AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icrp_ecoli_hinf_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 HI0054 109 uxu operon regulator (uxuR) #56 HI0055 27 mannonate dehydratase (uxuA) #57 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #58 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #59 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #60 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #61 HI0190 28 ferric uptake regulation protein (fur) #62 HI0191 96 flavodoxin (fldA) #63 HI0289 222 serine transporter (sdaC) #64 HI0351 172 UDP-glucose 4-epimerase (galE) #65 HI0518 83 purine-nucleoside phosphorylase (deoD) #66 HI0519 98 transport protein, putative #67 HI0521 212 conserved hypothetical protein #68 HI0604 300 adenylate cyclase (cyaA) #69 HI0615_HI0616 197 HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA) #70 HI0618 26 glp protein, putative #71 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #72 HI0680 31 rarD protein, putative #73 HI0681 300 transcriptional activator (ilvY) #74 HI0685_HI0686 200 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #75 HI0687 99 conserved hypothetical protein #76 HI0688 94 H. influenzae predicted coding region HI0688 #77 HI0690 229 glycerol uptake facilitator protein (glpF) #78 HI0727.1 260 cyaY protein (cyaY) #79 HI0745 225 L-asparaginase II (ansB) #80 HI0819 37 galactokinase (galK) #81 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #82 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #83 HI0954 47 deoxyuridinetriphosphatase (dut) #84 HI0956 21 conserved hypothetical protein #85 HI0957 66 catabolite gene activator (crp) #86 HI1027 58 L-xylulose kinase (lyx) #87 HI1028 30 conserved hypothetical protein #88 HI1030 71 conserved hypothetical transmembrane protein #89 HI1031 175 conserved hypothetical protein #90 HI1116 110 deoxyribose-phosphate aldolase (deoC) #91 HI1164 300 outer membrane protein P5 (ompA) #92 HI1350 273 cytidine deaminase (cdd) #93 HI1678 300 kpsF protein (kpsF) #94 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 GGCGTTACATACCGGATGCGGCTAC 1 6 0 ACCGGATGCG 0.80367 -279 GGTATGTAACGCCTGATGCGACGCTGACGC 1 23 1 GCCTGATGCG 0.993304 -262 CAGCGTGTAGGCCAGATAAGACGCGTCAGC 1 45 0 GCCAGATAAG 0.721799 -240 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 76 1 GCCGGATAAG 0.987864 -209 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 GCCGGATGCG 0.996028 -194 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 108 1 GCCTGATGCG 0.993304 -177 CAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 GCCTGATAAG 0.979653 -155 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 161 1 GCCGGATAAG 0.987864 -124 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 GCCGGATGCG 0.996028 -109 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 193 1 GCCTGATGCG 0.993304 -92 CAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 GCCTGATAAG 0.979653 -70 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 246 1 GCCGGATAAG 0.987864 -39 ACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GCCGGATGCG 0.996028 -24 GCAATCAATGTCGGATGCGGCGCGAGCGC 3 10 1 GTCGGATGCG 0.913477 -56 TGATATGTTGGTCGGATAAGGCGCTCGCGC 3 30 0 