AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_ecoli_reg_300.orf -o00561_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 yabB 300 orf, hypothetical protein #2 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #3 rpsB 300 30S ribosomal subunit protein S2 #4 tsf 257 protein chain elongation factor EF-Ts #5 pyrH 146 uridylate kinase #6 frr 291 ribosome releasing factor #7 yaeM 91 putative ATP-binding component of a transport system #8 yaeS 185 orf, hypothetical protein #9 cdsA 120 CDP-diglyceride synthetase #10 yaeT 29 orf, hypothetical protein #11 hlpA 121 histone-like protein, located in outer membrane or nucleoid #12 prpB 238 putative phosphonomutase 2 #13 lacZ 122 beta-D-galactosidase #14 lacI 76 transcriptional repressor of the lac operon #15 mhpR 76 transcriptional regulator for mhp operon #16 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #17 yaiN 166 putative alpha helix chain #18 ddlA_yaiB 462 ddlA: D-alanine-D-alanine ligase A, yaiB: orf, hypothetical protein #19 phoA 31 alkaline phosphatase #20 ybaD 90 orf, hypothetical protein #21 ribH 88 riboflavin synthase, beta chain #22 thiL 77 thiamin-monophosphate kinase #23 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #24 ybeX 89 putative transport protein #25 ybeZ 113 putative ATP-binding protein in pho regulon #26 yleA 145 orf, hypothetical protein #27 htrB 224 heat shock protein #28 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #29 cls 300 cardiolipin synthase, a major membrane phospholipid; novobiocin sensitivity #30 pgpB 169 non-essential phosphatidylglycerophosphate phosphatase, membrane bound #31 ycjL 121 probable amidotransferase subunit #32 ycjC 26 orf, hypothetical protein #33 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #34 ydcH 72 orf, hypothetical protein #35 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #36 msbB 119 suppressor of htrB, heat shock protein #37 yebA 78 orf, hypothetical protein #38 yebL 24 putative adhesin #39 pgsA 56 phosphatidylglycerophosphate synthetase = CDP-1,2-diacyl-sn-glycero-3-phosphate phosphatidyl transferase #40 uvrC 62 excinuclease ABC, subunit C; repair of UV damage to DNA #41 uvrY 300 putative 2-component transcriptional regulator #42 wcaA 34 putative regulator #43 BIME92 24 BIME #44 wza 300 putative polysaccharide export protein #45 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #46 trxC 206 putative thioredoxin-like protein #47 yfiP 44 orf, hypothetical protein #48 yfiQ 31 orf, hypothetical protein #49 pssA 110 phosphatidylserine synthase; phospholipid synthesis #50 plsC 233 1-acyl-sn-glycerol-3-phosphate acyltransferase #51 parC 137 DNA topoisomerase IV subunit A #52 b3020 132 putative transport periplasmic protein #53 b3022 204 orf, hypothetical protein #54 b3023 52 orf, hypothetical protein #55 ygiW 151 orf, hypothetical protein #56 ebgR 218 regulator of ebg operon #57 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #58 glpD 189 sn-glycerol-3-phosphate dehydrogenase (aerobic) #59 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #60 BIME167 47 BIME #61 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #62 BIME168 126 BIME #63 livH 47 high-affinity branched-chain amino acid transport