AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_rpxx_reg_300.orf -o00970_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 Purged sequences: RP851 21 unknown Input sequences: #1 RP064 249 DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE (dgtP) #2 RP085 300 CYSTEINYL-TRNA SYNTHETASE (cysS) #3 RP142 300 AMINOPEPTIDASE A (pepA) #4 RP143 91 unknown #5 RP144 98 unknown #6 RP145 72 ASPARAGINYL-TRNA SYNTHETASE (aspS) #7 RP208 300 METHIONYL-TRNA DEFORMYLASE (def) #8 RP221 300 THREONYL-TRNA SYNTHETASE (thrS) #9 RP306 217 unknown #10 RP307 130 CATIONIC AMINO ACID TRANSPORTER-1 (atrc1) #11 RP308 80 HISTIDYL-TRNA SYNTHETASE (hisS) #12 RP325 107 GLUTAMYL-TRNA SYNTHETASE (gltX1) #13 RP326 300 DNA TOPOISOMERASE I (topA) #14 RP371 252 LYSYL-tRNA SYNTHETASE (lysS) #15 RP382 300 unknown #16 RP384 141 PROLYL-TRNA SYNTHETASE (proS) #17 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #18 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #19 RP420 300 unknown #20 RP421 64 LEUCYL-TRNA SYNTHETASE (leuS) #21 RP468 74 TRYPTOPHANYL-TRNA SYNTHETASE (trpS) #22 RP556 300 TYROSYL-TRNA SYNTHETASE (tyrS) #23 RP617 300 PROBABLE ISOLEUCYL-TRNA SYNTHETASE (ileS) #24 RP622 74 3-DEMETHYLUBIQUINONE-9 3-METHYLTRANSFERASE (ubiG) #25 RP623 114 GLUTAMYL-TRNA SYNTHETASE (gltX2) #26 RP684 300 THYMIDYLATE KINASE (tmk) #27 RP687 300 VALYL-TRNA SYNTHETASE (valS) #28 RP780 245 unknown #29 RP782 175 unknown #30 RP849 40 GLYCYL-TRNA SYNTHETASE BETA CHAIN (glyS) #31 RP850 186 GLYCYL-TRNA SYNTHETASE ALPHA SUBUNIT (glyQ) #32 RP852 211 PROLINE/BETAINE TRANSPORTER (proP6) #33 RP854 163 unknown #34 RP855_RP856 190 RP855: unknown, RP856: ALANYL-TRNA SYNTHETASE (alaS) Motif number 1 TCTTATAAATTATATAATATATCTTAATAT 1 31 1 TATATAATAT 0.827547 -219 TCAACTTTTATCTTTAAAATTCTTGTATTT 1 151 1 TCTTTAAAAT 0.795043 -99 ATTAATTGTTTTTTTTATAAATGAGATATA 2 180 1 TTTTTTATAA 0.783871 -121 ATGTTAGTGATATATAATAACTTTAGTTAA 3 54 1 TATATAATAA 0.787428 -247 CATTAAGTAATATTTAATAATTACTCTATT 3 194 0 TATTTAATAA 0.862271 -107 TTATAAAGTATATATAATATAACGTGCAAA 5 48 1 TATATAATAT 0.827547 -51 CGGTAATAGTTGTATAATAAGCTCACCTAC 7 206 0 TGTATAATAA 0.657911 -95 AATTTTATTGTATATTATAAGTAAAAGATT 7 266 1 TATATTATAA 0.644299 -35 TCTATTTTTCTATTTTATATATTAACGATA 8 266 0 TATTTTATAT 0.798919 -35 AATTTTAATTTTTAAAATCTACGTGTAT 9 9 1 TTTTTAAAAT 0.850061 -209 ATAATCGTGTTGTTTAATAATTATCAATTT 9 109 0 TGTTTAATAA 0.764868 -109 TATCTTTCAATATATTAAAATGCTATAATC 9 133 0 TATATTAAAA 0.583032 -85 CAAGAGTATATTTATAATAAAGAATAATGA 11 29 0 TTTATAATAA 0.814114 -52 TTACAGCAAATATTTAAAAAGGTTATCGAT 13 69 1 TATTTAAAAA 0.799501 -232 TATACTGCTATGTTTTATATTTGAATTATT 13 153 1 TGTTTTATAT 0.673499 -148 TGTTCTTAAATGTTTAAAATATTGTTGCCG 13 185 0 TGTTTAAAAT 0.764868 -116 ATGTAATGAGTTTATAATAAATAG 13 287 1 TTTATAATAA 0.814114 -14 AATGTTTTATTTTTTTAAATTACACGAACT 14 97 0 TTTTTTAAAT 0.783871 -156 AATATTTTAATTTTTAATAATAGAAATTGG 15 91 0 TTTTTAATAA 0.850061 -210 TGAATAACATTCTATAAAAAATTTTTACTT 15 155 1 TCTATAAAAA 0.638915 -146 TTACTTTAAATTTTTTAAATTAACAATTAA 15 179 1 TTTTTTAAAT 0.783871 -122 