AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icrp_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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB 300 L-ribulokinase #3 lacA 65 thiogalactoside acetyltransferase #4 lacY 51 galactoside permease (M protein) #5 lacZ 122 beta-D-galactosidase #6 lacI 76 transcriptional repressor of the lac operon #7 mhpR 76 transcriptional regulator for mhp operon #8 tsx 298 nucleoside channel; receptor of phage T6 and colicin K #9 yajI 90 orf, hypothetical protein #10 nagD 47 N-acetylglucosamine metabolism #11 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #12 nagB 300 glucosamine-6-phosphate deaminase #13 fur 288 negative regulator #14 fldA 139 flavodoxin 1 #15 ybfE 70 orf, hypothetical protein #16 ybfF 184 orf, hypothetical protein #17 galE 260 UDP-galactose-4-epimerase #18 modF 67 ATP-binding component of molybdate transport system #19 modE 128 molybdate uptake regulatory protein #20 ompA 300 outer membrane protein 3a (II*;G;d) #21 dadA 300 D-amino acid dehydrogenase subunit #22 yohJ 238 orf, hypothetical protein #23 cdd 129 cytidine/deoxycytidine deaminase #24 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #25 ptsH 300 PTS system protein HPr #26 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #27 gutM 104 glucitol operon activator #28 srlR 66 regulator for gut (srl), glucitol operon #29 gutQ 31 orf, hypothetical protein #30 ansB 175 periplasmic L-asparaginase II #31 yggN 182 orf, hypothetical protein #32 yggH_mutY 160 yggH: orf, hypothetical protein, mutY: adenine glycosylase; G.C --> T.A transversions #33 yggX 27 orf, hypothetical protein #34 mltC 61 membrane-bound lytic murein transglycosylase C #35 nupG 153 transport of nucleosides, permease protein #36 tdcC 21 anaerobically inducible L-threonine, L-serine permease #37 tdcB 98 threonine dehydratase, catabolic #38 tdcA 188 transcriptional activator of tdc operon #39 crp 300 cyclic AMP receptor protein #40 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #41 ompR 191 response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis #42 malT 300 positive regulator of mal regulon #43 glpG 44 protein of glp regulon #44 glpE_glpD 189 glpE: protein of glp regulon, glpD: sn-glycerol-3-phosphate dehydrogenase (aerobic) #45 aldB 74 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) #46 yiaY 189 putative oxidoreductase #47 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #48 yibF 227 putative S-transferase #49 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #50 mtlD 229 mannitol-1-phosphate dehydrogenase #51 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #52 ivbL 300 ilvB operon leader peptide #53 rpmH 300 50S ribosomal subunit protein L34 #54 yidC 223 60 KD inner-membrane protein #55 thdF 105 GTP-binding protein in thiophene and furan oxidation #56 tnaL 242 tryptophanase leader peptide #57 cyaA 300 adenylate cyclase #58 rhaD 300 rhamnulose-phosphate aldolase #59 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #60 glpK 22 glycerol kinase #61 glpF 300 facilitated diffusion of glycerol #62 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #63 priA 202 primosomal protein N'(= factor Y)(putative helicase) #64 malF 153 part of maltose permease, periplasmic #65 malE_malK 364 malE: periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis, malK: ATP-binding component of transport system for maltose #66 lamB 71 phage lambda receptor protein; maltose high-affinity receptor #67 malM 242 periplasmic protein of mal regulon #68 melR 282 regulator of melibiose operon #69 uxuA 300 mannonate hydrolase #70 uxuB 80 D-mannonate oxidoreductase #71 deoC 257 2-deoxyribose-5-phosphate aldolase #72 deoA 126 thymidine phosphorylase #73 deoB 51 phosphopentomutase #74 deoD 56 purine-nucleoside phosphorylase #75 ybdM 85 similar to protein kinase #76 ybdN 131 ybdN #77 glpQ 98 glycerophosphoryl diester phosphodiesterase #78 glpT 296 glycerol-3-phosphate permease #79 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #80 ybfT 218 similar to glucosamine-6-phosphate isomerase #81 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #82 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #83 ycbD 29 similar to aldehyde dehydrogenase #84 yczA 300 yczA #85 ycbL 96 similar to two-component response regulator [YcbM] #86 yccC 216 similar to asparaginase #87 yclJ 212 similar to two-component response regulator [YclK] #88 ycnL 164 ycnL #89 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #90 mtlD 52 mannitol-1-phosphate dehydrogenase #91 ydcB 94 similar to holo- acyl-carrier protein synthase #92 ydcC 60 ydcC #93 dal 114 D-alanine racemase #94 glvA 300 6-phospho-alpha-glucosidase #95 yfiA 64 similar to hypothetical proteins #96 yfiB 105 similar to ABC transporter (ATP-binding protein) #97 yfiD 154 similar to hypothetical proteins #98 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #99 yhcU 110 yhcU #100 yhcV 136 similar to hypothetical