AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_rpxx_reg_300.orf -o00330_rpxx_300.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP064 249 DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE (dgtP) #2 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #3 RP153 300 GLUTAMYL-tRNA AMIDOTRANSFERASE SUBUNIT C (gatC) #4 RP254 225 UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE (lpxC) #5 RP255 300 unknown #6 RP382 300 unknown #7 RP384 141 PROLYL-TRNA SYNTHETASE (proS) #8 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) Motif number 1 AAAAATCTTATAAATTATATAATATATCTT 1 26 1 TAAATTATAT 0.855836 -224 ACCATCTTGAAAAATATTAAGATATATTAT 1 44 0 AAAATATTAA 0.801193 -206 TATTATAGTGTAAATAATATGAATTTAGTA 2 19 0 TAAATAATAT 0.90972 -156 ATTTTATTTAAAAATTTATTAAGATATGCT 2 50 0 AAAATTTATT 0.770169 -125 ATTTTTAAATAAAATAATTTTATTGAGATT 2 65 1 AAAATAATTT 0.819323 -110 GTTTTAATTAAAAATAATATCTTGTAGTTT 3 104 0 AAAATAATAT 0.943848 -197 TTTTTACGTAAAAATAATAAAACT 3 287 1 AAAATAATAA 0.849278 -14 ATTTTGTTACAAAATATTACATAATCACCA 4 148 0 AAAATATTAC 0.634858 -78 ATTTTGTAACAAAATATTATTTGTATAATT 4 163 1 AAAATATTAT 0.838836 -63 AATTTGCAATTAAATATTAACATTTAAATA 4 189 1 TAAATATTAA 0.771702 -37 TATTAACATTTAAATATATTTAAACAACCT 4 203 1 TAAATATATT 0.735678 -23 ACACCTCTTTAAAATACTAAAAAATATATT 5 54 1 AAAATACTAA 0.621468 -247 AAAATACTAAAAAATATATTATTACTTTCT 5 64 1 AAAATATATT 0.751794 -237 AAATAATATGAAAATATTTTAATGTAAGAA 5 90 0 AAAATATTTT 0.498156 -211 AATAATGAATTAAATAATATGAAAATATTT 5 101 0 TAAATAATAT 0.90972 -200 ATTTTTAAATTAAATAATAATTTATATACA 5 128 1 TAAATAATAA 0.768342 -173 TATTATCTTAAAAATTAAATAAAGAGATTC 5 222 0 AAAATTAAAT 0.790597 -79 TTATCGTGACTAAATACTTTTACCTATACC 6 62 1 TAAATACTTT 0.661557 -239 TCTATTATTAAAAATTAAAATATTGATACT 6 97 1 AAAATTAAAA 0.552984 -204 GGTCGATTAATAAATAGTATATCAGTATCA 6 120 0 TAAATAGTAT 0.745936 -181 ATTTAAAGTAAAAATTTTTTATAGAATGTT 6 160 0 AAAATTTTTT 0.79378 -141 ATTTTTACTTTAAATTTTTTAAATTAACAA 6 175 1 TAAATTTTTT 0.802261 -126 TGACTGTTAAAAAATAATTTTAATTGTTAA 6 198 0 AAAATAATTT 0.819323 -103 ACGGTATTTAAAAATATTTTTCCTTTGATA 6 244 0 AAAATATTTT 0.498156 -57 GATTACAAAAAAATTAAATATAACCTATA 6 282 0 AAAATTAAAT 0.790597 -19 AGCAATCTAATAAATTTTATTATTTCATGA 7 61 0 TAAATTTTAT 0.872976 -81 TAATAATAGGAAAATTATTAAACTAAAACA 7 117 1 AAAATTATTA 0.717923 -25 AAAATTGTTTTAGTTTAATA 7 132 0 AAAATTGTTT 0.692348 -10 AAAACAATATAAAATATATTTATAT 8 6 0 AAAATATATT 0.751794 -57 TATTATATACTAAATTTAATGAATTAAAGA 8 36 1 TAAATTTAAT 0.719931 -27 ********** Masking position 5 Map Score: 32.7471 Number of sites scoring better than the average of aligned sites = 2106 Number in coding regions = 1398 Number in noncoding regions = 708 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 2 ATAAAGCAACTTAAAATACAAGAATTTTAAA 1 163 0 TTAAATACAA 0.907753 -87 AGTTTAATTACTAAATTCATATT 2 3 1 TTTAATACTA 0.747856 -172 ATAAAATTATTTTATTTAAAAATTTATTAAG 2 57 0 TTTATTAAAA 0.948229 -118 TTTTTTATGTTTTAATTAAAAATAATATCTT 3 111 0 TTTAATAAAA 0.883592 -190 TAATTAGTTATTTTTCTAAAACTATCTTAAT 3 165 0 TTTTTTAAAA 0.753376 -136 TTTTATTATTTTTACGTAAAAATTTGCTTGT 3 278 0 TTTACTAAAA 0.900875 -23 TTATTTAAAGTTTATCTAAAATTTCATTTTT 5 24 0 TTTATTAAAA 0.948229 -277 TTAGATAAACTTTAAATAACACCTCTTTAAA 5 36 1 TTTAATAACA 0.77088 -265 TAACACCTCTTTAAAATACTAAAAAATATAT 5 52 1 TTAAATACTA 0.725874 -249 TGAAAATATTTTAATGTAAGAAAGTAATAAT 5 81 0 TTAATTAAGA 0.726789 -220 AAATTATTATTTAATTTAAAAATAATGAATT 5 120 0 TTAATTAAAA 0.943993 -181 TAAATAATAATTTATATACAATAAGACTACC 5 138 1 TTTATTACAA 0.90654 -163 ATTAAGATTATTATCTTAAAAATTAAATAAA 5 229 0 TTATCTAAAA 0.654643 -72 ATATTTTAATTTTTAATAATAGAAATTGGGT 6 89 0 TTTTATAATA 0.531027 -212 TTTAAAAAATTTAAAGTAAAAATTTTTTATA 6 167 0 TTAAATAAAA 0.948468 -134 ATTTTAATTGTTAATTTAAAAAATTTAAAGT 6 181 0 TTAATTAAAA 0.943993 -120 AGGAAAATTATTAAACTAAAACAATTTT 7 124 1 TTAAATAAAA 0.948468 -18 ***** ***** Masking position 7 Map Score: 17.7278 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 279 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 AAAAATCTTATAAATTATATAATATATCTTAATA 1 26 1 TAAATAATAA 0.818949 -224 TGGCAATTTCTAAACTACAAAACAACACCATCTT 1 66 0 TAAACAAAAA 0.962053 -184 TACCTTGGCTTAAAACACTAGATACAGTGTAAAG 1 109 1 TAAAAATAAA 0.808508 -141 TAAAGCAACTTAAAATACAAGAATTTTAAAGATA 1 159 0 TAAAAAAAAT 0.783912 -91 TCATATTATTTACACTATAATAAAGCATATCTTA 2 27 1 TACACAAAAA 0.802391 -148 ACATTAATAATAAACGATAATACAGCAATTTTAA 2 93 0 TAAACAAAAA 0.962053 -82 AATGTTATTCTAAAGTATATAAGAATCCGAATTC 2 122 1 TAAAGAATAA 0.726331 -53 ACTAAAATAGGTAAAAAAATCTTAAG 3 3 1 TAAAAAGTAA 0.827087 -298 TCAATGAATATAAACTACAAGATATTATTTTTAA 3 93 1 TAAACAAAAA 0.962053 -208 TATTTTTAATTAAAACATAAAAAAGAAATTTAAC 3 118 1 TAAAAAAAAA 0.958942 -183 CTTAATGAAATAAAATAGGATATAGAATATAGTA 3 206 1 TAAAAAGAAA 0.869083 -95 AATTTTTACGTAAAAATAATAAAACT 3 285 1 TAAAATATAA 0.723276 -16 AGTAGACCGGTAAACAAGATGAAA 4 1 0 TAAACAATAA 0.948095 -225 AATATTTTGTTACAAAATATTACATAATCACCAT 4 147 0 TACAAAATAA 0.729362 -79 TATCCATAATTAAAAAATGAAATTTTAGATAAAC 5 12 1 TAAAAAGAAT 0.507683 -289 AACACCTCTTTAAAATACTAAAAAATATATTATT 5 53 1 TAAAAATAAA 0.808508 -248 AATAATGAATTAAATAATATGAAAATATTTTAAT 5 97 0 TAAATAATAA 0.818992 -204 TCATTATTTTTAAATTAAATAATAATTTATATAC 5 123 1 TAAATAATAA 0.818985 -178 AATTCAATATCAAACTACAAGAAACAGCATAAAA 6 24 1 CAAACAAAAA 0.697879 -277 TTTCTATTATTAAAAATTAAAATATTGATACTGA 6 95 1 TAAAATAAAA 0.783911 -206 GATTACAAAAAAATTAAATATAACCTATAA 6 281 0 AAAAAATAAA 0.313978 -20 CATGAAATAATAAAATTTATTAGATTGCTTCATC 7 62 1 TAAAATATAA 0.723248 -80 GGAAAATTATTAAACTAAAACAATTTT 7 125 1 TAAACAAAAT 0.797487 -17 GTATATAATAAAAACAATATAAAATATATTTATA 8 12 0 AAAACAATAA 