TAGCTCACGGTATTTAAAAATATTTTTCCT 15 250 0 TATTTAAAAA 0.799501 -51 TTTATTAGACTTTATTATATCAATCTTAGG 17 76 1 TTTATTATAT 0.735314 -225 TACTGCAAATTTTTTAAAATACTAGTTATT 17 168 1 TTTTTAAAAT 0.850061 -133 ATAATACAAATTTTTAATATGTAAAACATT 17 281 1 TTTTTAATAT 0.905604 -20 AGCTATTAACTATTTAATATGTTC 19 5 0 TATTTAATAT 0.890413 -296 ATGAAAAAATTTTTTTAAATCAGGACTCCA 19 90 1 TTTTTTAAAT 0.783871 -211 CACTATATATTATATTAACATGATT 22 6 1 TATATTATAT 0.701176 -295 TTTCATATACTTTATAATAAATTAAATATA 22 102 1 TTTATAATAA 0.814114 -199 TTATTGCTGCTTTTTAAAATTAACCTTAAG 22 176 0 TTTTTAAAAT 0.850061 -125 ATTGTTATTTTCTTTTAAATATACCTTATA 23 140 1 TCTTTTAAAT 0.655073 -161 TTAGTCATTATCTATTATATTAAACCAAAT 23 262 1 TCTATTATAT 0.592331 -39 CAACACACTATATATAATATACTCGG 24 7 0 TATATAATAT 0.827547 -68 GAGTTATATATATTTAAAATAATAATAATA 25 94 1 TATTTAAAAT 0.862271 -21 CATAATCATATCTTTAAAAAAAATATTTAC 26 254 0 TCTTTAAAAA 0.723477 -47 TATGCTTTAGTTTTTAAAATTGCAATTTTT 26 280 1 TTTTTAAAAT 0.850061 -21 CATAAAAGTTTCTTTAATATCTTTAACCTA 27 140 0 TCTTTAATAT 0.834198 -161 GTTAAATTACTTTTTTATAATTGAATGCAT 27 167 0 TTTTTTATAA 0.783871 -134 ATACATAATCTTTATAATAATATTCTTAAC 27 268 1 TTTATAATAA 0.814114 -33 TTGTGATTTTTATATTAAATTTTTAAATTA 28 17 1 TATATTAAAT 0.644299 -229 TTATAAACCTTTTTTAATAATTG 29 4 0 TTTTTAATAA 0.850061 -172 TTAAAAAAGGTTTATAATATTCAGATATAC 29 17 1 TTTATAATAT 0.850327 -159 CAGATATACTTGTTTAATATGAAAAATTGA 29 38 1 TGTTTAATAT 0.808374 -138 ATAATATTGATATTTAAAATTAACAATTTC 31 32 1 TATTTAAAAT 0.862271 -155 GATAGCTTGCTTTTTTAAAAGTTGATCCTC 32 98 1 TTTTTTAAAA 0.711118 -114 TTACTTTATTTATTTAAAAAGATAATAAAA 32 188 0 TATTTAAAAA 0.799501 -24 ********** Masking position 5 Map Score: 34.7088 Number of sites scoring better than the average of aligned sites = 1320 Number in coding regions = 841 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 2 CACCATCTTGAAAAATATTAAGATATATTA 1 45 0 AAAAATATTA 0.799932 -205 ATTTTGTTTGAAAATTATTAGTCAATAAAT 2 233 0 AAAATTATTA 0.941955 -68 CAATATAAATAAAATTATCAAAATTCAAAA 3 266 1 AAAATTATCA 0.855575 -35 ACATATACATAAAATTATTAGCTTGTGCAA 6 26 0 AAAATTATTA 0.941955 -47 GGTAATAGTTAAAAGTATTACAAATGTTAG 8 172 1 AAAAGTATTA 0.73219 -129 ACAATATACTAAATTTATTTATTTGTAAAA 14 200 0 AAATTTATTT 0.762377 -53 GGGTATAGGTAAAAGTATTTAGTCACGATA 15 63 0 AAAAGTATTT 0.7153 -238 ATTTAAAGTAAAAATTTTTTATAGAATGTT 15 160 0 AAAATTTTTT 0.72557 -141 TTTTTACTTTAAATTTTTTAAATTAACAAT 15 176 1 AAATTTTTTA 0.558292 -125 ATTAACAATTAAAATTATTTTTTAACAGTC 15 197 1 AAAATTATTT 0.915059 -104 TTATCAAAGGAAAAATATTTTTAAATACCG 15 243 1 AAAAATATTT 0.650827 -58 TGAAATAATAAAATTTATTAGATTGCTTCA 16 64 1 AAATTTATTA 0.847293 -78 TAATAATAGGAAAATTATTAAACTAAAACA 16 117 1 AAAATTATTA 0.941955 -25 GTCTTACTGCAAATTTTTTAAAATACTAGT 17 164 1 AAATTTTTTA 0.558292 -137 TCACAAACTCAAAATTATCTTATTATACTT 19 39 0 AAAATTATCT 0.846153 -262 CTGATTTAAAAAAATTTTTTCATTAAATAT 19 83 0 AAAATTTTTT 0.72557 -218 CTATTAGTCAAAAATTATTTAAACTAATTG 19 234 0 AAAATTATTT 0.915059 -67 TATTAAAATAATTATATTAATAAA 21 5 1 AAAATAATTA 0.588113 -70 AAGCAGCAATAAATTTATTAGCAGGAAAAT 22 194 1 AAATTTATTA 0.847293 -107 TTTTTCTACAAAAATTATCTTCAAAAATAT 23 84 1 