GTCGGATAAG 0.774102 -36 AGCCTGGGGTGCCTAATGAGTGAGCTAACT 5 30 0 GCCTAATGAG 0.716625 -93 TGCTGACCTTGCCGGAGGCGGCCTTAGCAC 11 19 1 GCCGGAGGCG 0.908044 -242 GGTAGTCACTGCCCGATACGGACTTTACAT 17 79 1 GCCCGATACG 0.866528 -177 ACTATAGAATGCCTGATGCGCTACGCTCAT 18 45 1 GCCTGATGCG 0.993304 -60 AGTCCTGTATGCCTGATGAGCGTAGCGCAT 18 60 0 GCCTGATGAG 0.988747 -45 GGGGTTAATTGCCTGATGCGCTACGCTTAT 35 42 1 GCCTGATGCG 0.993304 -188 CATCCTGTAGGCCTGATAAGCGTAGCGCAT 35 57 0 GCCTGATAAG 0.979653 -173 GTTCTTGTAGGCCGGATAAGGCGCTTACGC 35 111 1 GCCGGATAAG 0.987864 -119 GAGGGGCAGCGCCGGATGCGGCGTAAGCGC 35 131 0 GCCGGATGCG 0.996028 -99 GCCTGATAAGACGCGACAGC 39 1 1 GCCTGATAAG 0.979653 -300 GGCAATCAATGCCTGATGCGACGCTGTCGC 39 23 0 GCCTGATGCG 0.993304 -278 GGCATTGATTGCCGGATGCGGCACAAGTGC 39 40 1 GCCGGATGCG 0.996028 -261 CGACCTGTAGGCCGGATAAGGCACTTGTGC 39 60 0 GCCGGATAAG 0.987864 -241 ACAGTTGTAGGCCTGATAAGACGCGACAGC 39 93 1 GCCTGATAAG 0.979653 -208 GGCAATCAATGCCTGATGCGACGCTGTCGC 39 115 0 GCCTGATGCG 0.993304 -186 GGCATTGATTGCCGGATGCGCACAAGTCGC 39 132 1 GCCGGATGCG 0.996028 -169 CGACCTGTAGGCCTGATAAGCGACTTGTGC 39 151 0 GCCTGATAAG 0.979653 -150 ATAGTTGTAGGCCTGATAAGACGCGACAGC 39 184 1 GCCTGATAAG 0.979653 -117 GGCAATCAATGCCTGATGCGACGCTGTCGC 39 206 0 GCCTGATGCG 0.993304 -95 CGACCCGTAGGCCGGATAAGGCGCTCGCGC 39 244 0 GCCGGATAAG 0.987864 -57 GCTGTGAAATGCCGGATGCGGCGTGAACGC 44 12 1 GCCGGATGCG 0.996028 -142 GGTTTTGTAGGCCGGACAAGGCGTTCACGC 44 32 0 GCCGGACAAG 0.762194 -122 ACGTATGTAGGCCTGATAAGACGCGTCAGC 44 65 1 GCCTGATAAG 0.979653 -89 GACAACAACTGCCTGATGCGACGCTGACGC 44 87 0 GCCTGATGCG 0.993304 -67 GGCAGTTGTTGTCGGATAAGGCGTGAAAGC 44 104 1 GTCGGATAAG 0.774102 -50 CAAAACCTGGGCCGGATAAGGCGTTTACGC 47 14 1 GCCGGATAAG 0.987864 -229 GGCGTTGGTTGCCGAATGCGGCGTAAACGC 47 34 0 GCCGAATGCG 0.87832 -209 GGCAACCAACGCCTGATGCGACGCTTGCGC 47 51 1 GCCTGATGCG 0.993304 -192 GCCGTTGTAGGCCTGATAAGACGCGCAAGC 47 73 0 GCCTGATAAG 0.979653 -170 TCAAATGTAGGCCGGATAAGGCGTTTACGC 47 105 1 GCCGGATAAG 0.987864 -138 CTGTTTTTATGCCGGATGCGGCGTAAACGC 47 125 0 GCCGGATGCG 0.996028 -118 TTCACTTTGATCCTGATGCGTTTGCCACCA 51 65 1 TCCTGATGCG 0.70771 -193 GATGCTTTACGCCTGATGCGCTGCGCTTAT 52 15 1 GCCTGATGCG 0.993304 -112 CGTCTCGTAGGCCTGATAAGCGCAGCGCAT 52 30 0 GCCTGATAAG 0.979653 -97 CTACCCGTAGGCCGGATAAGGCGTAGACGC 52 63 1 GCCGGATAAG 0.987864 -64 GGCGGCTTTTGCCGGATGCGTCTACGCCTT 52 80 0 GCCGGATGCG 0.996028 -47 ********** Masking position 6 Map Score: 192.213 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 212 Number in noncoding regions = 616 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 CGCGTCTTATCTGGCCTACACGCTGCGATT 1 50 1 CTGGCCTACA 0.935265 -235 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 71 0 CCGGCCTACA 0.995058 -214 CGCGTCTTATCAGGCCTACGCGCTGCGATT 1 135 1 CAGGCCTACG 0.986445 -150 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 156 0 CCGGCCTACA 0.995058 -129 CGCGTCTTATCAGGCCTACACGCTGCGATT 1 220 1 CAGGCCTACA 0.992047 -65 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 241 0 CCGGCCTACA 0.995058 -44 AGCACCCTCTCCGGCCAACGGTTCGACGCA 11 44 1 CCGGCCAACG 0.873389 -217 CTACGCTCATCAGGCATACAGGACTTCCGC 18 65 1 CAGGCATACA 0.818619 -40 CTACGCTTATCAGGCCTACAGGATGCATCA 35 62 1 CAGGCCTACA 0.992047 -168 AGCGCCTTATCCGGCCTACAAGAACGTGCA 35 