AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icrp_ecoli_bsub_100.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 tsx 298 nucleoside channel; receptor of phage T6 and colicin K #7 nagD 47 N-acetylglucosamine metabolism #8 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #9 nagB 300 glucosamine-6-phosphate deaminase #10 fur 288 negative regulator #11 galE 260 UDP-galactose-4-epimerase #12 ompA 300 outer membrane protein 3a (II*;G;d) #13 dadA 300 D-amino acid dehydrogenase subunit #14 cdd 129 cytidine/deoxycytidine deaminase #15 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #16 ptsH 300 PTS system protein HPr #17 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #18 gutM 104 glucitol operon activator #19 srlR 66 regulator for gut (srl), glucitol operon #20 gutQ 31 orf, hypothetical protein #21 ansB 175 periplasmic L-asparaginase II #22 nupG 153 transport of nucleosides, permease protein #23 tdcC 21 anaerobically inducible L-threonine, L-serine permease #24 tdcB 98 threonine dehydratase, catabolic #25 tdcA 188 transcriptional activator of tdc operon #26 crp 300 cyclic AMP receptor protein #27 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #28 ompR 191 response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis #29 malT 300 positive regulator of mal regulon #30 glpG 44 protein of glp regulon #31 glpE_glpD 189 glpE: protein of glp regulon, glpD: sn-glycerol-3-phosphate dehydrogenase (aerobic) #32 aldB 74 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) #33 yiaY 189 putative oxidoreductase #34 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #35 mtlD 229 mannitol-1-phosphate dehydrogenase #36 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #37 tnaL 242 tryptophanase leader peptide #38 cyaA 300 adenylate cyclase #39 rhaD 300 rhamnulose-phosphate aldolase #40 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #41 glpK 22 glycerol kinase #42 glpF 300 facilitated diffusion of glycerol #43 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #44 malF 153 part of maltose permease, periplasmic #45 malE_malK 364 malE: periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis, malK: ATP-binding component of transport system for maltose #46 lamB 71 phage lambda receptor protein; maltose high-affinity receptor #47 malM 242 periplasmic protein of mal regulon #48 melR 282 regulator of melibiose operon #49 uxuA 300 mannonate hydrolase #50 uxuB 80 D-mannonate oxidoreductase #51 deoC 257 2-deoxyribose-5-phosphate aldolase #52 deoA 126 thymidine phosphorylase #53 deoB 51 phosphopentomutase #54 deoD 56 purine-nucleoside phosphorylase #55 ybdM 85 similar to protein kinase #56 ybdN 131 ybdN #57 glpQ 98 glycerophosphoryl diester phosphodiesterase #58 glpT 296 glycerol-3-phosphate permease #59 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #60 ybfT 218 similar to glucosamine-6-phosphate isomerase #61 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #62 ycbD 29 similar to aldehyde dehydrogenase #63 yczA 300 yczA #64 ycbL 96 similar to two-component response regulator [YcbM] #65 yccC 216 similar to asparaginase #66 yclJ 212 similar to two-component response regulator [YclK] #67 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #68 mtlD 52 mannitol-1-phosphate dehydrogenase #69 dal 114 D-alanine racemase #70 yfiD 154 similar to hypothetical proteins #71 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #72 yhcV 136 similar to hypothetical proteins #73 glpF 178 glycerol uptake facilitator #74 glpD 140 glycerol-3-phosphate dehydrogenase #75 yhjM 103 similar to transcriptional regulator (LacI family) #76 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #77 tenA 248 transcriptional regulator #78 yjmC 104 similar to malate dehydrogenase #79 yjmE 24 similar to D-mannonate hydrolase #80 yjmG 47 similar to hexuronate transporter #81 yjmH 87 similar to transcriptional regulator (LacI family) #82 ykoG 300 similar to two-component response regulator [YkoH] #83 fruR 279 transcriptional