0.664434 -51 ***** * ** * * Masking position 4 Map Score: 24.9529 Number of sites scoring better than the average of aligned sites = 668 Number in coding regions = 429 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 ATTTTTACAAGGTAATTTTAA 1 1 0 GGAATTTTAA 0.516812 -249 ATTACCTTGTAAAAATCTTATAAATTATATA 1 16 1 AAAATCTTAT 0.721621 -234 CACCATCTTGAAAAATATTAAGATATATTAT 1 44 0 AAAATATTAA 0.845452 -206 CTTAAAATACAAGAATTTTAAAGATAAAAGT 1 154 0 AAAATTTTAA 0.97316 -96 TCACAGTATAAAGCAACTTAAAATACAAGAA 1 170 0 AACAACTTAA 0.553786 -80 TTTTAAATAAAATAATTTTATTGAGATTAAA 2 67 1 AAAATTTTAT 0.797138 -108 ACGATAATACAGCAATTTTAATCTCAATAAA 2 83 0 AGAATTTTAA 0.864479 -92 AATGAGCTTTGAGAATCTTAAAATACTGAAT 2 152 0 GAAATCTTAA 0.800419 -23 AAATAGGTAAAAAAATCTTAAGATCATTATA 3 15 1 AAAATCTTAA 0.959868 -286 GATTGATTCAAATACTTTTAAATGTCTACAA 3 55 0 AAACTTTTAA 0.776095 -246 AAACATAAAAAAGAAATTTAACGACTGTTTT 3 130 1 AAAAATTTAA 0.951644 -171 ATTTTTCTAAAACTATCTTAATTATCAAAAC 3 156 0 AATATCTTAA 0.731211 -145 AGGTTGTTTAAATATATTTAAATGTTAATAT 4 202 0 AAATATTTAA 0.691203 -24 AATAATATGAAAATATTTTAATGTAAGAAAG 5 88 0 AATATTTTAA 0.804835 -213 TTTTTAAGATAATAATCTTAATTATAATTAT 5 238 1 AAAATCTTAA 0.959869 -63 ACATTCTATAAAAAATTTTTACTTTAAATTT 6 161 1 AAAATTTTTA 0.794514 -140 TTGTTAATTTAAAAAATTTAAAGTAAAAATT 6 174 0 AAAAATTTAA 0.951555 -127 ACTGTTAAAAAATAATTTTAATTGTTAATTT 6 195 0 AAAATTTTAA 0.97316 -106 TCAAAGGAAAAATATTTTTAAATACCGTGAG 6 246 1 AAATTTTTAA 0.804836 -55 GATTACAAAAAAATTAAATATAACCTA 6 284 0 AAAAAATTAA 0.748064 -17 GAAGCAATCTAATAAATTTTATTATTTCATG 7 62 0 AAAAATTTTA 0.680795 -80 TTTATTATATACTAAATTTAATGAATTAAAG 8 34 1 ACAAATTTAA 0.652944 -29 TAATGAATTAAAGAAATTTAA 8 52 1 AAAAATTTAA 0.951644 -11 ** ******** Masking position 8 Map Score: 30.2391 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 335 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 AAGCCAAGGTATAATGAATATGGCAATTTC 1 90 0 ATAATGAATA 0.655683 -160 GTAAAGCTAGATAATCAACTTTTATCTTTA 1 137 1 ATAATCAACT 0.634339 -113 GAATCTTAAAATACTGAATTCGGATTCTTA 2 141 0 ATACTGAATT 0.966144 -34 TTTTAGAAAAATAACTAATTAGCTTTTATG 3 175 1 ATAACTAATT 0.742101 -126 TTAAATGTTAATATTTAATTGCAAATTATA 4 186 0 ATATTTAATT 0.850243 -40 TAATTTAAAAATAATGAATTAAATAATATG 5 110 0 ATAATGAATT 0.947075 -191 TAAGACTACCATACTGGATTAAAAGCTGAT 5 159 1 ATACTGGATT 0.900155 -142 TGTTTAGCAAATACTTAATTT 5 290 1 ATACTTAATT 0.935586 -11 TTGTAGTTTGATATTGAATTGTGATTAATA 6 14 0 ATATTGAATT 0.917727 -287 ACTTTTACCTATACCCAATTTCTATTATTA 6 77 1 ATACCCAATT 0.847126 -224 TTTATAGGTTATATTTAATTTTTTTGTAAT 6 280 1 ATATTTAATT 0.850243 -21 AATCTTGATAATCGATTTGTCTCTAGT 7 8 1 ATAATCGATT 0.776528 -134 TTTTTATTATATACTAAATTTAATGAATTA 8 32 1 ATACTAAATT 0.815317 -31 ********** Masking position 3 Map Score: 10.4579 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 