCTCGG 8 211 0 CGCGGGAGCC 0.383876 -57 CCGCGATGGCAGCGCCGCCCGGGGTGGACC 8 226 1 AGCGCCGCCC 0.989542 -42 GGGGTGGACCGGGTGCGCGCCCTCATGCAT 8 246 1 GGGTGCGCGC 0.507911 -22 CCCGGGCCCCGAGCGAGCGGTCAC 9 5 1 GGCCCCGAGC 0.955453 -98 ATTGACAGCACGCCCCAGGCGGACCATCGT 9 45 1 CGCCCCAGGC 0.702916 -58 CTTAATGAAAGCCGCCGCCG 9 93 1 GCCGCCGCCG 0.953466 -10 GGCGGCGGCGCCGGTAACGGCGC 10 4 1 GGCGGCGCCG 0.714846 -206 GCGCCGGTAACGGCGCGCGCCGGTTCGTTT 10 18 1 CGGCGCGCGC 0.508272 -192 CAACCCGATCGTCAGCGCGCACATGTTGCG 10 66 0 GTCAGCGCGC 0.843293 -144 CTGCGACACCGTCGGCAGGGCTTTCGATCC 10 146 0 GTCGGCAGGG 0.882325 -64 CCCGCACCTCCGACCAGCTCAGCAC 10 195 0 ACCTCCGACC 0.672747 -15 GGCTGGGTGAACCGCCCCGGTGAGTCCGGA 11 30 0 ACCGCCCCGG 0.738882 -271 ACTCAATATCGCCGACAGCCGGTGACGACC 11 61 0 GCCGACAGCC 0.678561 -240 AAAACCGCATGTCGCCGGGCAAATGGGTGG 11 131 0 GTCGCCGGGC 0.967004 -170 CGGCTAGCCCGGCTACGACCTCAGAAAACC 11 155 0 GGCTACGACC 0.642437 -146 TAGCCGGGCTAGCCGCGCGCTTCAGTGGTA 11 170 1 AGCCGCGCGC 0.962252 -131 ********** Masking position 6 Map Score: 112.845 Number of sites scoring better than the average of aligned sites = 74694 Number in coding regions = 69712 Number in noncoding regions = 4982 Number of orfs with sites within 600 bp upstream = 1490 Fraction of orfs with sites within 600 bp upstream = 0.239319 Motif number 2 TCGGCGCCACCCGCGAGGGCGGCCGCATAGT 1 53 0 CCGCGGGGCG 0.963957 -248 GAGCAGAAGGCCGCAGGTTCGAATCCTGCCG 1 131 0 CCGCAGTTCG 0.700795 -170 CGACACGTTGCGCCATGGGGCCCCGCCAGAG 1 204 1 CGCCAGGGGC 0.775935 -97 CAGTGGGTAGCCGCGATGCGCTACTCTGGCG 1 227 0 CCGCGTGCGC 0.899342 -74 CTATGGGCTGAGGTGGTTGGGCTTCGAATCC 1 269 0 AGGTGTTGGG 0.528646 -32 CCCGGCTCCGCCGCGCTTGCGATCGCCA 2 8 0 CCGCGTTGCG 0.982624 -210 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGG 2 31 1 CGGCGGTCGG 0.995705 -187 CCCGGCTCCGCCGCGCTTGCGATCGCCACCC 2 65 0 CCGCGTTGCG 0.982624 -153 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGG 2 88 1 CGGCGGTCGG 0.995705 -130 CCCGGCTCCGCCGCGCTTGCGATCGCCACCC 2 122 0 CCGCGTTGCG 0.982624 -96 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGG 2 145 1 CGGCGGTCGG 0.995705 -73 CCCGGCTCCGCCGCGCTTGCGATCGCCACCC 2 179 0 CCGCGTTGCG 0.982624 -39 GAGCCGGGTGCGGCGGGTCGGCACGC 2 202 1 CGGCGGTCGG 0.995705 -16 CCGTATTCGCCGCTGATGGCGATCACCGTTG 3 148 1 CGCTGTGGCG 0.6661 -109 TCAGCCAAATCGCCGAGTGCGCCAATCATCG 3 185 0 CGCCGGTGCG 0.992144 -72 TCCGGCGAGACGGCTCGCCGGGA 4 3 1 CGGCGGACGG 0.990656 -148 GCACGCATCTCGGTGTTTGGGGTGATAGCGG 