regulator (DeoR family) #84 xylR 300 transcriptional regulator #85 yncD 300 similar to alanine racemase #86 dhaS 229 aldehyde dehydrogenase #87 deoD 300 purine nucleoside phosphorylase #88 ilvA 248 threonine dehydratase #89 resD 80 two-component response regulator #90 resC 135 essential protein similar to cytochrome c biogenesis protein #91 ppiB 253 peptidyl-prolyl isomerase #92 drm 160 phosphodeoxyribomutase #93 yqkL 112 similar to transcriptional regulator (Fur family) #94 yqhL 190 similar to hypothetical proteins #95 yqgQ 109 yqgQ #96 yqgP 89 similar to hypothetical proteins #97 yqgO 66 yqgO #98 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #99 cdd 118 cytidine/deoxycytidine deaminase #100 yrkP 267 similar to two-component response regulator [YrkQ] #101 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #102 araA 207 L-arabinose isomerase #103 phoP 211 two-component response regulator #104 ccpA 274 transcriptional regulator (Lacl family) #105 gbsA 198 glycine betaine aldehyde dehydrogenase #106 yulE 25 similar to L-rhamnose isomerase #107 yulB 56 similar to transcriptional regulator (DeoR family) #108 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase #109 yutF 28 similar to N-acetyl-glucosamine catabolism #110 yutE 23 yutE #111 yutD 81 yutD #112 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #113 yurN 57 similar to sugar permease #114 yurO 80 similar to multiple sugar-binding protein #115 yurP 215 similar to opine catabolism #116 yvqA 277 similar to two-component response regulator [YvqB] #117 yvrI 300 yvrI #118 yvfL 39 similar to maltodextrin transport system permease #119 yvfK 140 similar to maltose/maltodextrin-binding protein #120 yvdH 39 similar to maltodextrin transport system permease #121 yvdG 95 similar to maltose/maltodextrin-binding protein #122 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #123 crh 23 catabolite repression HPr-like protein #124 yvcL 22 similar to hypothetical proteins #125 yvcJ 24 similar to hypothetical proteins #126 yvcI 300 similar to mutator MutT protein #127 nagA 181 N-acetylglucosamine-6-phosphate deacetylase #128 glcR 223 transcriptional regulator (DeoR family) #129 fnr 98 transcriptional regulator (FNR/CRP family) #130 narK 135 nitrite extrusion protein #131 galK 80 galactokinase #132 ywcC 300 alternate gene name: ipa-33d #133 msmX 120 multiple sugar-binding transport ATP-binding protein #134 galE 114 UDP-glucose 4-epimerase #135 yxjD 78 similar to 3-oxoadipate CoA-transferase #136 yxjC 153 similar to hypothetical proteins from B. subtilis #137 pdp 29 pyrimidine-nucleoside phosphorylase #138 nupC 115 pyrimidine-nucleoside transport protein #139 dra 105 deoxyribose-phosphate aldolase #140 yxdJ 108 similar to two-component response regulator [YxdK] #141 iolR 300 transcriptional regulator (DeoR family) #142 yxbG 116 alternate gene name: yxaU; similar to glucose 1-dehydrogenase #143 yycF 300 similar to two-component response regulator [YycG] Motif number 1 GTAGCCGCATCCGGTATGTAACGCC 1 6 1 CGCATCCGGT 0.678559 -279 GCGTCAGCGTCGCATCAGGCGTTACATACC 1 23 0 CGCATCAGGC 0.988086 -262 GCTGACGCGTCTTATCTGGCCTACACGCTG 1 45 1 CTTATCTGGC 0.543828 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 76 0 CTTATCCGGC 0.972913 -209 ATAAGCAAAGCGCATCCGGCATTCAACGCC 1 91 1 CGCATCCGGC 0.992327 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 1 108 0 CGCATCAGGC 0.988086 -177 GCTGGCGCGTCTTATCAGGCCTACGCGCTG 1 130 1 CTTATCAGGC 0.958391 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 161 0 CTTATCCGGC 0.972913 -124 ATAAGCAAAGCGCATCCGGCATTCAACGCC 1 176 1 CGCATCCGGC 0.992327 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 1 193 0 CGCATCAGGC 0.988086 -92 GCTGGCGCGTCTTATCAGGCCTACACGCTG 1 215 1 CTTATCAGGC 0.958391 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATC 1 246 0 CTTATCCGGC 0.972913 -39 ATAAGCAAAGCGCATCCGGCACGAAGGAGT 1 261 1 CGCATCCGGC 0.992327 -24 GCGCTCGCGCCGCATCCGACATTGATTGC 3 10 0 CGCATCCGAC 0.84483 -56 GCGCGAGCGCCTTATCCGACCAACATATCA 3 30 1 