181 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 ATAAGATTTTTACAAGGTAATTTTAA 1 6 0 TACAAGTAAT 0.915185 -244 ATTTTAAAGATAAAAGTTGATTATCTAGCTT 1 140 0 TAAAAGTGAT 0.872632 -110 ACATTAATAATAAACGATAATACAGCAATTT 2 96 0 TAAACGTAAT 0.814167 -79 GAATATAAACTACAAGATATTATTTTTAATT 3 98 1 TACAAGTATT 0.87971 -203 CATTAAGTCATAAAAGCTAATTAGTTATTTT 3 182 0 TAAAAGTAAT 0.962294 -119 AATATTTTGTTACAAAATATTACATAATCAC 4 150 0 TACAAATATT 0.617508 -76 TAAATATATTTAAATGTTAATATTTAATTGC 4 194 0 TAAATGTAAT 0.881923 -32 ATTTTTAAATTAAATAATAATTTATATACAA 5 128 1 TAAATATAAT 0.622471 -173 CATACTGGATTAAAAGCTGATAATCTAATAA 5 168 1 TAAAAGTGAT 0.872632 -133 AATTTAGGTATAATAGTTATTAGATTATCAG 5 184 0 TAATAGTATT 0.750125 -117 AGAAACAGCATAAAACTTATTATCGTGACTA 6 43 1 TAAAACTATT 0.691336 -258 AAAATAATTTTAATTGTTAATTTAAAAAATT 6 187 0 TAATTGTAAT 0.564512 -114 ATATGACTGTTAAAAAATAATTTTAATTGTT 6 200 0 TAAAAATAAT 0.849257 -101 CATGAAATAATAAAATTTATTAGATTGCTTC 7 62 1 TAAAATTATT 0.727134 -80 AAAAACAATATAAAATATATTTATAT 8 6 0 TAAAATTATT 0.727134 -57 ****** **** Masking position 2 Map Score: 12.3588 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 294 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 TAGTTTATATTCATTGATACTGCAGATTGAT 3 79 0 TCATTGATCT 0.919881 -222 CTGGAAATAATTACAGATACTATATAGTATC 4 33 1 TTACAGATCT 0.951462 -193 TAAGGTCCAATTACAGATACTATATAGTATC 4 48 0 TTACAGATCT 0.951462 -178 ACAACACCACTTATTGATGCTCACAATGGTG 4 122 1 TTATTGATCT 0.9739 -104 AAAAATTAAAATATTGATACTGATATACTAT 6 106 1 ATATTGATCT 0.885669 -195 TTATAGAATGTTATTCATTCTAGGTCGATTA 6 141 0 TTATTCATCT 0.94028 -160 CTAAATTGTGTTACTCATACTAGAGACAAAT 7 25 0 TTACTCATCT 0.950034 -117 ******** ** Masking position 7 Map Score: 4.49292 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 45 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GTAAAAATCTTATAAATTATATAATATATC 1 24 1 TATAAATTAT 0.865185 -226 AAAATATTAAGATATATTATATAATTTATA 1 34 0 GATATATTAT 0.690921 -216 TATTATAGTGTAAATAATATGAATTTAGTA 2 19 0 TAAATAATAT 0.754967 -156 TAAAATAGGATATAGAATATAGTATAACAA 3 216 1 TATAGAATAT 0.938857 -85 TTACAGATACTATATAGTATCTGTAATTAT 4 39 0 TATATAGTAT 0.813468 -187 CAATGGTGATTATGTAATATTTTGTAACAA 4 145 1 TATGTAATAT 0.705459 -81 AATACTAAAAAATATATTATTACTTTCTTA 5 66 1 AATATATTAT 0.601314 -235 AATAATGAATTAAATAATATGAAAATATTT 5 101 0 TAAATAATAT 0.754967 -200 TCTTATTGTATATAAATTATTATTTAATTT 5 134 0 TATAAATTAT 0.865185 -167 AAAAATTTTTTATAGAATGTTATTCATTCT 6 151 0 TATAGAATGT 0.69135 -150 TTAACAGTCATATAGATTATGTACCTTATC 6 218 1 TATAGATTAT 0.929847 -83 GTGAGCTATTTATAGGTTATATTTAATTTT 6 272 1 TATAGGTTAT 0.65911 -29 ATAAAAACAATATAAAATATATTTATAT 8 9 0 TATAAAATAT 0.881441 -54 TTAAATTTAGTATATAATAAAAACAATATA 8 25 0 TATATAATAA 0.617738 -38 ********** Masking position 2 Map Score: 6.9216 