AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_ecoli_reg_300.orf -o00300_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 thrL 189 thr operon leader peptide #2 thrA 81 aspartokinase I, homoserine dehydrogenase I #3 b0024 102 orf, hypothetical protein #4 ileS 42 isoleucine tRNA synthetase #5 slpA 29 probable FKBX-type 16KD peptidyl-prolyl cis-trans isomerase (a rotamase) #6 yaaF 65 orf, hypothetical protein #7 dapB 166 dihydrodipicolinate reductase #8 yabB 300 orf, hypothetical protein #9 dapD 30 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase #10 glnD 61 protein PII; uridylyltransferase acts on regulator of glnA #11 map_rpsB 367 map: methionine aminopeptidase, rpsB: 30S ribosomal subunit protein S2 #12 tsf 257 protein chain elongation factor EF-Ts #13 pyrH 146 uridylate kinase #14 frr 291 ribosome releasing factor #15 yaeM 91 putative ATP-binding component of a transport system #16 yaeS 185 orf, hypothetical protein #17 cdsA 120 CDP-diglyceride synthetase #18 yaeT 29 orf, hypothetical protein #19 hlpA 121 histone-like protein, located in outer membrane or nucleoid #20 ybdL 108 putative aminotransferase #21 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #22 ybeX 89 putative transport protein #23 ybeZ 113 putative ATP-binding protein in pho regulon #24 yleA 145 orf, hypothetical protein #25 htrB 224 heat shock protein #26 ydcH 72 orf, hypothetical protein #27 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #28 malX 174 PTS system, maltose and glucose-specific II ABC #29 cstC 300 acetylornithine delta-aminotransferase #30 msbB 119 suppressor of htrB, heat shock protein #31 yebA 78 orf, hypothetical protein #32 yebL 24 putative adhesin #33 wcaA 34 putative regulator #34 BIME92 24 BIME #35 wza 300 putative polysaccharide export protein #36 yffB 300 orf, hypothetical protein #37 dapA 79 dihydrodipicolinate synthase #38 lysA 121 diaminopimelate decarboxylase #39 prfB 90 peptide chain release factor RF-2 #40 dsbC 24 protein disulfide isomerase II #41 xerD 111 site-specific recombinase #42 asd 192 aspartate-semialdehyde dehydrogenase #43 dapF 300 diaminopimelate epimerase #44 metB 276 cystathionine gamma-synthase #45 lysC 300 aspartokinase III, lysine sensitive #46 lysU 236 lysine tRNA synthetase, inducible; heat shock protein #47 yjdL 58 putative