AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00040_ecoli_reg_300.orf -o00040_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: BIME6 21 BIME Input sequences: #1 araB 300 L-ribulokinase #2 ybaC 151 putative lipase (EC 3.1.1.-) #3 ychK 73 orf, hypothetical protein #4 hnr 91 Hnr protein #5 galU 201 glucose-1-phosphate uridylyltransferase #6 uxaB 226 altronate oxidoreductase #7 b1522 111 orf, hypothetical protein #8 yneH 63 putative glutaminase #9 b1525 76 putative aldehyde dehydrogenase #10 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #11 edd 234 6-phosphogluconate dehydratase #12 zwf 300 glucose-6-phosphate dehydrogenase #13 ugd 248 UDP-glucose 6-dehydrogenase #14 gnd 300 gluconate-6-phosphate dehydrogenase, decarboxylating #15 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #16 wcaK 61 putative galactokinase (EC 2.7.1.6). #17 BIME91 82 BIME #18 wcaJ 54 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase #19 cpsG 104 phosphomannomutase #20 gmd 25 GDP-D-mannose dehydratase #21 wcaA 34 putative regulator #22 BIME92 24 BIME #23 wza 300 putative polysaccharide export protein #24 araE 300 low-affinity L-arabinose transport system proton symport protein #25 kduD 29 2-deoxy-D-gluconate 3-dehydrogenase #26 kduI 286 homolog of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase #27 yqeF 251 putative acyltransferase #28 uxaC 300 uronate isomerase #29 agaZ 248 putative tagatose 6-phosphate kinase 2 #30 BIME157 76 BIME #31 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #32 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #33 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #34 dam 106 DNA adenine methylase #35 damX 91 putative membrane protein; interferes with cell division #36 aroB 56 3-dehydroquinate synthase #37 aroK 199 shikimate kinase I #38 yrfD 68 orf, hypothetical protein #39 xylB 71 xylulokinase #40 xylA 300 D-xylose isomerase #41 yiaK 200 putative dehydrogenase #42 yiaM 117 orf, hypothetical protein #43 rhaD 85 rhamnulose-phosphate aldolase #44 rhaB 287 rhamnulokinase #45 uxuA 300 mannonate hydrolase #46 uxuB 80 D-mannonate oxidoreductase Motif number 1 ATACGCAGATTTACTCTTGCTTTAAAATGAATA 9 45 0 TTACTTTTTT 0.498096 -32 CGCTTATCCTTTATGGTTATTTTACCGGTAACA 11 17 1 TTATGTTTTT 0.743119 -218 CAAAACTGCATTTCGATTTCTTTCAG 12 4 0 TTTCGTTTTT 0.977273 -297 ATTATAGCTTGTTCGATTTTTTTCGCCAGCATC 15 122 0 GTTCGTTTTT 0.836574 -53 AATACACTGATTTAGTTTAATTTTTCACACCCT 23 70 0 TTTAGTTTTT 0.755227 -231 TGAAACACTGTTTCGTTTTCTCTATAAAGGGAT 26 219 0 TTTCGTTTCT 0.836574 -68 TTGCCCTCCATTTTGTTTAATTTGTAGATGATA 27 21 0 TTTTGTTTTT 0.925962 -231 TTCGTAAAACTTTCGTTTCATTTCGTTTTGCCT 29 21 1 TTTCGTTTTT 0.977273 -228 GTGACTTTCATTATGTTTCTTTTGTGAATCAGA 29 121 1 TTATGTTTTT 0.743119 -128 AACCATTATCTTTCGTTTTATTTTTATCTCACC 29 160 1 TTTCGTTTTT 0.977273 -89 GATATTAATCTTTCGTTTTGTTTCAGTTGATAC 29 201 0 TTTCGTTTTT 0.977273 -48 CCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATC 30 43 1 TTTCTTTTTT 0.81098 -34 ATCCCTTTTGCTTCCTTTATCTTTTCTT 31 6 1 TTTTGTTTTT 0.925962 -186 CGATCACAAATTTCGTTTTATTTCTTTTTTCTC 31 43 1 TTTCGTTTTT 0.977273 -149 TCCATTGAACTTTCAGTTTCTTTTCTATAGATT 31 74 1 TTTCATTTTT 0.708719 -118 TTCACTTGCCTTTCGTTTCATTTCACTTGGTGA 31 124 0 TTTCGTTTTT 0.977273 -68 CGATTACGATTTTTGGTTTATTTCTTGATTTAT 40 60 1 TTTTGTTTTT 0.925962 -241 ***** ** *** Masking position 7 Map Score: 22.6414 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 26 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GCGTCTCGCGCGCTCCCGTCAGATTGTGTTAA 2 47 0 CGCCCGTCAG 0.965135 -105 TTCTGACAGGCGCAGGTGGCAATAGCATGCCA 4 39 1 CGCGGGGCAA 0.92593 -53 CTTTATTTGCCGCCGCTGTCAGCGAACATGCT 7 49 1 CGCGCGTCAG 0.994057 -63 AGGGCAAAAACGTTTCAGTCAGTGTAATAAAA 11 119 0 CGTTCGTCAG 0.912656 -116 ATTCACAACGCGTTTCATTCAGAGGATTTATG 11 178 0 CGTTCTTCAG 0.654502 -57 CGTTTTACGCCGCATCCGGCAACCGTTGTCGG 17 27 0 CGCTCGGCAA 0.973977 -56 ACGTCGCATCAGGCAATGAATGCGAA 19 5 1 CGCTCGGCAA 0.973977 -100 TAAAATTGGCCGCTTCGGTCAGGGCCAACTAT 19 62 1 CGCTCGTCAG 0.989007 -43 TTCACACCCTCTCAGCATGCAGTCGTTGATGA 23 48 0 CTCGCTGCAG 0.849667 -253 GAACAACTCACGCAGGTGTCAGGTCGGAAACA 24 236 0 CGCGGGTCAG 0.967792 -65 ATGTCTTACTCTCTGCTGGCAGGAAAAA 24 283 1 CTCGCGGCAG 0.96892 -18 AATATGCCTGAGCAGCAGTCAGAGACATAACT 27 140 0 AGCGCGTCAG 0.910565 -112 CCAGTACTGGCGCGGCCTGCAGCGAGATTTAC 28 141 1 CGCGCTGCAG 0.979864 -160 CAGCATCCAGCGCTTCAGGCAACTCCCGCAAC 34 39 0 CGCTCGGCAA 0.973977 -68 *** ** ***** Masking position 11 Map Score: 19.2306 Number of sites scoring better than the average of aligned sites = 1678 Number in coding regions = 1420 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 AAAGTCCACATTGATTATTTGCACGGCGTCACACTTT 1 166 1 TTATATGCGC 0.852465 -135 ATTCAGAGGATTTATGACTGAAACGCCTGTAACCGGA 11 157 0 TTATATACCC 0.861659 -78 AATGAAACGCGTTGTGAATCATCCTGCTCTGACAACT 11 191 1 GTGTATACGC 0.953326 -44 