proteins #101 yhxA 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #102 glpP 27 transcription antiterminator #103 glpF 178 glycerol uptake facilitator #104 glpD 140 glycerol-3-phosphate dehydrogenase #105 yhjM 103 similar to transcriptional regulator (LacI family) #106 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #107 yjbQ 234 similar to Na+/H+ antiporter #108 tenA 248 transcriptional regulator #109 yjlC 300 yjlC #110 yjlD 39 similar to NADH dehydrogenase #111 yjmA 197 similar to glucuronate isomerase #112 yjmB 67 similar to Na+:galactoside symporter #113 yjmC 104 similar to malate dehydrogenase #114 yjmE 24 similar to D-mannonate hydrolase #115 yjmG 47 similar to hexuronate transporter #116 yjmH 87 similar to transcriptional regulator (LacI family) #117 ykoG 300 similar to two-component response regulator [YkoH] #118 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #119 moeB 50 molybdopterin biosynthesis protein #120 yknU 223 similar to ABC transporter (ATP-binding protein) #121 yknW 109 yknW #122 fruR 279 transcriptional regulator (DeoR family) #123 xylR 300 transcriptional regulator #124 yncD 300 similar to alanine racemase #125 dhaS 229 aldehyde dehydrogenase #126 deoD 300 purine nucleoside phosphorylase #127 ilvA 248 threonine dehydratase #128 resD 80 two-component response regulator #129 resC 135 essential protein similar to cytochrome c biogenesis protein #130 resA 131 essential protein similar to cytochrome c biogenesis protein #131 ypuL 91 similar to hypothetical proteins #132 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #133 ypuI 54 similar to hypothetical proteins from B. subtilis #134 ypuG 280 similar to hypothetical proteins #135 ppiB 253 peptidyl-prolyl isomerase #136 drm 160 phosphodeoxyribomutase #137 ripX 300 integrase/recombinase #138 yqkL 112 similar to transcriptional regulator (Fur family) #139 spoIIM 100 spoIIM #140 yqkK 99 yqkK #141 yqkI 140 similar to Na+/H+ antiporter #142 ansB 44 L-aspartase #143 ansA 181 L-asparaginase #144 yqhL 190 similar to hypothetical proteins #145 yqgQ 109 yqgQ #146 yqgP 89 similar to hypothetical proteins #147 yqgO 66 yqgO #148 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #149 cdd 118 cytidine/deoxycytidine deaminase #150 yqfF 78 yqfF #151 yqfC 56 yqfC #152 yqfB 24 yqfB #153 yqfA 21 yqfA #154 yqeZ 130 yqeZ #155 rpsU 163 ribosomal protein S21 #156 yrkP 267 similar to two-component response regulator [YrkQ] #157 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #158 araA 207 L-arabinose isomerase #159 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #160 ysdC 183 similar to endo-1,4-beta-glucanase #161 phoP 211 two-component response regulator #162 citH 43 malate dehydrogenase #163 citC 163 isocitrate dehydrogenase #164 citZ 300 citrate synthase II #165 ccpA 274 transcriptional regulator (Lacl family) #166 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #167 ytxJ 23 alternate gene name: csb40; similar to general stress protein #168 ytxH 27 alternate gene name: csb40; similar to general stress protein #169 ytxG 161 alternate gene name: csb40; similar to general stress protein #170 murC 249 UDP-N-acetyl muramate-alanine ligase #171 ytpS 159 ytpS #172 ytpP 234 similar to thioredoxin H1 #173 gbsA 198 glycine betaine aldehyde dehydrogenase #174 yulE 25 similar to L-rhamnose isomerase #175 yulB 56 similar to transcriptional regulator (DeoR family) #176 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase #177 tlpB 113 methyl-accepting chemotaxis protein #178 mcpA 125 methyl-accepting chemotaxis protein #179 tlpA 176 methyl-accepting chemotaxis protein #180 mcpB 157 methyl-accepting chemotaxis protein #181 yutF 28 similar to N-acetyl-glucosamine catabolism #182 yutE 23 yutE #183 yutD 81 yutD #184 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #185 yurN 57 similar to sugar permease #186 yurO 80 similar to multiple sugar-binding protein #187 yurP 215 similar to opine catabolism #188 yurQ 102 yurQ #189 yurR 300 similar to opine catabolism #190 yvqA 277 similar to two-component response regulator [YvqB] #191 yvrI 300 yvrI #192 yvfL 39 similar to maltodextrin transport system permease #193 yvfK 140 similar to maltose/maltodextrin-binding protein #194 lacR 179 transcriptional regulator (LacI family) #195 yvfI 300 similar to transcriptional regulator (GntR family) #196 yvdH 39 similar to maltodextrin transport system permease #197 yvdG 95 similar to maltose/maltodextrin-binding protein #198 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #199 yvdE 205 similar to transcriptional regulator (LacI family) #200 yvdD 116 similar to hypothetical proteins #201 crh 23 catabolite repression HPr-like protein #202 yvcL 22 similar to hypothetical proteins #203 yvcJ 24 similar to hypothetical proteins #204 yvcI 300 similar to mutator MutT protein #205 nagA 181 N-acetylglucosamine-6-phosphate deacetylase #206 glcR 223 transcriptional regulator (DeoR family) #207 ywpH 76 