AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_ecoli_reg_300.orf -o00030_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 Input sequences: #1 talB 278 transaldolase B #2 gcd 193 glucose dehydrogenase #3 seqA 184 negative modulator of initiation of replication #4 pgm 25 phosphoglucomutase #5 prsA 150 phosphoribosylpyrophosphate synthetase #6 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #7 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #8 edd 234 6-phosphogluconate dehydratase #9 zwf 300 glucose-6-phosphate dehydrogenase #10 gnd 300 gluconate-6-phosphate dehydrogenase, decarboxylating #11 talA 288 transaldolase A #12 rpiA 55 ribosephosphate isomerase, constitutive #13 yqfE 141 orf, hypothetical protein #14 fba 214 fructose-bisphosphate aldolase, class II #15 pgk 49 phosphoglycerate kinase #16 epd 284 D-erythrose 4-phosphate dehydrogenase #17 yggD 21 putative transcriptional regulator #18 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #19 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #20 tktA 151 transketolase 1 isozyme #21 dam 106 DNA adenine methylase #22 damX 91 putative membrane protein; interferes with cell division #23 aroB 56 3-dehydroquinate synthase #24 aroK 199 shikimate kinase I #25 yrfD 68 orf, hypothetical protein #26 gntK 230 gluconokinase 2, thermoresistant #27 gntR 223 regulator of gluconate (gnt) operon #28 yhhW 122 orf, hypothetical protein #29 yhhX 300 putative regulator #30 rbsD 300 D-ribose high-affinity transport system; membrane-associated protein #31 rbsB 24 D-ribose periplasmic binding protein #32 rbsK 125 ribokinase #33 b3913 146 orf, hypothetical protein #34 yiiP 148 putative transport system permease protein #35 pfkA 180 6-phosphofructokinase I #36 pgi 300 glucosephosphate isomerase #37 rpiB 300 ribose 5-phosphate isomerase B #38 fbp 175 fructose-bisphosphatase #39 idnK 216 gluconate kinase, thermosensitive glucokinase #40 deoC 257 2-deoxyribose-5-phosphate aldolase #41 deoA 83 thymidine phosphorylase #42 deoB 51 phosphopentomutase Motif number 1 TGTATAAAAATGGCGGGCGATATCAACGCAGTGTCA 1 127 1 TGCGGCGACA 0.916037 -152 AGACGGTTATCGCCAGGCGAGACTGTTTCGGATTTC 1 163 0 CGCGGCGATT 0.945173 -116 GAATAAATCCCGGCAGCGGATAGCGTCAAGCCTGGC 3 110 0 CGCGCGGACT 0.926058 -75 ATACCGAAGCCGTCGGCGGGTAACATTTGTATCCGT 13 77 1 CGCGCGGACT 0.926058 -65 CATAAGTAAGTGACTGGGGTGAGCGAACGCAGACGC 