AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_ecoli_reg_300.orf -o00620_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: glcB 21 malate synthase G Input sequences: #1 leuA 92 2-isopropylmalate synthase #2 leuL 300 leu operon leader peptide #3 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #4 aceE 160 pyruvate dehydrogenase (decarboxylase component) #5 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #6 rpsB 300 30S ribosomal subunit protein S2 #7 tsf 257 protein chain elongation factor EF-Ts #8 pyrH 146 uridylate kinase #9 frr 291 ribosome releasing factor #10 yaeM 91 putative ATP-binding component of a transport system #11 yaeS 185 orf, hypothetical protein #12 cdsA 120 CDP-diglyceride synthetase #13 yaeT 29 orf, hypothetical protein #14 hlpA 121 histone-like protein, located in outer membrane or nucleoid #15 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #16 dnaE 36 DNA polymerase III, alpha subunit #17 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #18 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #19 yaiN 166 putative alpha helix chain #20 ybiY 31 putative pyruvate formate-lyase 2 activating enzyme #21 poxB 132 pyruvate oxidase #22 ybjW 137 putative prismane #23 ybjE 300 putative surface protein #24 pflB 54 formate acetyltransferase 1 #25 focA 300 probable formate transporter (formate channel 1) #26 mgsA 86 methylglyoxal synthase #27 b0964 91 orf, hypothetical protein #28 b0968 181 orf, hypothetical protein #29 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #30 ycjL 121 probable amidotransferase subunit #31 ycjC 26 orf, hypothetical protein #32 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #33 ldhA 207 fermentative D-lactate dehydrogenase, NAD-dependent #34 hrpA 257 helicase, ATP-dependent #35 ydcF 271 orf, hypothetical protein #36 aldA 196 aldehyde dehydrogenase, NAD-linked #37 sfcA 129 NAD-linked malate dehydrogenase (malic enzyme) #38 rpsV 101 30S ribosomal subunit protein S22 #39 b1481 281 orf, hypothetical protein #40 nemA 36 N-ethylmaleimide reductase #41 gloA 80 lactoylglutathione lyase #42 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #43 ppsA 300 phosphoenolpyruvate synthase #44 pabB 73 p-aminobenzoate synthetase, component I #45 yebK 300 orf, hypothetical protein #46 pykA 127 pyruvate kinase II, glucose stimulated #47 dld 195 D-lactate dehydrogenase, FAD protein, NADH independent #48 atoS 214 sensor protein AtoS for response regulator AtoC #49 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #50 atoB 30 acetyl-CoA acetyltransferase #51 ackA 300 acetate kinase #52 pta 74 phosphotransacetylase #53 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #54 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #55 cvpA 165 membrane protein required for colicin V production #56 