similar to single-strand DNA-binding protein #208 ywpG 174 ywpG #209 fnr 98 transcriptional regulator (FNR/CRP family) #210 narK 135 nitrite extrusion protein #211 ywiB 300 ywiB #212 galK 80 galactokinase #213 ywcC 300 alternate gene name: ipa-33d #214 msmX 120 multiple sugar-binding transport ATP-binding protein #215 yxkF 183 similar to hypothetical proteins #216 galE 114 UDP-glucose 4-epimerase #217 yxkA 129 similar to hypothetical proteins #218 yxjD 78 similar to 3-oxoadipate CoA-transferase #219 yxjC 153 similar to hypothetical proteins from B. subtilis #220 yxjB 300 similar to hypothetical proteins #221 pdp 29 pyrimidine-nucleoside phosphorylase #222 nupC 115 pyrimidine-nucleoside transport protein #223 dra 105 deoxyribose-phosphate aldolase #224 deoR 90 transcriptional regulator #225 yxxB 72 yxxB #226 yxeR 69 similar to ethanolamine transporter #227 yxeN 22 similar to amino acid ABC transporter (permease) #228 yxeM 24 similar to amino acid ABC transporter (binding protein) #229 yxeK 185 similar to monooxygenase #230 yxeI 154 similar to penicillin amidase #231 yxeH 39 similar to hypothetical proteins #232 yxeF 87 yxeF #233 yxdJ 108 similar to two-component response regulator [YxdK] #234 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #235 iolG 22 myo-inositol 2-dehydrogenase #236 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #237 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #238 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #239 iolA_iolR 415 iolA: methylmalonate-semialdehyde dehydrogenase, iolR: transcriptional regulator (DeoR family) #240 yxbG 116 alternate gene name: yxaU; similar to glucose 1-dehydrogenase #241 yycF 300 similar to two-component response regulator [YycG] Motif number 1 GGCGTTACATACCGGATGCGGCTAC 1 6 0 ACCGGATGCG 0.735794 -279 GGTATGTAACGCCTGATGCGACGCTGACGC 1 23 1 GCCTGATGCG 0.990633 -262 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 76 1 GCCGGATAAG 0.977812 -209 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 GCCGGATGCG 0.994803 -194 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 108 1 GCCTGATGCG 0.990633 -177 CAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 GCCTGATAAG 0.960545 -155 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 161 1 GCCGGATAAG 0.977812 -124 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 GCCGGATGCG 0.994803 -109 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 193 1 GCCTGATGCG 0.990633 -92 CAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 GCCTGATAAG 0.960545 -70 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 246 1 GCCGGATAAG 0.977812 -39 ACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GCCGGATGCG 0.994803 -24 GCAATCAATGTCGGATGCGGCGCGAGCGC 3 10 1 GTCGGATGCG 0.883539 -56 TGATATGTTGGTCGGATAAGGCGCTCGCGC 3 30 0 GTCGGATAAG 0.635901 -36 AGCCTGGGGTGCCTAATGAGTGAGCTAACT 5 30 0 GCCTAATGAG 0.578802 -93 TGCTGACCTTGCCGGAGGCGGCCTTAGCAC 17 19 1 GCCGGAGGCG 0.926441 -242 GGTAGTCACTGCCCGATACGGACTTTACAT 26 79 1 GCCCGATACG 0.783187 -177 ACTATAGAATGCCTGATGCGCTACGCTCAT 27 45 1 GCCTGATGCG 0.990633 -60 AGTCCTGTATGCCTGATGAGCGTAGCGCAT 27 60 0 GCCTGATGAG 0.981342 -45 ATGCAAAACTGCCTGATGCGCTACGCTTAT 31 33 1 GCCTGATGCG 0.990633 -150 ATCTTTCCAGGCCTGATAAGCGTAGCGCAT 31 48 0 GCCTGATAAG 0.960545 -135 CGTTTTCCATGCCGGATGCGGCGTAAACAC 31 102 0 GCCGGATGCG 0.994803 -81 AAAGTTAGTTGCCGGATGCAAGCATGATAA 32 95 0 GCCGGATGCA 0.833374 -66 TATGCAAGTTGCCGGAGGCGTGCTCCGGCA 34 17 0 GCCGGAGGCG 0.926441 -45 GGGGTTAATTGCCTGATGCGCTACGCTTAT 50 42 1 GCCTGATGCG 0.990633 -188 CATCCTGTAGGCCTGATAAGCGTAGCGCAT 50 57 0 GCCTGATAAG 0.960545 -173 GTTCTTGTAGGCCGGATAAGGCGCTTACGC 50 111 1 GCCGGATAAG 0.977812 -119 GAGGGGCAGCGCCGGATGCGGCGTAAGCGC 50 131 0 GCCGGATGCG 0.994803 -99 CTTTTCGTAGGGCGGATAAGCACCGCGCAT 55 60 1 GGCGGATAAG 0.653423 -46 TGCTTTGTGTGGCGGATGCGCGGTGCTTAT 55 75 0 GGCGGATGCG 0.891183 -31 GCCTGATAAGACGCGACAGC 58 1 1 GCCTGATAAG 0.960545 -300 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 23 0 GCCTGATGCG 0.990633 -278 GGCATTGATTGCCGGATGCGGCACAAGTGC 58 40 1 GCCGGATGCG 0.994803 -261 CGACCTGTAGGCCGGATAAGGCACTTGTGC 58 60 0 GCCGGATAAG 0.977812 -241 ACAGTTGTAGGCCTGATAAGACGCGACAGC 58 93 1 GCCTGATAAG 0.960545 -208 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 115 0 GCCTGATGCG 0.990633 -186 GGCATTGATTGCCGGATGCGCACAAGTCGC 58 132 1 GCCGGATGCG 0.994803 -169 CGACCTGTAGGCCTGATAAGCGACTTGTGC 58 151 0 GCCTGATAAG 0.960545 -150 ATAGTTGTAGGCCTGATAAGACGCGACAGC 58 184 1 GCCTGATAAG 0.960545 -117 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 206 0 GCCTGATGCG 0.990633 -95 CGACCCGTAGGCCGGATAAGGCGCTCGCGC 58 244 0 GCCGGATAAG 0.977812 -57 GCTGTGAAATGCCGGATGCGGCGTGAACGC 64 12 1 GCCGGATGCG 0.994803 -142 ACGTATGTAGGCCTGATAAGACGCGTCAGC 64 65 1 GCCTGATAAG 0.960545 -89 GACAACAACTGCCTGATGCGACGCTGACGC 64 87 0 GCCTGATGCG 0.990633 -67 GGCAGTTGTTGTCGGATAAGGCGTGAAAGC 64 104 1 GTCGGATAAG 0.635901 -50 CAAAACCTGGGCCGGATAAGGCGTTTACGC 67 14 1 GCCGGATAAG 0.977812 -229 GGCGTTGGTTGCCGAATGCGGCGTAAACGC 67 