AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_bsub_reg_100.orf -o00400_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pabB 166 para-aminobenzoate synthase (subunit A) #2 aroI 275 shikimate kinase #3 ykrV 94 similar to aspartate aminotransferase #4 aspB 22 aspartate aminotransferase #5 ypmA 142 ypmA #6 tyrA 48 prephenate dehydrogenase #7 trpE 215 anthranilate synthase #8 aroB 61 3-dehydroquinate synthase #9 aroF 69 chorismate synthase #10 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #11 aroC 111 3-dehydroquinate dehydratase #12 yqhS 86 similar to 3-dehydroquinate dehydratase #13 yqhR 226 yqhR #14 yqeG 300 similar to hypothetical proteins #15 pheB 60 chorismate mutase #16 obg 33 GTPase activity #17 spo0B 300 sporulation initiation phosphoprotein #18 pheS 300 phenylalanyl-tRNA synthetase (alpha subunit) #19 tyrS 300 tyrosyl-tRNA synthetase #20 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #21 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #22 eno 29 enolase #23 tpi 30 triose phosphate isomerase #24 pgk 300 phosphoglycerate kinase #25 ywfB 151 alternate gene name: ipa-80d #26 tyrZ 248 tyrosyl-tRNA synthetase Motif number 1 ATCATACAGAAAAAGACCCTTCCATCGAAG 2 33 1 AAAAGACCCT 0.903291 -243 ACTTCGACGCAAAAAAGCGTTAAAACCTTC 2 89 0 AAAAAAGCGT 0.924977 -187 AAATGGCTACAACAAAGCGCACTATAAGCT 2 166 1 AACAAAGCGC 0.876269 -110 ATACTAGTATCACAGAGCGGGAAATCCGCT 5 65 0 CACAGAGCGG 0.878787 -78 GAAAATAAGCAACAGAGCCGGCAACATATA 10 18 1 AACAGAGCCG 0.956866 -219 CAAAACAGAACAAAAACCGGCGGCGTTATA 10 44 0 CAAAAACCGG 0.716785 -193 TAGCAACTAAAAAAGAGCCTTAAAGGGCTC 11 14 0 AAAAGAGCCT 0.95216 -98 GTTGGCTGAAAAGAGAGCCTGGTGCCAGGC 15 16 1 AAGAGAGCCT 0.873382 -45 TTGTTTTTCTAACAAAGCCTTCTCTGTTAT 17 219 1 AACAAAGCCT 0.950415 -82 TGGAAAATAAAAAAAACCCGTCCCTTGTAC 18 240 0 AAAAAACCCG 0.885637 -61 CTTTTATGTAAACAAACCGTCATATGTCTT 18 270 0 AACAAACCGT 0.868137 -31 CGCTTTTGCAAACAAAGCCGGCCAGGCTTT 19 125 1 AACAAAGCCG 0.949434 -176 AAAAAAGCGTCCAGATATCA 20 1 1 AAAAAAGCGT 0.924977 -235 TTTTTTACAAAAAAAAGCGCCAGATGATAT 20 25 0 AAAAAAGCGC 0.861575 -211 TTTTTTTTGTAAAAAACCCTTGAACATTGC 20 39 1 AAAAAACCCT 0.88771 -197 GTTTCTCTATCACAGAGCGTTTTCTGAAAG 24 103 0 CACAGAGCGT 0.880967 -198 CATACAAACAAAAAAACCCTTTAAAAAGGG 25 41 0 AAAAAACCCT 0.88771 -111 CTCCCTGTTTCAGAGAGCCGGCGGTAGGTG 26 40 1 CAGAGAGCCG 