AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifruR_ecoli_bsub_300.orf -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 icdA 201 isocitrate dehydrogenase, specific for NADP+ #2 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #3 ppsA 300 phosphoenolpyruvate synthase #4 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #5 edd 234 6-phosphogluconate dehydratase #6 zwf 300 glucose-6-phosphate dehydrogenase #7 fruB 300 PTS system, fructose-specific IIA/fpr component #8 ptsH 300 PTS system protein HPr #9 ptsI 44 PEP-protein phosphotransferase system enzyme I #10 crr 40 PTS system, glucose-specific IIA component #11 fba 214 fructose-bisphosphate aldolase, class II #12 pgk 49 phosphoglycerate kinase #13 epd 284 D-erythrose 4-phosphate dehydrogenase #14 yggD 21 putative transcriptional regulator #15 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #16 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #17 pckA 300 phosphoenolpyruvate carboxykinase #18 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #19 mtlD 229 mannitol-1-phosphate dehydrogenase #20 b3913 146 orf, hypothetical protein #21 yiiP 148 putative transport system permease protein #22 pfkA 180 6-phosphofructokinase I #23 metA 156 homoserine transsuccinylase #24 aceB 268 malate synthase A #25 aceA 29 isocitrate lyase #26 aceK 182 isocitrate dehydrogenase kinase/phosphatase #27 ycnL 164 ycnL #28 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #29 mtlD 52 mannitol-1-phosphate dehydrogenase #30 yjdC 300 similar to transcriptional antiterminator (BglG family) #31 yjdD 147 similar to fructose phosphotransferase system enzyme II #32 ykvY 300 similar to Xaa-Pro dipeptidase #33 ykvZ 281 similar to transcriptional regulator (LacI family) #34 glcT 62 transcriptional antiterminator (BglG family) #35 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #36 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #37 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #38 moeB 50 molybdopterin biosynthesis protein #39 yknU 223 similar to ABC transporter (ATP-binding protein) #40 yknW 109 yknW #41 fruR 279 transcriptional regulator (DeoR family) #42 pps 300 phosphoenolpyruvate synthase #43 kdgK 37 2-keto-3-deoxygluconate kinase #44 kdgR 221 transcriptional regulator (LacI family) #45 ypqE 137 similar to phosphotransferase system enzyme II #46 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #47 