CTTATCCGAC 0.60192 -36 AGTTAGCTCACTCATTAGGCACCCCAGGCT 5 30 1 CTCATTAGGC 0.566744 -93 GTGCTAAGGCCGCCTCCGGCAAGGTCAGCA 11 19 0 CGCCTCCGGC 0.833087 -242 ATGTAAAGTCCGTATCGGGCAGTGACTACC 17 79 0 CGTATCGGGC 0.76328 -177 ATGAGCGTAGCGCATCAGGCATTCTATAGT 18 45 0 CGCATCAGGC 0.988086 -60 ATGCGCTACGCTCATCAGGCATACAGGACT 18 60 1 CTCATCAGGC 0.978471 -45 ATAAGCGTAGCGCATCAGGCAATTAACCCC 35 42 0 CGCATCAGGC 0.988086 -188 ATGCGCTACGCTTATCAGGCCTACAGGATG 35 57 1 CTTATCAGGC 0.958391 -173 GCGTAAGCGCCTTATCCGGCCTACAAGAAC 35 111 0 CTTATCCGGC 0.972913 -119 GCGCTTACGCCGCATCCGGCGCTGCCCCTC 35 131 1 CGCATCCGGC 0.992327 -99 GCTGTCGCGTCTTATCAGGC 39 1 0 CTTATCAGGC 0.958391 -300 GCGACAGCGTCGCATCAGGCATTGATTGCC 39 23 1 CGCATCAGGC 0.988086 -278 GCACTTGTGCCGCATCCGGCAATCAATGCC 39 40 0 CGCATCCGGC 0.992327 -261 GCACAAGTGCCTTATCCGGCCTACAGGTCG 39 60 1 CTTATCCGGC 0.972913 -241 GCTGTCGCGTCTTATCAGGCCTACAACTGT 39 93 0 CTTATCAGGC 0.958391 -208 GCGACAGCGTCGCATCAGGCATTGATTGCC 39 115 1 CGCATCAGGC 0.988086 -186 GCGACTTGTGCGCATCCGGCAATCAATGCC 39 132 0 CGCATCCGGC 0.992327 -169 GCACAAGTCGCTTATCAGGCCTACAGGTCG 39 151 1 CTTATCAGGC 0.958391 -150 GCTGTCGCGTCTTATCAGGCCTACAACTAT 39 184 0 CTTATCAGGC 0.958391 -117 GCGACAGCGTCGCATCAGGCATTGATTGCC 39 206 1 CGCATCAGGC 0.988086 -95 GCGCGAGCGCCTTATCCGGCCTACGGGTCG 39 244 1 CTTATCCGGC 0.972913 -57 GCGTTCACGCCGCATCCGGCATTTCACAGC 44 12 0 CGCATCCGGC 0.992327 -142 GCTGACGCGTCTTATCAGGCCTACATACGT 44 65 0 CTTATCAGGC 0.958391 -89 GCGTCAGCGTCGCATCAGGCAGTTGTTGTC 44 87 1 CGCATCAGGC 0.988086 -67 GCTTTCACGCCTTATCCGACAACAACTGCC 44 104 0 CTTATCCGAC 0.60192 -50 GCGTAAACGCCTTATCCGGCCCAGGTTTTG 47 14 0 CTTATCCGGC 0.972913 -229 GCGTTTACGCCGCATTCGGCAACCAACGCC 47 34 1 CGCATTCGGC 0.788244 -209 GCGCAAGCGTCGCATCAGGCGTTGGTTGCC 47 51 0 CGCATCAGGC 0.988086 -192 GCTTGCGCGTCTTATCAGGCCTACAACGGC 47 73 1 CTTATCAGGC 0.958391 -170 GCGTAAACGCCTTATCCGGCCTACATTTGA 47 105 0 CTTATCCGGC 0.972913 -138 GCGTTTACGCCGCATCCGGCATAAAAACAG 47 125 1 CGCATCCGGC 0.992327 -118 TGGTGGCAAACGCATCAGGATCAAAGTGAA 51 65 0 CGCATCAGGA 0.575143 -193 ATAAGCGCAGCGCATCAGGCGTAAAGCATC 52 15 0 CGCATCAGGC 0.988086 -112 ATGCGCTGCGCTTATCAGGCCTACGAGACG 52 30 1 CTTATCAGGC 0.958391 -97 GCGTCTACGCCTTATCCGGCCTACGGGTAG 52 63 0 CTTATCCGGC 0.972913 -64 AAGGCGTAGACGCATCCGGCAAAAGCCGCC 52 80 1 CGCATCCGGC 0.992327 -47 AAGGAGAAAATGCATCAGGCGGAGACAACT 138 11 1 TGCATCAGGC 0.570218 -105 ********** Masking position 5 Map Score: 172.245 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 197 Number in noncoding regions = 461 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 2 AATCGCAGCGTGTAGGCCAGATAAGACGCG 1 50 0 TGTAGGCCAG 0.945493 -235 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 71 1 TGTAGGCCGG 0.995478 -214 AATCGCAGCGCGTAGGCCTGATAAGACGCG 1 135 0 CGTAGGCCTG 0.986534 -150 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 156 1 TGTAGGCCGG 0.995478 -129 AATCGCAGCGTGTAGGCCTGATAAGACGCG 1 220 0 TGTAGGCCTG 0.993367 -65 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 241 1 TGTAGGCCGG 0.995478 -44 TGCGTCGAACCGTTGGCCGGAGAGGGTGCT 11 44 0 CGTTGGCCGG 0.868773 -217 GCGGAAGTCCTGTATGCCTGATGAGCGTAG 18 65 0 TGTATGCCTG 0.850176 -40 TGATGCATCCTGTAGGCCTGATAAGCGTAG 35 62 0 TGTAGGCCTG 0.993367 -168 TGCACGTTCTTGTAGGCCGGATAAGGCGCT 35 106 1 TGTAGGCCGG 0.995478 -124 GTTGCCGACCTGTAGGCCGGATAAGGCACT 39 65 0 TGTAGGCCGG 0.995478 -236 CGGCAACAGTTGTAGGCCTGATAAGACGCG 39 88 1 TGTAGGCCTG 0.993367 -213 ATTGCCGACCTGTAGGCCTGATAAGCGACT 39 156 0 TGTAGGCCTG 0.993367 -145 CGGCAATAGTTGTAGGCCTGATAAGACGCG 39 179 1 TGTAGGCCTG 0.993367 -122 ATGCACGACCCGTAGGCCGGATAAGGCGCT 39 249 0 CGTAGGCCGG 0.9908 -52 CCACGATGCTTGTAGGCATGCTGTAAACTT 42 229 0 TGTAGGCATG 0.850176 -72 GTTTCGGTTTTGTAGGCCGGACAAGGCGTT 44 37 0 TGTAGGCCGG 0.995478 -117 CCGAAACGTATGTAGGCCTGATAAGACGCG 44 60 1 TGTAGGCCTG 0.993367 -94 TGACAGCCGTTGTAGGCCTGATAAGACGCG 47 78 0 TGTAGGCCTG 0.993367 -165 GGCTGTCAAATGTAGGCCGGATAAGGCGTT 47 100 1 TGTAGGCCGG 0.995478 -143 AGATACGTCTCGTAGGCCTGATAAGCGCAG 52 35 0 CGTAGGCCTG 0.986534 -92 CGTATCTACCCGTAGGCCGGATAAGGCGTA 52 58 1 CGTAGGCCGG 0.9908 -69 ********** Masking