AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_bsub_reg_100.orf -o02020_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/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 ybdG 245 ybdG #2 ybdJ 91 similar to two-component response regulator [YbdK] #3 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #4 yczA 300 yczA #5 ycbL 96 similar to two-component response regulator [YcbM] #6 yccH 143 similar to two-component response regulator [YccG] #7 yclJ 212 similar to two-component response regulator [YclK] #8 ydbF 69 similar to two-component sensor histidine kinase [YdbG] #9 ydfH 300 similar to two-component sensor histidine kinase [YdfI] #10 yesL 114 similar to hypothetical proteins from B. subtilis #11 citS 126 two-component sensor histidine kinase #12 yfiJ 123 similar to two-component sensor histidine kinase [YfiK] #13 yhcY 148 similar to two-component sensor histidine kinase [YhcZ] #14 ykoG 300 similar to two-component response regulator [YkoH] #15 kinA 163 two-component sensor histidine kinase #16 kinC 189 two-component sensor histidine kinase #17 yocF 119 similar to two-component sensor histidine kinase [YocG] #18 resD 80 two-component response regulator #19 resC 135 essential protein similar to cytochrome c biogenesis protein #20 spo0A 275 two-component response regulator #21 yrkP 267 similar to two-component response regulator [YrkQ] #22 spo0B 300 sporulation initiation phosphoprotein #23 lytS 166 two-component sensor histidine kinase #24 phoP 211 two-component response regulator #25 ytsA 96 similar to two-component response regulator [YtsB] #26 ytrD 29 similar to cytochrome c oxidase subunit #27 ytrA 300 similar to transcriptional regulator (GntR family) #28 kinB 125 two-component sensor histidine kinase #29 kapB 45 kinase-associated protein B #30 yufL 120 similar to two-component sensor histidine kinase [YufM] #31 comA 80 two-component response regulator #32 comQ 184 transcriptional regulator #33 yvqA 277 similar to two-component response regulator [YvqB] #34 yvqF 33 yvqF #35 yvqG 249 yvqG #36 yvrI 300 yvrI #37 yvfT 132 similar to two-component sensor histidine kinase [YvfU] #38 yvcP 300 similar to two-component response regulator [YvcQ] #39 degU 82 two-component response regulator #40 degS 216 two-component sensor histidine kinase #41 ywpD 300 similar to two-component sensor histidine kinase #42 spo0F 165 two-component response regulator #43 yxjO 129 similar to transcriptional regulator (LysR