AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_ctra_reg_100.orf -o294_ctra_100.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCT00066 300 Chlamydia_trachomatis #2 RCT00068 66 Chlamydia_trachomatis #3 RCT00070 26 Chlamydia_trachomatis #4 RCT00071 195 Chlamydia_trachomatis #5 RCT00225 300 Chlamydia_trachomatis #6 RCT00227 16 Chlamydia_trachomatis #7 RCT00228 119 Chlamydia_trachomatis #8 RCT00230 300 Chlamydia_trachomatis #9 RCT00231 68 Chlamydia_trachomatis #10 RCT00232 27 Chlamydia_trachomatis #11 RCT00253 132 Chlamydia_trachomatis #12 RCT00281 167 Chlamydia_trachomatis #13 RCT00285 300 Chlamydia_trachomatis #14 RCT00405 132 Chlamydia_trachomatis #15 RCT00430 300 Chlamydia_trachomatis #16 RCT00507 100 Chlamydia_trachomatis #17 RCT00649 300 Chlamydia_trachomatis #18 RCT00738 300 Chlamydia_trachomatis #19 RCT00854 259 Chlamydia_trachomatis #20 RCT00776 22 Chlamydia_trachomatis Motif number 1 TTCCGCACCACTATCGAAAAAACTGACATCCC 4 27 0 CTTCAAAAAA 0.887883 -169 GAAATGCCTTCTAAATCAAAAACTCAGAAGGG 5 34 0 CTAACAAAAA 0.924213 -267 AAAAATCTAGCTTTAAATAAAACTAGAGTAAC 5 168 0 CTTAATAAAA 0.729747 -133 CTCGCAGAGTCTATAGCAAAAAAAATCTAGCT 5 188 0 CTTACAAAAA 0.969697 -113 CCGCAAACAAAAAGAAAAAACCG 7 107 0 CGAACAAAAA 0.837558 -13 TTTAATTTCTCTTAAAAAGAAA 11 1 0 CTAAAAGAAA 0.751112 -132 ATTATTGATTGGTTAAAAAAAATTACAATAAA 12 15 1 GGTAAAAAAA 0.674359 -153 AAACCATCCTCTTTACAAAAAATTGAGCAATA 12 49 0 CTTAAAAAAA 0.967212 -119 AAGCCAGCTCCTGTAAAAGAAATTATTGGGAG 14 97 0 CTTAAAGAAA 0.887883 -36 AGCAAGCAAGCGATATCAAAAAATTACTACCT 16 32 0 CGTACAAAAA 0.931177 -69 CGCTTGCTTGCTAAAAAAAAAAAAGGATAATA 16 52 1 CTAAAAAAAA 0.918311 -49 TCGAACAAAAGTTTATAAAAAAACTGGACCCG 17 27 0 GTTAAAAAAA 0.830433 -274 CTTTGAAGAGCTTTCTCAAAAACCTAGTCACC 18 142 0 CTTCCAAAAA 0.89573 -159 CGTGGATATTCTTTACCAAAAATAGCCTCTTT 18 195 0 CTTACAAAAA 0.969697 -106 GGATTTTTCTCTTTAGAAAAAAAGCTCGACCT 18 244 1 CTTAAAAAAA 0.967193 -57 ** ** ****** Masking position 10 Map Score: 15.1015 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 112 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 GCCTCCTGTAAGGAGCTCCCCCTCCAAAAAAAGAA 1 53 0 AGGACCCCTC 0.980297 -248 TCTATTTTAAAGGATACAAGCCTCCTGTAAGGAGC 1 72 0 AGGAAACCTC 0.988884 -229 CGATCCCCTAAGGACAAAAACCAACCGATATTTCT 1 157 0 AGGAAACCAC 0.918722 -144 AATAAAGGTTAGGGTATAAACCTCCCTAGCAGTAT 