AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -ipurR_aquae_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glnB 196 nitrogen regulatory PII protein #2 guaA 45 GMP synthase #3 purK 300 phosphoribosyl aminoimidazole carboxylase #4 carA 300 carbamoyl phosphate synthetase small subunit #5 oppB 300 transporter (OppBC family) #6 mtfB 300 mannosyltransferase B #7 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #8 purB 41 adenylosuccinate lyase #9 aq_598 99 putative protein #10 purD 35 phosphoribosylamine-glycine ligase #11 aq_765 33 putative protein #12 gcsH4 269 glycine cleavage system protein H #13 carB1 300 carbamoyl-phosphate synthase large subunit #14 aq_1173 115 hypothetical protein #15 purF 27 amidophosphoribosyltransferase #16 purE 24 phosphoribosylaminoimidazole carboxylase #17 purA 28 adenylosuccinate synthetase #18 aq_1292 68 hypothetical protein #19 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #20 prs 128 phosphoribosylpyrophosphate synthetase #21 purL 52 phosphoribosylformylglycinamidine synthase II #22 putative 27 putative protein #23 guaB 300 inosine monophosphate dehydrogenase #24 carB2 26 carbamoyl-phosphate synthase large subunit #25 hemN 300 oxygen-independent coproporphyrinogen II Motif number 1 ACTCCACACGGTACATTAGGAACCGTATTTTGA 3 33 0 GTCATGGAAC 0.986229 -268 AATGTACCGTGTGGAGTTGAAACCTTGCTTTAT 3 49 1 GTGATGAAAC 0.993652 -252 ACTCCACACGGTACATTAGGAACAAACTATGAA 3 107 0 GTCATGGAAC 0.986229 -194 AATGTACCGTGTGGAGTTGAAACCTCTTGATAG 3 123 1 GTGATGAAAC 0.993652 -178 CTCCACTACGGTACATTAGGAACAAAAGAATCG 3 178 0 GTCATGGAAC 0.986229 -123 ATGTACCGTAGTGGAGTTGAAACTTCGGTGATA 3 195 1 GTGATGAAAC 0.993652 -106 TATCCACACGGTACATTAGAAACTGATTTCTTT 3 245 0 GTCATGAAAC 0.992883 -56 ACTCCACACGGTACATTAGAAACAGAACTCTCA 4 38 0 GTCATGAAAC 0.992883 -263 AATGTACCGTGTGGAGTTAAAACTTCTTCCATT 4 54 1 GTGATAAAAC 0.976631 -247 ACTCCACACGGTACATTAGAAACAATAATCAAC 4 105 0 GTCATGAAAC 0.992883 -196 AATGTACCGTGTGGAGTTAAAACAGGTTTGAGA 4 121 1 GTGATAAAAC 0.976631 -180 ACTCCACACGGTACATTAGAAACTTCGTCAAGC 4 170 0 GTCATGAAAC 0.992883 -131 AATGTACCGTGTGGAGTTAAAACAAGGTTTTGA 4 186 1 GTGATAAAAC 0.976631 -115 ACTCCACACGGTACATTAGAAACCATCTGCAAC 4 235 0 GTCATGAAAC 0.992883 -66 AATGTACCGTGTGGAGTTAAAACGCAGATTGTA 4 251 1 GTGATAAAAC 0.976631 -50 AGGCTGTGAAGTTGACTTAACACCCGGTTACAA 