ytcD 183 ytcD #48 citC 163 isocitrate dehydrogenase #49 citZ 300 citrate synthase II #50 pykA 42 pyruvate kinase #51 pfk 183 6-phosphofructokinase #52 yttI 300 similar to acetyl-CoA carboxylase #53 pckA 300 phosphoenolpyruvate carboxykinase #54 pgk 300 phosphoglycerate kinase #55 gap 46 glyceraldehyde-3-phosphate dehydrogenase #56 yvbQ 297 yvbQ #57 araE 137 permease #58 crh 23 catabolite repression HPr-like protein #59 yvcL 22 similar to hypothetical proteins #60 yvcJ 24 similar to hypothetical proteins #61 yvcI 300 similar to mutator MutT protein #62 yvkC 300 similar to pyruvate,water dikinase Motif number 1 GTTCTTGTAGGCCGGATAAGGCGCTTACGCCGC 19 111 1 GCGGATGGCG 0.99708 -119 GAGGGGCAGCGCCGGATGCGGCGTAAGCGCCTT 19 128 0 GCGGATGGCG 0.99708 -102 CTGACTGTAGGCCGGATAAGGCGTTCACGCCGC 26 27 1 GCGGATGGCG 0.99708 -156 TGCACCGATTGCCGGATGCGGCGTGAACGCCTT 26 44 0 GCGGATGGCG 0.99708 -139 GGTGCACGATGCCTGATGCGACGCTTGCGCGTC 26 71 1 GCTGATGACG 0.985065 -112 ACGGCTGTAGGCATGATAAGACGCGCAAGCGTC 26 90 0 GCTGATGACG 0.985065 -93 CCGAACGTAGGCTGGATAAGGCGTTTACGCCGC 26 125 1 GCGGATGGCG 0.99708 -58 GCAGAGAATTGCCGGATGCGGCGTAAACGCCTT 26 142 0 GCGGATGGCG 0.99708 -41 ATCGTGCTTCGCTTGATCAGACGGTACGGAAGC 52 263 0 GCTGATGACG 0.985065 -38 CGGAGTTATCGCTTGAACAGACGGTTTCACGTT 54 234 1 GCTGAAGACG 0.893393 -67 ATAAAATATTGCTGGATAAAACGACGCGGCATG 56 105 1 GCGGATAACG 0.93397 -193 ** **** **** Masking position 6 Map Score: 28.1372 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 73 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 ACAAATCATTAACAAAAAATTGCTCTAAAGC 1 104 1 AACAAAAAAT 0.691036 -98 AGTCTTAAAAAGTAAAAAAATATATTTGCTT 3 182 1 AGTAAAAAAT 0.521491 -119 CAGTCAGTGTAATAAAAAAAGCCTCGTGGGT 5 105 0 AATAAAAAAG 0.883084 -130 GACAAAAGCAGATAAAAAAGTTGTTATTTTT 6 67 1 GATAAAAAAT 0.811237 -234 CGGCAAAACTGATAAAAAAATCATCGTTTTC 6 135 0 GATAAAAAAT 0.811237 -166 TAGGAAAAATGGCAAAAAATTGTGCAGCACA 7 116 1 GGCAAAAAAT 0.678527 -185 CAGCCTCTATGAGAAAAAAAGCGCCAACCTG 7 249 0 GAGAAAAAAG 0.680049 -52 ATATCAAGGTAATAAAAAAGGTCGCCGAAGC 16 20 0 AATAAAAAAG 0.883084 -281 ATTCATATTTGACAAAAAACTCCGTGATTCC 17 184 0 GACAAAAAAT 0.811841 -117 ACGTTTCGGAAATAAAAAAGGCACCCGAAGG 24 60 0 AATAAAAAAG 0.883084 -209 GTAAGTGGATGATAAAAAATGTGAAAATGTG 27 70 1 GATAAAAAAG 0.935777 -95 CGGAAGCTTCGGTAAAAAACGAAACTTTTGT 30 181 1 GGTAAAAAAG 0.876966 -120 TTTTCCCTATAACAAAAAAAGCAAGGAATAA 31 20 0 AACAAAAAAG 0.88349 -128 CGGAACCTATGGTAAAAAAAGCGATTTTAAT 31 64 1 GGTAAAAAAG 