AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -irpoH_rpxx_opreg_100.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP036 300 CLPB PROTEIN (clpB) #2 RP042 158 CELL CYCLE PROTEIN MESJ (mesJ) #3 RP043 50 CELL DIVISION PROTEIN FTSH (ftsH) #4 RP162 114 N UTILIZATION SUBSTANCE PROTEIN B (nusB) #5 RP184 122 DNAJ PROTEIN (dnaJ) #6 RP185 287 DNAK PROTEIN (dnaK) #7 RP319 264 HEAT SHOCK PROTEIN HSLV (hslV) #8 RP450 99 ATP-DEPENDENT PROTEASE LA (lon) #9 RP520 152 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT (clpP) #10 RP615 90 RIBOSOMAL PROTEIN S21 (rpsU) #11 RP627 300 10 KD CHAPERONIN (groES) #12 RP629 211 GRPE PROTEIN (grpE) #13 RP692 114 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX (clpX) #14 RP840 157 HEAT SHOCK PROTEIN HTPG (htpG) #15 RP860 270 unknown Motif number 1 ACTTTGTAACTTTTGACAAATTTACTATGATTA 1 17 1 TTTTAAATTT 0.869531 -284 TTCAAAATGCTTATAAAAAATTAAATGTTACTA 1 70 0 TTATAAATTA 0.829822 -231 CAAAGTAATATTATCAATTTTATCTTTCATATT 1 126 1 TTATATTTAT 0.863138 -175 AAATAACATATTTTCATTAATAAAGTGCAATAT 1 276 0 TTTTATATAA 0.751578 -25 AAATATAGCATTATTATTGTTTAATTGAATTGA 2 35 1 TTATATTTTA 0.728431 -124 ATTAGTAAACTTATAAAATTTTT 4 1 0 TTATAATTTT 0.828643 -114 TAATAAATTATTTTAAGATATAAGTTGCAAGGT 4 30 1 TTTTAAATAA 0.763388 -85 TCCAGAAAAATTATCACTCATAATGACTAAATT 4 72 0 TTATATATAA 0.490918 -43 AATTATTGTATTATGACTTTTTATTTGATATAG 6 21 0 TTATATTTTA 0.728431 -267 AAAAAACAACTTATAATTTATTTCTAGATCCTG 6 169 1 TTATATATTT 0.929017 -119 CAAGCTACCATTATTAATTATATTT 8 3 0 TTATATATAT 0.878373 -97 TTTATAGCAATTTTTAATTATATAATATAGTAT 8 47 0 TTTTATATAT 0.896661 -53 AATTAAAACCTTTTTAAAAATTTATATAGTTTA 8 76 0 TTTTAAATTT 0.869531 -24 CTATTCTAGCTTTTGATTATTATCTCACGCGTG 9 24 1 TTTTATTTAT 0.79658 -129 TATAAGTTAATTATAAGTTATAGTACAATAAAC 10 39 1 TTATATATAG 0.753659 -52 TATATATAGATTATTACTAATAAAGATGTAAAA 11 14 0 TTATATATAA 0.490918 -287 CTTTGCCACTTTTTAATTACTTAATATATATAG 11 38 0 TTTTATCTTA 0.696519 -263 AATTGCAAAATTATAATAACTTTTATGCTGTAT 11 74 1 TTATAACTTT 0.86981 -227 AAAATTTTTTTTATTAGAGATATATTTTTTTGC 11 201 0 TTATAAATAT 0.919618 -100 TAACCTCCAATTATTAAATCTTTAAATGTACAT 11 276 0 TTATAACTTT 0.86981 -25 GAAAAAAAATTTATTATATCTATATATATCTTA 12 162 1 TTATAACTAT 0.877264 -50 TAGTGTTCTTTTTTAAGATATATATAGATATAA 12 175 0 TTTTAAATAT 0.876998 -37 ATAGTTTTATTACATTTTTCTTCTGTCGT 14 7 1 TTATAATTTT 0.828643 -151 CTTGTCAACGTTATCAAATATTTACCATATTTC 14 62 0 TTATAAATTT 0.915172 -96 CTAAACCAATTTATAAATTCTTGTTTTTAGATT 14 134 0 TTATATCTTG 0.699442 -24 TAGTATACTATTTTCAATAATATTGATTTCAGC 15 39 1 TTTTATATAT 0.896661 -232 CAAATAAGCCTTTTTAATTATTTAGTGTTTCCC 15 99 1 