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 241 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 9 AATGAATATGGCAATTTCTAAACTACAAAA 1 78 0 GCAATTTCTA 0.964866 -172 CCATGTAGCTCCAATTTTTATTGCAGCTTA 1 202 0 CCAATTTTTA 0.970941 -48 CGATAATACAGCAATTTTAATCTCAATAAA 2 83 0 GCAATTTTAA 0.811632 -92 ACAACTGTATCCAAGTTCTAATTTTATCAG 3 242 1 CCAAGTTCTA 0.950525 -59 ATTACACAAGCAAATTTTTACGTAAAAATA 3 273 1 CAAATTTTTA 0.837882 -28 TTACCTATACCCAATTTCTATTATTAAAAA 6 81 1 CCAATTTCTA 0.981323 -220 ********** Masking position 6 Map Score: 2.72882 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 32 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: 1.11088e-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 11 CAAGAATTTTAAAGATAAAAGTTGATTATC 1 146 0 AAAGATAAAA 0.548625 -104 ACTAAAATAGGTAAAAAAATCTTAAG 3 7 1 ATAGGTAAAA 0.944257 -294 AAGCAAATTTTTACGTAAAAATAATAAAAC 3 280 1 TTACGTAAAA 0.664231 -21 GCCTTGAACATAAGGTCCAATTACAGATAC 4 59 0 TAAGGTCCAA 0.64556 -167 GTAATCCAATTTAGGTATAATAGTTATTAG 5 192 0 TTAGGTATAA 0.727535 -109 TTTGCTAAACATAGGTACATGGTATATAAC 5 271 0 ATAGGTACAT 0.790448 -30 GAAATTGGGTATAGGTAAAAGTATTTAGTC 6 69 0 ATAGGTAAAA 0.944257 -232 TTAAAAAATTTAAAGTAAAAATTTTTTATA 6 167 0 TAAAGTAAAA 0.571685 -134 TTTCCTTTGATAAGGTACATAATCTATATG 6 226 0 TAAGGTACAT 0.790448 -75 GTACCTTATCAAAGGAAAAATATTTTTAAA 6 238 1 AAAGGAAAAA 0.857602 -63 CCTATTATTATAAGGAAAAACCATTAGTTT 7 97 0 TAAGGAAAAA 0.857602 -45 CCTTATAATAATAGGAAAATTATTAAACTA 7 112 1 ATAGGAAAAT 0.681652 -30 ********** Masking position 3 Map Score: 3.53528 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 421 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 12 ACCTTGTAAAAATCTTATAAATTATATAAT 1 19 1 AATCTTATAA 0.62949 -231 CAGCAATTTTAATCTCAATAAAATTATTTT 2 75 0 AATCTCAATA 0.68329 -100 AAGATTCTCAAAGCTCATTTT 2 164 1 AAGCTCATTT 0.639621 -11 AAAAAATCTTAAGATCATTATATGACAGAA 3 24 1 AAGATCATTA 0.831719 -277 TAAGTCATAAAAGCTAATTAGTTATTTTTC 3 180 0 AAGCTAATTA 0.919475 -121 AGGTTGTTTAAATATATTTAAATGTTAATA 4 203 0 AATATATTTA 0.614135 -23 AAAAGCTGATAATCTAATAACTATTATACC 5 179 1 AATCTAATAA 0.891111 -122 TTGGATTACGAATCTCTTTATTTAATTTTT 5 213 1 AATCTCTTTA 0.868807 -88 TTTAATTTTTAAGATAATAATCTTAATTAT 5 233 1 AAGATAATAA 0.684689 -68 ACAATTTAGCAATCTCATGAAATAATAAAA 7 47 1 AATCTCATGA 0.831858 -95 TTGATGAAGCAATCTAATAAATTTTATTAT 7 68 0 AATCTAATAA 0.891111 -74 AACAATATAAAATATATTTATAT 8 4 0 AATATATTTA 0.614135 -59 ********** Masking position 2 Map Score: 3.44531 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 259 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 13 ********** No masking Map Score: 1.11088e-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: 1.11088e-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: 1.11088e-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