position 3 Map Score: 75.7851 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 3 TAACGCCTGATGCGACGCTGACGCGTCTTATCTGGC 1 29 1 TGCGCGCGCT 0.997326 -256 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 114 1 TGCGCGCGCT 0.997326 -171 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 199 1 TGCGCGCGCT 0.997326 -86 CAATGTCGGATGCGGCGCGAGCGCCTTATCCGACCA 3 16 1 TGCGCGCGCT 0.997326 -50 TGTGATGCGGCGTAGACTCATGTCTACGCCG 10 6 1 TGCGCGCTCT 0.942737 -283 TCCCTGACTCTGCGGCAATATGGCGTCTTTAGTATC 13 160 0 TGCGCAGGCT 0.774395 -141 CAGCGCCGGATGCGGCGTAAGCGCCTTATCCGGCCT 35 119 0 TGCGCGCGCT 0.997326 -111 CCGCCCGGTTTGCGCCGGCGGGGTTTTGGAATCGTG 36 25 0 TGCGCGGGTT 0.764364 -81 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 11 0 TGCGCGCGCT 0.997326 -290 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 103 0 TGCGCGCGCT 0.997326 -198 AGGCCTGATAAGCGACTTGTGCGCATCCGGCAATCA 39 137 0 AGCGCTCGCT 0.779515 -164 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 194 0 TGCGCGCGCT 0.997326 -107 AAATGCCGGATGCGGCGTGAACGCCTTGTCCGGCCT 44 18 1 TGCGCGCGCT 0.997326 -136 AACTGCCTGATGCGACGCTGACGCGTCTTATCAGGC 44 75 0 TGCGCGCGCT 0.997326 -79 GATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGG 45 255 1 AGCGCGGGCT 0.937163 -110 GGTTGCCGAATGCGGCGTAAACGCCTTATCCGGCCC 47 22 0 TGCGCGCGCT 0.997326 -221 CAACGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 47 57 1 TGCGCGCGCT 0.997326 -186 TTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 47 113 0 TGCGCGCGCT 0.997326 -130 ATTTGGGCGGAGCGTTGACTCCGCCTTTGTTATGTC 54 14 1 AGCGTGCGCT 0.769643 -43 **** ** *** * Masking position 16 Map Score: 63.8042 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 4 CAGATAAGACGCGTCAGCGTCGCATCAGGCGTTA 1 29 0 GCGGCGCGCA 0.99895 -256 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 114 0 GCGGCGCGCA 0.99895 -171 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 199 0 GCGGCGCGCA 0.99895 -86 GTCGGATAAGGCGCTCGCGCCGCATCCGACATTG 3 16 0 GCGGCGCGCA 0.99895 -50 GCGTAGACATGAGTCTACGCCGCATCACA 10 6 0 GAGACGCGCA 0.953515 -283 GCCGGATAAGGCGCTTACGCCGCATCCGGCGCTG 35 121 1 GCGACGCGCA 0.997041 -109 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 39 13 1 GCGGCGCGCA 0.99895 -288 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 39 105 1 GCGGCGCGCA 0.99895 -196 CTGATAAGACGCGACAGCGTCGCATCAGGCATTG 39 196 1 GCGGCGCGCA 0.99895 -105 GCCGGACAAGGCGTTCACGCCGCATCCGGCATTT 44 18 0 GCGACGCGCA 0.997041 -136 CTGATAAGACGCGTCAGCGTCGCATCAGGCAGTT 44 77 1 GCGGCGCGCA 0.99895 -77 GCCGGATAAGGCGTTTACGCCGCATTCGGCAACC 47 24 1 GCGACGCGCA 0.997041 -219 CTGATAAGACGCGCAAGCGTCGCATCAGGCGTTG 47 57 0 GCGGCGCGCA 0.99895 -186 GCCGGATAAGGCGTTTACGCCGCATCCGGCATAA 47 115 1 GCGACGCGCA 0.997041 -128 *** *** **** Masking position 14 Map Score: 58.0385 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 37 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 CAGATAAGACGCGTCAGCGTCGCATCAGGCGTT 1 30 0 GCGGCGTCGC 0.994048 -255 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTT 1 115 0 GCGGCGTCGC 0.994048 -170 CTGATAAGACGCGCCAGCGTCGCATCAGGCGTT 1 200 0 GCGGCGTCGC 0.994048 -85 GTCGGATAAGGCGCTCGCGCCGCATCCGACATT 3 17 0 GCGGCGCCGC 0.99806 -49 GCGTAGACATGAGTCTACGCCGCATCACA 10 7 0 GAGACGCCGC 0.93121 -282 GCCGGATAAGGCGCTTACGCCGCATCCGGCGCT 35 121 1 GCGACGCCGC 0.995931 -109 CTGATAAGACGCGACAGCGTCGCATCAGGCATT 39 13 1 GCGGCGTCGC 0.908965 -288 CTGATAAGACGCGACAGCGTCGCATCAGGCATT 39 105 1 GCGGCGTCGC 0.908965 -196 ATTGCCGGATGCGCACAAGTCGCTTATCAGGCC 39 139 1 GCGAAGTCGC 0.914873 -162 CTGATAAGACGCGACAGCGTCGCATCAGGCATT 39 196 1 GCGGCGTCGC 0.908965 -105 GCCGGACAAGGCGTTCACGCCGCATCCGGCATT 44 19 0 GCGACGCCGC 0.996076 -135 CTGATAAGACGCGTCAGCGTCGCATCAGGCAGT 44 77 1 GCGGCGTCGC 0.994048 -77 GCCGGATAAGGCGTTTACGCCGCATTCGGCAAC 47 24 1 GCGACGCCGC 0.995931 -219 CTGATAAGACGCGCAAGCGTCGCATCAGGCGTT 47 58 0 GCGGCGTCGC 0.997424 -185 GCCGGATAAGGCGTTTACGCCGCATCCGGCATA 47 115 1 GCGACGCCGC 0.995931 -128 TTTGGGCGGAGCGTTGACTCCGCCTTTGTTATG 54 15 1 GCGACTCCGC 0.928049 -42 *** ******* Masking position 3 Map Score: 54.5437 