14 132 1 TGCGGGGACA 0.847095 -83 TGTCCTGTATCGTCGGGCCTTATACTCGTCATACTT 14 183 0 CGCGGCCAAT 0.961909 -32 GCTTTATTCCAGGCTGGCGTAATAATAACCCTACAA 16 27 0 AGCGGCGAAT 0.945876 -258 ATGTCTTCTTCGGCTGGACAAACATTCCTTTTATTC 16 104 1 CGCGGACAAT 0.745742 -181 TCCAGCAAATCGTCCGGGGAAACCTTACCTGTCGCA 16 212 0 CGCGGGGACT 0.985399 -73 TTTAGGGTACCGTCCGGCGGTAAAAATAAAATACTC 19 256 0 CGCGGCGAAA 0.987218 -45 ACATGACGCGCGGCTTGCGGTAAATTGTTGGCAAAT 20 51 1 CGCTGCGAAT 0.87993 -101 TATATACACTCGTCTGCGGGTACAGTAATTAAGGTG 23 20 1 CGCGCGGAAT 0.942875 -37 CTTCTGATATTGTCCGGCTGGACAATGTTACCGATA 26 119 1 TGCGGCTAAT 0.813254 -112 GCCTGCAAAAAGGCAGGCTTCAAAGATGCCGTTGAG 27 13 0 AGCGGCTAAA 0.507195 -211 CATCAGCACGCGACCGGAGCGAGCGAGGAAGCCTGC 27 43 0 CGCGGAGACA 0.871905 -181 AGCCAGCACCCGGCTGGCTAAGTAATACTGGAAGCA 29 151 0 CGCGGCTGAT 0.82031 -150 AGAAAGGAGGCGTCTGGCGTTAGATTTCGACCTGAG 30 164 0 CGCGGCGAAT 0.994323 -137 TGCAAACATGCGTCAGGGGGTGTAAAACAACGTAAA 33 66 0 CGCGGGGGAA 0.884442 -81 CATTTTTCTGTGACTGGCGCTACAATCTTCCAAAGT 36 244 1 TGCGGCGAAT 0.970244 -57 TGCGATACTACGCCTGGCGGCATAATAATTTCACGT 39 163 0 CGCGGCGAAT 0.994323 -54 ** * **** * * * Masking position 4 Map Score: 22.3781 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 1018 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 GCCGGGCAAGCTGAGTTTCGGT 5 1 1 GCCGGAAGCT 0.946918 -150 AACTGTGCGGGCCAGGCATGATCCTTTCCAGG 5 82 0 GCCGGATGAT 0.971575 -69 AAGTTTCCGGGACCGCGATGGTCTCTTTTTTT 7 31 0 GACGCATGGT 0.797228 -256 AGATTAGCGTCCCTGGAAAGGTAACGAATTAT 7 76 1 CCCGGAAGGT 0.958615 -211 AATGCTCGCGGCCTGGAATGTTCGCAAATAAG 10 246 0 GCCGGATGTT 0.912198 -55 AAGCATAGCAGACAGGCATGGTATTGCTGGAT 11 186 0 GACGGATGGT 0.973658 -103 CGCAGTTTGCGACAGGTAAGGTTTCCCCGGAC 16 205 1 GACGGAAGGT 0.977184 -80 TTTCTCCACAGCCGGAGAAGGTGTAATTAGTT 21 78 1 GCCGAAAGGT 0.885498 -29 GCGATAAATCACCGGGTAAGATTAGCGTAAAA 24 171 0 ACCGGAAGAT 0.757289 -29 GCACTGTTTTCCCCGGGAAGGTTCTGATGTGT 27 157 1 CCCGGAAGGT 0.958616 -67 GACCCGATCTGCCTGGGATGATAGAGGGTGAA 28 61 0 GCCGGATGAT 0.971576 -62 TGTGGGGGAAGACAGGGATGGTGTCTATGGCA 34 27 0 GACGGATGGT 0.973663 -122 GTTTTGCACGGACGGGGAAGATGA 37 287 1 GACGGAAGAT 0.940247 -14 *** ** ***** Masking position 8 Map Score: 15.6453 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 264 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 CGTGATATCATCAGGGCAGACCGGTTACATC 1 225 1 TCAGGCAGAC 0.833335 -54 GCAACAAAGCGCAAGACACGCAGTATACCAG 