AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_ecoli_mtub_300.orf -o250_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yabB 300 orf, hypothetical protein #2 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #3 ftsZ 60 cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase #4 ddlA 300 D-alanine-D-alanine ligase A #5 murB 300 UDP-N-acetylenolpyruvoylglucosamine reductase #6 murB 26 murB #7 ftsZ 172 ftsZ #8 murE 22 murE #9 hypothetical 267 hypothetical protein Rv2160c #10 Rv2161c 102 hypothetical protein Rv2161c #11 PE_PGRS 209 PE_PGRS #12 Rv2166c 300 hypothetical protein Rv2166c #13 ddlA 77 ddlA #14 gpdA2 118 gpdA2 Motif number 1 CAGTTTGCGACGCGAGCGGCATTTTAGGAC 1 22 0 CGCGAGCGGC 0.528956 -279 TACGGCCTCAGGCGACAGGCACAAATCGGA 3 33 1 GGCGACAGGC 0.769904 -28 GGACAAATCCGCCGGGAGCGGATTTGAACG 5 90 1 GCCGGGAGCG 0.588145 -211 CGAAGCAACGGCCCGGAGGGTGGCGGGCAG 5 123 1 GCCCGGAGGG 0.659727 -178 CCCGGAGGGTGGCGGGCAGGACGCCCGCCA 5 134 1 GGCGGGCAGG 0.943754 -167 CCGAAAAAATGCCCGCCGCGTATCGGCGCG 7 11 1 GCCCGCCGCG 0.565422 -162 GTATCGGCGCGCCTGCACGGTTAGCAACCG 7 30 1 GCCTGCACGG 0.696492 -143 AGAACCGTATGGCTACGACGGTTGCTAACC 7 48 0 GGCTACGACG 0.803171 -125 AAGAACCGAGCCCCACCAGGGAGGAAGCCG 7 149 1 CCCCACCAGG 0.641977 -24 CTACCGACAGGGCGCGCACAC 8 2 0 GGCGCGCACA 0.67251 -21 CGCCGACGTCGGCCGCCAAAC 9 2 1 GCCGACGTCG 0.812274 -266 GCGCAGGATCTGCGCCCGGGTTTGGCGGCC 9 21 0 TGCGCCCGGG 0.53852 -247 TATCCATCGCGGCGCGCAGGATCTGCGCCC 9 34 0 GGCGCGCAGG 0.945368 -234 GATGGACAGCCCCGAGAGCCCCTTCACCGA 9 69 0 CCCGAGAGCC 0.482753 -199 CGGCGAGCTTGCCGGGCGGCTGGGCATGAG 9 98 1 GCCGGGCGGC 0.499883 -170 CCGGCATTTCGGCGCCAAGGAGCAGCTGCA 9 143 1 GGCGCCAAGG 0.936031 -125 ACACGCTCACGGCGGCCTCGACGGTCGCCA 9 175 0 GGCGGCCTCG 0.917545 -93 CGTGTTCGAAGCCGAGGTCGTGGCTCCCGC 9 200 1 GCCGAGGTCG 0.796703 -68 CCGAGGTCGTGGCTCCCGCGATGGCAGCGC 9 211 1 GGCTCCCGCG 0.561648 -57 CGATGGCAGCGCCGCCCGGGGTGGACCGGG 9 229 1 GCCGCCCGGG 0.528303 -39 CATGCATGAGGGCGCGCACCCGGTCCACCC 9 247 0 GGCGCGCACC 0.815473 -21 CCCGGGCCCCGAGCGAGCGGTCACG 10 6 1 GCCCCGAGCG 0.669202 -97 ACGATGGTCCGCCTGGGGCGTGCTGTCAAT 10 45 0 GCCTGGGGCG 0.700854 -58 CTTAATGAAAGCCGCCGCCG 10 93 1 GCCGCCGCCG 0.914675 -10 GGCGGCGGCGCCGGTAACGG 11 1 1 GGCGGCGGCG 0.567021 -209 