TTTTATATTT 0.890904 -172 TCAATCACAATTATTATATCTAGGGAAACACTA 15 121 0 TTATAACTAG 0.670165 -150 AATTTGAGTATTTTAATTGTTATCTAGACACTT 15 178 0 TTTTATTTAT 0.79658 -93 **** * * **** Masking position 6 Map Score: 28.3398 Number of sites scoring better than the average of aligned sites = 1367 Number in coding regions = 887 Number in noncoding regions = 480 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 TTTGTAACTTTTGACAAATTTACTATGATTATGTAT 1 19 1 TAAATTATAT 0.604043 -282 TTATAATGCTTGAAATATTGAAAAATCAAAAAGAGA 1 168 0 TATATAAAAT 0.8823 -133 TATCTCTTGTTATTTTAATTAAAAATCATTATATGA 1 223 1 TTTATAAAAT 0.840647 -78 TATATGAAAATAGTCTAGTTAAAAATATTGCACTTT 1 252 1 TTTATAAAAT 0.847039 -49 CACAGTATTCACGAATATTTTACAATACTAACATCC 2 123 1 AATATTAAAT 0.767376 -36 ATTTTATAAGTTTACTAATAAATTATTTTAAGATAT 4 15 1 TATATAATAT 0.932476 -100 GTCGTATAAAACAACTATTATAACATAATTTC 5 101 1 AATATTACAT 0.673853 -22 AACAAGCCCTTTAATTATTGTATTATGACTTTTTAT 6 30 0 TATATTATAT 0.941363 -258 ATTCCCAGGATCTAGAAATAAATTATAAGTTGTTTT 6 171 0 TAAATAATAT 0.567533 -117 AGGTCCACACTGGAATAATATAGAATACAACGCTAA 6 233 1 TATATTAAAT 0.897056 -55 TTAATTAAATTGAATTAGTCAAGTATGCTTGATAAA 7 49 1 TATATAATAT 0.932481 -216 AAGTTGTTAATTAAGTACTATAACATAATATTTTAT 7 219 0 TATATTACAT 0.845148 -46 AAATATAATTAATAATGGTAGCTTGA 8 1 1 ATTATAAAAT 0.664666 -99 CAATTTTTAATTATATAATATAGTATCAACTGGATT 8 37 0 TTTATTATAT 0.922239 -63 CAGTTTTTATGTTCTATTCTAGCTTTTGATTATTA 9 10 1 TTTATTACTT 0.556075 -143 TATAACATCTTTAATTAATCAAATTTTGGGAGAAAA 9 122 1 TATATAATTT 0.810556 -31 AAAGATATTGTGGTTTATTGTACTATAACTTATAAT 10 48 0 TTTATTATAT 0.922239 -43 TATAATGATTTTTTGTACTTTAAAATAGAAGTAAAA 11 136 1 TTTATTAAAT 0.865543 -165 CAAAATACTCTCAACTAATCTAATATTTAGTTTTAC 11 166 0 TATATTATAT 0.941364 -135 TGTACATACTATATATATTTTATTTTTGTTAGTTCA 11 247 0 ATTATTATTT 0.582402 -54 TTGTACTCCTAATAATATTAAAGAATCGGTATACGA 12 19 1 AATATAAAAT 0.73943 -193 AGATATATATAGATATAATAAATTTTTTTTCAACGG 12 157 0 ATTATAATTT 0.545433 -55 TAGATTTAGTAATTTTAGTATACTATTTTCAATAAT 15 24 1 ATTATTATAT 0.81784 -247 CAAGTATATTTGTAATAGTTAAATTTGTCAAATAAG 15 71 1 TATATAATTT 0.81099 -200 AGATAACAATTAAAATACTCAAATTTGTATTTTTAC 15 186 1 TATATAATTT 0.81099 -85 ACAGTTTTCATCATGTAATTTATTATGAGATCCATG 15 221 0 TTTATTATAT 0.922238 -50 * * ** * ** *** Masking position 9 Map Score: 23.1192 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 548 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 ATATTCGTGAATACTGTGATCAAACATAGTATG 2 108 0 ATACTGTAAA 0.831729 -51 ATTTTTCTGGATACCTTCGTCAAGTTACGGT 4 94 1 ATACCTTGAA 0.951252 -21 TTTTTACTGGATGACGTGGTTAAGCCATGGTAT 5 62 1 ATGACGTGAA 0.92183 -61 