AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mthe_reg_300.orf -o00051_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH331 208 mannosyltransferase #2 MTH332 119 LPS biosynthesis RfbU related protein #3 MTH338 190 LPS biosynthesis RfbU related protein #4 MTH343 48 rhamnosyl transferase #5 MTH347 60 O-antigen transporter #6 MTH348 194 rhamnosyl transferase #7 MTH442 195 excinuclease ABC subunit B #8 MTH443 41 excinuclease ABC subunit A #9 MTH444 133 sensory transduction histidine kinase #10 MTH446 97 sensory transduction regulatory protein #11 MTH447 109 sensory transduction regulatory protein #12 MTH448 74 unknown #13 MTH449 38 unknown #14 MTH661 119 ammonium transporter #15 MTH662 61 nitrogen regulatory protein P-II #16 MTH663 205 ammonium transporter #17 MTH839 253 unknown #18 MTH840 62 pseudouridylate synthase I #19 MTH1040 300 unknown #20 MTH1041 195 triosephosphate isomerase #21 MTH1405 82 DNA polymerase delta small subunit #22 MTH1406 48 fuculose-1-phosphate aldolase #23 MTH1583 44 conserved protein #24 MTH1584 112 phosphomannomutase #25 MTH1591 30 phosphonopyruvate decarboxylase #26 MTH1592 21 conserved protein #27 MTH1593 205 ribosomal protein S3a #28 MTH1594 72 conserved protein #29 MTH1598 300 conserved protein #30 MTH1759 70 mannose-1-phosphate guanyltransferase #31 MTH1762 159 DNA mismatch recognition protein MutS #32 MTH1763 28 collagenase #33 MTH1764 154 sensory transduction regulatory protein Motif number 1 CCAGTCCAGTCCAGTCCAGTCCATCCTATC 6 104 0 CCAGTCCAGT 0.969783 -91 CCAGTCCAGTCCAGTCCAGTCCAGTCCAGT 6 114 0 CCAGTCCAGT 0.969783 -81 TTTTATCAGTCCAGTCCAGTCCAGTCCAGT 6 124 0 CCAGTCCAGT 0.969783 -71 CATTCACTGTCTACTCCAGGATCTTTTATC 6 147 0 CTACTCCAGG 0.970489 -48 GGAACGCTGACCACTCCGGGCTGATGACAG 17 125 0 CCACTCCGGG 0.967288 -129 GTACAACGAGCTACTCCACTGGGACCTCAT 17 156 0 CTACTCCACT 0.953471 -98 TCTCTTATCTCCACACCAGGTGATCCT 18 46 1 CCACACCAGG 0.907332 -17 TTAATCTTACCGCCTCCACTGATGGCAGGA 19 238 0 CGCCTCCACT 0.852545 -63 TAGCACTGGCCTCCTCCAGGGGGAGGAGGT 28 19 1 CTCCTCCAGG 0.953697 -54 GCATAATAATCCACTCCACTACCATGTTCA 29 132 1 CCACTCCACT 0.979599 -169 AAAAGATCTTCTCCTCCGCTGGAGGACATA 33 85 1 CTCCTCCGCT 0.831249 -70 ********** Masking position 6 Map Score: 13.6032 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 252 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 