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #57 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #58 dedA 82 orf, hypothetical protein #59 usg 65 putative PTS system enzyme II A component #60 pdxB 98 erythronate-4-phosphate dehyrogenase #61 fucO 24 L-1,2-propanediol oxidoreductase #62 fucA 300 L-fuculose-1-phosphate aldolase #63 yqeF 251 putative acyltransferase #64 glcD 250 glycolate oxidase subunit D #65 tdcE 33 probable formate acetyltransferase 3 #66 tdcC 21 anaerobically inducible L-threonine, L-serine permease #67 tdcB 98 threonine dehydratase, catabolic #68 tdcA 188 transcriptional activator of tdc operon #69 mdh 300 malate dehydrogenase #70 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #71 pabA 31 p-aminobenzoate synthetase, component II #72 yhfG 104 orf, hypothetical protein #73 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #74 pckA 300 phosphoenolpyruvate carboxykinase #75 aldB 74 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) #76 yiaY 189 putative oxidoreductase #77 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #78 yibF 227 putative S-transferase #79 lldP 300 L-lactate permease #80 frwC 300 PTS system, fructose-like enzyme II component #81 pflD 50 formate acetyltransferase 2 #82 ppc 249 phosphoenolpyruvate carboxylase #83 argE 153 acetylornithine deacetylase #84 metA 156 homoserine transsuccinylase #85 aceB 268 malate synthase A #86 acs 300 acetyl-CoA synthetase Motif number 1 AAAAAACCCGCGCCATTGCGCGGGTTTTTTTAT 1 29 1 CGCCAGCGCG 0.993634 -64 TCGTCTTTCAGGCCGCAGCGGCGTTAGCTTCAC 5 240 0 GGCCGGCGGG 0.626718 -61 GCGAAGATAACGCATCTGCGGCGCGAAATATGA 7 110 1 CGCATGCGGG 0.699471 -148 GTTTGGTCACGGCCAGCGCGCAGCAACCGGAGC 9 97 1 GGCCAGCGCG 0.986545 -195 TAATACCCGTCGTCATCGCGGCGTTGTTTCTGT 12 57 1 CGTCAGCGGG 0.947555 -64 CGATTTTGTTCGCCAGAGCCCGGGGGTGCAGGG 23 14 0 CGCCAGCCCG 0.974412 -287 CGAACAAAATCGCCGCTGCGCGGTGCCCTCGAC 23 35 1 CGCCGGCGCG 0.978811 -266 GCGGGCAACGGCCCCGGAAAAGACCC 28 4 1 GGCAAGCCCG 0.744633 -178 ACGAGAGTATAGTCAGTGCGGTGATGATTTGCT 29 228 0 AGTCAGCGGG 0.699171 -73 AGTTTGTGAACGTCAGGGCGCAGAGATCCCCGG 32 218 0 CGTCAGCGCG 0.960013 -57 AAAACAAAAACACCATTGCGCAGGCAATGGTGT 37 42 0 CACCAGCGCG 0.861356 -88 TTATACTTGAGGCCGACGCCCTGGCGGTAAAGC 37 83 1 GGCCGGCCCG 0.950977 -47 AGGACAACATCGCCGTAGCGAAGAAACACGTGC 38 49 0 CGCCGGCGAG 0.950576 -53 ATTAATTTATCGCCATCGCGGCGTTATTTCATT 46 54 1 CGCCAGCGGG 0.941862 -74 TTTTGTAACCCGCCAAATCGGCGGTAACGAAAG 52 42 1 CGCCATCGGG 0.811346 -33 GGATTAAGGTCGCGGCAGCGGAGCAACATATCT 69 249 1 CGCGGGCGGG 0.732394 -52 AATTCCAGCAGGCCGGGACGCCGGTCTATTTTG 70 183 0 GGCCGACGCG 0.768936 -118 ACGCCGGGAGAGCAGAAGCGCGGGCAAGATTGC 72 26 0 AGCAGGCGCG 0.748124 -79 TCACATGGCAGGCCGTTGCCGTGCGCTCTTATC 80 36 0 GGCCGGCCGG 0.945775 -265 TATAAAGCCACGTAAAAGCGGTGACGTCAAATG 82 132 0 CGTAAGCGGG 0.779387 -118 AGCATATTCGCGCCAATGCGACGTGAAGGATAC 82 189 1 CGCCAGCGAG 0.947681 -61 ***** **** * Masking position 9 Map Score: 29.9201 Number of sites scoring better than the average of aligned sites = 1527 Number in coding regions = 1465 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 CAGTCAAACAAAAAACCCGCGCCATTGCGC 1 20 1 AAAAACCCGC 0.842609 -73 TCGGGCATAAAAAAACCCGCGCAATGGCGC 1 38 0 AAAAACCCGC 0.842609 -55 TCAACCGATGAAAAGCGTCGGTAGTTAAGC 2 122 1 AAAAGCGTCG 0.879466 -179 CTGACGCAATAAAAACGTCCCGCCAGCGTG 2 216 0 AAAAACGTCC 0.712513 -85 AAGCGCATATAAAAGCGCGGCAACTAAACG 4 52 1 AAAAGCGCGG 0.967193 -109 ATTTGTGGTATAAAGCGCGCCGGACTTCCG 6 129 1 TAAAGCGCGC 0.604099 -172 TCTAAAATCCTCGGAGATGTGAT 7 245 0 AAAATCCTCG 0.533525 -13 GGCTGCGCTGAAAAGCGACGTACAATGTCG 8 82 1 AAAAGCGACG 0.727603 -65 CTTGAACGACAAAAACGCCGCTCAGTAGAT 10 14 1 AAAAACGCCG 0.920992 -78 ATACTTCAGCAAAAGCGACCCCCA 12 5 0 AAAAGCGACC 0.727603 -116 TCTGGCGAACAAAATCGCCGCTGCGCGGTG 23 30 1 AAAATCGCCG 0.909603 -271 CATCCCTGTAAAACGCGCCCTCAGCCCACA 23 104 1 AAACGCGCCC 0.724715 -197 TGGTGGCGTCAAAATCGCCGAGGCGTTCCC 23 159 0 AAAATCGCCG 0.909603 -142 TAAAGACCGAAAAAGCCTGCGCACAGGCAC 26 18 0 AAAAGCCTGC 0.770166 -69 CTGATAAAGAAAAAACCCGGTAAGCATTTA 35 24 1 AAAAACCCGG 0.842609 -248 AGAATTAATAAAAAACCCGGCGCTAAATGC 35 47 0 AAAAACCCGG 0.842609 -225 CAAAGACGATAAAAGCCCCCCAGGG 37 115 1 AAAAGCCCCC 0.948312 -15 GTGACATCGAAAAAGCGTGCAGAGGAATGT 42 170 0 AAAAGCGTGC 0.862411 -131 CGATTACGGGAAAAGCGCGCAAAGTGCGGC 45 93 1 AAAAGCGCGC 0.967193 -208 ATCCGAATGAAATAACGCCGCGATGGCGAT 46 62 0 AATAACGCCG 0.623392 -66 GACAGGGCGTAAAATCGTGGGACACAT 55 149 1 AAAATCGTGG 0.647619 -17 GACGAAAACGAAAAGCCCGCTTAATAACTG 64 171 1 AAAAGCCCGC 0.940338 -80 AATAGCGCGGTTCTTTTGTA 71 1 1 AATAGCGCGG 0.807184 -31 AAAATCACCTAAAATCGCCCGCTCGCGGCA 73 51 0 AAAATCGCCC 0.909603 -220 GAAATGTTAAAAAATCGCCCCAAGTAACAC 82 19 0 AAAATCGCCC 0.909603 -231 TAAGAAGGTGAATAGCCCCG 83 1 0 AATAGCCCCG 0.722626 -153 ********** Masking position 2 Map Score: 21.5349 Number of sites scoring better than the average of aligned sites = 1142 Number in coding regions = 976 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 3 AATAAAAACGTCCCGCCAGCGTGAGTTCTG 2 209 0 TCCCGCCAGC 0.862298 -92 GCAGTTTGGTCACGGCCAGCGCGCAGCAAC 9 94 1 CACGGCCAGC 0.98608 -198 AAAAGCAAAACGCCGCCAGCCGATCCGCAA 10 46 0 CGCCGCCAGC 0.956139 -46 ACAATAATAACACGGCCTGCCGCAATCGTA 15 55 0 CACGGCCTGC 0.981749 -50 TGTGGGCTGCCCCGGCCTTCAGGGAACGCC 23 138 1 CCCGGCCTTC 0.893437 -163 GCGCAATGCGCCCGGCAATCTATACACAAA 32 36 1 CCCGGCAATC 0.666881 -239 TTAACCGCCACTCCGCAAGCCTGACATATC 35 167 0 CTCCGCAAGC 0.824624 -105 TTTCACACCGCCAGCTCAGCTGGCG 52 6 1 CACCGCCAGC 0.986081 -69 TACAAAACAGCACCGCCAGCTGAGCTGGCG 52 19 0 CACCGCCAGC 0.986081 -56 ATGCCTGCGTCACGGCATGCAAATTCTGCT 69 12 1 CACGGCATGC 0.907001 -289 AGACCGGCGTCCCGGCCTGCTGGAATTTAT 70 189 1 CCCGGCCTGC 0.986327 -112 AAAGCGTATGCCCCGACAGCTGTATGCATA 70 222 0 CCCCGACAGC 0.852666 -79 AGCGCACGGCAACGGCCTGCCATGTGACAA 80 42 1 AACGGCCTGC 