peptide transporter #48 cadA 79 lysine decarboxylase 1 #49 cadB 300 transport of lysine/cadaverine #50 yjeA 294 putative lysyl-tRNA synthetase Motif number 1 CTGTCAGGTGCGGGCTTTTTTCTGTGTTTC 2 20 0 CGGGCTTTTT 0.939557 -62 CCTGACAGTGCGGGCTTTTTTTTTCGACCA 2 42 1 CGGGCTTTTT 0.939557 -40 GGTAACAAGACCGGCATTTTCGCATAACTT 6 25 0 CCGGCATTTT 0.942473 -41 GGTCTTGTTACCGGCATTTTTTATGGAGAA 6 43 1 CCGGCATTTT 0.942473 -23 TGCGACGCGAGCGGCATTTTAGGACATATC 8 17 0 GCGGCATTTT 0.953304 -284 CCGGCGAATGCCGGCTTTTTTAATGCGATA 10 18 1 CCGGCTTTTT 0.980444 -44 CTCGAGCTTGCCGCCTTTCTGCAACTCGAA 12 38 0 CCGCCTTTCT 0.728523 -220 CCCTCAGGCGGCTCCTTTTTGATAA 13 6 0 GCTCCTTTTT 0.655263 -141 CCGCCTGAGGGCGGCTTCTTTTTGTGCCCA 13 25 1 GCGGCTTCTT 0.800078 -122 GATCTACTGAGCGGCGTTTTTGTCGTTCAA 15 15 0 GCGGCGTTTT 0.970305 -77 GGATCGGCTGGCGGCGTTTTGCTTTTTATT 15 50 1 GCGGCGTTTT 0.970305 -42 GTGGTTTTACACGGCTTTTTTTTGTATAGG 16 118 1 ACGGCTTTTT 0.915716 -68 CGTCGTCATCGCGGCGTTGTTTCTGTTGCC 17 64 1 GCGGCGTTGT 0.821841 -57 TTTGCGTGGCCCGGCGATCTTATATTGATC 19 59 0 CCGGCGATCT 0.588384 -63 GTGATTAACGACGGCGTTTTGATTAACTAA 22 49 1 ACGGCGTTTT 0.850353 -41 TGCAATGCTTGCGCCTTTTTCCTGTGGCGT 23 69 1 GCGCCTTTTT 0.925264 -45 ATATCATGCCGCGGATTTTTACTTTCCCAT 25 30 0 GCGGATTTTT 0.624274 -195 ATTTACAAGCGCGGCAATTTCGCCCAGTCT 25 125 1 GCGGCAATTT 0.804697 -100 CGCCAGCCAGGCGGCTTTTTTAACAACTGC 27 23 1 GCGGCTTTTT 0.984246 -40 GGAAATTACTGCGCCATTCTGAC 29 4 0 GCGCCATTCT 0.522155 -297 GCAGTCAGTACCGGCTTTTTTTATTTGGTG 30 35 1 CCGGCTTTTT 0.980444 -85 GGCGACAGAGCGGGCTATCTGTTGCACGTA 31 23 0 CGGGCTATCT 0.458694 -56 GCTACCGCCCCTGGCTTTTTAGCTACCAAT 35 100 0 CTGGCTTTTT 0.634482 -201 ACTCCAGATAAGTGCTTTTTTATGATTACG 38 97 0 AGTGCTTTTT 0.340879 -25 TGCGACTTATCCTGCTTTGTTAGCACGCAG 42 44 0 CCTGCTTTGT 0.52077 -149 TGCGACTTTGGCTGCTTTTTGTATGGTGAA 42 110 1 GCTGCTTTTT 0.905587 -83 GGTCGGCGGCGGTGCGTTTTTATCTGCAGG 43 161 0 GGTGCGTTTT 0.608671 -140 TATAATTTTAACGGCTATTTGGGATTTGCT 44 148 1 ACGGCTATTT 0.68679 -129 GTGTTGGGAGGGGCCTTTTTTACCTGGAGA 48 53 1 GGGCCTTTTT 0.793325 -27 ATAATATGTTGCGGCAATTTATTTGCCGCA 49 11 1 GCGGCAATTT 0.804697 -290 ACCATCAGATCGTGCTTTTTTTAGTCACTG 50 215 1 CGTGCTTTTT 0.704714 -80 ********** Masking position 10 Map Score: 40.5816 Number of sites scoring better than the average of aligned sites = 1579 Number in coding regions = 1341 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 