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 95 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 AATTTGCAGCAAAATAAAAATACGGCTTGA 9 14 0 AAAATAAAAA 0.85809 -287 GCAAATATTGTTAATAAAAACGTGGCACAG 10 150 0 TTAATAAAAA 0.688279 -139 TTGCCACGCCTAAATGAAAACCACAAGTCC 10 183 0 TAAATGAAAA 0.626454 -106 TATTTATGTTTAAATAAAAACAAATAA 24 8 0 TAAATAAAAA 0.745253 -91 TTCTAGACGGAGAATAAAAAAGAGCCGGAT 55 28 0 AGAATAAAAA 0.658655 -58 CCTGTCTTTCATAATAAAAAACGGATGTAA 57 51 0 ATAATAAAAA 0.820266 -48 TTTATCTTTTTTAATAAAAATTTATTTTTC 59 56 0 TTAATAAAAA 0.688279 -175 CAATTTTTTAAAAATAAAAAGGCTCCTGGT 67 12 0 AAAATAAAAA 0.85809 -161 AAGGCGGACAAAAATAAAAAATCCCCCTGC 71 36 0 AAAATAAAAA 0.85809 -58 AGAGAAGAAGAGAATAAAAAAACCACAACA 73 121 0 AGAATAAAAA 0.658655 -58 CCATTTCCTTATAATAAAAAGGGATAGAAA 76 59 1 ATAATAAAAA 0.820266 -65 TCCCCCTCTGAAAATAAAAAAACCACTTTC 77 222 0 AAAATAAAAA 0.85809 -27 TTTTTTTGGTAAAATAAAAAACTGCATATC 82 16 1 AAAATAAAAA 0.85809 -285 TTATGATGTTAAAATAAAAAATTGTATACG 82 209 0 AAAATAAAAA 0.85809 -92 TCTTCTTATTTTAATGAAAAAAGTCTTTTA 83 65 0 TTAATGAAAA 0.558645 -215 TTTTAATTATTAAATAAAAATAATTGTCTT 88 162 1 TAAATAAAAA 0.745253 -87 GCTTTACTAAAAAATAAAAATGAAACCTGA 91 118 0 AAAATAAAAA 0.85809 -136 GCCAGCTGTTATAATGAAAAAAAACTATTG 96 59 1 ATAATGAAAA 0.723468 -31 GCCGTCCTATTGAATAAAAAGCCGGGCTCT 102 27 1 TGAATAAAAA 0.482818 -181 AATTTGATGAATAATGAAAAATAATGTACA 104 134 1 ATAATGAAAA 0.723468 -141 TAAAGTTTGTTAAATAAAAATTTAATGTTT 105 159 0 TAAATAAAAA 0.745253 -40 GAAATCATATATAATGAAAACGGATACAAA 108 92 1 ATAATGAAAA 0.723468 -46 CTATATTTCTAAAATAAAAAATGTAAATTT 112 69 0 AAAATAAAAA 0.85809 -113 ATAACGTTATATAATAAAAACGAGGAGTGA 115 191 1 ATAATAAAAA 0.820266 -25 TTGTGGGATAAAAATGAAAAGAATATGTGA 116 191 1 AAAATGAAAA 0.776102 -87 TTTTTTTACCTAAATAAAAAATGACTTAGT 119 25 0 TAAATAAAAA 0.745253 -116 AGGGGAATAAAAAATAAAAACCAGAAAGGT 131 53 1 AAAATAAAAA 0.85809 -28 GGATAGTATGTAAATGAAAATAAATCATTT 132 165 1 TAAATGAAAA 0.626454 -136 TAAACACTATATAATGAAAACAGGTCATTT 134 77 1 ATAATGAAAA 0.723468 -38 AAAGATTAATATAATAAAAATAATGAAAAA 141 137 0 ATAATAAAAA 0.820266 -164 ACATAAATATATAATAAAAACCAAAAGTTA 141 251 0 ATAATAAAAA 0.820266 -50 ********** Masking position 5 Map Score: 27.6818 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 55 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TAGCCGCATCCGGTATGTAACGCCTGATGCGACGCT 1 12 1 CGGAAGCCTG 0.997083 -273 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 97 1 CGGAAGCCTG 0.997086 -188 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 182 1 CGGAAGCCTG 0.997086 -103 CGCGAAATACGGGCAGACATGGCCTGCCCGGTTATT 4 12 0 GGGAAGCCTG 0.970929 -40 CACAAGGAAGCGGTAGTCACTGCCCGATACGGACTT 17 68 1 CGGAAGCCCG 0.980352 -188 ATGGAGAAGGTGGGGTTAATTGCCTGATGCGCTACG 35 31 1 TGGGAGCCTG 0.86739 -199 CTTATTACAACGGCGTGAAACGCCTGTCAGGATCCA 38 37 0 CGGGAGCCTG 0.990031 -264 GTGCCGCATCCGGCAATCAATGCCTGATGCGACGCT 39 28 0 CGGAAGCCTG 0.997086 -273 TGTGCGCATCCGGCAATCAATGCCTGATGCGACGCT 39 120 0 CGGAAGCCTG 0.997086 -181 CGCGCATCCACGGCAATCAATGCCTGATGCGACGCT 39 211 0 CGGAAGCCTG 0.997086 -90 ACGCCTTATCCGACAACAACTGCCTGATGCGACGCT 44 92 0 CGAAAGCCTG 0.957509 -62 ACGCCGCATTCGGCAACCAACGCCTGATGCGACGCT 47 40 1 CGGAAGCCTG 0.997086 -203 GGTGGTACCGCGGAAAGAAAAGCCTTTTCGCCCCTT 101 152 1 CGGAAGCCTT 0.954183 -149 TTGCTGTGATCGCGATTTACAGCCTGACTGGTCTAG 135 25 1 CGCAAGCCTG 0.970926 -54 *** * * ***** Masking position 9 Map Score: 30.0925 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 36 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CACTCCATCCAAAAAAACGGGTATGGAGAAA 2 275 0 AAAAAAACGG 0.748676 -26 AGCTCACCATAAAAAAGCCGCATGTTGAATA 13 206 1 AAAAAAGCCC 0.922172 -95 ACAGAGCAGAAAAAAAGCAAGTGAAGAGATT 27 234 0 AAAAAAGCAG 0.830929 -37 TCAGACACATAAAAAAACGTCATCGCTTGCA 29 189 1 AAAAAAACGC 0.78105 -112 TTATGAATTTAAAAAAAGCACATTGTTTAAT 33 54 1 AAAAAAAGCC 0.866186 -136 CTGAAAGTGTAAAAAAGGGCGGGCAGCTTAC 33 160 0 AAAAAAGGGG 0.748842 -30 ACGCTTGTGTAAAAAAGCAACAAGGCGGCGA 34 75 0 AAAAAAGCAC 0.854764 -226 TCGTGAAACTAAAAAAACCAGGCGCGAAAAG 38 176 1 AAAAAAACCG 0.879665 -125 CCTCCCCCATAAAAAAGCCAGGGGGTGGAGG 45 94 0 AAAAAAGCCG 0.908212 -271 