2 55 1 GCAAGCACGC 0.962396 -139 GAGTTTTTCTGCAAGCCAGGCTTGACGCTAT 3 96 1 GCAAGCAGGC 0.98744 -89 CGAAAACTGTGCGGGCCAGGCATGATCCTTT 5 87 0 GCGGGCAGGC 0.980706 -64 AAAATCACAGGGCAGGGAAACCTGCCC 14 7 1 ACAGGCAGGG 0.870833 -208 ACAATTTACCGCAAGCCGCGCGTCATGTACA 20 48 0 GCAAGCGCGC 0.798505 -104 ATCGGATGATGAAGGGCACGCCCTTAACGAC 20 120 0 GAAGGCACGC 0.917729 -32 CAACAAGAAAGGTCAGGCCGCTTATCAA 22 8 1 AAAGGCAGGC 0.919959 -84 TAGTATAAAGGCAAGCCAGACGCATTGATAT 25 38 1 GCAAGCAGAC 0.924909 -31 GAAGCCTGCAAAAAGGCAGGCTTCAAAGATG 27 21 0 AAAAGCAGGC 0.813509 -203 ATAAAGAAAAGCAGGGCACGCGCCACCCTAA 32 74 1 GCAGGCACGC 0.986049 -52 TACACAAAATGCGGGTCTGGCTCTCTTTTAT 35 16 0 GCGGGCTGGC 0.88926 -165 CTGAATTGATTCAGGTCAGGCCAAATGGCGG 35 54 0 TCAGGCAGGC 0.970154 -127 AGGTGTTATCACAGGACTGGCTCCTCCAACA 36 11 1 ACAGGCTGGC 0.928406 -290 CTGCGCTAGCGCAGGCCAGAAGAGGCGCGTT 36 55 0 GCAGGCAGAA 0.776971 -246 TTTATTGGCGACAAGCCAGGAGAATGAA 40 240 1 ACAAGCAGGA 0.752738 -18 ***** ***** Masking position 5 Map Score: 16.2177 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 861 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 CAGAGCAGGATGATTCACAACGCGTTTCATTCAGAGGA 8 184 0 TCAAGCGTTC 0.906825 -51 ATCCTCTCGTTGATTCTAAAAGTTTTGCAGACGCTGCT 15 17 0 TCAAGTTTGC 0.84415 -33 CAAATGTCAATACCGCATATCGTGATGCATATTACATA 19 122 0 TCATGTGTGC 0.897368 -179 TTTTCCGGCGTAGCCCAAAACGCGCTGTCGTCAAGTCG 20 86 1 TCAAGCGTGT 0.91444 -66 GGTAATGTTTTTACGCTGAACGTGTTTCATCTATTTGA 24 25 1 TCAAGTGTTC 0.905223 -175 TCATGGTTAGTCGTGCTCAAAGTGGTGCCCCCACAATA 26 184 0 TCAAGTGTGC 0.986926 -47 TTGCCGCGTCGTTAGCACAATGCGATGCAATTGATTTA 27 94 1 GCAAGCGTGC 0.923853 -130 AAATGCATTTTTTTGCAAAAAGTGTTGGACAAGTGCGA 29 39 1 TCAAGTGTGG 0.898121 -262 TACTTGCTGCTGCAACGTAATGCGCTGCGTGCACCAGA 30 85 1 TCAAGCGTGC 0.987167 -216 TCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTG 34 82 1 TCAAGCATGC 0.84661 -67 CATTACTATGTTACGCATAACGTGATGTGCCTTGTAAT 39 103 1 TCAAGTGTGT 0.912955 -114 TCTTTTCCTTTTATGCCGAAGGTGATGCGCCATTGTAA 40 13 1 TCAAGTGTGC 0.986926 -245 AATTGTGATGTGTATCGAAGTGTGTTGCGGAGTAGATG 40 172 1 TCAGGTGTGC 0.928361 -86 * * ** *** *** Masking position 9 Map Score: 12.3911 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 149 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GACGCAACGTCAGCGCAACCGCCGACAAGA 1 196 0 CAGCGCAACC 0.759495 -83 AATAAGCATGTGGCGAAAACAGATTTTTAT 7 154 1 TGGCGAAAAC 0.568767 -133 