34 0 GCCGAATGCG 0.833374 -209 GGCAACCAACGCCTGATGCGACGCTTGCGC 67 51 1 GCCTGATGCG 0.990633 -192 GCCGTTGTAGGCCTGATAAGACGCGCAAGC 67 73 0 GCCTGATAAG 0.960545 -170 TCAAATGTAGGCCGGATAAGGCGTTTACGC 67 105 1 GCCGGATAAG 0.977812 -138 CTGTTTTTATGCCGGATGCGGCGTAAACGC 67 125 0 GCCGGATGCG 0.994803 -118 GATGCTTTACGCCTGATGCGCTGCGCTTAT 72 15 1 GCCTGATGCG 0.990633 -112 CGTCTCGTAGGCCTGATAAGCGCAGCGCAT 72 30 0 GCCTGATAAG 0.960545 -97 CTACCCGTAGGCCGGATAAGGCGTAGACGC 72 63 1 GCCGGATAAG 0.977812 -64 GGCGGCTTTTGCCGGATGCGTCTACGCCTT 72 80 0 GCCGGATGCG 0.994803 -47 AGTTGTCTCCGCCTGATGCATTTTCTCCTT 222 11 0 GCCTGATGCA 0.734252 -105 ********** Masking position 6 Map Score: 169.877 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 250 Number in noncoding regions = 484 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 GCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTA 1 29 0 AGCGCGCGCA 0.998536 -256 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 114 0 AGCGCGCGCA 0.998536 -171 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 199 0 AGCGCGCGCA 0.998536 -86 TGGTCGGATAAGGCGCTCGCGCCGCATCCGACATTG 3 16 0 AGCGCGCGCA 0.998536 -50 CGGCGTAGACATGAGTCTACGCCGCATCACA 13 6 0 AGAGCGCGCA 0.976474 -283 AGGCGGGATAAGGTGTTTACGCCGCATCCGGCATGG 31 90 1 AGTGCGCGCA 0.976474 -93 AGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTG 50 119 1 AGCGCGCGCA 0.998536 -111 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 11 1 AGCGCGCGCA 0.998536 -290 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 103 1 AGCGCGCGCA 0.998536 -198 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 194 1 AGCGCGCGCA 0.998536 -107 AGGCCGGACAAGGCGTTCACGCCGCATCCGGCATTT 64 18 0 AGCGCGCGCA 0.998536 -136 GCCTGATAAGACGCGTCAGCGTCGCATCAGGCAGTT 64 75 1 AGCGCGCGCA 0.998536 -79 GGGCCGGATAAGGCGTTTACGCCGCATTCGGCAACC 67 22 1 AGCGCGCGCA 0.998536 -221 GCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTG 67 57 0 AGCGCGCGCA 0.998536 -186 AGGCCGGATAAGGCGTTTACGCCGCATCCGGCATAA 67 113 1 AGCGCGCGCA 0.998536 -130 * *** ** **** Masking position 1 Map Score: 58.6391 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 24 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 AATCGCAGCGTGTAGGCCAGATAAGACGCG 1 50 0 TGTAGGCCAG 0.914325 -235 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 71 1 TGTAGGCCGG 0.992671 -214 AATCGCAGCGCGTAGGCCTGATAAGACGCG 1 135 0 CGTAGGCCTG 0.979402 -150 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 156 1 TGTAGGCCGG 0.992671 -129 AATCGCAGCGTGTAGGCCTGATAAGACGCG 1 220 0 TGTAGGCCTG 0.990862 -65 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 241 1 TGTAGGCCGG 0.992671 -44 TGCGTCGAACCGTTGGCCGGAGAGGGTGCT 17 44 0 CGTTGGCCGG 0.769476 -217 CTATGCTTGATGTATGCCTGAGTTCGCTGC 22 107 1 TGTATGCCTG 0.87371 -132 GCGGAAGTCCTGTATGCCTGATGAGCGTAG 27 65 0 TGTATGCCTG 0.87371 -40 TGATGCATCCTGTAGGCCTGATAAGCGTAG 50 62 0 TGTAGGCCTG 0.990862 -168 TGCACGTTCTTGTAGGCCGGATAAGGCGCT 50 106 1 TGTAGGCCGG 0.992671 -124 GTTGCCGACCTGTAGGCCGGATAAGGCACT 58 65 0 TGTAGGCCGG 0.992671 -236 CGGCAACAGTTGTAGGCCTGATAAGACGCG 58 88 1 TGTAGGCCTG 0.990862 -213 ATTGCCGACCTGTAGGCCTGATAAGCGACT 58 156 0 TGTAGGCCTG 0.990862 -145 CGGCAATAGTTGTAGGCCTGATAAGACGCG 58 179 1 TGTAGGCCTG 0.990862 -122 ATGCACGACCCGTAGGCCGGATAAGGCGCT 58 249 0 CGTAGGCCGG 0.983442 -52 CCACGATGCTTGTAGGCATGCTGTAAACTT 61 229 0 TGTAGGCATG 0.789659 -72 GTTTCGGTTTTGTAGGCCGGACAAGGCGTT 64 37 0 TGTAGGCCGG 0.992671 -117 CCGAAACGTATGTAGGCCTGATAAGACGCG 64 60 1 TGTAGGCCTG 0.990862 -94 TGACAGCCGTTGTAGGCCTGATAAGACGCG 67 78 0 TGTAGGCCTG 0.990862 -165 GGCTGTCAAATGTAGGCCGGATAAGGCGTT 67 100 1 TGTAGGCCGG 0.992671 -143 AGATACGTCTCGTAGGCCTGATAAGCGCAG 72 35 0 CGTAGGCCTG 0.979402 -92 CGTATCTACCCGTAGGCCGGATAAGGCGTA 72 58 1 CGTAGGCCGG 0.983442 -69 CCCCGTAACTTGTAGGTCTGGCTGTTTACG 195 78 0 TGTAGGTCTG 0.789659 -223 ********** Masking position 3 Map Score: 68.249 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 20 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 CAGATAAGACGCGTCAGCGTCGCATCAGGCGTTA 1 29 0 GCGGCGCGCA 0.997697 -256 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 114 0 GCGGCGCGCA 0.997697 -171 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 199 0 GCGGCGCGCA 0.997697 -86 GTCGGATAAGGCGCTCGCGCCGCATCCGACATTG 3 16 0 GCGGCGCGCA 0.997697 -50 CCTTGCGGGAGTGAAAAAGGCGCAAATTGCGTTT 8 252 0 GTGAAGCGCA 0.713605 -47 GCGTAGACATGAGTCTACGCCGCATCACA 13 6 0 GAGACGCGCA 0.957157 -283 TAAAAACCCAGCGTCCGCGTCGCTTTCCGCGCGT 15 21 1 GCGGCGCGCT 0.981069 -50 ATGTATGCCTGAGTTCGCTGCGCATTGCGTAATG 22 116 1 GAGGCTCGCA 0.810197 -123 CTCCAGTTACGTGAACGCTACGCATTATCCCTTA 30 145 0 GTGGCTCGCA 0.810197 -31 GCGGGATAAGGTGTTTACGCCGCATCCGGCATGG 31 92 1 GTGACGCGCA 0.957157 -91 GCCGGATAAGGCGCTTACGCCGCATCCGGCGCTG 50 121 1 GCGACGCGCA 0.994058 -109 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 13 1 GCGGCGCGCA 0.997697 -288 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 105 1 GCGGCGCGCA 0.997697 -196 ATTGCCGGATGCGCACAAGTCGCTTATCAGGCCT 58 139 1 GCGAAGCGCT 0.690578 -162 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 