AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -ipurR_aquae_opreg_300.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 aq_1104 45 putative protein #13 gcsH4 269 glycine cleavage system protein H #14 carB1 300 carbamoyl-phosphate synthase large subunit #15 aq_1173 115 hypothetical protein #16 purF 27 amidophosphoribosyltransferase #17 purE 24 phosphoribosylaminoimidazole carboxylase #18 purA 28 adenylosuccinate synthetase #19 aq_1292 68 hypothetical protein #20 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #21 prs 128 phosphoribosylpyrophosphate synthetase #22 purL 52 phosphoribosylformylglycinamidine synthase II #23 putative 27 putative protein #24 guaB 300 inosine monophosphate dehydrogenase #25 carB2 26 carbamoyl-phosphate synthase large subunit #26 hemN 300 oxygen-independent coproporphyrinogen II Motif number 1 TCAAAATACGGTTCCTAATGTACCGTGTGGAGT 3 33 1 GTTCCATGAC 0.986924 -268 ATAAAGCAAGGTTTCAACTCCACACGGTACATT 3 49 0 GTTTCATCAC 0.993975 -252 TTCATAGTTTGTTCCTAATGTACCGTGTGGAGT 3 107 1 GTTCCATGAC 0.986924 -194 CTATCAAGAGGTTTCAACTCCACACGGTACATT 3 123 0 GTTTCATCAC 0.993975 -178 CGATTCTTTTGTTCCTAATGTACCGTAGTGGAG 3 178 1 GTTCCATGAC 0.986924 -123 TATCACCGAAGTTTCAACTCCACTACGGTACAT 3 195 0 GTTTCATCAC 0.993975 -106 AAAGAAATCAGTTTCTAATGTACCGTGTGGATA 3 245 1 GTTTCATGAC 0.993245 -56 TGAGAGTTCTGTTTCTAATGTACCGTGTGGAGT 4 38 1 GTTTCATGAC 0.993245 -263 AATGGAAGAAGTTTTAACTCCACACGGTACATT 4 54 0 GTTTTATCAC 0.977802 -247 GTTGATTATTGTTTCTAATGTACCGTGTGGAGT 4 105 1 GTTTCATGAC 0.993245 -196 TCTCAAACCTGTTTTAACTCCACACGGTACATT 4 121 0 GTTTTATCAC 0.977802 -180 GCTTGACGAAGTTTCTAATGTACCGTGTGGAGT 4 170 1 GTTTCATGAC 0.993245 -131 TCAAAACCTTGTTTTAACTCCACACGGTACATT 4 186 0 GTTTTATCAC 0.977802 -115 GTTGCAGATGGTTTCTAATGTACCGTGTGGAGT 4 235 1 GTTTCATGAC 0.993245 -66 TACAATCTGCGTTTTAACTCCACACGGTACATT 4 251 0 GTTTTATCAC 0.977802 -50 TTGTAACCGGGTGTTAAGTCAACTTCACAGCCT 14 82 0 GTGTTATCAC 0.839839 -219 TTGTTGCAGAGTTCCTCGTCAACTTCCTTAATT 24 35 0 GTTCCCTCAC 0.909795 -266 ***** * ** ** Masking position 9 Map Score: 52.3332 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 GGTTTCAACTCCACACGGTACATTAGGAACC 3 42 0 CCCACGGTAC 0.999212 -259 GGTTTCAACTCCACACGGTACATTAGGAACA 3 116 0 CCCACGGTAC 0.999212 -185 GTTTCAACTCCACTACGGTACATTAGGAACA 3 187 0 CATACGGTAC 0.940522 -114 TCATTTTTATCCACACGGTACATTAGAAACT 3 254 0 CCCACGGTAC 0.999212 -47 