13 82 1 GTGATAACAC 0.832637 -219 AATTAAGGAAGTTGACGAGGAACTCTGCAACAA 23 35 1 GTGAGGGAAC 0.905386 -266 ** ** * ***** Masking position 5 Map Score: 52.5071 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 2 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GGTTCCTAATGTACCGTGTGGAGTTGAAACC 3 42 1 GTACCGTGGG 0.999134 -259 TGTTCCTAATGTACCGTGTGGAGTTGAAACC 3 116 1 GTACCGTGGG 0.999134 -185 TGTTCCTAATGTACCGTAGTGGAGTTGAAAC 3 187 1 GTACCGTATG 0.934985 -114 AGTTTCTAATGTACCGTGTGGATAAAAATGA 3 254 1 GTACCGTGGG 0.999134 -47 TGTTTCTAATGTACCGTGTGGAGTTAAAACT 4 47 1 GTACCGTGGG 0.999134 -254 TGTTTCTAATGTACCGTGTGGAGTTAAAACA 4 114 1 GTACCGTGGG 0.999134 -187 AGTTTCTAATGTACCGTGTGGAGTTAAAACA 4 179 1 GTACCGTGGG 0.999134 -122 GGTTTCTAATGTACCGTGTGGAGTTAAAACG 4 244 1 GTACCGTGGG 0.999134 -57 ******** ** Masking position 3 Map Score: 33.7864 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 4 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 CTTCCTTCCTCCTTGTAAGTTATT 1 183 0 TTCCTTCCTT 0.89129 -14 GGTTTCACCTCCCTTTATTCATCCATCTATAT 2 10 1 TCCCTTTCAT 0.766704 -36 TATTCCACGATTCTTTTGTTCCTAATGTACCGT 3 171 1 TTCTTTTCCT 0.898867 -130 TGTAAAATCTTCCCTTGCCTCCTCACTCAGGTC 5 111 0 TCCCTTTCCT 0.967137 -190 TTTACAGCAGCTCTTTGGTACTTCATAGAAGAA 5 138 1 CTCTTTACTT 0.571222 -163 GGGTATCCTGTCCTTTTCTTCTATGAAGTACCA 5 153 0 TCCTTTTCTA 0.612446 -148 TATTGAGAGCTTCTTTTCAACCTTCGAGCGATG 6 47 1 TTCTTTACCT 0.844713 -254 GATATCATGCTCCTTTGGGACTTGGACTTGCAG 7 17 1 TCCTTTACTT 0.934455 -47 TCCCTTCTTTCCTTTCCCTCCCT 8 1 1 TCCCTTTCCT 0.967137 -41 CGTAAACTCCTTACCACTTATATAATAAG 10 7 1 CTCCTTACTT 0.63849 -29 GGGATAGGGTTGCTTTAATACCTCCAGTTAGCG 12 219 1 TGCTTTACCT 0.726697 -51 GGTTACAAATTCCTTTATTTCTTTAATGTCTTT 13 206 0 TCCTTTTCTT 0.958838 -95 TTCCCTTACAGCCCTTACTTCTTCTATTATTGA 19 114 0 GCCCTTTCTT 0.913033 -31 CCTCGTCAACTTCCTTAATTCTTTCGGGCTTAT 23 22 0 TTCCTTTCTT 0.925176 -279 GCCTTAATGGGTCCTTACGACTTCCTGAACGTT 23 96 1 GTCCTTACTT 0.720096 -205 TTACTGCTGTTCCTTTAAGTCCTTAATGAGTGT 23 228 0 TCCTTTTCCT 0.956894 -73 GCAGTAAAAATCCTTTCCTCCTTTTTCCTTTTA 23 254 1 TCCTTTCCTT 0.939194 -47 TCCTCCTTTTTCCTTTTAACCTTTGAGTAATAT 23 269 1 TCCTTTCCTT 0.939194 -32 AATTAGTAATGCCTTTTCACCCTCAAAGATCAT 25 128 0 GCCTTTCCCT 0.833443 -173 TAGGTGGGGCTGCCTTATTTCTTGCAAATAAAC 25 195 1 TGCCTTTCTT 0.858034 -106 ****** **** Masking position 6 Map