196 1 GCGGCGCGCA 0.997697 -105 GCCGGACAAGGCGTTCACGCCGCATCCGGCATTT 64 18 0 GCGACGCGCA 0.994058 -136 CTGATAAGACGCGTCAGCGTCGCATCAGGCAGTT 64 77 1 GCGGCGCGCA 0.997697 -77 GCCGGATAAGGCGTTTACGCCGCATTCGGCAACC 67 24 1 GCGACGCGCA 0.994058 -219 CTGATAAGACGCGCAAGCGTCGCATCAGGCGTTG 67 57 0 GCGGCGCGCA 0.997697 -186 GCCGGATAAGGCGTTTACGCCGCATCCGGCATAA 67 115 1 GCGACGCGCA 0.994058 -128 ACGAACAACTGAGACTGAGCCGCAAATGGTTCAG 194 51 1 GAGGAGCGCA 0.865821 -129 *** *** **** Masking position 11 Map Score: 57.5792 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 175 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 GTTTGCAGCAATCCCTCTTTGCAGACCTTT 22 65 0 ATCCCTCTTT 0.417259 -174 ACCTCTTTCCATCCTCCTTGCCCCTACGCC 65 276 0 ATCCTCCTTG 0.832967 -89 GGAGCGTTGACTCCGCCTTTGTTATGTCAC 74 22 1 CTCCGCCTTT 0.367881 -35 GCAAACAACCTCCTTTTATTTCCATC 76 116 0 AACCTCCTTT 0.919925 -16 ATGTGTGGCGTGCCTCCTTTCCCGAAAAAC 78 245 0 TGCCTCCTTT 0.545651 -52 TAATAATTATCCCCCTTTGCTGTTTGTG 78 279 0 ATCCCCCTTT 0.849032 -18 AAAGATTTGTATCCTTCTTTTATAACAAAT 80 84 1 ATCCTTCTTT 0.656483 -135 GCCAGTATATATCCGTCTTTTTCAATAAAC 81 207 0 ATCCGTCTTT 0.294417 -94 CAACATAACCTCCTGTTATTTGTGTA 82 211 0 AACCTCCTGT 0.603344 -16 CATTGGCCGTCACCTCCTTTAAGAAACACA 84 231 0 CACCTCCTTT 0.671057 -70 TTGATATCCTCCTTTCTAACTCATC 84 286 0 ATCCTCCTTT 0.93754 -15 TTGTTGTCATATCCTTCTTTTTTTGTCTTT 86 106 0 ATCCTTCTTT 0.656483 -111 GTATGATAACCTCCTTTGCGTACGTAC 91 78 0 AACCTCCTTT 0.919925 -17 ATGACGACCTCCTTGATAACGTTTA 94 286 0 GACCTCCTTG 0.403969 -15 TTTATCCTCCTTGATAAATGTTA 97 142 0 ATCCTCCTTG 0.832967 -13 TACGTTTCCTCCTTGTTGTCACGGT 104 126 0 TTCCTCCTTG 0.554314 -15 TTGAATCATCCTCCTTTTTAAGTCGGA 106 107 0 ATCCTCCTTT 0.93754 -17 AATCAGAACCTCCTTTTTAAGTCAGG 107 219 0 AACCTCCTTT 0.919925 -16 TTCAAAACCTCCTTGAGAATATCTA 121 95 0 AACCTCCTTG 0.792392 -15 CTCATATCCTCCTGTAAATCTAAAT 126 286 0 ATCCTCCTGT 0.665259 -15 GGTGCTTCCTCCTTTAATGTGCTTT 134 6 1 TTCCTCCTTT 0.789189 -275 CTTGAAAGCCTCCTTTTTTTCTATAC 136 145 0 AGCCTCCTTT 0.82804 -16 CGGTCGAACCATCCGCCTTTTTCATCCTGA 137 243 0 ATCCGCCTTT 0.766211 -58 AATCTTTAACCTTCTTTCTCTTTGCTG 142 28 0 AACCTTCTTT 0.593937 -17 AGTGTTAGAACCTCCTTTCAAATCATAC 151 9 1 AACCTCCTTT 0.919925 -48 ACAAAAAGAACCCCCTTTCATCTCATGT 151 39 0 AACCCCCTTT 0.811476 -18 TTTAGTTCCTCCTTTTGGATTTTCA 157 286 0 TTCCTCCTTT 0.789189 -15 TTTTGTTCAACCTCCTTTATTTTAGAAA 159 179 0 AACCTCCTTT 0.919925 -18 CTCAAACCTCCTTGCTGCAGGATA 169 148 0 AACCTCCTTG 0.792392 -14 ATAAGCCTCCTTGACGTAAATAA 173 186 0 AGCCTCCTTG 0.615354 -13 TCTCGTTGACTCCTCCTTTAAGATAAATC 177 95 0 CTCCTCCTTT 0.727181 -19 TTCCTTTTGAACCTTCTTTCAATAATTTA 179 158 0 AACCTTCTTT 0.593937 -19 AGGGTAGCCTCCTTTTAACCTATTA 184 6 1 AGCCTCCTTT 0.82804 -176 GTTTCCCCCTTTGATTTCCGTT 198 101 0 TTCCCCCTTT 0.583788 -12 TAAAGTAATTGACCCCCTTTTTATAATGAA 204 80 1 GACCCCCTTT 0.433219 -221 GATATGTTCCTCCTGTTCCGGGCTGC 205 7 1 TTCCTCCTGT 0.331398 -175 AGATGATCCGCCTTTCTGGAATTTG 205 167 0 ATCCGCCTTT 0.766211 -15 CTAACATCCCCCTTTGTTATTGTAA 214 106 0 ATCCCCCTTT 0.849032 -15 AAGATGACCCTCCTTTGGTCCTGCAT 215 7 1 ACCCTCCTTT 0.57763 -177 GTGTCCAACCCTCTTTCACAGAAATC 225 57 0 AACCCTCTTT 0.354015 -16 TCTTTCCTCCTTTTTTGGGCGAA 232 75 0 TTCCTCCTTT 0.789189 -13 GATACGAGACCTCCTTTTTCTATTTGT 240 100 0 GACCTCCTTT 0.671057 -17 ********** Masking position 8 Map Score: 37.5307 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 64 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 AATAAATTAGTGGAATCGTTTACACAAGAATTTAGCC 17 165 0 TGAACGTCAA 0.96328 -96 TCGTAAAACGTGCTACCGATCACATTAAGAAATCAGC 22 171 0 TGTACGTCAA 0.938401 -68 AATGCAATTTAGCAACCGATTGCAATAAAACATTTAA 40 90 0 AGAACGTCAA 0.938401 -181 AGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAA 62 60 0 TGAACGTCAA 0.96328 -96 TGATAATTTAAGAAAGCGCTATCATGATAAGTTAATA 78 139 1 AGAACGTCAA 0.938401 -158 ACGACCTCCTTGATAACGTTTACAATTCCATTTATAC 94 271 0 TGTACGTCAT 0.781943 -30 GTTGTTGACATGTTACCGATTTCAGAAACTAGGATAA 105 57 0 TGTACGTCAA 0.938401 -47 GAAAATGAAATGTTAACGCTGTCATAAACATAAAAAA 111 73 0 TGTACGTCAA 0.938401 -125 TATTTCAAAATGTTAACGTTAACATTTTGATTTGTTT 111 151 0 TGTACGTCAT 0.781943 -47 GTATTCAAAATGAATACGTTTTCATTAGGAGGTGAAG 122 252 1 TGATCGTCAA 0.860629 -28 TCAGTCAAGAAGAAAACGCTGACAAAAAAGCCAGCTT 145 29 0 AGAACGTCAA 0.938401 -81 AAATATAAAGTGATAGCGGTACCATTATAGGTAAGAG 149 80 1 TGTACGTCAA 0.938401 -39 CCTTTATTTTAGAAAGCGCTTACAAATTAGATTATTT 159 157 0 AGAACGTCAT 0.781943 -40 TTACTATAAATGAAAGCGCTATCATAAACGTCTTTAT 161 52 1 TGAACGTCAA 0.96328 -160 ATAAAAACCAAGTATACGTTTTCATCATCTATAAAAA 165 70 1 AGATCGTCAA 0.781943 -205 CCCTTTTATTTGTATCCGTTTTCATTATATATGATTT 176 93 0 TGATCGTCAA 0.860629 -45 ACTTTCGATTTGTTACCGATAACAGAATG 197 3 0 TGTACGTCAA 0.938401 -93 ATTGTCCTATAGAAAGCGGTTACAACAACTTTCGATT 197 30 0 AGAACGTCAA 0.938401 -66 CTTTTCACCCTGTTACCGATAACAGAATAAGGCGC 198 9 0 TGTACGTCAA 0.938401 -104 ACTCAATATAAGAAAGCGTTTACAATAACAAAGGGGG 214 87 1 AGAACGTCAA 0.938401 -34 TCCGCGAACTAGAAAGCGTTTACAAAAACCTGTCCGC 219 111 0 AGAACGTCAA 0.938401 -43 CTCCTTTATTTGTATTCGCTTACAATTACTGTTTCCT 222 81 0 TGATCGTCAT 0.592429 -35 ** ** ** * ** * Masking