family) #44 yxjN 77 similar to hypothetical proteins from B. subtilis #45 yxdJ 108 similar to two-component response regulator [YxdK] #46 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CGGTTTATTGAAAAAGACGGATATATACTG 3 205 1 AAAAAGACGG 0.865413 -96 CAGATGAGTTAGAAAGGAGGATATCAA 4 284 1 AGAAAGGAGG 0.980023 -17 AAAGAAAAAGGCAGACGCGGTCTG 11 5 1 AAAAAGGCAG 0.95153 -122 GTGAAAATAAAAAAAGGCAGACCGCGTCTG 11 22 0 AAAAAGGCAG 0.95153 -105 TGATCTAGGTAGAAAGGACGGCTGGTGCT 11 108 1 AGAAAGGACG 0.927736 -19 TGAGAAAAAGAAAAAGCCGGATCATTTACA 13 32 0 AAAAAGCCGG 0.908645 -117 AATTATGCTAAAAAAGGCGGAGTGATATCA 16 11 1 AAAAAGGCGG 0.986583 -179 TTGGCACGCAAAAAAGGCGGAGATGATATC 16 34 0 AAAAAGGCGG 0.986583 -156 TGATAAAGGAGGTCTTCTAATA 17 3 1 ATAAAGGAGG 0.894523 -117 CTCCAACAATAAAAAGGAAGCCTTCTAGTA 17 33 0 AAAAAGGAAG 0.917258 -87 TAAATACACAAGAAAGGCCGCATAAAGAAA 19 51 0 AGAAAGGCCG 0.957867 -85 AATAAAGATAAAAAGGGCAGGCCAAACCG 19 117 1 AAAAGGGCAG 0.848031 -19 TAGTAAAAAGAGAAAGGCTGTATTAAGCAA 24 28 0 AGAAAGGCTG 0.851236 -184 TGCGCTATAGAAAAAGCCGGCTGTCTCAGC 25 24 0 AAAAAGCCGG 0.908645 -73 CAGATCGTATAGAAAGTAGGGAAGTAA 27 284 1 AGAAAGTAGG 0.708703 -17 AAGAGTGAGTAAAAGGGAGGAAAAC 31 66 1 AAAAGGGAGG 0.921894 -15 GGTTAAGGGAAGAAAGGAAGAGAAAAAGAG 33 145 0 AGAAAGGAAG 0.929067 -133 ACTAGGCAGAAGAAAGGAGGCGGACACCAG 34 12 1 AGAAAGGAGG 0.980023 -22 CTGCAGAAAAAGAAGGGAGGTATTTTCCTA 36 155 0 AGAAGGGAGG 0.933089 -146 TAACAAAAAGAAAAAGACCGATTTACTATT 38 211 1 AAAAAGACCG 0.627241 -90 ATTGTACGTTATAAAGGAGGATTCACTT 42 9 0 ATAAAGGAGG 0.894523 -157 ********** Masking position 4 Map Score: 29.8702 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 304 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 TGGAACAGTTTTTTTTCACATTTGACTTTGCCC 1 162 0 TTTTTCATTT 0.856518 -84 TTCAAAATGTTTTTGTCGTATTTTGTATGATTC 3 60 0 TTTTTCATTT 0.856518 -241 ATCATCTTTATTCTATCCCATTTCACGACATAA 6 98 0 TTCTTCATTT 0.738845 -46 GTACGTTTTATCTTTTCAAATTTACCTTTAAAA 9 83 0 TCTTTCATTT 0.7299 -218 TCACAGGGAATTTTCTCATTTTTCAAAATCCAT 11 66 0 TTTTTCTTTT 0.913805 -61 ACGTTTCCTTGTTTGTCAAATTTCATTTTTAGT 20 107 1 GTTTTCATTT 0.702166 -169 TATTCTATGTTTTTCTCTGTTTTTCGACTAAAA 20 133 0 TTTTTCTTTT 0.913805 -143 TATATAGCGGTTTTGTCGAATGTAAACATGTAG 20 212 1 TTTTTCATGT 0.6844 -64 ATCAATACTCCTTTCCCATTTATCACGGCAA 21 9 1 TCCTTCATTT 0.561542 -259 CGGTCTTTATATTTATCCATTGTAAGGCTCAAG 21 64 0 ATTTTCTTGT 0.424107 -204 CTCGCCACAAATTTGTCACATTTTCTAAAAAAA 21 126 0 ATTTTCATTT 0.533035 -142 TTCACAAGGCTTTTATCTATTGTAAAATAAAAC 23 59 0 TTTTTCTTGT 0.793868 -108 ATGTCACCTGTTCTTTCCGTTTTCATTCTAGCA 