AAAATTATCT 0.846153 -217 AATTATCTTCAAAAATATCAATTTCGTATT 23 96 1 AAAAATATCA 0.596129 -205 TACCTTATACAAAAATATTACAACTTTAGC 23 161 1 AAAAATATTA 0.799932 -140 TGCACTCTTGAAATTTATTAGTTTAGTATA 23 215 1 AAATTTATTA 0.847293 -86 AGTATCTAGGAAAATAATTTGCAATATATA 25 25 0 AAAATAATTT 0.524929 -90 TATCTTTAAAAAAAATATTTACTATTATTT 26 246 0 AAAAATATTT 0.650827 -55 ATAGAGCTTGAAAATTTTCTATATCATCTT 32 12 1 AAAATTTTCT 0.556122 -200 ATCATCTTTGAAAATTATTGGATACTAAAT 32 34 1 AAAATTATTG 0.688532 -178 CAAGAATCAAAAATTTATTTTGTCATACTG 33 99 0 AAATTTATTT 0.762377 -65 ********** Masking position 3 Map Score: 22.1423 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 580 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 ATCAACTTTTATCTTTAAAATTCTTGTATTTTAAGTTGCT 1 150 1 ATTTATTTAT 0.894681 -100 AAATTATGTTATGTTTTTTCTTGTGATAGTTTTACTTACT 2 24 1 ATTTTTTTAT 0.912271 -277 AGTGAAAACATATTTTTGAGTTGGAATTTTTTAGTTTAAA 2 135 1 TATTATTTTT 0.585452 -166 AATATTTGTTAATTTATATATTCAATTTATTGACTAATAA 2 209 1 AATTTTTTTT 0.794838 -92 TGTTAGTGATATATAATAACTTTAGTTAATACAAGTATAA 3 55 1 ATTAATTTAT 0.844042 -246 CATTAAGTAATATTTAATAATTACTCTATTAAGTAATACT 3 184 0 TATTATTTAT 0.707172 -117 CTAATTCCTTATATTTTGAATTTTGATAATTTTATTTATA 3 269 0 ATTTATTTAT 0.894505 -32 AAGAAAGTAAATCTTGCTAATTCCGGTAATAGTTGTATAA 7 219 0 ATTTATTTAT 0.894681 -82 AAGATTTACTTTCTTTGCATTTAATTTTATTGTATATTAT 7 244 1 TTTTATTTTT 0.689129 -57 ACATAATTCAATCTTAATCTTTTACTTATAATA 7 278 0 TATTTTTTTT 0.633536 -23 CCGACAAGTTATTTTCTTTATTAGTATATTTGAGTTATGG 8 134 0 ATTTTTTTAT 0.91227 -167 TTTTATTCTAATTTATCTATTTTTCTATTTTATATATTA 8 272 0 AATTTTTTAT 0.868851 -29 GTTGTTTAATAATTATCAATTTGTTGTAATATACGGTCAC 9 91 0 AATAATTTAT 0.775174 -127 AACAACACGATTATAGCATTTTAATATATTGAAAGATAGT 9 125 1 TTTATTTTAT 0.747232 -93 GTTGTAATTTAATTATAAATTTAGTATAATTTAATGTTTA 9 165 1 AATAATTTAT 0.775173 -53 AACTTCAATTACATTTTTTCATTATTCTTTATTATA 11 7 1 AATATTTTAT 0.808452 -74 AAATAACTAATTTTATTAATTGCTATACGT 12 88 0 AATAATTTAT 0.775078 -20 TAAATATCATATCTAAAGAATTAGTATACTGCTATGTTTT 13 129 1 ATTAATTTAT 0.844042 -172 GTATACTGCTATGTTTTATATTTGAATTATTATCGGCAAC 13 152 1 ATTTTTTTTT 0.858781 -149 ATCAGTGACAATATACTAAATTTATTTATTTGTAAAATAT 14 197 0 ATTAATTTAT 0.843975 -56 ATCAGTATCAATATTTTAATTTTTAATAATAGAAATTGGG 15 90 0 ATTTATTTAT 0.89468 -211 ATTCTATAAAAAATTTTTACTTTAAATTTTTTAAATTAAC 15 163 1 AATTATTTTT 0.759899 -138 TAAATTTTTTAAATTAACAATTAAAATTATTTTTTAACAG 15 185 1 AATTATTTTT 0.75975 -116 TTTATAGGTTATATTTAATTTTTTTGTAATC 15 280 1 ATTTTTTTAT 0.912271 -21 TGATGAAGCAATCTAATAAATTTTATTATTTCATGAGATT 16 57 0 ATTAATTTAT 0.844041 -85 TAAACACGTCTTTTTAAGTATTGGTGTTTTATTAGACTTT 17 49 1 TTTTTTTTTT 0.730718 -252 AATGATTATTATCTTTATTTTTGTCTTACTGCAAATTTTT 17 142 1 ATTTTTTTAT 0.912271 -159 TGAGGATAAAATATAGACTATTATACTAATTTCATGCTTC 17 210 0 ATTATTTTAT 0.868851 -91 TATAGCAAATTTCTTTAAATTTACTATAATGAATTGAGGA 17 244 0 TTTTATTTAT 0.791261 -57 AATGTTTTACATATTAAAAATTTGTATTATAGCAAATTTC 17 271 0 ATTTATTTTT 0.832271 -30 AATTATTTTTTGTTTTTAGATTTTATCTCAACAT 18 83 0 ATTTTTTTTT 0.858781 -24 AAGTTTTGTTTATTTCGCTTTTAAAATTCTGACTTTTGCT 19 168 0 TATTTTTTTT 0.633536 -133 