AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_ecoli_reg_300.orf -o00630_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 acnB 300 aconitate hydrase B #2 prpC 41 putative citrate synthase; propionate metabolism? #3 ybbT 229 orf, hypothetical protein #4 ybbU 77 putative regulator #5 gcl 89 glyoxylate carboligase #6 folD 300 5,10-methylene-tetrahydrofolate dehydrogenase; 5,10-methylene-tetrahydrofolate cyclohydrolase #7 gltA 300 citrate synthase #8 hyaA 300 hydrogenase-1 small subunit #9 purU 49 formyltetrahydrofolate deformylase; for purT-dependent FGAR synthesis #10 ychJ 73 orf, hypothetical protein #11 acnA 300 aconitate hydrase 1 #12 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #13 yeaU 81 putative tartrate dehydrogenase #14 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #15 edd 234 6-phosphogluconate dehydratase #16 zwf 300 glucose-6-phosphate dehydrogenase #17 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #18 hycA 211 transcriptional repression of hyc and hyp operons #19 fucO 24 L-1,2-propanediol oxidoreductase #20 fucA 300 L-fuculose-1-phosphate aldolase #21 glcB 21 malate synthase G #22 glcD 250 glycolate oxidase subunit D #23 b2997 188 putative hydrogenase subunit #24 b2998 118 orf, hypothetical protein #25 b3000 205 orf, hypothetical protein #26 ttdA 206 L-tartrate dehydratase, subunit A #27 mdh 300 malate dehydrogenase #28 def 129 peptide deformylase #29 dam 106 DNA adenine methylase #30 damX 91 putative membrane protein; interferes with cell division #31 aroB 56 3-dehydroquinate synthase #32 aroK 199 shikimate kinase I #33 yrfD 68 orf, hypothetical protein #34 fdoG 193 formate dehydrogenase-O, major subunit #35 metA 156 homoserine transsuccinylase #36 aceB 268 malate synthase A #37 aceA 29 isocitrate lyase #38 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #39 yjcQ 140 putative enzyme #40 yjcR 300 putative membrane protein Motif number 1 AAGGTGATTATCACCATGCGAATTAACGAAG 1 72 1 TCACCAGCGA 0.907498 -229 TCTCACAGGAGCGTGAAGAGAATCGCCTGCC 1 248 1 GCGTGAGAGA 0.796331 -53 TTGTCATAGTGCGGCAGGCGATTCTCTTCAC 1 260 0 GCGGCAGCGA 0.99143 -41 GCTCCGCAGAGCGGGATGCGACAGACA 5 7 0 GCGGGAGCGA 0.990369 -83 CAGATTTATCGCGTGAAGCGACCTCTTGCGA 6 196 0 GCGTGAGCGA 0.973262 -105 TCAGCATCTCACGTGAAGCGATGGTTTGCCT 8 205 1 ACGTGAGCGA 0.877626 -96 GCGCTTATGGTCGGCAAGCGACGTCCCTGTA 8 239 0 TCGGCAGCGA 0.987063 -62 TGTTATCAAATCGTTACGCGATGTTTGTGTT 11 219 1 TCGTTAGCGA 0.831165 -82 TTAATTTTTAACGGCAAGAGAGACAAAACAG 12 16 0 