GCGCAAAGTGCGGCAAAACTGATAAAAAAA 9 146 0 CGGCAAAACT 0.715452 -155 CGTGCGATTACGGGAAAAGCGCGCAAAGTG 9 166 0 CGGGAAAAGC 0.937228 -135 AATCACAGGGCAGGGAAACCTGCCCTTGTT 14 13 1 CAGGGAAACC 0.974576 -202 GCAAATCGTCCGGGGAAACCTTACCTGTCG 16 214 0 CGGGGAAACC 0.987831 -71 CAAATTTGCTCAGGGAAAACCTTGCAGGAG 16 261 1 CAGGGAAAAC 0.904719 -24 AGCAATTGAGCAGGGAAACCGGTGTTTTGA 19 211 0 CAGGGAAACC 0.974576 -90 GCTAACGACGCGGCAAAACCCCGGAAGCGT 27 80 0 CGGCAAAACC 0.955847 -144 AGAACCTTCCCGGGGAAAACAGTGCTTGTT 27 152 0 CGGGGAAAAC 0.952625 -72 GTCTCGCGATCAGGAAGACCCTCGCGGAGA 29 95 1 CAGGAAGACC 0.725312 -206 CTGACTGAGTTGGGAAAACCATCGTGACGT 30 272 0 TGGGAAAACC 0.816587 -29 ATAAACATTGCAGGGAAAGTTTT 38 163 1 CAGGGAAAGT 0.634251 -13 TAGACGCATCCGGCAAAAGCCGCCTCATAC 41 43 1 CGGCAAAAGC 0.893978 -41 ********** Masking position 8 Map Score: 10.8456 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 601 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 GATAACTTCTGCGTAGCATACATGAGGTTTTG 1 97 1 GCGTAGCACA 0.735904 -182 AACGTTGCAGACAAAGGACAAAG 4 2 1 ACGTTGCACA 0.954087 -24 TCCTTGAGATACGTTGCAGTTATAACCCTTAA 6 180 0 ACGTTGCATA 0.910161 -34 TAGGGCAAAAACGTTTCAGTCAGTGTAATAAA 8 120 0 ACGTTTCACA 0.928177 -115 CCGGTTACAGGCGTTTCAGTCATAAATCCTCT 8 158 1 GCGTTTCACA 0.942142 -77 GATTCACAACGCGTTTCATTCAGAGGATTTAT 8 179 0 GCGTTTCACA 0.942142 -56 CCTGCCCACAACGTGGCGCACATTATTACCCT 11 63 1 ACGTGGCGCA 0.774558 -226 ATTTTGTGTCAGGTTGCATATACCGAAGCCGT 13 58 1 AGGTTGCATA 0.609917 -84 CTTTTATTCCACGTTTCGCTTATCCTAGCTGA 16 131 1 ACGTTTCGTA 0.711288 -154 ATCGACTGAAACGCTTCAGCTAGGATAAGCGA 16 146 0 ACGCTTCATA 0.860562 -139 ACCGCAAGCCGCGCGTCATGTACATGGAACAT 20 40 0 GCGCGTCATA 0.76679 -112 ACAGCATCCAGCGCTTCAGGCAACTCCCGCAA 21 40 0 GCGCTTCACA 0.941007 -67 AATGCTTACCACGTTGCAATTAACCTGAAGCT 22 49 0 ACGTTGCATA 0.910161 -43 AAATACCTGCGCGCGTCAAATAGATGAAACAC 24 46 0 GCGCGTCATA 0.76679 -154 GCAACGTAATGCGCTGCGTGCACCAGATCAAT 30 96 1 GCGCTGCGCA 0.909339 -205 TTTACGATTCAGGCTGCAAACATGCGTCAGGG 33 84 0 AGGCTGCACA 0.758533 -63 ******** ** Masking position 12 Map Score: 10.6705 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 737 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 ACCTTGTTCCAGACGTTGCATCGCGCTCTTT 5 42 1 AACGTTGCAT 0.799088 -109 AGTCCTTGAGATACGTTGCAGTTATAACCCT 6 183 0 AACGTTGCAG 0.969169 -31 CATAGGGCAAAAACGTTTCAGTCAGTGTAAT 8 123 0 AACGTTTCAG 0.944161 -112 CTCCGGTTACAGGCGTTTCAGTCATAAATCC 8 156 1 