23 142 0 TTCTTCTTTT 0.834009 -25 TTAAGCAAGCCTTTCTCTCTTTTTA 24 3 0 CTTTTCTTTT 0.807207 -209 GCTTAATACAGCCTTTCTCTTTTTACTATAAAT 24 30 1 GCCTTCTTTT 0.473206 -182 CCGACATCCTATTTCTCTATTTTATGTCATCTT 24 164 0 ATTTTCTTTT 0.669664 -48 ACTCACCGCACTTTTTCCTTTTTTATCAAGTGT 25 71 0 CTTTTCTTTT 0.807207 -26 CACGTTACGTTTGTTTCGTTTTTTATGTTTCAT 27 140 0 TTGTTCTTTT 0.491332 -161 TTATTCCATTTTTTCTCCTTTTTACGAATTACG 30 23 1 TTTTTCTTTT 0.913805 -98 TTTTACTCACTCTTTTCCATTTTATAAAAAAGA 31 47 0 TCTTTCTTTT 0.827562 -34 AGGACAGCAGGTTTTTCGTTTTTTAACAATCAT 32 74 0 GTTTTCTTTT 0.807207 -111 TTTCACATATTCTTTTCATTTTTATCCCACAAT 33 190 0 TCTTTCTTTT 0.827562 -88 GCAGTTTACGTTTTATCGGTTTTCCTCACTTAC 36 193 0 TTTTTCTTTT 0.913805 -108 CCTTTTCGTATTTATAAGGAATT 38 1 1 CCTTTCATTT 0.516265 -300 TTTCTGAGCATTTTCTCTTTTGTTGTATACTGA 42 40 0 TTTTTCTTGT 0.793868 -126 ATGAATCCCTCTCTCTATTTTCTCGTTCTAT 43 9 1 CTCTTCTTTT 0.664915 -121 GTTGACGTTTTTCTTTCCTATTTTCGCTATGCT 44 32 1 TTCTTCATTT 0.738845 -46 ATCGCCAGTTGTTTATCTATTGTCATGCTGGTC 46 116 0 GTTTTCTTGT 0.603331 -185 **** ** **** Masking position 6 Map Score: 28.3467 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 738 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 3 CCGATTCCCCAAAATAAAAAGCGAGGATGT 3 156 1 AAAATAAAAA 0.924959 -145 GGATGTGATCAACATAAAACTGGAACGGTT 3 180 1 AACATAAAAC 0.572136 -121 TAACCTTTACAAAATCAAAAAACACACACG 5 56 0 AAAATCAAAA 0.921546 -41 ATTTACCTTTAAAATCATAAGGAACTTACT 9 67 0 AAAATCATAA 0.756338 -234 CGAAGGAGTGAAAATAAAAAAAGGCAGACC 11 29 0 AAAATAAAAA 0.924959 -98 GAGTTTCTGGAAAATAAAAACCGCATATGA 12 42 0 AAAATAAAAA 0.924959 -82 TTTTTTTGGTAAAATAAAAAACTGCATATC 14 16 1 AAAATAAAAA 0.924959 -285 TTATGATGTTAAAATAAAAAATTGTATACG 14 209 0 AAAATAAAAA 0.924959 -92 TTTTTATTTTAACATCATAATAGATGATAA 14 219 1 AACATCATAA 0.513439 -82 CGCGGGAATAAAGATAAAAAGGGCAGGCCA 19 111 1 AAGATAAAAA 0.742052 -25 AAGAGGGATCAAAATAAAAAAACTGCCGGA 20 22 0 AAAATAAAAA 0.924959 -254 ACCCTCTAAAAAAATCATAATCACCAATAT 20 183 0 AAAATCATAA 0.756338 -93 TATCTATTGTAAAATAAAACATGAGCCTTT 23 49 0 AAAATAAAAC 0.797301 -118 TGCTTTCGCTAAAATAAAATCATGAAACAT 24 131 1 AAAATAAAAT 0.497492 -81 GCAGTTATGAAACATAAAAAACGAAACAAA 27 134 1 AACATAAAAA 0.807334 -167 TTGTGGGATAAAAATGAAAAGAATATGTGA 33 191 1 AAAATGAAAA 0.66034 -87 AGGAAATAGGAAAATCAAACAGAATACATA 42 101 1 AAAATCAAAC 0.789404 -65 ACTTTTGACGAAAATCATAATATTGGGGTG 42 142 1 AAAATCATAA 0.756338 -24 TTAAGGTCAAAAGATAAAAAAAATAAAGGT 46 177 0 AAGATAAAAA 0.742052 -124 CGGCAGGAGGAAAATCAAAATG 46 289 1 AAAATCAAAA 0.921546 -12 ********** Masking position 5 Map Score: 18.9852 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 259 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 CAGGAAGGTTTTTTAATGAAATAATTTTTTATT 1 74 1 TTTATGAAAA 0.618921 -172 TTTTTATAAAACACACACGTTTT 5 1 1 TTTATAAAAA 0.745406 -96 AGTCCAAAGGTATGAAAAAAATATGAACAATCT 7 87 1 TATAAAAAAA 0.574579 -126 AGTTTTTTATTTTACCAAAAAAACAGGA 14 6 0 TTTCAAAAAA 0.891241 -295 AACGTCAATTTTTGAATAAAAGAAAGGGCACAC 15 37 0 TTTATAAAAA 0.745508 -127 TTTGTCACATTTTCTAAAAAAAATGATGACTCT 21 115 0 TTTAAAAAAA 0.893202 -153 TTACTCCGCATATTGCAAAAAAAACTCCAGTCA 22 16 0 TATCAAAAAA 0.569 -285 AACAATTGTTTTTCCCAGAAATATCATGTTCCT 22 191 0 TTTCAGAAAA 0.819795 -110 ACATGAGCCTTTTGGCAGAAAGATTTGAATCTG 23 28 0 TTTCAGAAAA 0.819861 -139 TTTCAGACGATTTTAAAAAAACAGTCAGCCGCA 23 98 1 TTTAAAAAAA 0.893239 -69 TTACATCATTTTTAAAAGAAATAAAGACGTTTA 24 76 0 TTTAAGAAAA 0.822895 -136 AATGTCCTGCTTTCGCTAAAATAAAATCATGAA 24 124 1 TTTCTAAAAA 0.741568 -88 TCAATCCTTTTTTTACAAAAAAACG 27 3 0 TTTCAAAAAA 0.890429 -298 TCTTTTCCATTTTATAAAAAAGACTTGGCCTGT 31 37 0 TTTAAAAAAA 0.893239 -44 TGGTCAACTTTTTTTAAAAAAGATAACTTTATT 46 88 0 TTTAAAAAAA 0.893197 -213 AAAATAAAGGTTTAGAAAAAAAACACATGTTTC 46 155 0 TTTAAAAAAA 0.893239 -146 *** ****** * Masking position 9 Map Score: 13.0397 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 166 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 CCTTCCTATAAGCAGGAAGGTTTTTTAATGA 1 62 1 AGAGGAAGGT 0.929523 -184 CAATATCAGGTGCAGGGAAACATTAGAGTTT 9 163 0 TGAGGGAAAC 0.76188 -138 CGTTTTCCAAAGCAGGAAGGTG 10 103 1 AGAGGAAGGT 0.929523 -12 AGGTATGATAAGAAGGGAATTGGGTATCGGG 12 93 1 AGAGGGAATT 0.71629 -31 ATAATACCAGCGTGGGGAAGTGCAGGTTGAC 14 101 0 CGGGGGAAGT 0.870637 -200 TGAAAGTAACAGAAGGAAAGCAGGGGGAAAA 18 59 1 AGAGGAAAGC 0.944469 -22 GAAGGAAAGCAGGGGGAAAAC 18 70 1 AGGGGAAAAC 0.636302 -11 GCCTTAGGTTTGGAGGGAAGTGAG 26 16 1 TGAGGGAAGT 0.951155 -14 TCGTATAGAAAGTAGGGAAGTAA 27 288 1 AGAGGGAAGT 0.976457 -13 ATGGAATGGGAGGGGGGAAGTCGTTATTGAG 32 128 1 AGGGGGAAGT 0.955163 -57 CTGCAGAAAAAGAAGGGAGGTATTTTCCTAT 36 154 0 AGAGGGAGGT 0.963487 -147 GGAAGACACTAGGCGGAAAGTAGTAGTTTAC 36 239 1 AGCGGAAAGT 0.751495 -62 CTAAATTAAATGAAGGAAAGCAAAAAAAAGT 36 268 0 TGAGGAAAGC 0.888706 -33 CATTTAATTTAGTAGGGAGGCGGT 36 287 1 AGAGGGAGGC 0.955847 -14 AACGCCGTGACGGAGGGAAATT 40 205 1 CGAGGGAAAT 0.724083 -12 CTGATTCCTCTGAAGGAAAGCCTGAAGCTAC 41 144 0 TGAGGAAAGC 0.888706 -157 CGCACTCCGGTGAGGGGAGGTTTCAATAAAG 46 64 1 TGGGGGAGGT 0.864188 -237 GTCATTCGGCAGGAGGAAAATCAAAATG 46 283 1 AGAGGAAAAT 0.805894 -18 ** ******** Masking position 8 Map Score: 17.0837 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 193 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 GCACCGTAATCAGCATGAGGGCCAGTATAT 3 227 0 CAGCATGAGG 0.669523 -74 AGAGAGTCGGTGGCAGGTGTGAACCGATCC 4 11 1 TGGCAGGTGT 0.907466 -290 GAAGCCCATTCGGCATCAGGGGAGGATCGG 4 34 0 CGGCATCAGG 0.927075 -267 CAATGTACGATGGCTGGTGGTGGCATAGCA 4 256 1 TGGCTGGTGG 0.773823 -45 TGTTGAGAGACGGCAGCAGCC 10 2 0 CGGCAGCAGC 0.942538 -113 TTTCACAGACCGGCAGGAATTTTCTTTCGA 10 41 1 CGGCAGGAAT 0.708737 -74 GTAGAAAGGACGGCTGGTGCT 11 116 1 CGGCTGGTGC 0.800792 -11 GAAACACAAGCGGCAGGTGGTCAT 16 176 1 CGGCAGGTGG 0.98598 -14 ATGCTGATTGCGGCATCTGTGATCGCTTGT 27 176 1 CGGCATCTGT 0.857452 -125 TTTTCATAATAGGCAGGTGTCGTGATGAAG 38 159 0 AGGCAGGTGT 0.748791 -142 CTTTTATGCTTAGCAGGAGGGTCAGCTAGC 40 11 0 TAGCAGGAGG 0.689899 -206 ATGGCGATCCCGGCATCTGTAGCTTCAGGC 41 126 1 CGGCATCTGT 0.857452 -175 ATTATGATGATGGCAGCAGTGTAAGAAACG 45 76 1 TGGCAGCAGT 0.882479 -33 TTCTTTGAACCGGCCGCAGGGCCGGTTCTC 46 14 0 CGGCCGCAGG 0.894668 -287 TGAAGTCATTCGGCAGGAGGAAAATCAAAA 46 279 1 CGGCAGGAGG 0.987647 -22 ********** Masking position 4 Map Score: 9.63338 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 678 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ACGACAAAAACATTTTGAAAATAAGCAGTAA 3 74 1 CATTTTGAAA 0.702623 -227 ATAATAGCACCATTTTAAACAGAAGGTTTTG 7 160 0 CATTTTAACA 0.817834 -53 GGAATTTTCTCATTTTTCAAAATCCATTTTC 11 62 0 CATTTTTAAA 0.882057 -65 TAGATCATACCATTTTTCACAGGGAATTTTC 11 84 0 CATTTTTACA 0.938801 -43 TGCCTCAGGGCATTTTTGACAGGAGTTTCTG 12 63 0 CATTTTTACA 0.938801 -61 TGATAAGAATCATTTTGTAAACAACGAAATC 14 243 1 CATTTTGAAA 0.702623 -58 ACAACGAAATCATTTTTTTCATATAGGGACG 14 263 1 CATTTTTTCA 0.843038 -38 CGTCTGAAAACATATTTCACAAGGCTTTTAT 23 76 0 CATATTTACA 0.567584 -91 CCTTTTACATCATTTTTAAAAGAAATAAAGA 24 82 0 CATTTTTAAA 0.882057 -130 GCACTTTTTCCTTTTTTATCAAGTGTATAGC 25 66 0 CTTTTTTTCA 0.571859 -31 AAAGTCAATCCTTTTTTTACAAAAAAACG 27 9 0 CTTTTTTACA 0.792311 -292 CACTCTTTTCCATTTTATAAAAAAGACTTGG 31 42 0 CATTTTAAAA 0.686395 -39 CCTCCCATTCCATTTTACTAAATGGGACATT 32 110 0 CATTTTATAA 0.433851 -75 GTTTGCCAAGCATTTTTTTCATTCGGTTTCA 35 102 0 CATTTTTTCA 0.843038 -148 ATAAAGTTATCTTTTTTAAAAAAAGTTGACC 46 89 1 CTTTTTTAAA 0.65033 -212 GACAAGGACCCATTCTTTACATGGGCCATAA 46 219 1 CATTCTTACA 0.660489 -82 ******* *** Masking position 6 Map Score: 8.8059 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 362 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 