0.751067 -209 ACAAACACAAAAAAGAGCCCATCCCAATAA 26 214 0 AAAAGAGCCC 0.909481 -35 ********** Masking position 6 Map Score: 24.6134 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 663 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 GGAAGAGAAATTCACTTTTTTCACTAACAA 1 95 1 TTCACTTTTT 0.871945 -72 TTTCAATCTTTACCTTGTTTTATTATACAC 11 79 0 TACCTTGTTT 0.523948 -33 TAAAAAAGCTCACACTTTTTGGCAGCTGCG 13 166 0 CACACTTTTT 0.776454 -61 TTATTGACATTTCATTTTTTGGGCACACTT 13 193 1 TTCATTTTTT 0.862578 -34 AATTTTTTTGCTCAGTTTTTCTTTAGGCGC 14 223 1 CTCAGTTTTT 0.728634 -78 ACCCGCACCCTTCCCTTTTTCTTTCTTTCA 14 280 0 TTCCCTTTTT 0.950562 -21 AAATATCATGTTCCTTTTTTCTGGCTTTGG 17 176 0 TTCCTTTTTT 0.946594 -125 TTTGCATCCTCCTTTTATGTAAACAAAC 18 283 0 CTCCTTTTAT 0.756739 -18 AAGATAAAGCTCCTTTTTTAATTAAAATA 19 282 0 CTCCTTTTTT 0.973231 -19 TCCCTGCACATTCATTTTTTATTTTGTAGT 20 203 0 TTCATTTTTT 0.862578 -33 TCTGTGTCACTCCCTTTTTTTGATGGTTG 21 10 1 CTCCCTTTTT 0.975271 -138 GAAGTTTCTCCTCGTTTTTTCTTAGCATTC 21 70 1 CTCGTTTTTT 0.896521 -78 GACATTATATCACGTTTTTTGACGAATGCT 21 93 0 CACGTTTTTT 0.682998 -55 CGGACTCCCTTTCCCTTTTTCCATGAAGAC 24 70 1 TTCCCTTTTT 0.950562 -231 AGCGGTTTGTCTCCCTGTTTCAGAGAGCCG 26 30 1 CTCCCTGTTT 0.907815 -219 TTTTCCTCCTTTTTTACAAACACAA 26 234 0 CTCCTTTTTT 0.973231 -15 ********** Masking position 6 Map Score: 18.5215 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 488 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 TTATATAGATACCGGCTTTACCGGTCAAGCTTAT 2 189 0 ACCGGTACGG 0.762717 -87 AGCCGCATAAAGCGGCTTTTGCGGTGTGGGAGTA 5 12 1 AGCGGTTCGG 0.960562 -131 TTTATTTAAAAGCGGATTTCCCGCTCTGTGATAC 5 55 1 AGCGGTCCGC 0.946858 -88 CTCTCCTTTTCGCGAGGGTTTCTCATGTAAAAAA 12 58 0 CGCGATTCTC 0.84286 -29 CTAGAGGTTTAGCGGTGTTTCCTGTACAATAGAG 13 58 0 AGCGGTTCTG 0.952473 -169 TCTCATTCTTGGCGGGGTCTGCTCGCACATACTC 17 68 0 GGCGGCTCTC 0.957957 -233 GCTCTCAGTCAGCGGCATTTTCTCCCTGGAAAGC 18 40 0 AGCGGTTCTC 0.985975 -261 TGTACGCGGTCCCGGCGACAACTCAAGAGGTGAA 18 99 0 CCCGGCACTC 0.876942 -202 TCGCCGGGACCGCGTACACTGCGCGTAAAGGTGA 18 115 1 CGCGTCTCGC 0.812116 -186 AGGGTGGTACCGCGGCCACAACTCGTCCCTTGTA 18 209 1 CGCGGCACTC 0.961535 -92 TGTCAATTCTAGCGGAAGTTTCTCCTCGTTTTTT 21 56 1 AGCGGTTCTC 0.985975 -92 CTGCTTAAAACGCGGTCGTTTCTCTATCACAGAG 24 116 0 CGCGGTTCTC 0.987869 -185 AAGCAGCTTTGCCGGCGCTTTCGCCTAAGGCCGC 24 144 1 GCCGGTTCGC 0.922513 -157 GATCTGCCCTAGCGGAGTTATCGCTTGAACAGAC 24 222 1 AGCGGTACGC 0.975341 -79 ***** ** *** Masking position 3 Map Score: 16.1642 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 353 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TCTAATTGCTTTATACACACTCTTGTGTAT 7 32 0 TTATACACAC 0.971018 -184 AATCGTTCTGTTATCCACACCAAAAAGTGG 14 85 1 TTATCCACAC 0.959766 -216 TTTAGACAAATTATAAACACGATACTCACA 14 121 0 TTATAAACAC 0.904337 -180 GTGGATAAATTTACACACACTATCCACTCT 14 164 0 TTACACACAC 0.959766 -137 GTGTGTAAATTTATCCACACCTGGTGAAGA 14 176 1 TTATCCACAC 0.959766 -125 TTATAATTCATAATACACACTTATACAGAC 17 245 1 TAATACACAC 0.825 -56 TAATACACACTTATACAGACTCCTAAATAA 17 255 1 TTATACAGAC 0.847215 -46 CTCTACTTTATTACCCAAACGCTTTTAAGT 20 108 0 TTACCCAAAC 0.769824 -128 ACAAAAAATTTTATAAAAACTCTACTTTAT 20 127 0 TTATAAAAAC 0.650531 -109 TCCTCCTTTTTTACAAACACAAAAAAGAGC 26 226 0 TTACAAACAC 0.870647 -23 ********** Masking position 7 Map Score: 9.66547 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 34 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 AAAAGTGAATTTCTCTTCCAAGAATAACAT 1 84 0 TTCTCTTCCA 0.711239 -83 TTTTTCATCCTCCAGTTTGAA 5 132 0 TTTTCATCCT 0.97714 -11 TCATGCCATCTTCTCATTCTCCTTGCCATA 7 183 1 TTCTCATTCT 0.861164 -33 TATGGCAATTTTTTCAGCCTGTCAATCTAG 13 88 0 TTTTCAGCCT 0.959834 -139 ACCCTTCCCTTTTTCTTTCTTTCAAAATGA 14 274 0 TTTTCTTTCT 0.813725 -27 CCAGGCTCTCTTTTCAGCCAACATTGA 15 8 0 TTTTCAGCCA 0.884686 -53 GAGATGTTTATTCTCATTCTTGGCGGGGTC 17 83 0 TTCTCATTCT 0.861164 -218 CTTTGGTTGATTTGCAGCCAGGCAGAACAT 17 152 0 TTTGCAGCCA 0.794788 -149 GTCAGCGGCATTTTCTCCCTGGAAAGCAGT 18 37 0 TTTTCTCCCT 0.760156 -264 TTTGCATCCTCCTTTTATGT 18 291 0 TTTGCATCCT 0.955711 -10 AAGACGAATGTTTGCATTCTCTTATTAGTA 19 199 1 TTTGCATTCT 0.861164 -102 TTTTTTCATCCTTTCCCTGCAC 20 224 0 TTTTCATCCT 0.97714 -12 TTTTCCTCCTTTTTTACAAA 26 239 0 TTTTCCTCCT 0.899137 -10 ********** Masking position 2 Map Score: 10.4011 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 505 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 GATAAATAGGAAGGGAGGAATGGCG 2 6 0 AAGGGAGGAA 0.929108 -270 TAATGCGATGAAGGGAGAAGAAGTC 9 55 1 AAGGGAGAAG 0.893855 -15 AAGAAAGAAAAAGGGAAGGGTGCGGGTT 14 283 1 AAGGGAAGGG 0.960522 -18 CTCTATTTTAAAGGGGGGATGCAA 15 47 1 AAGGGGGGAT 0.885392 -14 TCCCTTGTACAAGGGACGAGTTGTGGCCGC 18 220 0 AAGGGACGAG 0.985198 -81 