TTAATACCTTTTTATTTTACTCATTATAAAA 21 54 0 TATATTTTAT 0.653181 -21 ATTATTTATATTGTTTTTGGTTTTTCTATAAACAG 22 276 0 TTTATTTTTT 0.633536 -25 TAAAAGTTAATATTTGTTATTTTTGCTTGTG 23 2 0 TATTATTTTT 0.585452 -299 AACAAATATTAACTTTTAATTTAACTTATTACAAATTCAT 23 24 1 AATTATTTAT 0.844042 -277 AGAAAATAACAATTTTTCTTTTTCAGTAATACGAAATTGA 23 113 0 AATTTTTTAT 0.868851 -188 ATTCTAGAAATTATTATAATTTGGTTTAATATAATAGATA 23 270 0 TTTTATTTAT 0.791261 -31 ATAATTTGCAATATATACTGTTGAGATTTTA 25 2 0 ATTATTTTTT 0.794839 -113 ATATTCTGAGTTATATATATTTAAAATAATAATAATAA 25 87 1 TTTAATTTAT 0.707172 -28 TTGATTCTACATTTAATTTTTTCCTGTAATATTTTATTGT 26 81 1 ATTATTTTAT 0.868851 -220 TTTAAAAAAAATATTTACTATTATTTTTTTATTGCATGAT 26 232 0 ATTTTTTTTT 0.85878 -69 TGTGATTTTTATATTAAATTTTTAAATTATACGTTATATT 28 18 1 ATTTTTTTTT 0.858781 -228 GTTCTTTCTGAAGTTGATTCTTATACTACTCTTCATTTAT 28 75 0 AATTTTTTAT 0.868851 -171 TTAAATATCAATATTATTTATTCACATAATATGCAGTT 31 9 0 ATTTTTTTAT 0.91227 -178 ACAATTTTAGTTCTAATATATTAACTTTTT 31 167 1 TTTATTTTTT 0.633536 -20 ATCCTCATCTATCTACTCTCTTATTTTATTTGGGTTATGT 32 122 1 ATTATTTTAT 0.868851 -90 TTACTTGAGAAAGTACACTATTCCTTTTATTATCTTTTTA 32 164 1 AATATTTTTT 0.711666 -48 TAATAGTTTTTAGTATTTTATTGTTTTACTGAACACCGTA 33 32 0 TATATTTTAT 0.653181 -132 ** ** * ** ** * Masking position 11 Map Score: 58.3531 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 570 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 4 AAATTGAATATATAAATTAACAAATATTATATCTCATT 2 199 0 TAAAAATATT 0.725415 -102 TAATATGATGTATTAAGCACATTTTGTTTGAAAATTAT 2 245 0 TATAATTGTT 0.56124 -56 TATTTACAAAAAATTGTTGATGGCATTA 2 283 0 TATTAATGTT 0.713973 -18 ATAATCGCACTACTAAATATGTTATACTTGTATTAACT 3 78 0 TATAATTACT 0.766431 -223 TCTCATTAAGTAATATTTAATAATTACTCTATTAAGTA 3 189 0 TATAAATACT 0.896567 -112 TATTTTTGTGTAGAACGCAAAACCTACTGTAATAAAGA 4 13 1 TAAAAATACT 0.72922 -79 TAAGCTCACCTACTTTCAATCATTTATTTGCATGATTA 7 181 0 TATTAATATT 0.862671 -120 ACTATCTTTATATTTTACATCAACTACTAAAGAATTAC 8 27 0 TATTAATACT 0.864927 -274 TACTTTTAACTATTACCGACAAGTTATTTTCTTTATTA 8 151 0 TATAAATATT 0.894775 -150 ATGGTTTAATATCAAATTATTACTATAAACTAAA 12 7 1 TATAATTACT 0.766431 -101 TATTGATTTATACTAAATATGATCTATTCCTAGTAATT 13 17 0 TATAAATATT 0.894775 -284 GAATATTAGCTAATTTACAGCAAATATTTAAAAAGGTT 13 55 1 TATTAATATT 0.862671 -246 AAAACACCAATACTTAAAAAGACGTGTTTAGCTTTTTA 17 41 0 TATTAATGTT 0.713973 -260 TATTATACTTTATAAGCTATTAACTATTTAATATGTTC 19 11 0 TAAAAATATT 0.725417 -290 GAGCTTTGACTATTAGTCAAAAATTATTTAAACTAATT 19 235 0 TATAAATATT 0.894775 -66 TTAACTCACTTAATTTATAAATCATGTTAATATAATAT 22 17 0 TATTATTGTT 0.485848 -284 TAAGTTAAATTAAAAGTTAATATTTGTTATTTTTGCTT 23 14 0 TAAAAATGTT 0.512147 -287 TCTTTTTCAGTAATACGAAATTGATATTTTTGAAGATA 23 99 0 TATAATTATT 0.762981 -202 TTTATTAGTTTAGTATAAATTATGTATTTATCTCTTAG 23 228 1 TATAAATATT 0.894775 -73 TCTAGGAAAATAATTTGCAATATATACTGTTGAGATTT 25 13 0 TATTAATACT 0.864927 -102 TTTAAATATATATAACTCAGAATATACTCAGAACTTTT 25 74 0 TAAAAATACT 0.72922 -41 AATAACCACTTAATTATTAGCAAATACTTTACTTTAAA 26 183 0 TATTAATACT 0.864927 -118 ATTAAATTTTTAAATTATACGTTATATTCCAAGTGTAT 28 30 1 TAATATTATT 0.424896 -216 CTGAAGCTGTTACTTCAGATTTAGTACTGCGTACTTTT 