AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icrp_ecoli_hinf_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 HI0054 109 uxu operon regulator (uxuR) #76 HI0055 27 mannonate dehydratase (uxuA) #77 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #78 HI0096 300 H. influenzae predicted coding region HI0096 #79 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #80 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #81 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #82 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #83 HI0144 45 glucose kinase, putative #84 HI0145 300 conserved hypothetical protein #85 HI0190 28 ferric uptake regulation protein (fur) #86 HI0191 96 flavodoxin (fldA) #87 HI0289 222 serine transporter (sdaC) #88 HI0291 74 H. influenzae predicted coding region HI0291 #89 HI0292 76 mercuric ion scavenger protein (merP) #90 HI0351 172 UDP-glucose 4-epimerase (galE) #91 HI0352 300 conserved hypothetical protein #92 HI0518 83 purine-nucleoside phosphorylase (deoD) #93 HI0519 98 transport protein, putative #94 HI0521 212 conserved hypothetical protein #95 HI0604 300 adenylate cyclase (cyaA) #96 HI0615_HI0616 197 HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA) #97 HI0618 26 glp protein, putative #98 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #99 HI0680 31 rarD protein, putative #100 HI0681 300 transcriptional activator (ilvY) #101 HI0685_HI0686 292 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #102 HI0687 99 conserved hypothetical protein #103 HI0688 94 H. influenzae predicted coding region HI0688 #104 HI0690 229 glycerol uptake facilitator protein (glpF) #105 HI0727.1 260 cyaY protein (cyaY) #106 HI0745 225 L-asparaginase II (ansB) #107 HI0819 37 galactokinase (galK) #108 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #109 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #110 HI0954 47 deoxyuridinetriphosphatase (dut) #111 HI0956 21 conserved hypothetical protein #112 HI0957 66 catabolite gene activator (crp) #113 HI1027 58 L-xylulose kinase (lyx) #114 HI1028 30 conserved hypothetical protein #115 HI1030 71 conserved hypothetical transmembrane protein #116 HI1031 175 conserved hypothetical protein #117 HI1116 110 deoxyribose-phosphate aldolase (deoC) #118 HI1164 300 outer membrane protein P5 (ompA) #119 HI1350 273 cytidine deaminase (cdd) #120 HI1678 300 kpsF protein (kpsF) #121 HI1713 158 phosphocarrier protein HPr (ptsH) #122 HI1714 70 conserved hypothetical protein Motif number 1 GGCGTTACATACCGGATGCGGCTAC 1 6 0 ACCGGATGCG 0.690676 -279 GGTATGTAACGCCTGATGCGACGCTGACGC 1 23 1 GCCTGATGCG 0.988963 -262 CAGCGTGTAGGCCAGATAAGACGCGTCAGC 1 45 0 GCCAGATAAG 0.526425 -240 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 76 1 GCCGGATAAG 0.975853 -209 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 GCCGGATGCG 0.993641 -194 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 108 1 GCCTGATGCG 0.988963 -177 CAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 GCCTGATAAG 0.958633 -155 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 161 1 GCCGGATAAG 0.975853 -124 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 GCCGGATGCG 0.993641 -109 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 193 1 GCCTGATGCG 0.988963 -92 CAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 GCCTGATAAG 0.958633 -70 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 246 1 GCCGGATAAG 0.975853 -39 ACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GCCGGATGCG 0.993641 -24 GCAATCAATGTCGGATGCGGCGCGAGCGC 3 10 1 GTCGGATGCG 0.856322 -56 TGATATGTTGGTCGGATAAGGCGCTCGCGC 3 30 0 GTCGGATAAG 0.606512 -36 AGCCTGGGGTGCCTAATGAGTGAGCTAACT 