2 CACTGTCAGGTGCGGGCTTTTTTCTGTGTTT 2 21 0 TGCGGGCTTT 0.941925 -61 CACCTGACAGTGCGGGCTTTTTTTTTCGACC 2 40 1 TGCGGGCTTT 0.941925 -42 CCGGTAACAAGACCGGCATTTTCGCATAACT 6 26 0 GACCGGCTTT 0.967011 -40 CCGGTCTTGTTACCGGCATTTTTTATGGAGA 6 41 1 TACCGGCTTT 0.954989 -25 TTTGCGACGCGAGCGGCATTTTAGGACATAT 8 18 0 GAGCGGCTTT 0.967011 -283 AGCCGGCGAATGCCGGCTTTTTTAATGCGAT 10 16 1 TGCCGGCTTT 0.975275 -46 AGCCGCCTGAGGGCGGCTTCTTTTTGTGCCC 13 23 1 GGGCGGCTCT 0.888262 -124 AGGATCTACTGAGCGGCGTTTTTGTCGTTCA 15 16 0 GAGCGGCTTT 0.96701 -76 GCGGATCGGCTGGCGGCGTTTTGCTTTTTAT 15 48 1 TGGCGGCTTT 0.975275 -44 GCCGCCAGCCAGGCGGCTTTTTTAACAACTG 27 21 1 AGGCGGCTTT 0.876064 -42 ACGCAGTCAGTACCGGCTTTTTTTATTTGGT 30 33 1 TACCGGCTTT 0.954989 -87 CTTGCGACTTTGGCTGCTTTTTGTATGGTGA 42 108 1 TGGCTGCTTT 0.705973 -85 AGCGTTCGCAGTCGGGCGTTTCGCAAGTGGT 45 172 1 GTCGGGCTTT 0.714473 -129 CATGTGTTGGGAGGGGCCTTTTTTACCTGGA 48 50 1 GAGGGGCTTT 0.923389 -30 ******* *** Masking position 9 Map Score: 21.1501 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 229 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 CGCATCGCTACGCCGCCAGCCAAAAACGCTGA 7 97 0 CGCGCCGCCA 0.990511 -70 TCAATGGTATCACACCCGGGCAAATTGAGAAT 11 295 0 CACCCCGGCA 0.887495 -73 AAAAAGAAGCCGCCCTCAGGCGGCTCCTTTTT 13 16 0 CGCCTCGGCG 0.850328 -131 GGTTGCTGCGCGCTGGCCGTGACCAAACTGCC 14 93 0 CGCGGCGTGA 0.533866 -199 GGATGGCGAGCACTGCCCGGGGCCAAAATGGC 14 146 1 CACGCCGGGG 0.85063 -146 AAAAGCAAAACGCCGCCAGCCGATCCGCAAGG 15 44 0 CGCGCCGCCG 0.993942 -48 CAGTTCTTTGCGTGGCCCGGCGATCTTATATT 19 63 0 CGTGCCGGCG 0.951001 -59 CGCATTTTTTCGCCCGCAACCAAAATTTGTGG 25 159 0 CGCCGCACCA 0.69405 -66 ACTTTCCTAAGCCGCCAGCCAGGCGGCTTTT 27 10 1 AGCGCCGCCA 0.846593 -53 GCACTTTTATCACTGGCTGGCACGAACCCTGC 29 206 1 CACGGCGGCA 0.904167 -95 TTAACATCCATTCGCAGCCGGTACGCAGTC 30 9 1 CATCGCGCCG 0.514902 -111 CCTTTCAGACCGCAGCCCGTCAGGCTGAAGAG 43 113 0 CGCGCCGTCA 0.947501 -188 AAAAACGCACCGCCGCCGACCAAACCGGTAGA 43 170 1 CGCGCCACCA 0.941342 -131 CGATGATGAACGTGGCCAGCCGTTCAATCACC 45 105 0 CGTGCCGCCG 0.962717 -196 CAGAAGCGTTCGCAGTCGGGCGTTTCGCAAGT 45 168 1 CGCGTCGGCG 0.943472 -133 TTTTTTTAGTCACTGCCCACCGCTGTTTGATT 50 230 1 CACGCCACCG 0.882477 -65 *** *** **** Masking position 7 Map Score: 15.7305 Number of sites scoring better than the average of aligned sites = 2913 Number in coding regions = 2811 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 