4 40 1 CGGTGTTGGG 0.943451 -111 GTTCTCGGCACGCCACGACGGGCGGCCACCG 4 115 1 CGCCAGACGG 0.834911 -36 GGGCGTCGGTTCGCGTTAGGGTCCGCGCTCG 5 53 1 TCGCGTAGGG 0.809036 -37 TCAACCTTCTTCCCGCGAGCGCGGACCCTAA 5 68 0 TCCCGGAGCG 0.783263 -22 GTGTGCGCGCCCTGTCGGTAGG 7 8 1 CGCCCGTCGG 0.789437 -15 AGATCCTGCGCGCCGCGATGGATATCGCCTC 8 40 1 CGCCGGATGG 0.909024 -228 CGATGGACAGCCCCGAGAGCCCCTTCACCGA 8 69 0 CCCCGGAGCC 0.925345 -199 GGGCCTGTTCCGGCATTTCGGCGCCAAGGAG 8 134 1 CGGCATTCGG 0.847517 -134 CCGTCGAGGCCGCCGTGAGCGTGTTCGAAGC 8 181 1 CGCCGGAGCG 0.983034 -87 GGCGCTGCCATCGCGGGAGCCACGACCTCGG 8 211 0 TCGCGGAGCC 0.641578 -57 ACCCGGTCCACCCCGGGCGGCGCTGCCATCG 8 229 0 CCCCGGCGGC 0.780913 -39 CCCGGGCCCCGAGCGAGCGGTCACGCAAT 9 9 1 CCGAGGAGCG 0.76324 -94 AACCGGCGCGCGCCGTTACCGGCGCCGCCGC 10 12 0 CGCCGTACCG 0.945383 -198 TAACGGCGCGCGCCGGTTCGTTTCGGCTCCA 10 25 1 CGCCGTTCGT 0.785396 -185 CTGAGCTGGTCGGAGGTGCGGG 10 198 1 CGGAGTGCGG 0.606953 -12 TGAACCGCCCCGGTGAGTCCGGAGACTCTCT 11 22 0 CGGTGGTCCG 0.948451 -279 CGGTTCACCCAGCCGGGTCGTCACCGGCTGT 11 46 1 AGCCGGTCGT 0.345959 -255 CCCAGTTGTGCCCCACTTGGCCCCACTTGCC 11 102 1 CCCCATTGGC 0.73177 -199 GGCAAATGGGTGGCAAGTGGGGCCAAGTGGG 11 113 0 TGGCAGTGGG 0.821676 -188 CCTCAGAAAACCGCATGTCGCCGGGCAAATG 11 136 0 CCGCAGTCGC 0.886009 -165 GGTATCAAAGCGGCGTTTTGCCGTCTCTGTA 11 198 0 CGGCGTTTGC 0.828327 -103 ATGGTGGCTGAGGTGTTTGGGTGAGATGGAT 11 262 1 AGGTGTTGGG 0.528646 -39 ***** ***** Masking position 4 Map Score: 71.5493 Number of sites scoring better than the average of aligned sites = 41579 Number in coding regions = 38663 Number in noncoding regions = 2916 Number of orfs with sites within 600 bp upstream = 1238 Fraction of orfs with sites within 600 bp upstream = 0.198844 Motif number 3 CCAACTATGCGGCCGCCCTCGCGGGTGGCG 1 50 1 GGCCGCCCTC 0.918637 -251 TGGCGATCGCAAGCGCGGCGGAGC 2 5 1 GATCGCAAGC 0.990019 -213 ATTGGGTGGCGATCGCAAGCGCGGCGGAGC 2 62 1 GATCGCAAGC 0.990019 -156 ATTGGGTGGCGATCGCAAGCGCGGCGGAGC 2 119 1 GATCGCAAGC 0.990019 -99 ATTGGGTGGCGATCGCAAGCGCGGCGGAGC 2 176 1 GATCGCAAGC 0.990019 -42 GGTGCGGCGGGTCGGCACGC 2 208 1 GTCGGCACGC 0.886039 -10 CCCGCTTCCTGGCCGGAAGCAAGCAAACCC 3 26 0 GGCCGGAAGC 0.849673 -231 CGGCTCCGAGGATAGCCCGCTTCCTGGCCG 3 41 0 GATAGCCCGC 0.964588 -216 TTGCCGCTAGGACAGCCACCAATTCTTCTT 3 104 1 GACAGCCACC 0.858418 -153 TTGCAACGGTGATCGCCATCAGCGGCGAAT 3 152 0 GATCGCCATC 0.852715 -105 TCCGGCGAGACGGCTCGCCGGGAATGTC 4 9 1 GACGGCTCGC 0.922755 -142 