AGTTTTAACTCCACACGGTACATTAGAAACA 4 47 0 CCCACGGTAC 0.999212 -254 TGTTTTAACTCCACACGGTACATTAGAAACA 4 114 0 CCCACGGTAC 0.999212 -187 TGTTTTAACTCCACACGGTACATTAGAAACT 4 179 0 CCCACGGTAC 0.999212 -122 CGTTTTAACTCCACACGGTACATTAGAAACC 4 244 0 CCCACGGTAC 0.999212 -57 ** ******** Masking position 5 Map Score: 33.701 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 ACAATAAAAAGGAGGTAAAAA 1 2 0 GGAGGTAAAA 0.923399 -195 TAATAACTTACAAGGAGGAAGGAAG 1 182 1 CAAGGAGGAA 0.645514 -15 ATGAATAAAGGGAGGTGAAACC 2 3 0 GGAGGTGAAA 0.983658 -43 ATAATATATAGATGGATGAATAAAGGGAGG 2 18 0 GATGGATGAA 0.49477 -28 TGTACCGTGTGGAGTTGAAACCTTGCTTTA 3 51 1 GGAGTTGAAA 0.858116 -250 TGTACCGTGTGGAGTTGAAACCTCTTGATA 3 125 1 GGAGTTGAAA 0.858116 -176 GTACCGTAGTGGAGTTGAAACTTCGGTGAT 3 197 1 GGAGTTGAAA 0.858116 -104 TCAAGTACGTGAAGGAAAAACACAAAGAGG 5 229 1 GAAGGAAAAA 0.862977 -72 GTGGAAGGAGAAAGTGGTGTATG 6 4 1 GAAGGAGAAA 0.969181 -297 ACCATCGCTCGAAGGTTGAAAAGAAGCTCT 6 52 0 GAAGGTTGAA 0.903582 -249 GAGTTGATGTGGACGAGAAAATAATCAGGT 6 196 1 GGACGAGAAA 0.747835 -105 AACTCTACAAAGAGGTAAAAGCC 12 4 0 AGAGGTAAAA 0.560319 -42 TCCAGTTAGCGGTGGTTAAAACTTCTTGGA 13 241 1 GGTGGTTAAA 0.667473 -29 AAAACTTCTTGGAGGTGGAAGG 13 258 1 GGAGGTGGAA 0.982519 -12 ACGATGTTGTGAAGGAAGAAGGCTGTGAAG 14 63 1 GAAGGAAGAA 0.854675 -238 CGTGGAGTACGGAGGAGAATAAGTATAATC 14 274 1 GGAGGAGAAT 0.764549 -27 AATCCTAACAGGAGGTGGAAGGATGGGCGA 15 17 1 GGAGGTGGAA 0.982519 -99 GGAGGATTAAATGGCTGGGG 21 119 0 GGAGGATTAA 0.597482 -10 TTTACTTACCGAAGGAGGAAGCGA 22 5 0 GAAGGAGGAA 0.967068 -48 TTAAAAGGAAAAAGGAGGAAAGGATTTTTA 24 258 0 AAAGGAGGAA 0.75636 -43 TATATTACTCAAAGGTTAAAAGGAAAAAGG 24 273 0 AAAGGTTAAA 0.51479 -28 GCCTCTGGCGAAGGATAAATTGGATCTCT 26 10 1 GAAGGATAAA 0.902158 -291 TATGATCTTTGAGGGTGAAAAGGCATTACT 26 127 1 GAGGGTGAAA 0.765922 -174 ********** Masking position 9 Map Score: 27.1752 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 897 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 4 AATTGAACAAAGGTACTAAATCAGCTTAATTTC 1 66 0 AGGTAAAATA 0.79142 -131 AATAACTTACAAGGAGGAAGGAAG 1 183 1 AAGGAAAGGA 0.812337 -14 ATATAGATGGATGAATAAAGGGAGGTGAAACC 2 10 0 ATGAAAAGGA 0.700735 -36 ACGGTACATTAGGAACAAAAGAATCGTGGAATA 3 171 0 AGGAAAAAGA 0.960698 -130 GACCTGAGTGAGGAGGCAAGGGAAGATTTTACA 5 111 1 AGGAGAAGGA 0.828279 -190 GACGACTACAAGGTAATCAAGTACGTGAAGGAA 5 213 1 AGGTACAAGA 0.874412 -88 CATCGCTCGAAGGTTGAAAAGAAGCTCTCAATA 6 47 0 AGGTTAAAGA 0.778862 -254 TTGAATTTATAGGTATTCAGTTAAAAATCACCC 6 278 0 AGGTACAGTA 0.637805 -23 CTGCAAGTCCAAGTCCCAAAGGAGCATGATATC 7 17 0 AAGTCAAAGA 0.63349 -47 AGGGAGGGAAAGGAAAGAAGGGA 8 1 0 AGGAAAAGGA 0.97264 -41 CGCTAACTGGAGGTATTAAAGCAACCCTATCCC 13 219 0 AGGTAAAAGA 0.956176 -51 AAAGACATTAAAGAAATAAAGGAATTTGTAACC 14 206 1 AAGAAAAAGA 0.885782 -95 ATAAGCCCGAAAGAATTAAGGAAGTTGACGAGG 24 22 1 AAGAAAAGGA 0.918557 -279 ACACTCATTAAGGACTTAAAGGAACAGCAGTAA 24 228 1 AGGACAAAGA 0.859226 -73 TAAAAGGAAAAAGGAGGAAAGGATTTTTACTGC 24 254 0 AAGGAAAAGA 0.748517 -47 TATTACTCAAAGGTTAAAAGGAAAAAGGAGGAA 24 268 0 AGGTTAAGGA 0.836662 -33 GAAAAGAGCAAGGTATACAATTAGTAATGCCTT 26 146 0 AGGTACAATA 0.54768 -155 GTTTATTTGCAAGAAATAAGGCAGCCCCACCTA 26 195 0 AAGAAAAGGA 0.918557 -106 TAAAAGCCTCAGGAAAGAAGTAAAAATAGATGA 26 231 1 AGGAAAAGTA 0.860769 -70 ***** **** * Masking position 9 Map Score: 17.2789 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 762 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 ACACGGTACATTAGGAACCGTATTTTGAAG 3 31 0 TTAGGAACCG 0.962528 -270 ACACGGTACATTAGGAACAAACTATGAAGA 3 105 0 TTAGGAACAA 0.930606 -196 CTACGGTACATTAGGAACAAAAGAATCGTG 3 176 0 TTAGGAACAA 0.930606 -125 ACACGGTACATTAGAAACTGATTTCTTTTG 3 243 0 TTAGAAACTG 0.93253 -58 ACACGGTACATTAGAAACAGAACTCTCAGA 4 36 0 TTAGAAACAG 0.96267 -265 ACACGGTACATTAGAAACAATAATCAACAA 4 103 0 TTAGAAACAA 0.942056 -198 ACACGGTACATTAGAAACTTCGTCAAGCTT 4 168 0 TTAGAAACTT 0.725915 -133 ACACGGTACATTAGAAACCATCTGCAACAT 4 233 0 TTAGAAACCA 0.951535 -68 GAGTGATAAATTATAAACCGTATGATCTTT 26 107 1 TTATAAACCG 0.753265 -194 ********** Masking position 6 Map Score: 7.3552 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 19 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TTTTGTGAAATGGAAGAAGTTTTAACTCCA 4 65 0 TGGAAGAAGT 0.967157 -236 TAGAAGGAAACTCGCAAAAG 5 1 1 TAGAAGGAAA 0.587621 -300 TGGTACTTCATAGAAGAAAAGGACAGGATA 5 153 1 TAGAAGAAAA 0.78781 -148 GTGGAAGGAGAAAGTGGTGTA 6 2 1 TGGAAGGAGA 0.885319 -299 AGACCTTTTTGAGAAGAAGATAGAAATACC 14 160 1 GAGAAGAAGA 0.93341 -141 GAACAATTTATGGAAGAAATAGACAGCGTG 14 248 1 TGGAAGAAAT 0.879438 -53 GAGTACGGAGGAGAATAAGTATAATCTTTC 14 278 1 GAGAATAAGT 0.617882 -23 GGCTTAAGCGGGAAGAAGCTTTGAGAATA 15 97 0 GGGAAGAAGC 0.894448 -19 ACCTCAATAATAGAAGAAGTAAGGGCTGTA 20 111 1 TAGAAGAAGT 0.956415 -34 TAGAAGAAGTATTTTATCTT 23 1 1 TAGAAGAAGT 0.956415 -27 AAAAGCCTCAGGAAAGAAGTAAAAATAGAT 26 232 1 GGAAAGAAGT 0.68454 -69 ********** Masking position 5 Map Score: 6.08029 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 784 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 CAAAAGAATCGTGGAATACGCGGAAAACAGATA 3 156 0 GGGAATACGG 0.747314 -145 GTATCCTGAAGAGGAGTTTGGCGTCCAGAATCA 5 61 0 GGGAGTTTGG 0.980576 -240 AGTTAGGGTCGGAGAGTATCCTGAAGAGGAGTT 5 76 0 GAGAGTATCG 0.894346 -225 GGAGGCAAGGGAAGATTTTACAGCAGCTCTTTG 5 122 1 GAGATTTTAG 0.651097 -179 GCGATGGTTTGGAGAGTATGTAGTGAGCAAAAG 6 74 1 GAGAGTATGG 0.969378 -227 TAAAGAAAAGGAAGAGTTTGAGTTTGAAGGCAC 13 67 1 GAGAGTTTGT 0.905841 -203 TGCCGTTAACGAAGAGTACGTGGATGAGGACTA 13 172 1 GAGAGTACGG 0.963021 -98 TATCCCCGTCGGAGATTTTATAGTCCTCATCCA 13 192 0 GAGATTTTAG 0.651097 -78 AATAGACAGCGTGGAGTACGGAGGAGAATAAGT 14 265 1 GGGAGTACGG 0.967915 -36 ACATAGTAAAGGGGAGTTTGCATAAAGTAGAAT 20 17 0 GGGAGTTTGT 0.917656 -128 CGTACTTGTTGCAGAGTTCCTCGTCAACTTCCT 24 40 0 GAGAGTTCCG 0.905541 -261 CGTACTGAGCGAGGATTTTGATTCCGTACTTGT 24 64 0 GGGATTTTGT 0.734076 -237 * ******** * Masking position 5 Map Score: 7.23154 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 8 TTTGTTAACATGTTTACAATTGAACAAAGG 1 86 0 TGTTTACAAT 0.935111 -111 AAATTTTTCGTGTTTACAATTTTGTTAACA 1 106 0 TGTTTACAAT 0.935111 -91 TGATTATTTGTGTTTAAAATTCTTTAGAA 3 282 1 TGTTTAAAAT 0.915235 -19 TTTTAATTTCTTTTTACAATCTGCGTTTTA 4 268 0 TTTTTACAAT 0.823745 -33 AATGAGCATGTGTTTAAAGTTGGGATAATG 6 123 1 TGTTTAAAGT 0.902152 -178 TTTCGGTTAATGTTTAAAGTCATAGAAATG 9 36 1 TGTTTAAAGT 0.902152 -64 AAGTCTAAATTTTAAAGTTAAACTTTTT 11 9 1 ATTTTAAAGT 0.53873 -25 AAAAGAAAAGTTTAAAATATCAAG 17 7 0 AGTTTAAAAT 0.787539 -18 TATCAAAATTTTACAATGAGCTGAGTA 19 52 0 ATTTTACAAT 0.673138 -17 ********** Masking position 5 Map Score: 5.89324 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 30 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 9 TTTTTACCTCCTTTTTATTGTTGGAA 1 7 1 CCTCCTTTTT 0.939061 -190 CTTCCTTCCTCCTTGTAAGTTATTATG 1 180 0 CCTCCTTGTA 0.976337 -17 GGTTTCACCTCCCTTTATTCATCCATC 2 8 1 CCTCCCTTTA 0.917901 -38 GGAGTTGAAACCTCTTGATAGTATCTGTTT 3 135 1 CCTCTTGATA 0.737349 -166 CTGTCTATCTCCTCTTTGTGTTTTTCCTTC 5 239 0 CCTCTTTGTG 0.806232 -62 GGCTTTTACCTCTTTGTAGAGTTAAGTA 12 9 1 CCTCTTTGTA 0.931141 -37 TGCTTTAATACCTCCAGTTAGCGGTGGTTA 13 229 1 CCTCCAGTTA 0.861537 -41 CATCCTTCCACCTCCTGTTAGGATTTACTA 15 12 0 CCTCCTGTTA 0.972005 -104 AAAATCCTTTCCTCCTTTTTCCTTTTAACC 24 260 1 CCTCCTTTTT 0.939061 -41 ********** Masking