AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_ecoli_reg_100.orf -o00620_ecoli_100.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 aceE 160 pyruvate dehydrogenase (decarboxylase component) #4 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #5 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #6 dnaE 36 DNA polymerase III, alpha subunit #7 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #8 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #9 yaiN 166 putative alpha helix chain #10 ybiY 31 putative pyruvate formate-lyase 2 activating enzyme #11 poxB 132 pyruvate oxidase #12 pflB 54 formate acetyltransferase 1 #13 focA 300 probable formate transporter (formate channel 1) #14 mgsA 86 methylglyoxal synthase #15 b0964 91 orf, hypothetical protein #16 b0968 181 orf, hypothetical protein #17 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #18 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #19 ldhA 207 fermentative D-lactate dehydrogenase, NAD-dependent #20 aldA 196 aldehyde dehydrogenase, NAD-linked #21 sfcA 129 NAD-linked malate dehydrogenase (malic enzyme) #22 nemA 36 N-ethylmaleimide reductase #23 gloA 80 lactoylglutathione lyase #24 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #25 ppsA 300 phosphoenolpyruvate synthase #26 pabB 73 p-aminobenzoate synthetase, component I #27 pykA 127 pyruvate kinase II, glucose stimulated #28 dld 195 D-lactate dehydrogenase, FAD protein, NADH independent #29 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #30 atoB 30 acetyl-CoA acetyltransferase #31 ackA 300 acetate kinase #32 pta 74 phosphotransacetylase #33 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #34 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #35 cvpA 165 membrane protein required for colicin V production #36 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #37 fucO 24 L-1,2-propanediol oxidoreductase #38 fucA 300 L-fuculose-1-phosphate aldolase #39 yqeF 251 putative acyltransferase #40 glcD 250 glycolate oxidase subunit D #41 tdcE 33 probable formate acetyltransferase 3 #42 tdcC 21 anaerobically inducible L-threonine, L-serine permease #43 tdcB 98 threonine dehydratase, catabolic #44 tdcA 188 transcriptional activator of tdc operon #45 mdh 300 malate dehydrogenase #46 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #47 pabA 31 