AGCGTTTCAG 0.969169 -79 ATGATTCACAACGCGTTTCATTCAGAGGATT 8 182 0 AGCGTTTCAT 0.799088 -53 CGCATCAAAAAAGCATAGCAGACAGGCATGG 11 197 0 AGCATAGCAG 0.737882 -92 ATCCTAGCTGAAGCGTTTCAGTCGATTAAAT 16 152 1 AGCGTTTCAG 0.969169 -133 TGCTCAGGGAAAACCTTGCAGGAGATCT 16 267 1 AACCTTGCAG 0.838782 -18 ACGCAGCGCATTACGTTGCAGCAGCAAGTAC 30 84 0 TACGTTGCAG 0.769864 -217 CTGCTGCTTAATGCATTGCAGATGATTTGCT 34 91 1 AGCATTGCAG 0.961691 -58 CAAGTGAGAAACGCATTTCAGGATAATCCGT 38 60 1 AGCATTTCAG 0.934335 -116 TTTACTCCATAAACATTGCAGGGAAAGTTTT 38 155 1 AACATTGCAG 0.934335 -21 GACACCTCGGAAGCATTTAAGCGGTTTTAAC 39 32 1 AGCATTTAAG 0.483792 -185 * ********* Masking position 10 Map Score: 10.9141 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 542 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TCCCTCTTATTGCCGGTCGCGATGACTTTCCT 1 16 1 TCCGGTGCGA 0.87324 -263 TATGAATAAATCCCGGCAGCGGATAGCGTCAA 3 117 0 TCCGGCGCGG 0.968519 -68 CATGATCCTTTCCAGGCGGTGTATTAAAGAGC 5 66 0 TCAGGCGTGT 0.862895 -85 GCTTGCATCATACAGGATGCGTAAGATCAATA 6 50 1 TCAGGAGCGT 0.918285 -164 TTTTTACACTTTCAGGCCTCGTGCGGATTCAC 8 75 1 TCAGGCTCGT 0.759259 -160 TTGCGAACATTCCAGGCCGCGAGCATTCAGCG 10 251 1 TCAGGCGCGA 0.976408 -50 AGTCTGTAGACTCCGGCAGGGTAATAATGTGC 11 80 0 CCCGGCGGGT 0.876425 -209 GACGCAAGCAGCGTCTGCAAAACT 15 3 1 CCAAGCGCGT 0.867163 -47 AACAATTTACCGCAAGCCGCGCGTCATGTACA 20 48 0 CCAAGCGCGC 0.576522 -104 ATTACACCTTCTCCGGCTGTGGAGAAAGCTCC 21 73 0 CCCGGCGTGG 0.764376 -34 CATCATGGAACGCAGGCAGCGAAGAGCACCAA 24 105 0 CCAGGCGCGA 0.979368 -95 TGATTTATCATTCAGGCGGCATTTTGCTGTCT 24 138 1 TCAGGCGCAT 0.855176 -62 TCCTCGCTCGCTCCGGTCGCGTGCTGATGTAC 27 50 1 CCCGGTGCGT 0.913367 -174 CGCGGCAAAACCCCGGAAGCGTACATCAGCAC 27 70 0 CCCGGAGCGT 0.937916 -154 ATCGAAATCATTCAGGGGGCGAATACAA 28 105 1 TCAGGGGCGA 0.817107 -18 GAGTTTACGATTCAGGCTGCAAACATGCGTCA 33 87 0 TCAGGCGCAA 0.800072 -60 TGAATCATCTTACCTGCTGCGATACTACGCCT 39 184 0 TCCTGCGCGA 0.758139 -33 AGGCGGCTTTTGCCGGATGCGTCTACGCCTTA 41 36 0 TCCGGAGCGT 0.935753 -48 * ***** **** Masking position 6 Map Score: 16.7705 Number of sites scoring better than the average of aligned sites = 1897 Number in coding regions = 1771 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 GTGTGATCGTCATCACAATTCGAGCTTTAT 2 114 0 CATCACAATT 0.929856 -80 TTGTGATGACGATCACACATGTTAAAACCT 2 126 1 GATCACACAT 0.899972 -68 TCAGCGCGGTGATCACACCTGACAGGAGTA 10 277 1 GATCACACCT 0.802101 -24 ATCTGACTCACATCACACTTTTATCCCCTT 