7 69 1 AGGGAACCTC 0.980289 -51 CGAAAGGAGAAGGAGAGCATCCTTCTCCTTTCACC 9 15 1 AGGAACCCTC 0.976156 -54 GCCGTGGTAAAGGATCGACATCTTCAGCGTTGGAG 13 36 0 AGGACATCTC 0.974547 -265 AGTCAGAAACAGGAGCCAACCCCTCGAATAGGATG 13 115 1 AGGACACCCC 0.982008 -186 CTCTGAATAGAGAAACCAGTTCTTCTAAAAATCTA 15 88 0 AGAACATCTC 0.816412 -213 CATTATCTATGGGTACCATCCCTGCTCTGAGTTCT 15 139 1 GGGTCACCTC 0.815356 -162 GAGAATTATAGGGATCCATATCCCCCTCATTTCTA 15 231 0 GGGACATCCC 0.848723 -70 GTAGCTTGGAAGGCTACAGCTCTACCATTGAGCTA 17 166 0 AGGCAATCTC 0.867902 -135 CTTTAGAGAGAGAAAAAAAACCTTCGGCTTCCCAA 19 13 1 AGAAAACCTC 0.911757 -247 GCGACAGACAAGGGGACACCCCCTCTCTTCGCAGT 19 123 0 AGGGAACCCC 0.961694 -137 CTTATTGGGGAGGGTAGCTATCTGCAGTCTATAGG 19 224 1 AGGGACTCTC 0.89017 -36 **** * * *** * Masking position 12 Map Score: 13.5832 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 131 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 3 CTAGAGTAACCAATCCCTACAAGTCTACTCTT 5 146 0 CATCCCTAAA 0.966283 -155 TATTTTGCATCTATCCTCATAATCGATTATCT 7 41 0 CATCCTCAAA 0.884447 -79 GATAATTTGACTAGCCCTACAAATATAGGAAG 8 114 0 CAGCCCTAAA 0.795433 -187 CTTGAGTAGTCTCTTCCTAATATGTGGGGACG 8 174 1 CCTTCCTATA 0.865809 -127 AAGAATGGTGCTCTTCCCAGAAAGAGTAAGAA 8 232 1 CCTTCCCAAA 0.972512 -69 GTAGCACGCTCCCTTCTTATAAAAAAGAGTTA 11 110 0 CCTTCTTAAA 0.785822 -23 TCAAGATTTTGTATTCTTAAAAAATAGTT 13 282 1 GATTCTTAAA 0.505508 -19 TTTTTGTGGACTCTCCCAATAATTTCTTTTAC 14 85 1 CCTCCCAAAA 0.903737 -48 GAGTCGCCACCTCTTCCTACTAGCGATATGGG 15 189 1 CCTTCCTATA 0.865809 -112 TTCTAAGAAACCATCCCCATATCGCTAGTAGG 15 204 0 CATCCCCAAT 0.808069 -97 AGGGGGATATGGATCCCTATAATTCTCAGAGA 15 239 1 GATCCCTAAA 0.935883 -62 AAAAACCTTCGGCTTCCCAAAAACCTTTTTCT 19 28 1 GCTTCCCAAA 0.947423 -232 TTTGTGGAACGACTCCCCAAAATATACCGCGA 19 154 0 GCTCCCCAAA 0.977179 -106 GGAAGTCTGGGGATCCCCAGGATTCAAAGAGC 19 193 0 GATCCCCAGA 0.800845 -67 CAGATAGCTACCCTCCCCAATAAGGAAGTCTG 19 216 0 CCTCCCCATA 0.960944 -44 * ******* ** Masking position 9 Map Score: 9.8598 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 216 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TGCTAAACACAAGAGTCCTCTGAGGATAAGC 1 268 0 AAGAGTCTCT 0.852511 -33 CAATCCCTACAAGTCTACTCTTTCGCACATT 5 137 0 AAGTCTCTCT 0.987697 -164 CACACAGTCTCCTCTG 6 2 0 CAGTCTCTCT 0.949385 -15 TTATCTAGAAAAGTCTGCGCTAGGGATGAAG 8 269 0 AAGTCTCGCT 