p-aminobenzoate synthetase, component II #48 yhfG 104 orf, hypothetical protein #49 pckA 300 phosphoenolpyruvate carboxykinase #50 aldB 74 aldehyde dehydrogenase B (lactaldehyde dehydrogenase) #51 yiaY 189 putative oxidoreductase #52 lldP 300 L-lactate permease #53 frwC 300 PTS system, fructose-like enzyme II component #54 pflD 50 formate acetyltransferase 2 #55 ppc 249 phosphoenolpyruvate carboxylase #56 aceB 268 malate synthase A #57 acs 300 acetyl-CoA synthetase Motif number 1 GCCAGCACGCAGTCAAACAAAAA 1 1 1 GCCACGCAGT 0.941756 -92 AAAAACCCGCGCCATTGCGCGGGTTTTTTTATG 1 30 1 GCCGCGCGGG 0.990286 -63 CGTCTTTCAGGCCGCAGCGGCGTTAGCTTCACG 4 239 0 GCCGCGGCGT 0.992208 -62 TGGTTTTTATGCAAATACGGAGTAAATATTTGA 13 172 0 GCAACGGAGT 0.569534 -129 GATTTTTGTGCCTGTGCGCAGGCTTTTTCGGT 14 10 1 GCCGCGCAGG 0.991973 -77 AGCCGCCTCTGCCTTGGCTGCGTTCGCTCCCCC 18 132 0 GCCGCTGCGT 0.922292 -143 AAACAAAAACACCATTGCGCAGGCAATGGTGTT 21 41 0 ACCGCGCAGG 0.859728 -89 TTGCTTTACCGCCAGGGCGTCGGCCTCAAGTAT 21 85 0 GCCGCGTCGG 0.962487 -45 TTAATTTATCGCCATCGCGGCGTTATTTCATTC 27 55 1 GCCGCGGCGT 0.992208 -73 TTTGTAACCCGCCAAATCGGCGGTAACGAAAGA 32 43 1 GCCTCGGCGG 0.966745 -32 TGCCTTCGCTGAGGGTGCCGGTCT 33 2 1 GCCGCTGAGG 0.910012 -93 GACTTTTTATGCCTTTGCGGCATCGGGCAATGC 35 13 0 GCCGCGGCAT 0.863295 -153 GAATTTGCATGCCGTGACGCAGGCATG 45 5 0 GCCACGCAGG 0.96686 -296 ATTCCAGCAGGCCGGGACGCCGGTCTATTTTGC 46 182 0 GCCACGCCGG 0.984072 -119 CGCCGGGAGAGCAGAAGCGCGGGCAAGATTGCC 48 25 0 GCAGCGCGGG 0.904775 -80 AAATCTATGAGCCTTGTCGCGGTTAACACCCCC 49 229 1 GCCTCGCGGT 0.877246 -72 GCATATTCGCGCCAATGCGACGTGAAGGATACA 55 190 1 GCCGCGACGT 0.934296 -60 *** ******* Masking position 8 Map Score: 22.7391 Number of sites scoring better than the average of aligned sites = 1050 Number in coding regions = 1001 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 CTACCTTGCTGCACCCAGAAATCCATAGGGTATG 4 154 0 GCACCCGATC 0.876113 -147 TAACGCCGCTGCGGCCTGAAAGACGACGGGTATG 4 247 1 GCGGCCGAGC 0.933429 -54 TCTTACGATTGCGGCAGGCCGTGTTATTATTGTC 5 52 1 GCGGCAGCTT 0.746248 -53 GCTATCCGGGGCGGCCTTCCCTGCCGATTAGCCC 9 26 1 GCGGCCTCTC 0.820151 -141 TAAGCGCAATGCGCCCGGCAATCTATACACAAAA 18 33 1 GCGCCCGATT 0.930946 -242 GGGGATCTCTGCGCCCTGACGTTCACAAACTGCA 18 220 1 GCGCCCGCTC 0.994155 -55 CTTGAGGCCGACGCCCTGGCGGTAAAGCAAAGAC 21 88 1 ACGCCCGCGA 0.614731 -42 AAAGGCTCCCGGTCGTCTGGTGATAAAA 22 19 0 GCTCCCGCTT 0.944738 -18 TTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCC 24 247 1 GCGCCCGAGA 0.744928 -54 GTATCCTTTAGCAGCCTGAAGGCCTAAGTAGTAC 31 75 1 GCAGCCGAGC 0.717678 -226 ACGCTCTATGGCTCCCTGACGTTTTTTTAGCCAC 31 256 1 GCTCCCGCTT 0.944738 -45 TGCCGGTCTGGCACCCTGACTTGCAACTCCCGCC 33 26 1 GCACCCGCTC 0.968587 -69 CCACGATTTTACGCCCTGTCATCCTGTTCGGGGC 35 135 0 ACGCCCGCTC 0.95518 -31 TATCTCTTTAGCTACCGGTCAGACCATTTTTTTT 40 137 0 GCTACCGCGC 0.697549 -114 CATGCCTGCGTCACGGCATGCAAATTCTGCT 45 8 1 GCGTCAGCTC 0.660576 -293 AAATAGACCGGCGTCCCGGCCTGCTGGAATTTAT 46 185 1 GCGTCCGCTC 0.959348 -116 TCCTCAGTAAGCTGCCCGCCCTTTTTTACACTTT 51 154 1 GCTGCCGCTT 0.912164 -36 GCGCACGGCAACGGCCTGCCATGTGACAAATCTG 53 43 1 ACGGCCGCTT 0.817326 -258 AAGCTGCTCCCGGGCTTGCGAAAGCCCAT 53 282 0 GCTCCCGCTC 0.980184 -19 ****** * * * * Masking position 5 Map Score: 18.301 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 966 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TTAGAGTTACTGGATACAAAAACGGATGTCAACCC 2 245 0 TGGCAAAAGG 0.943937 -56 TTGCCGTTTGTTGTTTAAAAATTGTTAACAATTTT 4 68 1 TTGAAAAAGT 0.568659 -233 TGAATGTGGTCGGAAAACAAAGAGGAAAGGGGGGG 9 60 0 CGGACAAAGG 0.837428 -107 TGCAAACAAGTGGTTCACAAACGGGCAATTT 20 7 0 TGGACAAAGG 0.853896 -190 TTGCCCGACGTGGCAGCGAAAATGGTGCAAAAACC 28 30 1 TGGCGAAAGG 0.950392 -166 ATAGTGGGTATGGAAGACAAAATGTTTTGAACGTT 31 37 0 TGGACAAAGT 0.614328 -264 AATTGATACGTGGCTAAAAAAACGTCAGGGAGCCA 31 264 0 TGGAAAAAGT 0.759344 -37 GCCAAATCGGCGGTAACGAAAGAGGATAAACC 32 53 1 CGGCGAAAGG 0.944088 -22 CCCGAAACTTTGGATAAAAAAGTGGTCGAACCGCG 36 21 0 TGGAAAAAGG 0.920491 -135 CATGGTCTGTTGGGGGCAAAAATGGCATTATGCGT 36 81 1 TGGCAAAAGG 0.943937 -75 AAGATAAAACTGGCATCGAACCAGGTTCAGACAGA 36 121 1 TGGCGAACGG 0.658269 -35 TATTAATTGTTTGTGCCGAAAACGGTCATTCCGGG 38 34 1 TTGCGAAAGG 0.888945 -267 CTACCTCTCTCTGATTCAAAACAGGGCAATAATGT 38 273 0 CTGCAAAAGG 0.861118 -28 GTTATCTTAATTGTTTAAAAAAAGTGATTTTTATC 39 180 0 TTGAAAAAGT 0.568659 -72 GGTCACAGAGCTGGAAAAAAAATGGTCTGACCGGT 40 123 1 CTGAAAAAGG 0.810007 -128 GCTGCCAATTGCTACGAAATCGTTATAATGTGC 46 9 1 TTGCGAAAGT 0.685693 -292 TCCGTGATTCCTGTCACGAAACGGTTGCTATTATC 49 160 0 CTGCGAAAGT 0.657862 -141 GGGAGATGTCTGGTAAAGAAAAGGGCAATCCTCAT 52 53 0 TGGAGAAAGG 0.929443 -248 AGGTACGTTTCGGAAATAAAAAAGGCACCCGAAGG 56 60 0 CGGTAAAAGG 0.564556 -209 GTTATGCATGCTGTTGAAAAAGAGGAAGATACTGA 57 95 0 CTGAAAAAGG 0.810007 -206 *** ***** ** Masking position 9 Map Score: 16.6683 