16 72 0 CATCACACTT 0.954833 -213 GCGTGTTGTAGATCACAAATATTTATATGC 19 79 1 GATCACAAAT 0.849441 -222 ATTTGAAGTAGCTCACACTTATACACTTAA 26 72 1 GCTCACACTT 0.723729 -159 TTTCGAGGTTGATCACATTTCCGTAACGTC 30 247 1 GATCACATTT 0.806306 -54 GCACTAAAACCATCACATTTTTCTGTGACT 36 229 1 CATCACATTT 0.852223 -72 AATTCATTAACATCACAAATGTTTTTTGAT 37 251 1 CATCACAAAT 0.886571 -50 ACGTGATCTTCATCACAAATAATGACAGTT 39 60 0 CATCACAAAT 0.886571 -157 CTTCGATACACATCACAATTAAGGAAATCT 40 162 0 CATCACAATT 0.929856 -96 ATCTACTCCGCAACACACTTCGATACACAT 40 179 0 CAACACACTT 0.710027 -79 ********** Masking position 5 Map Score: 9.44878 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 44 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 CCGTCTTGTCGGCGGTTGCGCTGACGTTGC 1 193 1 GGCGGTTGCG 0.819166 -86 ATATACCGAAGCCGTCGGCGGGTAACATTT 13 75 1 GCCGTCGGCG 0.782056 -67 TTGCATGTGCTGCGTCTGCGTTCGCTCACC 14 149 0 TGCGTCTGCG 0.985253 -66 CCTTGATATGTCCGTTTGCGGACAAGCAAT 19 42 1 TCCGTTTGCG 0.918368 -259 GGTATATCAATGCGTCTGGCTTGCCTTTAT 25 42 0 TGCGTCTGGC 0.737544 -27 AAATACCACGGGCGTTTGCGAGGATCAACG 30 36 0 GGCGTTTGCG 0.963488 -265 CCGTGGTATTTGCGTCTGCGCGGCAAGCTG 30 55 1 TGCGTCTGCG 0.985253 -246 GCTGCAAACATGCGTCAGGGGGTGTAAAAC 33 74 0 TGCGTCAGGG 0.881618 -73 TCTTCTGGCCTGCGCTAGCGCAGGTAGTAC 36 63 1 TGCGCTAGCG 0.761888 -238 TGGTTTTAGTGCCGTTAGCGTAATGTTGAG 36 211 0 GCCGTTAGCG 0.81077 -90 TTGATCCTGATGCGTTTGCCACCACTGACG 40 71 1 TGCGTTTGCC 0.875517 -187 TTCAAATGAATGCGTCAGTGGTGGCAAACG 40 83 0 TGCGTCAGTG 0.731927 -175 TTTTGCCGGATGCGTCTACGCCTTATCCGG 41 31 0 TGCGTCTACG 0.814834 -53 ********** Masking position 3 Map Score: 9.2374 Number of sites scoring better than the average of aligned sites = 1409 Number in coding regions = 1344 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 ATCACGACGCAACGTCAGCGCAACCGCCGACA 1 199 0 AACGAGCGCA 0.93307 -80 TTTGGCACCGCAACAAAGCGCAAGACACGCAG 2 46 1 CAACAGCGCA 0.923879 -148 ATGAATAAATCCCGGCAGCGGATAGCGTCAAG 3 116 0 CCCGAGCGGA 0.7506 -69 GTGACGTTGTCACCGAAACTCAGCTTGCCCGG 5 12 0 CACCAACTCA 0.707288 -139 GTTATAACTGCAACGTATCTCAAGGACTTGTC 6 186 1 CAACATCTCA 0.27095 -28 AAACGCCTGTAACCGGAGCTCATAGGGCAAAA 8 142 0 AACCAGCTCA 0.779246 -93 GCGCGCTTTTCCCGTAATCGCACGGGTGGATA 9 172 1 CCCGATCGCA 0.877227 -129 CCCCTGCCCACAACGTGGCGCACATTATTACC 11 61 1 CAACGGCGCA 0.870805 -228 GGGGTGAGCGAACGCAGACGCAGCACATGCAA 14 147 1 AACGGACGCA 0.606517 -68 