AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_ecoli_reg_300.orf -o00640_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 rpsB 300 30S ribosomal subunit protein S2 #2 tsf 257 protein chain elongation factor EF-Ts #3 pyrH 146 uridylate kinase #4 frr 291 ribosome releasing factor #5 yaeM 91 putative ATP-binding component of a transport system #6 yaeS 185 orf, hypothetical protein #7 cdsA 120 CDP-diglyceride synthetase #8 yaeT 29 orf, hypothetical protein #9 hlpA 121 histone-like protein, located in outer membrane or nucleoid #10 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #11 dnaE 36 DNA polymerase III, alpha subunit #12 sdhC 300 succinate dehydrogenase, cytochrome b556 #13 BIME45 63 BIME #14 sucC 85 succinyl-CoA synthetase, beta subunit #15 ycjL 121 probable amidotransferase subunit #16 ycjC 26 orf, hypothetical protein #17 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #18 goaG 37 4-aminobutyrate aminotransferase #19 ydbO 284 orf, hypothetical protein #20 fliY 87 putative periplasmic binding transport protein #21 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #22 BIME89 108 BIME #23 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #24 atoS 214 sensor protein AtoS for response regulator AtoC #25 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #26 atoB 30 acetyl-CoA acetyltransferase #27 ackA 300 acetate kinase #28 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #29 dedA 82 orf, hypothetical protein #30 usg 65 putative PTS system enzyme II A component #31 pdxB 98 erythronate-4-phosphate dehyrogenase #32 b2654 300 orf, hypothetical protein #33 b2657 171 putative enzyme #34 b2658 138 orf, hypothetical protein #35 b2659 230 orf, hypothetical protein #36 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #37 yqeF 251 putative acyltransferase #38 iciA 141 replication initiation inhibitor, binds to 13-mers at oriC #39 sbm 203 methylmalonyl-CoA mutase (MCM) #40 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #41 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #42 acs 300 acetyl-CoA synthetase Motif number 1 TCGGCACATATTCCGGGGTGCCCTTTGGGGT 1 224 1 TTCCGGGGGC 0.916991 -77 CTCGAACTATTTTGGGGGAGTTATCAAGCCT 2 13 0 TTTGGGGGGT 0.650812 -245 AGCTCGAGAATTCCCGGGAGCTTACATCAGT 2 60 1 TTCCCGGGGC 0.793156 -198 TGCGGTTTAATGCCGGGCAGATCACATCTCC 2 225 1 TGCCGGGCGA 0.700028 -33 AAGAAGCCGCCCTCAGGCGGCTCCTTTTTGA 3 14 0 CCTCAGGCGC 0.913715 -133 AGCTAACCCTTGTGGGGCTGCGCTGAAAAGC 3 67 1 TGTGGGGCGC 0.838174 -80 GCGTAAGTATCGCGGGGGCGTAAGTCTGGTT 4 43 1 CGCGGGGGGT 0.732128 -249 GGCGTTATTGTTGCAGGCAGTTTGGTCACGG 4 78 1 TTGCAGGCGT 0.882863 -214 GCCATTTTGGCCCCGGGCAGTGCTCGCCATC 4 147 0 CCCCGGGCGT 0.870411 -145 CCTTGCGGATCGGCTGGCGGCGTTTTGCTTT 5 44 1 CGGCTGGCGC 0.720276 -48 CCCATTTGCACCGGAGGGTGCAGTTCTTTGC 9 84 0 CCGGAGGGGC 0.759069 -38 CTTACGATTGCGGCAGGCCGTGTTATTATTG 10 53 1 CGGCAGGCGT 0.900735 -52 TTCCGGAGACCTGGCGGCAGTATAGGCTGTT 12 70 0 CTGGCGGCGT 0.532244 -231 TGGCTCGGGATTGCAGGGTGTTCCGGAGACC 12 90 0 TTGCAGGGGT 0.84239 -211 TGTGTATAGATTGCCGGGCGCATTGCGCTTA 17 33 0 TTGCCGGGGC 0.773618 -242 AGGTAAGTGATTCGGGGGAGCGAACGCAGCC 17 119 1 TTCGGGGGGC 0.810235 -156 GCGCAGAGATCCCCGGGCCGTATGCCCGTTT 17 203 0 CCCCGGGCGT 0.870411 -72 AGTTTGTGAACGTCAGGGCGCAGAGATCCCC 17 220 0 CGTCAGGGGC 0.917687 -55 TACAGGTAAATTCCAGGCAGAAAAAAACCCC 21 56 0 TTCCAGGCGA 0.694569 -123 CCATCGGTCACCTGAGGCGGAGCTTCGCCCC 24 60 0 CCTGAGGCGA 0.369143 -155 CTACTTAGGCCTTCAGGCTGCTAAAGGATAC 27 75 0 CTTCAGGCGC 0.937517 -226 GCTAAAAAAACGTCAGGGAGCCATAGAGCGT 27 256 0 CGTCAGGGGC 0.917687 -45 TTATCCAAAGTTTCGGGCTGTTATGTTTTAA 28 39 1 TTTCGGGCGT 0.871797 -117 GCTCGGAACATTTCAGGCTGTAGCCAACGTA 29 21 1 TTTCAGGCGT 0.874108 -62 ACTCGTCATCTTTCAGGCTGTAACTACGTTG 29 45 0 TTTCAGGCGT 0.874108 -38 GCTGTAACATTGGCAGGGAGCTTTGCTATTT 30 30 1 TGGCAGGGGC 0.913291 -36 TTCGCAAGTATGCCTGGCCGCGAGATTATGG 31 34 1 TGCCTGGCGC 0.71548 -65 ATGGAGCGCATTTGAGGGTGTATCTGCAACT 34 85 1 TTTGAGGGGT 0.655533 -54 AATAGACAAATCTCAGGCGGCAAAAAACGAC 39 87 1 TCTCAGGCGC 0.902117 -117 ******** ** Masking position 6 Map Score: 27.3897 Number of sites scoring better than the average of aligned sites = 4019 Number in coding regions = 3788 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 AGTTTGGTCACGGCCAGCGCGCAGCAACCGGAGCG 4 96 1 CGCACGCCGC 0.859089 -196 ATTTTGGCCCCGGGCAGTGCTCGCCATCCTCACGT 4 140 0 CGCATGCCCC 0.603692 -152 TTTCTTGAACGACAAAAACGCCGCTCAGTAGATC 5 10 1 CGAAAACCGC 0.97836 -82 GACAGAATAAAAAGCAAAACGCCGCCAGCCGATCC 5 50 0 AACAAACCGC 0.882686 -42 GGCGATACTTCAGCAAAAGCGACCCCCA 7 4 0 CAAAAGCACC 0.56741 -117 CCGGCGGCAACAGAAACAACGCCGCGATGACGACG 7 64 0 CAAAAACCGC 0.982177 -57 ATCGCCGGGCCACGCAAAGAACTGCACCCTCCGGT 9 71 1 CACAAGACGC 0.732399 -51 TAAGAAACGACAATAATAACACGGCCTGCCGCAAT 10 59 0 CAAAAACCGC 0.982177 -46 AACTGCGCGTCATGCAAAACACTGCTTCCAGATGC 12 146 0 CACAAACCGC 0.97836 -155 TTTGTAAACACAAAAACAACTCCGCTACATCTTAT 20 17 0 CAAAAACCGC 0.982177 -71 AATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 21 44 0 AGAAAACCGC 0.882686 -135 CTAATCGTCCGATTAAAAACCCTGCAGAAACGGAT 21 115 1 GAAAAACCGC 0.935152 -64 GATAAACAGCCCTGCGTTATATGAG 21 164 0 GAAAAGCCGC 0.949214 -15 TGTGCAAATTCACAACTCAGCGGGACAACGT 