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 536 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CATCAGGATAGGTTTTGCAACGCGTGCATTTTGTCCC 2 41 1 GTTCACGCGC 0.947301 -260 TAAGCTCCTGGGGATTCTGGCGCTTGCTACCTTGCTG 4 177 0 GTTTGCGCGC 0.945434 -124 TTCCTTCTGCCGCCCGCTATCCGGGGC 9 1 1 TTTTCCGCGC 0.935381 -166 CAAATGAGTTGAATTTTTTCCGCATCCTCCGCTAAAA 13 103 0 GTTTCCGCCC 0.97382 -198 AGTTTTCCATGGATTTGCAACGCGTCCATTAAGGATA 16 143 1 GTTCACGCCC 0.901926 -39 CGGGCGCATTGCGCTTACCCGGCTTACAGAACAAAAA 18 13 0 GTTCCGGCAC 0.672673 -262 GTATAGCGGCGGCTTTACGCCGCTCGCAATGTTGGA 23 10 0 GTTCCCGCGC 0.991503 -71 TCTAGTTTGTGATATTTTTTCGCCACCACAAGGAGTG 28 165 1 GTTTTCGCCC 0.764697 -31 TAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAA 45 252 0 TTTCCCGCCC 0.922387 -49 GATTGTGACAGGCGTTTCACCGCCGTCTGTAAAGCGT 46 245 0 GTTCCCGCTC 0.919607 -56 TGATTTCTCGCGCGGGCAATCTTGCCC 48 1 1 TTTTGCGCGC 0.775256 -104 CTCACAAGACGCTGTTTTGCGGCATGCTTCCGGTTTA 53 122 1 GTTTCGGCGC 0.928888 -179 TTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTAT 53 220 1 CTTCCCGCGC 0.93163 -81 GTTCTTCTCCCGCTCGCAAGGGCGGGT 54 1 1 GTTTCCGCGC 0.986433 -50 * ** * **** ** Masking position 6 Map Score: 12.0357 Number of sites scoring better than the average of aligned sites = 693 Number in coding regions = 571 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 CATCGGTTGACATATTTCAGCATAAATTTTTGCATC 2 96 0 CATTGCATAA 0.629295 -205 CAATGACGCCCATTTCTTTGCATCGACAGAAAAGTA 16 102 0 CATTGCATGA 0.945403 -80 CGGAGTTTTCCATGGATTTGCAACGCGTCCATTAAG 16 140 1 CAGTGCAAGC 0.839838 -42 GCAAAGCTGACACCTTTCAGCATCGCTTTTCGCCAT 17 32 0 CATTGCATGC 0.985897 -269 TGATCCAAATCAAATTTTTGCAAAGCTGACACCTTT 17 51 0 CATTGCAAGC 0.965331 -250 TCGAAGAGAGCAGATTTGCGCAACGCTGGGATCAGT 25 149 1 CATTGCAAGC 0.965331 -152 TTGAGAAACACATTTCTGCGCATTTATCTTTGCATA 25 245 0 CATTGCATTA 0.749588 -56 GCGCACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 29 12 0 CATTGCATGC 0.985897 -184 GCACAGTGCGCAATTTTCTGCATAGCCGCTCATTCT 29 37 1 CATTGCATGC 0.985897 -159 TATGCCCCGACAGCTGTATGCATAGCGATAAATTCC 46 210 0 CATTGCATGC 0.985897 -91 TTGGCCCTACCAATTCTTCGCTTATCTGACCTCTGG 52 98 1 CATTGCTTTC 0.605597 -203 ** * * **** ** Masking position 2 Map Score: 9.01734 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 57 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ACCCGCGCAATGGCGCGGGTTTTTTGTTTGACTGCGTG 1 16 0 TGGGTTTTTT 0.959152 -77 ACCCGCGCCATTGCGCGGGTTTTTTTATGCCCGAAGCG 1 34 1 TTGGTTTTAT 0.479017 -59 GAACTCACGCTGGCGGGACGTTTTTATTGCGTCAGGGT 2 211 1 TGGGTTTTTT 0.959152 -90 ACCTACCTTCTTAAGTGGATTTTTTATTTACTGCGTAC 12 22 0 TTGGTTTTTT 0.919662 -33 TTTATTCGCCTGATGCTCCCTTTTAATTAACTGTTTTA 13 70 1 TGGTTTTTTT 0.686381 -231 GTATAGTCAGTGCGGTGATGATTTGCTTAACCTATGAA 17 217 0 TGGGATTTTT 0.653495 -84 CCATTGCCTGCGCAATGGTGTTTTTGTTTTTATCTGCT 21 45 1 CGAGTTTTTT 0.443212 -85 GTATATTTTTTGAAACGCTGTTTTTGTTTTCCTTTTGG 24 18 1 TGAGTTTTTT 0.686381 -283 CGTTCTACGCTTCTGTGCGTTTTTAATTTATGCTTTCA 25 11 0 TTGGTTTTTT 0.919662 -290 AGAAACACATTTCTGCGCATTTATCTTTGCATATTTAA 25 240 0 TTGGTTATTT 0.725868 -61 TGAATATTTTTTCAGCGCCATTTTTATTGATGCGCGGG 35 54 1 TTGGTTTTTT 0.919662 -112 TTATCCAAAGTTTCGGGCTGTTATGTTTTAATGTGCAA 36 39 1 TTGGTTATTT 0.725868 -117 TGAACAGTTATTAAGCGGGCTTTTCGTTTTCGTCTATC 40 167 0 TTGGTTTTTT 0.919662 -84 GTTGAAGTATTGTAGAGAGATTATTTTTC 41 15 1 TGGGTTATTT 0.844511 -19 ATTGGCGCAACGAAGGTATATTTTGTTTTTTGCCGGAG 46 90 1 CGGTTTTTTT 0.443212 -211 TCAGGCACCTTCGGGTGCCTTTTTTATTTCCGAAACGT 56 53 1 TCGGTTTTTT 0.752507 -216 AACGAAGGATCGTTGTGCTCTTTTCGTTCAGCACAACT 56 199 0 CGGGTTTTTT 0.895182 -70 ** * * **** ** Masking position 12 Map Score: 9.11227 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 147 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 GGTTCTACGTTTAGTTGCCGCGCTTTTATATGCGCTT 3 52 0 TTATTGCGTT 0.973546 -109 CTCTATATATTTATCTCCGGCGGTCATACCCGTCGTC 4 268 0 TTACTGCGAT 0.73408 -33 AGTGGATTTTTTATTTACTGCGTACTTCGACAACCA 12 10 0 TTATTGCGTT 0.973546 -45 GACGAAGTAATGATTTTTCGCGCCCTTTGGCTAACAC 16 46 1 TGATTGCGTT 0.873905 -136 GTATGCCCGTTTATTTCTGGCGACATTCTTTATATAC 18 178 0 TTATTGCGTT 0.973546 -97 TCCTTTTGGATTAATTTCAGCGTATAATGCGCGCCAA 24 47 1 TTATTGCGAA 0.697959 -254 CATCGCGGCGTTATTTCATTCGGATTTCATGTTCAAG 27 67 1 TTATTTCGTT 0.743572 -61 TATTGCACTGTTAATTGGTGCGAGGTT 39 235 1 TTATTGCGTT 0.973546 -17 ACCTACATATTTAATTCAGGCGAAGAGGTTTTATA 43 74 1 TTATTGCGAG 0.86307 -25 ACCTTTGGTGTTACTTGGGGCGATTTTTTAACATTTC 55 12 1 TTATTGCGTT 0.973546 -238 TAAGTTACGCTTATTTAAAGCGTCGTGAATTTAATGA 55 51 1 TTATTGCGTG 0.940562 -199 *** ** *** ** Masking position 3 Map Score: 5.17906 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ATCAGGATAGGTTTTGCAACGCGTGCATTTTG 2 42 1 GTTTGCACGC 0.922049 -259 AGCTGACACCTTTCAGCATCGCTTTTCGCCAT 17 32 0 TTTAGCACGC 0.908342 -269 CCAAATCAAATTTTTGCAAAGCTGACACCTTT 