5 30 0 GCCTAATGAG 0.54785 -93 TGCTGACCTTGCCGGAGGCGGCCTTAGCAC 17 19 1 GCCGGAGGCG 0.908389 -242 GGTAGTCACTGCCCGATACGGACTTTACAT 26 79 1 GCCCGATACG 0.754297 -177 ACTATAGAATGCCTGATGCGCTACGCTCAT 27 45 1 GCCTGATGCG 0.988963 -60 AGTCCTGTATGCCTGATGAGCGTAGCGCAT 27 60 0 GCCTGATGAG 0.979628 -45 ATGCAAAACTGCCTGATGCGCTACGCTTAT 31 33 1 GCCTGATGCG 0.988963 -150 ATCTTTCCAGGCCTGATAAGCGTAGCGCAT 31 48 0 GCCTGATAAG 0.958633 -135 CGTTTTCCATGCCGGATGCGGCGTAAACAC 31 102 0 GCCGGATGCG 0.993641 -81 AAAGTTAGTTGCCGGATGCAAGCATGATAA 32 95 0 GCCGGATGCA 0.686895 -66 TATGCAAGTTGCCGGAGGCGTGCTCCGGCA 34 17 0 GCCGGAGGCG 0.908389 -45 GGGGTTAATTGCCTGATGCGCTACGCTTAT 50 42 1 GCCTGATGCG 0.988963 -188 CATCCTGTAGGCCTGATAAGCGTAGCGCAT 50 57 0 GCCTGATAAG 0.958633 -173 GTTCTTGTAGGCCGGATAAGGCGCTTACGC 50 111 1 GCCGGATAAG 0.975853 -119 GAGGGGCAGCGCCGGATGCGGCGTAAGCGC 50 131 0 GCCGGATGCG 0.993641 -99 GTCTATCAACGCCTGATTAGTCCGCTACTC 54 25 1 GCCTGATTAG 0.545338 -199 CTTTTCGTAGGGCGGATAAGCACCGCGCAT 55 60 1 GGCGGATAAG 0.624613 -46 TGCTTTGTGTGGCGGATGCGCGGTGCTTAT 55 75 0 GGCGGATGCG 0.86548 -31 GCCTGATAAGACGCGACAGC 58 1 1 GCCTGATAAG 0.958633 -300 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 23 0 GCCTGATGCG 0.988963 -278 GGCATTGATTGCCGGATGCGGCACAAGTGC 58 40 1 GCCGGATGCG 0.993641 -261 CGACCTGTAGGCCGGATAAGGCACTTGTGC 58 60 0 GCCGGATAAG 0.975853 -241 ACAGTTGTAGGCCTGATAAGACGCGACAGC 58 93 1 GCCTGATAAG 0.958633 -208 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 115 0 GCCTGATGCG 0.988963 -186 GGCATTGATTGCCGGATGCGCACAAGTCGC 58 132 1 GCCGGATGCG 0.993641 -169 CGACCTGTAGGCCTGATAAGCGACTTGTGC 58 151 0 GCCTGATAAG 0.958633 -150 ATAGTTGTAGGCCTGATAAGACGCGACAGC 58 184 1 GCCTGATAAG 0.958633 -117 GGCAATCAATGCCTGATGCGACGCTGTCGC 58 206 0 GCCTGATGCG 0.988963 -95 CGACCCGTAGGCCGGATAAGGCGCTCGCGC 58 244 0 GCCGGATAAG 0.975853 -57 GCTGTGAAATGCCGGATGCGGCGTGAACGC 64 12 1 GCCGGATGCG 0.993641 -142 ACGTATGTAGGCCTGATAAGACGCGTCAGC 64 65 1 GCCTGATAAG 0.958633 -89 GACAACAACTGCCTGATGCGACGCTGACGC 64 87 0 GCCTGATGCG 0.988963 -67 GGCAGTTGTTGTCGGATAAGGCGTGAAAGC 64 104 1 GTCGGATAAG 0.606512 -50 CAAAACCTGGGCCGGATAAGGCGTTTACGC 67 14 1 GCCGGATAAG 0.975853 -229 GGCGTTGGTTGCCGAATGCGGCGTAAACGC 67 34 0 GCCGAATGCG 0.797461 -209 GGCAACCAACGCCTGATGCGACGCTTGCGC 67 51 1 GCCTGATGCG 0.988963 -192 GCCGTTGTAGGCCTGATAAGACGCGCAAGC 67 73 0 GCCTGATAAG 0.958633 -170 TCAAATGTAGGCCGGATAAGGCGTTTACGC 67 105 1 GCCGGATAAG 0.975853 -138 CTGTTTTTATGCCGGATGCGGCGTAAACGC 67 125 0 GCCGGATGCG 0.993641 -118 TTCACTTTGATCCTGATGCGTTTGCCACCA 71 65 1 TCCTGATGCG 0.561477 -193 GATGCTTTACGCCTGATGCGCTGCGCTTAT 72 15 1 GCCTGATGCG 0.988963 -112 CGTCTCGTAGGCCTGATAAGCGCAGCGCAT 72 30 0 GCCTGATAAG 0.958633 -97 CTACCCGTAGGCCGGATAAGGCGTAGACGC 72 63 1 GCCGGATAAG 0.975853 -64 GGCGGCTTTTGCCGGATGCGTCTACGCCTT 72 80 0 GCCGGATGCG 0.993641 -47 ********** Masking position 6 Map Score: 202.654 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 266 Number in noncoding regions = 638 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 AATCGCAGCGTGTAGGCCAGATAAGACGCG 1 50 0 TGTAGGCCAG 0.907448 -235 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 71 1 TGTAGGCCGG 0.993327 -214 AATCGCAGCGCGTAGGCCTGATAAGACGCG 1 135 0 CGTAGGCCTG 0.983342 -150 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 156 1 TGTAGGCCGG 0.993327 -129 AATCGCAGCGTGTAGGCCTGATAAGACGCG 1 220 0 TGTAGGCCTG 0.989263 -65 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 241 1 TGTAGGCCGG 0.993327 -44 TGCGTCGAACCGTTGGCCGGAGAGGGTGCT 17 44 0 CGTTGGCCGG 0.837117 -217 CTATGCTTGATGTATGCCTGAGTTCGCTGC 22 107 1 TGTATGCCTG 0.849057 -132 GCGGAAGTCCTGTATGCCTGATGAGCGTAG 27 65 0 TGTATGCCTG 0.849057 -40 TGATGCATCCTGTAGGCCTGATAAGCGTAG 50 62 0 TGTAGGCCTG 0.989263 -168 TGCACGTTCTTGTAGGCCGGATAAGGCGCT 50 106 1 TGTAGGCCGG 0.993327 -124 TTTTTCTTTTCGTAGGGCGGATAAGCACCG 55 55 1 CGTAGGGCGG 0.824307 -51 GTTGCCGACCTGTAGGCCGGATAAGGCACT 58 65 0 TGTAGGCCGG 0.993327 -236 CGGCAACAGTTGTAGGCCTGATAAGACGCG 58 88 1 TGTAGGCCTG 0.989263 -213 ATTGCCGACCTGTAGGCCTGATAAGCGACT 58 156 0 TGTAGGCCTG 0.989263 -145 CGGCAATAGTTGTAGGCCTGATAAGACGCG 58 179 1 TGTAGGCCTG 0.989263 -122 ATGCACGACCCGTAGGCCGGATAAGGCGCT 58 249 0 CGTAGGCCGG 0.989624 -52 CCACGATGCTTGTAGGCATGCTGTAAACTT 61 229 0 TGTAGGCATG 0.761334 -72 GTTTCGGTTTTGTAGGCCGGACAAGGCGTT 64 37 0 TGTAGGCCGG 0.993327 -117 CCGAAACGTATGTAGGCCTGATAAGACGCG 64 60 1 TGTAGGCCTG 0.989263 -94 TGACAGCCGTTGTAGGCCTGATAAGACGCG 67 78 0 TGTAGGCCTG 0.989263 -165 GGCTGTCAAATGTAGGCCGGATAAGGCGTT 67 100 1 TGTAGGCCGG 0.993327 -143 AGATACGTCTCGTAGGCCTGATAAGCGCAG 72 35 0 CGTAGGCCTG 0.983342 -92 CGTATCTACCCGTAGGCCGGATAAGGCGTA 72 58 1 CGTAGGCCGG 0.989624 -69 CTATTCATATCGTAGGCTGGACTTTAGCCC 82 233 0 CGTAGGCTGG 0.767554 -53 ********** Masking position 3 Map Score: 83.199 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 32 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 GCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTA 1 29 0 AGCGCGCGCA 0.997227 -256 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 114 0 AGCGCGCGCA 0.997227 -171 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTG 1 199 0 AGCGCGCGCA 0.997227 -86 TGGTCGGATAAGGCGCTCGCGCCGCATCCGACATTG 3 16 0 AGCGCGCGCA 0.997227 -50 CGGCGTAGACATGAGTCTACGCCGCATCACA 13 6 0 AGAGCGCGCA 0.922694 -283 ATTAAAAACCCAGCGTCCGCGTCGCTTTCCGCGCGT 15 19 1 CGCGCGCGCT 0.872994 -52 TTGTGACGGAAAACGAACGCCACGCAAAGCTGACCG 19 79 0 AACGCCCGCA 0.801693 -50 GATACTAAAGACGCCATATTGCCGCAGAGTCAGGGA 21 160 1 AGCCTGCGCA 0.872167 -141 AGGCGGGATAAGGTGTTTACGCCGCATCCGGCATGG 31 90 1 AGTGCGCGCA 0.922694 -93 GTTCCGGTTTACACCCTGCCGTCGCTGTGCTGCAAT 32 42 0 AACCCGCGCT 0.688831 -119 AGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTG 50 119 1 AGCGCGCGCA 0.997227 -111 CACGATTCCAAAACCCCGCCGGCGCAAACCGGGCGG 51 25 1 AACCCGCGCA 0.898826 -81 CACTGAAAGTATACGTGTTCCGCGCAGAACGCGCAA 52 72 0 AACGCCCGCA 0.801693 -229 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 11 1 AGCGCGCGCA 0.997227 -290 AGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATC 58 46 0 AGCATGCGCA 0.697464 -255 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 103 1 AGCGCGCGCA 0.997227 -198 TGATTGCCGGATGCGCACAAGTCGCTTATCAGGCCT 58 137 1 AGCGAGCGCT 0.76427 -164 GCCTGATAAGACGCGACAGCGTCGCATCAGGCATTG 58 194 1 AGCGCGCGCA 0.997227 -107 AGGCCGGACAAGGCGTTCACGCCGCATCCGGCATTT 64 18 0 AGCGCGCGCA 0.997227 -136 GCCTGATAAGACGCGTCAGCGTCGCATCAGGCAGTT 64 75 1 AGCGCGCGCA 0.997227 -79 CCTTGCCCCTACGCCCCACCGTCGCTTTGTGTGATC 65 255 0 AGCCCGCGCT 0.948967 -110 GGGCCGGATAAGGCGTTTACGCCGCATTCGGCAACC 67 22 1 AGCGCGCGCA 0.997227 -221 GCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTG 67 57 0 AGCGCGCGCA 0.997227 -186 AGGCCGGATAAGGCGTTTACGCCGCATCCGGCATAA 67 113 1 AGCGCGCGCA 0.997227 -130 GACATAACAAAGGCGGAGTCAACGCTCCGCCCAAAT 74 14 0 AGCGCACGCT 0.756236 -43 TTAGCAGAAAAAGCAAGTGTGCCGCAAGGGTAGCAA 79 192 0 AGCATGCGCA 0.697464 -81 * *** ** **** Masking position 13 Map Score: 73.5069 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 199 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 GCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCA 5 13 1 TTGTGATCAC 0.966678 -110 TGACGGGGAAAGATGTTGCGGGACGCACAAAATCGTCC 8 21 0 ATGTTGGCAC 0.366389 -278 AACGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 12 123 1 TTGTGATCAC 0.966678 -178 AGAGTCAGGGAGATGTGAGCCAGCTCACCATAAAAAAG 21 185 1 ATGTGATCAC 0.96482 -116 GCTGATTTCTTAATGTGATCGGTAGCACGTTTTACGAA 22 171 1 TTGTGAGCAC 0.909058 -68 