TCTGCGCAGCAAAAAAACAGCCTGGTCAGCC 61 22 0 AAAAAAACAC 0.813016 -205 ATGAAAAGACAAAAAAAGAAGGATATGACAA 65 102 1 AAAAAAAGAG 0.728621 -115 GCTATTATATAAAAAAGCATCAAAACAACCG 66 183 1 AAAAAAGCAC 0.854764 -30 ATGTCTAACGAAAAAAAGGCCAAATCATGTT 69 24 0 AAAAAAAGGC 0.725108 -91 AAACTGTAACAAAAAAAGACCTCTGTGCAGG 70 19 0 AAAAAAAGAC 0.76276 -136 AGAAGAGAATAAAAAAACCACAACAAACCGC 73 115 0 AAAAAAACCC 0.897477 -64 CTCTGAAAATAAAAAAACCACTTTCCCGCAA 77 216 0 AAAAAAACCC 0.897477 -33 TTATTTTACCAAAAAAACAGGA 82 2 0 AAAAAAACAG 0.784061 -299 CACTAAACATAAAAAAACCTCATGCATGTTG 83 18 0 AAAAAAACCC 0.897477 -262 ATCACCGGCCAAAAAAAGAACAATCATATAC 87 55 0 AAAAAAAGAC 0.76276 -246 CGCTCTAAACAAAAAAGCCGCAGCCACCTGC 92 13 0 AAAAAAGCCC 0.922172 -148 GACGTATAGAAAAAAAGGAGGCTTTCAAG 92 142 1 AAAAAAGGAG 0.784211 -19 AAACGCTGACAAAAAAGCCAGCTTCCTTTCC 95 22 0 AAAAAAGCCG 0.908212 -88 GAGGTGTAAGAAAAAAGCCAGAGCTTTGAAA 98 241 1 AAAAAAGCCG 0.908212 -60 TCGGAATAGAAAAAAAGCCAGAACCTTTTTC 98 268 0 AAAAAAGCCG 0.908212 -33 AATGGGCGTGAAAAAAAGCGCGCGATTATGT 99 48 1 AAAAAAAGCC 0.866186 -71 ATTATTCAATAAAAAAAGCCCTTCCGCCCAC 101 218 0 AAAAAAAGCC 0.866186 -83 TTTTCTTTTAAAAAAAGCCGGGGGCAGAGCC 102 51 0 AAAAAAGCCG 0.908212 -157 AGAAAGCATAAAAAAAGGCCGCACGGCGGCC 104 26 0 AAAAAAGGCG 0.879759 -249 ATTTATGGACAAAAAAAGGACACGGATAACT 126 135 0 AAAAAAAGGC 0.725108 -166 TTTTTCTCATAAAAAAAGGACAAAGCCCGAA 130 33 0 AAAAAAAGGC 0.725108 -103 GAAAGCTCCGAAAAAAGGAGCTTTCCTTTTT 136 20 1 AAAAAAGGAC 0.81315 -134 ATATCTTAACAAAAAAGGAAGTGTGCGAAGG 139 85 1 AAAAAAGGAG 0.784211 -21 AACACCGCACAAAAAAACACGCCATCTCGGC 140 25 0 AAAAAAACAG 0.784061 -84 ********* * Masking position 6 Map Score: 37.3599 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 198 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 9 GCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCA 5 13 1 TTGTGATCAC 0.954664 -110 TGACGGGGAAAGATGTTGCGGGACGCACAAAATCGTCC 6 21 0 ATGTTGGCAC 0.408826 -278 AACGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 9 123 1 TTGTGATCAC 0.954664 -178 AGAGTCAGGGAGATGTGAGCCAGCTCACCATAAAAAAG 13 185 1 ATGTGATCAC 0.939599 -116 GTTGCATAATTAATGAGATTCAGATCACATATAAAGCC 14 52 1 TTGAGATCAC 0.564173 -78 TTCATAAATTAAATGTGAATTGCCGCACACATTATTAA 15 148 0 ATGTGAGCAC 0.860752 -125 TCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTT 22 36 1 ATGTTATCAC 0.777768 -118 TTGAAAGTTAATTTGTGAGTGGTCGCACATATCCTGTT 25 107 1 ATGTGAGCAC 0.860752 -82 ACATTATTGATTCTGTTGATATGATCACGTTATACCCA 28 13 0 TTGTTGTCAC 0.702011 -179 ATAAACGCCATAATGTTATACATATCACTCTAAAATGT 31 99 0 TTGTTATCAC 0.82571 -91 ATCAAAACAAAAATGTGACACTACTCACATTTAAATGC 34 22 1 ATGTGATCAC 0.939599 -279 TACACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 34 95 1 TTGTGATCAC 0.954664 -206 CGACGGCCTTTTGTGTGATATCAATCACATAAATATAG 34 143 0 TTGTGATCAC 0.954664 -158 ACCTTGTAGATACTGCGAAATCTGGCACTGAATCGGTT 34 192 0 TTGCGAGCAC 0.728582 -109 GAAATTGTTTAAATGTGAATCGAATCACAATCGTTCGG 37 153 0 ATGTGATCAC 0.939599 -90 TCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACC 38 129 1 ATGTTATCAC 0.777768 -172 GTGTTACCGTTGATGTTGGCGGAATCACAGTCATGACG 38 250 1 TTGTTGTCAC 0.702011 -51 AATTTTCAGGAAATGCGGTGAGCATCACATCACCACAA 40 126 1 ATGCGGTCAC 0.712773 -162 CAATTCAGCAAATTGTGAACATCATCACGTTCATCTTT 40 161 1 ATGTGATCAC 0.939599 -127 CATTTTCGATTGATGTGGATTATGTCACCAGGAGAAGG 42 51 0 TTGTGGTCAC 0.912826 -250 TTCATGAAAATTCTGTAACCGTTTTCACGCGCTATCTG 43 60 1 TTGTAATCAC 0.713069 -96 TCGCCACGATTTTTGCAAGCAACATCACGAAATTCCTT 45 174 0 TTGCAATCAC 0.443593 -191 GAATTGGCGGTAATGTGGAGATGCGCACATAAAATCGC 45 208 0 TTGTGGGCAC 0.806237 -157 TTACCGCCAATTCTGTAACAGAGATCACACAAAGCGAC 45 233 1 TTGTAATCAC 0.713069 -132 GGTCAACCATTGTTGCGATGAATGTCACATCCTCTGAT 49 30 1 TTGCGATCAC 0.871057 -271 TATGAGAAAAACGTGTGATGTAATTCACAATCCTGTTT 130 53 1 ATGTGATCAC 0.939599 -83 * ***** **** Masking position 4 Map Score: 26.6393 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 46 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 CATTCTGTAACAAAGCGGGACCAAAGCCAT 2 96 1 CAAAGCGGGA 0.938751 -205 AATAAAATGGCATAGCGGGATATGCCGCGA 27 29 1 CATAGCGGGA 0.782977 -242 TTATTCCACACAAAAGGGGACAGTATAAAG 