TTTATCTGCTTTTGTCATTAACACGGCACACAGGCGT 12 46 0 TTGTATACGC 0.934342 -255 CGATGATTTTTTTATCAGTTTTGCCGCACTTTGCGCG 12 140 1 TTATATTCGC 0.956052 -161 TTGATCGAATTTCATCAGTTTTTCACCCGTAATATAA 14 152 1 TTATATTCCC 0.830235 -149 TTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCAT 19 30 0 GTGTATACGC 0.95332 -75 TTACGTGCCAGTTATGTCTCTGACTGCTGCTCAGGCA 27 131 1 GTATTTTCGC 0.714918 -121 TACTCTCAAAGTGGTAAATCTCGCTGCAGGCCGCGCC 28 149 0 GTGTATTCGC 0.941304 -152 GGAAATTGGTGTGATAACTTTGTCAGCATCGCACCAT 28 238 1 GTATATTCGC 0.968967 -63 CGGAGAAGGTGTAATTAGTTAGTCAGC 34 90 1 GTATATACGC 0.97547 -17 GACATCCACCTTAATTACTGTACCCGCAGACGAGTGT 36 25 0 TTATATTCGC 0.956052 -32 ATGATGATGATTTATCATTCAGGCGGCATTTTGCTGT 37 131 1 TTATATACGC 0.965164 -69 TCTTTTGAAATTCATCAATCAGATTGCCTTGTTAAAA 41 92 1 TTATATATGC 0.798431 -109 TCTAACTATATTAATAATTCAGGTTGCTGCACATGCG 42 54 1 TTATATATGC 0.798431 -64 GGCTATGTCTGTCATAATTCAAGTCGCATGTGCAGCA 42 78 0 GTATATATGC 0.850419 -40 ACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGA 44 26 0 GTATATTCCC 0.875301 -262 ** ** * * * * ** Masking position 9 Map Score: 16.7411 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 158 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 GGTTAACATAGTGCTACTCAGGCGGTTAATACG 3 38 0 GGCTTCAGGC 0.921855 -36 CATTATGTTCCCGCTTTTCATGCGATACATTAT 14 16 1 CGCTTCATGC 0.897336 -285 AGGCGTTTTACGCCGCATCCGGCAACCGTTGTC 17 29 0 CCCGTCCGGC 0.983669 -54 CGGCGTAAAACGCCTTATCCGTCCTACGGTTCT 17 47 1 CCCTTCCGTC 0.885461 -36 ACGTCGCATCAGGCAATGAATGCG 19 2 1 CTCGTCAGGC 0.889429 -103 ATCGTTACCCTTTTTCAGGCAATAGTTGGC 19 85 0 CCTTTCAGGC 0.869673 -20 ATGTCTCTGACTGCTGCTCAGGCATATTTCCTT 27 144 1 CGCTTCAGGC 0.991066 -108 CGACAGCATCCAGCGCTTCAGGCAACTCCCGCA 34 41 0 CGCGTCAGGC 0.984131 -66 TAACTAATTACACCTTCTCCGGCTGTGGAGAAA 34 78 0 CCCTTCCGGC 0.990804 -29 AAAGGTCAGGCCGCTTATCAAGCGGTCTATTAG 35 18 1 CGCTTCAAGC 0.897336 -74 AAAAACATTACCGCTTTTACGGCTGT 37 4 0 CGCTTACGGC 0.902155 -196 TGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 43 26 1 CCCTTCCGGC 0.990804 -60 * *** ****** Masking position 8 Map Score: 14.0673 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 546 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 GCGGGGTTACCGGTTGGGTTAGCGAGAAGAGCCAG 1 51 0 CGGTGGTGCA 0.77279 -250 TCAATATCAGCAGGCGGGATCGCATTTTCATGGCA 2 87 1 CAGGGGTGCT 0.990323 -65 TTCTGAAAAGGAGGCGAGTTAGCATAATTAAGACA 5 91 0 GAGGGGTGCT 0.929831 -111 AATTTGATGCCAGGTGAGGCTGCGTTTGTTTTGTT 16 25 0 CAGGGGCGCT 