GTTGCATAATTAATGAGATTCAGATCACATATAAAGCC 23 52 1 TTGAGATCAC 0.772304 -78 TTCATAAATTAAATGTGAATTGCCGCACACATTATTAA 24 148 0 ATGTGAGCAC 0.904307 -125 TCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTT 35 36 1 ATGTTATCAC 0.801975 -118 TTGAAAGTTAATTTGTGAGTGGTCGCACATATCCTGTT 38 107 1 ATGTGAGCAC 0.904307 -82 TTGCATTTTAAGAGGTGATTTTGATCACGGAATAAAAA 40 120 1 AGGTGATCAC 0.608149 -151 ACATTATTGATTCTGTTGATATGATCACGTTATACCCA 41 13 0 TTGTTGTCAC 0.639656 -179 ATAAACGCCATAATGTTATACATATCACTCTAAAATGT 44 99 0 TTGTTATCAC 0.810743 -91 ATCAAAACAAAAATGTGACACTACTCACATTTAAATGC 49 22 1 ATGTGATCAC 0.96482 -279 TACACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 49 95 1 TTGTGATCAC 0.966678 -206 CGACGGCCTTTTGTGTGATATCAATCACATAAATATAG 49 143 0 TTGTGATCAC 0.966678 -158 ACCTTGTAGATACTGCGAAATCTGGCACTGAATCGGTT 49 192 0 TTGCGAGCAC 0.707076 -109 AGCAAGGGAAAATTGAGGGGTTGATCACGTTTTGTACT 52 196 0 ATGAGGTCAC 0.570583 -105 GAAATTGTTTAAATGTGAATCGAATCACAATCGTTCGG 56 153 0 ATGTGATCAC 0.96482 -90 TCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACC 57 129 1 ATGTTATCAC 0.801975 -172 GTGTTACCGTTGATGTTGGCGGAATCACAGTCATGACG 57 250 1 TTGTTGTCAC 0.639656 -51 AATTTTCAGGAAATGCGGTGAGCATCACATCACCACAA 59 126 1 ATGCGGTCAC 0.732928 -162 CAATTCAGCAAATTGTGAACATCATCACGTTCATCTTT 59 161 1 ATGTGATCAC 0.96482 -127 CATTTTCGATTGATGTGGATTATGTCACCAGGAGAAGG 61 51 0 TTGTGGTCAC 0.923201 -250 TTCATGAAAATTCTGTAACCGTTTTCACGCGCTATCTG 62 60 1 TTGTAATCAC 0.692037 -96 TCGCCACGATTTTTGCAAGCAACATCACGAAATTCCTT 65 174 0 TTGCAATCAC 0.351761 -191 GAATTGGCGGTAATGTGGAGATGCGCACATAAAATCGC 65 208 0 TTGTGGGCAC 0.805529 -157 TTACCGCCAATTCTGTAACAGAGATCACACAAAGCGAC 65 233 1 TTGTAATCAC 0.692037 -132 GGTCAACCATTGTTGCGATGAATGTCACATCCTCTGAT 69 30 1 TTGCGATCAC 0.875083 -271 TTTATTTCCAAAATGAGAAGTTGATCACATTTATGAAA 84 117 1 ATGAGATCAC 0.762277 -184 TATTTTCTAAAACTGTGATCTTCCTCACGTTTTCAAAA 94 130 1 ATGTGATCAC 0.96482 -83 AAATGCAAAAAAATGTGACATAAATCACAATTTTTCGA 95 216 0 ATGTGATCAC 0.96482 -85 CGGTGTAAAGATTTGTGAAACACTTCACATTTTTGATT 101 117 0 ATGTGATCAC 0.96482 -176 AAGAAAGCGATTTTGTGATATTGATCACAATAATTTTC 101 168 0 TTGTGATCAC 0.966678 -125 TATTTTCTTATTTTGTGACAAAGATCACGGTTTATTTA 108 123 1 TTGTGATCAC 0.966678 -85 TATTCATTAAAACTGTGATCTTGATCACTTATTTGATA 119 162 0 ATGTGATCAC 0.96482 -112 * ***** **** Masking position 17 Map Score: 59.0283 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 5 TAGGCCAGATAAGACGCGTCAGCGTCGCATCAG 1 35 0 AAGACGCGGC 0.989257 -250 TAGGCCTGATAAGACGCGCCAGCGTCGCATCAG 1 120 0 AAGACGCGGC 0.989257 -165 TAGGCCTGATAAGACGCGCCAGCGTCGCATCAG 1 205 0 AAGACGCGGC 0.989257 -80 TTGGTCGGATAAGGCGCTCGCGCCGCATCCGAC 3 20 0 AAGGCGCTGC 0.987007 -46 TATCTGAAAAAAGACGCGGTTTCATGCCTGCAT 17 73 0 AAGACGCGTC 0.865907 -188 TAGGCCGGATAAGGCGCTTACGCCGCATCCGGC 50 118 1 AAGGCGCTGC 0.987007 -112 GCCTGATAAGACGCGACAGCGTCGCATCAG 58 8 1 AAGACGCGGC 0.989257 -293 TAGGCCGGATAAGGCACTTGTGCCGCATCCGGC 58 50 0 AAGGCACTGC 0.742157 -251 TAGGCCTGATAAGACGCGACAGCGTCGCATCAG 58 100 1 AAGACGCGGC 0.989257 -201 TAGGCCTGATAAGACGCGACAGCGTCGCATCAG 58 191 1 AAGACGCGGC 0.989257 -110 TAGGCCGGATAAGGCGCTCGCGCGCATCCACGG 58 234 0 AAGGCGCTGC 0.987007 -67 ATTTCGTACGAAGGCGCGAAATCATACAGAAAT 63 98 1 AAGGCGCGTC 0.93241 -105 TAGGCCGGACAAGGCGTTCACGCCGCATCCGGC 64 22 0 AAGGCGTTGC 0.934989 -132 TAGGCCTGATAAGACGCGTCAGCGTCGCATCAG 64 72 1 AAGACGCGGC 0.989257 -82 GTTGTCGGATAAGGCGTGAAAGCCTTATCCGTC 64 111 1 AAGGCGTGGC 0.973853 -43 TGGGCCGGATAAGGCGTTTACGCCGCATTCGGC 67 21 1 AAGGCGTTGC 0.934989 -222 TAGGCCTGATAAGACGCGCAAGCGTCGCATCAG 67 63 0 AAGACGCGGC 0.989257 -180 TAGGCCGGATAAGGCGTTTACGCCGCATCCGGC 67 112 1 AAGGCGTTGC 0.934989 -131 CATTATCTGAAAGGGGCGAAAGCCCCTCTGATT 67 160 1 AAGGGGCGGC 0.916997 -83 TAGGCCGGATAAGGCGTAGACGCATCCGGCAAA 72 70 