30 13 0 CAAAAGGGGA 0.768228 -32 TCTCCGTGAGGAGAGGGGCAGCGCCGGATG 35 143 0 GAGAGGGGCA 0.806393 -87 TGTGACATAACAAAGGCGGAGTCAACGCTC 54 23 0 CAAAGGCGGA 0.75309 -34 GCACAAACAGCAAAGGGGGATAATTATTA 58 278 1 CAAAGGGGGA 0.962026 -19 GAAAAAACACGAAAGGGGCAATGGGC 62 14 1 GAAAGGGGCA 0.955244 -16 AGATGAGTTAGAAAGGAGGATATCAA 63 285 1 GAAAGGAGGA 0.836687 -16 TTTTTATTTTCAGAGGGGGAATGATTT 77 232 1 CAGAGGGGGA 0.831757 -17 CAGGTCCTCACAAAGCAGCACTATCCAGCT 91 41 0 CAAAGCAGCA 0.573857 -213 TATTTTATGAGAAAGGGGCAGTTTAC 102 192 1 GAAAGGGGCA 0.955244 -16 TTATTTTAGCGAAAGCAGGACATTCCGACA 103 118 0 GAAAGCAGGA 0.756071 -94 TGAAACGAGAAAGCGGCATATCTGCTGC 108 9 1 GAAAGCGGCA 0.928124 -129 AACAAAAAAAGAAAGCAGCAGATATGCCGC 108 23 0 GAAAGCAGCA 0.652203 -115 CGGGTCAAAAGATAGGGGGACTTTTCTG 112 164 1 GATAGGGGGA 0.892521 -18 AAACGGAAATCAAAGGGGGAAAC 122 100 1 CAAAGGGGGA 0.962026 -13 CCGTAAAGAAAAGGGGAGATCTT 123 8 1 GAAAAGGGGA 0.821928 -16 TCAAATTCCAGAAAGGCGGATCATCT 127 166 1 GAAAGGCGGA 0.809427 -16 TGAATGGATAGATAACGGGAGGAGCAGGGG 128 13 0 GATAACGGGA 0.39662 -211 TTGAATCATTGAAAGGGGCAAGCCAA 130 120 1 GAAAGGGGCA 0.955244 -16 TTTCTTCATAGAAAACGGCAGATCATATGC 131 21 0 GAAAACGGCA 0.628181 -60 TTTACAATAACAAAGGGGGATGTTAG 133 105 1 CAAAGGGGGA 0.962026 -16 AGAAGAAAACGAAAGGGGCATCAAT 135 64 1 GAAAGGGGCA 0.955244 -15 TATCACTGCACATAGCGGGAAGACAAATAG 142 78 1 CATAGCGGGA 0.782977 -39 ********** Masking position 4 Map Score: 25.832 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 190 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 AACGCCTGATGCGACGCTGACGCGTCTTAT 1 30 1 GCGACGCTGA 0.981492 -255 AACGCCTGATGCGACGCTGGCGCGTCTTAT 1 115 1 GCGACGCTGG 0.990953 -170 AACGCCTGATGCGACGCTGGCGCGTCTTAT 1 200 1 GCGACGCTGG 0.990953 -85 AAATTCTCCGGCGACGCGGTTTTTAACAGG 13 43 0 GCGACGCGGT 0.928593 -258 CTCACCTAAAACGACGCTGATCCAGCGTGA 29 121 0 ACGACGCTGA 0.806896 -180 AATGCCTGATGCGACGCTGTCGCGTCTTAT 39 16 0 GCGACGCTGT 0.985725 -285 AATGCCTGATGCGACGCTGTCGCGTCTTAT 39 108 0 GCGACGCTGT 0.985725 -193 AATGCCTGATGCGACGCTGTCGCGTCTTAT 39 199 0 GCGACGCTGT 0.985725 -102 ACTGCCTGATGCGACGCTGACGCGTCTTAT 44 80 0 GCGACGCTGA 0.981492 -74 ATCACACAAAGCGACGGTGGGGCGTAGGGG 45 256 1 GCGACGGTGG 0.927489 -109 AACGCCTGATGCGACGCTTGCGCGTCTTAT 47 58 1 GCGACGCTTG 0.89616 -185 ********** Masking position 4 Map Score: 20.7251 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 140 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 AATAAATTAGTGGAATCGTTTACACAAGAATTT 11 169 0 TGAACGTTAC 0.922476 -92 AATGTTTTATTGCAATCGGTTGCTAAATTGCAT 27 93 1 TGAACGTTGC 0.813116 -178 GCGCGAAAAGTGGTAACGGTTACCTTTGACATA 38 197 1 TGTACGTTAC 0.758713 -104 ATGAAAATTCTGTAACCGTTTTCACGCGCTATC 43 63 1 TGAACGTTTC 0.971678 -93 TAACTTATCATGATAGCGCTTTCTTAAATTATC 58 140 0 TGTACGTTTC 0.900657 -157 GGCCTCTATCTGTAAGCGCTTTTATTAATTTTT 61 175 0 TGAACGTTTT 0.644564 -52 GTATAGGGACTGTAAGCGTTTTAACATAGAGTC 67 79 1 TGAACGTTTA 0.88025 -94 GTTGTTGACATGTTACCGATTTCAGAAACTAGG 75 61 0 TGTACGTTTC 0.900657 -43 CAATTCAATATGTATTCGTTTAACCACTAGGGG 77 54 1 TGATCGTTAA 0.453558 -195 GTATTCAAAATGAATACGTTTTCATTAGGAGGT 83 252 1 TGATCGTTTC 0.917829 -28 ATAGAATGTTTGTATACGCTTACGTTTGAAGCA 86 108 1 TGATCGTTAC 0.79483 -122 TCAACGGGAATGAAAACGGTTTATACTTGAGTT 92 85 1 TGAACGTTTA 0.88025 -76 CTGGCTTTTTTGTCAGCGTTTTCTTCTTGACTG 95 32 1 TGCACGTTTC 0.80331 -78 CTTTTGTATTTGAAAGCGTTTTATTTTATGAGA 102 171 1 TGAACGTTTA 0.880249 -37 AAGACGTTTATGATAGCGCTTTCATTTATAGTA 103 53 0 TGTACGTTTC 0.900657 -159 CCCTTTTATTTGTATCCGTTTTCATTATATATG 108 97 0 TGATCGTTTC 0.917829 -41 TCGGTAGGAATGAAAGCGCTTTAAAGATAATAT 119 104 0 TGAACGTTTA 0.88025 -37 CGAAAGTTGTTGTAACCGCTTTCTATAGGACAA 121 33 1 TGAACGTTTC 0.971678 -63 CCTTTGTTATTGTAAACGCTTTCTTATATTGAG 133 88 0 TGAACGTTTC 0.971678 -33 GACAGGTTTTTGTAAACGCTTTCTAGTTCGCGG 136 114 1 TGAACGTTTC 0.971678 -40 CTCCTTTATTTGTATTCGCTTACAATTACTGTT 138 85 0 TGATCGTTAC 0.79483 -31 ** ** ** **** Masking position 10 Map Score: 23.7004 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 54 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 CGCAATTAATGTGAGTTAGCTCACTCATTAGGCA 5 17 1 GTGAACTCAC 