AAAGGTGTACATTTGGAGCATAGCAGAACATTTGATGAATT 1 115 0 ATGGGAGAAT 0.97525 -131 TGTAAAGGTTAGGTGAGGAGATGCAGCGCATA 5 75 1 ATGGGAGCAT 0.924136 -22 GCTTTGGTTGATTTGCAGCCAGGCAGAACATTTTATGTATT 22 142 0 ATGGGAGAAT 0.969366 -159 AAAGATTTGAATCTGAAGCAGAGGAGAAGATC 23 2 0 ATGGGAGAAT 0.975355 -165 ACGCCTTTACAAATGAAGACGTAAAGGCGTTTACAGCTATA 28 12 0 ATGGAAGGTT 0.665842 -114 TAAATGGGACATTTAAAGGACAGCAGGTTTTTCGTTTTTTA 32 82 0 ATAGGAGGTT 0.665842 -103 GCGAATTGATACGTGCGGAAGGGAAGGACTTGACCGCAAAT 35 26 0 ATGGGAGGTT 0.961961 -224 CATAATAGGCAGGTGTCGTGATGAAGAAAATCATGCTGTTT 38 144 0 ATGGGAGAAT 0.975363 -157 AATGCTCAGAAAATGTCGTAAAGTAGACTATTATAATTAAA 42 61 1 ATGGGAGAAT 0.975363 -105 GTTATGGATAACTTGCAGTGAAGGAGATATTTC 43 107 1 ATGGGAGATT 0.958919 -23 CATGGGCCATAAGTGATGAAACGAATGTTATATAGATGAAA 46 238 1 ATGGGATGAT 0.771666 -63 * ** * * *** ** Masking position 15 Map Score: 6.37685 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TATTTGATCAGGCTGATATAAATAAATACTGT 2 30 0 GGCGATATAA 0.937988 -62 TAAAAAGCGAGGATGTGATCAACATAAAACTG 3 170 1 GGAGTGATAA 0.906067 -131 GAGTTAGAAAGGAGGATATCAA 4 289 1 GGAGATATAA 0.829895 -12 TCAGACTTTTGGATGAGAAAAAGAAAAAGCCG 13 43 0 GGAGAGAAAA 0.825208 -106 GTGCTGTTTTGGCTGAGATAAAGCGCGGAAGA 14 164 0 GGCGAGATAA 0.976286 -137 ACGCAAAAAAGGCGGAGATGATATCACTCCGC 16 27 0 GGCGAGATAT 0.826647 -163 TATCTTAGGCGGCGGTAATCAAAAATTGGCAC 16 57 0 GGCGTAATAA 0.769563 -133 CACTACACATTGCCGTGATAAATGGGAAAGGA 21 19 0 TGCGTGATAA 0.682116 -249 CATTAAGGGAGGCAGTTATGAAACATAAAAAA 27 123 1 GGCGTTATAA 0.916579 -178 AGGGAAGAAAGGAAGAGAAAAAGAGCGAGGAA 33 138 0 GGAGAGAAAA 0.825208 -140 CCAGAATACCGGCAGTGATCAACAGTTTGCCA 35 125 0 GGCGTGATAA 0.967644 -125 CAATCAAGGCGGCGGATAACAATTAAAAGTGT 41 32 0 GGCGATAAAA 0.843204 -269 *** ***** ** Masking position 8 Map Score: 6.79607 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 216 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 CACCTCCTTTAAGAAACACAAAAAACCCCCGTC 4 218 0 AAGAAAAAAA 0.757733 -83 ACTTTTGGATGAGAAAAAGAAAAAGCCGGATCA 13 38 0 GAGAAAAAAA 0.647221 -111 ACCATAAGAATAGAAGGAGAATACTCATTTTCT 15 71 1 TAGAAAAATA 0.876187 -93 GAGAAAAACATAGAATAACAAAGATATGCCACT 20 149 1 TAGAAAAAAG 0.831025 -127 AGACCCCGCCAAGAATGAGAATAAACATCTCAA 22 82 1 AAGAAAAATA 0.694372 -219 AAGGCTTTGTTAGAAAAACAATTGTTTTTCCCA 22 207 0 TAGAAAAATT 0.473455 -94 GAAAACATGCTAGAATGAAAACGGAAAGAACAG 23 135 1 TAGAAAAACG 0.706225 -32 CGATCATCACAAGAACAAGAAAAAAAGAACAAG 27 201 0 AAGAAAAAAA 0.757733 -100 CACTAAATATTAGAAGTAAAATATAAAATTCCT 28 62 0 TAGAAAAATA 0.876187 -64 ATTGTATCGGTAGAACGAAAAAAAAGACTTGTT 