27 7 1 AACAAACCGC 0.882686 -294 TGGTTTACTCCAGAAATAGCAAAGCTCCCTGCCAA 30 39 0 CAAAAGCAGC 0.861989 -27 TTGTATCCGTGGTTAAAAGCGCAGCTTAAAAGATC 38 25 0 GGAAAGCCGC 0.938778 -117 GACAAACCCACGTAAAAAGCTCACCGTAGGCGCAA 39 143 1 CGAAAGCCCC 0.924844 -61 TGCTGACCTTCAAAAATTACCCTGCCGTTTATTTG 42 163 1 CAAATACCGC 0.89264 -138 ** ** *** * ** Masking position 6 Map Score: 17.3419 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 923 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 3 TCAGTGATATAGTCTGCGCCATCTGATCGT 6 57 1 AGTCTGCGCC 0.841043 -129 GAAAGGACGCTGTCTGACCCGCAAGCAGAC 12 184 1 TGTCTGACCC 0.792491 -117 GGCCCGGGGATCTCTGCGCCCTGACGTTCA 17 215 1 TCTCTGCGCC 0.941901 -60 AATACTCTTTTCTCTGCCCCTTATTCCCGC 23 103 0 TCTCTGCCCC 0.973362 -163 CATAATGCCATTTTTGCCCCCAACAGACCA 28 83 0 TTTTTGCCCC 0.883983 -73 TTTAATGTTATATCTGCCCCGATAAAACGG 35 11 1 TATCTGCCCC 0.981918 -220 CTAAACATATTATCTGCCCCGTTTTATCGG 35 29 0 TATCTGCCCC 0.981918 -202 ATTAACGCCCTATCTACCCCTCTATTGGTG 37 83 1 TATCTACCCC 0.795764 -169 TGCTGTTGTCTGCTCCTGGTAAATGC 38 126 0 TGTCTGCTCC 0.912899 -16 AAAATGAGGGTATTTGCGCCTACGGTGAGC 39 161 0 TATTTGCGCC 0.885986 -43 TATTTGCTCCGTAAAACGCA 39 194 0 TATTTGCTCC 0.775225 -10 ACGCCGGTCTATTTTGCCCCAGAGTGTCAA 40 169 0 ATTTTGCCCC 0.63061 -132 ********** Masking position 5 Map Score: 11.6069 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 239 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 CCTCAGGCGGCTCCTTTTTGATAA 3 5 0 CTCCTTTTTG 0.758764 -142 CTGAGGGCGGCTTCTTTTTGTGCCCATCTT 3 29 1 CTTCTTTTTG 0.943509 -118 TTTTACACGGCTTTTTTTTGTATAGGCTTC 6 122 1 CTTTTTTTTG 0.859872 -64 CGTTCCATCTTTTGTTCGCCAAACTTTA 10 9 1 CTTTTGTTCG 0.879661 -96 AAATACCTTGCTTCTTTTCGTACAACCCTG 24 26 0 CTTCTTTTCG 0.912746 -189 TTTATATTCCTTCTGTTTGTAGGGGTGCC 26 12 0 CTTCTGTTTG 0.969481 -19 AAAAGTAGGACATCTGTTTGCAATTACTTT 32 214 1 CATCTGTTTG 0.801442 -87 GTTGTCCTCACTTCTTTTTGTATTCCTTGA 39 45 1 CTTCTTTTTG 0.943509 -159 TTTTTACCCTTCTGTTTTTTTGACCTTA 41 9 1 CTTCTGTTTT 0.830335 -181 TTTCTTTAATCTTTTGTTTGCATATTTTTA 41 105 1 CTTTTGTTTG 0.92108 -85 GCTTTTGTTCTCCTTGTAGGA 42 290 0 CTTTTGTTCT 0.529668 -11 ********** Masking position 5 Map Score: 8.38797 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 69 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AAGTCTGGTTATAAGGCGTTATTGTTGCAG 4 64 1 ATAAGGCGTT 0.848818 -228 CGTAAACCCTGTCAGGGAATAAAAAACGC 6 167 1 GTCAGGGAAT 0.795854 -19 AAAAGCAGATATCAGGCGATACTTCAGCAA 7 23 0 ATCAGGCGAT 0.956862 -98 TGTAGACCGGATAAGGCATTATCGCCTTCT 13 32 1 ATAAGGCATT 0.838248 -32 AGCGCAGCGCATCAGGCAATTTGGCGTTGC 22 41 0 ATCAGGCAAT 