0.972578 -37 GCTAAAAAGCCAGGGGCGGTAGCGTGTCTGGATGC 23 107 1 CAGGGGTGCT 0.990323 -194 TTCCTCTCAACGAGTGAGCTAGCTTGCTTATGGTG 28 269 0 CGAGGGTGCT 0.894802 -32 GTCAATGGGCAAGGTGGGCTTGCATTTGCTTAATA 29 67 0 AAGGGGTGCT 0.940355 -182 CGTTTTGTTTCAGTTGATACTGCGTCATGGTGAGA 29 186 0 CAGTGTCGCT 0.739151 -63 AACTTGACGTCGGGCGTTGTCGCTTTCACTTGCCT 31 146 0 CGGGGTTGCT 0.974513 -46 ACAGTAATTAAGGTGGATGTCGCGTT 36 41 1 AGGTGTTGCT 0.593354 -16 TAACATTACCCAGGCGTTCTGGCGTAGACGATTAT 42 15 0 CAGGGTTGCT 0.970595 -103 GGCGTTGCATCGGATGAGATGGCGTATAAGTTCTA 45 181 0 CGGAGGTGCT 0.920771 -120 **** * * * ** * Masking position 13 Map Score: 9.82386 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 310 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CCTACCTGACGCTTTTTATCGCAACTCTCT 1 241 1 GCTTTTTATC 0.689652 -60 CCAGAATTTTTATCTACACTTAAG 4 5 1 AATTTTTATC 0.726762 -87 TAAAATGAATAATATTAAGCCACTTATTCA 9 26 0 AATATTAAGC 0.597586 -51 ATCAGTGTCAGATTTTTACCCAATGGAAAA 12 110 1 GATTTTTACC 0.660523 -191 TTATTAAGTTAATATTAAGCAGTGAAATTT 13 88 0 AATATTAAGC 0.597586 -161 AGTACTTTTAGATATTTAGCCAGAAAACGT 14 103 1 GATATTTAGC 0.872238 -198 ACCGCCCCTGGCTTTTTAGCTACCAATACA 23 97 0 GCTTTTTAGC 0.730616 -204 AATGACGGCAGATATTTATCGGTAAGGAGG 26 21 0 GATATTTATC 0.847551 -266 TAAAAAAAGTGATTTTTATCACAAAGGAAA 27 170 0 GATTTTTATC 0.891407 -82 AGATTACTGCGATATTAATCTTTCGTTTTG 29 214 0 GATATTAATC 0.790097 -35 CTTTTCTATAGATTTTAATCAACGAAAGAC 31 93 1 GATTTTAATC 0.847551 -99 GGCACTCCCCGATATTAATCGGGAAGTACA 32 38 0 GATATTAATC 0.790097 -129 CAATTTTTAGCAACTAAACAG 40 2 1 AATTTTTAGC 0.763747 -299 AACAATTACAGATTTTTATCTTTCGATTAC 40 37 1 GATTTTTATC 0.891407 -264 CGCATATTGAAATTTTAAGCCAAAAAAGCG 41 157 1 AATTTTAAGC 0.686622 -44 ********** Masking position 8 Map Score: 10.1189 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 161 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 TTTTACACTTTCAGGCCTCGTGCGGATTCA 11 76 1 TCAGGCCTCG 0.973316 -159 TGCGAACATTCCAGGCCGCGAGCATTCAGC 14 252 1 CCAGGCCGCG 0.975822 -49 CGGTGCGAATGCAGGCGTCG 22 1 0 GCAGGCGTCG 0.949615 -24 GACTGGTCTTTCAGGCATCCAGACACGCTA 23 126 0 TCAGGCATCC 0.782104 -175 AAATCTCGCTGCAGGCCGCGCCAGTACTGG 28 141 0 GCAGGCCGCG 0.990845 -160 ACAAGAAAGGTCAGGCCGCTTATCAAGCGG 35 13 1 TCAGGCCGCT 0.944744 -79 ATCATGGAACGCAGGCAGCGAAGAGCACCA 37 106 0 GCAGGCAGCG 0.967385 -94 GATTTATCATTCAGGCGGCATTTTGCTGTC 37 139 1 TCAGGCGGCA 0.913114 -61 TGCGCTACCATCAGGACGCGACAAA 41 6 0 TCAGGACGCG 0.957962 -195 