28 137 1 TATTATTACT 0.70795 -109 TCCACCTATCTACTTTTCATTATTTACTTATT 29 154 1 TATTAATACT 0.864927 -22 ATTCATTATCTAATACTCATTAAATATTAATAATGAAA 31 98 0 TATAAATATT 0.894775 -89 ** ** * * **** Masking position 15 Map Score: 22.7992 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 106 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 AGGTATAATGAATATGGCAATTTCTAAACTA 1 83 0 ATATGGCAAT 0.79838 -167 AACTCAACACATTATAGCAATATCATGCATT 7 62 0 ATATAGCAAT 0.940683 -239 AAACAACACGATTATAGCATTTTAATATATT 9 124 1 ATATAGCATT 0.847385 -94 GATACACCATAGTTTGGCAATTATATCCATT 10 24 1 ATTTGGCAAT 0.756642 -107 TAAAATTCCTAATAAAGCAATACAATTAGAA 10 64 0 ATAAAGCAAT 0.575721 -67 TTTATTAGGAATTTTAGCATATACGAGAATG 10 79 1 ATTTAGCATA 0.671791 -52 AAGCCACACACGTATAGCAATTAATAAAATT 12 79 1 CTATAGCAAT 0.731358 -29 AAAATAAAACATTATAGCATTTTTTCTGGAT 14 114 1 ATATAGCATT 0.847385 -139 TGAGTAACACAATTTAGCAATCTCATGAAAT 16 39 1 ATTTAGCAAT 0.92566 -103 ATTAAAATGTTATTTAGCAATGATTATTATC 17 124 1 TTTTAGCAAT 0.825939 -177 AAAAATTTGTATTATAGCAAATTTCTTTAAA 17 265 0 ATATAGCAAA 0.881594 -36 TTCACTGGACTATTTAGCAAAGTTATGTTGT 18 48 1 TTTTAGCAAA 0.690193 -59 TTCCATATGTTCTTTAGCAAAAGTCAGAATT 19 153 1 TTTTAGCAAA 0.690193 -148 AGGGTCTAGTTTTATAGCAATAACATTACCA 22 133 0 TTATAGCAAT 0.858022 -168 AAATATTACAACTTTAGCATTAGAAAGTTCT 23 173 1 ATTTAGCATT 0.813421 -128 ACAAAGTGGTAATATAGCAAAACAAATTTGT 27 67 1 ATATAGCAAA 0.881594 -234 * ********* Masking position 3 Map Score: 11.4508 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 133 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 GATATATTATATAATTTATAAGATTTTTAC 1 24 0 ATAATTTATA 0.658228 -226 ATAATATTTGTTAATTTATATATTCAATTT 2 207 1 TTAATTTATA 0.879345 -94 TATAATAACTTTAGTTAATACAAGTATAAC 3 66 1 TTAGTTAATA 0.686656 -235 AATTACTCTATTAAGTAATACTATTCCGAT 3 176 0 TTAAGTAATA 0.679023 -125 TTAAATCTCATTAAGTAATATTTAATAATT 3 202 0 TTAAGTAATA 0.679023 -99 TTAATCTTCCTTAATTGATACATATATTTT 7 131 1 TTAATTGATA 0.736646 -170 TAAATAAACATTAAATTATACTAAATTTAT 9 179 0 TTAAATTATA 0.788844 -39 CCGTATATTTTTAGTTTATAGTAATAATTT 12 24 0 TTAGTTTATA 0.686656 -84 TTCTTGCACTTTAATTAATAATCAGTGACA 14 227 0 TTAATTAATA 0.879345 -26 AAATAACATTTTAATTGATATATAAATAAG 17 109 0 TTAATTGATA 0.736646 -192 AACATATTAAATAGTTAATAGCTTATAAAG 19 12 1 ATAGTTAATA 0.366721 -289 ATCTGTCGTTTAATTTATGTGTAATCATG 20 46 0 TTAATTTATG 0.587163 -19 ATTAACTCACTTAATTTATAAATCATGTTA 22 26 0 TTAATTTATA 0.879345 -275 ATTAAGTGAGTTAATTAATATGAGCTTGTA 22 41 1 TTAATTAATA 0.879345 -260 AGATAAATACATAATTTATACTAAACTAAT 23 231 0 ATAATTTATA 0.658228 -70 TCAGAACTTTTTAAATTATAATTTGATTAG 25 55 0 TTAAATTATA 0.788844 -60 AAATATAGATTTAAATAATGATATTATCAT 26 144 0 TTAAATAATG 0.421644 -157 TATTAAATTTTTAAATTATACGTTATATTC 28 29 1 TTAAATTATA 0.788844 -217 TATTATGTGAATAAATAATATTGATATTTA 31 18 1 ATAAATAATA 0.496782 -169 TGCAATAACATTAAATAATATATCTTACC 34 10 0 TTAAATAATA 0.788844 -181 ********** Masking position 6 Map Score: 11.2114 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 178 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 ATTTCTAAACTACAAAACAACACCATCTTG 1 65 