CATAAAAAATGCCGGTAACAAGACCGGCATTTTCGCA 6 31 0 GCGGTAGCGG 0.993149 -35 TTTATATCTGTGCGGTTTAATGCCGGGCAGATCACAT 12 215 1 TCGGTTGCGG 0.97793 -43 CTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTC 14 68 1 GCGTTTTCGG 0.724877 -224 TTAAACATATTACGGGTAATCGTCTGGATTATTAGGC 14 188 0 TCGGGCGCGG 0.798292 -104 CACCGGAGGGTGCAGTTCTTTGCGTGGCCCGGCGATC 19 70 0 TCAGTTGGGG 0.617026 -52 GGGGACGTCTGCCAGTCAAATGCCTGGCAAA 22 5 0 GCAGTTGCGG 0.93562 -85 AGCGAGGATTTTCGTTTTTCAGACGGGATATTAAATC 26 44 0 TCGTTAGCGG 0.902976 -29 TCCATTCGCAGCCGGTACGCAGTCAGTACCGGCTTTT 30 17 1 GCGGTAGCGT 0.898206 -103 GGGGCGGTGCGAATGCAGGCGTCG 34 6 0 GCGGTATCGG 0.943933 -19 TCAGCATGCAGTCGTTGATGAGAAAGGGTTATTACGG 35 32 0 GCGTTAGAGG 0.67434 -269 AAAAGCCAGGGGCGGTAGCGTGTCTGGATGCCTGAAA 35 111 1 GCGGTTGCGG 0.992071 -190 CTAGTCAAAATGCGGTGATAAGAGCGGGATTGTACCC 39 43 0 TCGGTAGGGG 0.941419 -48 TTTATCTGCAGGCGGGAAATAGAGCGGACCTTTCAGA 43 136 0 GCGGGAGGGG 0.929437 -165 CCTGGGCTTTGTCGGTGAAATGTCAGGCACCAGAGTA 44 238 0 GCGGTTGCGG 0.992071 -39 * **** ** * ** Masking position 3 Map Score: 12.7335 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 656 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TATGCGAAAATGCCGGTCTTGTTACCGGCATT 6 29 1 TGCCGGTCTT 0.948242 -37 TGTCCTAAAATGCCGCTCGCGTCGCAAACTGA 8 21 1 TGCCGCTCCT 0.961994 -280 GGATCGGAAGTCCGGCGCGCTTTATACCACAA 11 159 1 TCCGGCGCCT 0.668814 -209 GCTCGAGAATTCCCGGGAGCTTACATCAGTAA 12 61 1 TCCCGGGACT 0.648176 -197 CGCTCGCTCATCCCGGTCACTTACTGATGTAA 12 81 0 TCCCGGTCCT 0.931677 -177 TGCGGTTTAATGCCGGGCAGATCACATCTCCG 12 225 1 TGCCGGGCGT 0.948371 -33 AGGTCAGATATGCCGTGGTTTTACACGGCTTT 16 104 1 TGCCGTGGTT 0.735084 -82 TTTGCCAGGCATTTGACTGGCAGA 22 3 1 TGCCAGGCTT 0.665143 -87 TTCTCAGGCCTGCCGTTCCGGTGGGCCTTGTT 23 11 1 TGCCGTTCGT 0.716457 -103 TAGCCAGGAATGCAGGGCGCATAGTGTAATGC 24 103 0 TGCAGGGCCT 0.773362 -43 TGCTATATCATGCCGCGGATTTTTACTTTCCC 25 32 0 TGCCGCGGTT 0.894363 -193 TGGGCGAAATTGCCGCGCTTGTAAATAACAAA 25 119 0 TGCCGCGCTT 0.970016 -106 TTGGGTACAATCCCGCTCTTATCACCGCATTT 39 41 1 TCCCGCTCTT 0.879743 -50 AAATCTTCCCGTTCTTTTCAGACA 40 7 0 TCCCGTTCTT 0.705673 -18 CCCTGATAATTGCCGCGGACTTTCTGCGTGCT 42 21 1 TGCCGCGGCT 0.931445 -172 TGTATAAATGTGCCGGTCTCCTCTTGGCACAT 42 142 0 TGCCGGTCCT 0.967107 -51 ******** * * Masking position 1 Map Score: 13.1188 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 