ACGGCAGAGA 0.712349 -216 ATTTTGATGGTCAGGAAGTGAGAACCCA 13 64 1 TCAGGAGTGA 0.729924 -18 ATCATGGAACGCAGGCAGCGAAGAGCACCAA 32 105 0 GCAGGCGCGA 0.808862 -95 CCCTGCACACGCAGCAAGCGAATGTAAATGG 34 142 1 GCAGCAGCGA 0.975898 -52 TGATAGTCGATCGTTAAGCGATTCAGCACCT 36 18 1 TCGTTAGCGA 0.834681 -251 GAAACGTACCTCAGCAGGTGAATAAATTTTA 36 84 1 TCAGCAGTGA 0.754672 -185 TGCACGGTCTGCGGCACGCGACCTGGTCGCC 39 83 0 GCGGCAGCGA 0.991443 -58 TTGAGTTGCATCGCCATGCGAGAGAGAACTG 40 24 0 TCGCCAGCGA 0.954486 -277 TTGACGCTCATCACGAGGCGAGTTATTCAGC 40 173 1 TCACGAGCGA 0.850431 -128 ****** **** Masking position 11 Map Score: 21.4413 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 643 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GTAGATCGAAGGGGATGCGCCTATTTTGTCA 6 256 0 GGGGATGGCC 0.884891 -45 GTAAAGCCAGGTTGATGTGCGAAGGCAAATT 7 235 1 GTTGATGGCG 0.935763 -66 AATATTGGTCCTGGATGGGCGCGTTTTCTCT 11 71 1 CTGGATGGCG 0.965288 -230 CGTGCGATTACGGGAAAAGCGCGCAAAGTGC 16 165 0 CGGGAAAGCG 0.84001 -136 AATCGCACGGGTGGATAAGCGTTTACAGTTT 16 187 1 GTGGATAGCG 0.924578 -114 ACGCCTGTTTGGGGATGGGCGTGTCGATGAG 17 40 1 GGGGATGGCG 0.986355 -85 TAATCACTTACGTGATGTGCGTGTTTTGCGA 22 56 0 CGTGATGGCG 0.981774 -195 AGCCAGACTACGGGATACGCGCTGGCGAATC 25 60 0 CGGGATAGCG 0.978412 -146 TATCCGCAGTTGTGATAAGCGCAGTGTATTT 26 18 1 TGTGATAGCG 0.78603 -189 TAATAGACCGCTTGATAAGCGGCCTGACCTT 30 19 0 CTTGATAGCG 0.90133 -73 CGGCAATCCCGGTGATCGGCGCTTATTATCC 40 108 1 GGTGATCGCG 0.896722 -193 TAACTCGCCTCGTGATGAGCGTCAAAATAAG 40 167 0 CGTGATGGCG 0.981774 -134 ******* *** Masking position 5 Map Score: 16.1953 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 284 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 3 GAGGATAAGAAAATCACGCAACTTGCGGATTTAAAAGG 3 23 0 AAACCACGCG 0.93371 -207 AATTTTGTCAAAAAAACCCGCTCCGCAGAGCGGGATGC 5 19 0 AAAACCTGCG 0.728358 -71 GAGCCAAATAAAAAACGGGTAAAGCCAGGTTGATGTGC 7 217 1 AAAAGAACCG 0.920427 -84 GCAACCGGCTAAACATCCCCACCGCCCGGCCAAAAGAA 8 36 1 AAAACACCCG 0.975342 -265 TAGCGGTAGAAAAACGCACCACTGCCTGACAGGCCAGT 12 71 0 AAACCACCCG 0.967756 -161 CTGAAAGAAATCGAAATGCAGTTTTGTCAGA 16 4 1 AAAACAAGCG 0.920427 -297 GATTACGGGAAAAGCGCGCAAAGTGCGGCAAAACTGAT 16 153 0 AAACCAAGCG 0.897719 -148 ACCGTAAGAAAATTACAAGTATACCCTGGCTTAAGTAC 16 246 1 AATAGATCCG 0.630342 -55 GCCCATCCCCAAACAGGCGTAACGCCTGCAAAACGGGC 17 22 0 AAAAGAACCG 0.920427 -103 TGTTTTCGTCAAAAATGACAATCACCTGAGGAATGCCT 17 96 1 AAAACATCCG 0.947102 -29 AATGGGGTTATAAAAAGAGAACTTGCAGTTATTTACTG 20 126 1 TAAAGACGCG 0.53758 -175 TTAAGAACAGAAAAATTGGTCCTACCTGTGCACGAGGT 22 17 0 