1 AAGGCGTAGC 0.693927 -57 CAGCACAAAGAAGCCGCTACGGCT 79 259 1 AAGCCGCTGC 0.881174 -14 ACTGAATTAGAAGGCGCGGTTGCTGGTACGGAT 81 99 1 AAGGCGCGGC 0.994942 -174 ******** ** Masking position 2 Map Score: 54.6139 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 99 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 TATCTCCTGCTGAACGCCCTTTTTATCCAGC 21 133 0 TAACGCCCTT 0.8404 -168 TTCCATTAACCGCCCCTGACGATGCTC 35 7 1 TACCGCCCCT 0.81624 -147 CTCAGTAAGCTGCCCGCCCTTTTTTACACTT 46 156 1 TCCCGCCCTT 0.906017 -34 GTGGTTATGTTAAACGCCCTTCTCCGTGTGA 47 51 1 TAACGCCCTT 0.8404 -47 CTTTCCTTATTTACCGCGCTTTTCCGCACCT 53 145 0 TACCGCGCTT 0.897391 -156 GGCGGTCAACTGACCGCCCTTATTTTAGCGA 55 23 0 TACCGCCCTT 0.983658 -83 GGCGGTCAGTTGACCGCCTTTTTTCTTTTCG 55 36 1 TACCGCCTTT 0.872717 -70 GATGTGATGCTCACCGCATTTCCTGAAAATT 59 126 0 TACCGCATTT 0.9038 -162 AAATAAAAACAAACCGCACTTTTATAGCACT 77 29 1 AACCGCACTT 0.828851 -74 TCCGCAGAATTGACCGCACTTTGTGTTGAAA 78 234 1 TACCGCACTT 0.988021 -67 AGATAGAAAATTGCCGCACTTATAATGATCC 82 189 1 TGCCGCACTT 0.950596 -97 TCGCTGAAAATTACCGCACTTTTTATAAAAA 87 62 1 TACCGCACTT 0.988021 -161 CGGTCATTTTTTACCGCACTTTTTAATTGAT 92 20 0 TACCGCACTT 0.988021 -64 CGGTAAAAAATGACCGCACTTTATTCATTTT 92 35 1 TACCGCACTT 0.988021 -49 CGGCGAATTTTCACCGCACTTTTTGTAAACG 93 12 0 TACCGCACTT 0.988021 -87 CACAAAAAATTGACCGCACTTTTAGGAAGAT 96 85 1 TACCGCACTT 0.988021 -113 ACCAGAAAACTAACCGCACTTTTTA 100 5 0 TACCGCACTT 0.988021 -296 CGCTAAATTTTACCCGCACTTTAAATTGAAG 100 49 1 TCCCGCACTT 0.929624 -252 TTGTTAATTTTGGCCGCACTTCCCTACAATG 101 220 1 TGCCGCACTT 0.950596 -73 AGCAATTTGCCCACCGCCTTTTTTAAGCTAA 102 11 0 CACCGCCTTT 0.677523 -89 TGGAGAATTGCTAACGCCCTTAATAAAACCA 103 65 0 CAACGCCCTT 0.617375 -30 CTCTTCATTTCAACCGCACTTCTAAGGAGTG 104 205 1 CACCGCACTT 0.961938 -25 GCTTTATAATTTGCCGCATTTTATCAGATTT 105 225 1 TGCCGCATTT 0.686696 -36 GGCTCAAGTATAACCGCACTTGGGTTATCTT 106 44 1 TACCGCACTT 0.988021 -182 TATAGGATAATAAGCGCACTTTTGAACGTTC 118 112 1 TAGCGCACTT 0.80888 -189 GGGATTTTATTGACCGCACTAGTGATTGCCC 120 241 0 TACCGCACTA 0.804174 -60 AGGGAAAAAACGACCGCACTTTT 122 58 1 CACCGCACTT 0.961938 -13 * ********* Masking position 6 Map Score: 52.3155 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 80 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 GGCCAGATAAGACGCGTCAGCGTCGCATCAGG 1 34 0 GCGCGCAGCG 0.993868 -251 GGCCTGATAAGACGCGCCAGCGTCGCATCAGG 1 119 0 GCGCGCAGCG 0.993868 -166 GGCCTGATAAGACGCGCCAGCGTCGCATCAGG 1 204 0 GCGCGCAGCG 0.993868 -81 TTCGCGGTATGGCATGATAGCGCCCGGAAGAG 6 34 1 GCATGTAGCG 0.534043 -43 AGCGCGATGAGTCACGCCAACGCCCACGCGCG 15 48 0 GCACGCAACG 0.842305 -23 AATGACGTACGAAACGTCAGCGGTCAACACCC 25 145 1 GAACGCAGCG 0.664809 -156 GCATGATAAGGCCGTGGCTGCGGAAAGTTCCG 32 72 0 GCGTGCTGCG 0.923345 -89 AGCGCCGGATGCGGCGTAAGCGCCTTATCCGG 50 122 0 GGGCGAAGCG 0.720806 -108 GCCTGATAAGACGCGACAGCGTCGCATCAGG 58 10 1 GCGCGCAGCG 0.993868 -291 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 58 102 1 GCGCGCAGCG 0.993868 -199 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 58 193 1 GCGCGCAGCG 0.993868 -108 GGCATTGATTGCCGTGGATGCGCGCGAGCGCC 58 223 1 GCGTGATGCG 0.723015 -78 TGGAATAAATGGCGCGATAACGCTCATTTTAT 61 143 1 GCGCGTAACG 0.715444 -158 GGCCTGATAAGACGCGTCAGCGTCGCATCAGG 64 74 1 GCGCGCAGCG 0.993868 -80 GGCCTGATAAGACGCGCAAGCGTCGCATCAGG 67 62 0 GCGCGAAGCG 0.972318 -181 CCGATGCAACGCCACGGCTGCGGTCTGGTTGT 69 203 1 GCACGCTGCG 0.923345 -98 TATCCACCGGCATGGCTGCGCGCCGTGCCG 70 9 1 GCATGCTGCG 0.748246 -72 AGAGCAGACCGCCGTGTAAACGGTAAGGGTGA 120 46 0 GCGTGAAACG 0.536497 -255 * **** ***** Masking position 6 Map Score: 36.7551 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 330 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TAGCCGCATCCGGTATGTAACGCCTGATGCGACGCT 1 12 1 CGGTATGCCG 