0.876966 -84 TAGAAATAAAAAAGGACTTTGTTCT 33 5 1 AATAAAAAAG 0.883084 -277 ATTTAATGCAGATAAAAAAGGACGATGTCGA 33 35 0 GATAAAAAAG 0.935777 -247 ATCTGCATTAAATAAAAAAATCATCAAATGT 33 53 1 AATAAAAAAT 0.690192 -229 GACAGCGTTTGACAAAAAAAGTACAATAGTT 52 119 1 GACAAAAAAG 0.936013 -182 GTCCCGCTATGACAAAAAACGTCCCGTCATA 56 239 0 GACAAAAAAG 0.936013 -59 TATAATGTCCAGCAAAAAAGGAAGGAACGTT 56 271 1 AGCAAAAAAG 0.787665 -27 TTTATTTATGGACAAAAAAAGGACACGGATA 61 138 0 GACAAAAAAG 0.936013 -163 TTGATGATGTAATAAAAAAAGTGCCGCTGAT 62 38 0 AATAAAAAAG 0.883084 -263 ********* * Masking position 6 Map Score: 25.882 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 180 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 AGTCCAAAGTGCTGAAACCATTCAAGAGTCAA 2 84 0 GCTGAACCTT 0.941411 -217 TATTACACTGACTGAAACGTTTTTGCCCTATG 5 122 1 ACTGAACGTT 0.972232 -113 AGGATTTATGACTGAAACGCCTGTAACCGGAG 5 156 0 ACTGAACGCT 0.879543 -79 ACAAGATCGCGCTGAAACGTTTCAAGAAAGCA 7 203 0 GCTGAACGTT 0.992006 -98 TCTCATAGAGGCTGAATCGTTTCAATTCAGCA 7 266 1 GCTGAACGTT 0.992006 -35 AAAAGCCAAAGCTGAATCGATTTTATGATTTG 8 82 1 GCTGAACGTT 0.992006 -219 GCTTATCCTAGCTGAAGCGTTTCAGTCGATTA 13 148 1 GCTGAACGTT 0.992006 -137 GAAATCTGGCACTGAATCGGTTAACTGTCCAG 18 182 0 ACTGAACGTT 0.972232 -119 ATCACTTCCTGCTGAATTGATTCAGGTCAGGC 22 64 0 GCTGAATGTT 0.915549 -117 GAGGTAAGGTGCTGAATCGCTTAACGATCGAC 24 23 0 GCTGAACGTT 0.992006 -246 ****** ** ** Masking position 6 Map Score: 17.3705 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 AAGGAAAACAAAAACAGCGTTTCAAAAAATAT 2 20 0 AAAACGCTTT 0.944036 -281 ATTTTTTATGAAAACAGCATTTCATTTTTATG 3 83 1 AAAACGCTTT 0.944036 -218 AATATCTGACAAAACTGCATTTCGATTTCTTT 6 14 0 AAAACGCTTT 0.944062 -287 CAGCAACAGTGAAATGGCATTTTGACTATTCG 7 26 0 GAAATGCTTT 0.874756 -275 TATTATCGCAGAAATAGCATTTTAGGTGTGGA 17 135 0 GAAATGCTTT 0.874756 -166 ATTTTCGCTAAAAATGGCATTTAAATGTGAGT 18 44 0 AAAATGCTTT 0.926343 -257 AAAGAGTATAAAAATCGCTTTTTTCCGGAAGC 30 156 1 AAAATGCTTT 0.919727 -145 TGTTATAGGGAAAAATGCCTTTATTACCGGAA 31 37 1 AAAAAGCTTT 0.913669 -111 TCAGCTCATTAAAATCGCTTTTTTTACCATAG 31 70 0 AAAATGCTTT 0.919727 -78 AGGAAACCTCCTTTAAAGTGTGAA 31 134 0 GAAACTCTTT 0.670091 -14 CGTTAAGAGCATAACTGCTTTTCGTCTGAAAA 32 101 1 ATAACGCTTT 0.590857 -200 ATTTTAATGAAAAAAGTCTTTTATATTCATAG 41 56 0 AAAAATCTTT 0.696293 -224 GCCTAAACCGAAAATAGCGTTTACAATGAAAT 41 219 1 AAAATGCTTT 0.926317 -61 TGAATGTTAGGAAAAATCATTTTATTTTCTAT 48 87 1 GAAAATCTTT 0.560185 -77 ATTTCCCCGAAAAAACGCCTTTATTTGCGGGT 49 16 0 