AGGATAAATATTTAAGAGAGGTTCATTTAACTGT 1 119 1 TTTAGGGTTC 0.979621 -90 ATCATGATTATGTGTGAGGTGTTCTCATTAAGGA 1 184 1 TGTAGTGTTC 0.933711 -25 GATCTTAAGGTTTTTCAGAGGCTCTCTTGAAATC 2 80 0 TTTAGGGCTC 0.97824 -40 CCCCACTCGCATTTTGAGGGGCTACAGGAGTTGC 3 79 1 ATTAGGGCTA 0.733949 -112 ATGTCCTCTTTTTACTAGGTGCTCGGCCTCAATC 3 116 0 TTTAGTGCTC 0.873831 -75 TATCATTTCATGGATAAGAGGTTCCATGAAACGC 9 43 1 TGGAGGGTTC 0.945109 -91 ATTAGTCCTCAGTGATAGCGGTTCCATAAAGGAG 11 79 1 AGTAGGGTTC 0.973275 -31 TGTTCGTCCCTGTGGAAGTGGCTCCTTTACATCC 17 91 1 TGTAGGGCTC 0.98844 -163 GTGCGGGAGTTGTTGAAGGGGTTCATGAATGAAT 20 113 0 TGTAGGGTTC 0.989181 -83 ACACTGAGTTATTGAGGGGGGTTCTCTATCCGGT 29 222 0 ATTGGGGTTC 0.782884 -79 AAGTATTCTCTGTTGAAGCGGTTACTCCCAGATT 31 87 0 TGTAGGGTTA 0.933711 -73 *** ** ***** Masking position 13 Map Score: 9.24675 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 114 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 3 TACATATTGATGAGGTTTTTATGTAGGATAA 1 95 1 TGAGGTTTTA 0.774565 -114 CATTTGGACTTGTAGTTATTACGAAAACCTC 3 150 0 TGTAGTATTA 0.652921 -41 GAGTTAAGCGTGAGGAGATGATGCC 4 34 1 TGAGGAATGA 0.926644 -15 CACAATAGAATGAGGTTCTTATTTTAAGTGA 7 172 1 TGAGGTCTTA 0.835701 -24 ACATTTTCTGGTAATGAGAATTAAGGC 8 7 1 TCTGGTATGA 0.726982 -35 TAAGGTGTCTTGAGCTCATTAACCGTAATGA 10 65 1 TGAGCTATTA 0.758641 -33 GACGTCAGGCTGAAGTTATGATGGTACACGC 12 54 1 TGAAGTATGA 0.796883 -21 TTTCAGTAATTGAGGTTATTATCTAAACTTG 16 41 1 TGAGGTATTA 0.975692 -165 TATATAGTGGTGATGTGATTAAGGTTCATGG 19 190 1 TGATGTATTA 0.694308 -111 CTTTATTCATTGAGGTAATGTGATTAAAAAT 24 11 1 TGAGGTATGT 0.855813 -102 TGGGGTGCTGTGTGGTCATGAATATGAACAG 27 24 0 TGTGGTATGA 0.948594 -182 TGAGAACCATTGAGATGATTAAACATGACCT 29 36 1 TGAGATATTA 0.679751 -265 GTGGTGGATGTGAGGTCATGTTTAATCATCT 29 48 0 TGAGGTATGT 0.855775 -253 ATGCACAGTCTGAGGAAATCAAACAGTATAT 29 105 0 TGAGGAATCA 0.709573 -196 ACCATGTTCATGTGGAGATTATTTAAGAAAA 29 152 1 TGTGGAATTA 0.85926 -149 TTCTGGTTATTATAATGTAATT 30 2 1 TCTGGTATTA 0.731059 -69 TCAGAAAGAGTGGGGATATTAGGTGCAATAA 31 51 0 TGGGGAATTA 0.690631 -109 ****** **** Masking position 9 Map Score: 9.37292 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 333 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TGTTAATGAGATACATGAAAATCTCTACGTATATTA 1 34 1 AACTGAATTT 0.706673 -175 TTCTGGGTGAATCCATGAAAATATGTCTTTTTAGCA 3 34 1 ACCTGAATTT 0.965005 -157 AACTTTATGTATCCTGGCAAAGGTATATATAAGTTG 