AAAAGCCCCG 0.855568 -234 AGAGCTGGAAAAAAAATGGTCTGACCGGTAGCTAAAGA 22 129 1 AAAAGCTCCG 0.728358 -122 GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCA 26 43 1 AAAACATCCG 0.947102 -164 ATAGAAGAAATAATCTTTCTAACTCCTGAACACATCTC 28 93 1 TAACCAACCG 0.713945 -37 TTAGCGTAAAAAAGACAGCAAAATGCCGCCTGAATGAT 32 144 0 AAAACAAGCG 0.920427 -56 CGCAAAGAAAAATAACTCCCACTCCCTGCACACGCAGC 34 119 1 AATACACCCG 0.889226 -75 TCGTCACGTCAAAACTGACGACAGCCTGTTTTTCGTCA 38 50 1 AAACCACCCG 0.967756 -148 CGGTATAAATAATTCCGACAAATGCCAGATTGATATTT 40 208 0 AATCCAACCG 0.791473 -93 *** * * ** ** * Masking position 2 Map Score: 15.5963 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 564 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 AAAGGTGATTATCACCATGCGAATTAACGAA 1 71 1 ATCACCAGCG 0.69572 -230 GTCTCACAGGAGCGTGAAGAGAATCGCCTGC 1 247 1 AGCGTGAGAG 0.502208 -54 ATTGTCATAGTGCGGCAGGCGATTCTCTTCA 1 261 0 TGCGGCAGCG 0.90401 -40 CGCTCCGCAGAGCGGGATGCGACAGACA 5 8 0 AGCGGGAGCG 0.955751 -82 TCAGATTTATCGCGTGAAGCGACCTCTTGCG 6 197 0 CGCGTGAGCG 0.714964 -104 TTTTGTCAGAAGCGGGGCGCGCTGTCAGGTT 6 233 0 AGCGGGGGCG 0.791996 -68 TTTACCTGCAAGCGCCCAGAGCTCTGTACCC 7 159 1 AGCGCCCGAG 0.877915 -142 TCTTTCACAGAGCGGCGAGCCAAATAAAAAA 7 201 1 AGCGGCGGCC 0.921164 -100 AATACTTTCTGGCGACGTGCGCCAGTGCAGA 8 157 1 GGCGACGGCG 0.51154 -144 GGCGCTTATGGTCGGCAAGCGACGTCCCTGT 8 240 0 GTCGGCAGCG 0.711111 -61 GCCGACCATAAGCGCCCGGTGTCCTGCCGGT 8 255 1 AGCGCCCGTG 0.686365 -46 TGGGTGAATCCGCACGAGGCCTGAAAGTGTA 15 79 0 CGCACGAGCC 0.581476 -156 TTCGACACTCATCGACACGCCCATCCCCAAA 17 47 0 ATCGACAGCC 0.462192 -78 CCTTCGTTTTAGCGCCCCGCCGCAGTATCAT 23 60 1 AGCGCCCGCC 0.919793 -129 AAGCTCCGACAGCATCCAGCGCTTCAGGCAA 29 49 0 AGCATCCGCG 0.820987 -58 CCGCTTGATAAGCGGCCTGACCTTTCTTGTT 30 12 0 AGCGGCCGAC 0.818992 -80 CATCATGGAACGCAGGCAGCGAAGAGCACCA 32 106 0 CGCAGGCGCG 0.680257 -94 TCCCTGCACACGCAGCAAGCGAATGTAAATG 34 141 1 CGCAGCAGCG 0.861995 -53 AAAGAACGCCAGCAGCCTGACCACCGGTAAT 39 33 0 AGCAGCCGAC 0.592153 -108 TGAAGAGTTAAGCGAGCGGCGACCAGGTCGC 39 66 1 AGCGAGCGCG 0.899203 -75 TTGCACGGTCTGCGGCACGCGACCTGGTCGC 39 84 0 TGCGGCAGCG 0.870033 -57 CAGAATCACCAGCAGGCAGCCTACCCAGAGT 39 114 0 AGCAGGCGCC 0.864326 -27 TTTGAGTTGCATCGCCATGCGAGAGAGAACT 40 25 0 ATCGCCAGCG 0.878723 -276 TTTGACGCTCATCACGAGGCGAGTTATTCAG 40 172 1 ATCACGAGCG 0.58089 -129 ******* *** Masking position 3 Map Score: 16.4189 Number of sites scoring better than the average of aligned sites = 4935 Number in coding regions = 4738 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 5 