17 51 0 TTTTGCAAGC 0.958461 -250 AGTTGTATATTTTTTGAAACGCTGTTTTTGTT 24 14 1 TTTTGAACGC 0.832028 -287 AGAGAGCAGATTTGCGCAACGCTGGGATCAGT 25 153 1 TTTCGCACGC 0.964325 -148 ACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 29 12 0 TTTTGCAAGC 0.958461 -184 AGTGCGCAATTTTCTGCATAGCCGCTCATTCT 29 41 1 TTTTGCAAGC 0.958461 -155 GCGTTGAATATTTTTTCAGCGCCATTTTTATT 35 50 1 TTTTTCACGC 0.832028 -116 AATGTCACCTTTTCCGCAGCGCAAAAACTGCG 46 61 0 TTTCGCACGC 0.964325 -240 CCCCGACAGCTGTATGCATAGCGATAAATTCC 46 210 0 TGTTGCAAGC 0.898589 -91 TTTTATCCACTGTTTGCTCCGCCTGCGATTGC 53 221 1 TGTTGCTCGC 0.754038 -80 *** **** *** Masking position 3 Map Score: 7.19303 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 237 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 GGGTTTTTTTATGCCCGAAGCGAGGCGCTC 1 50 1 ATGCCCGAAG 0.786361 -43 TCGCCTTATGCCCGATGATATTCCTTT 11 8 1 ATGCCCGATG 0.902352 -125 CCCGGGCCGTATGCCCGTTTATTTCTGGCG 18 193 0 ATGCCCGTTT 0.973713 -82 ACATGCCACAATACCCGTATTGAATGCTTA 19 42 0 ATACCCGTAT 0.537382 -166 AAATTGCCCGTTTGTGAACCACT 20 4 1 TTGCCCGTTT 0.901872 -193 GTCAGGAGTCATGCCCGTTTGCAAACAAGT 20 31 0 ATGCCCGTTT 0.973713 -166 ACGCATTGCCCGATGCCGCAAAGGC 35 6 1 TTGCCCGATG 0.696312 -160 ACCTGGTTCGATGCCAGTTTTATCTTTGGG 36 117 0 ATGCCAGTTT 0.744809 -39 CACAAATCAGATGACCGTATTAATTGTTTG 38 17 1 ATGACCGTAT 0.785164 -284 CAAGCCCGGAATGACCGTTTTCGGCACAAA 38 43 0 ATGACCGTTT 0.901724 -258 GAATAGAAAAATGACCGTTTTGATAAATAT 38 76 1 ATGACCGTTT 0.901724 -225 ********** Masking position 2 Map Score: 7.69044 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 228 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 AGGGAAGGCCGCCCCGGATAGCGGGCGGCAG 9 17 0 GCCCCGGAAG 0.923102 -150 TCAATGCATACCCCCCTATAGTATATAACAC 9 116 0 CCCCCCTAAG 0.954259 -51 ATATAGAATACCCCCCTATAGTATATTGC 9 148 1 CCCCCCTAAG 0.954259 -19 CGGGCAACGGCCCCGGAAAAGACCCACGGAT 16 12 1 CCCCGGAAAG 0.874686 -170 ATATTTTTTCGCCACCACAAGGAGTGGAAA 28 176 1 GCCACCACAG 0.842297 -20 GTTAGAATGCGCCCCGAACAGGATGACAGGG 35 125 1 GCCCCGAAAG 0.960874 -41 TGCCATTTTTGCCCCCAACAGACCATGAATG 36 77 0 GCCCCCAAAG 0.982255 -79 CAACCACTAACCCACCAATAGAGGGGTAGAT 39 94 0 CCCACCAAAG 0.91048 -158 GGGCAAGATTGCCCGCGCGAGAAATCA 48 7 0 GCCCGCGCAG 0.801521 -98 GCGGTTAACACCCCCAAAAAGACTTTACTAT 49 247 1 CCCCCAAAAG 0.880557 -54 CCAGACATCTCCCCCCACAAGAATTGGCCCT 52 75 1 CCCCCCACAG 0.976386 -226 ******** ** Masking position 10 Map