0.779892 -259 CCACTGTTTGCTCCGCCTGCGATTGCCTAT 80 227 1 CTCCGCCTGC 0.951676 -74 ********** Masking position 3 Map Score: 16.0442 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 864 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 GAGCACTGCCCGGGGCCAAAATGGCAAATAAAATAG 9 153 1 CGAAAAGGCA 0.856293 -139 AGAATGTCGCCAGAAATAAACGGGCATACGGCCCGG 32 186 1 CAAAACGGCA 0.765077 -89 TCATTTAAAAGAAAATTAATCAGGCAGACTACTGCC 34 165 1 GAAATCGGCA 0.537799 -93 GCAAACAAGTGGTTCACAAACGGGCAATTT 36 5 0 GGAAACGGCA 0.958951 -192 GTGAACCACTTGTTTGCAAACGGGCATGACTCCTGA 36 24 1 TGAAACGGCA 0.769579 -173 AGAACTCAACGACTCAAAAACAGGCACTCACGTTGG 42 118 1 GAAAACGGCA 0.935429 -183 TATCTGCTTTTGTCATTAACACGGCACACAGGCGTA 45 204 1 TGAACAGGCA 0.547354 -97 ATTGATACGTGGCTAAAAAAACGTCAGGGAGCCATA 51 262 0 GGAAAAGTCA 0.525837 -39 CCGATTTGGCGGGTTACAAAACAGCACCGCCAGCTG 52 27 0 GGAAAAAGCA 0.757758 -48 TTGCAAGTCAGGGTGCCAGACCGGCACCCTCAGCGA 53 16 0 GGAGACGGCA 0.701396 -79 GTTACGGTGAGAATAGCAAAAGGGCAGAGCCAGTGG 56 29 0 GAAAAAGGCA 0.942649 -41 ATGGTCTGTTGGGGGCAAAAATGGCATTATGCGTCC 57 82 1 GGAAAAGGCA 0.963644 -74 ACCTCTCTCTGATTCAAAACAGGGCAATAATGTTGT 62 270 0 GAAACAGGCA 0.839876 -31 GGCCTGCGTTCAAAAATAAAATGGCATAGCGGGATA 73 15 1 CAAAAAGGCA 0.78701 -256 TTAACAAACAGAGCAGAAAAAAAGCAAGTGAAGAGA 73 236 0 GAAAAAAGCA 0.659841 -35 AAATTCTTATGAATTTAAAAAAAGCACATTGTTTAA 76 48 1 GAAAAAAGCA 0.659841 -142 ATGGCCTGGTGATGGGAAAAAGGGCAGAAAATGTTG 78 170 0 GAAAAAGGCA 0.942649 -58 GGAGATGTCTGGTAAAGAAAAGGGCAATCCTCATCA 79 51 0 GGAAAAGGCA 0.963644 -250 GTGAATGTTTTACGTTTAACCTGGCAACCAGACATA 83 29 0 TAAACCGGCA 0.397927 -125 GGTACGTTTCGGAAATAAAAAAGGCACCCGAAGGTG 85 58 0 GGAAAAGGCA 0.963644 -211 ** **** **** Masking position 8 Map Score: 15.7549 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 295 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TGGATTTCTGGGTGCAGCAAGGTAGCAAGCGCCAGAAT 5 163 1 GGCAAGGCAA 0.973038 -138 TAACGCCGCTGCGGCCTGAAAGACGACGGGTATGACCG 5 247 1 GGCAAGGACG 0.90561 -54 AATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAAT 7 33 1 GGCAAGGCAA 0.973038 -225 TAACGCATCTGCGGCGCGAAATATGAAGGGGGAGAGCC 7 117 1 GGCAATGAAG 0.670911 -141 GGAGAGAAAGGAGGCACTAACGGTTAAATAGCCCGATG 21 38 0 GGCAAGTAAA 0.908247 -95 GCCCGACCCGGTAGCCGTAAGGGATAAGTCGAGGGCAC 23 57 0 GGCAAGTAAG 0.934244 -244 TTATTAACTGTTAGCTATAATGGCGAAAAGCGATGCTG 29 13 1 TGCAAGGAAA 0.586845 -288 GGCGAAAAGCGATGCTGAAAGGTGTCAGCTTTGCAAAA 29 34 1 GGCAAGTCAG 0.947097 -267 AATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGAAT 32 65 1 GGCAAGGCAA 0.973038 -210 CAAGGCAGAGGCGGCTTGAAGGATGAAGTGTATATAAA 32 149 1 GGCAAGGAAG 0.976252 -126 GAATCCAGCCGCTGCTGCAAGGCCGTAAAGGTCAATTT 34 226 0 GGCAAGGTAA 0.801197 -32 GCCCGACGTGGCAGCGAAAATGGTGCAAAAACCGTAGT 47 32 1 GGCAAGGCAA 0.973038 -164 GTATCCTTTAGCAGCCTGAAGGCCTAAGTAGTACATAT 51 75 1 GGCAAGTAAG 0.934244 -226 CTGTTGGAATGTTGCGCTAATGCATAAGCGACTGTTAA 69 109 1 GGCAAGTAAG 