32 23 0 TAGAAAAAAA 0.906908 -162 TTTGTTATGATAGAATGATAAAGGTAAAATTTT 38 185 0 TAGAAAAAAG 0.831025 -116 CTAGAGTATATAGAACAATAATACAAGGAGGCG 39 54 1 TAGAAAAATA 0.876187 -29 AGTATACCTATAGAACGAGAAAATAGAGAGAGG 43 18 0 TAGAAAAAAA 0.906908 -112 AATAAAGGTTTAGAAAAAAAACACATGTTTCAC 46 153 0 TAGAAAAACA 0.826449 -148 ***** * **** Masking position 8 Map Score: 6.65982 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 56 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 TTATTTTGGGGAATCGGGAGAAAACCTGCAAAT 3 140 0 GATCGGGGAA 0.681229 -161 AGCCCATTCGGCATCAGGGGAGGATCGGTTCAC 4 29 0 GATCAGGGGG 0.833315 -272 TCCTCTCTTGGTAACGGGGAGAGAAACCCGGCA 4 95 0 GAACGGGAAG 0.804703 -206 CCCGTCCTATGCAAAGGACGAGGGTCTCGCGGT 4 191 0 GAAAGGAGGG 0.880181 -110 GGTGAAACAGGTAAAGGAAGTGGATAAGGT 9 281 1 GAAAGGAGGG 0.880181 -20 AGGGAATTGGGTATCGGGAGTGATGAGC 12 106 1 GATCGGGGGA 0.938954 -18 TTTTCATATAGGGACGGGAGAGGATGGTCAAAT 14 278 1 GGACGGGGGG 0.958441 -23 GCGAAAAGGGAGTGATGTCATGGCA 19 3 1 GAAAGGGGGA 0.880181 -133 TTAGTAAAATGGAATGGGAGGGGGGAAGTCGTT 32 120 1 GAATGGGGGG 0.929428 -65 GCGGAACGGGGAAGGATTTGCGGTC 35 3 1 GAACGGGAGG 0.96738 -247 GTCAAACAGGGGATCGGATATGGT 37 119 1 GATCGGAAGG 0.772489 -14 AGCAGTGTAAGAAACGGGAGTGGTTCAGT 45 90 1 GAACGGGGGG 0.992611 -19 * ****** * ** Masking position 7 Map Score: 7.40746 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 190 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 AAAGCAATTTGCAGGTTTTCTCCCGATTCCCC 3 134 1 GCAGGTTCTC 0.889707 -167 AGTAGGCGATGCCGGGTTTCTCTCCCCGTTAC 4 86 1 GCCGGTTCTC 0.987993 -215 GAGGGAATGCGCCGCATATGACATAAAGTTCA 12 13 1 GCCGCTTGAC 0.881056 -111 ATGACCACCTGCCGCTTGTGTTTCTCTACTTA 16 168 0 GCCGCTTGTT 0.724104 -22 TATAGAAAAAGCCGGCTGTCTCAGCCGGCTCG 25 17 0 GCCGGTTCTC 0.987993 -80 GTTGATCACTGCCGGTATTCTGGTTTTTTTCG 35 134 1 GCCGGATCTG 0.821086 -116 GAAAGCGCCAGCCGGTTATGTGCTGAACACTG 41 196 0 GCCGGTTGTG 0.959188 -105 ACTTGATGATGCCGGATATGACTGGTTTCGAA 41 273 1 GCCGGTTGAC 0.960503 -28 CGGCCGCAGGGCCGGTTCTCCCT 46 2 0 GCCGGTTCCC 0.962004 -299 ***** * **** Masking position 9 Map Score: 3.46546 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 189 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TGTAATTGAAAAACGTGTGTGTTTTATAAAAA 5 10 0 AACGTTGTTT 0.688267 -87 ATAAGTGTAATTACGTGTGTGTTTTTTGATTTT 5 43 1 TACGTTGTTT 0.655866 -54 CTGCTTTGGAAAACGCTTTCATTTTAAAGTAAT 10 85 0 AACGCTTCTT 0.907739 -30 TAAGGGATCAAAGCGCGTTTCTTCCGCGCTTTA 14 145 1 AGCGCTTTTT 0.907739 -156 ACGTTTATGATAGCGCTTTCATTTATAGTAAAA 24 50 0 TGCGCTTCTT 0.896418 -162 