CGCCGGTAACGGCGCGCGCCGGTTCGTTTC 11 19 1 GGCGCGCGCC 0.499755 -191 GGGCGGTTCACCCAGCCGGGTCGTCACCGG 12 43 1 CCCAGCCGGG 0.661805 -258 ACTCAATATCGCCGACAGCCGGTGACGACC 12 61 0 GCCGACAGCC 0.803627 -240 CCATTTGCCCGGCGACATGCGGTTTTCTGA 12 135 1 GGCGACATGC 0.449616 -166 TGAAGCGCGCGGCTAGCCCGGCTACGACCT 12 164 0 GGCTAGCCCG 0.850528 -137 AGATGGATTTGGCAGGGAGGTGCCCC 12 285 1 GGCAGGGAGG 0.718529 -16 GCCTCGCACGGGCCGGCACG 13 1 1 GCCTCGCACG 0.940911 -77 GCCTCGCACGGGCCGGCACGACCGAAAACT 13 11 1 GGCCGGCACG 0.941422 -67 CAGGCAGACGGGCTCCCACGAGCTGCAGTT 13 37 0 GGCTCCCACG 0.944746 -41 AACCTGCAGAGGCTACCGGGTCAGGCAGAC 13 58 0 GGCTACCGGG 0.927901 -20 CGTGGATCGACGCTGGCAGGATGACTTC 14 9 0 CGCTGGCAGG 0.7641 -110 CGACGGCATTGCCGCCACGGTCGTGGCCGG 14 49 1 GCCGCCACGG 0.878571 -70 GTGCCTGGGCCCCGGCCACGACCGTGGCGG 14 60 0 CCCGGCCACG 0.835321 -59 GTGGCCGGGGCCCAGGCACGGTCCCGACGG 14 71 1 CCCAGGCACG 0.691249 -48 CGGTCCCGACGGCAACCGCGGCGCAGATTA 14 89 1 GGCAACCGCG 0.925826 -30 ********** Masking position 3 Map Score: 62.1927 Number of sites scoring better than the average of aligned sites = 12257 Number in coding regions = 11797 Number in noncoding regions = 460 Number of orfs with sites within 600 bp upstream = 335 Fraction of orfs with sites within 600 bp upstream = 0.0538066 Motif number 2 TATAAAGTGTCAGTTTGCGACGCGAGCGGCATTTTA 1 26 0 CAGGCGCGAG 0.700787 -275 AAGAAAAAATCCCTCATCGTCATCACCGTTTTAAAA 1 86 0 CCCGCATCAC 0.61792 -215 TCGCCTGAGGCCGTAATCATCGTCGGCCTCATAAAA 3 12 0 CCGACGTCGG 0.739315 -49 CAGTACGTTGCACGCTTTGTCAGCAGAAGATTGCAA 4 195 1 CACGCAGCAG 0.508125 -106 GGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCG 5 123 0 CCGCCCGGGC 0.965504 -178 TGATGCCTGGCAGTTTATGGCGGGCGTCCTGCCCGC 5 145 0 CAGGCGGGCG 0.861568 -156 GGCTAGTTTACCGTATCTGTGGGGGGATGGCTTGTA 5 250 0 CCGGGGGGGG 0.977239 -51 CCGAAAAAATGCCCGCCGCGTATCGG 7 1 1 CCGAGCCCGC 0.846073 -172 CGGTTGCTAACCGTGCAGGCGCGCCGATACGCGGCG 7 24 0 CCGGGCGCCG 0.990015 -149 AGCAGACACACCGAAGAACCGAGCCCCACCAGGGAG 7 136 1 CCGCGAGCCC 0.915132 -37 CCTACCGACAGGGCGCGCACAC 8 3 0 CCGGGCGCAC 0.99026 -20 GGATCTGCGCCCGGGTTTGGCGGCCGACGTCGGCG 9 10 0 CCGGCGGCCG 0.99318 -258 AACCCGGGCGCAGATCCTGCGCGCCGCGATGGATAT 9 29 1 CAGGGCGCCG 0.920817 -239 GCCCCGAGAGCCCCTTCACCGAGGCGATATCCATCG 9 55 0 