7 119 1 ACCGGAAGTT 0.985916 -77 GGAACCTCTTATCCATGAAATGATAAGAGTGGATCA 9 32 0 ACCTGAAGTA 0.892529 -102 AGACACCTTAAGCCTGGAAATTTTATTGTGGGCTCT 10 39 0 ACCGGAATTT 0.98476 -59 CTTATAAGAAATCCGGTTAAGGATATTTAAG 15 41 1 ACCGTAAGTT 0.923676 -21 TATACACCTGAACCCTGCAACTGTATGTTGATGTAA 22 17 1 ACCTGAATTT 0.964978 -32 AATCATGGTTAACCAGTTAAATATGAATTTTTTGAA 27 130 1 ACCGTAATTA 0.756398 -76 ATCCATATATATCCAGGGAAATTTATAGTTGGG 31 137 1 ACCGGAATTT 0.98476 -23 ATCCATCAGGAGCCGGGAAAAGATCTTCTCCTCCGC 33 68 1 ACCGGAAGTT 0.985917 -87 * ** ** ** * * * Masking position 9 Map Score: 9.05847 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 42 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 ATAAAATTTCCAGGCTTAAGGTGTCTTGAGCTCA 10 49 1 CGCTAGGTGT 0.983555 -49 TTACCGGGTTTCAGTGTTGAGCGTATC 12 4 1 CGGTCAGTGT 0.916564 -71 AACATATTCTCCGGATCCAGGTGTTCATGCTCCA 17 46 1 CGATAGGTGT 0.937709 -208 TGGAGTAGCTCGTTGTACCGGTGTCATCCAGGGC 17 168 1 CTGTCGGTGT 0.984615 -86 CGCATCCCCACATAGTGAAGGTGTTAAATGCAGA 20 62 0 CTGTAGGTGT 0.983353 -134 TATCTCATAGTATGGTTGAGGTGTATTATAAAAT 20 161 0 TTGTAGGTGT 0.837684 -35 CATACAGTTGCAGGGTTCAGGTGTATATAACAT 22 10 0 CGGTAGGTGT 0.991457 -39 AAAATTCATACGGAGTGAAGGTCTGACTTTATCC 24 37 1 CGGTAGGTCT 0.937609 -76 TAGAGTATTCCATACTGGCGGTGTATGTAACTCT 27 95 1 CTCTCGGTGT 0.970572 -111 GGTCTCCCTCCCGGTGTGCAGCAGGTG 29 284 0 CCCTCGGTGT 0.936938 -17 * * ** ****** Masking position 6 Map Score: 8.79162 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 55 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 6 CATGTATCTCATTAACAGGGAATGTGAACATAC 1 18 0 ATTACAGGAT 0.587362 -191 AGATCCTGGAGTAGACAGTGAATGCAGATCCTC 6 153 1 GTAACAGGAT 0.894061 -42 GTTTTAAACATAAATCAGAGGATGGTAATGATA 7 13 0 TAATCAGGAT 0.811607 -183 GAGTCTCATATCTGACAGGGTATCCCACGTGTT 7 79 0 TCTACAGGAT 0.906173 -117 TGTACCGGTGTCATCCAGGGCATGGTTCATACC 17 181 1 TCACCAGGAT 0.954232 -73 AGTTTTTGATGAATTCAGGGTATGAACCATGCC 17 199 0 GAATCAGGAT 0.664709 -55 AATAAAACCTTTTAACAGAGTATTGGGGCGCCA 19 73 1 TTTACAGGAT 0.874817 -228 GCTTTTTTCAGCATTCAGAGGATTCTAATCATG 19 115 0 GCATCAGGAT 0.858137 -186 TTTGCCTGTAATATCCAGCGCATCCCCACATAG 20 81 0 ATACCAGGAT 0.755022 -115 AATTCAAATATTATCCAGTGAATGGGGCTGTTA 24 86 1 TTACCAGGAT 0.937738 -27 TCTGAGGAAATCAAACAGTATATGGAGACGTCT 29 95 0 TCAACAGAAT 0.572579 -206 TTTGATTTCCTCAGACTGTGCATAATAATCCAC 29 113 1 TCAACTGGAT 0.684399 -188 