system; membrane component #64 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein #65 yiaY 189 putative oxidoreductase #66 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #67 yibF 227 putative S-transferase #68 secB 62 protein export; molecular chaperone; may bind to signel sequence #69 grxC 141 glutaredoxin 3 #70 yibN 244 orf, hypothetical protein #71 rfaS 36 lipopolysaccharide core biosynthesis #72 rfaQ 300 lipopolysaccharide core biosynthesis #73 trxA 76 thioredoxin 1 #74 rhoL 140 rho operon leader peptide #75 rho 84 transcription termination factor Rho; polarity suppressor #76 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #77 wecD 106 orf, hypothetical protein #78 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #79 pldA 146 outer membrane phospholipase A #80 b3913 146 orf, hypothetical protein #81 yiiP 148 putative transport system permease protein #82 pfkA 180 6-phosphofructokinase I #83 BIME199 56 BIME #84 sbp 164 periplasmic sulfate-binding protein #85 cdh 106 CDP-diacylglycerol phosphotidylhydrolase #86 tpiA 107 triosephosphate isomerase #87 yiiQ 100 orf, hypothetical protein #88 glpK 22 glycerol kinase #89 glpF 300 facilitated diffusion of glycerol #90 plsB_dgkA 110 plsB: glycerol-3-phosphate acyltransferase, dgkA: diacylglycerol kinase #91 melA 282 alpha-galactosidase #92 psd 96 phosphatidylserine decarboxylase; phospholipid synthesis #93 yjeQ 64 orf, hypothetical protein #94 mdoB 292 phosphoglycerol transferase I #95 yjjA 45 putative glycoprotein/receptor #96 dnaT 106 DNA biosynthesis; primosomal protein i #97 yjjB 137 orf, hypothetical protein #98 yjjP 300 putative structural protein Motif number 1 TGCGACGCGAGCGGCATTTTAGGACATATC 1 17 0 GCGGCATTTT 0.894508 -284 CCTGCATATGGCCCCCTTTTTCACTTTTAT 4 190 1 GCCCCCTTTT 0.821839 -68 GATCTACTGAGCGGCGTTTTTGTCGTTCAA 7 15 0 GCGGCGTTTT 0.943274 -77 GGATCGGCTGGCGGCGTTTTGCTTTTTATT 7 50 1 GCGGCGTTTT 0.943274 -42 CGTCGTCATCGCGGCGTTGTTTCTGTTGCC 9 64 1 GCGGCGTTGT 0.873265 -57 GGCCGCGAATCCCCCGTTTTGTCGTGGTAA 18 406 1 CCCCCGTTTT 0.898209 -57 CAAAAGCGTTGCGCCTTTGTTGTATCGTCA 20 24 1 GCGCCTTTGT 0.747753 -67 TCCATGATCGCCGGCCTTTTCTTTTTTACC 22 42 1 CCGGCCTTTT 0.906834 -36 TGCAATGCTTGCGCCTTTTTCCTGTGGCGT 25 69 1 GCGCCTTTTT 0.877358 -45 TAATGCTTTGCTGCCGTTGTGACCAGTATG 26 79 0 CTGCCGTTGT 0.740863 -67 TGTATGTATTGTCGCATTTTTTCGCCCGCA 27 173 0 GTCGCATTTT 0.700824 -52 CAGTGCTTTTCCCGCGTTTTTATTTGCCAG 29 226 1 CCCGCGTTTT 0.912734 -75 TTTCCTGGAACTGGCGTTTTCAGTTATGAT 30 123 1 CTGGCGTTTT 0.891042 -47 CGCCAGCCAGGCGGCTTTTTTAACAACTGC 35 23 1 GCGGCTTTTT 0.894508 -40 GCAGTCAGTACCGGCTTTTTTTATTTGGTG 36 35 1 CCGGCTTTTT 0.899726 -85 GCTACCGCCCCTGGCTTTTTAGCTACCAAT 44 100 0 CTGGCTTTTT 0.806582 -201 CGCATCTTGTGCCCCGTTTTCTCCTCTGCG 47 22 1 GCCCCGTTTT 0.892922 -23 GTCTGAGAGACTGGCATTGTACGTCACCTG 50 200 0 CTGGCATTGT 0.633434 -34 GCGGGGGCAACTCGCTTTTTTCTTTACCGG 52 22 1 CTCGCTTTTT 0.712544 -111 CAATACGCCTGTGGCATTGTTCGCTCAAAC 52 78 0 GTGGCATTGT 0.620208 -55 CTGATGTGCGCCCCCATTGTAGAGGAAGTG 56 179 0 CCCCCATTGT 0.650907 -40 CGTGCCCCATCTCCCATTTTCCCTCACCCA 61 70 1 CTCCCATTTT 0.676509 -169 TCTAAACCCGCCCGCATTTTACGGGCGGTG 63 17 0 CCCGCATTTT 0.842108 -31 ACAGAAAAAAGTGCCTTTGTCAGCATAAAA 64 84 0 GTGCCTTTGT 0.579431 -217 AGTAAGCTGCCCGCCCTTTTTTACACTTTC 