AAAAAGCTTT 0.913545 -285 TCATAGCCAAAAAAAATCATTTCTGCTTTCTT 56 212 0 AAAAATCTTT 0.696351 -86 ***** ** *** Masking position 4 Map Score: 15.6015 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 128 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CTTTAGAGCAATTTTTTGTTAATGATTTGTA 1 103 0 ATTTTTGTTA 0.586577 -99 TGAACCTTCAATTTTATTTTTTATGAAAACA 3 68 1 ATTTTTTTTT 0.864308 -233 CCGCACGAGTATTTTATTTTTACCGCCGGAC 16 250 1 ATTTTTTTTT 0.864308 -51 AATTATCCTTATTTTATTTTTAGGGTACCGT 16 279 0 ATTTTTTTTT 0.864308 -22 TAGTGTCACATTTTTGTTTTGATGGTTTGTT 18 14 0 TTTTTTTTTG 0.544416 -287 ACCAGGAGCCTTTTTATTTTTAAAAAATTGT 28 12 1 TTTTTTTTTT 0.804569 -161 TGTCTCTATGATTTTGTTTTATAATGTAAAC 30 209 1 ATTTTTTTTA 0.690417 -92 TATTCCTTGCTTTTTTTGTTATAGGGAAAAA 31 21 1 TTTTTTGTTA 0.478361 -127 ACCAGATATCTTTTTGTGTTTTTAGCTGAAA 33 198 0 TTTTTTGTTT 0.723695 -84 GCATGAGGTTTTTTTATGTTTAGTGATTTCT 41 24 1 TTTTTTGTTT 0.723695 -256 TCTTGTCAATATTTTTTTTTGAAGGGGAGAT 42 275 1 ATTTTTTTTG 0.648985 -26 TTTAGAAAACATTTTATTTTTCTTATATAGA 48 114 0 ATTTTTTTTT 0.864308 -50 TTTACCTATAATTTTTTTTTTCCATTCTGTG 49 48 0 ATTTTTTTTT 0.864308 -253 AAATGTAAGCATTTTCTTTTTGGGGGAGAGA 49 195 1 ATTTTTTTTT 0.864308 -106 GGAAGCATACTTTTTCTTTTTCGTGAATATA 52 238 0 TTTTTTTTTT 0.804569 -63 CCTTTATCGTTTTTTGTGTTTTGCTAATTGT 53 270 0 TTTTTTGTTT 0.723695 -31 CTGTATGCCTATTTTCTTTTATTCTCGGAAT 62 81 0 ATTTTTTTTA 0.690417 -220 TTCTTCATTCATTTTGTTTTTCTCTCTAGTC 62 264 0 ATTTTTTTTT 0.864308 -37 ***** ***** Masking position 5 Map Score: 14.5681 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 83 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 GCTTGCGAAAACTGTAAACGCTTATCCACCCGTG 6 192 0 ATGAACGTTA 0.892463 -109 GAATATTGTGAGTGGAATCGCATTCCTGAATGAA 17 62 0 ATGAACGATT 0.892454 -239 TTGTATAGGGACTGTAAGCGTTTTAACATAGAGT 28 77 1 ATGAACGTTT 0.970907 -96 TTTGTTTTATAATGTAAACGGTTTCTTATATAGT 30 221 1 ATGAACGTTT 0.970907 -80 AAATCAGCTCATTAAAATCGCTTTTTTTACCATA 31 71 0 ATAAACGTTT 0.6382 -77 TCTGTCTTCCATTGTAACAGGTTTTACCGGTGTT 32 243 0 ATGAAAGTTT 0.6382 -58 TAAAAGGGCAAATGTAAACGGTTAAACTGGAAGA 35 142 1 ATGAACGTTA 0.892463 -97 ACAATGATTTTCTGTAAGCGTTTATTCTACATAT 39 81 1 TTGAACGTTA 0.673616 -143 ATACAATTTCATTGTAAACGCTATTTTCGGTTTA 41 222 0 ATGAACGTAT 0.740629 -58 TTCACCTCCTAATGAAAACGTATTCATTTTGAAT 41 254 0 ATGAACGATT 0.892463 -26 TTGTAACGGTTTTGAAATCGGTTTCAAATATATG 44 180 1 TTGAACGTTT 0.892463 -42 TTCAATTTAAAGTGTAACCCAATTTTGATGTCTG 48 57 0 ATGAACCATT 0.684722 -107 CAGCCAGTAAAATGTAAGCATTTTCTTTTTGGGG 