GTTTTTTTGAATACCGTGGACAAGCTGCGATGT 6 143 0 ATACCGTGAA 0.995037 -145 TTTGATTTAGATACCATTGACAATGGATGGTAT 9 92 1 ATACCATGAA 0.951587 -61 GAAAAATAAAATAACGTAGCAAATTTTTCAAAT 12 112 1 ATAACGTGAA 0.982631 -100 TTAAATGATTATACCGTTGAAAAAAAATTTATT 12 144 1 ATACCGTGAA 0.995037 -68 TCGTCCTGAGATACCGCTACCAAGTAGCGGAAT 13 22 0 ATACCGCAAA 0.921866 -93 ATATTTCTGGATACCGTAAGGAATATGAGACGA 14 36 0 ATACCGTAAA 0.98263 -122 TAAATATTTGATAACGTTGACAAGACATGAGAT 14 71 1 ATAACGTGAA 0.982628 -87 ******* * ** Masking position 2 Map Score: 11.4492 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 23 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 TAAATTTGTCAAAAGTTACAAAGTCCGATT 1 7 0 AAAATAAAGT 0.951046 -294 AAATGCTTATAAAAAATTAAATGTTACTAAAGAT 1 65 0 AAAAAAATGT 0.430703 -236 GAGATCTCAAAAAAATATGAAAGATAAAATTGAT 1 138 0 AAAATAAAGA 0.895469 -163 TGAAATATTGAAAAATCAAAAAGAGATCTCAAAA 1 160 0 AAAATAAAGA 0.895469 -141 ATTTATTAGTAAACTTATAAAATTTTT 4 4 0 AAACTAAATT 0.828076 -111 TATGCTTGATAAACTTCAAAAATTTGCGTTGTTG 7 72 1 AAACTAAATT 0.828076 -193 AACCTTTTTAAAAATTTATATAGTTTATAGCAAT 8 69 0 AAAATATAGT 0.699148 -31 TAAGTAATTAAAAAGTGGCAAAGTAAAATTGCAA 11 48 1 AAAATAAAGT 0.951046 -253 GTGGCAAAGTAAAATTGCAAAATTATAATAACTT 11 62 1 AAAATAAATT 0.947026 -239 TTCAAGGGGGAAAAATAAAAATTTTTTTTATTAG 11 217 0 AAAATAATTT 0.859534 -84 TTGAACTAACAAAAATAAAATATATATAGTATGT 11 246 1 AAAATATATA 0.505134 -55 TCCAATTATTAAATCTTTAAATGTACATACTATA 11 270 0 AAATTAATGT 0.700861 -31 ATACGAAAGCAAATTTCAAAAAGAGCAAAATGTT 12 49 1 AAATTAAAGA 0.76069 -163 ATAACGTAGCAAATTTTTCAAATTAAATGATTAT 12 122 1 AAATTAAATT 0.87728 -90 TGTATAAACTAAAAAAAGAAAATTA 13 100 1 AAAAAAAATT 0.69829 -15 CGGTATCCAGAAATATGGTAAATATTTGATAACG 14 53 1 AAATTAAATA 0.759976 -105 TCTAAAAACAAGAATTTATAAATTGGTTTAGT 14 136 1 AGAATAAATT 0.649103 -22 ATAGTATACTAAAATTACTAAATCTATACAATAT 15 16 0 AAAATAAATC 0.724173 -255 TGTAATAGTTAAATTTGTCAAATAAGCCTTTTTA 15 81 1 AAATTAAATA 0.759971 -190 AGATCCATGTAAAAATACAAATTTGAGTATTTTA 15 196 0 AAAATAATTT 0.859534 -75 AAAATTACTAATTTATTGCTACAT 15 257 0 AAAATAATTT 0.836087 -14 **** * ***** Masking position 10 Map Score: 16.3574 Number of sites scoring better than the average of aligned sites = 802 Number in coding regions = 513 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 AAAAATTAAATGTTACTAAAGATTTTATATGATA 1 54 0 TGTAAAAATT 0.869694 -247 TTTGATGAATTGCTAGGAAAAATTGTATTCAAAA 1 96 0 TGTAAAAATT 0.869694 -205 CAAAAAAATATGAAAGATAAAATTGATAATATTA 1 131 0 TGAATAAATT 0.204718 -170 GAAAATAGTCTAGTTAAAAATATTGCACTTTATT 1 257 1 TATTAAAATT 0.546198 -44 TATTGCACTTTATTAATGAAAATATGTTATTTAT 1 277 1 TATAGAAATA 