65 159 1 CCGCCCTTTT 0.891444 -31 TCAACATTTTCTGCCCTTTTTCCCATCACC 67 169 1 CTGCCCTTTT 0.792383 -59 TTGAAACTCGGCCCCATTTTCAAATCTACA 72 18 1 GCCCCATTTT 0.809607 -283 ACGTAAACACGTGGCGTTTTTGGCATAAGA 76 16 0 GTGGCGTTTT 0.88543 -224 ACGTGTTTACGTGGCGTTTTGCTTTTATAT 76 34 1 GTGGCGTTTT 0.88543 -206 GAGAGCCAGACCCGCATTTTGTGTATAAAA 82 22 1 CCCGCATTTT 0.842108 -159 GTAAAGGAATCTGCCTTTTTCCGAAATCA 83 10 0 CTGCCTTTTT 0.778674 -47 CGGATTTCTTCCGCCTTTTTAATCCCTCAA 84 43 1 CCGCCTTTTT 0.883313 -122 CGTTAGAATCGTCCCCTTTTTTTCAGGATC 92 27 1 GTCCCCTTTT 0.681923 -70 ACCGCGAAACGCCGCGTTTTAGCTGTTACC 94 11 1 GCCGCGTTTT 0.908123 -282 CGGCTCTCTCCTGCCCTTTTCCCTGCTCCT 94 50 1 CTGCCCTTTT 0.792383 -243 ********** Masking position 7 Map Score: 42.9463 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 880 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 TCCTAAAATGCCGCTCGCGTCGCAAACTGACACTT 1 23 1 CCGCCGTGCA 0.950363 -278 AAACCTTCAGTGGCACGTTTGGCGAAATTCAGAAT 3 28 0 TGGCCGTGCA 0.647663 -273 ACACACGTATCGGCACATATTCCGGGGTGCCCTTT 3 215 1 CGGCCATCCG 0.834524 -86 TTTGTACGCTCCGGTTGCTGCGCGCTGGCCGTGAC 6 102 0 CCGGTGGGCC 0.585795 -190 GCCATTTTGGCCCCGGGCAGTGCTCGCCATCCTCA 6 143 0 CCCCGGGGCC 0.605973 -149 TAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTT 7 39 1 CGGACGTGCG 0.861877 -53 CAGGGAAGGCCGCCCCGGATAGCGGGCGGCAGAAG 17 14 0 CGCCCGTGCG 0.987803 -153 TAAAATCCGCCCCCCTGCGGGGCCATACTCGAACC 21 52 1 CCCCTGGGCA 0.425582 -37 TTACACTATGCGCCCTGCATTCCTGGCTACTATTT 26 106 1 CGCCTGTCCG 0.779202 -40 ACGCATATTTCGGCGCGATTGCCCCTCAAGCCAAC 29 67 1 CGGCCGTCCC 0.961201 -234 TACCCCCACCCCCGACGCTGACCAGTGCTTTTCCC 29 204 1 CCCGCGGCCG 0.759112 -97 GTATAGATTGCCGGGCGCATTGCGCTTACCCGGCT 33 26 0 CCGGCGTGCC 0.946198 -249 CAGAGATCCCCGGGCCGTATGCCCGTTTATTTCTG 33 196 0 CGGGCGTCCG 0.957055 -79 GTTAAAAAAGCCGCCTGGCTGGCGGCTTAGGAAAG 35 12 0 CCGCTGTGCG 0.91436 -51 GATAGTGTAGCGGCGCAACTTGCCCCGCACCAAAT 36 57 0 CGGCCATGCC 0.881929 -63 TTCGGGTAATCTGCGCGCTTCGCGCAGCGCTGGTG 46 20 0 CTGCCGTGCC 0.761454 -187 TACCCGAAGTCCGCGCGGTTCGCCATGATTTCGTA 46 47 1 CCGCCGTGCA 0.946853 -160 GTGAATAGCGCCGCCGGACGTGCTCCGACGGCGAT 51 18 0 CCGCGGGGCC 0.761689 -120 CATTATCTGCCGCGTCGAGTCACAGGAGATCAACG 51 52 0 CGCGCGTACG 0.54911 -86 TTACCGCTCCCGGGACGCGTTCCCGGGAATAATTT 54 14 1 CGGGCGTCCG 0.957055 -39 CATAAAATAACGGCACAAAGGGCGGAATAATTCAC 64 56 0 CGGCCAGGCG 0.724431 -245 AAAAATCATTCGGGTCGGATTGCTGCGAAAGAAAT 72 122 1 CGGGCGTGCG 0.986497 -179 AAGCTCAAATCGCCGCGGGTGGCAAATACACAGCC 78 195 0 CGCCCGTGCA 0.948043 -47 GGAAGAAATCCGCCTCATATTGCTGACAAAGTGCG 84 20 0 CGCCCATGCG 0.887381 -145 GTTAACCTTCTGGCACGCTTTGCTCATCACAACAC 84 121 1 TGGCCGTGCC 0.795809 -44 GGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTG 86 53 0 CGCCCGGGCG 0.978784 -55 GCGGCACGCCTTGCAGATTACGGTTT 89 2 1 CGGCCGTGCG 0.964651 -299 TTTCAGGATCCGGCATGTAGGCCGGATCAGGAACG 92 47 1 CGGCTGGCCG 0.805196 -50 ACAGCTAAAACGCGGCGTTTCGCGGT 94 2 0 CGCGCGTGCG 0.972285 -291 CTCACTAAACCGGGCCGTTTAGCCAACGTTTAAGC 94 220 0 CGGGCGTGCA 0.941625 -73 GCAAAGCCGACCGCAGGAATGGCGGCGAGGATCAT 97 40 0 CCGCGGTGCG 0.921257 -98 **** ** * ** * Masking position 13 Map Score: 36.8324 Number of sites scoring better than the average of aligned sites = 2429 Number in coding regions = 2322 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 