AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_ecoli_reg_100.orf -o00600_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 Input sequences: #1 caiA 30 probable carnitine operon oxidoreductase #2 caiT 300 probable carnitine transporter #3 yabB 300 orf, hypothetical protein #4 lacZ 122 beta-D-galactosidase #5 ybjU 36 putative arylsulfatase #6 poxB 132 pyruvate oxidase #7 gatZ 28 putative tagatose 6-phosphate kinase 1 #8 gatY 197 tagatose-bisphosphate aldolase 1 #9 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #10 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #11 agaZ 248 putative tagatose 6-phosphate kinase 2 #12 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #13 yiaM 117 orf, hypothetical protein #14 rfaS 36 lipopolysaccharide core biosynthesis #15 rfaQ 300 lipopolysaccharide core biosynthesis #16 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #17 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #18 aslA 300 arylsulfatase #19 melA 282 alpha-galactosidase #20 sgaT 291 orf, hypothetical protein Motif number 1 ACTGATTATTAATCAAAATTAACGAAAAAACGCCCTC 2 100 1 AAAAAAGAAA 0.980457 -201 ATTAAATGTTAACAAAAATAAAACAAACGGGAACGCA 2 240 1 AAAAAACAAA 0.934648 -61 TTATTCGAGGAGTGAAAGGCAAAAAAACGGCCTCCCG 8 81 0 AAAAAAAAAA 0.900944 -117 TGTTTTCGATTTCAAAATATAATGAAATTATTTGTTT 8 160 0 TAAAAAGAAA 0.883307 -38 ATATTTTGAAATCGAAAACAAACGACAGGAT 8 177 1 AAAAAAGACA 0.962641 -21 TAATAGGCAAAACGAAATGAAACGAAAGTTTTACGAA 11 21 0 AAAAAAGAAA 0.980457 -228 CTGATTCACAAAAGAAACATAATGAAAGTCACTGAAA 11 116 0 AAAAAAGAAA 0.980457 -133 TCATGGTGAGATAAAAATAAAACGAAAGATAATGGTT 11 160 0 AAAAAAGAAA 0.980457 -89 CGCAGTATCAACTGAAACAAAACGAAAGATTAATATC 11 197 1 AAAAAAGAAA 0.980457 -52 TGATCGTTGAAAGAAAAGATAAAGGAAGCAAAAGGGA 12 12 0 AAAAAAGGAA 0.856572 -180 AATGGAGAAAAAAGAAATAAAACGAAATTTGTGATCG 12 43 0 AAAAAAGAAA 0.980457 -149 TCTTTCGTTGATTAAAATCTATAGAAAAGAAACTGAA 12 85 0 AAAAATGAAA 0.883307 -107 GACATCACCAAGTGAAATGAAACGAAAGGCAAGTGAA 12 120 1 AAAAAAGAAA 0.980457 -72 TAATCATAAAAATCAAATAGATAAAAAATAGCATTTC 15 68 0 AAAAATAAAA 0.578472 -233 TGTCAGGATTAATCAAAACCAATCACATATTGATTCG 20 33 0 AAAAAACACA 0.880178 -259 ATCTTTCCATACTCAAAATCAACAACAACTTCCCTGG 20 111 0 AAAAAAAACA 0.823682 -181 TCACTCTAATTTTCAAAAGTAATCACAACAAGATTAT 20 265 0 TAAAAACACA 0.525688 -27 * *** ** **** Masking position 7 Map Score: 24.8643 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 