0 TACAAAACAA 0.80491 -185 GTGATTAAGCTGCAATAAAAATTGGAGCTA 1 197 1 TGCAATAAAA 0.891114 -53 GGCAATGCCTTACAAAACAAAGGATAACT 1 231 1 TACAAAACAA 0.80491 -19 TATTTACAAAAAATTGTTGATGGC 2 287 0 TACAAAAAAT 0.6272 -14 TATAACTTTATACAAGAAAAACTTTAATGA 5 23 0 TACAAGAAAA 0.857813 -76 TGTATATGTATACAATGAAAGAAATATACA 6 47 1 TACAATGAAA 0.781781 -26 TAAAATTAAATGCAAAGAAAGTAAATCTTG 7 243 0 TGCAAAGAAA 0.633105 -58 ACTTATAATATACAATAAAATTAAATGCAA 7 258 0 TACAATAAAA 0.925051 -43 TATACGGTGTTACAATACAAGATTTCGTGG 12 47 1 TACAATACAA 0.850295 -61 TTAATTAAAGTGCAAGAAAAATAA 14 239 1 TGCAAGAAAA 0.800014 -14 GATTACAAAAAAATTAAATATAA 15 288 0 TACAAAAAAA 0.899654 -13 AGAAACAATATACAATAAAATATTACAGGA 26 102 0 TACAATAAAA 0.925051 -199 CTTTAAAATCTACAATAAATATAGATTTAA 26 160 0 TACAATAAAT 0.698439 -141 AAGTATATCATGCAATAAAAAAATAATAGT 26 226 1 TGCAATAAAA 0.891114 -75 ********** Masking position 5 Map Score: 9.72126 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 107 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TTGCAAGTATTATAATCAACTTAAAATTAAATCTCAT 3 221 0 TATAACTAAT 0.891309 -80 CCTTAATTGATACATATATTTTATGCTGTCTGATATT 7 139 1 TACAATTAGT 0.858102 -162 GACCGTATATTACAACAAATTGATAATTATTAAACAA 9 93 1 TACAATTAAT 0.717903 -125 AACATTAAATTATACTAAATTTATAATTAAATTACAA 9 166 0 TATAATTAAT 0.866808 -52 GTTTGGCAATTATATCCATTTCAAGCTTATTCTAATT 10 35 1 TATAATTAGT 0.939264 -96 ATATACGGTATATATAGAATTAAAAGTAATGCATAAT 13 240 1 TATAATTAAT 0.866809 -61 AAATATAACCTATAAATAGCTCACGGTATTTAAAAAT 15 259 0 TATAACTAGT 0.951187 -42 TAGACTTTATTATATCAATCTTAGGATACTTATTTAT 17 81 1 TATAACTAGT 0.951187 -220 TATAGACTATTATACTAATTTCATGCTTCTTATTACT 17 202 0 TATAATTAGT 0.939264 -99 TTAAATTTACTATAATGAATTGAGGATAAAATATAGA 17 233 0 TATAATTAGT 0.939264 -68 AAACTGGTCTTATCACAAACTCAAAATTATCTTATTA 19 44 0 TATCACTAAT 0.671875 -257 ACATTACCATTATATTTAATTTATTATAAAGTATATG 22 105 0 TATAATTATT 0.574669 -196 CAGTTTTCTCTACAGACACTTTATGGTCTTTTTAGAG 22 242 0 TACAATTAGT 0.858102 -59 TTATTTTAAATATATATAACTCAGAATATACTCAGAA 25 79 0 TATAACTAAT 0.891309 -36 AGATCCATAATATAAAAAGCTGAAGCTGTTACTTCAG 28 118 1 TATAACTAGT 0.951187 -128 ACTATTAATATATCTGGACCTAATGATAAATCCACAG 33 65 1 TATCACTAGT 0.829517 -99 **** * ** * * * Masking position 8 Map Score: 12.6713 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 21 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 GTTATTATATATCACTAACATTTTATGTAATAAA 3 41 0 ATATACATTT 0.848379 -260 ATTAAGGAAGATTAATAATATATTATAGTGTGAT 7 112 0 ATATATATTT 0.934679 -189 ATACTCTTGTATCACTAAAATCTTCTACATAACT 8 85 0 ATATAAATTT 0.780627 -216 AGTTATTTTCTTTATTAGTATATTTGAGTTATGG 8 134 0 TTATATATTT 0.683442 -167 TTTAGTATAAATCAATAGAATATTAGCTAATTTA 13 38 1 ATATAAATTT 0.780627 -263 AGGTCGATTAATAAATAGTATATCAGTATCAATA 15 117 0 ATATATATTC 0.769561 -184 TAAATTAACAATTAAAATTATTTTTTAACAGTCA 15 194 1 ATAAATATTT 0.534727 -107 ATAATCATTGCTAAATAACATTTTAATTGATATA 17 117 0 CTATACATTT 0.566329 -184 TTATTTAGCAATGATTATTATCTTTATTTTTGTC 17 133 1 ATATATATTT 0.93461 -168 TTACTTCACAATAACTAGTATTTTAAAAAATTTG 17 173 0 ATATATATTT 0.934679 -128 AGTCCAGTGAATCAATACAATATTGTTGATCCTG 18 25 0 ATATAAATTT 