CGCCGGGAATGTCCGCACGCATCTCGGTGT 4 26 1 GTCCGCACGC 0.951829 -125 CGCCACGACGGGCGGCCACCGATCACAGAG 4 125 1 GGCGGCCACC 0.785084 -26 CAAGCTCGCCGATGGACAGCCCCGAGAGCC 8 79 0 GATGGACAGC 0.866617 -189 CGGCCTCGACGGTCGCCAGCTGCAGCTGCT 8 163 0 GGTCGCCAGC 0.985151 -105 CGGATTGCGTGACCGCTCGCTCGGGGCCCG 9 13 0 GACCGCTCGC 0.968123 -90 ATCCGGCATTGACAGCACGCCCCAGGCGGA 9 38 1 GACAGCACGC 0.949563 -65 CGTGTTTAACGATGGTCCGCCTGGGGCGTG 9 53 0 GATGGTCCGC 0.904104 -50 CCGCCAACCCGATCGTCAGCGCGCACATGT 10 70 0 GATCGTCAGC 0.959775 -140 ATTGTTATAGGATCGAAAGCCCTGCCGACG 10 137 1 GATCGAAAGC 0.903191 -73 CACCCAGCCGGGTCGTCACCGGCTGTCGGC 11 51 1 GGTCGTCACC 0.734692 -250 ********** Masking position 5 Map Score: 43.4453 Number of sites scoring better than the average of aligned sites = 7111 Number in coding regions = 6634 Number in noncoding regions = 477 Number of orfs with sites within 600 bp upstream = 366 Fraction of orfs with sites within 600 bp upstream = 0.0587857 Motif number 4 CTTACCCCGACGAATTTGAGAGCGAGACCACGAA 1 15 1 CGATTTGAGG 0.671115 -286 TGCCCCCGGCAGGATTCGAACCTGCGGCCTTCTG 1 125 1 AGGTTCGACG 0.718254 -176 CCCTGAGCTACGGGGGCGCACGACGACACGTTGC 1 181 1 CGGGGCGCGC 0.874778 -120 ACCACCGCAACGGATTCGAAGCCCAACCACCTCA 1 258 1 CGGTTCGACC 0.715976 -43 CCGCCGCACCCGGCTCCGCCGCGCTTGCGATCGC 2 13 0 CGGTCCGCCC 0.977195 -205 CGGGTCGGCACGGTTTGGATTGGGTGGCGATCGC 2 44 1 CGGTTGGAGG 0.979365 -174 CCGCCGCACCCGGCTCCGCCGCGCTTGCGATCGC 2 70 0 CGGTCCGCCC 0.977195 -148 CGGGTCGGCACGGTTTGGATTGGGTGGCGATCGC 2 101 1 CGGTTGGAGG 0.979365 -117 CCGCCGCACCCGGCTCCGCCGCGCTTGCGATCGC 2 127 0 CGGTCCGCCC 0.977195 -91 CGGGTCGGCACGGTTTGGATTGGGTGGCGATCGC 2 158 1 CGGTTGGAGG 0.979365 -60 CCGCCGCACCCGGCTCCGCCGCGCTTGCGATCGC 2 184 0 CGGTCCGCCC 0.977195 -34 TGCTTGCTTCCGGCCAGGAAGCGGGCTATCCTCG 3 31 1 CGGCAGGACG 0.706918 -226 TACTGCCTTGCCGCTAGGACAGCCACCAATTCTT 3 97 1 CCGTAGGAGC 0.61459 -160 CGAGGTTCGCCGTATTCGCCGCTGATGGCGATCA 3 139 1 CGTTTCGCCG 0.811518 -118 CGCCAATCATCGACTTTGCAACGGTGATCGCCAT 3 163 0 CGATTTGCCG 0.805531 -94 GCCAAATCGCCGAGTGCGCCAATCATCGACTTTG 3 179 0 CGATGCGCAC 0.367513 -78 CGATGCTCAACGAGTTGGAACCGGACCAGGTTCT 4 86 1 CGATTGGACG 0.901075 -65 GATCTGCGCCCGGGTTTGGCGGCCGACGTCGGCG 8 11 0 CGGTTTGGGC 0.657946 -257 GCTTGCCGGGCGGCTGGGCATGAGCAAGTCGGGC 8 104 1 CGGTGGGCGG 0.944761 -164 ACGCTCACGGCGGCCTCGACGGTCGCCAGCTGCA 8 169 0 CGGCTCGAGC 0.936563 -99 GCCACGACCTCGGCTTCGAACACGCTCACGGCGG 8 190 0 CGGTTCGAAG 0.53815 -78 CAGCGCCGCCCGGGGTGGACCGGGTGCGCGCCCT 