position 10 Map Score: 26.1294 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AATTTGCAGCAAAATAAAAATACGGCTTGAAAC 12 8 0 AAAAAAAACC 0.930455 -293 AACCGCTAAGCACAGAAAAGCACTCCCCTTTTGTGC 19 44 1 CAAAAAAGCC 0.877437 -85 AGAAATCGCAAAGAAAAAAATTCTCCGGCGACGCGG 21 54 0 AAAAAAAACC 0.930455 -247 CAAATTCAGACACATAAAAAAACGTCATCGCTTGCA 42 184 1 CAAAAAAACC 0.962204 -117 TGATTGATATCACACAAAAGGCCGTCGACTGGACAG 49 154 1 CAAAAAAGCC 0.877437 -147 ACAGCAACATCATACAAGAAATCCCCCAAAATCATG 79 163 1 CAAAAGAACC 0.839618 -68 TCCTTTAAGAAACACAAAAAACCCCCGTCCTATGCA 84 211 0 AAAAAAAACC 0.930455 -90 ATGGTGCTATTATATAAAAAAGCATCAAAACAACCG 87 178 1 TAAAAAAACC 0.836025 -35 CAATTTTTTAAAAATAAAAAGGCTCCTGGTT 89 6 0 AAAAAAAACC 0.930455 -167 TTTTTGACGGCAAACGAAAACCCTCCCGAAAAGGAG 96 19 0 CAAGAAAACC 0.775654 -87 ATAAAACTGTAACAAAAAAAGACCTCTGTGCAGGAC 97 17 0 AAAAAAAACC 0.930455 -138 AAGGCGGACAAAAATAAAAAATCCCCCTGCCGTTAT 98 30 0 AAAAAAAACC 0.930455 -64 TCCCCCTCTGAAAATAAAAAAACCACTTTCCCGCAA 108 216 0 AAAAAAAACC 0.930455 -33 CGATTAAGCGCACAAAAAAATACACCATTCGGTCAA 117 70 1 CAAAAAAACC 0.962204 -231 GAAATCACTAAACATAAAAAAACCTCATGCATGTTG 122 18 0 AAAAAAAACC 0.930455 -262 TGCAATTTACAAAAGAAAAAAGCTACAATAAGCTTA 125 35 0 AAAAAAAACC 0.930455 -195 TGGAAGCAAACATAAAAAAACTCTCCCTGAAAAAGG 132 22 0 CAAAAAAACC 0.962204 -101 TCTGTCGCTCTAAACAAAAAAGCCGCAGCCACCTGC 136 13 0 TAAAAAAACC 0.836025 -148 ATGGCAAAGAAAAGGACATCTTTCTAAGAG 154 5 1 CAAAAAAGCC 0.877437 -126 TTTTTTTATGTATAAAAAAAGACATCTCTCTTAGAA 154 32 0 TAAAAAAACC 0.836025 -99 AACGAGAAAGCATAAAAAAAGGCCGCACGGCGGCCT 165 25 0 CAAAAAAACC 0.962204 -250 AAGGGTTTTTTACAAAAAAAAGCGCCAGATGATATC 166 24 0 TAAAAAAACC 0.836025 -212 GCTTTTTAACAAAAAAAGAAAGCAGCAGATATGCCG 176 24 0 AAAAAGAACC 0.733424 -114 TATTGTTTACCATATAAAAAAACAGCGCTTTGATAG 179 27 0 CAAAAAAACC 0.962204 -150 AAACCTGATCCATAGGAAAATACCTCCCTTCTTTTT 191 143 1 CAAGAAAACC 0.775654 -158 TGATAGTTTTAAGATAAAAGTACAACATAGATCTGC 211 29 0 AAAAAAAGCC 0.790022 -272 CGCAACACCGCACAAAAAAACACGCCATCTCGGCGG 233 23 0 CAAAAAAACC 0.962204 -86 GCGGCCGGTTCAAAGAAGAAGACGTCATTGATAAAG 241 27 1 CAAAAGAACC 0.839618 -274 ** * ***** * * Masking position 9 Map Score: 35.3629 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 39 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TAGCCGCATCCGGTATGTAACGCCTGATGCGACGC 1 12 1 CGGAAAGCCT 0.994356 -273 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGC 1 97 1 CGGAAAGCCT 0.982822 -188 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGC 1 182 1 CGGAAAGCCT 0.982822 -103 CTTATTACAACGGCGTGAAACGCCTGTCAGGATCC 57 38 0 CGGGAAGCCT 0.967729 -263 GTGCCGCATCCGGCAATCAATGCCTGATGCGACGC 58 29 0 CGGAAAGCCT 0.992633 -272 TGTGCGCATCCGGCAATCAATGCCTGATGCGACGC 58 121 0 CGGAAAGCCT 0.992633 -180 CGCGCATCCACGGCAATCAATGCCTGATGCGACGC 58 212 0 CGGAAAGCCT 0.992633 -89 ACGCCGCATTCGGCAACCAACGCCTGATGCGACGC 67 40 1 CGGAAAGCCT 0.994353 -203 AGAAAGCACTCGGAAAGGAATGCTTTTGGCAATGC 111 28 0 CGGAAAGCTT 0.926745 -170 AGCGCAGAAGCGGGAGAAAAAGCCTTTGCTTCTGG 134 104 0 CGGAAAGCCT 0.99436 -177 TCTATTAAAACGGTAAGGAAGGTCTTAAA 144 5 0 CGGAAAGTCT 0.926745 -186 GGTGGTACCGCGGAAAGAAAAGCCTTTTCGCCCCT 157 152 1 CGGAAAGCCT 0.99436 -149 *** * ** **** Masking position 9 Map Score: 25.1927 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 13 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 CACAGAAAAGCACTCCCCTTTTGTGCGGTCAG 19 54 1 CTCCCCTTTT 0.900467 -75 TCTCCTGCTGAACGCCCTTTTTATCCAGCATA 21 130 0 AGCCCTTTTT 0.785705 -171 CGCTTTATACTGTCCCCTTTTGTGTGGAATA 43 10 1 CTCCCCTTTT 0.900467 -35 CAGTAAGCTGCCCGCCCTTTTTTACACTTTCA 46 158 1 CGCCCTTTTT 0.891013 -32 ATCAACATTTTCTGCCCTTTTTCCCATCACCA 48 168 1 TGCCCTTTTT 0.695968 -60 CAGAGGGGCTTTCGCCCCTTTCAGATAATGAC 67 158 0 TGCCCCTTTC 0.58641 -85 AGCCGGTTATCCGGCTCTTTTTTATTCTCCGT 75 20 1 CGCTCTTTTT 0.796283 -66 GGGGTGTTTTCTGGCTCTTTTTGTTTTTCGGG 78 223 1 CGCTCTTTTT 0.796283 -74 GCCCATTGCCCCTTTCGTGTTTTTTC 83 14 0 AGCCCCTTTC 0.694279 -16 TCCGAGCCCCTTTTCTTCATTTTG 91 3 1 CGCCCCTTTT 0.933096 -92 GTTAAATGGCTCCTTTTCGAAGCGGAA 99 6 1 AGCTCCTTTT 0.749404 -105 TATTTTTAGAAAAGCTCTTTTTGTATCAGAGA 100 31 1 AGCTCTTTTT 0.636758 -106 CCTTTCCTCTAACTCCCTTTTTAAACGGCTCG 100 78 1 ATCCCTTTTT 0.703997 -59 AAATAATAAAACATCCCCTTTCTCAAGAAGAA 101 156 0 ATCCCCTTTC 0.595651 -145 TTGGCTGTTGTGGTCTCTTTTTCTATTTACCG 104 98 1 TTCTCTTTTT 0.415188 -43 AGTATCGTTTCTATCCCTTTTTATTATAAGGA 106 64 0 CTCCCTTTTT 0.84135 -60 CCTTTGGGATCAATCTCTTTTTTGAAAATGAA 111 101 0 CTCTCTTTTT 0.717157 -97 GATGAAATCTCCTTTTCTTATCTATA 125 5 1 ATCTCCTTTT 0.659846 -225 CAATTGGCTCCTTTTGGTTCTAATT 127 4 1 TGCTCCTTTT 0.651213 -245 GCCATGACATCACTCCCTTTTCGC 129 3 0 CTCCCTTTTC 0.658174 -133 CGGTTTGGCCTGCCCTTTTTATCTTTATTC 129 116 0 CGCCCTTTTT 0.891013 -20 CGTTTACTCTCCCTTTTTCAGGGAGAGT 132 7 1 CTCCCTTTTT 0.84135 -116 AACAGAAAAACATGCCCTTTTTCAAAAAGAAA 139 26 0 CGCCCTTTTT 0.891013 -75 GTGATCACTCCCTTTTTTATTTTCATA 140 83 0 CTCCCTTTTT 0.84135 -17 GAACTTCCGCTCCTTTTTCACCTTGAG 143 6 1 TGCTCCTTTT 0.651213 -176 GAAAAGCCTTTTCGCCCCTTTTAGCTATCGCA 157 168 1 TGCCCCTTTT 0.796131 -133 GTAAACTGCCCCTTTCTCATAAAATA 158 192 0 AGCCCCTTTC 