49 186 1 ATGAACATTT 0.687312 -115 TCATATTGACATTGCAAACCCTTTTACGATAAGA 53 133 0 ATGAACCTTT 0.897258 -168 TTTCGTGCTGTATGCAAACCATTTTGAAGGAGGA 54 267 1 TTGAACCTTT 0.684722 -34 TGAAGGTTTAAATGAAAACGCTTTACTCAACATT 57 99 1 ATGAACGTTT 0.970907 -39 * ** ** ** *** Masking position 7 Map Score: 10.5181 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 119 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GCAAGTTTCTCCCATCCTTCTCAACTTAAAGA 2 268 1 CCCCCTTCTC 0.980544 -33 TCCAATCCCACCCTCTCCACATGGAGA 19 6 1 TCCCCCTCTC 0.946828 -224 AGGCAATTAACCCCACCTTCTCCATGTGGAGA 19 24 0 CCCCCTTCTC 0.980544 -206 CCGGCGCTGCCCCTCTCCTCACGGAGAGGGTT 19 146 1 CCCTCCTCAC 0.803979 -84 TTTCCCTCACCCAAACCCTCTCCGTGAGGAGA 19 159 0 CCACCCTCTC 0.852679 -71 AAAGCCTCACCCCAGCCCTCTCGGGTAAAAAC 19 189 1 CCCCCCTCTC 0.987755 -41 TAGACACCATCCCTGTCTTCCCCCACATGCTG 21 32 1 CCCTCTTCCC 0.910564 -117 CTCTTCCCAACCTCCTCTTAGTTGAGG 43 21 0 CCCCCTCCTC 0.945848 -17 TGTATTTTCTCCCTTCTCATTCACTTCA 45 120 0 TTCCCTTCTC 0.607195 -18 ACAATCCATTCTCCTCACAGGCACCA 47 168 0 TCCTCTCCTC 0.554299 -16 GAAAAGGGATCTCCATCCTCCCTATGAAACCT 51 100 0 CTCTCCTCCC 0.693639 -84 TTCCCTGCCCTCCCGAATGTTGAG 57 124 0 CCCCCCTCCC 0.980591 -14 *** ******* Masking position 7 Map Score: 9.22457 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 116 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CACACATTCCTCTGCACGCTTTTTCGATGTCACCT 2 167 1 TCTGGCTTTC 0.946742 -134 AAACTTGCTTTCTGGGCGCACTGCCGGAAAGCGAA 2 241 0 TCTGGCTGCC 0.739253 -60 TTTGCCGCACTTTGCGCGCTTTTCCCGTAATCGCA 6 159 1 TTTGGCTTCC 0.962816 -142 GATTTAACCTTTTGAGAACATTTTCCACACCTAAA 17 112 1 TTTGACTTTC 0.91885 -189 GCGAAGAAGATTTGATCGCCATTTCAACGAGGTGA 29 22 1 TTTGGCTTTC 0.980877 -31 ACGTATTCATTTTGAATACAATTTCATTGTAAACG 41 236 0 TTTGACTTTC 0.91885 -44 ATGAAAATATTTTGGTAACGGTTTCAAAGAAAATT 44 49 1 TTTGACTTTC 0.91885 -173 ATCTCATATATTTGAAACCGATTTCAAAACCGTTA 44 183 0 TTTGCCTTTC 0.869139 -39 AACATTATTTTTGAATGCGCTGTCAACCTTGTCG 52 10 1 TTTGGCTGTC 0.941876 -291 TATTGTTTTTTGTGTGTGCATTTCCATTGTTTTCC 53 195 0 TGTGGCTTCC 0.829823 -106 TTTAAGCAGCTTTGCCGGCGCTTTCGCCTAAGGCC 54 141 1 TTTGGCTTTC 0.980877 -160 ATAGAATAATCTTGTTTGCATTTTCTGTCA 57 6 0 CTTGGCTTTC 0.889989 -132 ACTTTCTGCGTTTGACAGCATTTTCCTGAAAACCT 62 173 1 TTTGGCTTTC 0.980877 -128 **** ** **** Masking position 12 Map Score: 10.1521 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 81 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ATCCGTATCGCAGGACGCAAACGCATATGC 