ACCATCCTTAACGATTCAGCCACTTTTTTATG 1 129 1 ACGTTCAGCA 0.980474 -172 TTTTTAACTGGCCTGTCAGGCAGTGGTGCGTT 12 65 1 GCCGTCAGCA 0.955125 -167 TAGGGCAAAAACGTTTCAGTCAGTGTAATAAA 15 120 0 ACGTTCAGCA 0.980474 -115 CCGGTTACAGGCGTTTCAGTCATAAATCCTCT 15 158 1 GCGTTCAGCA 0.989638 -77 GATTCACAACGCGTTTCATTCAGAGGATTTAT 15 179 0 GCGTTCATCA 0.936359 -56 TATTGATTTTGCGATTGAGGCAAAATATATGC 23 140 1 GCGTTGAGCA 0.917716 -49 AATATACCCTACCGTTCAGCCAAAACAACATC 27 69 0 ACCTTCAGCA 0.922874 -232 ACAGCATCCAGCGCTTCAGGCAACTCCCGCAA 29 40 0 GCGTTCAGCA 0.989638 -67 AACGCGACATCCACCTTAATTAC 31 44 0 ACGGACATCA 0.667888 -13 GACAGCCATCACGCGGCAGACATT 38 3 0 ACGGGCAGCA 0.91647 -195 ACGAAATACCGCGTGACAGCCATCACGCGGCA 38 17 0 GCGGACAGCA 0.961282 -181 *** ***** ** Masking position 8 Map Score: 11.3249 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 220 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GCATCCCGCTCTGCGGAGCGGGTTTTTTTGAC 5 19 1 CTGCGAGCGG 0.844932 -71 CTTTCAGTCTCAGCGACGGTGCGCCTCACCTT 6 165 1 CAGCGCGGGC 0.867615 -136 AAGCGACCTCTTGCGAAGGTGAGGCGCACCGT 6 180 0 TTGCGAGGGA 0.771353 -121 GCTCGCCGCTCTGTGAAAGAGGGGAAAACCTG 7 189 0 CTGTGAAGGG 0.717638 -112 TTCTGGCGACGTGCGCCAGTGCAGAAGGATGA 8 163 1 GTGCGCAGGC 0.903878 -138 TCTCTCCTCCTTGCGACACCGGCAGGACACCG 8 271 0 TTGCGCACGG 0.913286 -30 CTTGACCCCGCTGCGGCGGGGTTGTCATTTGC 11 150 1 CTGCGCGGGT 0.942444 -151 GTAGGTCAATTTGCGAAGGCGGATTATTTTGT 12 114 1 TTGCGAGGGG 0.936506 -118 CAAGCAATAATTGTGCCAGTGTTGATTATCCC 18 39 1 TTGTGCAGGT 0.586069 -173 TATCATGATACTGCGGCGGGGCGCTAAAACGA 23 63 0 CTGCGCGGGC 0.986224 -126 AGAATGAATATTGCGCCAGAGCAGGGAATGGC 26 60 0 TTGCGCAGGC 0.975756 -147 TAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG 26 161 1 TTGTGCGGGA 0.640811 -46 CATGCCTGCGTCACGGCATGCAAATTC 27 6 1 CTGCGCACGC 0.93698 -295 TGGATTAAGGTCGCGGCAGCGGAGCAACATAT 27 248 1 TCGCGCAGGG 0.844636 -53 TTATTTTTCTTTGCGGAAGGGGCCGCAAAGGT 34 102 0 TTGCGAAGGG 0.921294 -92 GCTGGTTTTTCTGCGCCATTGCCAGCCTTATT 40 141 1 CTGCGCATGC 0.789127 -160 ***** *** ** Masking position 5 Map Score: 11.504 Number of sites scoring better than the average of aligned sites = 1883 Number in coding regions = 1792 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 ATCCTGCTATTCTGCCCGTTGCGGTACTGG 1 196 1 TCTGCCCGTT 0.86288 -105 TCAACCTGGCTTTACCCGTTTTTTATTTGG 7 220 0 TTTACCCGTT 0.939917 -81 TTCCTTCTCTTTTACTCGTTTAGCAACCGG 8 14 1 TTTACTCGTT 0.669871 -287 TTTGCCGCACTTTGCGCGCTTTTCCCGTAA 16 159 1 TTTGCGCGCT 0.97268 -142 CTGTACTGCTTTTACGAGCTTGCGAAAACT 16 213 0 TTTACGAGCT 0.770331 -88 