Score: 22.4528 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 749 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 TTTTTACCTCCTTTTTATTGT 1 2 1 TTTTACCTCC 0.948083 -195 CTTCCTTCCTCCTTGTAAGTTATTA 1 182 0 TTCCTCCTTG 0.424447 -15 GGTTTCACCTCCCTTTATTCAT 2 3 1 TTTCACCTCC 0.983004 -43 CCTCCCTTTATTCATCCATCTATATATTAT 2 18 1 TTCATCCATC 0.337795 -28 TAAAGCAAGGTTTCAACTCCACACGGTACA 3 51 0 TTTCAACTCC 0.931051 -250 TATCAAGAGGTTTCAACTCCACACGGTACA 3 125 0 TTTCAACTCC 0.931051 -176 ATCACCGAAGTTTCAACTCCACTACGGTAC 3 197 0 TTTCAACTCC 0.931051 -104 ATGGAAGAAGTTTTAACTCCACACGGTACA 4 56 0 TTTTAACTCC 0.810014 -245 CTCAAACCTGTTTTAACTCCACACGGTACA 4 123 0 TTTTAACTCC 0.810014 -178 CAAAACCTTGTTTTAACTCCACACGGTACA 4 188 0 TTTTAACTCC 0.810014 -113 ACAATCTGCGTTTTAACTCCACACGGTACA 4 253 0 TTTTAACTCC 0.810014 -48 CCTCTTTGTGTTTTTCCTTCACGTACTTGA 5 229 0 TTTTTCCTTC 0.859775 -72 CATACACCACTTTCTCCTTCCAC 6 4 0 TTTCTCCTTC 0.951027 -297 AGAGCTTCTTTTCAACCTTCGAGCGATGGT 6 52 1 TTCAACCTTC 0.799872 -249 ACCTGATTATTTTCTCGTCCACATCAACTC 6 196 0 TTTCTCGTCC 0.701531 -105 AAAAGTACCTTATCTCCACCATCTTACGAA 12 15 0 TATCTCCACC 0.276445 -255 TCCAAGAAGTTTTAACCACCGCTAACTGGA 12 241 0 TTTAACCACC 0.663082 -29 CCTTCCACCTCCAAGAAGTTTT 12 258 0 TTCCACCTCC 0.978093 -12 CTTCACAGCCTTCTTCCTTCACAACATCGT 13 63 0 TTCTTCCTTC 0.825577 -238 GATTATACTTATTCTCCTCCGTACTCCACG 13 274 0 ATTCTCCTCC 0.720294 -27 TCGCCCATCCTTCCACCTCCTGTTAGGATT 14 17 0 TTCCACCTCC 0.978093 -99 CCCCAGCCATTTAATCCTCC 20 119 1 TTAATCCTCC 0.463401 -10 TCGCTTCCTCCTTCGGTAAGTAAA 21 5 1 TTCCTCCTTC 0.937464 -48 TAAAAATCCTTTCCTCCTTTTTCCTTTTAA 23 258 1 TTCCTCCTTT 0.332252 -43 AGAGATCCAATTTATCCTTCGCCAGAGGC 25 10 0 TTTATCCTTC 0.816644 -291 AGTAATGCCTTTTCACCCTCAAAGATCATA 25 127 0 TTTCACCCTC 0.662684 -174 ********** Masking position 2 Map Score: 33.2684 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 889 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 5 GGAAATTGCATAATAACTTACAAGGAGGAAGGAAG 1 172 1 TTAACGGAGG 0.962917 -25 AAAATACGGTTCCTAATGTACCGTGTGGAGTTGAAACC 3 35 1 TTAACTGTGG 0.918235 -266 CACGGTACATTAGGAACAAACTATGAAGACATAGAAAG 3 96 0 TGAACTGAAG 0.494519 -205 AGAAATCAGTTTCTAATGTACCGTGTGGATAAAAATGA 3 247 1 TTAACTGTGG 0.918235 -54 AGAGTTCTGTTTCTAATGTACCGTGTGGAGTTAAAACT 4 40 1 TTAACTGTGG 0.918235 -261 TGATTATTGTTTCTAATGTACCGTGTGGAGTTAAAACA 4 107 