1 135 1 CAGGACGCAA 0.81007 -67 TCAGCAGCGTCAGCAGCCAATCAGCAACAG 7 49 0 CAGCAGCCAA 0.883072 -252 ACTTCTGTTTCAGCACGCAAGGAAAGCCGT 7 169 0 CAGCACGCAA 0.95958 -132 CGCGCTTTTAGAGCACGCAATTTTTCATAC 11 47 1 GAGCACGCAA 0.81007 -168 AAGCGTAGCGCATCAGGCAATTAACCCCAC 19 40 0 CATCAGGCAA 0.884007 -190 ATGCATTAAGCAGCAGGCAAATTGAGGATA 21 77 0 CAGCAGGCAA 0.976763 -72 TGAATCAATTCAGCAGGAAGTGATTGTTAT 22 72 1 CAGCAGGAAG 0.833735 -109 GTTCACGCCGCATCCGGCAATCGGTGCACG 26 49 1 CATCCGGCAA 0.778121 -134 GTTTACGCCGCATCCGGCAATTCTCTGCTC 26 147 1 CATCCGGCAA 0.778121 -36 ACAGGAAGAGGAGCAGGAAATAAAATGCAT 32 186 1 GAGCAGGAAA 0.661913 -115 AGATTCAAATCAGCCGGCAAATGTGATTAT 47 83 1 CAGCCGGCAA 0.950786 -101 GTTTTAGTTCCAGCAGCCAGTAAAATGTAA 49 173 1 CAGCAGCCAG 0.776548 -128 GGTTTGCATACAGCACGAAAAACGTGAAAC 54 257 0 CAGCACGAAA 0.860225 -44 GAGACGATGACAGGACGAAGGTTAG 61 286 1 CAGGACGAAG 0.337228 -15 ********** Masking position 2 Map Score: 9.37579 Number of sites scoring better than the average of aligned sites = 958 Number in coding regions = 841 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 10 GTAATCAGGCGAGAGAAAACTCTG 4 23 1 GAGAGAAAAC 0.511604 -14 CGTGCGATTACGGGAAAAGCGCGCAAAGTG 6 166 0 CGGGAAAAGC 0.76542 -135 TTTCAGCACGCAAGGAAAGCCGTAAAGTTA 7 162 0 CAAGGAAAGC 0.804216 -139 TTAATCGTTACAGGAAAAGCCAAAGCTGAA 8 68 1 CAGGAAAAGC 0.866015 -233 AATCACAGGGCAGGGAAACCTGCCCTTGTT 11 13 1 CAGGGAAACC 0.98142 -202 GCAAATCGTCCGGGGAAACCTTACCTGTCG 13 214 0 CGGGGAAACC 0.963853 -71 CAAATTTGCTCAGGGAAAACCTTGCAGGAG 13 261 1 CAGGGAAAAC 0.964138 -24 AGCAATTGAGCAGGGAAACCGGTGTTTTGA 16 211 0 CAGGGAAACC 0.98142 -90 GTGTCTATGGCAAGGAAAACAGGGTTTA 21 9 0 CAAGGAAAAC 0.772807 -140 CAATGAAATACAGAAAAACCGGACGGCTGA 39 26 0 CAGAAAAACC 0.676751 -198 GGCGTTTTTTCGGGGAAATCACAGAATGGA 49 29 1 CGGGGAAATC 0.804882 -272 TAATAAATAACAGAGAAACCGGTTGCTGGG 53 46 1 CAGAGAAACC 0.913163 -255 CACCTATATTGAGGGAAAACAATGGAAATG 53 182 1 GAGGGAAAAC 0.840296 -119 ********** Masking position 6 Map Score: 7.81035 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 276 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 GCCTGGAATAAAGCTTCCCACAAAAGGGGATAAAAGTGT 13 49 1 ACTCAAAGGG 0.796574 -236 GAGCACAACGATCCTTCGTTCACAGTGGGGAAGTTTTCG 24 217 1 ACTCTAGGGG 0.91669 -52 GCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGG 26 9 1 ACTTTAGAGG 0.886566 -174 TCATGCCTACAGCCGTTGCCGAACGTAGGCTGGATAAGG 26 107 1 ACTTCAGAGG 0.820934 -76 AGGAAATAAAATGCATTAGAAAATGAAGGCGTCGTGAAA 32 200 