CCCCCCTCAATAACTCAGTGTATGTGCATCTTA 29 235 1 TAATCAGGAT 0.811513 -66 ATAAGTATTTTTTTCCAGCGAATATGCAATTAC 30 27 0 TTTCCAGGAT 0.851866 -44 GAGTAACCGCTTCAACAGAGAATACTTTCCACA 31 94 1 TTCACAGGAT 0.758972 -66 TTATAATGCTTCAGACACAGAATTATTTAGGAT 33 118 1 TCAACACGAT 0.665045 -37 *** **** * ** Masking position 12 Map Score: 8.3758 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 162 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ATTTATTACATATTGATGAGGTTTTTATGTA 1 89 1 TATTGATGGG 0.956747 -120 ACTTTTCGTATGATGATGTGGGGTGCGACAG 6 40 1 TGATGATGGG 0.9351 -155 TCATTAACCGTAATGAAGAGGAACCGGA 10 80 1 TAATGAAGGG 0.860117 -18 TGTTCGTCCCTGTGGAAGTGGCTCCTTTACA 17 91 1 TGTGGAAGGG 0.973618 -163 TCCTGCCATCAGTGGAGGCGGTAAGATTAAG 19 238 1 AGTGGAGGGG 0.811502 -63 GTGCGGGAGTTGTTGAAGGGGTTCATGAATG 20 116 0 TGTTGAAGGG 0.981072 -80 TATCTCATAGTATGGTTGAGGTGTATTATAA 20 164 0 TATGGTTGGG 0.689063 -32 TCCACTACCATGTTCATGTGGAGATTATTTA 29 146 1 TGTTCATGGG 0.870328 -155 TACACTGAGTTATTGAGGGGGGTTCTCTATC 29 226 0 TATTGAGGGG 0.948289 -75 AAGTATTCTCTGTTGAAGCGGTTACTCCCAG 31 90 0 TGTTGAAGGG 0.981072 -70 ******** ** Masking position 8 Map Score: 7.42019 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 264 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 CATCCTTTCTCTGATGAGTTAATCCCTATGAG 5 34 0 CTGAGGTTAA 0.912527 -27 TAAGTTGACCCTGAAATATAATCCCACAATAG 7 148 1 CTGAAATAAT 0.821156 -48 TAAGATGATGCTGATATATAAATCTTTCGGAT 16 103 0 CTGAAATAAA 0.910218 -103 CTGAGAAATTATATTACTTCTT 18 1 1 CTGAAATTAT 0.910234 -62 TGTTAAACCAGTGAAAAATTAAATTGTAAACA 20 16 0 GTGAAATTAA 0.856901 -180 TTACAGGGCAGTGAAGGATTAAA 21 70 1 GTGAGATTAA 0.866446 -13 TAGAGAGCGCCTGAGAAGTAAAGAGTAAAGCA 29 187 1 CTGAAGTAAA 0.813435 -114 TTTACTCTTCCTGATAGATTAACCATC 33 6 0 CTGAAATTAA 0.957253 -149 TTCCCGGCTCCTGATGGATTAACCACGATCCT 33 55 0 CTGAGATTAA 0.960414 -100 AATTCTGTGTCTGAAGCATTATAAAGTTATGT 33 110 0 CTGAGATTAT 0.916568 -45 **** * ***** Masking position 4 Map Score: 5.485 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 28 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 AACTCCTGTAGCCCCTCAAAATGCGAGTGGGGGGT 3 76 0 GCCCTCAAGG 0.882197 -115 AGGAATGCCGGGACCTCCAGAAGTG 5 1 0 GGCCTCGAGG 0.997141 -60 AAAATCAGCCGGACCTCTGGAAGAGCAGAGATCCG 9 88 0 GGCCTCGAGG 0.997141 -46 ACTGGTGTCTGGTCTTCAAGACATGC 10 2 0 GGCTTCGAAG 0.8707 -96 CGGTGTGTTCGTCCCTGTGGAAGTGGCTCCTTTAC 17 86 1 GTCCTGGAGG 