919 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 TAACCAGCGCATCGCTACGCCGCCAGCCAAAA 7 104 0 ATCGCCGCCG 0.986344 -63 GAGCGAAGATAACGCATCTGCGGCGCGAAATA 12 108 1 AACGCCTGCG 0.969762 -150 TGCCGGGCAGATCACATCTCCGAGGATTTTAG 12 235 1 ATCACCTCCG 0.763976 -23 CCGCGTAAGTATCGCGGGGGCGTAAGTCTGGT 14 41 1 ATCGCGGGCG 0.973651 -251 GAACGACAAAAACGCCGCTCAGTAGATCCTTG 15 17 1 AACGCCTCAG 0.716473 -75 CAACAGAAACAACGCCGCGATGACGACGGGTA 17 60 0 AACGCCGATG 0.68125 -61 TCAATATAAGATCGCCGGGCCACGCAAAGAAC 19 61 1 ATCGCGGCCA 0.726131 -61 TAAATTATTAAACGCCAGGGCGACAGAGCGGG 31 39 0 AACGCGGGCG 0.980721 -40 TGCAGATAAAAACGCACCGCCGCCGACCAAAC 43 163 1 AACGCCGCCG 0.990043 -138 ATGTCACGGTAACGCCTGTACGGTAAACTATG 44 85 0 AACGCGTACG 0.817383 -192 CAGCCGTTCAATCACCTCGGCGATGCACCCCC 45 89 0 ATCACCGGCG 0.909383 -212 GTCTACTCGCAACGCGACGGCGAGACAAATTT 50 270 0 AACGCCGGCG 0.990043 -25 ***** ***** Masking position 1 Map Score: 9.79004 Number of sites scoring better than the average of aligned sites = 1036 Number in coding regions = 998 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ATTGTCGCTTCCGTCCAGTCTGTGTATACGAA 11 125 1 CGTCAGTCTG 0.876519 -243 CTGTGTGTGACTGTCTGGTCTGACTGAGACAA 14 251 1 CGTTGGTCTG 0.983934 -41 TAAAAAAAGCCGGTACTGACTGCGTACCGGCT 30 26 0 CGTCTGACTG 0.844092 -94 TCAGAACGGTTCTGTCTGCTTGCTTTTA 37 7 1 CGTCTGTCTG 0.971729 -73 GCGTCTCTACCGGTTTGGTCGGCGGCGGTGCG 43 175 0 CGTTGGTCGG 0.952317 -126 CCCACATCAACTGTGTGGTCTGGTCTCAATTT 44 36 0 CGTTGGTCTG 0.988439 -241 GATCGGTACACTGTATTATCTGCCTCGACTAT 46 167 0 CGTTTATCTG 0.803803 -70 ATCTTATCGCCAGTTTGGTCTGGTCAGGAAAT 49 225 1 CGTTGGTCTG 0.976607 -76 ATAGGTACAACAGTATAGTCTGATGGATAAGT 50 105 1 CGTTAGTCTG 0.963441 -190 * ** ******* Masking position 4 Map Score: 9.74693 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CATATTGCCCGTTGCAGTCAGAATGAAAAGCT 1 8 0 GTTGCGCGAG 0.951606 -182 AAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTT 2 29 1 GCACCGCGGG 0.953957 -53 TTATCAAAAAGGAGCCGCCTGAGGGCGGCTTCTTT 13 11 1 GGAGCGCGGG 0.93503 -136 AGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCA 14 77 1 GTTGCGCGTG 0.960359 -215 GTACGCTCCGGTTGCTGCGCGCTGGCCGTGACCAA 14 99 0 GTTGCGGGTG 0.925004 -193 CGTTGTTTCTGTTGCCGCCGGTGGGGTTCGCCATT 17 78 1 GTTGCGCGGG 0.978757 -43 GGTGTACGGTTCCTGCGAGATGGGAAAGTAAAA 25 9 1 GTTCCGGGTG 0.862728 -216 AAAATTTGTGGCTGAAGACTGGGCGAAATTGCCGC 25 135 