GCGCTATCATAAACGTCTTTATTTCTTTTAAAA 24 67 1 AACGTTTTTT 0.87482 -145 GTAAACGCCTTTACGTCTTCATTTGTAAAGGCG 28 19 1 TACGTTTCTT 0.860084 -107 TTTCTAGAATATACGCATTCTTTCATTATAATT 40 126 1 AACGCTTCTT 0.907739 -91 CATAACCGGCTGGCGCTTTCGTTTCAACAAAAG 41 208 1 TGCGCTTCTT 0.896418 -93 CACCGGGACAATACGCTTTTGTTGAAACGAAAG 41 223 0 AACGCTTTTT 0.90615 -78 TTACGTTTACATGCGTATTTGTTTATCACTGAT 43 68 0 AGCGTTTTTT 0.876867 -62 ATCTGCCGGTTGACGTTTTTCTTTCCTATTTTC 44 24 1 TACGTTTTTT 0.857803 -54 ACCGCCGAGATGGCGTGTTTTTTTGTGCGGTGT 45 22 1 TGCGTTTTTT 0.860084 -87 * **** *** ** Masking position 8 Map Score: 6.06836 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 229 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 14 GCCAGCGGCACCGTAATCAGCATGAGGGCCA 3 233 0 CCGTAATCGC 0.803301 -68 GGAGAGAAACCCGGCATCGCCTACTATCCGT 4 80 0 CCGGCATCCC 0.97083 -221 TTTTTATTTTCCAGAAACTCCTGTCAAAAAT 12 52 1 CCAGAAACCC 0.935283 -72 AAAAAAACTGCCGGAAACTCCGGCAG 20 6 0 CCGGAAACCC 0.975207 -270 AAATTTGTGGCGAGCATCAGCTTTCATAAAT 21 145 1 CGAGCATCGC 0.744502 -123 ATCACAGATGCCGCAATCAGCATTGGCACGT 27 168 0 CCGCAATCGC 0.858213 -133 GCAATCAGCGCGGGAAACCCCAAATTGCCGA 36 88 1 CGGGAAACCC 0.903601 -213 GACGTCATTGCCAGAAACAGCATGATTTTCT 38 130 1 CCAGAAACGC 0.935284 -171 GCTACAGATGCCGGGATCGCCATTAAAGCAT 41 118 0 CCGGGATCCC 0.92546 -183 CCAGTCATATCCGGCATCATCAAGTCACAGC 41 267 0 CCGGCATCTC 0.837366 -34 AGAGACCAGAAACCGCCGAGATGGCG 45 6 1 CCAGAAACGC 0.93527 -103 ******** ** Masking position 6 Map Score: 5.05414 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 352 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 CAAATGTGAAAAAAAACTGTTCCAAAGTTA 1 171 1 AAAAAACTGT 0.618516 -75 TGTGATCAACATAAAACTGGAACGGTTTAT 3 183 1 ATAAAACTGG 0.657017 -118 AATGAAATACAAAAAACTGGTATAATCTTA 13 100 1 AAAAAACTGG 0.942982 -49 TATTTTACCAAAAAAACAGGA 14 2 0 AAAAAACAGG 0.657017 -299 TTGGTAAAATAAAAAACTGCATATCCTAAG 14 21 1 AAAAAACTGC 0.865622 -280 GATCAAAATAAAAAAACTGCCGGAAACTCC 20 16 0 AAAAAACTGC 0.865622 -260 TTTATAACGGAAACGACTTGGCACAGGCCA 31 15 1 AAACGACTTG 0.681688 -66 CATTTTATAAAAAAGACTTGGCCTGTGCCA 31 33 0 AAAAGACTTG 0.86071 -48 AAAAGACTTGGAAACAAGTC 32 1 1 AAAAGACTTG 0.86071 -184 AGAACGAAAAAAAAGACTTGTTTCCAAGTC 32 15 0 AAAAGACTTG 0.86071 -170 TGCTAAGCATAAAAGACTGCCTATACAAAT 40 26 1 AAAAGACTGC 0.881826 -191 GACAATAGATAAACAACTGGCGATAAAGGT 46 125 1 AAACAACTGG 0.851451 -176 ********** Masking position 6 Map Score: 6.4393 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 186 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269