GTGGTATAAAGCGCGCCGGACTTCCGATCC 3 133 1 GCGCGCCGGA 0.941041 -168 ACCCCAAAGGGCACCCCGGAATATGTGCCG 3 225 0 GCACCCCGGA 0.600005 -76 ACTGATGTAAGCTCCCGGGAATTCTCGAGC 4 61 0 GCTCCCGGGA 0.92403 -197 CCTTCATATTTCGCGCCGCAGATGCGTTAT 4 116 0 TCGCGCCGCA 0.926326 -142 GAGATGTGATCTGCCCGGCATTAAACCGCA 4 225 0 CTGCCCGGCA 0.79708 -33 GTCACGGCCAGCGCGCAGCAACCGGAGCGT 6 102 1 GCGCGCAGCA 0.631019 -190 TTTGCCATTTTGGCCCCGGGCAGTGCTCGC 6 151 0 TGGCCCCGGG 0.660687 -141 GTTCTTTGCGTGGCCCGGCGATCTTATATT 11 63 0 TGGCCCGGCG 0.807946 -59 AGCGCACCGCAAAGTTAAGAA 12 2 1 GCGCACCGCA 0.882169 -237 TGGCATGATAGCGCCCGGAAGAGAGTCAAT 14 43 1 GCGCCCGGAA 0.867091 -34 GCAGGGAAGGCCGCCCCGGATAGCGGGCGG 17 20 0 CCGCCCCGGA 0.960579 -147 TCTCCCGGCTCGAAAGGGAA 21 1 1 TCTCCCGGCT 0.587044 -88 GGTTCGAGTATGGCCCCGCAGGGGGGCGGA 21 57 0 TGGCCCCGCA 0.845827 -32 ATTACACTATGCGCCCTGCATTCCTGGCTA 26 105 1 GCGCCCTGCA 0.924444 -41 TGAGGGGCAATCGCGCCGAAATATGCGTAT 29 65 0 TCGCGCCGAA 0.456547 -236 TAAGCGCAATGCGCCCGGCAATCTATACAC 33 33 1 GCGCCCGGCA 0.989862 -242 AACGGGCATACGGCCCGGGGATCTCTGCGC 33 204 1 CGGCCCGGGG 0.742222 -71 GCGGCGCAACTTGCCCCGCACCAAATAAAA 36 53 0 TTGCCCCGCA 0.7265 -67 AGGTTGTTCTCCCGGCTTATGAGCTGG 42 18 0 TCTCCCGGCT 0.587044 -17 GGCACAAGATGCGCCCCGGTAAGA 47 5 0 GCGCCCCGGT 0.870215 -40 TTGTTACCGCTCCCGGGACGCGTTCCCG 54 9 1 GCTCCCGGGA 0.92403 -44 CCCGGGACGCGTTCCCGGGAATAATTTCGC 54 22 1 GTTCCCGGGA 0.475758 -31 TTTGCCTCCCTGCGAAATTATTCC 54 39 0 CCTCCCTGCG 0.511205 -14 CGCGTTTTATGCTCGCGGGGTAACATGACA 61 182 0 GCTCGCGGGG 0.74273 -57 CATTTTGCTGCCGCCCTGCAACATGAAATT 69 95 1 CCGCCCTGCA 0.868367 -47 ATATACGACCGCTCGCGGCAAGCCGATGCC 70 92 1 GCTCGCGGCA 0.890524 -153 TTTTTTCGTCGCGCCCCGCAAAATTGCATT 70 134 1 GCGCCCCGCA 0.98845 -111 GCTGTATTTGCCGCACCGCGCAGGTATACT 70 179 1 CCGCACCGCG 0.730673 -66 TAAAAACTGGACGCCCGGCGTGAGTCATGC 74 40 1 ACGCCCGGCG 0.776222 -101 ACTCGCTTTTGCGCCAGGCGACGTAGTGGG 78 164 0 GCGCCAGGCG 0.613529 -78 AGGAAGATGGCCGCCCCGCAGGGCAGCAGG 86 59 0 CCGCCCCGCA 0.978788 -49 CGCTCATGTTTCGCGCGGCGCTACGCAAAC 90 73 0 TCGCGCGGCG 0.905967 -38 AGCGTAACGCCCGCACGGGAACGTTGAACA 97 80 0 CCGCACGGGA 0.708633 -58 GCGAATTATCTCTCGCCGCAAACAAACTAT 98 199 0 TCTCGCCGCA 0.74785 -102 ********** Masking position 4 Map Score: 30.5835 Number of sites scoring better than the average of aligned sites = 2687 Number in coding regions = 2537 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 CCGCGTAAGTATCGCGGGGGCGTAAGTCTGGT 6 41 1 ACGCGGGGCG 0.968498 -251 CAGAAACAACGCCGCGATGACGACGGGTATTA 9 57 0 GCGCGTGACG 0.980432 -64 TTAATCACCAACGGCGGGGACGTCTGCCAGTC 24 25 0 AGGCGGGACG 0.860116 -65 GCCGACGTAAATCGCGTTGGCTTGAGGGGCAA 29 85 0 ACGCGTGGCT 0.923735 -216 GAACGGAAGTGGGGCGCTGGCGCATGCAGCGT 29 124 0 GGGCGTGGCG 0.987639 -177 AGCCCGCTCTGTCGCCCTGGCGTTTAATAATT 37 37 1 GCGCCTGGCG 0.927348 -42 TAAAAAGCCAGGGGCGGTAGCGTGTCTGGATG 44 109 1 GGGCGTAGCG 0.953944 -192 ATCATGGCGAACCGCGCGGACTTCGGGTAATC 46 44 0 ACGCGGGACT 0.663742 -163 GAAAGATGACAAGGCGGTGACGGCGTGGGTGA 61 93 0 AGGCGTGACG 0.930369 -146 CATTCCAGTTAACGCGCTGGCTGTATTTGCCG 70 160 1 ACGCGTGGCT 0.923734 -85 TGTTGAGCCTGGGGCGGTAGCGTGCTTTTTTC 72 204 1 GGGCGTAGCG 0.953944 -97 TAATCTTAATGCCGCGCTGGCGATGTTAGGAA 76 67 1 GCGCGTGGCG 0.992981 -173 CCTGACGCCAGACGCGTTAGCGCCGTGGTCAC 77 83 1 GCGCGTAGCG 0.973458 -24 TGGAATAAATGGCGCGATAACGCTCATTTTAT 