0.97515 -32 GTGAAAGGAGAAGGATGCTCTCCTTCTCCTT 9 18 0 AAGGATCTCT 0.857797 -51 AAGTCTTCGCTTCCCTCTAGA 14 1 1 AAGTCTCGCT 0.97515 -132 GATTATTATCAAGTCTCCTCTGAATAGAGAA 15 109 0 AAGTCTCTCT 0.987697 -192 TCAAAGAGCTAAGGCTTTTCTCGCAACATTT 18 40 0 AAGGCTTTCT 0.841167 -261 GAGCAAGATTAGGACTTCTCTGCTATCCTTA 18 87 0 AGGACTCTCT 0.890823 -214 ****** **** Masking position 6 Map Score: 7.31297 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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 5 AAAAACTCTATTTTAAAGGATACAAGCCTC 1 83 0 TTTTAAAGGA 0.503888 -218 GCATAGAATGTGCGAAAGAGTAGACTTGTA 5 131 1 TGCGAAAGAG 0.789386 -170 CCGAGTATACTGCTAGGGAGGTTTATACCC 7 80 0 TGCTAGGGAG 0.727826 -40 CCCCCGAACCTGCTAGAGGGGTTGCTTTTC 8 41 1 TGCTAGAGGG 0.965304 -260 GCTCAATTTTTTGTAAAGAGGATGGTTTTG 12 53 1 TTGTAAAGAG 0.862387 -115 ATCTTCAGCGTTGGAGAGAGAATGTTCATC 13 22 0 TTGGAGAGAG 0.703715 -279 GAGGTTGCCGTGGTAAAGGATCGACATCTT 13 47 0 TGGTAAAGGA 0.840153 -254 TTGAAGCTATTTCTAAAGGAGGTTGCCGTG 13 65 0 TTCTAAAGGA 0.854453 -236 ATATAGAGATTTCTAGAGGGAAGCGAAGAC 14 13 0 TTCTAGAGGG 0.951682 -120 GTGGCGACTCTGGTAGAGGGTTCTTAGAAC 15 169 0 TGGTAGAGGG 0.946327 -132 TGCAATCTTCTTTTAGAGAAATTTTATTTT 17 88 0 TTTTAGAGAA 0.503869 -213 TAGGGGATCTCGCTAGAGGAAAGAGGCTAT 18 176 1 CGCTAGAGGA 0.758637 -125 AGGCTATTTTTGGTAAAGAATATCCACGAG 18 199 1 TGGTAAAGAA 0.788279 -102 CGAGCTTTTTTTCTAAAGAGAAAAATCCCT 18 242 0 TTCTAAAGAG 0.907407 -59 TTTTTTCTCTCTCTAAAGAG 19 1 0 CTCTAAAGAG 0.724954 -259 ********** Masking position 5 Map Score: 8.3857 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 286 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CGATAAGCGAGGTTCTTTTTTTGGAGGGGG 1 41 1 GGTTCTTTTT 0.859025 -260 AGGCTCTTATGTCTTTTTTTCATACTAGAA 1 231 1 GTCTTTTTTT 0.85987 -70 GTGTTTAGCAGGCTGTTTCTTA 1 289 1 GGCTGTTTCT 0.931555 -12 GTATAGGGACGGCTCTTTGTTTTGTTGAGC 4 75 1 GGCTCTTTGT 0.937863 -121 CAGTATACTCGGTTTTTTCTTTTTGTTTGC 7 98 1 GGTTTTTTCT 0.900975 -22 TTGCTTTTCGGGCTTTTTTTCGTTGTTTTC 8 62 1 GGCTTTTTTT 0.971303 -239 GTTGGTTTTTGGTTGTTTTTGATTATTGTT 11 70 1 GGTTGTTTTT 0.807072 -63 TAAGCCTCGAGTCTTTTTGTGGACTCTCCC 14 72 1 GTCTTTTTGT 0.813746 -61 TACAGGAGCTGGCTTTTTCGCCCCTCATC 14 114 1 GGCTTTTTCG 0.82198 -19 AATATACGGGGTCTCTTTGTCAGGGTTTTG 16 80 1 GTCTCTTTGT 0.732363 -21 AGAGGAAAGAGGCTATTTTTGGTAAAGAAT 18 190 1 GGCTATTTTT 0.842161 -111 GGGCTCAAAGGGATTTTTCTCTTTAGAAAA 18 234 1 GGATTTTTCT 0.734427 -67 GATAAGGTCGAGCTTTTTTTCTAAAGAGAA 18 250 0 AGCTTTTTTT 0.673234 -51 GGAAGCCGAAGGTTTTTTTTCTCTCTCTAA 19 15 0 GGTTTTTTTT 0.906794 -245 ********** Masking position 6 Map Score: 11.4532 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 156 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 7 TGTATCCTTTAAAATAGAGTTTTTCTTATGAT 1 89 1 AAAATAGATT 0.88251 -212 TTCATACTAGAAAATATAAGCTTATCCTCAGA 1 249 1 AAAATATACT 0.519766 -52 AGTGGTGCGGAAAAAAACGATTCGTGTAGTAT 4 47 1 AAAAAAACTT 0.636855 -149 TACTCTACTTAAAACAGCTGCTATACAAGCCT 4 134 0 AAAACAGCCT 0.551095 -62 GGATAGATGCAAAATAAAGGTTAGGGTATAAA 7 57 1 AAAATAAATT 0.925819 -63 AGAAAGAGTAAGAATAAAACTTCATCCCTAGC 8 250 1 AGAATAAATT 0.612844 -51 TGTTTGTATTAAAATAACTCTTTTTTATAAGA 11 96 1 AAAATAACTT 0.903328 -37 TTATCATAGGAAAATAAACGCACAAAACCATC 12 73 0 AAAATAAACA 0.444338 -95 CAAAGTGCAAAAAATAAAAGCTGATGGCTTCA 12 114 1 AAAATAAACT 0.903339 -54 CATGATTTTGGAAATAACGCTTGTGCTCTAGG 13 154 1 GAAATAACTT 0.542373 -147 CGCAACCATCAAAACAAAACTTCAAATATAAA 15 30 1 AAAACAAATT 0.783697 -271 AAGCATCAGCAAAATAAAAATTTTTATATTTG 15 52 0 AAAATAAATT 0.925819 -249 GCTGATGCTTAAAATAGATTTTTAGAAGAACT 15 74 1 AAAATAGATT 0.86005 -227 TTTGCAAGCCAAAATAAAATTTCTCTAAAAGA 17 78 1 AAAATAAATT 0.925345 -223 TTCTTTACCAAAAATAGCCTCTTTCCTCTAGC 18 187 0 AAAATAGCCT 0.808772 -114 TTAGAGAGAGAAAAAAAACCTTCGGCTTCCCA 19 15 1 AAAAAAAATT 0.700807 -245 ******** ** Masking position 6 Map Score: 8.1654 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 102 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 8 AAGAGCCTCCAGATAATCGATACGGGGACA 1 209 0 AGATAATCGA 0.96886 -92 TCTAGCACCTAGATAATCGATTATGAGGAT 7 31 1 AGATAATCGA 0.96886 -89 CAATTACAATAGAGAATCGAGGATAATTTG 8 137 0 AGAGAATCGA 0.948052 -164 AAATCTTGAGAGTCAATCGGGTTTTTATAG 13 261 0 AGTCAATCGG 0.9372 -40 ATAGGAAGGAAGTCAATCGAACAAAAGTTT 17 45 0 AGTCAATCGA 0.947371 -256 ACCTTATCTTAGATAATCGGGTATTCTCAG 18 272 1 AGATAATCGG 0.962678 -29 ********** Masking position 5 Map Score: 4.40384 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 9 TAAGAAACAGCCTGCTAAACACAAGAGTC 1 282 0 GCCTGCTAAA 0.980588 -19 CCAACGAAATGCCTTCTAAATCAAAAACTC 5 41 0 GCCTTCTAAA 0.944657 -260 GGCTTCAGTGGCTGGCTAAAATGTACGCAT 12 139 1 GCTGGCTAAA 0.957044 -29 GATATCGCTTGCTTGCTAAAAAAAAAAAAG 