0.673898 -273 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 97 1 CGGCACGCCG 0.995725 -188 AAAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 182 1 CGGCACGCCG 0.995725 -103 CGCGAAATACGGGCAGACATGGCCTGCCCGGTTATT 4 12 0 GGGCACGCCG 0.960112 -40 ACGAGCAGGACTGCACACTGTGCTACATGAAAGTGG 14 15 0 CTGCACGCTC 0.454109 -125 CCAGGCTTGACGCTATCCGCTGCCGGGATTTATTCA 16 59 0 CGCTACGCCG 0.700611 -126 CCGAGTTTTTCTGCAAGCCAGGCTTGACGCTATCCG 16 76 0 CTGCACGCTG 0.840384 -109 GTCGGTAGTGCTGACCTTGCCGGAGGCGGCCTT 17 8 1 GTGCTCGCCG 0.508726 -253 CACAAGGAAGCGGTAGTCACTGCCCGATACGGACTT 26 68 1 CGGTACGCCG 0.976564 -188 TCAACTATCTCTGTAACCCTTGCCCGTAAATTC 45 52 1 CTGTACGCCG 0.903614 -23 GTTAATGTGGCGGCAGAGGTAGCCGGACCTTGTAGA 49 220 0 CGGCAGGCCG 0.978673 -81 ATCCTCCACCCGGCGCGCCATGCTGGTTTCCACTGG 53 81 1 CGGCGCGCTG 0.875568 -220 CTTATTACAACGGCGTGAAACGCCTGTCAGGATCCA 57 37 0 CGGCGAGCCG 0.897698 -264 GTGCCGCATCCGGCAATCAATGCCTGATGCGACGCT 58 28 0 CGGCACGCCG 0.995725 -273 TGTGCGCATCCGGCAATCAATGCCTGATGCGACGCT 58 120 0 CGGCACGCCG 0.995725 -181 CGCGCATCCACGGCAATCAATGCCTGATGCGACGCT 58 211 0 CGGCACGCCG 0.995725 -90 AAACCGTAATCTGCAAGGCGTGCCGC 61 1 0 CTGCAGGCCC 0.619949 -300 ACATACGTTTCGGTTTTGTAGGCCGGACAAGGCGTT 64 37 0 CGGTTGGCCG 0.610895 -117 ACGCCTTATCCGACAACAACTGCCTGATGCGACGCT 64 92 0 CGACAAGCCG 0.525121 -62 ACGCCGCATTCGGCAACCAACGCCTGATGCGACGCT 67 40 1 CGGCACGCCG 0.995725 -203 ACCGGCATGGCTGCGCGCCGTGCCGGTTCCTTCTTC 70 16 1 CTGCGCGCCG 0.940316 -65 TAGACGCATCCGGCAAAAGCCGCCTCATACTCTTTT 72 86 1 CGGCAAGCCC 0.82178 -41 CACTGGTCGTCGGCTCACGCCGCCCGGACGTTATCC 120 84 1 CGGCTCGCCG 0.978036 -217 ***** * *** * Masking position 12 Map Score: 38.4731 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 823 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 TGACGCCGTGCAAATAATCAATGTGGACTTTT 2 165 0 CATAATCAAT 0.797431 -136 TGTGCCGCATCCGGCAATCAATGCCTGATGCG 58 33 0 CGCAATCAAT 0.939416 -268 TTGTGCGCATCCGGCAATCAATGCCTGATGCG 58 125 0 CGCAATCAAT 0.939416 -176 AATCAATCAATCAATCAATCAATCA 91 4 1 CACAATCAAT 0.973457 -297 ATCAATCAATCAATCAATCAATCAATCAATCA 91 16 1 CACAATCAAT 0.973457 -285 ATCAATCAATCAATCAATCAATCAATCAATCA 91 28 1 CACAATCAAT 0.973457 -273 ATCAATCAATCAATCAATCAATCAATCAATCA 91 40 1 CACAATCAAT 0.973457 -261 ATCAATCAATCAATCAATCAATCAATCAATCA 91 52 1 CACAATCAAT 0.973457 -249 ATCAATCAATCAATCAATCAATCAATCAATCA 91 68 1 CACAATCAAT 0.973457 -233 ATCAATCAATCAATCAATCAATCAATCAATCA 91 80 1 CACAATCAAT 0.973457 -221 ATCAATCAATCAATCAATCAATCAATCAATCA 91 92 1 CACAATCAAT 0.973457 -209 ATCAATCAATCAATCAATCAATCAAAGTCTGT 91 104 1 CACAATCAAT 0.973457 -197 TAAGAAAGCTCAGTCAATAAATGTAAAATAAA 116 101 0 CGCAATAAAT 0.624683 -75 ACTATCGCGGCTAACAATAAATTTTGATTTAA 119 209 1 CACAATAAAT 0.797431 -65 AATGCTACCTCGACTAATCAATAATTAAAAAT 121 137 0 CATAATCAAT 0.797431 -22 * * ******** Masking position 6 Map Score: 26.3486 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 7 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 82 0 TGCGCTGCTA 0.984573 -203 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 167 0 TGCGCTGCTA 0.984573 -118 TCGTGCCGGATGCGCTTTGCTTATCCGGCCTAC 1 252 0 TGCGCTGCTA 0.984573 -33 AAACCCAGCGTCCGCGTCGCTTTCCGCGCGTGG 15 24 1 TCCGCCGCTT 0.767076 -47 CTGAGTTCGCTGCGCATTGCGTAATGCCGGGGA 22 124 1 TGCGCTGCTA 0.858774 -115 ACATCAAAAATGCGCGACGCATCGCAAATT 23 8 0 TGCGCCGCTC 0.985158 -122 GAATGCCTGATGCGCTACGCTCATCAGGCATAC 27 51 1 TGCGCCGCCA 0.942936 -54 AACTGCCTGATGCGCTACGCTTATCAGGCCTGG 31 39 1 TGCGCCGCTA 0.991587 -144 AATTGCCTGATGCGCTACGCTTATCAGGCCTAC 50 48 1 TGCGCCGCTA 0.991587 -182 ACTCCAAACCTGCGCAATGCCTCAATTCCGTAG 54 90 0 TGCGCTGCTC 0.97289 -134 GTGTGGCGGATGCGCGGTGCTTATCCGCCCTAC 55 66 0 TGCGCTGCTA 0.980192 -40 AATTTTTCGATCCGCCTCGCATCGTGAGCGGT 62 10 0 TCCGCCGCTC 