106 0 CCGGCCTACA 0.995058 -124 AGTGCCTTATCCGGCCTACAGGTCGGCAAC 39 65 1 CCGGCCTACA 0.995058 -236 CGCGTCTTATCAGGCCTACAACTGTTGCCG 39 88 0 CAGGCCTACA 0.992047 -213 AGTCGCTTATCAGGCCTACAGGTCGGCAAT 39 156 1 CAGGCCTACA 0.992047 -145 CGCGTCTTATCAGGCCTACAACTATTGCCG 39 179 0 CAGGCCTACA 0.992047 -122 AGCGCCTTATCCGGCCTACGGGTCGTGCAT 39 249 1 CCGGCCTACG 0.99156 -52 AAGTTTACAGCATGCCTACAAGCATCGTGG 42 229 1 CATGCCTACA 0.825366 -72 AACGCCTTGTCCGGCCTACAAAACCGAAAC 44 37 1 CCGGCCTACA 0.995058 -117 CGCGTCTTATCAGGCCTACATACGTTTCGG 44 60 0 CAGGCCTACA 0.992047 -94 CGCGTCTTATCAGGCCTACAACGGCTGTCA 47 78 1 CAGGCCTACA 0.992047 -165 AACGCCTTATCCGGCCTACATTTGACAGCC 47 100 0 CCGGCCTACA 0.995058 -143 CTGCGCTTATCAGGCCTACGAGACGTATCT 52 35 1 CAGGCCTACG 0.986445 -92 TACGCCTTATCCGGCCTACGGGTAGATACG 52 58 0 CCGGCCTACG 0.99156 -69 GGGCTAAAGTCCAGCCTACGATATGAATAG 60 233 1 CCAGCCTACG 0.81656 -53 ********** Masking position 8 Map Score: 85.5711 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 0.998127 -256 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 114 1 TGCGCGCGCT 0.998127 -171 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 199 1 TGCGCGCGCT 0.998127 -86 CAATGTCGGATGCGGCGCGAGCGCCTTATCCGACCA 3 16 1 TGCGCGCGCT 0.998127 -50 TGTGATGCGGCGTAGACTCATGTCTACGCCG 10 6 1 TGCGCGCTCT 0.957068 -283 TCCCTGACTCTGCGGCAATATGGCGTCTTTAGTATC 13 160 0 TGCGCAGGCT 0.896337 -141 CAGCGCCGGATGCGGCGTAAGCGCCTTATCCGGCCT 35 119 0 TGCGCGCGCT 0.998127 -111 CCGCCCGGTTTGCGCCGGCGGGGTTTTGGAATCGTG 36 25 0 TGCGCGGGTT 0.814556 -81 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 11 0 TGCGCGCGCT 0.998127 -290 GATTGCCGGATGCGGCACAAGTGCCTTATCCGGCCT 39 46 1 TGCGCATGCT 0.685169 -255 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 103 0 TGCGCGCGCT 0.998127 -198 AGGCCTGATAAGCGACTTGTGCGCATCCGGCAATCA 39 137 0 AGCGCTCGCT 0.826352 -164 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGC 39 194 0 TGCGCGCGCT 0.998127 -107 AAATGCCGGATGCGGCGTGAACGCCTTGTCCGGCCT 44 18 1 TGCGCGCGCT 0.998127 -136 AACTGCCTGATGCGACGCTGACGCGTCTTATCAGGC 44 75 0 TGCGCGCGCT 0.998127 -79 GATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGG 45 255 1 AGCGCGGGCT 0.95255 -110 GGTTGCCGAATGCGGCGTAAACGCCTTATCCGGCCC 47 22 0 TGCGCGCGCT 0.998127 -221 CAACGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 47 57 1 TGCGCGCGCT 0.998127 -186 TTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 47 113 0 TGCGCGCGCT 0.998127 -130 ATTTGGGCGGAGCGTTGACTCCGCCTTTGTTATGTC 54 14 1 AGCGTGCGCT 0.809987 -43 **** ** *** * Masking position 16 Map Score: 71.2852 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 56 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 TAACGCCTGATGCGACGCTGACGCGTCTTATCTG 1 29 1 TGCGCGCCGC 0.998529 -256 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAG 1 114 1 TGCGCGCCGC 0.998529 -171 CAACGCCTGATGCGACGCTGGCGCGTCTTATCAG 1 199 1 TGCGCGCCGC 0.998529 -86 CAATGTCGGATGCGGCGCGAGCGCCTTATCCGAC 3 16 1 TGCGCGCCGC 0.998529 -50 TGTGATGCGGCGTAGACTCATGTCTACGC 10 6 1 TGCGCGTCTC 0.931583 -283 CAGCGCCGGATGCGGCGTAAGCGCCTTATCCGGC 35 121 0 TGCGCGTCGC 0.996133 -109 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 13 0 TGCGCGCCGC 0.998529 -288 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 105 0 