36 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 CCTCGTGGACGCGTTAATGGCTAACTCATAA 2 195 0 GGTTAATGGC 0.818554 -106 GTAAACATCGGGTTTTTTACCTCGGTATGCC 3 188 1 GTTTTTTACC 0.729217 -113 AAGTGCGCGTGTTTTTATGCCGGATGCGGTG 8 33 0 GTTTTATGCC 0.951416 -165 TCGGGAGGCCGTTTTTTTGCCTTTCACTCCT 8 80 1 GTTTTTTGCC 0.966548 -118 TGTCCGGCAATCGTTTTTGCCGGACAGTGCT 10 25 1 TGTTTTTGCC 0.669185 -123 TAAACACGTGGCGTTTTTGGCATAAGACAAA 16 12 0 GGTTTTTGGC 0.966421 -228 AAACTGGCTGGGCTTAATGCCACCACTCAGC 17 68 0 GCTTAATGCC 0.658615 -174 AGCCCAGCCAGTTTTTCTGGCATATCTGGGG 17 85 1 GTTTTCTGGC 0.809588 -157 TGAGATATAAGCTTTTTTACCCACTACGTCG 17 145 1 GTTTTTTACC 0.729219 -97 CAGCCGACTCGCTTTTGCGCCAGGCGACGTA 17 169 0 GTTTTGCGCC 0.686683 -73 CGAGTCGGCTGTGTATTTGCCACCCGCGGCG 17 189 1 GGTATTTGCC 0.766144 -53 GGCGATTTGAGCTTTTTTGCCAAAACGCACC 17 216 1 GTTTTTTGCC 0.966545 -26 GCTGTTTTTAGTTTTAACGGCAATTAATATA 18 60 0 GTTTAACGGC 0.537568 -241 CTGAAAAGCAGAGTTTTCGGCCTCATGATAC 19 122 0 GGTTTTCGGC 0.9128 -161 CAGTAAATCTGAGTTTATGGGAATAAATTAC 19 153 0 GGTTTATGGG 0.737693 -130 CGCAGGATCTGAGTTTATGGGAATGCTCAAC 19 192 1 GGTTTATGGG 0.737693 -91 ACCATTTTTTGACTTTTTGCCAGGGAAGTTG 20 92 1 GCTTTTTGCC 0.925505 -200 * ********* Masking position 4 Map Score: 12.7713 Number of sites scoring better than the average of aligned sites = 1482 Number in coding regions = 1283 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 AATGTGATACCAATCACAGAATACAGCTTA 2 154 1 CAATCACAGA 0.882568 -147 TATCCGCTCACAATTCCACACAACATACGA 4 80 0 CAATTCCACA 0.971357 -43 GAGCGGATAACAATTTCACACAGGAAACAG 4 101 1 CAATTTCACA 0.866641 -22 AACTCCCCAGCAATTACACAAACTACCATC 10 125 1 CAATTACACA 0.973164 -23 CTTAACCAGACAATCACACAAAAGAGTCGC 15 243 1 CAATCACACA 0.983062 -58 ACGGTCAGTTCAATCCCACACTGTGGCTGG 17 34 1 CAATCCCACA 0.98191 -208 CCGCGGGTGGCAAATACACAGCCGACTCGC 17 188 0 CAAATACACA 0.8077 -54 CCAGGTTGAGCATTCCCATAAACTCAGATC 19 197 0 CATTCCCATA 0.652005 -86 TAATCAAAACCAATCACATATTGATTCGAA 20 31 0 CAATCACATA 0.899413 -261 TTAGTTAATTGAATTACACATTCCATTAAA 20 147 0 GAATTACACA 0.896282 -145 GATAGAGTGGGATTCACACAACGAAACAAT 20 194 0 GATTCACACA 0.756034 -98 GACCCGCAAATAATTCCACATGGATAGAGT 20 216 0 TAATTCCACA 0.747658 -76 ********** Masking position 8 Map Score: 10.2532 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AATCGAAAACAAACGACAGGAT 8 186 1 AAACGACAGG 0.943824 -12 AAACGAAATGAAACGAAAGTTTTACGAAAG 11 19 0 AAACGAAAGT 0.975745 -230 TTAATAGGCAAAACGAAATGAAACGAAAGT 11 29 0 AAACGAAATG 0.925684 -220 AAAGTCACTGAAACGAGAGTAGCTTGCGTC 11 99 0 AAACGAGAGT 0.91442 -150 GATAAAAATAAAACGAAAGATAATGGTTTT 11 158 0 AAACGAAAGA 0.975745 -91 AACTGAAACAAAACGAAAGATTAATATCGC 11 206 1 AAACGAAAGA 0.975745 -43 AAAAGAAATAAAACGAAATTTGTGATCGTT 12 41 0 AAACGAAATT 0.887912 -151 AGATTTTAATCAACGAAAGACATCACCAAG 12 102 1 CAACGAAAGA 0.903838 -90 AAGTGAAATGAAACGAAAGGCAAGTGAAAG 12 129 1 AAACGAAAGG 0.984437 -63 ********** Masking position 6 Map Score: 11.2479 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 31 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TGTCCTAAAATGCCGCTCGCGTCGCAAACTGAC 3 21 1 TGCCCGCGTC 0.982677 -280 CGTGTTTTTATGCCGGATGCGGTGTAAACATAC 8 24 0 TGCCGGCGGT 0.972934 -174 GCCTGAAACCTGCGGCGCGCATTTCAATCGCTG 9 90 1 TGCGCGCATT 0.805873 -61 GAGAGTAGCTTGCGTCAATGGGCAAGGTGGGCT 11 82 0 TGCGCTGGGC 0.794919 -167 GTAGCTGTTGAGCCTGGGGCGGTAGCGTGCTTT 15 199 1 AGCCGGCGGT 0.820373 -102 GAAATGGCTTTTCCACTAGCGACTCTTTTGTGT 15 258 0 TTCCCGCGAC 0.757239 -43 GACTCGCTTTTGCGCCAGGCGACGTAGTGGGTA 17 162 0 TGCGCGCGAC 0.978919 -80 GCTGTGTATTTGCCACCCGCGGCGATTTGAGCT 17 196 1 TGCCCGCGGC 0.994254 -46 GGAGGATGACTGCGAGTGGGAGCACGGTTTTCA 19 56 1 TGCGGGGAGC 0.910849 -227 ACTCAGATCCTGCGTGAAGCAGCAGTAAATCTG 19 173 0 TGCGGGCAGC 0.977207 -110 TGGAATTATTTGCGGGTCGCGTCACATTTAATC 20 228 1 TGCGGGCGTC 0.982676 -64 **** * ***** Masking position 3 Map Score: 7.49634 Number of sites scoring better than the average of aligned sites = 1884 Number in coding regions = 1493 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 6 CGTAGCAAAAAGAAATTTTCAAT 2 1 1 CGAGCAAAGA 0.961137 -300 ATGCCGCTCGCGTCGCAAACTGACACTTTATAT 3 30 1 CGCGCAAAGA 0.883852 -271 GTCCAACGTGCGAAGCAAATTAACGTTATGAAT 3 128 0 CGAGCAAAAA 0.639575 -173 AAGCCAGTCACAAGGCATACCGAGGTAAAAAAC 3 199 0 CAGGCATAGA 0.633675 -102 ATAGGGAAGCCGTAGCAAAGTGCGCGTGTTTTT 8 48 0 CGAGCAAAGC 0.953151 -150 AGATTAATATCGCAGTAATCTGAACTGGAGAGG 11 223 1 CGAGTAATGA 0.709544 -26 TCATTTCTTTCGCAGCAATCCGACCCGAATGAT 15 126 0 CGAGCAATGA 0.971466 -175 CACGTGTTTACGTGGCGTTTTGCTTTTATATCT 16 33 1 CGGGCGTTGC 0.90442 -207 ACATCGCCAGCGCGGCATTAAGATTACAGATAT 16 60 0 CGGGCATTGA 0.970751 -180 TCTGCTGAGTGGTGGCATTAAGCCCAGCCAGTT 17 65 1 GGGGCATTGC 0.743822 -177 ATTTGCCACCCGCGGCGATTTGAGCTTTTTTGC 17 203 1 CGGGCGATGA 0.940598 -39 GACATGAAACCGGAGCATTTTGC 18 288 1 CGAGCATTGC 0.953151 -13 ** ****** ** Masking