0 GCTGAGCGGG 0.920268 -90 GGGGCGGTGCGAATGCAGGCGTCG 34 10 0 GGGGCGGGAG 0.677947 -15 AGCCCGTCAGGCTGAAGAGAGTAAGTAATACAGTG 43 97 0 GCTGAGGGAG 0.714996 -204 AGCCTGACGGGCTGCGGTCTGAAAGGTCCGCTCTA 43 119 1 GCTGCGCGAG 0.964444 -182 GTCAGTTTCTGTACCCGCGTGATTGGAGTAA 43 280 1 GTACCGGGTG 0.800635 -21 ATCGTGTAATGCACCTGTCGGCGTGATAATGCATA 44 115 1 GCACCGCGGG 0.953953 -162 CAAGGGAAGAGCGGAAGACGGGTGGGCGCAGAGCG 45 237 0 GCGGAGCGTG 0.722939 -64 TTACCCTGAAGTACGTGGCTGTGGGATAAAAACAA 50 25 0 GTACGGCGGG 0.614618 -270 ***** * * * * * Masking position 7 Map Score: 9.33412 Number of sites scoring better than the average of aligned sites = 1392 Number in coding regions = 1315 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 AAAATGCCGCTCGCGTCGCAAACTGACACT 8 27 1 TCGCGTCGCA 0.862901 -274 TATTCCCACTTTGCCCCACAATTTCCCACT 8 266 0 TTGCCCCACA 0.921166 -35 CCTTCATATTTCGCGCCGCAGATGCGTTAT 12 116 0 TCGCGCCGCA 0.984663 -142 AGGAAATTATTCACGCCACAGGAAAAAGGC 23 81 0 TCACGCCACA 0.908863 -33 CTGGGCGAAATTGCCGCGCTTGTAAATAAC 25 122 0 TTGCCGCGCT 0.746053 -103 GCGGCGCAACTTGCCCCGCACCAAATAAAA 30 53 0 TTGCCCCGCA 0.949068 -67 GCGGGGCAAGTTGCGCCGCTACACTATCAC 30 64 1 TTGCGCCGCT 0.965762 -56 TTTTTTATGATTACGCCACATCATAAAAAG 38 82 0 TTACGCCACA 0.881392 -40 ATCGCTTTAGTCACGGCACAATAAGGCATA 41 60 1 TCACGGCACA 0.72727 -52 TTGCGCCCCTTATGGTCACT 41 102 0 TTGCGCCCCT 0.866087 -10 ATAAAAACGATCGCGCCACTGGCGATGGTC 43 228 1 TCGCGCCACT 0.959575 -73 ********** Masking position 1 Map Score: 8.00134 Number of sites scoring better than the average of aligned sites = 848 Number in coding regions = 685 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 TCGGTATCACCGACGCTGATGGACAGAATTA 11 347 1 CGACGCTGTG 0.962601 -21 TCATATTTCGCGCCGCAGATGCGTTATCTTC 12 112 0 CGCCGCAGTG 0.918224 -146 TACTTTTGTACGCTCCGGTTGCTGCGCGCTG 14 110 0 CGCTCCGGTG 0.921638 -182 TGGGGGTCGCTTTTGCTGAAGTATCGCC 17 8 1 CGCTTTTGTG 0.891127 -113 CAGACGTCCCCGCCGTTGGTGATTAACGACG 22 31 1 CGCCGTTGTG 0.9626 -59 AATACGTTTGCGATGTGGGTGAATAAAAAGA 29 102 0 CGATGTGGTG 0.66563 -199 AGTTAGCCTCCGCCGTTTATGCACTTTTATC 29 186 1 CGCCGTTTTG 0.850341 -115 GTAAGCTTCTCGATTCTGCTGTGGCTTTTGC 41 14 1 CGATTCTGTG 0.891127 -98 TTGCGCCCCTTATGGTCACTCATT 41 98 0 CGCCCCTTTG 0.915452 -14 TTGGGCAACGCGCCTCTTCTGGCCTGCGCTA 45 18 0 CGCCTCTTTG 0.899661 -283 CGACTGCGAACGCTTCTGGTGACAACCCAGG 45 155 0 CGCTTCTGTG 0.962088 -146 