TCCCTTGTACAAGGGACGGGTTTTTTTTAT 18 234 1 AAGGGACGGG 0.984188 -67 TGTTTACATAAAAGGAGGATGCAAA 18 286 1 AAAGGAGGAT 0.755734 -15 CGTTTACACGAAGGGACGATTGATTATCGC 19 239 0 AAGGGACGAT 0.960712 -62 CGTGTAAACGAAGGGGCGTTTTTTATTTTA 19 259 1 AAGGGGCGTT 0.70941 -42 GAAAGCGGACAAGGGAAGGGGACGGACTCC 24 48 1 AAGGGAAGGG 0.960522 -253 TTCATGGAAAAAGGGAAAGGGAGTCCGTCC 24 67 0 AAGGGAAAGG 0.754805 -234 CCATCCCAATAAGGGACGTGGCTCAATGCA 26 196 0 AAGGGACGTG 0.954612 -53 TGTTTGTAAAAAAGGAGGAAAA 26 237 1 AAAGGAGGAA 0.623808 -12 ********** Masking position 2 Map Score: 14.28 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 147 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 AAAGCAATGTTGTTAGTGAAAAAAGTGAATTT 1 102 0 TGTTATAAAA 0.55358 -65 CATTTCAAGATTTTTTTAGAAGGTGAGAATAG 3 73 1 TTTTTTGAAG 0.858535 -22 TAGGATGGTGTTTTATTTAAAAGCGGATTTCC 5 44 1 TTTTATAAAA 0.731515 -99 CTTTTTGCTGAAAAATATGTTAT 9 2 1 TTTTTCGAAA 0.737846 -68 AAAGCTGATTTTTTTATTGAAACAATACAATT 10 159 1 TTTTTTGAAA 0.907638 -78 CACGTACAACTTTTTTTTGAAAATTTCTATTA 11 50 0 TTTTTTGAAA 0.959371 -62 TATTTTCAAATTTTACTCGCAGCTGCCAAAAA 13 149 1 TTTTATGCAG 0.416945 -78 AGTGTGAGCTTTTTTATTGACATTTCATTTTT 13 180 1 TTTTTTGACA 0.831914 -47 AGAAACCCAATTTTTGTCGAAATTTTTTTGCT 14 203 1 TTTTTTGAAA 0.95999 -98 GCAAGTTCGATTTTTTTCGACAATCATTTTGA 14 251 1 TTTTTTGACA 0.850164 -50 ATGACTGGAGTTTTTTTTGCAATATGCGGAGT 17 15 1 TTTTTTGCAA 0.898398 -286 AAAACAATTGTTTTTCTAACAAAGCCTTCTCT 17 212 1 TTTTTTACAA 0.792571 -89 GCGTTTTTTATTTTAATTAAAAAAGGAGCTTT 19 274 1 TTTTATAAAA 0.474887 -27 CTGGCGCTTTTTTTTGTAAAAAACCCTTGAAC 20 32 1 TTTTTTAAAA 0.596861 -204 TAAAGTAGAGTTTTTATAAAATTTTTTGTATT 20 128 1 TTTTTTAAAT 0.434632 -108 GAACTGTCAATGTTTTTTGAAAATATTGATAA 25 78 0 TGTTTTGAAA 0.89817 -74 CTCTTTTTTGTGTTTGTAAAAAAGGAGGAAAA 26 227 1 TGTTTTAAAA 0.653998 -22 ***** * **** Masking position 4 Map Score: 10.7653 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 403 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 8 CACTGCGCGTAAAGGTGAACCGGAATCTGATT 18 131 1 AAGGTGACCG 0.83962 -170 GTCTGAAATAAGGGTGGTACCGCGGCCACAAC 18 199 1 AGGTGGACCG 0.988145 -102 TCTTATTAGTAGGGTGGTACCGCGATAATCAA 19 218 1 AGGTGGACCG 0.988145 -83 TCAAAAAAAGGGAGTGACACAGA 21 2 0 GGGTGAACAG 0.803282 -146 CTGCTATAAGGAAGTGGAACAG 23 19 1 GAGTGGACAG 0.861717 -12 GGAAAAAGGGAAAGGGAGTCCGTCCCCTTCCC 24 60 0 AAGGGATCCG 0.810776 -241 CAGCACGAAAAACGTGAAACCGTCTGTTCAAG 24 245 0 AAGTGAACCG 0.970547 -56 AGTAGCAAAGAACGGGAAACCGTTATTCGAAT 26 126 1 AAGGGAACCG 0.964514 -123 GTCTTCAACCAGGGTGGTACCGCGTGCATTGA 26 172 1 AGGTGGACCG 0.988145 -77 ** **** **** Masking position 10 Map Score: 6.26242 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 92 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 ATGATAAATAGGAAGGGAGGAATGGCG 2 8 0 GGAAGGGAGG 0.671214 -268 GGCGTGTCCTGAAATGGAGTATGACTAACA 5 95 1 GAAATGGAGT 0.587295 -48 CACTCCTTATGGCAAGGAGAATGAGAAGAT 7 190 0 GGCAAGGAGA 0.891051 -26 ATAAAGGGTTGAATGGCAGTGTGCATCAGA 10 95 1 GAATGGCAGT 0.609742 -142 AGATCGTTGGGAAAGGCAGAGGTCTGATGC 10 117 0 GAAAGGCAGA 0.943673 -120 AAAATCAGCTGAAAAGCTGATTTTTTTATT 10 147 1 GAAAAGCTGA 0.710983 -90 AAGACAGCGAGACTGGGAGAGTAGAG 10 221 1 GACTGGGAGA 0.85715 -16 AAACCCTCGCGAAAAGGAGAGATTGT 12 71 1 GAAAAGGAGA 0.912584 -16 TAAAGAAATAGGCAGGTTGATAAT 13 5 0 GGCAGGTTGA 0.437701 -222 CCTCTAGATTGACAGGCTGAAAAAATTGCC 13 85 1 GACAGGCTGA 0.867373 -142 CACCTAGAATGAAATGCAGAGTATGTGCGA 17 50 1 GAAATGCAGA 0.720751 -251 TTGATTTGCAGCCAGGCAGAACATTTTATG 17 146 0 GCCAGGCAGA 0.909029 -155 TTTTCTCCCTGGAAAGCAGTTGATCAGAAA 18 27 0 GGAAAGCAGT 0.680468 -274 TAAAGATTGAGACAAGTAGAATATCCTTAC 19 31 1 GACAAGTAGA 0.675801 -270 TCTTGACATTGCAAAGGTGTGAATCAA 21 131 1 GCAAAGGTGT 0.384297 -17 TGGAAAAAGGGAAAGGGAGTCCGTCCCCTT 24 63 0 GAAAGGGAGT 0.902314 -238 GCCTAGGAGATCCTCCTTCA 24 291 0 GCCTAGGAGA 0.573777 -10 GGCTCTCTGAAACAGGGAGACAAACCGCTA 26 29 0 AACAGGGAGA 0.56452 -220 ********** Masking position 6 Map Score: 7.35613 Number of sites scoring better than the average of aligned sites = 1089 Number in coding regions = 880 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 10 TGCTACCCTATTCTCTAACTCAACTCATTCT 7 59 0 TTCTCTAATC 0.793024 -157 TAGTATTTTATCCTCTCATGCCATCTTCTCA 7 168 1 TCCTCTCAGC 0.943017 -48 TCTCATGCCATCTTCTCATTCTCCTTGCCAT 7 181 1 TCTTCTCATC 0.78985 -35 TGCTCTCACTCCTTATGGCAA 7 205 0 TGCTCTCATC 0.94102 -11 TCTCCACATTTTCTCTAATGCGGTCAATTTG 8 13 0 TTCTCTAAGC 0.547609 -49 TCGTCTCAAATCCTTTCAATCTTTACCTTGT 11 91 0 TCCTTTCATC 0.954161 -21 GCTAACCATTTCCTTTCACTCTATTGTACAG 13 40 1 TCCTTTCATC 0.954161 -187 CCTTCCCTTTTTCTTTCTTTCAAAATGATTG 14 271 0 TTCTTTCTTC 0.710584 -30 GCGTTAAAAATGCTCTCAGTCAGCGGCATTT 18 54 0 TGCTCTCATC 0.94102 -247 GGAATCTGATTCCGTTATGTCAATGAAGCTG 