0.592458 -24 TCGTGAATACTGTGATCAAACATAGTATGTCATT 2 103 0 TGGAAAAATA 0.696167 -56 AGGATGTTAGTATTGTAAAATATTCGTGAATACT 2 126 0 TATGAAAATT 0.41383 -33 TAAAATAATTTATTAGTAAACTTATAAAATTTTT 4 11 0 TATAAAATTA 0.374892 -104 AATACAACGCTAATAATAAACAAAAAGAAAACGA 6 256 1 TATAAAAAAA 0.375704 -32 CATTCTACTTTAGAATAAAATATTATGTTATAGT 7 205 1 TAAAAAAATT 0.888699 -60 TACTATATTATATAATTAAAAATTGCTATAAACT 8 48 1 TAAAAAAATT 0.887117 -52 AATCAAAAGCTAGAATAGAACATAAAAACTG 9 8 0 TAAAGAAATA 0.539184 -145 GCGTGTTTAGTGAGATCAAAAATAATAACAATGT 9 52 1 TGGAAAAATA 0.696187 -101 AATCAAATTTTGGGAGAAAATATTA 9 138 1 TGGAAAAATT 0.748758 -15 TATAGATTATTACTAATAAAGATGTAAAACAG 11 9 0 TATAAAAATG 0.526935 -292 TATTTTAAAGTACAAAAAATCATTATAAATACCA 11 129 0 TAAAAATATT 0.256561 -172 AAAATAGAAGTAAAACTAAATATTAGATTAGTTG 11 157 1 TAAAAAAATT 0.888699 -144 GAGAGTATTTTGCAAAAAAATATATCTCTAATAA 11 190 1 TGAAAAAATA 0.804929 -111 AATATATCTCTAATAAAAAAAATTTTTATTTTTC 11 208 1 TATAAAAATT 0.908514 -93 TTGAACTAACAAAAATAAAATATATATAGTATGT 11 246 1 AAAAAAAATA 0.215288 -55 ATATAGTATGTACATTTAAAGATTTAATAATTGG 11 269 1 TAATAAAATT 0.491803 -32 TTAATATTATTAGGAGTACAAATTATATT 12 6 0 TAGAACAATT 0.350893 -206 GTACTCCTAATAATATTAAAGAATCGGTATACGA 12 21 1 TATAAAAAAT 0.439041 -191 CATACATATTTAGTACGAAAAATAAAATAACGTA 12 96 1 TATAAAAATA 0.884204 -116 TATAATCATTTAATTTGAAAAATTTGCTACGTTA 12 123 0 TATTAAAATT 0.546178 -89 ATTATACCGTTGAAAAAAAATTTATTATATCTAT 12 151 1 TGAAAAATTA 0.245402 -61 AAAAGAACACTAATATAAAAAATATT 12 196 1 TATAAAAATA 0.88407 -16 GTCTTGTCAACGTTATCAAATATTTACCATATTT 14 63 0 CGTAAAAATT 0.306577 -95 CTGAAATCAATATTATTGAAAATAGTATACTAAA 15 37 0 TATAGAAATA 0.571301 -234 CTTGCCACAATACAACAAAATATACAGTCAATCA 15 147 0 TAAAAAAATA 0.859936 -124 GAGATCCATGTAAAAATACAAATTTGAGTATTTT 15 197 0 TAAAACAATT 0.493263 -74 ** ** *** *** Masking position 10 Map Score: 17.9454 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 627 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 6 ATTTTTAATTAAAATAACAAGAGATACATA 1 219 0 AAAATAACAA 0.550418 -82 ATATCAATTCAATTAAACAATAATAATGCT 2 41 0 AATTAAACAA 0.516112 -118 ATCGTCGTATAAAACAACTATTATAACATA 5 98 1 AAAACAACTA 0.717068 -25 AAAAAGTCATAATACAATAATTAAAGGGCT 6 32 1 AATACAATAA 0.762787 -256 CACGGTATTCAAAAAAACAACTTATAATTT 6 158 1 AAAAAAACAA 0.905975 -130 GAACTATTGTAGAACAACAACGCAAATTTT 7 90 0 AGAACAACAA 0.880809 -175 TATAAGTTATAGTACAATAAACCACAATAT 10 50 1 AGTACAATAA 0.65551 -41 CTTTATATGTAGTAAAACAATGATACAGCA 11 99 0 AGTAAAACAA 0.898185 -202 TCTATTTTAAAGTACAAAAAATCATTATAA 11 135 0 AGTACAAAAA 0.57044 -166 TTAAAATAGAAGTAAAACTAAATATTAGAT 11 155 1 AGTAAAACTA 0.641616 -146 