16 47 1 GCTTGCTAAA 0.983851 -54 TTTTATTTTGGCTTGCAAAAAGATAGGAAG 17 67 0 GCTTGCAAAA 0.937594 -234 TCTTTGAAGAGCTTTCTCAAAAACCTAGTC 18 145 0 GCTTTCTCAA 0.882744 -156 ********** Masking position 9 Map Score: 3.17015 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 10 GTTCTCTCTGTTCTCTTTTCTTCCTATATT 8 95 1 TTCTCTTTTC 0.972886 -206 TTATCCTCGATTCTCTATTGTAATTGGATA 8 141 1 TTCTCTATTG 0.891623 -160 GATGCTCTCCTTCTCCTTTCGGATT 9 6 0 TTCTCCTTTC 0.967476 -63 GAGAGCATCCTTCTCCTTTCACCTATTGGT 9 27 1 TTCTCCTTTC 0.967476 -42 AAGAACTGGTTTCTCTATTCAGAGGAGACT 15 99 1 TTCTCTATTC 0.972886 -202 GGAAGACTTGCTCTCTATTCTTCTCCCGGC 19 79 0 CTCTCTATTC 0.929177 -181 ********** Masking position 4 Map Score: 3.90224 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 52 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ATCCCATGTGGCGATAGGCCGGGTCTAGCG 1 119 1 GCGATAGGCC 0.950425 -182 TCTACTATCGGCGCTAGACCCGGCCTATCG 1 130 0 GCGCTAGACC 0.95741 -171 AATGATCTTTGTTCTAAGCCAGACTATACT 4 162 0 GTTCTAAGCC 0.75007 -34 TATGCTTCTCGCCCTAAGCCCTTCTGAGTT 5 16 1 GCCCTAAGCC 0.907532 -285 GATTATCTAGGTGCTAGACCTAAATAGGCT 7 19 0 GTGCTAGACC 0.930227 -101 AGAAAAGTCTGCGCTAGGGATGAAGTTTTA 8 264 0 GCGCTAGGGA 0.91009 -37 TTATTTCAAAGAGCTAAGGCTTTTCTCGCA 18 46 0 GAGCTAAGGC 0.933451 -255 ATATCCACGAGAGCTAGGGCTCAAAGGGAT 18 218 1 GAGCTAGGGC 0.939034 -83 ********** Masking position 6 Map Score: 2.64029 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 AAAACTAGAGTAACCAATCCCTACAAGTCTA 5 151 0 TAACCATCCC 0.652665 -150 AAAAGCCCGAAAAGCAACCCCTCTAGCAGGT 8 48 0 AAAGCACCCC 0.901432 -253 GCCAATCTCATAGGCGTCCCCACATATTAGG 8 189 0 TAGGCGCCCC 0.846193 -112 ACTTGGTCAGAAGCCAATCTCATAGGCGTCC 8 201 0 AAGCCATCTC 0.860432 -100 TAAACGCACAAAACCATCCTCTTTACAAAAA 12 60 0 AAACCACCTC 0.945222 -108 GCGTACATTTTAGCCAGCCACTGAAGCCATC 12 136 0 TAGCCACCAC 0.824037 -32 ATCCTTTACCACGGCAACCTCCTTTAGAAAT 13 56 1 ACGGCACCTC 0.669555 -245 TCAGAAACAGGAGCCAACCCCTCGAATAGGA 13 117 1 GAGCCACCCC 0.949694 -184 TCTAGGTGTAAAACTGCCCTCATACTCACTT 13 180 1 AAACTGCCTC 0.590106 -121 AGGGGCGAAAAAGCCAGCTCCTGTAAAAGAA 14 108 0 AAGCCACTCC 0.913203 -25 CATTTCTAAGAAACCATCCCCATATCGCTAG 15 208 0 AAACCACCCC 0.969771 -93 GACCCGACCGAAGCCGAGCCCA 17 2 0 AAGCCGGCCC 0.815947 -299 CACCGTACTCAAGCTAACTTCCATGCCAGAG 18 115 0 AAGCTACTTC 0.506415 -186 AGACTGCAGATAGCTACCCTCCCCAATAAGG 