CCCCGAGGCG 0.497522 -213 GGCAAGCTCGCCGATGGACAGCCCCGAGAGCCCCTT 9 75 0 CCGCGCCCCG 0.946692 -193 CGCCGAAATGCCGGAACAGGCCCGACTTGCTCATGC 9 121 0 CCGGCCCGAC 0.971609 -147 CTCACGGCGGCCTCGACGGTCGCCAGCTGCAGCTGC 9 164 0 CCTGCGCCAG 0.593603 -104 GGTCGTGGCTCCCGCGATGGCAGCGCCGCCCGGGGT 9 215 1 CCCGCAGCGC 0.85252 -53 GGGCGCGCACCCGGTCCACCCCGGGCGGCGCTGCCA 9 232 0 CCGCCCGGGC 0.972429 -36 CCCGGGCCCCGAGCGAGCGGTCACGCAATCCGGC 10 9 1 CCGGGGTCAC 0.915984 -94 GTCACGCAATCCGGCATTGACAGCACGCCCCAGGCG 10 30 1 CCGGCAGCAC 0.981336 -73 CCGGCGCGCGCCGTTACCGGCGCCGCCGCC 11 5 0 CCGGCGCCGC 0.985777 -205 GTTGTTGGAGCCGAAACGAACCGGCGCGCGCCGTTA 11 25 0 CCGACCGGCG 0.907021 -185 TTCCGCCAACCCGATCGTCAGCGCGCACATGTTGCG 11 66 0 CCGCGCGCGC 0.959549 -144 TCCCAGACCTGCGACACCGTCGGCAGGGCTTTCGAT 11 148 0 GCGGCGGCAG 0.81161 -62 CCCGCACCTCCGACCAGCTCAGCACAACTTCACGA 11 185 0 CCGCCAGCAC 0.945898 -25 GGTGAACCGCCCCGGTGAGTCCGGAGACTCTCTGAT 12 19 0 CCCGCCGGAG 0.945204 -282 TCGCCGACAGCCGGTGACGACCCGGCTGGGTGAACC 12 47 0 CCGGCCCGGC 0.842289 -254 GATATTGAGTCCGGTTTGAGCCCCAGTTGTGCCCCA 12 81 1 CCGACCCCAG 0.894246 -220 CCCAGTTGTGCCCCACTTGGCCCCACTTGCCACCCA 12 102 1 CCCGCCCCAC 0.938266 -199 CCTCAGAAAACCGCATGTCGCCGGGCAAATGGGTGG 12 131 0 CCGCCCGGGC 0.973053 -170 CGCGGCTAGCCCGGCTACGACCTCAGAAAACCGCAT 12 151 0 CCGGCCTCAG 0.967812 -150 CGTCTCTGTACCACTGAAGCGCGCGGCTAGCCCGGC 12 172 0 CCAGGCGCGG 0.78438 -129 GCCTCGCACGGGCCGGCACGACCGAAAAC 13 4 1 TCGGCGGCAC 0.725795 -74 CCGAAAACTGCAGCTCGTGGGAGCCCGTCTGCCTGA 13 32 1 CAGGGAGCCC 0.746872 -46 TCTGCCTGACCCGGTAGCCTCTGCAGGTT 13 59 1 CCGCCTGCAG 0.844077 -19 GGCGGCAATGCCGTCGAAGTGTGCCGCGTGGATCGA 14 29 0 CCGGGTGCCG 0.907299 -90 GACGGCATTGCCGCCACGGTCGTGGCCGGGGCCCAG 14 50 1 CCGGCGTGGC 0.917438 -69 GCCGTCGGGACCGTGCCTGGGCCCCGGCCACGACCG 14 66 0 CCGGGCCCCG 0.980883 -53 CTAATCTGCGCCGCGGTTGCCGTCGGGACCGTGCCT 14 84 0 CCGGCGTCGG 0.500247 -35 *** * ****** Masking position 1 Map Score: 77.6304 Number of sites scoring better than the average of aligned sites = 8267 Number in coding regions = 7891 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 3 TTACGGAGCTGAGGAAAAGCTTGTCAAGCCAGT 1 224 0 GAGGAGCTTG 0.554306 -77 GGGAAATTGTGGGGCAAAGTGGGAATAAGGGGT 1 269 1 GGGGAGTGGG 0.986615 -32 GTGGGAATAAGGGGTGAGGCTGGC 1 287 1 