1 ACTTAAGAGG 0.95649 -101 AGACAGAACAATGCATTGCAAATGGCAGGGAGGAACAAG 32 270 1 ACTTAAGAGG 0.95649 -31 ATTGTATGAAACGCATTCCAGATCAAGGGGATTTAGAAA 33 242 1 ACTTAAAGGG 0.739193 -40 TGATTCGATCAGGCATCAGTGATTGAGGGAAAAAAACGG 35 48 1 ACTCTAGGGG 0.91669 -191 AAATTTCCAAAAACCTTCAATATTGAAGGCTTTTCATA 40 10 0 ACTTAAGAGG 0.95649 -100 CAATCATACAACACATCTTACAAAGGAGGAACATC 47 7 0 ACTCAAGAGG 0.968123 -177 GGTGAAGAGAACCCTTCACAAAAGGGAGGTAATCATTTG 52 191 1 ACTCAAGAGG 0.968124 -110 AAAAAAGTGTATTCATTATAAAAAGGGGGTCAATTACTT 61 82 0 ACTTAAGGGG 0.957266 -219 CCGCTTCAAGATGCCTCCCACAATGAAGAGACATTGACA 61 238 0 ACTCAAGAGA 0.666718 -63 * * ** * * * *** Masking position 12 Map Score: 8.64541 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 TCACCTCTCCTTCGAGCGCTACT 1 189 0 CACCTCCTTC 0.674521 -13 CGAACAATCCTTTTGTGATAAAT 3 288 0 GAACTCCTTT 0.733825 -13 TCGGCTGGACAAACATTCCTTTTATTCCACGT 13 113 1 AAACTCCTTT 0.770184 -172 AAAAACACCCCTTCTTATGTTTGC 18 287 0 AAACCCCTTC 0.932965 -14 TTGCCATAGACACCATCCCTGTCTTCCCCCAC 21 26 1 CACCCCCTGT 0.682112 -123 GAAAAGAGCACAACGATCCTTCGTTCACAGTG 24 212 1 CAACTCCTTC 0.830543 -57 ATATAAACCCTCCCTGTTTTGTTTGTC 28 156 0 AACCCCCTGT 0.678017 -17 GCAAACGGAACAACCCCCCTGCGATTGAACGT 32 142 1 CAACCCCTGC 0.879289 -159 GAACGAGAATGAACTTCCCGTTTTTTTCCCTC 35 72 0 GAACCCCGTT 0.650563 -167 TCTACATCTCCCCTTCAAAAAAAAAT 42 285 0 CATCCCCTTC 0.726873 -16 ATGAAACCTTCCTTTATCGTTTTTT 53 286 0 AAACTCCTTT 0.770184 -15 GCTTTTAGACGAACTGCCCTGTGCCGAAAAAG 54 185 1 GAACCCCTGT 0.803814 -116 CGCTTTAATGAAACAGCCCTTTCTACGGGAAG 56 14 1 AAACCCCTTT 0.906501 -284 ATCCCAATATAAACAGCCCTTCCCGTAGAAAG 56 32 0 AAACCCCTTC 0.932955 -266 CTATGACAAAAAACGTCCCGTCATAGCCAAAA 56 232 0 AAACCCCGTC 0.764601 -66 GACTCAAACGTTCCTTCCTTTTTTGCT 56 281 0 AAACTCCTTC 0.827873 -17 AAGATCTCCCCTTTTCTTTACGG 58 10 0 GATCCCCTTT 0.599506 -14 **** ****** Masking position 2 Map Score: 8.9089 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 261 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 TATTTTTTTTCATAACATGATCAGTGTCAG 6 91 1 CATAACATGA 0.817116 -210 GTACGAAAGTAAGAACATGATGAAGAAAAG 30 37 0 AAGAACATGA 0.809764 -264 CCTCTCAACCAAAAACATGAAATTAAACCC 33 90 0 AAAAACATGA 0.920895 -192 CTTACAGCTAAAAATCATGACAACGAATTC 35 187 0 AAAATCATGA 0.596639 -52 CGGGGCAATAACATGATAAGATGACA 38 7 1 AATAACATGA 0.920895 -44 AATTTATTAGAAAAACATGAAACTTTTTGA 40 44 1 AAAAACATGA 0.920895 -66 TTATATAGAAAATAAAATGATTTTTCCTAA 48 93 0 AATAAAATGA 0.642022 -71 AGAGTGTTGTAAAAACATGAGGCTTACTTA 