19 223 0 TAGCTACCTC 0.803519 -37 ****** **** Masking position 11 Map Score: 6.91266 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 150 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 CCTCCTGTAAGGAGCTCCCCCTCCAAAAAA 1 57 0 GGAGCTCCCC 0.930113 -244 CTTTTTCAAAGTATGTCCCCGTATCGATTA 1 196 1 GTATGTCCCC 0.932302 -105 CCCTCGAATAGGATGTGCCCATGATTTTGG 13 135 1 GGATGTGCCC 0.944736 -166 TTATAGGGATCCATATCCCCCTCATTTCTA 15 231 0 CCATATCCCC 0.845675 -70 TTTCCTCTAGCGAGATCCCCTACTCTTTGA 18 168 0 CGAGATCCCC 0.937355 -133 CGAAGAGAGGGGGTGTCCCCTTGTCTGTCG 19 127 1 GGGTGTCCCC 0.931008 -133 AAGGAAGTCTGGGGATCCCCAGGATTCAAA 19 197 0 GGGGATCCCC 0.499774 -63 ********** Masking position 6 Map Score: 2.31056 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 33 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 ATACGGGGACATACTTTGAAAAAGTATACG 1 190 0 ATACTTTGAA 0.62578 -111 TATAGGGACGGCTCTTTGTTTTGTTGAGCG 4 76 1 GCTCTTTGTT 0.738264 -120 AGAACAGAGAGAACTTTGAAAACAACGAAA 8 79 0 GAACTTTGAA 0.805678 -222 TTTATTTTTTGCACTTTGATCTTTGGTTTA 12 102 0 GCACTTTGAT 0.907504 -66 CTGGTAGAGGGTTCTTAGAACTCAGAGCAG 15 160 0 GTTCTTAGAA 0.677611 -141 AAAAGCCTTAGCTCTTTGAAATAAAAATAT 18 52 1 GCTCTTTGAA 0.97727 -249 GAGATCCCCTACTCTTTGAAGAGCTTTCTC 18 157 0 ACTCTTTGAA 0.907697 -144 AAAATGCATCGCTCTTTGAATCCTGGGGAT 19 183 1 GCTCTTTGAA 0.97727 -77 ********** Masking position 5 Map Score: 2.56376 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 79 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 GTTCTTTTTTTGGAGGGGGAGCTCCTTACA 1 52 1 TGGAGGGGGA 0.796899 -249 GTGTAGTATAGGGACGGCTCTTTGTTTTGT 4 70 1 GGGACGGCTC 0.874989 -126 AGCCTCTATCAGGAAGCCTAAGATACTATA 4 109 0 AGGAAGCCTA 0.837458 -87 CTGCTTAAGATGGAAGGCGCTTCATTTTGA 5 260 1 TGGAAGGCGC 0.903696 -41 CTAATATGTGGGGACGCCTATGAGATTGGC 8 190 1 GGGACGCCTA 0.942099 -111 TGTAAACAGTTGGAAGCGGAGTTGAAGCTA 13 86 0 TGGAAGCGGA 0.936598 -215 GATTTCTAGAGGGAAGCGAAGACTT 14 6 0 GGGAAGCGAA 0.847599 -127 ACCGGTAGCTTGGAAGGCTACAGCTCTACC 17 175 0 TGGAAGGCTA 0.944294 -126 AAAGGTTTTTGGGAAGCCGAAGGTTTTTTT 19 26 0 GGGAAGCCGA 0.977209 -234 CTTCCTTATTGGGGAGGGTAGCTATCTGCA 19 220 1 GGGGAGGGTA 0.824605 -40 ********** Masking position 6 Map Score: 3.48424 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 79 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617