0.953437 -68 TGTGGGTACAGTCAGGCAATAGCAAGGGGA 25 151 0 GTCAGGCAAT 0.935812 -45 AGCTTAAAAGATCAGGGATTTGCGCTA 38 8 0 ATCAGGGATT 0.889087 -134 GATATGTGCTATCAGGCATTATTTGATGGA 39 11 0 ATCAGGCATT 0.967719 -193 GATAGCACATATCAGGCGTTGTCCTCACTT 39 28 1 ATCAGGCGTT 0.970129 -176 GTGTGATTGTGACAGGCGTTTCACCGCCGT 40 256 0 GACAGGCGTT 0.764919 -45 ********** Masking position 4 Map Score: 7.17166 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 421 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 ATGTGATCTGCCCGGCATTAAACCGCACAGATATA 2 217 0 CCCGCATACG 0.756444 -41 CCGGGCAGTGCTCGCCATCCTCACGTACTTTTGTA 4 131 0 CTCGCACCCG 0.872765 -161 GCGAGCACTGCCCGGGGCCAAAATGGCAAATAAAA 4 151 1 CCCGGGCATG 0.818968 -141 TGTGTTAATACCCGTCGTCATCGCGGCGTTGTTTC 7 52 1 CCCGCGCCCG 0.960708 -69 CGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAA 12 191 1 CCCGAACACG 0.936167 -110 GGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAG 12 218 1 CCCGCGCCGG 0.591118 -83 AACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAG 12 255 1 CCCGAGCCGG 0.655073 -46 ACCGACAATGCCCGGAAGCGATACGAAATATTCGG 14 16 1 CCCGAACTCG 0.86442 -70 AACGTGCTTCCCCGCCACCGGCGGGGTTTTTTTCT 21 34 1 CCCGCACCGG 0.527381 -145 TGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACC 23 203 0 CCCGCGCATC 0.862588 -63 TTCGTACAACCCTGAAAGCCTCGCGCTAC 24 5 0 CCTGAACCCG 0.654646 -210 AGAATCCCCACGACTAAAGGCCAGAACGTT 34 119 0 CCCCCGCAGG 0.832666 -20 ACAAATGTTACCCGCCGACGGCTTCGGTATATGCA 38 56 1 CCCGCGCCTC 0.932428 -86 AAGCGTATGCCCCGACAGCTGTATGCATAGCGATA 40 216 0 CCCGCACTTG 0.904485 -85 **** ** * * ** Masking position 1 Map Score: 9.20578 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 685 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TTGTGGTATAAAGCGCGCCGGACTTCCGATC 1 131 1 AAGCCGCCGG 0.993771 -170 TACAATGGCGAACCCCACCGGCGGCAACAGA 7 85 0 AACCCACCGG 0.972666 -36 CGATCAATATAAGATCGCCGGGCCACGCAAA 9 58 1 AAGACGCCGG 0.946849 -64 TCTGACCCGCAAGCAGACCGGAGGAAGGAAA 12 196 1 AAGCGACCGG 0.972666 -105 TTACCTGAGTAAGCTCATCGGGATTCGCTCA 17 94 0 AAGCCATCGG 0.918242 -181 GGCAGAAAAAAACCCCGCCGGTGGCGGGGAA 21 41 0 AACCCGCCGG 0.982591 -138 CCCACGTAAAAAGCTCACCGTAGGCGCAAAT 39 149 1 AAGCCACCGT 0.918243 -55 CGATAAATTCCAGCAGGCCGGGACGCCGGTC 40 190 0 CAGCGGCCGG 0.937466 -111 **** ****** Masking position 2 Map Score: 6.40884 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 204 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 8 CCTTGCGGATCGGCTGGCGGCGTTTTGCTT 5 44 1 CGGCTGGCGG 0.817321 -48 TTCCCTGACAGGGTTTACGGTACTCAGGAA 6 156 0 GGGTTTACGG 0.924572 -30 TTATTCCCTGGGGACTACGGGCACAGAGGT 12 256 