8 235 1 CGGGTGGAGG 0.932745 -33 ACGGCGCGCGCCGGTTCGTTTCGGCTCCAACAAC 10 27 1 CCGTTCGTCG 0.603662 -183 CGCTGACGATCGGGTTGGCGGAAGCTCTTTTAAG 10 79 1 CGGTTGGCAG 0.923671 -131 GCCCTGCCGACGGTGTCGCAGGTCTGGGATTCGT 10 155 1 CGGGTCGCGC 0.964609 -55 CGCCGACAGCCGGTGACGACCCGGCTGGGTGAAC 11 48 0 CGGGACGACG 0.627045 -253 GATATTGAGTCCGGTTTGAGCCCCAGTTGTGCCC 11 81 1 CCGTTTGACC 0.818172 -220 CAGTTGTGCCCCACTTGGCCCCACTTGCCACCCA 11 104 1 CCATTGGCCC 0.728059 -197 AGGTCGTAGCCGGGCTAGCCGCGCGCTTCAGTGG 11 164 1 CGGCTAGCCC 0.629483 -137 CGGCAAAACGCCGCTTTGATACCCCAGTTATGGG 11 206 1 CCGTTTGACC 0.818845 -95 *** ***** * * Masking position 8 Map Score: 48.0389 Number of sites scoring better than the average of aligned sites = 14114 Number in coding regions = 13127 Number in noncoding regions = 987 Number of orfs with sites within 600 bp upstream = 649 Fraction of orfs with sites within 600 bp upstream = 0.10424 Motif number 5 GTCGTCGTGCGCCCCCGTAGCTCAGGGGATAGAG 1 174 0 GCCCTAGCCA 0.905489 -127 TCCAGCAATCGCAGCATCTGCATACGTACTGCCT 3 71 1 GCAGCTGCTA 0.492307 -186 GAGACGGCTCGCCGGGAATGTCCGCACGCATCTC 4 17 1 GCCGATGTCG 0.689934 -134 GCTTACCGACGCCCGAACTGTGCACCAGCGGTAC 5 14 1 GCCCCTGTCA 0.968265 -76 GCGAACCGACGCCCGTCCTGTACCGCTGGTGCAC 5 33 0 GCCCCTGTCC 0.987714 -57 CCGCCGAACGTGCACGCACTGCGAAG 6 3 1 GCCGGTGCCG 0.972844 -81 CGAACAATTGGCCGAATCTTCGCAGTGCGTGCAC 6 20 0 GCCGCTTCCA 0.901816 -64 CCAATTGTTCGCAGCTGTTGCACGTTCGGCGAGT 6 43 1 GCAGTTGCCG 0.903534 -41 ATCGCGGCGCGCAGGATCTGCGCCCGGGTTTGGC 8 25 0 GCAGCTGCCC 0.982013 -243 CCGATGGACAGCCCCGAGAGCCCCTTCACCGAGG 8 67 0 GCCCGAGCCC 0.947295 -201 GCCGGAACAGGCCCGACTTGCTCATGCCCAGCCG 8 114 0 GCCCTTGCCA 0.985433 -154 ACGGTCGCCAGCTGCAGCTGCTCCTTGGCGCCGA 8 151 0 GCTGCTGCCC 0.937689 -117 TGGCAGCGCCGCCCGGGGTGGACCGGGTGCGCGC 8 232 1 GCCCGTGGCC 0.919675 -36 TCGTCAGCGCGCACATGTTGCGCAAAAGTTGTTG 10 54 0 GCACTTGCCA 0.926433 -156 GGTTCACCCAGCCGGGTCGTCACCGGCTGTCGGC 11 47 1 GCCGCGTCCC 0.742335 -254 TCCGGTTTGAGCCCCAGTTGTGCCCCACTTGGCC 11 90 1 GCCCTTGTCC 0.977709 -211 GCCCCACTTGGCCCCACTTGCCACCCATTTGCCC 11 111 1 GCCCTTGCAC 0.892748 -190 GCGGCGTTTTGCCGTCTCTGTACCACTGAAGCGC 11 186 0 GCCGCTGTCC 0.986395 -115 CCCCACAATCCCCCACTTTGCCCCATAACTGGGG 11 227 0 CCCCTTGCCC 0.921014 -74 **** **** ** Masking position 2 Map Score: 30.0066 Number of sites scoring better than the average of aligned sites = 6558 Number in coding regions = 6086 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 