0.498501 -106 ACGATATTTGGTGACAAAACTCACAAAAGACACG 9 127 0 GTGAACTCAC 0.770514 -174 TCAGGGAGATGTGAGCCAGCTCACCATAAAAAAG 13 189 1 GTGAACTCAC 0.550624 -112 CATAATTAATGAGATTCAGATCACATATAAAGCC 14 56 1 GAGAAATCAC 0.667386 -74 GGGCAAAAATGTTATCCACATCACAATTTCGTTT 22 40 1 GTTAAATCAC 0.831469 -114 TTTTTATTCCGTGATCAAAATCACCTCTTAAAAT 27 124 0 GTGAAATCAC 0.511098 -147 ACGCCATAATGTTATACATATCACTCTAAAATGT 31 99 0 GTTAAATCAC 0.831469 -91 AAACAAAAATGTGACACTACTCACATTTAAATGC 34 26 1 GTGATCTCAC 0.77757 -275 GGTAATTGACGTGACGTTCATCACAAAACGCTTG 34 99 0 GTGATATCAC 0.647845 -202 CTATATTTATGTGATTGATATCACACAAAAGGCC 34 143 1 GTGAAATCAC 0.666608 -158 TTGTTTAAATGTGAATCGAATCACAATCGTTCGG 37 153 0 GTGAGATCAC 0.754724 -90 TCAGCAAGGTGTTAAATTGATCACGTTTTAGACC 38 133 1 GTTATATCAC 0.730006 -168 TCAGCAAATTGTGAACATCATCACGTTCATCTTT 40 165 1 GTGATATCAC 0.752526 -123 CGCCAATTCTGTAACAGAGATCACACAAAGCGAC 45 237 1 GTAAAATCAC 0.690307 -128 TCTGAAATTGGTTAACCACATCACAAGAATTTCA 49 119 0 GTTAAATCAC 0.878706 -182 AAACAGGATTGTGAATTACATCACACGTTTTTCT 130 57 0 GTGAAATCAC 0.676083 -79 **** * ***** Masking position 4 Map Score: 14.9091 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 44 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 14 AGCTTTAACGAAAGTGAATGAGGGCAGC 31 6 0 AAAGAAGAGG 0.969834 -184 CTCCCGAGGAAAAGAGTATGAGGCGGCTTTTGC 52 98 0 AAAGTAGAGG 0.720844 -29 TGTATGATGGAAATAAAAGGAGGTTGTTTGC 56 111 1 AAAAAAGAGG 0.895653 -21 CTTTCCCGAAAAACAAAAAGAGCCAGAAAACAC 58 226 0 AAAAAAGAGC 0.553074 -71 CAAAAAACTGAAAAGGAAGGAGGCACTTGC 78 85 1 AAAGAAGAGG 0.969834 -20 ATAGGGATTTAAAACAAGAAAGGAATCTGTAC 88 227 1 AAAAAGAAGG 0.60553 -22 GCTGCTTGTGAAATTGAAGGAGGTCAAACTGCT 91 11 0 AAAGAAGAGG 0.969834 -243 TAAAAAGAGAGAAAGGCTTGCTTAAT 103 4 1 AAAGAGAAGG 0.851843 -208 CATTTATAGTAAAAAGAGAAAGGCTGTATTAAG 103 31 0 AAAGAGAAGG 0.851843 -181 TTAATTTTCTAAAGGAAAAGAGGGTCAGT 105 7 0 AAAAAAGAGG 0.895653 -192 AAAACTGATAAAGGGAGAGAGCCGT 106 10 1 AAAGAGGAGC 0.805411 -16 AAAGGAAGAGAAAAAGAGCGAGGAAGATGTAGG 116 130 0 AAAGAGGAGG 0.96634 -148 TGACTGCAGAAAAAGAAGGGAGGTATTTTCCTA 117 155 0 AAAAAGGAGG 0.88459 -146 ATAGTTTCGTAAATAGAAGGAGGAAAAGAG 121 76 1 AAAGAAGAGG 0.969834 -20 GATTGCTGAGAAAAGGAATGAGGGC 128 209 1 AAAGAAGAGG 0.969834 -15 AGTGTAGAAGAAAACGAAAGGGGCATCAAT 135 59 1 AAAGAAGGGG 0.79284 -20 GCGGGAAGACAAATAGAAAAAGGAGGTCTCGTA 142 92 1 AAAGAAAAGG 0.865569 -25 *** *** **** Masking position 3 Map Score: 13.0118 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 GCGTTCACGTAACTGGAGGAATGAA 21 161 1 AACTGGAGGA 0.644589 -15 TGGGGGAGGAGGCGGGAGGATGAGAACACGG 45 116 1 GGCGGGAGGT 0.740904 -249 TGATGGAAATAAAAGGAGGTTGTTTGC 56 115 1 AAAAGGAGGT 0.854686 -17 ATAAAAATCTGGAGGGAGGCTGTTTAAAG 58 9 0 GGAGGGAGGT 0.695981 -288 TGTTTTTCGGGAAAGGAGGCACGCCACACAT 58 244 1 GAAAGGAGGA 0.918444 -53 CCACCACACCGACAGGAGGCATCCC 59 216 1 GACAGGAGGA 0.93363 -15 ATACACAAATAACAGGAGGTTATGTTG 61 210 1 AACAGGAGGT 0.880194 -17 AGATGAGTTAGAAAGGAGGATATCAA 63 285 1 GAAAGGAGGT 0.897154 -16 CCGAAATAACGGCAGGGGGATTTTTTATTTT 71 25 1 GGCAGGGGGT 0.709064 -69 TATTATAAGGAAATGGAGGTACACTTTAAAA 76 44 0 AAATGGAGGA 0.592159 -80 ATCCGACTTAAAAAGGAGGATGATTCAA 76 106 1 AAAAGGAGGT 0.854686 -18 AAACTGAAAAGGAAGGAGGCACTTGC 78 89 1 GGAAGGAGGA 0.907656 -16 CATAAAAAATGACTGGAGGTTTGTTACGG 86 211 1 GACTGGAGGT 0.675703 -19 ACAGAAGGAAAGCAGGGGGAAAAC 89 67 1 AGCAGGGGGA 0.679633 -14 CGTATAGAAAAAAAGGAGGCTTTCAAG 92 144 1 AAAAGGAGGT 0.854686 -17 AAACCCTATTGGCAGGAGGGATATC 97 52 1 GGCAGGAGGA 0.924686 -15 ATGAAAATCCAAAAGGAGGAACTAAA 101 285 1 AAAAGGAGGA 0.883627 -16 ATAATAGGTTAAAAGGAGGCTACCCT 112 6 0 AAAAGGAGGT 0.854686 -176 TGCAGAAAAAGAAGGGAGGTATTTTCCTATG 117 153 0 GAAGGGAGGA 0.772007 -148 TTTCGTAAATAGAAGGAGGAAAAGAG 121 80 1 AGAAGGAGGA 0.868891 -16 GGCAGCCCGGAACAGGAGGAACATATC 127 7 0 AACAGGAGGA 0.904622 -175 CAGATTTTATAAAAGGGGGGAAAACACCTCA 127 91 1 AAAAGGGGGA 0.660538 -91 GAAGTCATTCGGCAGGAGGAAAATCAAAATG 143 280 1 GGCAGGAGGA 0.924686 -21 ********* * Masking position 6 Map Score: 21.1063 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 50 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405