1 TTAACTGTGG 0.918235 -194 TTGACGAAGTTTCTAATGTACCGTGTGGAGTTAAAACA 4 172 1 TTAACTGTGG 0.918235 -129 TGCAGATGGTTTCTAATGTACCGTGTGGAGTTAAAACG 4 237 1 TTAACTGTGG 0.918235 -64 GACTACAAGGTAATCAAGTACGTGAAGGAAAAACACAA 5 216 1 TTAACGAAGG 0.923975 -85 AAAGAGGAGATAGACAGGTACTTTAAGGAAACGAAGTT 5 252 1 TAAACTAAGG 0.949734 -49 AGGTATTCAGTTAAAAATCACCCAGAGGGTTATAAATT 6 263 0 TAAACAGAGG 0.883372 -38 TCTATGACTTTAAACATTAACCGAAAGGGATAAAATTT 9 24 0 TAAACAAAGG 0.780003 -76 GAATACTATTTTTAAAAAATCTATAAGGAG 9 80 1 TAATCTAAGG 0.824697 -20 GTTAGCGGTGGTTAAAACTTCTTGGAGGTGGAAGG 12 245 1 GAATCGGAGG 0.477963 -25 CCGGTCGGTGTAGATATTGACTTGGAAGTTTGTTTTGA 13 26 1 TAAACGGAAG 0.855303 -275 CCCGAAATACTCAAAAAAGACATTAAAGAAATAAAGGA 13 191 1 TAAACTAAAG 0.743819 -110 CTTTACTATGTCCATAAACACCTGAAGGCAAAGTTCAC 19 39 1 TAAACGAAGG 0.947384 -106 TGAACTAAACTCCAGAGGAACCATAAGGACACTCACGA 23 170 1 TAAACTAAGG 0.949734 -131 GCTTTTGATATTGACACACTCATTAAGGACTTAAAGGA 23 213 1 TAATCTAAGG 0.824697 -88 TACTCAAAGGTTAAAAGGAAAAAGGAGGAAAGGATTTT 23 260 0 TAAAAGGAGG 0.604689 -41 AAATAAACAATTAAAAGCCTCAGGAAAGAAGTAAAAAT 25 220 1 TAATCGAAAG 0.407911 -81 * * * ** ***** Masking position 6 Map Score: 22.5805 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 259 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 CAAAAGAATCGTGGAATACGCGGAAAACAGATA 3 156 0 GGGAATACGG 0.783557 -145 GTATCCTGAAGAGGAGTTTGGCGTCCAGAATCA 5 61 0 GGGAGTTTGG 0.984075 -240 AGTTAGGGTCGGAGAGTATCCTGAAGAGGAGTT 5 76 0 GAGAGTATCG 0.911984 -225 GGAGGCAAGGGAAGATTTTACAGCAGCTCTTTG 5 122 1 GAGATTTTAG 0.695519 -179 GCGATGGTTTGGAGAGTATGTAGTGAGCAAAAG 6 74 1 GAGAGTATGG 0.974843 -227 TAAAGAAAAGGAAGAGTTTGAGTTTGAAGGCAC 12 67 1 GAGAGTTTGT 0.921728 -203 TGCCGTTAACGAAGAGTACGTGGATGAGGACTA 12 172 1 GAGAGTACGG 0.969585 -98 TATCCCCGTCGGAGATTTTATAGTCCTCATCCA 12 192 0 GAGATTTTAG 0.695519 -78 AATAGACAGCGTGGAGTACGGAGGAGAATAAGT 13 265 1 GGGAGTACGG 0.973634 -36 ACATAGTAAAGGGGAGTTTGCATAAAGTAGAAT 19 17 0 GGGAGTTTGT 0.9317 -128 CGTACTTGTTGCAGAGTTCCTCGTCAACTTCCT 23 40 0 GAGAGTTCCG 0.921475 -261 CGTACTGAGCGAGGATTTTGATTCCGTACTTGT 23 64 0 GGGATTTTGT 0.771639 -237 * ******** * Masking position 5 Map Score: 7.35425 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 305 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ACCTTTGTTCAATTGTAAACATGTTAACAA 1 85 1 AATTGTAAAC 0.92586 -112 