GGGGAGCTGG 0.985005 -14 CGACAAAACGGGGGATTCGCGGCCTTCTGAAAG 4 235 0 GGGGTGCGGC 0.996431 -66 GCCACCCTCCGGGCCGTTGCTTCGCAACGTTCA 5 114 0 GGGCTGCTTC 0.818654 -187 GCAACGGCCCGGAGGGTGGCGGGCAGGACGCCC 5 127 1 GGAGTGCGGG 0.966688 -174 CGTATCTGTGGGGGGATGGCTTGTAGATATGAC 5 242 0 GGGGTGCTTG 0.973262 -59 GATCTGCGCCCGGGTTTGGCGGCCGACGTCGGC 9 12 0 CGGGTGCGGC 0.964613 -256 CTCGGTGAAGGGGCTCTCGGGGCTGTCCATCGG 9 68 1 GGGCTGGGGC 0.888148 -200 AGCGCCGCCCGGGGTGGACCGGGTGCGCGCCCT 9 236 1 GGGGGCCGGG 0.952716 -32 TGGTCCGCCTGGGGCGTGCTGTCAATGCCGGAT 10 38 0 GGGGTCTGTC 0.835163 -65 GGTGGCAAGTGGGGCCAAGTGGGGCACAACTGG 12 103 0 GGGGAGTGGG 0.986615 -198 GGGGCAAAGTGGGGGATTGTGGGGTATGGTGGC 12 237 1 GGGGTGTGGG 0.993013 -64 **** * ***** Masking position 3 Map Score: 16.5955 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 571 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CATTTTAAAACGGTGATGACGATGAGGGAT 1 84 1 CGGTGATGAC 0.785274 -217 TTTTTATGAGGCCGACGATGATTACGGCC 3 10 1 GGCCGACGAT 0.689221 -51 CGTTCAAATCCGCTCCCGGCGGATTTGTCC 5 90 0 CGCTCCCGGC 0.693135 -211 CCGCCACCCTCCGGGCCGTTGCTTCGCAAC 5 119 0 CCGGGCCGTT 0.390835 -182 CGTATCTGTGGGGGGATGGCTTGTAGATAT 5 245 0 GGGGGATGGC 0.519207 -56 AACCGTGCAGGCGCGCCGATACGCGGCGGG 7 22 0 GCGCGCCGAT 0.932612 -151 CAGAACCGTATGGCTACGACGGTTGCTAAC 7 49 0 TGGCTACGAC 0.423722 -124 CGTAGCCATACGGTTCTGACTACGAGCAAC 7 61 1 CGGTTCTGAC 0.511277 -112 GTGTGCGCGCCCTGTCGGTAGG 8 7 1 GCGCCCTGTC 0.48231 -16 CGCCGACGTCGGCCGCCAAA 9 1 1 CGCCGACGTC 0.833703 -267 CGCCAAACCCGGGCGCAGATCCTGCGCGCC 9 24 1 GGGCGCAGAT 0.530506 -244 ATCCTGCGCGCCGCGATGGATATCGCCTCG 9 42 1 CCGCGATGGA 0.564869 -226 CCGGCAAGCTCGCCGATGGACAGCCCCGAG 9 83 0 CGCCGATGGA 0.32381 -185 AGCTGCTCCTTGGCGCCGAAATGCCGGAAC 9 140 0 TGGCGCCGAA 0.533216 -128 CTCACGGCGGCCTCGACGGTCGCCAGCTGC 9 170 0 CCTCGACGGT 0.292161 -98 GTCGTGGCTCCCGCGATGGCAGCGCCGCCC 9 216 1 CCGCGATGGC 0.939317 -52 TGGACCGGGTGCGCGCCCTCATGCATGC 9 250 1 GCGCGCCCTC 0.647931 -18 ATGCCGGATTGCGTGACCGCTCGCTCGGGG 10 17 0 GCGTGACCGC 0.43906 -86 TCCGCCTGGGGCGTGCTGTCAATGCCGGAT 10 38 0 GCGTGCTGTC 0.515726 -65 CGGCGGCGGCTTTCATTAAG 10 93 0 CGGCGGCGGC 0.95379 -10 GGCGGCGGCGCCGGTAACGGCGCGC 11 6 1 CGGCGCCGGT 0.978207 -204 CGGTAACGGCGCGCGCCGGTTCGTTTCGGC 11 22 1 GCGCGCCGGT 0.948723 -188 CGGTTCGTTTCGGCTCCAACAACTTTTGCG 11 38 1 CGGCTCCAAC 0.44522 -172 CGCAACATGTGCGCGCTGACGATCGGGTTG 11 66 1 GCGCGCTGAC 0.938746 -144 GGATCGAAAGCCCTGCCGACGGTGTCGCAG 11 146 1 CCCTGCCGAC 0.859325 -64 GCTGGGTGAACCGCCCCGGTGAGTCCGGAG 12 29 0 CCGCCCCGGT 0.864431 -272 CGCCGACAGCCGGTGACGACCCGGCTGGGT 12 52 0 CGGTGACGAC 0.933332 -249 GACTCAATATCGCCGACAGCCGGTGACGAC 12 62 0 CGCCGACAGC 0.498049 -239 CCACCCATTTGCCCGGCGACATGCGGTTTT 12 131 1 GCCCGGCGAC 0.627237 -170 GCGGCTAGCCCGGCTACGACCTCAGAAAAC 12 156 0 CGGCTACGAC 0.884792 -145 CAGTTTTCGGTCGTGCCGGCCCGTGCGAGG 13 12 0 TCGTGCCGGC 0.746688 -66 TCAGGCAGACGGGCTCCCACGAGCTGCAGT 13 38 0 GGGCTCCCAC 0.509849 -40 CCGCGTGGATCGACGCTGGCAGGATGACTT 14 12 0 CGACGCTGGC 0.594786 -107 GCCTGGGCCCCGGCCACGACCGTGGCGGCA 14 58 0 CGGCCACGAC 0.924513 -61 GGCCCAGGCACGGTCCCGACGGCAACCGCG 14 79 1 CGGTCCCGAC 0.864617 -40 ACGGCAACCGCGGCGCAGATTAGTGTGTGT 14 97 1 CGGCGCAGAT 0.662642 -22 ********** Masking position 8 Map Score: 31.0546 Number of sites scoring better than the average of aligned sites = 19818 Number in coding regions = 19040 Number in noncoding regions = 778 Number of orfs with sites within 600 bp upstream = 491 Fraction of orfs with sites within 600 bp upstream = 0.0788628 Motif number 5 AAAAGCTTGTCAAGCCAGTCACAAGGCATACCGAGGT 1 206 0 CAGCAAAGGC 0.986064 -95 TTCTTAAATTCATACGATGCAAAAGGCATCGCTACAA 2 11 0 CAACAAAGGC 0.993139 -43 TTAAGAGAAAAAAACTCACCGCATGGCCATTTAAGCC 4 85 1 AAACGATGGC 0.852614 -216 GAAGATTGCAACAATCTTTCAGAAGGCCGCGAATCCC 4 220 1 ACACAAAGGC 0.869446 -81 CAAATAAAACGAAAGGCTCAGTCGAAA 5 1 1 CAACGAAGGC 0.994663 -300 CGACAAACAACAGATAAAACGAAAGGCCCAGTCTTTC 5 34 0 CAACGAAGGC 0.994663 -267 TGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACG 5 169 1 CAACAAAGGC 0.993139 -132 GCTAACCGTGCAGGCGCGCCGATACGCGGCGGGCATT 7 18 0 CAGCGTACGC 0.813917 -155 TTCAGTGGTACAGAGACGGCAAAACGCCGCTTTGATA 12 190 1 CAACAAACGC 0.977822 -111 ** * ** ***** Masking position 10 Map Score: 8.5108 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 81 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 GAATAAGGGGTGAGGCTGGC 1 291 1 TGAGGCTGGC 0.956054 -10 TTTTTATGAGGCCGACGATGATTACG 3 7 1 TGAGGCCGAC 0.852679 -54 CAACAATCTTTCAGAAGGCCGCGAATCCCC 4 228 1 TCAGAAGGCC 