GTTGACGACATCAGGAGGCCAGT 44 4 0 TCAGGAGGCC 0.832086 -284 ********** Masking position 3 Map Score: 9.22265 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 626 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTTGCACGGCGTCACACTTTGCTATGCCATAG 1 183 1 GTACATTTGC 0.938602 -118 CATGATCCGCGCCACACTTTTCTCATAAAACT 6 95 1 GCACATTTTC 0.889666 -132 TAAAAATTGTTCTACAATCTGCGCAAGATCAT 11 49 0 TCACATCTGC 0.805875 -186 TATCAGTTTTGCCGCACTTTGCGCGCTTTTCC 12 152 1 GCGCATTTGC 0.980591 -149 TGGATAAGCGTTTACAGTTTTCGCAAGCTCGT 12 198 1 TTACATTTTC 0.53003 -103 ATCGGCAATTTGCATTCCGTCGA 28 2 1 TCGCATTTGC 0.955686 -299 TATCATTCAGGCGGCATTTTGCTGTCTTTTTT 37 143 1 GCGCATTTGC 0.980435 -57 CGTGAACTACGGCACACTTTGCGCTACCATCA 41 23 0 GGACATTTGC 0.899671 -178 CGTGATGATGTTCACAATTTGCTGAATTGTGG 44 158 0 TTACATTTGC 0.867091 -130 ATTACCCTTTGCTGCAATTTGCAGCAACAACC 45 80 1 GCGCATTTGC 0.980591 -221 ** *** ***** Masking position 6 Map Score: 5.50323 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 307 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 AGCGGATCCTACCTGACGCTTTTTATCGCAACTCT 1 234 1 AACCTTTTTA 0.666519 -67 GGATTCACCCACGAGGCTTTTTTTATTACACTGAC 11 99 1 AGCTTTTTTA 0.900843 -136 ATGAAAAAAAATAACAACTTTTTTATCTGCTTTTG 12 69 0 AAATTTTTTA 0.866114 -232 CCAATGGAAAACGATGATTTTTTTATCAGTTTTGC 12 129 1 AGATTTTTTA 0.810967 -172 CGTATATTGCACCGGGCTTTTTTTTGCCAAATATC 13 44 1 AGCTTTTTTT 0.726689 -205 TCATCATGACAATCGAAGTTTTTTTTCAAAAGCCT 14 51 1 AAATTTTTTT 0.654386 -250 ATATTTAGCCAGAAAACGTATTTTATCAAATCGCA 14 114 1 AACTATTTTA 0.574199 -187 CCTGCGGATGAAATCAATTTTTTTAGGACTGATGC 23 175 1 AAATTTTTTA 0.866114 -126 CGTGATCGACACTGCACTTTTTTTAATCCTTAACT 26 129 1 AACTTTTTTA 0.931979 -158 TTTGTGATAAAAATCACTTTTTTTAAACAATTAAG 27 175 1 AACTTTTTTA 0.931979 -77 TACCACTTTGAGAGTAATTTTTTTAACTACGTTTA 28 170 1 AAATTTTTTA 0.86613 -131 AAAGTTGAATAATATAATTTTTTTAAATATATTAT 32 125 0 AAATTTTTTA 0.866114 -42 CGGTAGCGATACCGGGCATTTTTTTAAGGAACGAT 39 43 1 AGCTTTTTTT 0.726689 -29 TATCTTGAAAAATCGACGTTTTTTACGTGGTTTTC 44 84 0 AACTTTTTTA 0.931979 -204 * ** ******* Masking position 1 Map Score: 6.90716 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 50 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 TTTGTTACAGAATGCTTTTAATAAGCGGGG 1 80 0 AATGCTTTTA 0.738174 -221 CACCCACGAGGCTTTTTTTATTACACTGAC 11 104 1 GCTTTTTTTA 0.821457 -131 GGAAAACGATGATTTTTTTATCAGTTTTGC 12 134 1 GATTTTTTTA 0.831072 -167 GGTGCACTGTACTGCTTTTACGAGCTTGCG 12 219 0 ACTGCTTTTA 