0.867976 -168 GGAACTGGGAGGCCCTCCCGAAATGGAGGTCAACC 28 46 0 GGCCTCGAAG 0.985651 -27 TGGTTCTCATGGCCCTCCTGTGGGGCGTTATCAG 29 10 0 GGCCTCGTGG 0.984255 -291 GATTAACCACGATCCTCGGTAGGGGAAGATTTTTT 33 36 0 GACCTCTAGG 0.834785 -119 TATAAAGTTATGTCCTCCAGCGGAGGAGAAGATCT 33 88 0 TGCCTCGCGG 0.900824 -67 ** **** ** * * Masking position 6 Map Score: 5.37993 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 221 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 GGTTCATTTAACTGTTAAAAGTAGAATGTCA 1 138 1 ACTGTAAAAG 0.952354 -71 GGGGGTAAAGACTGCTAAAAAGACATATTTT 3 51 0 ACTGTAAAAA 0.926479 -140 ACTGGACTGGACTGATAAAAGATCCTGGAGT 6 134 1 ACTGTAAAAG 0.952354 -61 GCCCCAATACTCTGTTAAAAGGTTTTATTTT 19 71 0 TCTGTAAAAG 0.887775 -230 TCCTCTGAATGCTGAAAAAAGCATTATATAA 19 126 1 GCTGAAAAAG 0.937938 -175 TTCTGAATTAGATGTTAAAAACCACCTTACA 21 44 1 GATGTAAAAA 0.744009 -39 AGTGAATGGGGCTGTTAAAAA 24 102 1 GCTGTAAAAA 0.962999 -11 TTGCATATTCGCTGGAAAAAAATACTTATTA 30 31 1 GCTGAAAAAA 0.905015 -40 **** ****** Masking position 7 Map Score: 4.47562 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 19 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 TGGGGTGCGACAGATTTTTACTGCTGTAGGT 6 58 1 CAGATTTTTC 0.86225 -137 TTACCATCCTCTGATTTATGTTTAAAACAAG 7 18 1 CTGATTTATT 0.853097 -178 AGAGGTCCGGCTGATTTTTCTGACTCTCCTC 9 105 1 CTGATTTTTT 0.853097 -29 ACACAGATTTAAACATGGTTCACA 15 4 1 CAGATTTAAC 0.81972 -58 CTATATCCGAAAGATTTATATATCAGCATCA 16 99 1 AAGATTTATT 0.711956 -107 TGCTGATTTAATTTAAAAGGCTT 19 3 1 CTGATTTAAT 0.808369 -298 AAAAGGCTTTCAGATTTTTTTAGGGCCCCAT 19 25 1 CAGATTTTTT 0.918011 -276 CCACCATGTCAAGATTTAAATACTCCCTTAT 27 57 1 AAGATTTAAT 0.642275 -149 CGGTTACTCCCAGATTTTACTTCAGAAAGAG 31 72 0 CAGATTTTAT 0.890511 -88 ACCTGATTTTAACCGGAGGAAAT 32 3 1 CTGATTTTAC 0.702227 -26 TCGGTAGGGGAAGATTTTTTTACTCTTCCTG 33 25 0 AAGATTTTTT 0.711956 -130 GCTTCAGACACAGAATTATTTAGGATTATTT 33 125 1 CAGAATTATT 0.564627 -30 ********* * Masking position 4 Map Score: 5.07402 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 50 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TTTTCATCTCTCCATGTTCGAGGATCT 6 178 0 CTCTCCATGT 0.76321 -17 AAACGCATGGCTCTTCACGGATCTCTGCTC 9 71 1 CTCTTCACGG 0.803169 -63 CTTCACGGATCTCTGCTCTTCCAGAGGTCC 9 83 1 CTCTGCTCTT 0.871648 -51 ATTTTTCTGACTCTCCTCTTCTGGTC 9 118 1 CTCTCCTCTT 0.96734 -16 TTATTGTGGGCTCTTCACTGGTGTCTGGTC 10 23 0 CTCTTCACTG 