0 GGGACTACGG 0.947037 -45 ATGCCTTATCCGGTCTACAGTGCAGGTGAA 13 21 0 CGGTCTACAG 0.769005 -43 ACGAAATATTCGGTCTACGGTTTAAAAGAT 14 38 1 CGGTCTACGG 0.94721 -48 TGCGCTTACCCGGCTTACAGAACAAAAAGA 17 11 0 CGGCTTACAG 0.742329 -264 AGAAATAAACGGGCATACGGCCCGGGGATC 17 197 1 GGGCATACGG 0.897206 -78 GACGATAACAGGGTTGACGGCGATTGAGCC 23 192 1 GGGTTGACGG 0.934148 -74 GACGGCGATTGAGCCGACGGGTGGAAACCC 23 207 1 GAGCCGACGG 0.887482 -59 CAAATGTTACCCGCCGACGGCTTCGGTATA 38 57 1 CCGCCGACGG 0.611451 -85 GAGGGTATTTGCGCCTACGGTGAGCTTTTT 39 156 0 GCGCCTACGG 0.947004 -48 CCAGCAGGCCGGGACGCCGGTCTATTTTGC 40 182 0 GGGACGCCGG 0.795967 -119 ********** Masking position 8 Map Score: 5.49582 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 451 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 TCGAATTTTCTATTATAGAAAACCTTCAGTGGCACGTT 1 44 0 TTAAACTTCA 0.604254 -257 GGCGGCTTCTTTTTGTGCCCATCTTGTAAATTCAGCTA 3 34 1 TTCATCTGTA 0.63787 -113 TGCCGCCAGGTCTCCGGAACACCCTGCAATCCCGAGCC 12 82 1 TTCACCTGCA 0.857847 -219 GTGTTCTGTCCATCCTTCAGTAATCGTTA 14 67 0 TTCATCTTCA 0.965983 -19 CCCGGCAATCTATACACAAAATCATTCAAGTTGCATCA 17 46 1 TTAATCTTCA 0.767344 -229 ACATTCTTTATATACACTTCATCCTTCAAGCCGCCTCT 17 155 0 TTCATCTTCA 0.965982 -120 AATTCACAACTCAGCGGGACAACGTTCAAAACATTTTG 27 17 1 TACAACTTCA 0.564058 -284 AGACTCAAGATATTTCTTCCATCATGCAAAAAAAATTT 27 174 1 TTCATCTGCA 0.966596 -127 CACCGACATTTATGATTAACATCATGCACTGCAAATTT 27 206 0 TTCATCTGCA 0.966596 -95 TAATCATAAATGTCGGTGTCATCATGCGCTACGCTCTA 27 226 1 TTCATCTGCG 0.80847 -75 GCTGTTATGTTTTAATGTGCAACATTCATGGTCTGTTG 28 55 1 TTCAACTTCA 0.929294 -101 GCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACT 29 51 0 TTCATCTTCA 0.965983 -32 ACTTACAATTGATTAAAGACAACATTCACAGTGTGGTT 42 30 0 GTCAACTTCA 0.657264 -271 TTATGCCACATATTATTAACATCCTACAAGGAGAACAA 42 269 1 TTCATCTACA 0.817404 -32 * * **** **** Masking position 11 Map Score: 7.00941 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 103 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 GGTTCGCCATTGTAACGCTGGTGGTCTGC 7 102 1 TGTAAGCGTG 0.943822 -19 CACAAAGGAATGTAGTGGTAGTGTAGCGATGAC 9 19 1 TGTAGGGATG 0.962136 -103 CTATGCGATCTGTATAGCAACTGCGGAAAACAT 19 98 1 TGTATGCATG 0.771914 -187 AAACTGGAATCGTAAAGGTGATGAC 19 270 1 CGTAAGGGTG 0.726234 -15 AAGAATAAGATGTAGCGGAGTTGTTTTTGTGTT 20 13 1 TGTAGGGGTG 0.980363 -75 CTGTTTGCAGTGTAGAGCCATTGTTTGTAAACA 20 42 0 TGTAGGCATG 0.968058 -46 TCCTTCTGTTTGTAGGGGTGCCG 26 1 0 TGTAGGGGCG 0.903862 -30 TGGAATTCATTGTAGAGCTGCTGATAGGTAGAG 34 25 0 TGTAGGCGTG 0.983483 -114 AGCAGGAATATGGAGCGCATTTGAGGGTGTATC 34 76 1 TGGAGGCTTG 0.753628 -63 CACCGCCGTCTGTAAAGCGTATGCCCCGACAGC 