0.725021 -82 TGTGAATCATGATGTTTTTAGCATCCTGAT 13 204 0 GATGTTTTTA 0.821457 -45 GGATGAAATCAATTTTTTTAGGACTGATGC 23 180 1 AATTTTTTTA 0.887068 -121 TCGACACTGCACTTTTTTTAATCCTTAACT 26 134 1 ACTTTTTTTA 0.88018 -153 GATAAAAATCACTTTTTTTAAACAATTAAG 27 180 1 ACTTTTTTTA 0.88018 -72 CTTTGAGAGTAATTTTTTTAACTACGTTTA 28 175 1 AATTTTTTTA 0.887068 -126 TGAATAATATAATTTTTTTAAATATATTAT 32 125 0 AATTTTTTTA 0.887068 -42 TAAAAGCGGTAATGTTTTTACGCTGAACGT 37 18 1 AATGTTTTTA 0.88018 -182 ********** Masking position 10 Map Score: 5.32471 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 51 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 CATCAGACATTGCCGTCACTGCGTCTTTTA 1 21 1 TGCCGTCACT 0.966355 -280 TGGACTTTTCTGCCGTGATTATAGACACTT 1 144 0 TGCCGTGATT 0.903214 -157 TACCTTTATTTGCCGCCGCTGTCAGCGAAC 7 46 1 TGCCGCCGCT 0.965342 -66 CCTCTCAGCATGCAGTCGTTGATGAGAAAG 23 43 0 TGCAGTCGTT 0.787561 -258 GATAAATATCTGCCGTCATTAATCTGTTGA 26 31 1 TGCCGTCATT 0.947667 -256 GTTATCTTTCTGCCGTCGCAAATCATAAGT 28 33 0 TGCCGTCGCA 0.903762 -268 AATCAGGTAATGCCGCGGGTGATGGATGAT 40 269 0 TGCCGCGGGT 0.808057 -32 GCGCAAAGTGTGCCGTAGTTCACGATCTCG 41 31 1 TGCCGTAGTT 0.846247 -170 ATTGATTGCCGTGGATGCGCGCGAGC 43 7 1 TGCCGTGGAT 0.869203 -79 CCTTCTTCCTTGCCGTCACTCTTTGAAGAC 46 44 1 TGCCGTCACT 0.966355 -37 ********** Masking position 1 Map Score: 6.09962 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 536 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 ATAACGACATGTCGCAGCAATTTAATCCATA 24 198 1 GTCGCACAAT 0.894468 -103 AACCTCGCACCAATTAACAGTGCA 27 238 0 CTCGCACAAT 0.894564 -14 TGACAAAGTTATCACACCAATTTCCAGAGTC 28 232 0 ATCACACAAT 0.939371 -69 AAAGATTAATATCGCAGTAATCTGAACTGGA 29 221 1 ATCGCATAAT 0.87595 -28 TAATAAATACATCACTACAATATCGCAACAA 32 95 1 ATCACTCAAT 0.735199 -72 TCACTACAATATCGCAACAATAATATATTTA 32 106 1 ATCGCACAAT 0.973134 -61 ATCTAAAATCGCCTTAATATTGGTTTGA 33 8 1 ATCGCCTAAT 0.777541 -31 TGAGCATCACATCACCACAATTCAGCAAATT 44 144 1 ATCACCCAAT 0.883381 -144 TGTGACATTCATCGCAACAATGGTTGACCAA 45 28 0 ATCGCACAAT 0.973134 -273 GGTTAACCACATCACAAGAATTTCACTCTCA 45 113 0 ATCACAGAAT 0.719488 -188 ****** **** Masking position 9 Map Score: 5.07378 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 136 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 GACGTAATTTGAAAGGAGTTTTTGT 2 137 1 GAAAGGAGTT 0.90154 -15 ATGATCCAGGAAAAGGCGTTTTTCCTCGAT 6 60 1 AAAAGGCGTT 0.90154 -167 ATTTATGACTGAAACGCCTGTAACCGGAGC 11 155 0 GAAACGCCTG 