0.929004 -146 TTACGCCTGATGCGCTGCGCTTATCAGGCCTAC 72 21 1 TGCGCCGCTA 0.991587 -106 ***** *** ** Masking position 1 Map Score: 25.9823 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 49 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 GTAGGCCGGATAAGCAAAGCGCATCCGGCATT 1 82 1 TAAGCAGCGC 0.984645 -203 TTATCAGGCCTACGCGCTGCGATTTTGTAGGC 1 141 1 TACGCGGCGA 0.826553 -144 GTAGGCCGGATAAGCAAAGCGCATCCGGCATT 1 167 1 TAAGCAGCGC 0.984645 -118 GTAGGCCGGATAAGCAAAGCGCATCCGGCACG 1 252 1 TAAGCAGCGC 0.984645 -33 CTTTATCTCAAAAGCGTTGCGCCTTTGTTGTA 9 64 0 AAAGCGGCGC 0.926937 -27 AATATTGCCCTGAGCAAGGAGCCAGGGCAGGG 11 18 0 TGAGCAGAGC 0.680739 -42 TCCCCGGCATTACGCAATGCGCAGCGAACTCA 22 125 0 TACGCAGCGC 0.952962 -114 GTATGCCTGATGAGCGTAGCGCATCAGGCATT 27 52 0 TGAGCGGCGC 0.983656 -53 CCAGGCCTGATAAGCGTAGCGCATCAGGCAGT 31 40 0 TAAGCGGCGC 0.991682 -143 GTAGGCCTGATAAGCGTAGCGCATCAGGCAAT 50 49 0 TAAGCGGCGC 0.991682 -181 GTAGGGCGGATAAGCACCGCGCATCCGCCACA 55 66 1 TAAGCAGCGC 0.984645 -40 GTAGGCCTGATAAGCGCAGCGCATCAGGCGTA 72 22 0 TAAGCGGCGC 0.991682 -105 TTCGTCTGTTTGAGCGTAGCGAGTTCAGAAAA 100 138 1 TGAGCGGCGA 0.88392 -163 ****** **** Masking position 5 Map Score: 20.6027 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 72 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 TCTGTAATCAGATTGTTAGATCATCTGCTAC 12 57 1 GATTGTAGAT 0.865568 -244 TAAAAACATGAATTGTTTGATTTCGCGCATA 24 52 1 AATTGTTGAT 0.799404 -221 TTGATTGATTGATTGATTGATT 91 2 0 GATTGTTGAT 0.983741 -299 TTGATTGATTGATTGATTGATTGATTGATTG 91 14 0 GATTGTTGAT 0.983741 -287 TTGATTGATTGATTGATTGATTGATTGATTG 91 26 0 GATTGTTGAT 0.983741 -275 TTGATTGATTGATTGATTGATTGATTGATTG 91 38 0 GATTGTTGAT 0.983741 -263 TTGATTGATTGATTGATTGATTGATTGATTG 91 58 0 GATTGTTGAT 0.983741 -243 TTGATTGATTGATTGATTGATTGATTGATTG 91 70 0 GATTGTTGAT 0.983741 -231 TTGATTGATTGATTGATTGATTGATTGATTG 91 82 0 GATTGTTGAT 0.983741 -219 TTGATTGATTGATTGATTGATTGATTGATTG 91 94 0 GATTGTTGAT 0.983741 -207 GACAGACTTTGATTGATTGATTGATTGATTG 91 106 0 GATTGTTGAT 0.983741 -195 ATTATTAGTGGATAGCTTGATATTTTTCTTA 95 62 0 GATAGTTGAT 0.925136 -239 TGTTAGCCGCGATAGTTTGATTAAATATTCA 119 194 0 GATAGTTGAT 0.925136 -80 ***** ***** Masking position 2 Map Score: 25.0736 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 TCCGGGTGCGTGTTGTGTTTGTTTTTATGCAAGTTGCC 34 34 0 TTTTTTTTTT 0.880733 -28 GCACATATCCTGTTCATTTCATTTTGATACACTTCATG 38 131 1 TTTTTTTTTT 0.880733 -58 ATTTAGAATCTCTTCACTTGCTTTTTTTCTGCTCTGTT 40 228 1 TTTTTTTTTT 0.880733 -43 ATGTGCTTTTTATTAGATTAATTTTGATAATCAATAAT 46 92 1 TTTTTTTTTT 0.880733 -98 GTGCGGTTTGTTTTTATTTCATTTTACGAGCTTAAAA 77 10 0 TTTTTTTTTG 0.603855 -93 CGTAAAACTATTTTAAATTTGTTTTTTTACTCTTAGAA 84 76 0 TTTTTTTTTT 0.880733 -225 AATTTTTCCTTATTTTTAATAATGAATAAA 92 64 0 TTTTTTTTTT 0.880733 -20 AAATTCGGCTTATTCTACTTGTTTTCTTATGAAAAGTC 93 42 0 TTTCTTTTTT 0.813773 -57 ATTTATTACCTTTTATATTCCGTTTTATCATAAAAGGA 94 11 1 TTTTTGTTTT 0.603855 -202 GCGTGTTTTCTTTTTGCCTACTTTTGCTTTGCACGAGC 100 218 1 TTTCTTTTTT 0.813773 -83 ACTTTCTTATTTTTTATTTTCTTTTATGATTCGCAAAT 101 73 0 TTTTTTTTTG 0.603855 -220 ACACTTCACATTTTTGATTTTTTTTACTTTCTTATTTT 101 98 0 TTTTTTTTTT 0.880733 -195 TGATTACACTTTTTATATTATTTTTTCTTACATTTTGG 101 249 1 TTTTTTTTTT 0.880733 -44 AATTTCGTTATTTTACTTTAATTTTATTGAATGCCCAA 109 69 0 TTTTTTTTTT 0.880733 -56 ATATTCTCCTTAGTTTTTTATGGGCTGGA 113 40 0 TTTCTGTTTT 0.474242 -19 TATTTTCCTCCTTTTATTTATGTTTTAC 117 93 0 TTTCTTTTTT 0.813773 -18 TCTTTTGAATTTTTTGTTTAGTTTTTATCCAAAATAAC 118 55 0 TTTTTTTTTT 0.880733 -246 ATAAATAAACTATTTAGCTTATTTTTATGATTTAATTC 121 29 1 TTTCTTTTTT 0.813773 -130 TGCGGTCGTTTTTTCCCTTGTTTTTGGTAAAATGAAAA 122 38 0 TTTTTTTTTT 0.880733 -33 * ** ** **** * Masking position 9 Map Score: 16.4685 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 28 