ATGTTAACAAAATTGTAAACACGAAAAATT 1 105 1 AATTGTAAAC 0.92586 -92 ACAAATAATCATTTTTATCCACACGGTACA 3 263 0 ATTTTTATCC 0.650719 -38 TTCTAAAGAATTTTAAACACAAATAATC 3 283 0 AATTTTAAAC 0.915113 -18 TCATTATCCCAACTTTAAACACATGCTCAT 6 124 0 AACTTTAAAC 0.59394 -177 AGAGCATGGAATTTATAACCCTCTGGGTGA 6 254 1 ATTTATAACC 0.688614 -47 CACGATTAAAAATTTTATCCCTTTCGGTTA 9 15 1 AATTTTATCC 0.816735 -85 ACCTCCAAGAAGTTTTAACCACCGCTAACT 12 244 0 AGTTTTAACC 0.687723 -26 CCGTCTCCAGTTTTGTAAACGATCTTCACG 13 130 0 TTTTGTAAAC 0.665479 -171 AAATAAAGGAATTTGTAACCTTTGCAATAG 13 219 1 ATTTGTAACC 0.849917 -82 CTTGATATTTTAAACTTTTCTTTT 16 6 1 TATTTTAAAC 0.804236 -19 CCAGAAATAATATTATATACAATCCTCTCC 20 16 0 TATTATATAC 0.414824 -113 TTAGAGTTTTTATTTTAACCTTATAATTTT 21 32 0 TATTTTAACC 0.816735 -21 ACGAGTGATAAATTATAAACCGTATGATCT 25 105 1 AATTATAAAC 0.829954 -196 AGGCATTACTAATTGTATACCTTGCTCTTT 25 147 1 AATTGTATAC 0.826357 -154 ********** Masking position 7 Map Score: 7.54528 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 91 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TTTTTACCTCCTTTTTATTGTTGGAA 1 7 1 CCTCCTTTTT 0.9489 -190 CTTCCTTCCTCCTTGTAAGTTATTATG 1 180 0 CCTCCTTGTA 0.890049 -17 GGTTTCACCTCCCTTTATTCATCCATC 2 8 1 CCTCCCTTTA 0.926838 -38 GTTAAAACTTCTTCCATTTCACAAAATCAA 4 69 1 CTTCCATTTC 0.895262 -232 AACTCAAACTCTTCCTTTTCTTTACCGAGC 12 61 0 CTTCCTTTTC 0.93203 -209 TGCTTTAATACCTCCAGTTAGCGGTGGTTA 12 229 1 CCTCCAGTTA 0.946848 -41 ACCGGTAAGTCTTCCAGTTC 13 1 0 CTTCCAGTTC 0.875783 -300 CATCCTTCCACCTCCTGTTAGGATTTACTA 14 12 0 CCTCCTGTTA 0.966191 -104 AAAATCCTTTCCTCCTTTTTCCTTTTAACC 23 260 1 CCTCCTTTTT 0.9489 -41 ********** Masking position 3 Map Score: 6.73616 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 161 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 9 ATTTCCGTGCCAATTTCAGAATACGCTTTTACA 1 145 0 CAATTCAATA 0.778694 -52 AAGTTATCGTCAACTTCAAAATACGGTTCCTAA 3 18 1 CAACTCAATA 0.972888 -283 ACCGAAGTTTCAACTCCACTACGGTACATTAGG 3 191 0 CAACTCAACG 0.915228 -110 CATTAGAAACCATCTGCAACATATTCAAGTTCA 4 222 0 CATCTCAATA 0.949564 -79 ACGCCAAACTCCTCTTCAGGATACTCTCCGACC 5 70 1 CCTCTCAATA 0.901985 -231 TCGTCCACATCAACTCCACCACAGCCATCTCTC 6 179 0 CAACTCAACA 0.978817 -122 TCCTTCACAACATCGTCAAAACAAACTTCCAAG 13 46 0 CATCGCAACA 0.922162 -255 CTGGACAATGCCACTCCAGTACACCTCAATAAT 19 89 1 CCACTCAACA 0.957604 -56 