TGCGCGCCGC 0.998529 -196 CAATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 196 0 TGCGCGCCGC 0.998529 -105 GTAGGCCGGATAAGGCGCTCGCGCGCATCCACGG 39 234 0 TAAGCGCCGC 0.871083 -67 AAATGCCGGATGCGGCGTGAACGCCTTGTCCGGC 44 18 1 TGCGCGTCGC 0.996133 -136 AACTGCCTGATGCGACGCTGACGCGTCTTATCAG 44 77 0 TGCGCGCCGC 0.998529 -77 GGTTGCCGAATGCGGCGTAAACGCCTTATCCGGC 47 24 0 TGCGCGTCGC 0.996133 -219 CAACGCCTGATGCGACGCTTGCGCGTCTTATCAG 47 57 1 TGCGCGCCGC 0.998529 -186 TTATGCCGGATGCGGCGTAAACGCCTTATCCGGC 47 115 0 TGCGCGTCGC 0.996133 -128 GTAGGCCGGATAAGGCGTAGACGCATCCGGCAAA 52 69 1 TAAGCGTCGC 0.719453 -58 **** *** *** Masking position 1 Map Score: 63.6827 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 75 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 AACGCCTGATGCGACGCTGACGCGTCTTATCTG 1 30 1 GCGACGCCGC 0.994963 -255 AACGCCTGATGCGACGCTGGCGCGTCTTATCAG 1 115 1 GCGACGCCGC 0.994963 -170 AACGCCTGATGCGACGCTGGCGCGTCTTATCAG 1 200 1 GCGACGCCGC 0.994963 -85 AATGTCGGATGCGGCGCGAGCGCCTTATCCGAC 3 17 1 GCGGCGCCGC 0.998239 -49 ACATATCATAACGGAGTGATCGCA 3 52 1 ACGGAGTCGC 0.739455 -14 TGTGATGCGGCGTAGACTCATGTCTACGC 10 7 1 GCGGCGTCTC 0.923586 -282 AGCGCCGGATGCGGCGTAAGCGCCTTATCCGGC 35 121 0 GCGGCGTCGC 0.996511 -109 AATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 13 0 GCGACGCCGC 0.952047 -288 AATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 105 0 GCGACGCCGC 0.952047 -196 GGCCTGATAAGCGACTTGTGCGCATCCGGCAAT 39 139 0 GCGACTTCGC 0.861565 -162 AATGCCTGATGCGACGCTGTCGCGTCTTATCAG 39 196 0 GCGACGCCGC 0.952047 -105 TAGGCCGGATAAGGCGCTCGCGCGCATCCACGG 39 234 0 AAGGCGCCGC 0.888582 -67 AATGCCGGATGCGGCGTGAACGCCTTGTCCGGC 44 19 1 GCGGCGTCGC 0.996569 -135 ACTGCCTGATGCGACGCTGACGCGTCTTATCAG 44 77 0 GCGACGCCGC 0.994963 -77 GTTGCCGAATGCGGCGTAAACGCCTTATCCGGC 47 24 0 GCGGCGTCGC 0.996511 -219 AACGCCTGATGCGACGCTTGCGCGTCTTATCAG 47 58 1 GCGACGCCGC 0.996453 -185 TATGCCGGATGCGGCGTAAACGCCTTATCCGGC 47 115 0 GCGGCGTCGC 0.996511 -128 CCGATAATCAGAGGGGCTTTCGCCCCTTTCAGA 47 165 0 GAGGGGCCGC 0.823746 -78 TAGGCCGGATAAGGCGTAGACGCATCCGGCAAA 52 70 1 AAGGCGTCGC 0.802635 -57 CATAACAAAGGCGGAGTCAACGCTCCGCCCAAA 54 15 0 GCGGAGTCGC 0.958333 -42 ******* *** Masking position 3 Map Score: 61.3291 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 271 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 TGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGC 5 13 0 GTGATCACAA 0.96548 -110 GGACGATTTTGTGCGTCCCGCAACATCTTTCCCCGTCA 6 21 1 GTGCCAACAT 0.388139 -278 ACGATATTTGGTGACAAAACTCACAAAAGACACGCGTT 9 123 0 GTGATCACAA 0.96548 -178 CTTTTTTATGGTGAGCTGGCTCACATCTCCCTGACTCT 13 185 0 GTGATCACAT 0.967409 -116 CATAATTAATGAGATTCAGATCACATATAAAGCCACAA 14 56 1 GAGATCACAT 0.546177 -74 TTAATAATGTGTGCGGCAATTCACATTTAATTTATGAA 15 148 1 GTGCTCACAT 0.898772 -125 AAACGAAATTGTGATGTGGATAACATTTTTGCCCCTGA 22 36 0 GTGATAACAT 0.851518 -118 AACAGGATATGTGCGACCACTCACAAATTAACTTTCAA 25 107 0 GTGCTCACAT 0.898772 -82 TTTTTATTCCGTGATCAAAATCACCTCTTAAAATGCAA 27 120 0 GTGATCACCT 0.772081 -151 TGGGTATAACGTGATCATATCAACAGAATCAATAATGT 28 13 1 GTGACAACAA 0.666475 -179 ACATTTTAGAGTGATATGTATAACATTATGGCGTTTAT 31 99 1 GTGATAACAA 0.843836 -91 GCATTTAAATGTGAGTAGTGTCACATTTTTGTTTTGAT 34 22 0 GTGATCACAT 0.967409 -279 