position 5 Map Score: 6.61139 Number of sites scoring better than the average of aligned sites = 950 Number in coding regions = 874 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 TTCAATATTGTTTTATGGATCACCAATATTGA 2 28 1 TTTTTGATCA 0.897679 -273 ATAGAGGGCGTTTTTTCGTTAATTTTGATTAA 2 108 0 TTTTTCTTAA 0.798656 -193 ATTATGTTTCTTTTGTGAATCAGATCAGAAAA 11 130 1 TTTTTGATCA 0.897679 -119 TCTATTTGATTTTTATGATTAAAGTATATTTT 15 84 1 TTTTTGTTAA 0.943328 -217 TTAAAGTATATTTTGTGTATAAAAATCATTCG 15 102 1 TTTTTGATAA 0.93336 -199 TAGCGTGCTTTTTTCTGCTTAACTTAACCAGA 15 221 1 TTTTTGTTAA 0.943328 -80 TTTTGTGTGATTGTCTGGTTAAGTTAAGCAGA 15 234 0 TTGTTGTTAA 0.758142 -67 ACACGTGGCGTTTTTGGCATAAGACAAAT 16 8 0 TTTTGGATAA 0.725055 -232 ATTGAATGAATTTTATCATTCATAATAAGTAT 18 18 0 TTTTTCTTCA 0.713006 -283 TTCCAATTCATTTTCTGGATAAATAAATAATT 18 171 1 TTTTTGATAA 0.93336 -130 CAACAAGATTATTTATGATTAAATGTGACGCG 20 245 0 ATTTTGTTAA 0.678971 -47 **** ** **** Masking position 12 Map Score: 6.48534 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 74 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 AGTGGGAATAAGGGGTGAGGCTGGC 3 286 1 AGGGGGAGGC 0.980098 -15 CATCTGACGGAGGGGGAAGGGATGGGAGAGA 6 69 0 AGGGGAAGGG 0.970784 -64 AAATTATTCGAGGAGTGAAAGGCAAAAAAAC 8 90 0 AGGAGGAAAG 0.748156 -108 ATCATCCTGTCAGGGAGAGGGATCTCAATTA 18 228 1 CAGGGGAGGG 0.910905 -73 CTGATATTCCAGGAAAGAGAGCCATCC 19 7 0 AGGAAGAGAG 0.858851 -276 GAATTATGGCAGGAGTGAGGGAGGATGACTG 19 37 1 AGGAGGAGGG 0.991476 -246 CTCGCCCCTCTGGGAAGAGGGTGAAAACCGT 19 79 0 TGGGAGAGGG 0.933902 -204 CTCTTCCCAGAGGGGCGAGGGGACTCTCCGA 19 91 1 AGGGGGAGGG 0.99665 -192 ***** ***** Masking position 8 Map Score: 4.65743 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 101 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 AGCAAATATAAAGTGTCAGTTTGCGACGCG 3 38 0 AAGTGTCAGT 0.748825 -263 TTTCCTTGTTAAATGGCAGGTGCG 7 5 0 AAATGGCAGG 0.953817 -24 GTGTAAACATACGTGGCAGTGCTAT 8 6 0 ACGTGGCAGT 0.897869 -192 GCACAAGGGGACCTGGCTGGTTGCCGGATA 9 39 0 ACCTGGCTGG 0.870204 -112 TTTTACTAAAAAGTAGCAGGTAAATGCATT 10 86 0 AAGTAGCAGG 0.720762 -62 AGCATTTCGATAATGTCAGTACGGCCTATG 15 46 0 TAATGTCAGT 0.612658 -255 ATGCCAGAAAAACTGGCTGGGCTTAATGCC 17 78 0 AACTGGCTGG 0.860884 -164 TATGTAATCATCCTGTCAGGGAGAGGGATC 18 222 1 TCCTGTCAGG 0.893096 -79 AATATCAGAATTATGGCAGGAGTGAGGGAG 19 30 1 TTATGGCAGG 0.782995 -253 AATAACTTCATCATGGCAGGCGAATCTGCA 19 242 0 TCATGGCAGG 0.94957 -41 