6 CTCGCGGGTGGCGCCGATCACATTGTTGTAG 1 67 1 GCGCCGACAC 0.990737 -234 TCGCGGCTACCCACTGACCACCGCAACGGAT 1 242 1 CCACTGACAC 0.922871 -59 CCGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 26 0 CCGCCGCCCC 0.990473 -192 CCGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 83 0 CCGCCGCCCC 0.990473 -135 CCGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 140 0 CCGCCGCCCC 0.990473 -78 GCGTGCCGACCCGCCGCACCCGGCTCCGCCG 2 197 0 CCGCCGCCCC 0.990473 -21 GCTATCCTCGGAGCCGTCCAGCAATCGCAGC 3 55 1 GAGCCGTCAG 0.892973 -202 TTTCCTTCCCCCGCTGATCACGTCATACGGG 3 228 0 CCGCTGACAC 0.986267 -29 CGACGGGCGGCCACCGATCACAGAGGGCAGC 4 130 1 CCACCGACAC 0.963549 -21 ACCGACGCCCGAACTGTGCACCAGCGGTACA 5 18 1 GAACTGTCAC 0.706035 -72 AACTGTGCACCAGCGGTACAGGACGGGCGTC 5 29 1 CAGCGGTCAG 0.846054 -61 CAACCTGAGAGCTGAACACTCGCCGAACG 6 65 0 GAGCTGACAC 0.944848 -19 CACCTCCGACCAGCTCAGCACAACTTCACGA 10 185 0 CAGCTCACAC 0.802986 -25 GGACTCACCGGGGCGGTTCACCCAGCCGGGT 11 33 1 GGGCGGTCAC 0.837919 -268 CGGGCTAGCCGCGCGCTTCAGTGGTACAGAG 11 174 1 GCGCGCTCAG 0.634423 -127 ******* *** Masking position 4 Map Score: 21.8453 Number of sites scoring better than the average of aligned sites = 9553 Number in coding regions = 8924 Number in noncoding regions = 629 Number of orfs with sites within 600 bp upstream = 498 Fraction of orfs with sites within 600 bp upstream = 0.0799872 Motif number 7 CCTGCGGCCTTCTGCTCCGGAGGCAGACGC 1 145 1 TCTGCTCCGG 0.858891 -156 CGCACGACGACACGTTGCGCCATGGGGCCC 1 197 1 CACGTTGCGC 0.927551 -104 GGGCTTCGAATCCGTTGCGGTGGTCAGTGG 1 252 0 TCCGTTGCGG 0.675723 -49 CCCGCCGCACCCGGCTCCGCCGCGCTTGCG 2 18 0 CCGGCTCCGC 0.974321 -200 CCCGCCGCACCCGGCTCCGCCGCGCTTGCG 2 75 0 CCGGCTCCGC 0.974321 -143 CCCGCCGCACCCGGCTCCGCCGCGCTTGCG 2 132 0 CCGGCTCCGC 0.974321 -86 CCCGCCGCACCCGGCTCCGCCGCGCTTGCG 2 189 0 CCGGCTCCGC 0.974321 -29 GTGCCGAGAACCTGGTCCGGTTCCAACTCG 4 96 0 CCTGGTCCGG 0.972254 -55 CGACGCCCGTCCTGTACCGCTGGTGCACAG 5 31 0 CCTGTACCGC 0.859125 -59 CGGTTCGCGTTAGGGTCCGCGCTCGCGGGA 5 59 1 TAGGGTCCGC 0.877761 -31 GCAGTGCGTGCACGTTCGGCGG 6 3 0 CACGTTCGGC 0.927511 -81 GCAGCTGTTGCACGTTCGGCGAGTGTTCAG 6 53 1 CACGTTCGGC 0.927511 -31 GCAAGTCGGGCCTGTTCCGGCATTTCGGCG 8 127 1 CCTGTTCCGG 0.966424 -141 CCCGGTCCACCCCGGGCGGCGCTGCCATCG 8 229 0 CCCGGGCGGC 0.811212 -39 CCGGGGTGGACCGGGTGCGCGCCCTCATGC 8 244 1 CCGGGTGCGC 0.977193 -24 TGCGTGACCGCTCGCTCGGGGCCCGGG 9 8 0 CTCGCTCGGG 0.590542 -95 CGTGTTTAACGATGGTCCGCCTGGGGCGTG 9 