18 152 1 TCCGTTATTC 0.401786 -149 GATATTCTACTTGTCTCAATCTTTACCTTTT 19 25 0 TTGTCTCATC 0.671768 -276 ACGGATCAGGTCCGTTCTTTCACTACTGAAA 19 152 0 TCCGTTCTTC 0.771355 -149 GACATTGTCTTCCGCTCATTCGAATAACGGT 26 144 0 TCCGCTCATC 0.963562 -105 ******** ** Masking position 6 Map Score: 7.09322 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 328 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 11 CGCCGGGAGTTTTTTTATATTTCGTGCATC 1 32 1 TTTTTTATAT 0.755203 -135 CTCTATTTTCTTTTTTACTTGTTTTTAATT 1 136 0 TTTTTTACTT 0.846836 -31 TTTCTTTACTTTTTTCATTTAACCATATAT 3 30 1 TTTTTCATTT 0.617143 -65 AGTAGGATGGTGTTTTATTTAAAAGCGGAT 5 42 1 TGTTTTATTT 0.617143 -101 ATACACACTCTTGTGTATTTCTAAGCTGTT 7 20 0 TTGTGTATTT 0.607536 -196 GCCGGCTCTGTTGCTTATTTTCACAATGA 10 10 0 TTGCTTATTT 0.500335 -227 AAAAGCTGATTTTTTTATTGAAACAATACA 10 158 1 TTTTTTATTG 0.758331 -79 TTTAAGGCTCTTTTTTAGTTGCTATTCATA 11 20 1 TTTTTTAGTT 0.673472 -92 GAAGTGAACATTTTTTACATGAGAAACCCT 12 48 1 TTTTTTACAT 0.52876 -39 AAGTGTGAGCTTTTTTATTGACATTTCATT 13 179 1 TTTTTTATTG 0.758331 -48 AATCATTTAATTTCTTATTTAGGAGTCTGT 17 269 0 TTTCTTATTT 0.758331 -32 GGGACGGGTTTTTTTTATTTTCCAAAGACA 18 246 1 TTTTTTATTT 0.938277 -55 ATATGACGGTTTGTTTACATAAAAGGAGGA 18 275 1 TTGTTTACAT 0.263658 -26 CGAAGGGGCGTTTTTTATTTTAATTAAAAA 19 267 1 TTTTTTATTT 0.938277 -34 ATAAAGCTCCTTTTTTAATTAAAATAAAAA 19 278 0 TTTTTTAATT 0.58187 -23 TTATAAAATTTTTTGTATTTCAGTATTTCC 20 141 1 TTTTGTATTT 0.829088 -95 TGCACATTCATTTTTTATTTTGTAGTTATC 20 199 0 TTTTTTATTT 0.938277 -37 TTTAAAGGGTTTTTTTGTTTGTATGGGAAT 25 46 1 TTTTTTGTTT 0.758331 -106 ATGGGCTCTTTTTTGTGTTTGTAAAAAAGG 26 222 1 TTTTGTGTTT 0.500335 -27 ********** Masking position 1 Map Score: 10.8264 Number of sites scoring better than the average of aligned sites = 1072 Number in coding regions = 677 Number in noncoding regions = 395 Number of orfs with sites within 600 bp upstream = 369 Fraction of orfs with sites within 600 bp upstream = 0.0592676 Motif number 12 GGCGAACCGGGAGTTTTGGCTTTTT 1 6 0 GAGTTTTGGC 0.978358 -161 TTCACCTCTTGAGTTGTCGCCGGGACCGCG 18 99 1 GAGTTGTCGC 0.979557 -202 TACAAGGGACGAGTTGTGGCCGCGGTACCA 18 213 0 GAGTTGTGGC 0.985901 -88 GAGTTTTGTCTCTCCTTTTG 22 20 0 GAGTTTTGTC 0.896494 -10 TGCCCTAGCGGAGTTATCGCTTGAACAGAC 24 226 1 GAGTTATCGC 0.945606 -75 ********** Masking position 5 Map Score: 2.23699 