0.904671 -75 CTCTCTACTTTTTTTATTCT 14 1 1 CTCTCTACTT 0.948731 -119 ATCACTCTCCTTTTGGATGTGCCT 14 106 0 CTCTCCTTTT 0.836604 -14 CGCGTTACCTCGCTCTACTTGCACTCGCAG 19 276 1 CGCTCTACTT 0.794204 -25 CGCTCTCTATCTCTTTTCTTAAATAATCTC 29 166 0 CTCTTTTCTT 0.865472 -135 ATGTGCTTTACTCTTTACTTCTCAGGCGCT 29 192 0 CTCTTTACTT 0.904019 -109 ********** Masking position 4 Map Score: 3.10634 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 179 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TCCCTGCATCAGTGAGGTATCTGA 9 2 1 CCTCACAGTG 0.973442 -132 GTCTTGAAGACCAGACACCAGTGAAGAGCCCAC 10 15 1 CCGCACAGTG 0.995855 -83 GGGGCAATGTCCAGACATTAGTCCTCAGTGATA 11 63 1 CCGCATAGTC 0.929322 -47 TTACCGGGTTTCAGTGTTGAGCGTAT 12 4 1 CCGTTCAGTG 0.866114 -71 CCTTTACATCCCTGTCATCAGCCCGGAGTGGTC 17 114 1 CCGCACAGCC 0.985552 -140 GCGGGTAGATCCTGCCATCAGTGGAGGCGGTAA 19 229 1 CCGCACAGTG 0.995855 -72 AACTGCCATACCCATCAGCAGCGACCTTCGATG 31 14 1 CCACACAGCG 0.961536 -146 ** * ** ***** Masking position 10 Map Score: 3.39201 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 94 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 TTAAAATAGCATCATTTATAAAGGTATAAACTAC 2 14 1 ATATTATAGG 0.870114 -106 CAGACTCAACTTTATGTATCCTGGCAAAGGTATA 7 112 1 TTATTATTGG 0.917494 -84 TTTAACATATTTCAGTAATTGAGGTTATTATCTA 16 32 1 TTAGAATAGG 0.791834 -174 CTTACAGTTTTTGATGAATTCAGGGTATGAACCA 17 203 0 TTATAATAGG 0.942132 -51 GAAACAAAGGTTTATATATAGTGGTGATGTGATT 19 176 1 TTATTATTGG 0.917494 -125 TATTACCTAATTAATTTATGGAGGGAGAAC 23 25 1 TTATTATAGG 0.954953 -20 CTTTATTCATTGAGGTAATGTGATT 24 2 1 TTATCATAGG 0.946164 -111 AAGGTCTGACTTTATCCATATTGGTGATTAACAA 24 54 1 TTATCATTGG 0.902145 -59 AGATCATAAATCTAGGAAGGTGGGTT 25 3 1 ATATAATAGG 0.83726 -28 ** ** *** *** Masking position 8 Map Score: 2.49387 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 17 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 CTTTACCCCCCACTCGCATTTTGAGGGGCT 3 72 1 CACTCGCATT 0.985042 -119 GATTAAGAGACACTCGCGTTACCTCGCTCT 19 262 1 CACTCGCGTT 0.967196 -39 GCTCTACTTGCACTCGCAGTAGCA 19 287 1 CACTCGCAGT 0.974778 -14 TATTTTACTGCACACACATTTTAAAACTTT 21 16 1 CACACACATT 0.898075 -67 GAATACTTTCCACACGCACTCTGAATCCAT 31 113 1 CACACGCACT 0.964249 -47 ********** Masking position 2 Map Score: 0.587595 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 8 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185