89 143 1 GCGCGTAACG 0.928513 -158 * **** ***** Masking position 5 Map Score: 18.3076 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 1161 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 AAAAAGGAGCCGCCTGAGGGCGGCTTCTTTTT 5 16 1 CGCCTGGGCG 0.861779 -131 AAAAGCAAAACGCCGCCAGCCGATCCGCAAGG 7 44 0 CGCCGCAGCG 0.62649 -48 TTTCTGTTGCCGCCGGTGGGGTTCGCCATTGT 9 83 1 CGCCGGGGGT 0.930146 -38 GCCATTGTAACGCTGGTGGTCTGC 9 107 1 CGCTGGGGCT 0.944492 -14 AGTATGGCCCCGCAGGGGGGCGGATTTTAGCA 21 49 0 CGCAGGGGCG 0.878892 -40 GGAAGTGGGGCGCTGGCGCATGCAGCGTCAGG 29 120 0 CGCTGGGCTG 0.638202 -181 CACTGGTCAGCGTCGGGGGTGGGGGTATAATG 29 199 0 CGTCGGGGGG 0.925886 -102 TCCGGTAAGCCGTTGGTGACGGGCGTGACCAT 41 138 1 CGTTGGGAGG 0.702749 -163 CTTCGCGCAGCGCTGGTGGAGAAAAGC 46 6 0 CGCTGGGGGA 0.823152 -201 GGGTTGAATACGCTGCCGGATGACGACTTAAC 50 64 0 CGCTGCGGTG 0.902189 -170 GAATTTTTATCGTTTCCGGGGGTTGAATACGC 50 83 0 CGTTTCGGGG 0.598023 -151 ACGTGAATAGCGCCGCCGGACGTGCTCCGACG 51 23 0 CGCCGCGGCG 0.975802 -115 AACAATAAGTCGCTGGGGGCCTAATTGCAGCT 69 43 0 CGCTGGGGCT 0.944492 -99 CTTAATGCCGCGCTGGCGATGTTAGGAAAATT 76 71 1 CGCTGGGAGT 0.715893 -169 GAAGAAAAAACGCTGCTGACGG 78 1 0 CGCTGCGAGG 0.898646 -241 AAGCTCAAATCGCCGCGGGTGGCAAATACACA 78 198 0 CGCCGCGGGG 0.9791 -44 AGACCTGCTGCCCTGCGGGGCGGCCATCTTCC 86 56 1 CCCTGCGGCG 0.778717 -52 GCGGCGCTGCTGGCCTTTGGAGAGTT 93 49 0 CGCTGCGGCT 0.927683 -16 TCCCCGTTTCTGGCGGTATACTGCGA 95 5 1 CGTTTCGGGG 0.598132 -41 TTTCTGTTAGCGTTGGCGCAGGATATGATCCT 97 16 1 CGTTGGGCGG 0.718478 -122 GCGGGCGTTACGCTGGTGTGCGCTGCTTGGCT 97 96 1 CGCTGGGTCG 0.80761 -42 ****** ** ** Masking position 1 Map Score: 17.1353 Number of sites scoring better than the average of aligned sites = 2663 Number in coding regions = 2574 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 GGAGCCGCCTGAGGGCGGCTTCTTTTTGTGC 5 21 1 GGGGCGGCTT 0.989909 -126 ATAATATTTCGTGCGCTGCTTCCCTTTCGAG 21 19 0 GGCGCTGCTT 0.973843 -70 GGCCCCGCAGGGGGGCGGATTTTAGCATAAT 21 45 0 GGGGCGGATT 0.960474 -44 AAGCCGCCTGGCTGGCGGCTTAGGAAAGT 35 9 0 GTGGCGGCTT 0.865977 -54 TACATATTCAGCGGGCTGATTTTCATTTTTG 41 54 1 GGGGCTGATT 0.927411 -247 GCTGCGCGAAGCGCGCAGATTACCCGAAGTC 46 27 1 GGCGCAGATT 0.800477 -180 ATGCCGGGGAGGGCGCTGTTTCCTCCCGCTT 50 12 1 GGCGCTGTTT 0.784942 -222 CGCTTTTCCAGAGAGCGGCTTTTAACAATGC 50 156 1 GGAGCGGCTT 0.916351 -78 CCCGTAAAATGCGGGCGGGTTTAGAAAGGTT 63 22 1 GGGGCGGGTT 0.934443 -26 GTAAAAAAGGGCGGGCAGCTTACTGAGGATT 65 152 0 GGGGCAGCTT 0.957334 -38 CTGGCGTCAGGAGCGGTGCTTCAGACGTAAT 77 63 0 GGCGGTGCTT 0.784218 -44 CGCCATTCCTGCGGTCGGCTTTGCGATGGTG 97 51 1 GGGTCGGCTT 0.865977 -87 TTACGCTGGTGTGCGCTGCTTGGCTCGATAG 97 103 1 GGCGCTGCTT 0.973843 -35 * ********* Masking position 10 Map Score: 12.1006 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 299 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 7 CCCGGGAATTCTCGAGCTTGCCGCCTTTCTGC 4 46 0 CCAGCTTGCC 0.910681 -212 GTTATCTTCGCTCGCTCATCCCGGTCACTTAC 4 89 0 CCCTCATCCC 0.919829 -169 CTCTTCCGGGCGCTATCATGCCATACCGCGAA 14 34 0 CCATCATGCC 0.670581 -43 CTCTCGCTCTTCCTCAATATGGTA 16 21 0 CCCTCTTCCT 0.669103 -14 TTCTCAGGCCTGCCGTTCCGGTGG 25 3 1 CCGGCCTGCC 0.933148 -111 CATCGGGATTCGCTCACTTGCCGCCTTGATGC 33 78 0 CCCACTTGCC 0.833904 -197 GATAAGTCTCCTTACTCATCCCGAGGTTAGTT 46 185 1 CTCTCATCCC 0.533745 -22 