CCTGAAAAAATAGTGTCAGGATTAATCAAA 20 53 0 TAGTGTCAGG 0.910138 -239 ********** Masking position 4 Map Score: 4.15869 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 1239 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 TATTCCCACTTTGCCCCACAATTTCCCACT 3 266 0 TTGCCCCACA 0.96096 -35 ACCTGGCTGGTTGCCGGATACCGTTAAAAG 9 29 0 TTGCCGGATA 0.95962 -122 GCAAAAACGATTGCCGGACAGTGTGTAAGG 10 15 0 TTGCCGGACA 0.991434 -133 GCAATCGTTTTTGCCGGACAGTGCTGCCGT 10 31 1 TTGCCGGACA 0.991434 -117 ATAATTCAGGTTGCTGCACATGCGACTTGA 13 67 1 TTGCTGCACA 0.943208 -51 ********** Masking position 8 Map Score: 3.56388 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TTCGGGTGAATAGAGGGCGTTTTTTCGTTAATT 2 116 0 TGGGCGTTTT 0.982999 -185 GGTGATGACGATGAGGGATTTTTTCTTACAGCT 3 95 1 AGGGATTTTT 0.825428 -206 AGCCGTAGCAAAGTGCGCGTGTTTTTATGCCGG 8 41 0 AGGGCGTGTT 0.95862 -157 CCTGGGGCGGTAGCGTGCTTTTTTCTGCTTAAC 15 211 1 TGGGCTTTTT 0.965511 -90 ACCCGCGGCGATTTGAGCTTTTTTGCCAAAACG 17 210 1 ATGGCTTTTT 0.825428 -32 CTTTGGGTGCGTTTTGGCAAAAAAG 17 227 0 TGGGCGTTTT 0.982999 -15 TTGGAAAATCAGGAGAGCGTTTTCAATCCTACC 18 144 0 AGGGCGTTTT 0.986892 -157 * * * ******* Masking position 10 Map Score: 2.68921 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 150 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 TAGCTCACTCATTAGGCACCCCAGGCTTTACACT 4 33 1 ATGGCCCCAG 0.684598 -90 TTATTCGCACCTTTGGAGCGCCTGAAACCTGCGG 9 71 1 CTGGCGCCTG 0.907301 -80 TAAAAATTTTACTAAACTCCCCAGCAATTACACA 10 111 1 ATAACCCCAG 0.507715 -37 GGCAAGTGAAAGCGACAACGCCCGACGTCAAGTT 12 147 1 ACACCGCCCG 0.890957 -45 TAATCGTCTACGCCAGAACGCCTGGGTAATGTTA 13 16 1 CCAGCGCCTG 0.970944 -102 GAAAAAAGCACGCTACCGCCCCAGGCTCAACAGC 15 202 0 CCACCCCCAG 0.96753 -99 CAGGAATTTTCCTAACATCGCCAGCGCGGCATTA 16 73 0 CTACCGCCAG 0.964739 -167 AATGCCACCACTCAGCAGAGCCAGCCACAGTGTG 17 50 0 CCGCAGCCAG 0.930921 -192 AGGTCTGCCCCCCAGATATGCCAGAAAAACTGGC 17 91 0 CCGATGCCAG 0.714669 -151 CTTTTTTACCCACTACGTCGCCTGGCGCAAAAGC 17 156 1 CCACCGCCTG 0.980146 -86 TGCCTTACATATCAACTGCGCCAGAGGTAGGATT 18 119 1 ACACCGCCAG 0.9722 -182 GGAGGTTTTCTGCAGATTCGCCTGCCATGATGAA 19 232 1 TCGACGCCTG 0.764513 -51 GATGAAGTTATTCAAGCAAGCCAGGAGATCTGC 19 260 1 TCAGAGCCAG 0.638042 -23 * * ** ****** Masking position 11 Map Score: 4.418 Number of sites scoring better than the average of aligned sites = 3359 Number in coding regions = 3263 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 13 