position 3 Map Score: 5.50092 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 137 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 TGCTTTATCAGAGAATAGTATTCTTTCTATG 3 74 1 GAGATAGTAT 0.961584 -227 AGGGAATAGGATATCAGAAGGG 8 30 0 GGGATAGGAT 0.974947 -12 AATCTCCGACGGGGATAGGGTTGCTTTAATA 13 208 1 GGGATAGGGT 0.956591 -62 ACACAGGAGAGGATTGTATATAATATTAT 21 9 1 GAGATTGTAT 0.817707 -120 TTGCCATTTTGAGTATAGTGTCGTTGTCGGG 24 138 0 GAGATAGTGT 0.934098 -163 AAGGAAAAAGGAGGAAAGGATTTTTACTGCT 24 253 0 GAGAAAGGAT 0.876771 -48 TCTCTATACTGGGGATAGGATTTATTATTGC 26 37 1 GGGATAGGAT 0.974947 -264 TATGAGAATAATATAGGTGAAAAA 26 287 0 GAGATAATAT 0.736507 -14 *** ******* Masking position 5 Map Score: 4.77819 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTACAATTGAACAAAGGTACTAAATCAGCTT 1 72 0 AAAAGGTACT 0.968935 -125 AATACGCGGAAAACAGATACTATCAAGAGGT 3 144 0 AACAGATACT 0.968936 -157 AAGAGGAGATAGACAGGTACTTTAAGGAAAC 5 253 1 AACAGGTACT 0.98597 -48 TATATTAGAGAAACAGGTACTCAGCTCATTG 19 35 1 AACAGGTACT 0.985971 -34 TGCAACACCAAAAAAGATACTTATTAAAGCA 26 65 0 AAAAGATACT 0.93263 -236 * ********* Masking position 5 Map Score: 2.59066 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 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 12 GGAATTTAAATAAACATTTTAGCTCAACTCA 1 33 1 TAAACATTTA 0.52723 -164 ACAATTTTGTTAACATGTTTACAATTGAACA 1 90 0 TAACATTTTA 0.533537 -107 GAAATTAAAATAAAAACTCTAAT 4 288 1 TAAAAATCTA 0.904129 -13 AGGGAGATCATAACAGATTTATTGGACAGAG 6 227 1 TAACAGTTTA 0.671164 -74 CTCCCACGATTAAAAATTTTATCCCTTTCGG 9 11 1 TAAAAATTTA 0.587642 -89 TAGTATTCACTAACCATTCTATCATTTCTAT 9 57 0 TAACCATCTA 0.754948 -43 ATACTATTTTTAAAAAATCTATAAGGAG 9 82 1 TAAAAATCTA 0.904129 -18 ACCACTTATATAATAAGTTTAAC 10 23 1 TAATAATTTA 0.666751 -13 CAGGAAAAAAGTTTAACTTTAAAAT 11 19 0 AAAAAATTTA 0.566147 -15 CTTAACAAGTTTAAATATACACC 16 15 0 TAACAATTTA 0.904121 -13 TATCAAAATTTTACAATGAGCTG 19 56 0 TCAAAATTTA 0.643067 -13 AAGGTTAAAATAAAAACTCTAAA 22 40 1 TAAAAATCTA 0.904129 -13 ****** **** Masking position 3 Map Score: 3.64982 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 48 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 CTCAGAAGAACCGAGAGCTTTTTCTATTAAC 4 9 0 CAGAGCTTTT 0.95276 -292 TTCACAAAATCAAAGAGTTGTTGATTATTGTTT 4 86 1 CAGAGTTGTG 0.623993 -215 CAAAAGTCCTCTCAAACCTGTTTTAACTCCACA 4 130 0 CAAACCTGTT 0.919363 -171 TGGAGTACGTCAGAAACCTGATTCTGGACGCCA 5 43 1 CAAACCTGTT 0.919361 -258 CCGACCCTAACTTTGACCTGAGTGAGGAGGCAA 5 97 1 CTGACCTGGT 0.875566 -204 TATGAAGTACCAAAGAGCTGCTGTAAAATCTTC 5 132 0 CAGAGCTGTG 0.954684 -169 AGATGGCTTATTGAGAGCTTCTTTTCAACCTTC 6 39 1 TAGAGCTTTT 0.613776 -262 GTTATGATCTCCCTGACCTGATTATTTTCTCGT 6 208 0 CTGACCTGTT 0.948276 -93 AAACTGGAGACGGAGACCTTTTTGAGAAGAAGA 14 147 1 CAGACCTTTT 0.944167 -154 TACCCGTATTCTCAAAGCTTCTTCCCGCTTAAG 15 91 1 CAAAGCTTTT 0.833219 -25 CAAAATTTTACAATGAGCTGAGTACCTGTTTCT 19 43 0 CTGAGCTGGT 0.893528 -26 * ******* ** Masking position 6 Map Score: 3.5781 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 104 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 TTGATTTTGTGAAATGGAAGAAGTTTTAAC 4 69 0 GAAATGGAAG 0.906596 -232 GAGTGAGGAGGCAAGGGAAGATTTTACAGC 5 116 1 GCAAGGGAAG 0.941274 -185 AGGTAATCAAGTACGTGAAGGAAAAACACA 5 223 1 GTACGTGAAG 0.891421 -78 AGAAGGGAGGGAAAGGAAAGAAGGGA 8 7 0 GAAAGGAAAG 0.756605 -35 GCTCGGTAAAGAAAAGGAAGAGTTTGAGTT 13 61 1 GAAAAGGAAG 0.932922 -209 GAACTGGAAGACTTACCGGT 14 1 1 GAACTGGAAG 0.913162 -300 TGACGATGTTGTGAAGGAAGAAGGCTGTGA 14 61 1 GTGAAGGAAG 0.800138 -240 CTCAGTATCCGTACGTGAAGATCGTTTACA 14 117 1 GTACGTGAAG 0.891421 -184 AGTAAGGGCTGTAAGGGAAGAGCCGGA 20 128 1 GTAAGGGAAG 0.977696 -17 CTTCTACAACGTTCAGGAAGTCGTAAGGAC 24 106 0 GTTCAGGAAG 0.745305 -195 ********** Masking position 8 Map Score: 6.19244 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 642 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 15 AAGTTATCGTCAACTTCAAAATACGGTTCCT 3 18 1 CAACTCAAAA 0.96515 -283 AGCAAGGTTTCAACTCCACACGGTACATTAG 3 47 0 CAACCCACAC 0.917651 -254 CAAGAGGTTTCAACTCCACACGGTACATTAG 3 121 0 CAACCCACAC 0.917651 -180 TTCCATTTCACAAAATCAAAGAGTTGTTGAT 4 80 1 CAAATCAAAG 0.807026 -221 TATTCAAGTTCAGCTTCAAAACCTTGTTTTA 4 203 0 CAGCTCAAAA 0.852413 -98 ATCATTATCCCAACTTTAAACACATGCTCAT 6 124 0 CAACTTAAAC 0.718969 -177 ACGGTGCCTTCAAACTCAAACTCTTCCTTTT 13 72 0 CAAATCAAAC 0.845988 -198 TCCTTCACAACATCGTCAAAACAAACTTCCA 14 48 0 CATCTCAAAA 0.795788 -253 GGTGTTAAGTCAACTTCACAGCCTTCTTCCT 14 75 0 CAACTCACAG 0.938179 -226 ATGAGTGTGTCAATATCAAAAGCGGGCATCG 24 205 0 CAATTCAAAA 0.707568 -96 TTAATAAGTGCAACACCAAAAAAGATACTTA 26 73 0 CAACCCAAAA 0.93933 -228 AATGCCTTTTCACCCTCAAAGATCATACGGT 26 123 0 CACCTCAAAG 0.849876 -178 **** ****** Masking position 8 Map Score: 5.99132 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 110 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912