GGTAATTGACGTGACGTTCATCACAAAACGCTTGTGTA 34 95 0 GTGATCACAA 0.96548 -206 CTATATTTATGTGATTGATATCACACAAAAGGCCGTCG 34 143 1 GTGATCACAA 0.96548 -158 AACCGATTCAGTGCCAGATTTCGCAGTATCTACAAGGT 34 192 1 GTGCTCGCAA 0.66116 -109 CCGAACGATTGTGATTCGATTCACATTTAAACAATTTC 37 153 1 GTGATCACAT 0.967409 -90 GGTCTAAAACGTGATCAATTTAACACCTTGCTGATTGA 38 129 0 GTGATAACAT 0.851518 -172 CGTCATGACTGTGATTCCGCCAACATCAACGGTAACAC 38 250 0 GTGACAACAA 0.666475 -51 TTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAATT 40 126 0 GTGACCGCAT 0.719127 -162 AAAGATGAACGTGATGATGTTCACAATTTGCTGAATTG 40 161 0 GTGATCACAT 0.967409 -127 CCTTCTCCTGGTGACATAATCCACATCAATCGAAAATG 42 51 1 GTGACCACAA 0.91184 -250 CAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAA 43 60 0 GTGATTACAA 0.709871 -96 AAGGAATTTCGTGATGTTGCTTGCAAAAATCGTGGCGA 45 174 1 GTGATTGCAA 0.363334 -191 GCGATTTTATGTGCGCATCTCCACATTACCGCCAATTC 45 208 1 GTGCCCACAA 0.755724 -157 GTCGCTTTGTGTGATCTCTGTTACAGAATTGGCGGTAA 45 233 0 GTGATTACAA 0.709871 -132 ATCAGAGGATGTGACATTCATCGCAACAATGGTTGACC 49 30 0 GTGATCGCAA 0.867082 -271 TGAAATTCTTGTGATGTGGTTAACCAATTTCAGAATTC 49 119 1 GTGATAACCT 0.395577 -182 TTTTGAAAACGTGAGGAAGATCACAGTTTTAGAAAATA 67 130 0 GTGATCACAT 0.967409 -83 TCGAAAAATTGTGATTTATGTCACATTTTTTTGCATTT 68 216 1 GTGATCACAT 0.967409 -85 AATCAAAAATGTGAAGTGTTTCACAAATCTTTACACCG 74 25 1 GTGATCACAT 0.967409 -176 GAAAATTATTGTGATCAATATCACAAAATCGCTTTCTT 74 76 1 GTGATCACAA 0.96548 -125 TAAATAAACCGTGATCTTTGTCACAAAATAAGAAAATA 81 123 0 GTGATCACAA 0.96548 -85 TATCAAATAAGTGATCAAGATCACAGTTTTAATGAATA 92 162 1 GTGATCACAT 0.967409 -112 **** ***** * Masking position 14 Map Score: 60.7292 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 38 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 7 AAGTGTAAAAAAGGGCGGGCAGCTTACTGAG 33 156 0 AAGGGCGGGA 0.722714 -34 AATTTTCAGGAAATGCGGTGAGCATCACATC 40 126 1 AAATGCGGTA 0.875011 -162 GAAGGATGAAAAGTGTGGCAAACCGTAATCT 42 25 0 AAGTGTGGCA 0.674958 -276 AGTGCTATAAAAGTGCGGTTTGTTTTTATTT 57 29 0 AAGTGCGGTT 0.865408 -74 GGATCATTATAAGTGCGGCAATTTTCTATCT 60 189 0 AAGTGCGGCA 0.978002 -97 TTTTTATAAAAAGTGCGGTAATTTTCAGCGA 63 62 0 AAGTGCGGTA 0.987663 -161 ATCAATTAAAAAGTGCGGTAAAAAATGACCG 65 20 1 AAGTGCGGTA 0.987663 -64 AAAATGAATAAAGTGCGGTCATTTTTTACCG 65 35 0 AAGTGCGGTA 0.987663 -49 CGTTTACAAAAAGTGCGGTGAAAATTCGCCG 66 12 1 AAGTGCGGTA 0.987663 -87 ATCTTCCTAAAAGTGCGGTCAATTTTTTGTG 69 85 0 AAGTGCGGTA 0.987663 -113 TAAAAAGTGCGGTTAGTTTTCTGGT 73 5 1 AAGTGCGGTA 0.987663 -296 CTTCAATTTAAAGTGCGGGTAAAATTTAGCG 73 49 0 AAGTGCGGGA 0.958741 -252 CATTGTAGGGAAGTGCGGCCAAAATTAACAA 74 128 0 AAGTGCGGCA 0.978002 -73 CACTCCTTAGAAGTGCGGTTGAAATGAAGAG 77 205 0 AAGTGCGGTG 0.905032 -25 AAATCTGATAAAATGCGGCAAATTATAAAGC 78 225 0 AAATGCGGCA 0.79541 -36 AAGATAACCCAAGTGCGGTTATACTTGAGCC 79 44 0 AAGTGCGGTA 0.987663 -182 GAACGTTCAAAAGTGCGCTTATTATCCTATA 91 112 0 AAGTGCGCTA 0.847139 -189 GGGCAATCACTAGTGCGGTCAATAAAATCCC 93 241 1 TAGTGCGGTA 0.858325 -60 ********* * Masking position 2 Map Score: 38.4644 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 28 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TAGCCGCATCCGGTATGTAACGCCTGATGCGACGCT 1 12 1 CGGTAAGCCG 0.968018 -273 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 97 1 CGGCAAGCCG 0.994946 -188 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 182 1 CGGCAAGCCG 0.994946 -103 CCGGTTGGGTTAGCGAGAAGAGCCAGTAAAAGACGC 2 41 0 TAGCGAGCCG 0.486312 -260 CGCGAAATACGGGCAGACATGGCCTGCCCGGTTATT 4 12 0 GGGCAAGCCG 0.928054 -40 CACAAGGAAGCGGTAGTCACTGCCCGATACGGACTT 17 68 1 CGGTAAGCCG 0.967798 -188 AATGGCATAGCGGGATATGCCGCGAGCGGGCGATTT 27 34 1 CGGGAGGCGG 0.70363 -237 GTTAATGTGGCGGCAGAGGTAGCCGGACCTTGTAGA 34 220 0 CGGCAGGCCG 0.990326 -81 ATGGAGAAGGTGGGGTTAATTGCCTGATGCGCTACG 35 31 1 TGGGGAGCCG 0.769587 -199 AAACGCCTGTCAGGATCCACTGCCAGACCTCATTTT 38 20 0 CAGGAAGCCG 0.896337 -281 CTTATTACAACGGCGTGAAACGCCTGTCAGGATCCA 38 37 0 CGGCGAGCCG 0.990914 -264 GTGCCGCATCCGGCAATCAATGCCTGATGCGACGCT 39 28 0 CGGCAAGCCG 0.994946 -273 TGTGCGCATCCGGCAATCAATGCCTGATGCGACGCT 39 120 0 CGGCAAGCCG 0.994946 -181 CGCGCATCCACGGCAATCAATGCCTGATGCGACGCT 39 211 0 CGGCAAGCCG 0.994946 -90 ACGCCTTATCCGACAACAACTGCCTGATGCGACGCT 44 92 0 CGACAAGCCG 0.886894 -62 ACGCCGCATTCGGCAACCAACGCCTGATGCGACGCT 47 40 1 CGGCAAGCCG 0.994946 -203 TAGACGCATCCGGCAAAAGCCGCCTCATACTCTTTT 52 86 1 CGGCAGGCCC 0.857829 -41 CCCCTGTTTACGGGGGAAGGTGCCCGAAGGGCGGAA 60 91 1 CGGGGGGCCG 0.956787 -195 TTAAAAAGTGCGGTAAAAAATGACCGCACTTTATTC 65 25 1 CGGTAAGACG 0.546696 -59 CACTGGTCGTCGGCTCACGCCGCCCGGACGTTATCC 93 84 1 CGGCTGGCCG 0.897473 -217 CCGAGCTACACAGGGCAGAGTGCCGGATAACGTCCG 93 108 0 CAGGGAGCCG 0.827165 -193 ***** * *** * Masking position 12 Map Score: 40.3255 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 559 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 CCAGATAAGACGCGTCAGCGTCGCATCAGGC 1 33 0 CGCGCAGCGT 0.998161 -252 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 118 0 CGCGCAGCGT 0.998161 -167 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 203 0 CGCGCAGCGT 0.998161 -82 CCTGGTGTCTCGCTTCAGCATGACCCAGGTC 26 79 0 CGCTCAGCAT 0.891282 -222 TTCCAGCCTGCGCGACAGCAAACATAAGAAG 34 270 1 CGCGCAGCAA 0.929595 -31 CCTGATAAGACGCGACAGCGTCGCATCAGGC 39 12 1 CGCGCAGCGT 0.998161 -289 CCTGATAAGACGCGACAGCGTCGCATCAGGC 39 104 1 CGCGCAGCGT 0.998161 -197 CCTGATAAGACGCGACAGCGTCGCATCAGGC 39 195 1 CGCGCAGCGT 0.998161 -106 CCTGATAAGACGCGTCAGCGTCGCATCAGGC 44 76 1 CGCGCAGCGT 0.998161 -78 CCTGATAAGACGCGCAAGCGTCGCATCAGGC 47 61 0 CGCGAAGCGT 0.979349 -182 **** ****** Masking position 7 Map Score: 29.3515 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 10 AAATTAAATGTGAATTGCCGCACACATTATTAA 15 148 0 TATGCCGCAC 0.804721 -125 ACAAGTGGGCAAATTTACCGCACAGTTTACGTC 31 147 0 AATACCGCAC 0.984913 -43 AATGAAATAAAAACAAACCGCACTTTTATAGCA 57 25 1 AAAACCGCAC 0.848161 -78 AACAAGATAGAAAATTGCCGCACTTATAATGAT 60 185 1 AATGCCGCAC 0.962304 -101 TTTGTCGCTGAAAATTACCGCACTTTTTATAAA 63 58 1 AATACCGCAC 0.984913 -165 GAAAATCACCATTCTTACCACACAAAATAGTGA 64 111 1 ATTACCACAC 0.696554 -62 AGTGCGGTAAAAAATGACCGCACTTTATTCATT 65 31 1 AATACCGCAC 0.984913 -53 AAGTCGGCGAATTTTCACCGCACTTTTTGTAAA 66 14 0 ATTACCGCAC 0.978852 -85 AACTCACAAAAAATTGACCGCACTTTTAGGAAG 69 81 1 AATACCGCAC 0.984913 -117 AAATACCAGAAAACTAACCGCACTTTTTA 73 7 0 AATACCGCAC 0.984913 -294 AATACGCTAAATTTTACCCGCACTTTAAATTGA 73 45 1 ATTCCCGCAC 0.871001 -256 AATGTTGTTAATTTTGGCCGCACTTCCCTACAA 74 124 1 ATTGCCGCAC 0.947644 -77 AACACTCTTCATTTCAACCGCACTTCTAAGGAG 77 201 1 ATCACCGCAC 0.854439 -29 