Score: 7.77368 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 70 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 CCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTC 4 197 0 GATTATTAAC 0.941394 -104 ACAGTACAGCGCAACTTATTTTGTTAAAAACATGTAA 7 7 0 GATTATTAAC 0.941394 -70 ACAAATTACCGATATTTAACCTTATAATTAC 13 1 0 GATTACTAAC 0.847717 -300 GCTCCCCCGAATCACTTACCTGAGTAAGCTCATCGGGATTC 18 99 0 AATTATTAAC 0.780024 -176 GGCGACTCCTGTGATTTATATGTTTGTTTTCGGTGAATACA 20 165 0 GATTATTGTC 0.683061 -32 TTCATATTCAATTAGTTAAATAACTAAATCCAATAATCTCA 29 101 1 AATTATTAAC 0.780024 -95 AACCTTACGTGCCAGTTATGTCTCTGACTGCTGCTCAGGCA 39 127 1 GATTATTGAC 0.948999 -125 AACGACCTACGTTAATTACCTCATTGACGGCATGAAGTGTA 44 158 0 GATTATTGAC 0.948999 -31 TGTTAATTACGTAAGTTAGGTTCCTGATTACGGCAATTAAA 45 141 1 GATTATTGAC 0.948999 -160 TCCTGATTACGGCAATTAAATGCATAAACGCTAAACTTGCG 45 162 1 GATTATTAAC 0.941394 -139 CATATAAACCAAGATTTAACCTTTTGAGAACATTTTCCACA 49 100 1 AATTACTGAC 0.587389 -201 ATAAATAGCAGGAATTTACGTCATTAAATTCACGACGCTTT 55 67 0 GATTATTAAC 0.941387 -183 * * *** * *** * Masking position 8 Map Score: 5.81124 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 12 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 CCTGTCTTATTGAGCTTTCCGGCGAGAGTTCAA 3 87 1 TGGCTTTCGC 0.949085 -74 CGCAGCGGCGTTAGCTTCACGCCCTCACCCCAG 4 227 0 TTGCTTCCGC 0.949085 -74 CCCTTTCCTCTTTGTTTTCCGACCACATTCACC 9 64 1 TTGTTTTCGC 0.886639 -103 ACCTTTCAGCATCGCTTTTCGCCATTATAGCTA 17 24 0 ATGCTTTCGC 0.961849 -277 TTTTATCGTCTTTGCTTTACCGCCAGGGCGTCG 21 96 0 TTGCTTTCCC 0.960475 -34 TAATACCGGATTCGCTTTCCGGCAGTGCGCCCA 24 231 1 TTGCTTTCGC 0.987621 -70 TCGACTTTTTATGCCTTTGCGGCATCGGGCAAT 35 15 0 ATCCTTTCGC 0.785555 -151 CAAGGGCGGGTTCGCTTTCCCACAGGAGTTCCT 54 27 1 TTGCTTTCCC 0.960475 -24 ATGCTCGGGCTTTGCTTTTCGTCGTCTTTTATA 55 161 0 TTGCTTTCGC 0.987621 -89 ** ***** ** * Masking position 7 Map Score: 5.84829 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 63 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 CTACGTTTAGTTGCCGCGCTTTTATATGCGCT 3 53 0 TGCCGCGTTT 0.943373 -108 TGTTTTAGTATAGCGGCGGCTTTACGCCGCTC 23 22 0 TGCGGCGCTT 0.810999 -59 CAAGAGTCAATTGGCGCGCATTATACGCTGAA 24 62 0 TGGCGCGATT 0.96859 -239 TGCTAAATTGTTGGCGCTAATTATTTCATGCT 26 21 1 TGGCGCTATT 0.941949 -53 ATTTTCTGCATAGCCGCTCATTCTCCTTATAA 29 49 1 TGCCGCTATT 0.950766 -147 GTCATCCTGTTCGGGGCGCATTCTAACAGAAA 35 120 0 TGGGGCGATT 