0.694279 -16 AAGCAAGCCTTTCTCTCTTTTTA 161 2 0 TTCTCTTTTT 0.415188 -210 TTAATACAGCCTTTCTCTTTTTACTATAAATG 161 32 1 CTCTCTTTTT 0.717157 -180 ATATAACATCTCCTTTTCAATAAATTT 164 284 0 ATCTCCTTTT 0.659846 -17 CATTCATTTCTCCTTTTTTATGCTACC 178 109 0 ATCTCCTTTT 0.659846 -17 CTACATCTTCCTCGCTCTTTTTCTCTTCCTTT 190 131 1 CGCTCTTTTT 0.796283 -147 TCCTTAAGGGAAATCTCTTTTTTATTTCTCTT 199 103 1 ATCTCTTTTT 0.53208 -103 AAGATCTCCCCTTTTCTTTACGG 201 9 0 ATCCCCTTTT 0.802266 -15 TTGGCTTGCCCCTTTCAATGATTCAA 210 120 0 CGCCCCTTTC 0.835085 -16 TTAAAAAAGGAAAGCTCCTTTTTTCGGAGCTT 219 22 0 AGCTCCTTTT 0.749404 -132 TCGGCTGTTTCCGTCCCCTTTCCATATGTACG 219 78 0 CTCCCCTTTC 0.766613 -76 GGTTTTCTCCTTTTTCAAACGTAT 226 56 0 TTCTCCTTTT 0.547742 -14 TTGATCAGTCCCCTTTTCAATTCAGAT 230 138 0 CTCCCCTTTT 0.900467 -17 * ********* Masking position 9 Map Score: 35.0398 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 159 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 10 CCAGATAAGACGCGTCAGCGTCGCATCAGGC 1 33 0 CGCGCAGCGT 0.995688 -252 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 118 0 CGCGCAGCGT 0.995688 -167 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 203 0 CGCGCAGCGT 0.995688 -82 CCTGATAAGACGCGACAGCGTCGCATCAGGC 58 12 1 CGCGCAGCGT 0.995688 -289 CCTGATAAGACGCGACAGCGTCGCATCAGGC 58 104 1 CGCGCAGCGT 0.995688 -197 CCTGATAAGACGCGACAGCGTCGCATCAGGC 58 195 1 CGCGCAGCGT 0.995688 -106 CCTGATAAGACGCGTCAGCGTCGCATCAGGC 64 76 1 CGCGCAGCGT 0.995688 -78 CCTGATAAGACGCGCAAGCGTCGCATCAGGC 67 61 0 CGCGAAGCGT 0.952769 -182 GATGAAAGCCGGCGCCAGCCTGTATAATAAA 224 21 1 GGCGCAGCCT 0.942889 -70 GGCGGGATATGGCGACAGCCTTCCTGCCGAA 234 27 1 GGCGCAGCCT 0.942889 -59 **** ****** Masking position 7 Map Score: 22.7009 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 51 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 AGGCGGCCTTAGCACCCTCTCCGGCCAACGGTTC 17 34 1 AGCACCCCGG 0.549192 -227 AACACCTGTTAAAAACCGCGTCGCCGGAGAATTT 21 39 1 AAAACCTCGC 0.852348 -262 ACAGGTAACAAAAAACCAGTCCGCGAAGTTGATA 35 105 1 AAAACCCCGC 0.97546 -49 TGGGTGAGGGAAAAGCCTCACCCCAGCCCTCTCG 50 178 1 AAAACCCCCC 0.680687 -52 ACACGATTCCAAAACCCCGCCGGCGCAAACCGGG 51 24 1 AAAACCCGGC 0.896686 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCGCCGG 51 43 0 AAAACCCCGG 0.918973 -63 GCAGATAACAAAAAACCCCGCCGGAGCGAGGTTT 52 157 0 AAAACCCCGG 0.918973 -144 TATCCGGATGAACAACCAGACCGCAGCCGTGGCG 69 212 0 AACACCCCGC 0.910607 -89 TTTGCTGCGCAGAATCCCGGCCGGACAGTGATTT 82 40 1 AGAACCCCGG 0.826203 -187 AAAGCAATTCAGAAGCCCATTCGGCATCAGGGGA 84 41 0 AGAACCTCGG 0.408413 -260 CTCCGTCTCTAAAATCCTCTACGCTTAAATAGAT 88 32 0 AAAACCACGC 0.636967 -133 TAAAAATAGAAAAGCCCTTGCCGCATGA 100 5 0 AAAGCCCCGC 0.869539 -132 TGAAATACAGAAAAACCGGACGGCTGAAATGCCG 120 19 0 AAAACCCGGC 0.896686 -205 GTGTTAATTTGAAAACCTAACCGCAGGAAGGAGG 126 118 0 GAAACCCCGC 0.775753 -183 ACCAAACGCAACAATCCAGACCGCGTTGAATTTA 148 140 1 ACAACCCCGC 0.926927 -161 CCGCGGAAAGAAAAGCCTTTTCGCCCCTTTTAGC 157 159 1 AAAACCTCGC 0.852348 -142 ATTCAATAAAAAAAGCCCTTCCGCCCACAATCAG 157 212 0 AAAACCCCGC 0.97546 -89 AAGCATAAAAAAAGGCCGCACGGCGGCCTTTTGG 165 20 0 AAAGCCCGGC 0.592716 -255 AGCTATCAGCAGAAACCAAGCCGCTAAACAAGGG 171 60 0 AGAACCCCGC 0.943379 -100 AATAATATTGACAATCCTACCCGCGGACTTTAAT 187 137 1 ACAACCCCGC 0.926927 -79 TTCGACAAGCCCCATCGCTTTTAGCGCA 195 283 0 ACAACCTCGC 0.648152 -18 AAGCGTTTACAAAAACCTGTCCGCATCGGCTGTT 219 101 0 AAAACCCCGC 0.97546 -53 ACGACGAACAGCCGAACGGCGTCCATGTGC 238 7 1 AACACCCGGC 0.689843 -68 **** ** **** Masking position 7 Map Score: 21.8314 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 206 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 CGATAAAACAAGGATGAGAA 48 1 0 AGGATGAGAA 0.803317 -227 CACCAGGAGAAGGATGAAAAGTGTGGCAAA 61 34 0 AGGATGAAAA 0.935583 -267 AGGAGGCGGGAGGATGAGAACACGGCTTCT 65 122 1 AGGATGAGAA 0.803317 -243 AGGGGCAAGGAGGATGGAAAGAGGTTGCCG 65 281 1 AGGATGGAAA 0.840666 -84 CTCTGGGAAGAGGGTGAAAACCGTGCTCCC 68 201 1 AGGGTGAAAA 0.840666 -82 CACTATGTGAAAGAGGAAAAATC 69 288 1 AAGAGGAAAA 0.647902 -13 GTTATTATGTATGATGGAAATAAAAGGAGG 76 104 1 ATGATGGAAA 0.624035 -28 CTTATCTATAAGGAGGAGAAATC 77 86 1 AGGAGGAGAA 0.760277 -13 AACAAGGGTGATGATGAAAAATAAAGTGAT 107 129 0 ATGATGAAAA 0.820437 -106 TGAATATGGCAAGATGAAAAACTGGGTAGT 109 147 1 AAGATGAAAA 0.703243 -154 GAGGTTATATAAGATGAAAATAAGTTAGTT 123 60 0 AAGATGAAAA 0.703243 -241 GAAGGAAAGCAGGGGGAAAAC 128 70 1 AGGGGGAAAA 0.803803 -11 ATATCTTATGATGATGAAAAAGCGCGATTC 133 20 0 ATGATGAAAA 0.820437 -35 ACCGGTAAACAGGATGAAAACTTTCAATGC 137 107 0 AGGATGAAAA 0.935583 -194 GAAATGGATCAGGATGAAAAAGGCGGATGG 137 235 1 AGGATGAAAA 0.935583 -66 AATGCGGCGTAGGAGGGAAAGAC 138 100 1 AGGAGGGAAA 0.803803 -13 TAATCAGCTCAAGGTGAAAAAGGAGCGGAA 143 15 0 AAGGTGAAAA 0.462617 -167 TGATCTTTAAAGGATGAAAATCCAAAAGGA 157 272 1 AGGATGAAAA 0.935583 -29 GTTTTTATAGATGATGAAAACGTATACTTG 165 78 0 ATGATGAAAA 0.820437 -197 GTGCAGGGAAAGGATGAAAAAA 166 224 1 AGGATGAAAA 0.935583 -12 TTAACGAAACATGAGGAAAAGTCAAAAAGA 173 72 1 ATGAGGAAAA 0.780118 -127 TGTCCCAATAATGAGGAGAAAAGCAAAGCA 190 76 1 ATGAGGAGAA 0.499428 -202 CGTAAATAGAAGGAGGAAAAGAG 197 83 1 AGGAGGAAAA 