49 246 0 AAAAACATGA 0.920895 -55 TATGATTAAACATAACATGATCATTGCCCT 51 141 0 CATAACATGA 0.817116 -43 ATACAGCACGAAAAACGTGAAACCGTCTGT 54 250 0 AAAAACGTGA 0.686747 -51 GAAAGTCCTAAATAAAATGAATAGTTAAGT 62 149 0 AATAAAATGA 0.642022 -152 ********** Masking position 4 Map Score: 3.51129 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 49 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ATCGCAGGACGCAAACGCATATGCAACGTGG 1 141 1 GCAAAGCATA 0.781196 -61 CGCAGACGCAGCACATGCAACTTGAAGTATG 11 159 1 GCACAGCAAC 0.686588 -56 TGAAATTGATGCAAATTCAACCGGTAAAGTA 17 35 0 GCAAATCAAC 0.933952 -266 ACAAGAACGTGCAAATTCAACAAATTGTGAT 19 88 0 GCAAATCAAC 0.933952 -142 ACTTTGGAATGCAAAATGAAATCTGTTGCCG 22 148 0 GCAAATGAAA 0.809059 -33 CATTTAAAATGCAAAATCAAAAACAATTTCC 24 159 0 GCAAATCAAA 0.924282 -110 ACATTACATAGCAAACTCAAAGAGTATAAAA 30 138 1 GCAAATCAAA 0.924282 -163 ATCTACTTGAGCAAATTGATAGTATAAGTAT 30 255 0 GCAAATGATA 0.601032 -46 AAATTCATCAGCAAACGGAACAACCCCCCTG 32 132 1 GCAAAGGAAC 0.801506 -169 TAAAAGCATAGCAAAAGCAAAGGCTCAACGC 37 94 0 GCAAAGCAAA 0.909438 -43 ATAAAAAAGAGCAGATTCAAATCAGCCGGCA 47 71 1 GCAGATCAAA 0.69686 -113 TCCAGTTACAGCAAAATCATCTGAATTAAGG 61 176 1 GCAAATCATC 0.834091 -125 ***** ***** Masking position 5 Map Score: 5.55927 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 162 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 ATGCGCGTTATTAGGCTATAATGCGGCAATTCATAAT 1 24 0 TACTTAGCGC 0.885018 -178 AGAACAATTTTTACACTTTCAGGCCTCGTGCGGATTC 5 68 1 TACTTAGCTC 0.869188 -167 CTTGCTGAATTGAAACGATTCAGCCTCTATGAGAAAA 7 263 0 TACGTCGCTC 0.891419 -38 TGATGCAAATTCAACCGGTAAAGTATCGATTCACCAC 17 23 0 TACGTAGTTC 0.774336 -278 GTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCT 19 117 1 TACGTAGCGC 0.982269 -113 CTACATACGCTTATACGTTTAGACATCCAGATAGCTG 23 115 0 TACGTAACTC 0.790273 -42 GTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAT 26 33 1 TACGTAGCGC 0.982269 -150 GTAGGCATGATAAGACGCGCAAGCGTCGCATCAGGCA 26 80 0 TACGGAGCTC 0.891419 -103 GTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCAAT 26 131 1 TACGTAGCGC 0.982269 -52 AACGTGTTACTGATTCGATCAGGCATCAGTGATTGAG 35 38 1 TACGTAGCTC 0.979518 -201 CCGCCTTTTTTAACCAGATTATGCGTCTATGCCAGAT 45 19 1 TAAGTAGCTC 0.774336 -119 AACCGTCTGTTCAAGCGATAACTCCGCTAGGGCAGAT 54 223 0 TACGTATCGC 0.813606 -78 * * ** * * ** ** Masking position 3 Map Score: 8.02053 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 98 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038