GCGGCAAAACCCCGGAAGCGTACATCAGCACG 27 69 0 CCCGAGCGTA 0.670043 -155 TGGTTATTTACACCTTAGCGCAAAGCGGACGT 29 260 0 CACCAGCGCA 0.987486 -41 GCCACCCTAACACGGTGGCGCATTTTATGGAC 32 95 1 CACGGGCGCA 0.963795 -31 TTGTTTTACACCCCCTGACGCATGTTTGCAGC 33 72 1 CCCCGACGCA 0.867236 -75 TTGAGTGTAAACCCTTAGCGCAGTGAAGCATT 36 184 0 ACCCAGCGCA 0.945004 -117 TGGCGCGATTCACCTGAGCGCAACATTGAGAT 38 98 1 CACCAGCGCA 0.987486 -78 GAATTATTTGAACCAGATCGCATTACAGTGAT 40 116 1 AACCATCGCA 0.82044 -142 **** ****** Masking position 12 Map Score: 10.1883 Number of sites scoring better than the average of aligned sites = 1157 Number in coding regions = 1101 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 GGCGTAATATCTGACAAAACTGCATTTCGATTTCT 9 16 0 CTACAAGCAT 0.948045 -285 AATAAAGCTTCCCACAAAAGGGGATAAAAGTGTGA 16 55 1 CCACAAGGAT 0.677213 -230 AAGGTTAATGCTTACCACGTTGCAATTAACCTGAA 22 52 0 CTACCAGCAA 0.963215 -40 TCGCATTGTGCTAACGACGCGGCAAAACCCCGGAA 27 84 0 CTACGAGCAA 0.947304 -140 TCGAAGTGATCCAACGAATGTGCAAATAGTATAAC 35 97 0 CCACGAGCAA 0.885448 -84 GTTAAAGACACTCACCATCCAGCAACATCTATCAT 37 144 0 CTACCAGCAA 0.963215 -157 AGGTGTCTACCTGACCAGTGAGGAATTT 39 4 0 CTACCAGGAA 0.875029 -213 CACGAAACTTCTTACAATGGCGCATCACCTTCGGC 40 27 0 CTACAAGCAT 0.948045 -231 AGGAAATCTACTTACAAGTTTGCATCACTGTAATG 40 136 0 CTACAAGCAT 0.948045 -122 TGTTAGAATACTAACAAACTCGCAAGGTGAATTTT 40 208 1 CTACAAGCAA 0.963918 -50 ** **** **** Masking position 7 Map Score: 6.06645 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 52 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 TGTTAGGGGGATGTAACCGGTCTGCCCTGAT 1 234 0 ATTAACCGGT 0.659431 -45 TCTTTTATTGATCTTACGCATCCTGTATGAT 6 56 0 ATTTACGCAT 0.906431 -158 AATTGCCAGAATCTAACGGCTTTCGGCAATT 6 106 0 ATTAACGGCT 0.761193 -108 GCGCAAGATCATGTTACCGGTAAAATAACCA 8 30 0 ATTTACCGGT 0.923046 -205 GTTTTGTCAGATATTACGCCTGTGTGCCGTG 9 31 1 ATTTACGCCT 0.939205 -270 GACTTCATTATGTTCCCGCTTTTCATGCGA 10 10 1 ATTTCCCGCT 0.715197 -291 TTACGGCTTTATATTACGGGTGAAAAACTGA 10 166 0 ATTTACGGGT 0.959268 -135 AACATTACCGCTTTTACGGCTGT 24 3 0 CTTTACGGCT 0.714622 -197 CGGCTGGACAATGTTACCGATAACAGTTACC 26 133 1 ATTTACCGAT 0.863135 -98 AGAATTAAAAATGTTACGGGTAACTGTTATC 26 151 0 ATTTACGGGT 0.959267 -80 GCTTTTCTTTATATTACACGTTCATCTGTCG 32 55 0 ATTTACACGT 0.592133 -71 TCATCTTCCCCGTCCGTGCAAAA 37 288 0 ATTTCCCCGT 0.700889 -13 TCTGCCGCTCATTTTACGCATATGTCGGGCA 38 31 1 ATTTACGCAT 0.906432 -145 TCGCGCCAGCAAATTACGGATTATCCTGAAA 