AAGCTCCCGACAACGACACTATACTCAAAATGG 23 133 1 CAACGCAATA 0.946074 -168 ***** ** *** Masking position 8 Map Score: 4.68355 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ATTTTAGCTCAACTCAAGGAAATTAAGCTGAT 1 48 1 AATAAGGAAA 0.90652 -149 GCTCTTTGGTACTTCATAGAAGAAAAGGACAG 5 147 1 ACTATAGAAG 0.782823 -154 GTAATCAAGTACGTGAAGGAAAAACACAAAGA 5 225 1 ACTAAGGAAA 0.960636 -76 ATAGACAGGTACTTTAAGGAAACGAAGTTCTT 5 261 1 ACTAAGGAAA 0.960636 -40 TTAATGTTTAAAGTCATAGAAATGATAGAATG 9 42 1 AATATAGAAA 0.472272 -58 AAGCTCGGTAAAGAAAAGGAAGAGTTTGAGTT 12 59 1 AAAAAGGAAG 0.622889 -211 CCTTCCACCTCCAAGAAGTTTTAACCAC 12 252 0 ACTCAAGAAG 0.780078 -18 CTCAAAAAAGACATTAAAGAAATAAAGGAATT 13 200 1 ACTAAAGAAA 0.87523 -101 GCAATAGAACAATTTATGGAAGAAATAGACAG 13 242 1 AATATGGAAG 0.832862 -59 GTCCATAAACACCTGAAGGCAAAGTTCACGAA 19 48 1 ACTAAGGCAA 0.793774 -97 AAGCCCGAAAGAATTAAGGAAGTTGACGAGGA 23 24 1 GATAAGGAAG 0.709983 -277 AGCTTCTACAACGTTCAGGAAGTCGTAAGGAC 23 106 0 ACTCAGGAAG 0.925038 -195 CTCATTAAGGACTTAAAGGAACAGCAGTAAAA 23 231 1 ACTAAGGAAC 0.882477 -70 ** * ******* Masking position 11 Map Score: 4.75816 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 759 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 ATAGAAGAAAAGGACAGGATACCCGACTGGG 5 162 1 AGGAAGGATA 0.967914 -139 TCAGAAGGGAGGGAAAGGAAAGAAGGGA 8 8 0 GGGAAGGAAA 0.928236 -34 AGGGAATAGGATATCAGAAGGGA 8 29 0 GGAAAGGATA 0.889884 -13 ATCTCCGACGGGGATAGGGTTGCTTTAATAC 12 209 1 GGGAAGGGTT 0.961483 -61 ACACAGGAGAGGATTGTATATAATA 20 5 1 AGGAAGGATT 0.975174 -124 AGGAAAAAGGAGGAAAGGATTTTTACTGCTG 23 252 0 AGGAAGGATT 0.975174 -49 CTCTATACTGGGGATAGGATTTATTATTGCT 25 38 1 GGGAAGGATT 0.987824 -263 **** ****** Masking position 6 Map Score: 6.43825 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 113 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 CTTCCTTCCTCCTTGTAAGTTATT 1 183 0 CTTCCTCCTT 0.949089 -14 TTTTGTGAAAAATGCTCCTTTATCACCGAA 3 218 0 AATGCTCCTT 0.864043 -83 CCATACACCACTTTCTCCTTCCAC 6 5 0 CTTTCTCCTT 0.872361 -296 ACTTTAAACACATGCTCATTCCTTATGTTA 6 113 0 CATGCTCATT 0.946371 -188 ACCTCATCATCATGATCATTATCCCAACTT 6 139 0 CATGATCATT 0.630971 -162 TTATAAATTCCATGCTCTGTCCAATAAATC 6 242 0 CATGCTCTGT 0.805356 -59 TATCCGATATCATGCTCCTTTGGGACTTGG 7 12 1 CATGCTCCTT 0.984823 -52 TCGCTTCCTCCTTCGGTAAGTAA 21 4 1 CTTCCTCCTT 0.949089 -49 AATTGTATACCTTGCTCTTTTCATATTTAT 