CTTGTCAAGCCAGTCACAAGGCATACCGAG 3 208 0 CAGTCACAAG 0.474833 -93 AGCTGTTTCCTGTGTGAAATTG 4 111 0 CTGTTTCCTG 0.629997 -12 AATGTGATAACGGTAACAAGTTTAGTTCAT 6 97 0 CGGTAACAAG 0.670808 -36 CACTTTGCTACGGCTTCCCTATCGGGAGGC 8 59 1 CGGCTTCCCT 0.789216 -139 GGCAAAAAAACGGCCTCCCGATAGGGAAGC 8 71 0 CGGCCTCCCG 0.960438 -127 TAACGGTATCCGGCAACCAGCCAGGTCCCC 9 33 1 CGGCAACCAG 0.927874 -118 GTCGCATGTGCAGCAACCTGAATTATTAAT 13 63 0 CAGCAACCTG 0.826124 -55 CCAGGCTCAACAGCTACCTGAATACTGATA 15 186 0 CAGCTACCTG 0.874544 -115 AAACTAAAAACAGCATCAATAATCAACGCG 18 77 1 CAGCATCAAT 0.340266 -224 CAAAATGCTCCGGTTTCATGTCATCAAAAT 18 280 0 CGGTTTCATG 0.823591 -21 GCAGAGTTTTCGGCCTCATGATACTCGGAG 19 116 0 CGGCCTCATG 0.930547 -167 AGATTTACTGCTGCTTCACGCAGGATCTGA 19 174 1 CTGCTTCACG 0.758131 -109 AGAAAACCTCCGGCTTCCAGGTTGAGCATT 19 213 0 CGGCTTCCAG 0.967216 -70 ********** Masking position 7 Map Score: 3.52972 Number of sites scoring better than the average of aligned sites = 3059 Number in coding regions = 2915 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 14 CCGTAAACTCCTTTCAGTGGGAAATTGTGG 3 251 1 CTTTCAGTGG 0.941565 -50 GATGATATTCCTTTCATCGGGCTATTTAAC 6 24 1 CTTTCATCGG 0.912089 -109 ATATACATATCTTTTAACGGTATCCGGCAA 9 19 1 CTTTTAACGG 0.886453 -132 TCGCTGTTCTCTTTCAGCGAAATAACAAGA 9 117 1 CTTTCAGCGA 0.962947 -34 AGCTACTCTCGTTTCAGTGACTTTCATTAT 11 105 1 GTTTCAGTGA 0.861953 -144 TTTATCTTTTCTTTCAACGATCACAAATTT 12 26 1 CTTTCAACGA 0.955597 -166 ATGGGGCCGAGTTTCAATGAATCG 15 5 0 GTTTCAATGA 0.837939 -296 GCTGTTTTTAGTTTTAACGGCAATTAATAT 18 61 0 GTTTTAACGG 0.827552 -240 ********** Masking position 6 Map Score: 2.5184 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 378 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 AATAAATATTCGTTTTCACAGTGGAATTAACT 2 278 1 CGTTTTCACT 0.8807 -23 AATCCCTCATCGTCATCACCGTTTTAAAATGA 3 83 0 CGTCATCACT 0.984926 -218 AACTTGTTACCGTTATCACATTCAGGAGATGG 6 105 1 CGTTATCACT 0.9763 -28 TTTTTGTGATCGTTATCTCGATATTTAAAAAC 8 132 1 CGTTATCTCT 0.8807 -66 CGAAAATAAACGGCAGCACTGTCCGGCAAAAA 10 38 0 CGGCAGCACT 0.907641 -110 AAAGTAAGTGCGTTATCAGTATTCAGGTAGCT 15 173 1 CGTTATCAGT 0.9456 -128 CCGTCAGCAGCGTTTTTTCTTCC 17 2 1 CGTCAGCAGT 0.939802 -240 TGCTTAATTACGTCATCATTTTGATGACATGA 18 263 1 CGTCATCATT 0.909976 -38 ********* * Masking position 12 Map Score: 2.55689 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 178 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234