0.931938 -46 TTGTGTTGTGTGGCAGCTGATTTTTGCGCGCT 40 212 0 TGCAGCTATT 0.683655 -39 TAACCCGGATTTGCCGCTTATACTTGTGGCAA 48 58 1 TGCCGCTATA 0.827638 -47 GGCAAATTGTTAGCCGCTTTTTCAACTATCTC 50 31 1 TGCCGCTTTT 0.89757 -44 TTGGTGTTACTTGGGGCGATTTTTTAACATTT 55 16 1 TGGGGCGTTT 0.861113 -234 TCACGTCGCATTGGCGCGAATATGCTCGGGCT 55 183 0 TGGCGCGATA 0.884463 -67 * ****** *** Masking position 11 Map Score: 4.43152 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 207 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 ATTAAGGATAAGGAGAGCAGCA 16 170 1 AGGAGACAGC 0.940542 -12 ATACGGCCCGGGGATCTCTGCGCCCTGACGT 18 211 1 GGGATCCTGC 0.673554 -64 CCTCGCTCTAAGGATAGGTGACATCGAAAAA 24 186 0 AGGATAGTGA 0.811851 -115 AGGCTGCTAAAGGATACCTGATAGTGGGTAT 31 61 0 AGGATACTGA 0.837301 -240 TGAAATGAACAGGATATGTGCGACCACTCAC 44 121 0 AGGATAGTGC 0.921534 -68 TTTTTGCCGGAGGATAGCAGCAGATCGCTGC 46 116 1 AGGATACAGC 0.921799 -185 GGGTTACGCCGGGAGAGCAGAAGCGCGGGCA 48 33 0 GGGAGACAGA 0.690454 -72 ATATTGGCTAAGGAGCAGTGAA 49 289 1 AGGAGCGTGA 0.689672 -12 ACGTGTGACAAGGAGATGAGCAACAGACTCA 52 246 1 AGGAGAGAGC 0.929889 -55 CGTGGACTCCAGGAGACCTGCA 52 289 1 AGGAGACTGC 0.949489 -12 TTCTGTTTACAGGATAAGAGCGCACGGCAAC 53 24 1 AGGATAGAGC 0.908115 -277 ****** **** Masking position 4 Map Score: 4.34943 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 79 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 ACAAAAAACCCGCGCCATTGCGCGGGTTTT 1 27 1 CGCGCCATTG 0.941429 -66 CGATTAGCCCCCCCCCCTTTCCTCTTTGTT 9 50 1 CCCCCCCTTT 0.765365 -117 AATGATTTTTCGCGCCCTTTGGCTAACACT 16 54 1 CGCGCCCTTT 0.9701 -128 GGATTTGCAACGCGTCCATTAAGGATAAGG 16 153 1 CGCGTCCATT 0.577258 -29 GCGTATAATGCGCGCCAATTGACTCTTGAA 24 66 1 CGCGCCAATT 0.953151 -235 TGTTTTGTAACCCGCCAAATCGGCGGTAAC 32 40 1 CCCGCCAAAT 0.781537 -35 ATATTTTTTCAGCGCCATTTTTATTGATGC 35 57 1 AGCGCCATTT 0.677121 -109 TGGTAAATTGCCCTCCATTTTGTTTAATTT 39 31 0 CCCTCCATTT 0.683526 -221 AACCTCGCACCAATTAACAGTGCAA 39 237 0 CGCACCAATT 0.615836 -15 TCACAATATTCCCGCCATATAAACCAAGAT 49 85 1 CCCGCCATAT 0.848452 -216 CAGTAAGCTGCCCGCCCTTTTTTACACTTT 51 158 1 CCCGCCCTTT 0.965436 -32 GGAAAGCGAACCCGCCCTTGCGAGCGGGAG 54 17 0 CCCGCCCTTG 0.933778 -34 CGAGCATATTCGCGCCAATGCGACGTGAAG 55 187 1 CGCGCCAATG 0.911274 -63 ********** Masking position 6 Map Score: 8.63794 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 663 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639