0.568285 -73 TTTGTCCTACTCAGGAGAGCGTTCACCGAC 5 67 0 TCAGGAGAGC 0.865634 -234 GCAACGGCCCGGAGGGTGGCGGGCAGGACG 5 127 1 GGAGGGTGGC 0.835608 -174 AGGGTGGCGGGCAGGACGCCCGCCATAAAC 5 139 1 GCAGGACGCC 0.958309 -162 AGGCCATCCGTCAGGATGGCCTTCTGCTTA 5 184 0 TCAGGATGGC 0.968956 -117 CGTATCTGTGGGGGGATGGCTTGTAGATAT 5 245 0 GGGGGATGGC 0.743682 -56 CGTTTTTGCATCAGGAAAGCAGCT 5 287 1 TCAGGAAAGC 0.715767 -14 AGCAGGTCAGGCTACCCTTACGGGCC 6 7 1 TCAGGCTACC 0.7931 -20 TGCTAACCGTGCAGGCGCGCCGATACGCGG 7 26 0 GCAGGCGCGC 0.869698 -147 GCCCCACCAGGGAGGAAGCCGAACG 7 158 1 GGAGGAAGCC 0.890134 -15 TGGCGACCGTCGAGGCCGCCGTGAGCGTGT 9 175 1 CGAGGCCGCC 0.830169 -93 GCATGCATGAGGGCGCGCACCCGG 9 254 0 GCATGAGGGC 0.745701 -14 ACAGCACGCCCCAGGCGGACCATCGTTAAA 10 49 1 CCAGGCGGAC 0.879803 -54 GGCTACCGGGTCAGGCAGACGGGCTCCCAC 13 48 0 TCAGGCAGAC 0.869352 -30 ATCGACGCTGGCAGGATGACTTC 14 4 0 GCAGGATGAC 0.934261 -115 ********** Masking position 10 Map Score: 13.3616 Number of sites scoring better than the average of aligned sites = 3093 Number in coding regions = 2879 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 7 ATTTTACGTCCAACGTGCGAAGCAAATTAA 1 138 0 CAACGTGCGA 0.981612 -163 AATTGTGGGGCAAAGTGGGAATAAGGGGTG 1 273 1 CAAAGTGGGA 0.950663 -28 TACTGGTGAAGAAAGTGCGTTATCTCAAAG 4 170 0 GAAAGTGCGT 0.962559 -131 CCGTCTAACACAAAGTGCATACATTACCAC 4 267 0 CAAAGTGCAT 0.905364 -34 CGTTGCTTCGCAACGTTCAAATCCGCTCCC 5 103 0 CAACGTTCAA 0.736339 -198 CGTTAAACACGAACGTTCGTGCTTAATGAA 10 72 1 GAACGTTCGT 0.85215 -31 CTCTTTTAAGGAAAGTGCGACATCCTGTTT 11 103 1 GAAAGTGCGA 0.970994 -107 AGTTATGGGGCAAAGTGGGGGATTGTGGGG 12 231 1 CAAAGTGGGG 0.896697 -70 ********** Masking position 3 Map Score: 4.48625 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 262 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 ATGCCGCTCGCGTCGCAAACTGACACTTTA 1 30 1 CGTCGCAAAC 0.889642 -271 CGCTGATATTAGCCGTAAACATCGGGTTTT 1 174 1 AGCCGTAAAC 0.927489 -127 TTTTCCTCAGCTCCGTAAACTCCTTTCAGT 1 239 1 CTCCGTAAAC 0.963234 -62 TCTTTACGCCATTAACTTCTTAAATT 2 38 0 CGCCATTAAC 0.952652 -16 AATATATTCTCTTCGTTAACTTATAATTAA 4 59 1 CTTCGTTAAC 0.821491 -242 GCAGGACGCCCGCCATAAACTGCCAGGCAT 5 149 1 CGCCATAAAC 0.963234 -152 CCGTCGAGGCCGCCGTGAGCGTGTTCGAAG 9 181 1 CGCCGTGAGC 0.931997 -87 