38 75 0 AATTACGGAT 0.514439 -101 TTACATTACTATGTTACGCATAACGTGATGT 39 100 1 ATTTACGCAT 0.906432 -117 ACCTGCTGCGATACTACGCCTGGCGGCATAA 39 174 0 ATCTACGCCT 0.662066 -43 ** ******** Masking position 11 Map Score: 5.52454 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 135 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 ACGTTGCATCGCGCTCTTTAATACACCGCCTG 5 54 1 GCGCCTTTAT 0.861705 -97 AAAAGGGGGCGCTCTCTTTTATTGATCTTACG 6 69 0 GCTCCTTTTT 0.951551 -145 GGACCGCGATGGTCTCTTTTTTTGTTGTACGG 7 22 0 GGTCCTTTTT 0.909117 -265 TAAGTTATTCGCGCCTTTTTATAATTCGTTAC 7 96 0 GCGCTTTTTT 0.877265 -191 GCCGCACTTTGCGCGCTTTTCCCGTAATCGCA 9 162 1 GCGCCTTTTC 0.83967 -139 CCTTGTTTCAGCGCGCTTTTAGAGCACGCAAT 14 36 1 GCGCCTTTTG 0.83967 -179 AGGTGCTTCGGCGACCTTTTTTATTACCTTGA 19 16 1 GCGACTTTTT 0.758258 -285 GCGGCATTTTGCTGTCTTTTTTACGCTAATCT 24 153 1 GCTGCTTTTT 0.917298 -47 CCAGCCGGGTGCTGGCTTTTTTTTTGATCTTT 29 170 1 GCTGCTTTTT 0.917298 -131 CTTCATAAGGGGGCGTTTTTGTTTTCATGGTT 30 198 1 GGGCTTTTTT 0.784504 -103 CACATGCTGTGGGGGTTTTTTTTATCCTCAAT 34 55 1 GGGGTTTTTT 0.672767 -94 TGCGGGTCTGGCTCTCTTTTATACTGA 35 6 0 GCTCCTTTTT 0.951551 -175 AGGCCAAATGGCGGTATTTTATACACAAAATG 35 36 0 GCGGATTTTT 0.73802 -145 AGATTGTTGCGGTCGCTTTACTCCATAAACAT 38 139 1 GGTCCTTTAT 0.634514 -37 AAACTCGCAAGGTGAATTTTATTGGCGACAAG 40 223 1 GGTGATTTTT 0.439746 -35 **** ***** * Masking position 7 Map Score: 7.15492 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 414 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 15 TGTTAGGGGGATGTAACCGGTCTGCCCTGA 1 235 0 ATGTAACCGG 0.898999 -44 GCGCAAGATCATGTTACCGGTAAAATAACC 8 31 0 ATGTTACCGG 0.97288 -204 ACTGAAACGCCTGTAACCGGAGCTCATAGG 8 148 0 CTGTAACCGG 0.892751 -87 TGGGCAGGGGCTGTTGCCCACACACTTTAT 11 41 0 CTGTTGCCCA 0.563794 -248 TATAACACTGATGTTACCTGCTTAATCCAG 11 162 1 ATGTTACCTG 0.778605 -127 ACGGATACAAATGTTACCCGCCGACGGCTT 13 83 0 ATGTTACCCG 0.905593 -59 CGGCTGGACAATGTTACCGATAACAGTTAC 26 133 1 ATGTTACCGA 0.846781 -98 AGAATTAAAAATGTTACGGGTAACTGTTAT 26 152 0 ATGTTACGGG 0.822858 -79 AAAATGAAATCTGTTGCCGGAAGTCTTCTT 35 137 0 CTGTTGCCGG 0.969111 -44 TAGATGATAGATGTTGCTGGATGGTGAGTG 37 141 1 ATGTTGCTGG 0.745615 -160 TATGAGGCGGCTTTTGCCGGATGCGTCTAC 41 42 0 CTTTTGCCGG 0.711992 -42 ********** Masking position 4 Map Score: 5.20189 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 339 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159