53 0 GATGGTCCGC 0.724643 -50 TCAGCGCGCACATGTTGCGCAAAAGTTGTT 10 55 0 CATGTTGCGC 0.888877 -155 ********** Masking position 4 Map Score: 34.2427 Number of sites scoring better than the average of aligned sites = 9348 Number in coding regions = 8791 Number in noncoding regions = 557 Number of orfs with sites within 600 bp upstream = 421 Fraction of orfs with sites within 600 bp upstream = 0.0676197 Motif number 8 CATGCGTGAGGCTAGATCAACCCTTGTGCCCCC 1 99 1 GCAGTAACCC 0.948025 -202 TCGAAGCCCAACCACCTCAGCCCATAGGATGGA 1 273 1 ACACTAGCCC 0.685367 -28 GCGTGCCGACCCGCCGCACCCGG 2 205 0 GCTGCACCCG 0.660367 -13 CTGGCCGGAAGCAAGCAAACCCCCGCAACCTTG 3 15 0 GCAGAACCCC 0.991864 -242 CTGGACGGCTCCGAGGATAGCCCGCTTCCTGGC 3 43 0 CCAGAAGCCC 0.935672 -214 CTGCCTTGCCGCTAGGACAGCCACCAATTCTTC 3 99 1 GCAGAAGCCA 0.799524 -158 TTGGCTGACTGCAACAAAACCCCGTATGACGTG 3 208 1 GCACAACCCC 0.990743 -49 CATCGATTATGCCAGGTCAACCGCTATCACCCC 4 58 0 GCAGTAACCG 0.872282 -93 GCCGACGTCGGCCGCCAAACCCGGGCGCAGATC 8 12 1 GCGCAACCCG 0.926797 -256 CCGATGGACAGCCCCGAGAGCCCCTTCACCGAG 8 68 0 GCCCAAGCCC 0.893352 -200 ATCCGGCATTGACAGCACGCCCCAGGCGGACCA 9 38 1 GAAGAGCCCC 0.715892 -65 TGACGACCCGGCTGGGTGAACCGCCCCGGTGAG 11 36 0 GCGGTAACCG 0.683316 -265 CCAGTTGTGCCCCACTTGGCCCCACTTGCCACC 11 103 1 CCACTGCCCC 0.881275 -198 GCAAAACGCCGCTTTGATACCCCAGTTATGGGG 11 208 1 GCTTAACCCC 0.709385 -93 CCCACAATCCCCCACTTTGCCCCATAACTGGGG 11 227 0 CCACTGCCCC 0.881275 -74 AAACACCTCAGCCACCATACCCCACAATCCCCC 11 247 0 GCACAACCCC 0.990743 -54 ** ** * ***** Masking position 11 Map Score: 14.0354 Number of sites scoring better than the average of aligned sites = 2336 Number in coding regions = 2129 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 9 GCCGATCACATTGTTGTAGCCATGCGTGAGG 1 79 1 TTGTTGAGCC 0.989763 -222 GGCACAAGGGTTGATCTAGCCTCACGCATGG 1 98 0 TTGATCAGCC 0.963331 -203 ATACGGGGTTTTGTTGCAGTCAGCCAAATCG 3 204 0 TTGTTGAGTC 0.948792 -53 CAGGCCCGACTTGCTCATGCCCAGCCGCCCG 8 110 0 TTGCTCTGCC 0.922086 -158 TGCGCAAAAGTTGTTGGAGCCGAAACGAACC 10 39 0 TTGTTGAGCC 0.989763 -171 ****** **** Masking position 5 Map Score: 1.21299 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 153 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ********** No masking Map Score: 3.45567e-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: 3.45567e-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: 3.45567e-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