GCTGAGGCTTTGCCCGTTTTGCAGGCGT 17 9 1 TTTGCCCGTT 0.973445 -116 TGTCAGGTTACCCGTTTAACAGAGAT 18 196 0 GTTACCCGTT 0.728668 -16 ATGTGCGTGTTTTGCGAGTTAAGAACAGAA 22 43 0 TTTGCGAGTT 0.871545 -208 AGACCATTTTTTTTCCAGCTCTGTGACCTT 22 121 0 TTTTCCAGCT 0.681938 -130 GCAGCTGATTTTTGCGCGCTGCTTCTGTGA 22 202 0 TTTGCGCGCT 0.97268 -49 TTCATTCTTATTTTCGCGTTGATTCACGAA 26 84 1 TTTTCGCGTT 0.875465 -123 CAGATTGATATTTGCCCGCTGAATAACTCG 40 191 0 TTTGCCCGCT 0.976992 -110 ********** Masking position 3 Map Score: 8.58332 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 419 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 TGACAATGAGAGCGAGGAGAACCGTC 1 285 1 AGCGAGGAGA 0.951868 -16 GCCAGTGCAGAAGGATGAGCTTTCGTTTTC 8 177 1 AAGGATGAGC 0.787486 -124 CCGGTGTCGCAAGGAGGAGAGACGTGCGAT 8 281 1 AAGGAGGAGA 0.959518 -20 CAAATTGATAAAAGAGGAGAAACCTTGTGG 11 186 0 AAAGAGGAGA 0.856441 -115 CCCTGTCATTAAGGAGGAGCT 11 290 1 AAGGAGGAGC 0.974226 -11 TTCGTAAAGCAACAAGGAGAAGG 19 12 1 AACAAGGAGA 0.888279 -13 GCGAAAACGAGGAGATAAACA 21 6 1 AACGAGGAGA 0.97872 -16 GAACGCAGGCAGCGAAGAGCACCAACTCTC 32 100 0 AGCGAAGAGC 0.755606 -100 ACAATGTCGAAACAAGGAGCAATCC 34 179 1 AACAAGGAGC 0.926897 -15 TCGGATCCATGACGAGGAGCTGCACG 36 253 1 GACGAGGAGC 0.938636 -16 ********** Masking position 5 Map Score: 7.06218 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 60 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 GAGTATAAAGAGGCGGTAGTTTAAATTTTGAC 1 19 1 AGGCGGGTTT 0.814845 -282 CCGCTCTGCGGAGCGGGTTTTTTTGACAAAAT 5 24 1 GAGCGGTTTT 0.748973 -66 TATAGACCTGAAGCGGTAAATTACCAGGCTGA 6 29 1 AAGCGGAATT 0.920972 -272 GTAAATTACCAGGCTGAAAATTCTTTTTATAT 6 44 1 AGGCTGAATT 0.668573 -257 AGTGCTACTCAGGCGGTTAATACGCCGTTATT 10 33 1 AGGCGGAATA 0.68145 -41 GTTAAAAATTAAGCTGAATTTTATAGCATTTT 12 35 1 AAGCTGTTTT 0.63064 -197 CAATTTGCGAAGGCGGATTATTTTGTGGCAAA 12 120 1 AGGCGGTATT 0.914597 -112 ATATTTATCAAAACGGTCATTTTTCTATTCCT 20 74 0 AAACGGATTT 0.770409 -227 ATATTTTTAAGAGCGGTCATTTTTAATGGGGT 20 102 1 GAGCGGATTT 0.807992 -199 GTGGGTAATTAAACGGCTAATTCAATAGTGTG 20 232 1 AAACGGAATT 0.684485 -69 AACAGTTATTAAGCGGGCTTTTCGTTTTCGTC 22 171 0 AAGCGGTTTT 0.927451 -80 TGGTAGTTTGTGGCGGTGAATTTTTCCAGACA 26 164 1 TGGCGGAATT 0.563775 -43 TGGTCATTGTAAACGGCAATTTTGTGGATTAA 27 224 1 AAACGGATTT 0.769784 -77 GCCGCTTATCAAGCGGTCTATTAGCTTCAGGT 30 27 1 AAGCGGTATT 0.892041 -65 ACAGCCGTAAAAGCGGTAATGTTTTTACGCTG 32 11 1 AAGCGGATGT 0.669138 -189 TTTATCATTCAGGCGGCATTTTGCTGTCTTTT 32 141 1 AGGCGGTTTT 0.943082 -59 GGAATTATCCAGGCTGTTTTTTTGAGTTGCAT 40 44 0 AGGCTGTTTT 0.688756 -257 