25 157 1 CTTGCTCTTT 0.934955 -144 ********** Masking position 6 Map Score: 6.68273 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 110 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 ATGAAGACATAGAAAGAATACTATTCTCTGAT 3 80 0 AGAAAAATAT 0.938439 -221 ACGGTACATTAGAAACAGAACTCTCAGAAGAA 4 32 0 AGAAAAGAAT 0.843289 -269 ACGGTACATTAGAAACAATAATCAACAACTCT 4 99 0 AGAAAAATAT 0.938442 -202 GATTGTAAAAAGAAATTAAAATAAAAACTCTA 4 277 1 AGAAATAAAT 0.776729 -24 ATCCCGAGATAGAAAATATATTGAACTCCGTT 12 135 1 AGAAATATAT 0.848044 -135 CAAGCCTTCCAGAAATAATATTATATACAATC 20 22 0 AGAAAAATAT 0.938441 -107 TAGAAGAAGTATTTTATCTTAAT 22 2 1 AGAAGAGTAT 0.830174 -26 GCCTCAGGAAAGAAGTAAAAATAGATGATAAC 25 236 1 AGAAGAAAAT 0.843289 -65 ***** **** * Masking position 4 Map Score: 1.60801 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 78 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CAGAAGAACCGAGAGCTTTTTCTATTAAC 4 10 0 GAGAGCTTTT 0.95993 -291 ATGGCTTATTGAGAGCTTCTTTTCAACCTT 6 41 1 GAGAGCTTCT 0.986049 -260 CTTTTCTTTACCGAGCTTCTCCCTGAGAAT 12 47 0 CCGAGCTTCT 0.944002 -223 ACTGGAGACGGAGACCTTTTTGAGAAGAAG 13 149 1 GAGACCTTTT 0.847307 -152 CCCGTATTCTCAAAGCTTCTTCCCGCTTAA 14 93 1 CAAAGCTTCT 0.849585 -23 TGTCGTTGTCGGGAGCTTCTACAACGTTCA 23 121 0 GGGAGCTTCT 0.969411 -180 ********** Masking position 4 Map Score: 0.802372 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 84 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 TGAAGTTGACGATAACTTCAATCTG 3 5 0 GATAACTCAA 0.59447 -296 AAATTAAAATAAAAACTCTAAT 4 289 1 AAAAACTTAA 0.911271 -12 TTTTTAACTGAATACCTATAAATTCAA 6 284 1 AATACCTTAA 0.696818 -17 CTATTTTTAAAAAATCTATAAGGAG 9 85 1 AAAATCTTAA 0.566153 -15 CCACTTATATAATAAGTTTAAC 10 24 1 AATAAGTTAA 0.924268 -12 CAGGAAAAAAGTTTAACTTTAAAATT 11 18 0 AAAAAGTTAA 0.911267 -16 TACGGAGGAGAATAAGTATAATCTTTCTTA 13 281 1 AATAAGTTAA 0.924268 -20 CTTAACAAGTTTAAATATACACCT 15 14 0 AACAAGTTAA 0.789708 -14 AAAAGAAAAGTTTAAAATATCAAG 16 10 0 GAAAAGTTAA 0.78067 -15 CTAATATATCAATAACTATAATTTAAATTGG 18 12 0 AATAACTTAA 0.924268 -57 AGGTTAAAATAAAAACTCTAAA 21 41 1 AAAAACTTAA 0.911271 -12 CACTCGTATTAATAAGTGCAACACCAAAAAA 25 81 0 AATAAGTCAA 0.808786 -220 ******* *** Masking position 4 Map Score: 6.47916 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 71 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665