40 232 0 TGTAAGCTTG 0.820889 -69 AAGCGTTAAATGTAGGGGTATTGGCAGTTTTGT 42 238 0 TGTAGGGATG 0.962136 -63 ***** ** * ** Masking position 4 Map Score: 6.07996 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 82 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CGAGTTGCAGAAAGGCGGCAAGCTCGAGAAT 2 40 1 AAGGCGGCAA 0.88208 -218 GGCGAACCCCACCGGCGGCAACAGAAACAAC 7 79 0 ACGGCGGCAA 0.922915 -42 CAAGTTGCATCAAGGCGGCAAGTGAGCGAAT 17 72 1 CAGGCGGCAA 0.967947 -203 TCTGTATAGCAACTGCGGAAAACATTAATGC 19 106 1 ACTGCGGAAA 0.865906 -179 CAGGTAAATTCCAGGCAGAAAAAAACCCCGC 21 54 0 CAGGCAGAAA 0.921875 -125 CGATTAAAAACCCTGCAGAAACGGATAATCA 21 124 1 CCTGCAGAAA 0.921875 -55 CCAAAACTTGCTATGCAGAAATTTGCACAGT 25 13 1 CATGCAGAAA 0.880561 -183 GAATGAGCGGCTATGCAGAAAATTGCGCACT 25 41 0 CATGCAGAAA 0.880561 -155 TAGACAAATCTCAGGCGGCAAAAAACGACGT 39 89 1 TAGGCGGCAA 0.747506 -115 GCAGTTTTTGCGCTGCGGAAAAGGTGACATT 40 62 1 CCTGCGGAAA 0.963057 -239 AACATTGACACTCTGGGGCAAAATAGACCGG 40 165 1 CCTGGGGCAA 0.762552 -136 TCTGATCACGCTCGGCAGAAATCACGCTCTG 41 68 0 CCGGCAGAAA 0.949715 -122 * ********* Masking position 10 Map Score: 10.0851 Number of sites scoring better than the average of aligned sites = 958 Number in coding regions = 911 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 CTGGACGGAAGCGACAATCTCACTTTGTGTA 1 179 1 GCGAAATCTC 0.952349 -122 TTGCAGAAAGGCGGCAAGCTCGAGAATTCCC 2 44 1 GCGGAAGCTC 0.834348 -214 CTAACAAATAGCGCGACTCTCTGTAGCCGGA 6 17 0 GCGCACTCTC 0.944841 -169 GCCGGAGAAGGCGATAATGCCTTATCCGGTC 13 36 0 GCGAAATGCC 0.81398 -28 GGCGGCAAGTGAGCGAATCCCGATGAGCTTA 17 85 1 GAGCAATCCC 0.792345 -190 TATTTCAAAGGGGCGAAGCTCCGCCTCAGGT 24 51 1 GGGCAAGCTC 0.751896 -164 GTGTCATCATGCGCTACGCTCTATGGCTCCC 27 241 1 GCGCACGCTC 0.904078 -60 GGACAAGTGTGCCATAATCTCGCGGCCAGGC 31 45 0 GCCAAATCTC 0.661118 -54 GGTAGATAGGGCGTTAATCTCCCATACTTAA 37 70 0 GCGTAATCTC 0.858585 -182 TAGCGCAAATCCCTGATCTTTTA 38 3 1 GCGCAATCCC 0.982264 -139 TTTTTTGCTGGCGACAAACCCACGTAAAAAG 39 131 1 GCGAAAACCC 0.741434 -73 CTCACCGTAGGCGCAAATACCCTCATTTTGA 39 162 1 GCGCAATACC 0.813805 -42 TACCTTCGTTGCGCCAATGTCACCTTTTCCG 40 77 0 GCGCAATGTC 0.921254 -224 **** ****** Masking position 6 Map Score: 6.5693 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 482 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 TTCGTATACACAGACTGGACGGAAGCGACAATCTCACTT 1 165 1 CATGGAACGC 0.882448 -136 CAAAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGA 2 30 1 CGTGCAACGC 0.974887 -228 CCTGATTAAACATATTACGGGTAATCGTCTGGATTATTA 4 191 0 CATACGACGC 0.788098 -101 GATTGCCGGGCGCATTGCGCTTACCCGGCTTACAGAACA 17 17 