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 TTGATTATTTGCACGGCGTCACACTTTGCTATGCCA 2 176 1 GCGTCACATT 0.743508 -125 CCTAATGAGTGAGCTAACTCACATTAATTGCGTTGC 5 13 0 GAATCACATA 0.864026 -110 GATATTTGGTGACAAAACTCACAAAAGACACGCGTT 12 123 0 GAATCACAAA 0.674136 -178 TCATATGCCTGACGGAGTTCACACTTGTAAGTTTTC 20 119 1 GAATCACATT 0.953948 -182 TTTTTATGGTGAGCTGGCTCACATCTCCCTGACTCT 21 185 0 GAGTCACACT 0.561452 -116 TAATTAATGAGATTCAGATCACATATAAAGCCACAA 23 58 1 GAATCACAAT 0.870867 -72 AATAATGTGTGCGGCAATTCACATTTAATTTATGAA 24 150 1 GCATCACATT 0.8481 -123 GTCTGAATTTGCACTGTGTCACAATTCCAAATCTTT 42 159 0 GCGTCACATT 0.743508 -142 ATTTCACTCTGATGGATATCTCACTTCAGGCTTTCT 48 72 0 GAATCTCATT 0.702026 -156 ATTTAAATGTGAGTAGTGTCACATTTTTGTTTTGAT 49 22 0 GAGTCACATT 0.914927 -279 ATATTTATGTGATTGATATCACACAAAAGGCCGTCG 49 145 1 GAATCACAAA 0.674136 -156 GAACGATTGTGATTCGATTCACATTTAAACAATTTC 56 155 1 GAGTCACATT 0.914927 -88 AGATGAACGTGATGATGTTCACAATTTGCTGAATTG 59 161 0 GATTCACATT 0.624591 -127 AACACACTTCGATACACATCACAATTAAGGAAATCT 71 162 0 GAATCACATT 0.953948 -96 TCATAAATGTGATCAACTTCTCATTTTGGAAATAAA 84 117 0 GAATCTCATT 0.702026 -184 TTGAAAACGTGAGGAAGATCACAGTTTTAGAAAATA 94 130 0 GAATCACATT 0.953948 -83 AAAAAAATGTGACATAAATCACAATTTTTCGAAAAA 95 212 0 GAATCACATT 0.953948 -89 AAAGATTTGTGAAACACTTCACATTTTTGATTTTTT 101 113 0 GAATCACATT 0.953948 -180 AAATTATTGTGATCAATATCACAAAATCGCTTTCTT 101 170 1 GAATCACAAA 0.674136 -123 CTTATTTTGTGACAAAGATCACGGTTTATTTACAAT 108 129 1 GAATCACGTT 0.653658 -79 AAGAAAATAGGATCTAGATCACAAAATCAGTAAAAT 116 34 1 GAATCACAAA 0.674136 -142 TCAAATAAGTGATCAAGATCACAGTTTTAATGAATA 119 164 1 GAATCACATT 0.953948 -110 ** * ***** ** Masking position 9 Map Score: 19.2904 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 16 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 TCAGAGTGAAATAATTAGGAAAATATTTATATCA 48 96 1 ATAATAGAAT 0.623519 -132 TGTTAAACACAAAACCAACAAGGTCCCCA 52 282 1 AAAACAAAAT 0.638806 -19 TTAACGAGCAAAAACGAGAAATATCGAACTTAAA 61 191 0 AAAACAGAAT 0.619181 -110 ATAGTTAAACATAACAAGTAATTTTATTCTGTCA 75 33 0 ATAACAGAAT 0.346963 -77 GATTTTCAATAAAATAAAAAACCTGTTGCTAAAA 90 84 0 AAAATAAAAT 0.846462 -89 TCTTGGCAAGAAAATAAAAAAAGTATTTTTTAAT 91 244 1 AAAATAAAAT 0.846462 -57 ATAATGAATAAAAATGAATAAAGTGCGGTCATTT 92 42 0 AAAATAAAAT 0.846462 -42 CAATGGTAACAAAATAGACAATTTTGAAAACGTG 94 155 0 AAAATGAAAT 0.696837 -58 CTATCCACTAATAATAGAAAATATAGATTTTTAT 95 78 1 ATAATGAAAT 0.428933 -223 TGCCGCCTGAAAAATTGGAAATTTGTAGGAAATT 100 104 1 AAAATGGAAT 0.678779 -197 TATTTCCTGAAAAATTGGAAATTTGCTTAACGGA 100 172 0 AAAATGGAAT 0.678779 -129 TAGATGACACATAATTAAAAAGTTGGAGAAAAAA 101 13 0 ATAATAAAAT 0.64305 -280 GAAAGTAAAAAAAATCAAAAATGTGAAGTGTTTC 101 105 1 AAAATAAAAT 0.846462 -188 AAGTGCGGCCAAAATTAACAACATTTTGAGTGTA 101 207 0 AAAATAAAAT 0.846462 -86 TGAGAAAGAAAAAATGAAAAAATTACTATTAATT 105 154 0 AAAATAAAAT 0.846462 -107 ACAAAATAAGAAAATAAGCAAAATTTTTTATGAT 108 105 0 AAAATAGAAT 0.835208 -103 TCTAGATCACAAAATCAGTAAAATTATTTTAACA 116 46 1 AAAATAGAAT 0.835208 -130 CAATAAATGTAAAATAAATAAATTATTTATAAAT 116 85 0 AAAATAAAAT 0.846462 -91 ATAATTTACAAAAATAAGAAAGCTCAGTCAATAA 116 113 0 AAAATAGAAT 0.835208 -63 ACCATAGTCAAAAATAAAGAATTTTTGCTACAAT 117 57 1 AAAATAAAAT 0.846461 -54 TTATCCTATAAAAATTGAAAAGATCAAATTCTTT 118 88 0 AAAATGAAAT 0.696837 -213 GAGATTGTGAATAATAAATAAACTATTTAGCTTA 121 16 1 ATAATAAAAT 0.64305 -143 TTAAAAATATAAAACCAGAAAATTGCCCTAGTAT 121 111 0 AAAACAGAAT 0.619181 -48 CGACTAATCAATAATTAAAAATATAAAACCAGAA 121 125 0 ATAATAAAAT 0.64305 -34 TGTTTTTGGTAAAATGAAAAAAATTTTTGCATAG 122 24 0 AAAATAAAAT 0.846462 -47 ***** ** ** * Masking position 14 Map Score: 17.0323 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 52 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185