GGCGGCGGCGCCGGTAACGGCGCGCGCC 11 9 1 CGCCGGTAAC 0.964372 -201 ********** Masking position 8 Map Score: 5.15927 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 839 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 AAAACTCACCGCATGGCCATTTAAGCCAGGA 4 95 1 GCATGGCCTT 0.930991 -206 TACTGGTGAAGAAAGTGCGTTATCTCAAAGA 4 169 0 GAAAGTGCTT 0.45879 -132 CCAGTCTTTCGACTGAGCCTTTCGTTTTATT 5 13 0 GACTGAGCTT 0.807404 -288 TCAGTCGAAAGACTGGGCCTTTCGTTTTATC 5 28 1 GACTGGGCTT 0.979585 -273 TTAATTTGATGCCTGGCAGTTTATGGCGGGC 5 156 0 GCCTGGCATT 0.75006 -145 CCATCCGTCAGGATGGCCTTCTGCTTAATTT 5 180 0 GGATGGCCTC 0.939732 -121 CCATCCTGACGGATGGCCTTTTTGCGTTTCT 5 195 1 GGATGGCCTT 0.956423 -106 CCTACCGACAGGGCGCGCACAC 8 6 0 GACAGGGCCG 0.742933 -17 GGGCTCTCGGGGCTGTCCATCGGCGAGCTTG 9 78 1 GGCTGTCCTC 0.881824 -190 CTTGCCGGGCGGCTGGGCATGAGCAAGTCGG 9 105 1 GGCTGGGCTG 0.97876 -163 CGACACCGTCGGCAGGGCTTTCGATCCTATA 11 142 0 GGCAGGGCTT 0.971029 -68 TCGGGACCGTGCCTGGGCCCCGGCCACGACC 14 67 0 GCCTGGGCCC 0.934634 -52 ******** ** Masking position 5 Map Score: 7.49691 Number of sites scoring better than the average of aligned sites = 1412 Number in coding regions = 1314 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 10 GGAAATTGTGGGGCAAAGTGGGAATAAGGGG 1 270 1 GGCAAAGTGG 0.928805 -31 CAGGCGACAGGCACAAATCGGAGAGAAACT 3 41 1 GACAAATCGG 0.979326 -20 CTCCTGAGTAGGACAAATCCGCCGGGAGCGG 5 80 1 GACAAATCCG 0.926831 -221 GCTTCGCAACGTTCAAATCCGCTCCCGGCGG 5 98 0 GTCAAATCCG 0.898375 -203 GGCTGGGCATGAGCAAGTCGGGCCTGTTCCG 9 115 1 GGCAAGTCGG 0.979518 -153 CACAACTGGGGCTCAAACCGGACTCAATATC 12 81 0 GTCAAACCGG 0.897759 -220 GCCAAGTGGGGCACAACTGGGGCTCAAACCG 12 92 0 GACAACTGGG 0.885498 -209 TGGCAAGTGGGGCCAAGTGGGGCACAACTGG 12 103 0 GCCAAGTGGG 0.893029 -198 GCATGTCGCCGGGCAAATGGGTGGCAAGTGG 12 124 0 GGCAAATGGG 0.983643 -177 CCCAGTTATGGGGCAAAGTGGGGGATTGTGG 12 228 1 GGCAAAGTGG 0.928805 -73 * ********* Masking position 6 Map Score: 7.56131 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 317 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: 5.44519e-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: 5.44519e-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: 5.44519e-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