0.934244 -192 GTGGATTAAGGTCGCGGCAGCGGAGCAACATATCTTAG 69 247 1 GGCAGGGCAA 0.820685 -54 CAGTTTTTGCGCTGCGGAAAAGGTGACATTGGCGCAAC 70 63 1 GGCAAGGACA 0.869868 -238 GACGTCAAATGCTGCGAAATCGCTTCAGCAAACGAATA 82 105 0 GGCATGTCAG 0.605029 -145 * ** ** * **** Masking position 9 Map Score: 15.3781 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 199 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TGTCTTATTGAGCTTTCCGGCGAGAGTTCAAT 4 89 1 AGCTTCCGGG 0.741386 -72 CGACGGATAGAACGACCCGGTGGTGGTTAGGG 5 112 1 AACGCCCGGG 0.677946 -189 CGTATCGGCACATATTCCGGGGTGCCCTTTGG 6 220 1 CATATCCGGG 0.650861 -81 AAAAAGAAGCCGCCCTCAGGCGGCTCCTTTTT 8 16 0 CGCCTCAGGG 0.887821 -131 GGATGGCGAGCACTGCCCGGGGCCAAAATGGC 9 146 1 CACTCCCGGG 0.95812 -146 CAGTTCTTTGCGTGGCCCGGCGATCTTATATT 14 63 0 CGTGCCCGGG 0.689131 -59 CAAAGAACTGCACCCTCCGGTGCAAATGGGAT 14 85 1 CACCTCCGGG 0.943521 -37 TTCTGCCGCCCGCTATCCGGGGCGGCCTTCCC 19 15 1 CGCTTCCGGG 0.958121 -152 TTACCGTTATCACATTCAGGAGATGGAGAACC 21 111 1 CACATCAGGG 0.869381 -22 AAATGGGCGTCATTGTCCGGAGTTTTCCATGG 28 123 1 CATTTCCGGG 0.83983 -59 TCTAATGCGTCACTTCCAGGTGGCGTAAGCAA 29 115 0 CACTCCAGGG 0.934211 -186 AAAAGTTTAACATTATCAGGAGAGCATT 29 283 1 CATTTCAGGG 0.765018 -18 ATACCGGATTCGCTTTCCGGCAGTGCGCCCAG 42 233 1 CGCTTCCGGA 0.799141 -68 CGTTGACTGAAACAACCAGGTGTTGCTTGAAC 46 97 0 AACACCAGGG 0.387572 -31 CTTCCATACCCACTATCAGGTATCCTTTAGCA 51 56 1 CACTTCAGGA 0.765018 -245 GCCATAATCTCGCGGCCAGGCATACTTGCGAA 60 34 0 CGCGCCAGGA 0.579199 -65 GGCAAATGGACACGTTCAGGGAGGCATCAA 72 85 1 CACGTCAGGA 0.705068 -20 CCCTTTTTTACACTTTCAGGAGTGTGTT 76 172 1 CACTTCAGGG 0.949292 -18 TTACCTCAGGCACCTTCGGGTGCCTTTTTTAT 85 48 1 CACCTCGGGG 0.684149 -221 **** ***** * Masking position 7 Map Score: 10.355 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 866 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 ATAACGTTGAGTTTTCTGGAACCTGTCCCATTGAACTCT 4 111 0 GTCTGATCCC 0.602839 -50 TGACTGGGGTGAGGGCGTGAAGCTAACGCCGCTGCGGCC 5 224 1 GGCGGATCGC 0.812435 -77 AATTCGACGTCTGATGCTGTACACAGCGCCAACAATTAT 6 75 1 CGGCGACCGC 0.533163 -226 CGTTTGGTTAGGGGGCCTGCATATGGCCCCCTTTTTCAC 7 175 1 GGCCGATCCC 0.786683 -83 ATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAA 9 27 1 GTCGGATCGC 0.920642 -265 AACAAAATAAGTTGCGCTGTACTGTGCGCGCAACGACAT 17 23 1 GTGCGAGCGC 0.918516 -54 ATCTTGCTTACGCCACCTGGAAGTGACGCATTAGAGATA 29 112 1 CCCCGATCGC 0.785929 -189 TCAGGTAAGTGATTCGGGGGAGCGAACGCAGCCAAGGCA 32 117 1 GTGGGAGCGC 0.733161 -158 ATGTTTAACCGTTCAGTTGAAGGTTGCGCCTACACTAAG 33 68 1 GTGTGATCGC 0.871126 -140 ACAGCACGAGGATAAGCAGGATATTCCGAATAAAATCCG 39 59 1 GTGCGATCGA 0.800856 -223 TACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAG 42 234 1 GTCCGAGCCC 0.716812 -67 ATTATTTCATGCTACCCGGCACATAGCCAGTAGAGTCAG 44 40 1 GTCCGATCCA 0.474524 -34 TTTTTTATCAGTTTTGCCGCACTTTGCGCGCTTTTCCCG 45 99 0 GTGCGATCGC 0.977771 -202 ATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGG 48 180 0 CTCCGATCGA 0.63235 -35 ACCAAAACTTGCTATGCAGAAATTTGCACAGTGCGCAAT 49 12 1 GTGCGATCAC 0.636264 -184 AGAATGAGCGGCTATGCAGAAAATTGCGCACTGTGCAAA 49 34 0 GTGCGATCGC 0.977771 -162 TACATTATGCCATTGGCTGAAAATTACGCAAAATGGCAT 51 135 1 CTGCGATCGC 0.945613 -166 GGTCTGGCACCCTGACTTGCAACTCCCGCCGAAATCCTG 53 30 1 CTCTGATCGC 0.742999 -65 ATGTGTCCCACGATTTTACGCCCTGTCATCC 55 145 0 GGCCCATCGC 0.476958 -21 CGGCGTCCCGGCCTGCTGGAATTTATCGCTATGCATACA 70 193 1 GCCTGATCGC 0.588023 -108 GCTCTCCCGGCGTAACCCGGATTTGCCGCTTATACTTGT 72 46 1 CTCCGATCGC 0.949528 -59 AAATAAAATGGCATAGCGGGATATGCCGCGAGCGGGCGA 73 28 1 GAGCGATCGC 0.758866 -243 ACGTGAGATGGGTCAGGAGGACATATCGCGCA 77 4 0 GTGGGATCGC 0.914688 -94 TGCAGGTCTCCTGGAGTCCACGCACATCGTGTA 79 278 0 GTCCGACCGC 0.893316 -23 CACAATTCTACTTTTGCGTGATCTGTCGCCCAAATACTA 86 198 1 CTGCTATCGC 0.375772 -103 * * ** * * * *** Masking position 11 Map Score: 18.6865 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 1203 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 ACGTTTTTATTGCGTCAGGGTTGACATCCG 2 228 1 TGCGTCAGGG 0.953068 -73 TTCTTACGATTGCGGCAGGCCGTGTTATTA 15 51 1 TGCGGCAGGC 0.818532 -54 GGGGGGGCTAATCGGCAGGGAAGGCCGCCC 19 34 0 ATCGGCAGGG 0.897415 -133 GCGCAATTTTGGCGGCAGGGATCTACCGCC 22 20 0 GGCGGCAGGG 0.945651 -118 GCAGTTTGTGAACGTCAGGGCGCAGAGATC 32 223 0 AACGTCAGGG 0.949093 -52 TGGCTAAAAAAACGTCAGGGAGCCATAGAG 51 259 0 AACGTCAGGG 0.949093 -42 TAACTGATAAGGGCAGGGCCACTGGCTC 56 9 1 AAGGGCAGGG 0.805486 -61 CATGCCTGCGTCACGGCATGCAAATT 69 7 1 TGCGTCACGG 0.7034 -294 GTTTTGGCTGAACGGTAGGGTATATTGTCA 69 75 1 AACGGTAGGG 0.736425 -226 GCGCAAAAACTGCGTCAGGGAGGACGAGGT 70 45 0 TGCGTCAGGG 0.953068 -256 TGTGCAAATAAACGGCAGGGTAATTTTTGA 86 172 0 AACGGCAGGG 0.972572 -129 ********** Masking position 7 Map Score: 7.2961 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 282 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 GCGCATATAAAAGCGCGGCAACTAAACGTAG 4 54 1 AAGCGCGGAA 0.96054 -107 GCAAGGTAGCAAGCGCCAGAATCCCCAGGAG 5 179 1 AAGCGCCAAA 0.565115 -122 AATTTACAAGATGGGCACAAAAAGAAGCCGC 8 35 0 ATGGGCACAA 0.609515 -112 TTTGTAATTAAAGCGCAAGAATATCTTTAAA 23 201 1 AAGCGCAAAA 0.830291 -100 GTGTTAGCCAAAGGGCGCGAAAAATCATTAC 28 52 0 AAGGGCGCAA 0.890705 -130 AGGTCATTTAAAGCGCAGTAATGGCGATAAT 30 89 1 AAGCGCAGAA 0.93015 -33 TCAGCGTATAATGCGCGCCAATTGACTCTTG 42 63 1 ATGCGCGCAA 0.860179 -238 GCAAAGATAAATGCGCAGAAATGTGTTTCTC 43 248 1 ATGCGCAGAA 0.823394 -53 ATTACGGGAAAAGCGCGCAAAGTGCGGCAAA 45 95 1 AAGCGCGCAA 0.946153 -206 ATTTTTATTGATGCGCGGGAAGGAAATCCCT 55 73 1 ATGCGCGGAA 0.894988 -93 TGATTCAAAACAGGGCAATAATGTTGTTCCT 62 266 0 CAGGGCAAAA 0.470149 -35 TTCACAGAAGCAGCGCGCAAAAATCAGCTGC 64 201 1 CAGCGCGCAA 0.872951 -50 ACCTTTTCCGCAGCGCAAAAACTGCGTCAGG 70 56 0 CAGCGCAAAA 0.656727 -245 GGGAGAGCAGAAGCGCGGGCAAGATTGCCCG 72 23 0 AAGCGCGGCA 0.85872 -82 AAGTGTAAAAAAGGGCGGGCAGCTTACTGAG 76 156 0 AAGGGCGGCA 0.738157 -34 TGATGGGAAAAAGGGCAGAAAATGTTGATGG 