0 CGTGCGACGC 0.966108 -258 CAAAATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGA 17 62 1 CATGCAACGC 0.987163 -213 CTGACGTTCACAAACTGCATATATCTGATAGACGTGAAA 17 235 1 CATGCAATGT 0.814836 -40 GAGAAGAGAGAACATTGCGGTAACACGCTTTTACCGCTA 24 104 0 AATGCGACGT 0.763669 -111 TACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTT 35 61 1 CATGCAACCT 0.683324 -170 CGCCAGCAAAAAAAATGCATTCAGACGTCGTTTTTTGCC 39 105 0 AATGCAACGC 0.938686 -99 ACTTGACGGACATTGTGCAGCGATCTGCTGCTATCCTCC 40 124 0 CATGCAATGT 0.814836 -177 TGGAATTTATCGCTATGCATACAGCTGTCGGGGCATACG 40 209 1 CGTGCAATGC 0.885434 -92 ATACGCTTTACAGACGGCGGTGAAACGCCTGTCACAATC 40 243 1 CAGGCGACGC 0.899051 -58 GCAAAAGTAGAATTGTGCAAATAAACGGCAGGGTAATTT 42 176 0 AATGCAACGC 0.938686 -125 ** **** * ** * Masking position 13 Map Score: 4.87847 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 643 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 14 TCGCTTCCGTCCAGTCTGTGTATACGAAATGGA 1 160 0 CCATTGTGTT 0.885253 -141 AGCGACAATCTCACTTTGTGTAACAACACACAC 1 188 1 TCATTGTGTA 0.827293 -113 TAGCACACTTCCACTGTGTGTGACTGTCTGGTC 4 238 1 CCATTGTGTA 0.982088 -54 CTTTACGATTCCAGTTTTCGTGAATTAATTAAA 19 254 0 CCATTTCGTA 0.869313 -31 CAGTGTAGAGCCATTGTTTGTAAACACAAAAAC 20 35 0 CCATTTTGTA 0.939284 -53 TCAAAAACAGCCATTTTTTGTTAGTCGCCGAAA 23 131 0 CCATTTTGTA 0.939284 -135 TGAGTCTATGCCATTTTGCGTAATTTTCAGCCA 27 148 0 CCATTGCGTA 0.959308 -153 AAATTGCCCTCCATTTTGTTTAATTTGTAGATG 37 24 0 CCATTGTTTA 0.827293 -228 CACTATGACACAATTTTGTGTCAGGTTGCATAT 38 84 0 CAATTGTGTA 0.827293 -58 GCCCCTATGTGTAACAAATAACCA 42 2 1 CCCTTGTGTA 0.919577 -299 *** * ***** * Masking position 7 Map Score: 4.93259 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 77 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 CCGGCGCGCTTTATACCACAAATACGTCGTGG 1 120 0 TAACCACAAA 0.822652 -181 TCACTTTGTGTAACAACACACACGTATCGGCA 1 198 1 TAAACACACA 0.758682 -103 TGACGACGGGTATTAACACAAAAGCAGATATC 7 40 0 TTAACACAAA 0.937793 -81 CGCCCGGCAATCTATACACAAAATCATTCAAG 17 44 1 TTTACACAAA 0.679612 -231 AATAGTTAAGTAAAATCACAAATTTTGTATGT 19 189 0 TAATCACAAA 0.887741 -96 GTGAATTAATTAAAAACACGAATCACATTGTT 19 236 0 TAAACACGAA 0.758682 -49 AGCCATTGTTTGTAAACACAAAAACAACTCCG 20 28 0 TTAACACAAA 0.937792 -60 AAAAAGTGATTTTTATCACAAAGGAAATATGC 37 165 0 TTATCACAAA 0.88774 -87 ATTCCTTGAATCACATCACAAAATAGACAAAT 39 66 1 TAATCACAAA 0.887741 -138 GTTTGCATATTTTTAACACAAAATACACACTT 41 120 1 TTAACACAAA 0.937792 -70 * * ******** Masking position 8 Map Score: 2.20201 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 22 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