ATAGGGCTCAAGTATAACCGCACTTGGGTTATC 79 40 1 ATTACCGCAC 0.978852 -186 TTTTTATAGGATAATAAGCGCACTTTTGAACGT 91 108 1 AATAGCGCAC 0.827539 -193 GGCACGGTGCGCTCTTACCGCACCCTTTCACCC 93 19 1 GTTACCGCAC 0.862641 -282 ATTGGGGATTTTATTGACCGCACTAGTGATTGC 93 243 0 TATACCGCAC 0.913332 -58 * * * ******* Masking position 12 Map Score: 25.8862 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 64 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TAGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 83 1 AACAAGCGCA 0.963735 -202 CGGCCTACAAAATCGCAGCGCGTAGGCCTGAT 1 143 0 AACGAGCGCG 0.839425 -142 TAGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 168 1 AACAAGCGCA 0.963735 -117 TAGGCCGGATAAGCAAAGCGCATCCGGCACGA 1 253 1 AACAAGCGCA 0.963735 -32 TGAAAATTTAATTCGTATCGCAAATTAAACGC 9 96 1 ATCGATCGCA 0.862368 -205 AATTAATGAGATTCAGATCACATATAAAGCCA 14 59 1 ATCAATCACA 0.707309 -71 TATGCCTGATGAGCGTAGCGCATCAGGCATTC 18 51 0 GACGAGCGCA 0.728662 -54 CAAAAATGTTATCCACATCACAATTTCGTTTT 22 43 1 ATCAATCACA 0.707309 -111 TACGCGTACTAACCAAATCGCGCAACGGAAGG 26 46 1 AACAATCGCG 0.828211 -255 TAAAACATTTAAACAGATCACAAAATCACCTA 27 70 0 AACAATCACA 0.895661 -201 TAGGCCTGATAAGCGTAGCGCATCAGGCAATT 35 48 0 AACGAGCGCA 0.962013 -182 TTTAAATGTGAATCGAATCACAATCGTTCGGG 37 152 0 AACGATCACA 0.891073 -91 GAAATTGGTTAACCACATCACAAGAATTTCAC 49 118 0 AACAATCACA 0.895661 -183 CCGGATGAACAACCAGACCGCAGCCGTGGCGT 49 211 0 AACAACCGCA 0.890042 -90 GAATTATTTGAACCAGATCGCATTACAGTGAT 51 116 1 AACAATCGCA 0.958942 -142 ACACACTTCGATACACATCACAATTAAGGAAA 51 165 0 ATCAATCACA 0.707309 -93 TAGGCCTGATAAGCGCAGCGCATCAGGCGTAA 52 21 0 AACGAGCGCA 0.962013 -106 AATGAAATAAAAACAAACCGCACTTTTATAGC 57 25 1 AACAACCGCA 0.890042 -78 CCATAATATAAAACGAATCACATTTGTGATAA 88 35 1 AACGATCACA 0.891073 -37 ** ** ****** Masking position 7 Map Score: 19.3268 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 78 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 12 AAAGCGCATCCGGCATTCAACGCCTGATGC 1 97 1 CGGCATTCAA 0.923928 -188 AAAGCGCATCCGGCATTCAACGCCTGATGC 1 182 1 CGGCATTCAA 0.923928 -103 ATAATGTGTGCGGCAATTCACATTTAATTT 15 151 1 CGGCAATTCA 0.891104 -122 CTTAACATCGCGGCAACTCAAGAAACGGCA 15 192 1 CGGCAACTCA 0.836742 -81 TATTACCAAACGGCAACCTAATCTAATCAG 17 209 0 CGGCAACCTA 0.798585 -47 AAGCATATTTCGGCAATCCAGAGACAGCGG 26 236 1 CGGCAATCCA 0.970619 -65 GTGCCGCATCCGGCAATCAATGCCTGATGC 39 34 0 CGGCAATCAA 0.968246 -267 TGTGCGCATCCGGCAATCAATGCCTGATGC 39 126 0 CGGCAATCAA 0.968246 -175 CGCGCATCCACGGCAATCAATGCCTGATGC 39 217 0 CGGCAATCAA 0.968246 -84 ACGCCGCATCCGGCATTTCACAGCA 44 6 0 CGGCATTTCA 0.765228 -148 ACGCCGCATTCGGCAACCAACGCCTGATGC 47 40 1 CGGCAACCAA 0.950244 -203 ********** Masking position 5 Map Score: 12.5489 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 129 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 GTCGGATGCGGCGCGAGCGCCTTATCCGAC 3 20 1 GCGCGAGCGC 0.938011 -46 ATGTGTGTAAACGTGAACGCAATCGATTAC 6 139 1 ACGTGAACGC 0.913353 -160 TCCTCCAGTTACGTGAACGCTACGCATTAT 21 151 0 ACGTGAACGC 0.913353 -25 GCCGGATGCGGCGTAAGCGCCTTATCCGGC 35 121 0 GCGTAAGCGC 0.947826 -109 GAATGCGGCTTCGTAAGCGCGG 37 3 0 TCGTAAGCGC 0.747986 -240 CCGTGGATGCGCGCGAGCGCCTTATCCGGC 39 234 1 GCGCGAGCGC 0.938011 -67 GCCGGATGCGGCGTGAACGCCTTGTCCGGC 44 22 1 GCGTGAACGC 