0.918552 -13 TATCGGTAACAGGGTGAAAAGGATTGTTCC 198 25 1 AGGGTGAAAA 0.840666 -88 ATTTTATAAAAGGGGGGAAAACACCTCAGC 205 94 1 AGGGGGGAAA 0.598119 -88 TCAAAGTGGAATGATGAAAAGGACGTGTCA 211 279 1 ATGATGAAAA 0.820437 -22 TATTTGTTGTATGATGGAAACGGGGAAACC 220 113 1 ATGATGGAAA 0.624035 -188 GTCATTCGGCAGGAGGAAAATCAAAATG 241 283 1 AGGAGGAAAA 0.918552 -18 ********** Masking position 9 Map Score: 23.0197 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 52 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 82 0 TGCGCGCTTA 0.987787 -203 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 167 0 TGCGCGCTTA 0.987787 -118 TCGTGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 252 0 TGCGCGCTTA 0.987787 -33 ATACAACAAAGGCGCAACGCTTTTGAGATAAAG 9 63 1 GGCGCGCTTT 0.868587 -28 TCCCCTTTTGTGCGGTCAGCTTTGCGTGGCGTT 19 67 1 TGCGGGCTTT 0.803874 -62 CTGAGTTCGCTGCGCATTGCGTAATGCCGGGGA 22 124 1 TGCGCGCGTA 0.902092 -115 GAATGCCTGATGCGCTACGCTCATCAGGCATAC 27 51 1 TGCGCGCTCA 0.902092 -54 AACTGCCTGATGCGCTACGCTTATCAGGCCTGG 31 39 1 TGCGCGCTTA 0.987787 -144 TGTAAAAAAGGGCGGGCAGCTTACTGAGGATTT 46 151 0 GGCGGGCTTA 0.863761 -39 AATTGCCTGATGCGCTACGCTTATCAGGCCTAC 50 48 1 TGCGCGCTTA 0.987787 -182 GTGTGGCGGATGCGCGGTGCTTATCCGCCCTAC 55 66 0 TGCGCGCTTA 0.987787 -40 TTACGCCTGATGCGCTGCGCTTATCAGGCCTAC 72 21 1 TGCGCGCTTA 0.987787 -106 ***** ***** Masking position 10 Map Score: 14.4859 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 17 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 TGCTAAGGCCGCCTCCGGCAAGGTCAGCAC 17 18 0 GCCTCCGGCA 0.546669 -243 GCCGGAGCACGCCTCCGGCAACTTGCATAA 34 18 1 GCCTCCGGCA 0.546669 -44 GCGCGATATGTCCTCCTGACCCATCTCACG 47 12 1 TCCTCCTGAC 0.657353 -86 GGGGTTCTTCCTCATTCCAGGACGGATA 64 136 0 TCCTCATTCC 0.488557 -18 CGTGTTCTCATCCTCCCGCCTCCTCCCCCA 65 116 0 TCCTCCCGCC 0.906302 -249 CTCGCAGTCATCCTCCCTCACTCCTGCCAT 68 232 1 TCCTCCCTCA 0.677401 -51 CTTTAAACAGCCTCCCTCCAGATTTTTAT 78 10 1 GCCTCCCTCC 0.918285 -287 AAATAAAAAATCCCCCTGCCGTTATTTCGG 98 25 0 TCCCCCTGCC 0.831522 -69 GCGGTCTCCTCCTTACCGATTGTTTT 107 7 1 TCCTCCTTAC 0.662032 -228 CGTATATCCTCCGTCCTTTATATCAA 110 24 0 TCCTCCGTCC 0.835789 -16 GCAAGTGCCTCCTTCCTTTTCAGTTT 113 89 0 GCCTCCTTCC 0.944553 -16 CATGTCCCACCCCTCCTTCCTGCGGTTAGG 126 107 1 CCCTCCTTCC 0.944553 -194 TGCCCCCTTCCCCCTATTGCA 130 121 0 GCCCCCTTCC 0.851501 -11 ACCGTTTCCTCCCGCCCGCTCTAGTG 139 85 0 TCCTCCCGCC 0.906302 -16 AAGAAGTCCCCCTTCATGTAAAAGCT 141 125 0 TCCCCCTTCA 0.517246 -16 GATATCCCTCCTGCCAATAGGGTTT 147 52 0 CCCTCCTGCC 0.943451 -15 GGCGGTGTATCCCTCCTTCCTTTTATAATA 154 110 0 CCCTCCTTCC 0.944553 -21 TCTCTTTCCCTCCCTCCGAATACACCA 155 147 0 CCCTCCCTCC 0.918285 -17 GTTCCAAACCCTCCTTCATCAGTCCTGC 160 166 0 CCCTCCTTCA 0.783639 -18 ACCGCCTCCCTACTAAATTAAAT 191 288 0 GCCTCCCTAC 0.595191 -13 CTTTCTCCCCCCTGACTTGTCTTT 203 9 0 CCCCCCTGAC 0.42355 -16 GCCCTCATTCCTTTTCTCAGC 206 213 0 CCCTCATTCC 0.520824 -11 TCTTATTGCCTCCTTCATTAGTAAACA 239 399 0 GCCTCCTTCA 0.783639 -17 ATTTTGATTTTCCTCCTGCCGAATGACTTC 241 280 0 TCCTCCTGCC 0.936155 -21 ********** Masking position 5 Map Score: 16.137 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 = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 AATATTTATCTTTCATTTTGCGATCAAAATAAC 26 158 1 TTTCATTTTA 0.823418 -98 TTATTTGTTTTTATTTAAACATAAATAATCC 37 9 1 TTTTATTTAA 0.743283 -90 ATCCTGTTCATTTCATTTTGATACACTTCATGC 38 137 1 TTTCATTTTA 0.823418 -52 CGCTATGCCATTTTATTTTTGAACGCAGGCCAA 40 13 0 TTTTATTTTA 0.835318 -258 CCAGGAGCCTTTTTATTTTTAAAAAATTGTCAC 89 13 1 TTTTATTTTA 0.835317 -160 AGTACTTTTATTTCATTTTCGTAAAATGTAACA 97 53 1 TTTCATTTTA 0.823418 -102 AAAACGTTGATTTTATTTACGAAAGGGGTTAGA 106 15 0 TTTTATTTAA 0.743283 -109 AAAGTGGTTTTTTTATTTTCAGAGGGGGAATGA 108 223 1 TTTTATTTTA 0.835318 -26 AGCGTTAACATTTCATTTTCAAAAAAGAGATTG 111 90 1 TTTCATTTTA 0.823418 -108 TACAAACACATTTTATTTACAAATTATTTTAAA 113 30 0 TTTTATTTAA 0.743283 -75 ATATGCAGTTTTTTATTTTACCAAAAAAACAGG 117 12 0 TTTTATTTTA 0.835318 -289 GTATACAATTTTTTATTTTAACATCATAATAGA 117 210 1 TTTTATTTTA 0.835317 -91 AGACAATTATTTTTATTTAATAATTAAAAAAAT 127 158 0 TTTTATTTAA 0.743283 -91 CTTCTGTTACTTTCATTTTATCAAATCGTGAGA 128 41 0 TTTCATTTTA 0.823418 -40 TCACTCCCTTTTTTATTTTCATAGTAATGATAA 140 73 0 TTTTATTTTA 0.835318 -27 GTATCAAAGGTTTCATTTTTTTATGTATAAAAA 154 50 0 TTTCATTTTA 0.823418 -81 TTTGAAAGCGTTTTATTTTATGAGAAAGGGGCA 158 179 1 TTTTATTTTA 0.835318 -29 AACATTAAATTTTTATTTAACAAACTTTATTTA 173 160 1 TTTTATTTAA 0.743283 -39 TTCTTCCATTTTTTATTTTAAAACTTTTTTAAG 180 94 1 TTTTATTTTA 0.83531 -64 AATTTACATTTTTTATTTTAGAAATATAGCAAA 184 70 1 TTTTATTTTA 0.835317 -112 CTAAGTCATTTTTTATTTAGGTAAAAAAATTTA 193 26 1 TTTTATTTAA 0.743283 -115 TGGAATTCTCTTTTATTTATGGACAAAAAAAGG 204 147 0 TTTTATTTAA 0.743283 -154 CTCACAATACTTTCATTTTATCACTTTCGGGCT 205 47 1 TTTCATTTTA 0.823418 -135 AATGATTTATTTTCATTTACATACTATCCAGTC 213 161 0 TTTCATTTAA 0.726908 -140 TCTATGCCTTTTTCATTTATCTAAAAATGAATG 220 260 1 TTTCATTTAA 0.726908 -41 ********* * Masking position 7 Map Score: 21.4717 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 31 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096