TATCAACTTGCGATCCTGATGTGTTAATAAA 49 117 1 CGATCCTGTG 0.908124 -184 ******** ** Masking position 10 Map Score: 7.06145 Number of sites scoring better than the average of aligned sites = 1567 Number in coding regions = 1521 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 AAATTAACAAAAGAGAATAGCT 7 155 1 AAGAGATAGC 0.580729 -12 AAGTGGGAATAAGGGGTGAGGCTGGC 8 285 1 AAGGGTGAGG 0.780577 -16 CGAAATATGAAGGGGGAGAGCCCTTATAGAC 12 133 1 AGGGGAGAGC 0.964777 -125 AAGATGTGCCAAGAGGAGACCGGCACATTTA 42 139 1 AAGAGAGACC 0.809134 -54 CTATCATCGCAGGAGAAGACGTAAAAG 43 7 0 AGGAGAGACG 0.821201 -294 GCCTTGGCACAAGGGAAGAGCGGAAGACGGG 45 250 0 AAGGGAGAGC 0.961951 -51 TAGCTCGTACAAGGGAAGTGGCTTGCCACTT 47 12 1 AAGGGAGTGG 0.919664 -47 ATGAGCAAAAAAGGGAAGTGGCAAGCCACTT 47 27 0 AAGGGAGTGG 0.919664 -32 AAATGAAATTAGGAGAAGAGC 49 290 1 AGGAGAGAGC 0.944983 -11 GTACCTATAAAGGAGCAGTGGAATAGCGTTC 50 82 0 AGGAGAGTGG 0.886071 -213 ***** ***** Masking position 1 Map Score: 3.7712 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 94 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 12 GCATAACTTAGGCTGCTAATGAC 6 3 0 GGCTGCAATG 0.967997 -63 GATGAAGCCGGCGAATGCCGGCTTTTT 10 7 1 GCCGGCAATG 0.948498 -55 CAAAGGGCACCCCGGAATATGTGCCGATACG 11 71 1 CCCGGATATG 0.649401 -297 TGGTTAGGGGGCCTGCATATGGCCCCCTTTT 12 179 1 GCCTGCTATG 0.948789 -79 CTGCACCCTCCGGTGCAAATGGGATGGTAAG 19 92 1 CGGTGCAATG 0.86697 -30 ATGACCTACTCCCTGATTATGTGACAGATAA 28 15 1 CCCTGATATG 0.800995 -160 GTAATGTTTGCGCTGTAAATGTAGATTGCAG 29 234 0 CGCTGTAATG 0.666365 -67 ACTGCGTACCGGCTGCGAATGGATGTTAA 30 9 0 GGCTGCAATG 0.967997 -111 AGGTTGTTCTCCCGGCTTATGAGCTGGTTTG 33 14 0 CCCGGCTATG 0.865662 -21 GGGGCGGTGCGAATGCAGGCGTCG 34 10 0 CGGTGCAATG 0.86697 -15 TCTGTCAATAGCCTGCGGATGAAATCAATTT 35 164 1 GCCTGCGATG 0.893004 -137 AAAACATTTTGCCTGCAAATGATTATCAGGA 36 233 0 GCCTGCAATG 0.975622 -68 GCACCTGTCGGCGTGATAATGCATATAATTT 44 125 1 GCGTGAAATG 0.766322 -152 CTTGTGCCAAGGCTGAAAATGGATCCCCTGA 45 268 1 GGCTGAAATG 0.896848 -33 ****** **** Masking position 9 Map Score: 13.7914 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 301 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 GTTGCAGTCAGAATGAAAAGCT 1 2 0 GAATGAAAAC 0.889474 -188 AGTTGAGACAGAATAAAAAGCAAAACGCCGC 15 60 0 GAATAAAAAC 0.95448 -32 CCCTGTCAGGGAATAAAAAACGC 16 173 1 GAATAAAAAC 0.95448 -13 TGAATAAAAAGAATAAAAAACGCAATGTTAT 29 83 0 