0.933804 -132 GTCGGATAAGGCGTGAAAGCCTTATCCGTC 44 114 1 GCGTGAAAGC 0.828513 -40 GCCGAATGCGGCGTAAACGCCTTATCCGGC 47 24 0 GCGTAAACGC 0.92059 -219 GCCGGATGCGGCGTAAACGCCTTATCCGGC 47 115 0 GCGTAAACGC 0.92059 -128 GCCGGATAAGGCGTAGACGCATCCGGCAAA 52 73 1 GCGTAGACGC 0.815724 -54 ********** Masking position 2 Map Score: 12.5312 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 175 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 14 GTTTGCAACAAGGGCGAAAGTCAGTACAAT 6 99 1 AGGGCGAAAG 0.811359 -200 CATTATCTCAAGAGCAAATTCTGTCACTTC 10 228 1 AGAGCAAATT 0.740201 -61 TAAGCCTAATGGAGCGAATT 11 251 1 GGAGCGAATT 0.862028 -10 TACAAACAAGTGGGCAAATTTACCGCACAG 31 155 0 TGGGCAAATT 0.76655 -35 TTATCTGAAAGGGGCGAAAGCCCCTCTGAT 47 162 1 GGGGCGAAAG 0.839416 -81 TCTTTATGTAGGGGCGAATTACATTCGCCC 59 25 1 GGGGCGAATT 0.947582 -248 TTGAGATTATAGGGCGAATGTAATTCGCCC 59 36 0 AGGGCGAATG 0.929984 -237 TCTTTATGTAGGGGCGAATTACATTCGCCC 59 161 1 GGGGCGAATT 0.947582 -112 TTGTGATTATAGGGCGAATGTAATTCGCCC 59 172 0 AGGGCGAATG 0.929984 -101 AAACAATCATAGGGCAAATTGTCCTTACGT 59 200 1 AGGGCAAATT 0.891818 -73 GTAAATTATTGGAGCAAAAGAATTTCTTTT 60 151 1 GGAGCAAAAG 0.500313 -135 AGAATCTCAAAGAGCAAATTCTAAAATTGT 63 108 0 AGAGCAAATT 0.740201 -115 GTCAATTTGTAGAGCAAAATCCGCTCCAAC 63 171 0 AGAGCAAAAT 0.479869 -52 ATAAAACTTGGGGGCGTATTGTAGCTTGCA 69 37 1 GGGGCGTATT 0.592165 -161 TTACACCGTTTGAGCGAATGCGAAAATTAT 74 55 1 TGAGCGAATG 0.646457 -146 AAAAAGGCGGTGGGCAAATTGCTTAGTCGC 75 19 1 TGGGCAAATT 0.76655 -81 GTAATAAAGTAGGGCAAATTCAAAACCCTA 91 185 1 AGGGCAAATT 0.891818 -116 ********** Masking position 8 Map Score: 11.6411 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 207 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 TTACTATGGCTAAATGGTAAAAAACGAACTTCAG 15 21 0 TAATTAAAAA 0.742099 -252 AATCAGGCTGTTAATCATAAATAAGACCACGGGC 15 235 1 TAATTAAAAA 0.742091 -38 TTATTTATGTTTAAATAAAAACAAATAA 24 5 0 TAAAAAAAAA 0.809974 -94 AAAATTCTTATGAATTTAAAAAAAGCACATTGTT 33 47 1 TAATAAAAAA 0.809976 -143 ATTATCAAAATTAATCTAATAAAAAGCACATTGT 33 89 0 TAATAATAAA 0.529719 -101 TTTTTCGTCGTGAAACTAAAAAAACCAGGCGCGA 38 169 1 TAAAAAAAAA 0.809977 -132 ACCTTCGGCATAAAAGGAAAAGAAG 51 2 0 TAAAAAAAAA 0.809977 -256 GCTCGTAAAATGAAATAAAAACAAACCGCACTTT 57 17 1 TAAAAAAAAA 0.809976 -86 ATCAATAGATTAAATTTAATATAAAAAAGGAAAT 62 69 1 TAATAATAAA 0.529711 -28 ATGGTGATTTTCAATAAAATAAAAAACCTGTTGC 64 89 0 TAATAATAAA 0.529719 -84 TTAGGGAGTATAAATGCAAAAAAATGTGACATAA 68 231 0 TAATAAAAAA 0.809977 -70 AAGTATGAACTAAATCATAAAAAATTTTGCTTAT 81 92 1 TAATTAAAAA 0.742099 -116 TTCAATAAAATTAAAGTAAAATAACGAAATTGTG 82 76 1 TAAAAAAAAA 0.809973 -49 GCTCAGTCAATAAATGTAAAATAAATAAATTATT 89 92 0 TAATAAAAAA 0.809976 -84 AAAACCATAGTCAAAAATAAAGAATTTTTGCTAC 90 54 1 TAAATAAAAA 0.742099 -57 CTACAATAGGTAAAACATAAATAAAAGGAGGAAA 90 84 1 TAAATAAAAA 0.742099 -27 TTATTTTGGATAAAAACTAAACAAAAAATTCAAA 91 56 1 TAAATAAAAA 0.742099 -245 ATTGAGATTGTGAATAATAAATAAACTATTTAGC 94 13 1 TAATTAAAAA 0.742099 -146 GTATCCTTTTTCAAAGCAAAATAATCAAGAATAA 94 81 0 TAAAAAAAAA 0.809977 -78 TAATCAATAATTAAAAATATAAAACCAGAAAATT 94 121 0 TAAATATAAA 0.431941 -38 * *** **** ** Masking position 1 Map Score: 11.625 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 52 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887