78 166 0 AAGGGCAGAA 0.860651 -62 ******** ** Masking position 11 Map Score: 8.67287 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 610 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 GGATAATCCGGCTACAGAGAGTCGCGCTAT 11 6 1 ATCCCAGAGA 0.982289 -180 GGCGGCAGGGATCTACCGCCAGAGAGGTA 22 5 0 ATCCCAGAGA 0.982289 -133 TTTATTCACAATCCTGCCACAGAGATAGCGCAATA 34 63 1 ATCCCAGAGA 0.982289 -195 AACATTATTCATCTTGCAGCAGAGAATTGTATTTT 35 110 0 ATCCCAGAGA 0.982289 -162 GTTAATTAACATCAATCATCAGAGAGACGGAATCG 36 128 0 ATCCCAGAGA 0.982289 -69 TTCATAACCATCAGTCCTCAATGACGATTAAACA 37 10 1 ATCCCAATGA 0.63257 -120 TCGGCGGTGTATCATATTCCAGAGAAGAGAGAACA 48 129 0 ATCTCAGAGA 0.84465 -86 AAATGGCATTATGCGTCCCCAAAGATAAAACTGGC 57 100 1 ATGCCAAAGA 0.768862 -56 CTCCCTGCCAATGTTACAGCAGAGAGCATGAAGAA 59 15 0 ATGCCAGAGA 0.944112 -51 *** * ****** Masking position 11 Map Score: 6.09651 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 12 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 AATGAATTTAAATTCGTTTTAATTGAATTAAAA 3 12 1 AATTTTTTAT 0.728806 -289 GCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAA 10 56 1 TTTTTTTTAT 0.782924 -36 AGCAGTAGAGTATTCGTTTTCATTTAAAGATAT 23 221 0 TATTTTTTAT 0.756886 -80 TATGCATAACATTTCCTTTTAATTGCAACTTTA 23 257 1 ATTTTTTTAT 0.756886 -44 TAATTTTTAAAATTTATTTTTATTTGGATAATC 25 141 1 AATTTTTTAT 0.728806 -160 GCGAGTAAGCTTTTGATTTTCATAGGTTAAGCA 29 199 1 TTTTTTTTAT 0.782924 -102 CGCAATGGTGTTTTTGTTTTTATCTGCTTTATA 37 55 1 TTTTTTTTAT 0.782924 -75 GAACCTTCAATTTTATTTTTTATGAAAACAGCA 43 69 1 TTTTTTTTAT 0.782924 -232 TGAAAACAGCATTTCATTTTTATGGTTTCGTTT 43 91 1 ATTTTTTTAT 0.756886 -210 AAAAAGTTGTTATTTTTTTTCATAACATGATCA 45 171 0 TATTTTTTAT 0.756886 -130 TTATTTGTTTTTATTTAAACATAA 67 2 1 TATTTTTTAT 0.756886 -97 TATCCTGTTCATTTCATTTTGATACACTTCATG 68 136 1 ATTTTTTTAT 0.756886 -53 TTAAAATGGAAATTGTTTTTGATTTTGCATTTT 85 152 1 AATTTTTTAT 0.728806 -117 **** **** ** Masking position 12 Map Score: 5.37003 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 39 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 AATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAG 5 198 1 ACTCAGGTGA 0.962506 -103 AATTCCCGGGAGCTTACATCAGTAAGTGACCGGGATGAG 7 68 1 ACTCCGGTGA 0.97993 -190 CAGCAACCGGAGCGTACAAAAGTACGTGAGGATGGCGAG 9 117 1 ACTCAGGTGA 0.962506 -175 TATACTTAGCACACTTCCACTGTGTGTGACTGTCTGGTC 9 232 1 AATCCGGTGA 0.92363 -60 AATCCCGATGAGCTTACTCAGGTAAGTGATTCGGGGGAG 32 100 1 ACTCAGGTGA 0.962506 -175 ACATCGAAAAAGCGTGCAGAGGAATGTGTGCTTGTGTCT 42 158 0 ACTCAGGTGT 0.864306 -143 CATTAGCGCAACATTCCAACAGGTGGTGACAATATACCC 69 92 0 AATCCGGTGA 0.923631 -209 GCATAGCGATAAATTCCAGCAGGCCGGGACGCCGGTCTA 70 188 0 AATCCGGGGA 0.6949 -113 AACACACTCCTGAAAGTGTAAAAAAGGGC 76 171 0 ACCCCGGTGT 0.716431 -19 TAACCTGGCAACCAGACATAAGAAGGTGAATAGCCCCG 83 10 0 ACGCAGGTGA 0.84261 -144 TTATTTCCGAAACGTACCTCAGCAGGTGAATAAATTTTA 85 76 1 ACTCCGGTGA 0.97993 -193 * * * * * * **** Masking position 1 Map Score: 4.70268 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 68 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 GCATCTAATCAACGAGGAAAAAGGGGACAAAA 2 69 0 ACGAGGAAAA 0.813447 -232 AAACCCTGTCAGGGAATAAAAAACGC 11 170 1 AGGAATAAAA 0.804827 -16 TTATGCAAATACGGAGTAAATATTTGATTATC 25 167 0 AGGAGTAAAA 0.732212 -134 AAAGGAATAAAAGGCAGAAATAAAAGTCAGGA 36 54 0 AGGCAGAAAA 0.842732 -143 ACATCGCCGTAGCGAAGAAACACGTGCTAAAC 38 44 0 ACGAAGAAAA 0.868005 -58 TCGGGCAACAAAGGAAGAAAAATCCAT 47 6 0 AGGAAGAAAA 0.920913 -190 GATAGTGGGTATGGAAGACAAAATGTTTTGAA 51 41 0 AGGAAGACAA 0.629437 -260 TTTTTGCATGATGGAAGAAATATCTTGAGTCT 51 174 0 AGGAAGAAAA 0.920913 -127 GATGTGGCTTAACGAGGAAAAAGACGT 54 20 1 ACGAGGAAAA 0.813447 -17 CGATGCCGCAAAGGCATAAAAAGTCGATGGCG 55 21 1 AGGCATAAAA 0.654894 -145 GATTTTGATCACGGAATAAAAAGTGATCGTCA 73 136 1 AGGAATAAAA 0.804827 -135 GGTTGCTATTATCGCAGAAATAGCATTTTAGG 74 141 0 ACGCAGAAAA 0.751628 -160 CATATTTTTGATGGAGGAAACAATAGGCAATC 80 247 0 AGGAGGAAAA 0.885335 -54 CGCTTCAGCAAACGAATAAATAGCAGGAATTT 82 91 0 ACGAATAAAA 0.699593 -159 * ******** * Masking position 8 Map Score: 7.40599 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 GTAAGTGACTGGGGTGAGGGCGTGAAGCTAACGC 5 219 1 GGGGAGGGGG 0.991502 -82 GTAAGTGACCGGGATGAGCGAGCGAAGATAACGC 7 89 1 GGGGAGCGGG 0.991502 -169 GGCGCGAAATATGAAGGGGGAGAGCCCTTATAGA 7 129 1 ATGGGGGGGG 0.736057 -129 ACAAAAGTACGTGAGGATGGCGAGCACTGCCCGG 9 132 1 GTGGATGGGG 0.734693 -160 TACCATATTGAGGAAGAGCGAGAG 18 21 1 AGGGAGCGGG 0.966557 -14 AAAACAAAGAGGAAAGGGGGGGGGGCTAATCGGC 19 48 0 GGAGGGGGGG 0.864581 -119 TACGGCTACCGGGTCGGGCGCGAGGTAACATCCC 23 76 1 GGGGGGCGGG 0.9865 -225 ACATGGATGTGGGCTGAGGGCGCGTTTTACAGGG 23 107 0 GGGGAGGGGG 0.991502 -194 AATCACAGTGAGTGTGAGCGCGAGTAAGCTTTTG 29 180 1 AGTGAGCGGG 0.716313 -121 AATAGCAAAAGGGCAGAGCCAGTGGCCCTGCCCT 56 20 0 GGGGAGCCGG 0.931626 -50 ACCAATAGAGGGGTAGATAGGGCGTTAATCTCCC 63 78 0 GGGGATAGGG 0.735503 -174 *** ***** * * Masking position 6 Map Score: 5.6976 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 64 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 TGAATTTCGCCAAACGTGCCACTGAAGGTTT 6 32 1 CAAAGTGCCA 0.821347 -269 CAAATTTTTGCAAAGCTGACACCTTTCAGCA 29 46 0 CAAACTGACA 0.91512 -255 ACTTTATTCACAATCCTGCCACAGAGATAGC 34 61 1 CAATCTGCCA 0.839377 -197 CGCCACTCCGCAAGCCTGACATATCTTTTAA 35 161 0 CAAGCTGACA 0.954919 -111 AGTCTGCCTGCAAGTCTGACAGGGCAACTAT 53 72 1 CAAGCTGACA 0.954919 -23 GTTAACCGGACAAGTGTGCCATAATCTCGCG 60 52 0 CAAGGTGCCA 0.900325 -47 CCGACACCTGCAAGACAGACAGGTGGATTAT 67 35 0 CAAGCAGACA 0.748778 -64 CAATGTCCGTCAAGTCTAACATTGACACTCT 70 148 1 CAAGCTAACA 0.649201 -153 TGCCATGTGACAAATCTGCCAAAAGCTGGAC 80 59 1 CAAACTGCCA 0.945034 -242 AAATACTAAACAAAACTGCCAATACCCCTAC 86 229 1 CAAACTGCCA 0.945034 -72 **** ****** Masking position 3 Map Score: 4.69722 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357