GAATAAAAAC 0.95448 -218 GCAGTTAATTGAATAAAAATTTAACTGGCAT 35 206 0 GAATAAAAAT 0.885108 -95 CGATTTATGAGAATAAATACTCATTTAAGGG 36 266 0 GAATAAATAT 0.656531 -35 ATCATAAAAAGAATAAAAAATATCGATTTAT 38 62 0 GAATAAAAAT 0.885108 -60 AGGCAATCCATAATGAAAAACGTGTTTAAGG 43 62 1 TAATGAAAAC 0.747264 -239 TTGATATCACTAATAAATAACCATCAAAATG 46 93 0 TAATAAATAC 0.656531 -144 TAAATTTATGTAATAAAAATTATGCGGCAAA 49 32 0 TAATAAAAAT 0.73893 -269 CCTGATGTGTTAATAAAAAACCTCAAGTTCT 49 131 1 TAATAAAAAC 0.885108 -170 ********* * Masking position 6 Map Score: 6.1743 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 69 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 14 GAAGCTGCTATCAGACACTCTTTTTTTAATC 1 53 0 TCAGCACTCT 0.741466 -137 GAAAAAAAAAGCCCGCACTGTCAGGTGCGGG 2 36 0 GCCCCACTGT 0.938202 -46 TTCACTGATATCCCTCCCTGTTTATCATTAA 7 56 1 TCCCCCCTGT 0.947481 -111 GTCTATAAGGGCTCTCCCCCTTCATATTTCG 12 133 0 GCTCCCCCCT 0.694834 -125 GGGGCCATATGCAGGCCCCCTAACCAAACGT 12 174 0 GCAGCCCCCT 0.868166 -84 GACCAGACAGTCACACACAGTGGAAGTGTGC 14 240 0 TCACCACAGT 0.582766 -52 GGAAACATACGCACTCCCTGTTA 26 3 0 GCACCCCTGT 0.976058 -70 GCAACAGATAGCCCGCTCTGTCGCCCTGGCG 31 28 1 GCCCCTCTGT 0.78927 -51 GTTTAATTTTTCACACCCTCTCAGCATGCAG 35 58 0 TCACCCCTCT 0.932872 -243 CGTGTTTAAGGCACTCACTGTATTACTTACT 43 82 1 GCACCACTGT 0.948597 -219 ATCGTTTTTATCCGGCACCGTGGATTGCGTT 43 208 0 TCCGCACCGT 0.675475 -93 CCTCGGCGATGCACCCCCTCAGGTGTTATCA 45 76 0 GCACCCCTCA 0.733291 -225 CCCAGGGGATTCAGCCCCTGTAGCCGATGAT 45 130 0 TCAGCCCTGT 0.90906 -171 **** ****** Masking position 6 Map Score: 4.63849 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 238 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 15 CCGTAAACCCTGTCAGGGAATAAAAAACGC 16 166 1 TGTCAGGAAT 0.965958 -20 CAAAAGCAGATATCAGGCGATACTTCAGCAA 17 23 0 TATCAGGGAT 0.910155 -98 TCACCGGCCTATAAGGAAATTATTCACGCC 23 94 0 TATAAGGAAT 0.666412 -20 TGCAAATGATTATCAGGAAATATAACATTAT 36 220 0 TATCAGGAAT 0.94706 -81 CCGCGGCAATTATCAGGGAATTTGAGTT 42 8 0 TATCAGGAAT 0.94706 -185 AACTACCTCGTGTCAGGGGATCCATTTTCAG 45 280 0 TGTCAGGGAT 0.941411 -21 AACCAGAGAATGTCACGCAATCCATTGTAAA 49 62 1 TGTCACGAAT 0.824449 -239 AGTTTGGTCTGGTCAGGAAATAGTTATACAT 49 236 1 GGTCAGGAAT 0.882858 -65 ******* *** Masking position 5 Map Score: 3.23153 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 29 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493