GAAACCATGAAGACGGGAATTATCCAGGCTGT 40 59 0 AGACGGATTA 0.381247 -242 ****** **** Masking position 6 Map Score: 10.9418 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 728 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 10 AGCGTAGTGAAACTTTTGCACAAAACAATACAAAC 8 114 0 ATTGCCAAAA 0.960948 -187 ATGTTCTTTTTGATTTCGCGCAAAAAGATTCAGAA 12 155 1 TTTGCCAAAA 0.775904 -77 AAATTGTTCTACAATCTGCGCAAGATCATGTTACC 15 43 0 ATCGCCAAGA 0.743742 -192 GACGAAATTCATCTTTAGCTTAAAAATCTCTTTAA 18 117 1 ATTGCTAAAA 0.963385 -95 CAATAAATTAAAAGTTGGCACAAAAAATGCTTAAA 18 155 1 ATTGCCAAAA 0.960948 -57 CGCAAAAGTCGTTCTTTGCCTAAAATATCGCTATA 24 64 1 GTTGCTAAAA 0.845851 -55 ATACGTGCTTATGCTTTGCTTAAAAAAACACCAAC 25 118 1 ATTGCTAAAA 0.963385 -88 CACGGCATGCAAATTCTGCTTAAAAGTAAATTAAT 27 22 1 ATCGCTAAAA 0.94279 -279 TAGATGAAACACGTTCAGCGTAAAAACATTACCGC 32 23 0 ATCGCTAAAA 0.94279 -177 ATCACCGGGTAAGATTAGCGTAAAAAAGACAGCAA 32 161 0 ATTGCTAAAA 0.963385 -39 ACCCCACATAAAATGTGGCATAAAAGATGCATACT 38 126 1 AGTGCTAAAA 0.832074 -72 * ** ** ***** Masking position 12 Map Score: 5.49143 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 45 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 CTTGATTCGCCATTTATTCGTCATCAATGGATC 7 125 1 CATTTTTCGA 0.881751 -176 TGAAGAGAATCAGGGCTTCGCAACCCTGTCATT 11 267 1 CAGGGTTCGA 0.962653 -34 TGCGCAAGATCATGTTACCGGTAAAATAACCAT 15 29 0 CATGTACCGA 0.766044 -206 AAAAGCAGTACAGTGCACCGTAAGAAAATTACA 16 230 1 CAGTGACCGA 0.698705 -71 ATTTCATCGGCATGTTTTCGTCAAAAATGACAA 17 84 1 CATGTTTCGA 0.942771 -41 GCCGCAGTATCATGATATCGATAACCATAATAA 23 78 1 CATGAATCGA 0.590991 -111 AAATATATGCCAGGTCTTCGCAACGGAATAACT 23 162 1 CAGGTTTCGA 0.931282 -27 AAACTAGAAACATTGTTTCGAAATTGAACGGTG 25 24 0 CATTGTTCGA 0.934135 -182 TATTTTTGCCCAGTTTTTCGTCACTCTGTGAGC 25 88 0 CAGTTTTCGA 0.859834 -118 GGATTGCTCCTTGTTTCGACATTGTCACGTC 34 173 0 CCTTGTTCGA 0.708854 -21 AGCTCCTCGTCATGGATCCGAAAACTTCCCCAC 36 241 0 CATGGTCCGA 0.945994 -28 TTCCCGTCTTCATGGTTTCGGGATGCTCATTAT 40 72 1 CATGGTTCGA 0.969071 -229 ***** **** * Masking position 13 Map Score: 5.50675 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 140 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 CAGAGAGAGGATTCCATCTG 6 291 0 CAGAGAGAGG 0.907653 -10 TGGGCGCTTGCAGGTAAAGGATCCATTGAT 7 147 0 CAGGTAAAGG 0.607729 -154 TTATTGTTTCCAGGGAGATTATTT 10 60 1 CAGGGAGATT 0.638301 -14 ACTGGCCTGTCAGGCAGTGGTGCGTTTTTC 12 71 1 CAGGCAGTGG 0.916775 -161 TTTTGATGGTCAGGAAGTGAGAACCCA 13 65 1 CAGGAAGTGA 0.677115 -17 TGTTTTGAATCAGAGAGAGGTAGCTA 20 285 1 CAGAGAGAGG 0.907653 -16 TGCGCCAGAGCAGGGAATGGCAATGTTTTG 26 51 0 CAGGGAATGG 0.949442 -156 CTGCTTATGGCAGGGAGATAAGG 28 4 0 CAGGGAGATA 0.816816 -126 GCTGCGTGTGCAGGGAGTGGGAGTTATTTT 34 127 0 CAGGGAGTGG 0.986981 -67 CCCGTAATATCAGGGAATGACCCCACATAA 38 107 1 CAGGGAATGA 0.841237 -91 CCGGTAATGGCAGGGAGTTGAGCGCGCTCA 39 11 0 CAGGGAGTTG 0.949442 -130 ********** Masking position 6 Map Score: 7.18507 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 367 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 13 TATTCCAACTTTTGTATTGATGTTGTTCTC 3 127 1 TTTGTATTGA 0.811041 -103 CAGGTCTATATTTGTGTTGAATATATTT 6 9 0 TTTGTGTTGA 0.956135 -292 ATCCACACAGTTTGTATTGTTTTGTGCAAA 8 105 1 TTTGTATTGT 0.840968 -196 CGGTTATTATTTTGTGTTGAGATAAC 11 7 0 TTTGTGTTGA 0.956135 -294 ATATTTCATATTTGTGTTGATCATAGGCTA 11 46 0 TTTGTGTTGA 0.956135 -255 CTTTTATCAATTTGGGTTGTTATCAAATCG 11 202 1 TTTGGGTTGT 0.862532 -99 TTACGCGATGTTTGTGTTATCTTTAATATT 11 232 1 TTTGTGTTAT 0.749927 -69 GGTCATCTGATTTGTGTTTTTT 20 3 0 TTTGTGTTTT 0.749927 -298 GCTTCGCTTTGTTGTGTTGTGTGGCAGCTG 22 225 0 GTTGTGTTGT 0.862532 -26 ********** Masking position 7 Map Score: 4.59331 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 31 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 TTATGCAAGTCGGTTGCAGGCG 4 3 0 CGGTTGCAGG 0.961902 -75 GAGCTCTGGGCGCTTGCAGGTAAAGGATCC 7 153 0 CGCTTGCAGG 0.945456 -148 CTATGAGCTCCGGTTACAGGCGTTTCAGTC 15 149 1 CGGTTACAGG 0.951483 -86 GGTGGATAAGCGTTTACAGTTTTCGCAAGC 16 196 1 CGTTTACAGT 0.841847 -105 TCCCGGACCTCGTGCACAGGTAGGACCAAT 22 11 1 CGTGCACAGG 0.934574 -240 CACTCGTCTGCGGGTACAGTAATTAAGGTG 31 26 1 CGGGTACAGT 0.892188 -31 ATCTATTTGACGCGCGCAGGTATTTAGCAT 32 53 1 CGCGCGCAGG 0.948179 -147 TCGCTTGCTGCGTGTGCAGGGAGTGGGAGT 34 133 0 CGTGTGCAGG 0.957182 -61 AACGATCCTTCGTTCACAGTGGGGAAGTTT 36 223 1 CGTTCACAGT 0.814492 -46 ********** Masking position 8 Map Score: 6.42457 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 309 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 CGGGTTTTTTTGACAAAATTTGAAAGTTGG 5 37 1 TGACAAAATT 0.794498 -53 AAGAAATACCTGACAATATAAAAAGAATTT 6 61 0 TGACAATATA 0.934647 -240 GCCCCGCTTCTGACAAAATAGGCGCATCCC 6 246 1 TGACAAAATA 0.949038 -55 TTGAACCAGGTCACAAAATATAAGCTTGTG 20 171 1 TCACAAAATA 0.781662 -130 TAAACAAGCATGAAAAAATAGCGTGCGCAA 24 39 1 TGAAAAAATA 0.707217 -80 TCGCTATATATGACAATATATAGCGAATGA 24 91 1 TGACAATATA 0.934647 -28 CAACAGGTGGTGACAATATACCCTACCGTT 27 85 0 TGACAATATA 0.934647 -216 ********** Masking position 5 Map Score: 1.784 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617