ATATATCTCTAATAAAAAAAATTTTTATTT 11 209 1 AATAAAAAAA 0.633898 -92 TGTTGTGATCAATAAAACATTTTGCTCTTT 12 68 0 AATAAAACAT 0.516112 -144 TAGTACGAAAAATAAAATAACGTAGCAAAT 12 106 1 AATAAAATAA 0.712729 -106 CGAAATCTTTAACACAACAACCCGCAATCA 13 52 1 AACACAACAA 0.768356 -63 TGTATAAACTAAAAAAAGAAAATTA 13 100 1 AAAAAAAGAA 0.633842 -15 AGAAAAATGTAATAAAACTAT 14 2 0 AATAAAACTA 0.751581 -156 AACAAATCTAAAAACAAGAATTTATAAATT 14 130 1 AAAACAAGAA 0.6917 -28 CACTTGCCACAATACAACAAAATATACAGT 15 153 0 AATACAACAA 0.950792 -118 AGATCCATGTAAAAATACAAATTTGAGTAT 15 200 0 AAAAATACAA 0.408064 -71 ********** Masking position 7 Map Score: 9.64949 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 282 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 ATTCAAAATGCTTATAAAAAATTAAATGTT 1 74 0 CTTATAAAAA 0.788594 -227 AAAAAGAGATCTCAAAAAAATATGAAAGAT 1 147 0 CTCAAAAAAA 0.73635 -154 GATATAAAACCTAATAAAAATTTTATCGGT 3 30 0 CTAATAAAAA 0.95416 -21 AAAATTATCACTCATAATGACTAAATTATA 4 69 0 CTCATAATGA 0.779087 -46 AGCACTATATCAAATAAAAAGTCATAATAC 6 17 1 CAAATAAAAA 0.688973 -271 GAATACAACGCTAATAATAAACAAAAAGAA 6 255 1 CTAATAATAA 0.905975 -33 TAAAATTACTCTCCTAAAAAGATATTGTGG 10 71 0 CTCCTAAAAA 0.883963 -20 TAGATTATTACTAATAAAGATGTAAAACAG 11 11 0 CTAATAAAGA 0.868009 -290 AAATATATCTCTAATAAAAAAAATTTTTAT 11 207 1 CTAATAAAAA 0.95416 -94 CCCCCTTGAACTAACAAAAATAAAATATAT 11 241 1 CTAACAAAAA 0.781345 -60 ATAATTTGTACTCCTAATAATATTAAAGAA 12 14 1 CTCCTAATAA 0.779087 -198 AAAAAGAACACTAATATAAAAAATATT 12 195 1 CTAATATAAA 0.68893 -17 TTACATGGATCTCATAATAAATTACATGAT 15 218 1 CTCATAATAA 0.917782 -53 ********** Masking position 6 Map Score: 11.9329 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 128 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TATTAATGAAAATATGTTATTTAT 1 287 1 AATATGTTAT 0.88139 -14 GATCAAACATAGTATGTCATTAAACACATA 2 94 0 AGTATGTCAT 0.918458 -65 AGGTATTGAAGGATGTTAGTATTGTAAAA 2 140 0 AGGATGTTAG 0.828842 -19 GTTTTATACGACGATGTCATACCATGGCTT 5 83 0 ACGATGTCAT 0.946655 -40 GAAATTATGTTATAATAGTTGTT 5 110 0 ATTATGTTAT 0.881368 -13 CTTGTTGAACACGATGTCATTTCCACAACA 6 60 1 ACGATGTCAT 0.946655 -228 AGAATAAAATATTATGTTATAGTACTTAAT 7 216 1 ATTATGTTAT 0.881368 -49 TGATTAATTAAAGATGTTATACCATCCATT 9 113 0 AAGATGTTAT 0.921779 -40 ********** Masking position 4 Map Score: 2.96012 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 25 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 AGAGATACATAACTGCATATAGAATATTATA 1 199 0 AACTCATATA 0.948944 -102 TAACTAGACTATTTTCATATAATGATTTTTA 1 242 0 ATTTCATATA 0.596606 -59 TTTGCAGTTGATCTTCATATAATAATCATTC 7 179 1 ATCTCATATA 0.937835 -86 