0.876254 -80 TCCTCTGAATGAAACGCGTTGTGAATCATC 11 184 1 GAAACGCGTT 0.974053 -51 GATGCGGCGTAAAACGCCTTATCCGTCCTA 17 43 1 AAAACGCCTT 0.856478 -40 AAAGTTTTACGAAAGGACTTACT 29 4 0 GAAAGGACTT 0.880842 -245 TTGCTTAATAGAAAGGCGTTAATAGGCAAA 29 47 0 GAAAGGCGTT 0.978947 -202 GAAAGAAAAAGAAAGGCCTTACGGGGGAAG 30 37 0 GAAAGGCCTT 0.974053 -40 TCAAATAGATGAAACACGTTCAGCGTAAAA 37 33 0 GAAACACGTT 0.786337 -167 ********** Masking position 4 Map Score: 4.79714 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 74 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 ACTTTTGTTACGCGTTTTTGTCATGGCTTT 1 118 0 CGCGTTTTTG 0.842195 -183 GATCCTACCTGACGCTTTTTATCGCAACTC 1 238 1 GACGCTTTTT 0.784275 -63 TTTCTCCATACCCGTTTTTTTGGATGGAGT 1 275 1 CCCGTTTTTT 0.854307 -26 TCCAGGAAAAGGCGTTTTTCCTCGATTAAA 6 64 1 GGCGTTTTTC 0.886025 -163 TCACCCACGAGGCTTTTTTTATTACACTGA 11 103 1 GGCTTTTTTT 0.843634 -132 CCGCACTTTGCGCGCTTTTCCCGTAATCGC 12 163 1 CGCGCTTTTC 0.85338 -138 TATTGCACCGGGCTTTTTTTTGCCAAATAT 13 48 1 GGCTTTTTTT 0.843634 -201 TCATTATGTTCCCGCTTTTCATGCGATACA 14 15 1 CCCGCTTTTC 0.668912 -286 TTTGTTCGTTGCCGCTTTTT 16 1 0 GCCGCTTTTT 0.81448 -61 ATCGACACTGCACTTTTTTTAATCCTTAAC 26 133 1 CACTTTTTTT 0.607972 -154 TGATAAAAATCACTTTTTTTAAACAATTAA 27 179 1 CACTTTTTTT 0.607972 -73 TATACTACCGCGCGTTTGTTTATAAACTGC 38 15 0 CGCGTTTGTT 0.681762 -54 AGCGATACCGGGCATTTTTTTAAGGAACGA 39 47 1 GGCATTTTTT 0.571006 -25 TTTTTTTGATCGCTTTTTTGGCTTAAAATT 41 167 0 CGCTTTTTTG 0.630249 -34 TTGAAAAATCGACGTTTTTTACGTGGTTTT 44 85 0 GACGTTTTTT 0.829227 -203 CGCGAATTCAGGCGCTTTTTAGACTGGTCG 44 243 1 GGCGCTTTTT 0.926728 -45 ********** Masking position 6 Map Score: 7.57933 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 711 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 15 ACGGGTGGTTAACTGAGCGGCGAATGTTAAC 2 21 1 AACTAGCGGC 0.789547 -131 TGCAATCCACAACGAAGCGGCGTAACATCAC 15 61 1 AACGAGCGGC 0.971091 -114 GTTGGCCCTGACCGAAGCGGCCAATTTTATT 19 60 0 ACCGAGCGGC 0.981403 -45 CAAGGCCAGTACTGGCGCGGCCTGCAGCGAG 28 136 1 ACTGCGCGGC 0.968922 -165 ATAATCAGGTAATGCCGCGGGTGATGGATGA 40 270 0 AATGCGCGGG 0.764904 -31 CATCCGATGCAACGCCACGGCTGCGGTCTGG 45 200 1 AACGCACGGC 0.970984 -101 TATCCACCGGCATGGCTGCGCGCCGT 46 6 1 ACCGCATGGC 0.856125 -75 GGAAGAAGGAACCGGCACGGCGCGCAGCCAT 46 22 0 ACCGCACGGC 0.981403 -59 **** ****** Masking position 1 Map Score: 3.44105 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 677 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159