GCGCTGTTTCCTCCCGCTTGCAAGGAACGCCG 50 24 1 CCCGCTTGCA 0.836327 -210 TGCCTGACTCCAGCTTCCCTTATAAATTC 53 8 1 CCAGCTTCCC 0.919619 -197 AACCCCCGCCTCCCTGTTACTTTA 53 191 0 CCCGCCTCCC 0.974427 -14 GTAAATCTGGCATCGGCTTGCCGCGAGCGGTC 70 98 0 CTGGCTTGCC 0.67753 -147 CTTGTAATTTCCAACGCTTCCCGTTTTATCTT 74 117 1 CACGCTTCCC 0.764792 -24 TAGACACCATCCCTGTCTTCCCCCACATGCTG 81 32 1 CCGTCTTCCC 0.936284 -117 GTCATCCTCCCTCACTCCTGCCATAATTCTGA 91 34 0 CCCTCCTGCC 0.954788 -249 GCACGGTTTTCACCCTCTTCCCAGAGGGGCGA 91 77 1 CCCTCTTCCC 0.97278 -206 TGCAGAAAACCTCCGGCTTCCAGGTTGAGCAT 91 214 0 CCGGCTTCCA 0.702169 -69 GCTGACGCGGCTCTCTCCTGCCCTTTTCCCTG 94 43 1 CCCTCCTGCC 0.954788 -250 * * ******** Masking position 9 Map Score: 11.1313 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 264 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 ATGCGGTGAGTTTTTTTCTCTTAATTATAAGTTA 18 237 0 TTTTTTCCTA 0.937319 -226 AACGGAAATCTATTTTACCCTGAACTGACGATAC 20 45 0 TATTTTCCTA 0.595433 -46 TGGGCCTTGTTTTTTCTCTCTTTATCCCCATCTT 25 32 1 TTTTTCCCTA 0.825307 -82 CTAAATTTTATTTTTTTCCCTTAAGAAGTTGTTA 55 77 1 TTTTTTCCTA 0.937319 -75 ATGCTGGACATTTTTCATTCTCTAATGTT 64 6 0 TTTTTCTCTA 0.625896 -295 AGACTGTTCTTTTTTTATACTGCACTGTTTTTGC 64 220 0 TTTTTTTCTA 0.841161 -81 CTGCCCGCCCTTTTTTACACTTTCAGGAGTGTGT 65 165 1 TTTTTTCCTC 0.685669 -25 TAGCTCCTGTTTTTTTACCCTGAAATTTCATGTT 69 114 0 TTTTTTCCTA 0.937319 -28 GGTAGCGTGCTTTTTTCTGCTTAACTTAACCAGA 72 219 1 TTTTTTTCTA 0.841161 -82 AGATATAAGCTTTTTTACCCACTACGTCGCCTGG 78 147 1 TTTTTTCCAA 0.595433 -95 TGTGGGGGTTTTTTTTATCCTCAATTTGCCTGCT 81 62 1 TTTTTTTCTA 0.841161 -87 TAGCCAATCTTTTTTTATTCTTTAATGTTTGGTT 84 90 1 TTTTTTTCTA 0.841161 -75 CTTTTTTTCCCTGTACCTCAAAGAG 85 92 0 TTTTTTCCTA 0.937319 -15 ACATCGCATTTTTTTGACACTAGAATTGCAGCAA 94 152 1 TTTTTGCCTA 0.71966 -141 ****** * ** * Masking position 5 Map Score: 7.10599 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 29 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TGGGGCTGCGCTGAAAAGCGACGTACAATG 5 79 1 CTGAAAAGCG 0.913199 -68 GCGATACTTCAGCAAAAGCGACCCCCA 9 8 0 AGCAAAAGCG 0.728146 -113 GATCCTTTATCTCAAAAGCGTTGCGCCTTT 20 12 1 CTCAAAAGCG 0.883638 -79 TTCTGTAAGCCGGGTAAGCGCAATGCGCCC 33 19 1 CGGGTAAGCG 0.790716 -256 ATCAGTTTGACGCAAAAGCGTTTTTAAAAA 40 14 1 CGCAAAAGCG 0.968145 -49 AGCCGCTCTCTGGAAAAGCGTATTGTTAAT 50 146 0 TGGAAAAGCG 0.86743 -88 TTAATGGAAAAGCGGGGGCAACTC 52 5 1 TGGAAAAGCG 0.86743 -128 GATGCCAGGTCAGATAAGCGAAACGCATCC 60 24 0 CAGATAAGCG 0.683495 -24 AGATGGGGCACGGATAAGCGGGAAAATATA 61 52 0 CGGATAAGCG 0.956397 -187 CCCAGTAGGCCTGATAAGCGCAGCGCATCA 62 75 0 CTGATAAGCG 0.845115 -52 CGTCGCCTGGCGCAAAAGCGAGTCGGCTGT 78 171 1 CGCAAAAGCG 0.968145 -71 GCAAGGGTAACGCAAAATCGTGACAAATAA 85 60 0 CGCAAAATCG 0.687469 -47 ********** Masking position 6 Map Score: 7.98478 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 296 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TCCGGTGAATGTGGTCGGAAAACAAAGAGGAAAGGGGGG 17 61 0 GTTCAAAAGG 0.969001 -106 TATTCTCTTCGTTAACTTATAATTAAGAGAAAAAAACTC 18 225 1 GTACAATAGG 0.82517 -238 ATCCATATGCGTAAACTCATAACAATGCGCTTTCAAAAG 29 260 1 GTACAAAAGG 0.973785 -41 CACACAAAACGTATTCTTTAAGGAAAGTGATTGACCATA 53 78 0 GTTCAGAAGG 0.923061 -127 CGGGTCACCTGTTTTCAGTAAATAAAGCGCGTTTCTTTG 56 135 0 GTTCAAAAGG 0.969001 -84 AAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAA 65 62 0 GTTCAAAAGG 0.969001 -128 ACCCTTAAGTGTTGTCCTTAAATACTGCGCAATGTAATG 68 25 0 GTTCAAACGG 0.854794 -38 CGATGGCGCTGTTAACACCAAAGAAGGCGTTTTCCCAGG 77 19 0 GTACAAAAGG 0.973785 -88 TAAACTTATCGTTAACGAGCAAAAACGAGAAATATCGAA 89 197 0 GTACAAAAGG 0.973785 -104 TTGTGTCGCAGTATACCGCCAGAAACGGGGA 95 3 0 GTACAGAAGG 0.934455 -43 GTTTTAGCTTGTTAACATTAAAAAACGTGCCCGGTTATC 98 101 1 GTACAAAAGG 0.973785 -200 ** ** ** ** * * Masking position 11 Map Score: 10.1901 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 20 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ATGCTGTACACAGCGCCAACAATTATTGGT 3 88 1 CAGCGCCAAC 0.927599 -213 GCTCCGGTTGCTGCGCGCTGGCCGTGACCA 6 100 0 CTGCGCGCTG 0.535952 -192 GTGATATAGTCTGCGCCATCTGATCGTAAG 8 60 1 CTGCGCCATC 0.977433 -126 ACGCAAAGAACTGCACCCTCCGGTGCAAAT 11 82 1 CTGCACCCTC 0.797688 -40 GCATTACACTATGCGCCCTGCATTCCTGGC 26 103 1 ATGCGCCCTG 0.713054 -43 CCGGGGATCTCTGCGCCCTGACGTTCACAA 33 218 1 CTGCGCCCTG 0.935593 -57 TCCACCAGCGCTGCGCGAAGCGCGCAGATT 46 18 1 CTGCGCGAAG 0.760519 -189 CGGGAGGAAACAGCGCCCTCCCCGGCATA 50 10 0 CAGCGCCCTC 0.964158 -224 TCACAAAATACTGCGCTAACCCCTTAATCA 64 185 1 CTGCGCTAAC 0.730757 -116 TCCTTAAATACTGCGCAATGTAATGCCAAC 68 20 0 CTGCGCAATG 0.825474 -43 TTGGTGTTAACAGCGCCATCGTGCGCATTA 77 37 1 CAGCGCCATC 0.952501 -70 GGATCATATCCTGCGCCAACGCTAACAGAA 97 17 0 CTGCGCCAAC 0.965121 -121 TCGAGCCAAGCAGCGCACACCAGCGTAACG 97 101 0 CAGCGCACAC 0.752069 -37 ********** Masking position 6 Map Score: 8.84501 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 1130 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 TATATTTGCTGTGGAAAATAGTGAGTCATTTTAAAACG 1 58 1 GGAAAGGAGA 0.833386 -243 ACTCCTTTCAGTGGGAAATTGTGGGGCAAAGTGGGAAT 1 257 1 GGAATGGGGA 0.850406 -44 CGACGTATTTGTGGTATAAAGCGCGCCGGACTTCCGAT 3 123 1 GGAAAGGCGG 0.857536 -178 CGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCA 13 81 1 GGATTGGCGT 0.525453 -42 AATAAGTTGCGCTGTACTGTGCGCGCAACGACATTTTG 15 32 0 GGATTGGCGA 0.936026 -45 GCAACGTACTGGTGAAGAAAGTGCGTTATCTCAAAGAT 18 330 0 GGAAAGGCGA 0.981707 -133 AAAATTTGTGGCTGAAGACTGGGCGAAATTGCCGCGCT 27 132 0 GGAATGGCGA 0.975266 -93 TTTTGGTTGCGGGCGAAAAAATGCGACAATACATACAA 27 166 1 GCAAAAGCGA 0.536318 -59 TTAAACGCCAGGGCGACAGAGCGGGCTATCTGTTGCAC 37 26 0 GCAAAGGGGA 0.669389 -53 TTCGAATTATGAGCGAATATGCGCGAAATCAAACAATT 45 62 0 GCATTGGCGA 0.792911 -211 AAAATTTAGTGCTGTACAGAGCGCGTTACAACACGGTT 55 48 0 GGAAAGGCGA 0.981707 -104 CTGCCGCTTCGACGTAAACTGTGCGGTAAATTTGCCCA 58 36 0 GGAATGGCGA 0.975266 -154 GCATAAAATAACGGCACAAAGGGCGGAATAATTCACTA 64 54 0 AGAAAGGCGA 0.703153 -247 TGCGGGGCGCGACGAAAAAAAAGCGTAAATCTGGCATC 70 116 0 GGAAAAGCGA 0.815496 -129 ACACTAGCACGTCAAAGTAAGTGCGTTATCAGTATTCA 72 160 1 GAATAGGCGA 0.811863 -141 GTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGG 72 211 0 GGAAAGACGA 0.703153 -90 AATCGCGACAGAAAGATTTTGGGAGCAA 80 129 1 GAATTGGAGA 0.228111 -18 TGTGTGCCTCGTCATAAAATGAGCGTTATCGCGCCATT 89 150 0 GAAATGGCGA 0.895229 -151 AGAGGCGAGAAAAAGGGCGAAAGAGAGTAGTT 94 271 0 GAAAAGGCGA 0.920819 -22 * * * * ** *** * Masking position 6 Map Score: 11.8553 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 415 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 CTTTTGCTGAAGTATCGCCTGATATCTGCTT 9 20 1 ATATCGCCTG 0.863239 -101 CGATCAATATAAGATCGCCGGGCCACGCAAA 