AATTGCTATAAACTATATAAATTTTTAAAAA 8 68 1 AACTTATAAA 0.694734 -32 ATTAGTAATAATCTATATATATTAAGTAATT 11 26 1 ATCTTATATA 0.921371 -275 ATCATTGTTTTACTACATATAAAGTGGTATT 11 105 1 TACTCATATA 0.854512 -196 TAAATGTACATACTATATATATTTTATTTTT 11 256 0 TACTTATATA 0.820211 -45 AATTTATTATATCTATATATATCTTAAAAAA 12 169 1 ATCTTATATA 0.921371 -43 ACATGATGAAAACTGTATGTAGCAATAAATT 15 241 1 AACTTATGTA 0.771327 -30 **** ****** Masking position 7 Map Score: 2.94343 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 53 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ATGAGTGATAATTTTTCTGGATACCTTCGT 4 84 1 ATTTTTCTGG 0.966176 -31 CATTCTATGCATTGTTCTGGGGGCACAATT 6 99 1 ATTGTTCTGG 0.977868 -189 TTGTTCTACAATAGTTCTGGTACTTACACG 7 103 1 ATAGTTCTGG 0.977866 -162 AATATTTACCATATTTCTGGATACCGTAAG 14 49 0 ATATTTCTGG 0.966176 -109 ********** Masking position 5 Map Score: 1.86366 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 TAATGCTTGAAATATTGAAAAATCAAAAAGA 1 170 0 ATATTGAAAA 0.76373 -131 TTTTTTGAATACCGTGGACAAGCTGCGATGT 6 143 0 ACGTGGACAA 0.903494 -145 TTTAAGTGTAAGCCTTGAAAATTCAAGGAAC 7 13 1 ACCTTGAAAA 0.938485 -252 TGATTTAGATACCATTGACAATGGATGGTAT 9 94 1 ACATTGACAA 0.957295 -59 CTCATATTTTAACCTTGACATATAAGTTAAT 10 19 1 ACCTTGACAT 0.812612 -72 AAATGATTATACCGTTGAAAAAAAATTTATT 12 146 1 ACGTTGAAAA 0.956938 -66 AATATTTGATAACGTTGACAAGACATGAGAT 14 73 1 ACGTTGACAA 0.972412 -85 TGAAATCAATATTATTGAAAATAGTATACTA 15 39 0 ATATTGAAAA 0.76373 -232 * ********* Masking position 8 Map Score: 2.87459 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 28 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TACTTTGATGAATTGCTAGGAAAAATTGTATTCAAA 1 97 0 AATTCGAAAT 0.785871 -204 GATATATATCAGATCCACGCAACAATTCTATGTGTT 2 66 1 AGATCGAAAT 0.983487 -93 TTTGCACACTAAATCCAGGTGATAAAAGCGTGCGTT 5 27 1 AAATCGAAAA 0.88034 -96 ATTTATTTCTAGATCCTGGGAATAAATCACCGAATA 6 184 1 AGATCGAAAA 0.949549 -104 TAAGCCTTGAAAATTCAAGGAACAATAATTAATTAA 7 21 1 AAATCGAAAT 0.958816 -244 ATCTCACTAAACACGCGTGAGATAATAATCAAAAGC 9 32 0 ACACCGAAAT 0.869712 -121 CTTTTGATTTAGATACCATTGACAATGGATGGTATA 9 90 1 AGATCTAAAT 0.853779 -63 ATTGTTATCTAGACACTTGCCACAATACAACAAAAT 15 160 0 AGACCGAAAT 0.966792 -111 ATTTATTATGAGATCCATGTAAAAATACAAATTTGA 15 204 0 AGATCGAAAT 0.983487 -67 **** * * * *** Masking position 12 Map Score: 4.28571 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 25 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: 2.9654e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 2.9654e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 2.9654e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0