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 TCATTGTGAAAATAAGCAACAGAGC 10 5 1 TGTGAAAATA 0.825407 -232 ACAACTTTTTTTTGAAAATTTCTATTATATG 11 46 0 TTTGAAAATT 0.917323 -66 GCGAGTAAAATTTGAAAATAACGGGTATAAT 13 138 0 TTTGAAAATA 0.946807 -89 TTTTTCTTTCTTTCAAAATGATTGTCGAAAA 14 264 0 TTTCAAAATA 0.77385 -37 TCATATGTCTTTGGAAAATAAAAAAAACCCG 18 250 0 TTGGAAAATA 0.825407 -51 TTTGAAAATCAAAAGGAGAGA 22 1 1 TTTGAAAATA 0.946807 -29 GTCAATGTTTTTTGAAAATATTGATAATTAT 25 74 0 TTTGAAAATT 0.917323 -78 CCAACCAATCTTTTAAAATTTTAAGTAAATT 25 126 0 TTTTAAAATT 0.590023 -26 ********* * Masking position 6 Map Score: 1.66638 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 127 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 14 GTCATACTCCATTTCAGGACACGCCATACTAGTATC 5 84 0 ATTTCGGACA 0.977409 -59 AAACAATACAATTTCCTGATAAAACAAGCTATACTA 10 178 1 ATTTCTGACA 0.964635 -59 ATTGCTAACCATTTCCTTTCACTCTATTGTACAGGA 13 37 1 ATTTCTTATA 0.657576 -190 TCTTATATGCATTTCATGGTAGATTAAAGATAACTT 14 47 0 ATTTCTGATA 0.945045 -254 GGAACATGATATTTCTGGGAAAAACAATTGTTTTTC 17 192 1 ATTTCGGACA 0.977409 -109 GGTGAAGCCAATTTCCGGCTGCGTTAAAAATGCTCT 18 69 0 ATTTCGGGTA 0.878712 -232 AGAATTGACAATTTCAGGGCATAATACAACCATCAA 21 30 0 ATTTCGGATA 0.964635 -118 ATGTCATGAGATTTCTTGACATTGCAAAGGTGTGAA 21 118 1 ATTTCTGACA 0.964635 -30 ***** ** * ** Masking position 1 Map Score: 2.39586 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 TATGCCATGTCTGCGACGAATGTTATTCTT 1 65 1 CTGCGACGAA 0.743214 -102 TATTTTAATACTTCGACGCAAAAAAGCGTT 2 98 0 CTTCGACGCA 0.93275 -178 CTTCGGCGAAATCCTCCTAA 2 266 0 CTTCGGCGAA 0.951291 -10 TACATCACTCTTTAGACAAATTATAAACAC 14 131 0 TTTAGACAAA 0.771229 -170 AGCAAAAAAATTTCGACAAAAATTGGGTTT 14 205 0 TTTCGACAAA 0.818974 -96 TCAGTTTTTCTTTAGGCGCAAGTTCGATTT 14 234 1 TTTAGGCGCA 0.935705 -67 CCGGTTCACCTTTACGCGCAGTGTACGCGG 18 124 0 TTTACGCGCA 0.757737 -177 CGCCCCTTCGTTTACACGAAGGGACGATTG 19 247 0 TTTACACGAA 0.766469 -54 ATATCACGTTTTTTGACGAATGCTAAGAAA 21 87 0 TTTTGACGAA 0.760219 -61 GGGCAGCGGCCTTAGGCGAAAGCGCCGGCA 24 153 0 CTTAGGCGAA 0.935705 -148 TGCCCTGGCTTTTAGACGAACTGCCCTGTG 24 178 1 TTTAGACGAA 0.938543 -123 TCGCAGTCTTTTTCGGCACAGGGCAGTTCG 24 194 0 TTTCGGCACA 0.811723 -107 ********** Masking position 10 Map Score: 6.77131 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 224 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822