11 58 1 AGATCGCCGG 0.959471 -64 AACGCGGTGAAACATTGCCTGAAACGTTAAC 12 75 1 ACATTGCCTG 0.673 -164 AGACCGTTCCATGATCGCCGGCCTTTTCTTT 22 35 1 AGATCGCCGG 0.959471 -43 GACAATACATACAATTGCCCGAATAGGTTGA 27 190 1 AAATTGCCCG 0.790287 -35 ATTTTGTGTATAGATTGCCGGGCGCATTGCG 33 37 0 TGATTGCCGG 0.610683 -238 GCGATAAACGCCTGGCTGGCTGGT 40 49 0 AAAACGCCTG 0.522782 -14 GACTGGTGTTATTATTGCCCGCTTATGTCGT 49 44 1 ATATTGCCCG 0.790287 -67 CCCGCTTGCAAGGAACGCCGGATGAAACGTT 50 36 1 AGAACGCCGG 0.804252 -198 TCAAAGGGGCAATATTGCCGGAGATACTACA 51 85 0 ATATTGCCGG 0.879697 -53 TCCGGCAAAAACGATTGCCGGACAGTGTGTA 57 18 0 AGATTGCCGG 0.944858 -130 TGACAAATGTAAAATTGCCTGATGCGCTGCG 62 56 1 AAATTGCCTG 0.820424 -71 GAAAAATATCAGTATGGCCTGGTGATGGGAA 67 188 0 ATATGGCCTG 0.690707 -40 GAACGACAAAACAATGGCCTGGAGGCTACC 92 77 1 AAATGGCCTG 0.690707 -20 CGGTTTAGTGAGGATCGCCCGTTGTCAGAAC 94 243 1 AGATCGCCCG 0.924243 -50 * ********* Masking position 4 Map Score: 7.54117 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 417 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 GAACTATTTTGGGGGAGTTATCAAGCCTTA 4 9 0 GGGAGTTATC 0.686948 -249 TTCGCGCCGCAGATGCGTTATCTTCGCTCGCT 4 105 0 AAGCGTTATC 0.816971 -153 AACGCAATTAATGTGAGTTAGCTCACTCATTA 13 15 1 AGGAGTTAGC 0.812796 -108 CTGGTGAAGAAAGTGCGTTATCTCAAAGATGT 18 328 0 AGGCGTTATC 0.97464 -135 TGTGACCAGTATGAGCGTTATCAGCCCTTAGG 26 60 0 AGGCGTTATC 0.97464 -86 CAGTACCCAGAAGTGAGTAATCTTGCTTACGC 28 93 1 AGGAGTAATC 0.737319 -208 ACTAACTATCAGTAGCGTTATCCCTATTTCTG 41 268 1 ATGCGTTATC 0.71682 -33 ATGAGCGAATATGCGCGAAATCAAACAATTCA 45 60 0 AGGCGAAATC 0.53652 -213 GGGATGAGTAAGGAGACTTATCGGCAACGACG 46 175 0 AGGACTTATC 0.593353 -32 AAGCTCATAAATGTTCGTTATCGAACATATTA 58 145 0 AGTCGTTATC 0.684994 -45 AGAAAGCCTGAAGTGAGATATCCATCAGAGTG 67 72 1 AGGAGATATC 0.737319 -156 ACGTCAAAGTAAGTGCGTTATCAGTATTCAGG 72 168 1 AGGCGTTATC 0.97464 -133 TCCTGACGCCAGACGCGTTAGCGCCGTGGTCA 77 82 1 AAGCGTTAGC 0.545101 -25 TCGTCATAAAATGAGCGTTATCGCGCCATTTA 89 148 0 AGGCGTTATC 0.97464 -153 CGGTGATAAAAAGCGAATTATCTCTCGCCGCA 98 209 0 AGGAATTATC 0.496092 -92 * * ******** Masking position 10 Map Score: 6.87991 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 292 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 AGCTTGTCAAGCCAGTCACAAGGCATACCG 1 210 0 GCCAGTCACA 0.948381 -91 GCCAGCCTCACCCCTTATTC 1 291 0 GCCAGCCTCA 0.967112 -10 GGACGGAAGCGACAATCTCACTTTGTGTAA 3 181 1 GACAATCTCA 0.694632 -120 TTCAATCGTTGACAGTCTCAGGAAAGAAAC 5 127 1 GACAGTCTCA 0.919522 -20 GGCAGTGCTCGCCATCCTCACGTACTTTTG 6 133 0 GCCATCCTCA 0.698527 -159 AGTCAGACCAGACAGTCACACACAGTGGAA 6 246 0 GACAGTCACA 0.89665 -46 GGGGACGTCTGCCAGTCAAATGCCTGGCAA 24 12 0 GCCAGTCAAA 0.568647 -78 GACGTACAATGCCAGTCTCTCAGACCTTCA 50 205 1 GCCAGTCTCT 0.73702 -29 CAACTTATTCGCCAGCCTTCAAAGGGGCAA 51 104 0 GCCAGCCTTC 0.540328 -34 TGCGACAACCTCATACTCAAGAG 70 4 1 GACAACCTCA 0.734366 -241 AACTTAACCAGACAATCACACAAAAGAGTC 72 241 1 GACAATCACA 0.633332 -60 ACTCAGCAGAGCCAGCCACAGTGTGGGATT 78 45 0 GCCAGCCACA 0.957135 -197 TTTAATCGGAGCCAGTCATAACAAAAGGTA 87 75 1 GCCAGTCATA 0.699213 -26 ACGGATGAGAGACAGCCTCCTCTCCTCCGT 96 30 1 GACAGCCTCC 0.81437 -77 ********** Masking position 4 Map Score: 5.61798 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 472 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789