0.780627 -82 AAATTATGTTATAAATACCATTTTTATTAATATA 21 23 0 ATATACATTT 0.848379 -52 AGCTTGTATGATAATCAATATATCAAGTATAGAC 22 63 1 ATACATATTC 0.422506 -238 TAGCAATAACATTACCATTATATTTAATTTATTA 22 116 0 ATACATATTT 0.75815 -185 TTATTATTATTATTTTAAATATATAT 25 99 0 ATATATATTT 0.93461 -16 AAAAAAAATATTTACTATTATTTTTTTATTGCAT 26 235 0 TTATATATTT 0.683442 -66 GTATTATAGACTGATTACTATTTTCCAAATTAAA 29 119 1 CTATATATTT 0.769561 -57 AATTTTAAATATCAATATTATTTATTCACATAAT 31 19 0 ATATATATTA 0.683442 -168 CTTATATTTCATTATTAATATTTAATGAGTATTA 31 92 1 ATATATATTA 0.683442 -95 ** * ** *** ** Masking position 11 Map Score: 11.1505 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 150 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 ATGCACATGCTGTTTCATTACAAGATGAGA 3 140 1 TGTTTCATTA 0.701242 -161 GTAATATTCATTTCATTAAAGTTTTTCT 5 9 1 CATTTCATTA 0.809434 -90 TCTACATAACTTTATCATTAAAGGTTAGTA 8 66 0 TTTATCATTA 0.672253 -235 TCAATTACATTTTTTCATTATTCTTTATTA 11 15 1 TTTTTCATTA 0.884101 -66 ATTAATTAAGTATTTCATTAAGCTGAAAAC 13 97 1 TATTTCATTA 0.909433 -204 TAAATTTTATTATTTCATGAGATTGCTAAA 16 51 0 TATTTCATGA 0.576817 -91 AAACTAATGGTTTTTCCTTATAATAATAGG 16 97 1 TTTTTCCTTA 0.508599 -45 ATTTTATCCTCAATTCATTATAGTAAATTT 17 238 1 CAATTCATTA 0.424349 -63 TTAAAAAAATTTTTTCATTAAATATCTAAA 19 78 0 TTTTTCATTA 0.884101 -223 GCTTTTATCATATTTCAATAGATTTACAAG 28 221 1 TATTTCAATA 0.478963 -25 CACCTATCTACTTTTCATTATTTACTTATT 29 156 1 CTTTTCATTA 0.763328 -20 ACAGAACTTATATTTCATTATTAATATTTA 31 86 1 TATTTCATTA 0.909433 -101 TTCGAACATCTAATTCATTATCTAATACTC 31 118 0 TAATTCATTA 0.635226 -69 AGGGACAGCGTATATCATTAAACATTTAGT 32 57 0 TATATCATTA 0.729821 -155 ATACTGTGGATTTATCATTAGGTCCAGATA 33 75 0 TTTATCATTA 0.672253 -89 ********** Masking position 10 Map Score: 8.74209 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 101 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 AAACTATGGTGTATCAATTTTACTTAAT 10 8 0 GTATCAATTT 0.915882 -123 ATGGTTTAATATCAAATTATTACTATAAA 12 9 1 ATATCAAATA 0.660068 -99 TATTTGTAAAATATCAAATTAAGCTCAGTCA 14 180 0 ATATCAAATA 0.660068 -73 TCACAATTCAATATCAAACTACAAGAAACAG 15 20 1 ATATCAAATA 0.660069 -281 TAGTATATCAGTATCAATATTTTAATTTTTA 15 105 0 GTATCAATTT 0.915882 -196 AGACTTTATTATATCAATCTTAGGATACTTA 17 82 1 ATATCAATTT 0.903839 -219 AAGTTATGTTGTAACAATGTTGAGATAAAAT 18 67 1 GTAACAATTT 0.709262 -40 ATCTTCAAAAATATCAATTTCGTATTACTGA 23 100 1 ATATCAATTC 0.687117 -201 TTAAAAGAAAATAACAATTTTTCTTTTTCAG 23 127 0 ATAACAATTT 0.678037 -174 TAGGACCTTGGTATCAATTTTTCATATTAAA 29 50 0 GTATCAATTT 0.915882 -126 TTAATTTTAAATATCAATATTATTTATTCAC 31 24 0 ATATCAATTT 0.903839 -163 GGGCAACCTCGTATCAAAGTTCTGATATTGC 34 90 1 GTATCAAATT 0.849559 -101 ******** ** Masking position 6 Map Score: 6.25028 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 52 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 AAATTATGTTATGTTTTTTCTTGTGATAGTTTT 2 24 1 ATGTTTTCTG 0.807549 -277 TTTAATGCACATGCTGTTTCATTACAAGATGAG 3 136 1 ATGTTTTCAT 0.744674 -165 TTGATAATGCATGATATTGCTATAATGTGTTGA 7 57 1 ATGTTTGCTT 0.926372 -244 GAATTAAAAGATGGTAATTCTTTAGTAGTTGAT 8 14 1 ATGTATTCTT 0.88751 -287 GCTTATTCTAATTGTATTGCTTTATTAGGAATT 10 59 1 ATTTTTGCTT 0.433714 -72 ACATAGCAGTATACTAATTCTTTAGATATGATA 13 133 0 ATATATTCTT 0.45855 -168 ATGATAGGCGATGGTAATTCTGTTTTGTGTTCT 13 209 0 ATGTATTCTT 0.88751 -92 AATAAGTTTTATGCTGTTTCTTGTAGTTTGATA 15 31 0 ATGTTTTCTG 0.807549 -270 ATCAAAACTAATGGTTTTTCCTTATAATAATAG 16 93 1 ATGTTTTCCT 0.710262 -49 AAACAAAACTTTGTTTTTTCTATATATGTATGA 19 197 1 TTGTTTTCTT 0.806918 -104 TATAATGGTAATGTTATTGCTATAAAACTAGAC 22 128 1 ATGTTTGCTT 0.926372 -173 TATATTGTTTTTGGTTTTTCTATAAACAGTTTT 22 272 0 TTGTTTTCTT 0.806918 -29 AGTTGATGATTCTTTTTAATGTCAT 24 60 0 TTGTATTCTT 0.662401 -15 ATTTTATTGTATATTGTTTCTTTTACCATATTC 26 111 1 ATATTTTCTT 0.643345 -190 TTTTAAAGATATGATTATGCTTTAGTTTTTAAA 26 265 1 ATGTATGCTT 0.855224 -36 ATATTATTTAATGTTATTGCATTCTAACTGGAG 34 19 1 ATGTTTGCAT 0.685896 -172 *** * ***** * Masking position 8 Map Score: 8.13245 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 108 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 TATTGCAGCTTAATCACAGTATAAAGCAACTTAA 1 180 0 TATACATAAA 0.916667 -70 AAAAAATTGTTGATGGCATTATAATATGATGTAT 2 270 0 TATGCATAAA 0.776548 -31 TAACTTTAGTTAATACAAGTATAACATATTTAGT 3 71 1 TATCAATAAA 0.762076 -230 ATAAATAAAATTATCAAAATTCAAAATATAAGGA 3 270 1 TATAAATTAA 0.747963 -31 AATTATAAAAATATAACGGAATCTGC 4 76 0 TATAAATAAA 0.910065 -16 AATTTCTCCATTATCACACTATAATATATTATTA 7 100 1 TATACATAAA 0.916628 -201 AACAACACGATTATAGCATTTTAATATATTGAAA 9 125 1 TATGCATTAA 0.504163 -93 ACTAAATTTATAATTAAATTACAACACTATCTTT 9 156 0 TATAAATAAA 0.910236 -62 TTGCCGATAATAATTCAAATATAAAACATAGCAG 13 157 0 TATCAATAAA 0.762109 -144 TATTCGCTCCTAATAAAAATAAAAACCT 14 5 0 TATAAATAAA 0.910236 -248 CACTGATTATTAATTAAAGTGCAAGAAAAATAA 14 230 1 TATAAATGAA 0.63514 -23 TTTTATTAATCACAATTCAATATCAAACTA 15 7 1 TATACATTAA 0.762995 -294 AATAGGAAAATTATTAAACTAAAACAATTTT 16 121 1 TATAAATAAA 0.910235 -21 TTAAGACACGTGATGACATTAAAAAGAATCATCA 24 48 1 TATACATAAA 0.916668 -27 CTAGATACTCTAATCAAATTATAATTTAAAAAGT 25 46 1 TATAAATAAA 0.910233 -69 * ** *** ** ** Masking position 8 Map Score: 11.7006 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 80 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 ATTACAAGATGAGAAGATATATCGGAATAGTA 3 156 1 GAGAAGTAAT 0.953822 -145 TTTTTCCTTTGATAAGGTACATAATCTATATG 15 226 0 GATAAGTAAT 0.9616 -75 ATGAATTTGTAATAAGTTAAATTAAAAGTTAA 23 32 0 AATAAGTAAT 0.736592 -269 AATATTTTTGTATAAGGTATATTTAAAAGAAA 23 148 0 TATAAGTAAT 0.736592 -153 TCTTGATCAGGAGAAGATATATCTAAGCCTTT 26 26 1 GAGAAGTAAT 0.953822 -275 ATTTAACGACGATAAGTTACATGCTGTACAAA 27 190 1 GATAAGTAAT 0.9616 -111 TAAAATAAGAGAGTAGATAGATGAGGATCAAC 32 118 0 GAGTAGTAAT 0.765046 -94 GAACACCGTAGATAAGATAAATATGGTACAC 33 10 0 GATAAGTAAT 0.9616 -154 GGTAAGATATATTATTTAATGT 34 1 1 GGTAAGTAAT 0.854032 -190 ****** ** ** Masking position 5 Map Score: 4.63367 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 15 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 CTTTACACTGTATCTAGTGTTTTAAGCCAAGGTATA 1 107 0 TATTAGTTTG 0.965761 -143 TAACACCGTATATTTTTAGTTTATAGTAATAATTTG 12 23 0 TATTTGTTAG 0.685493 -85 TTAGATATGATATTTACTGTTTTCAGCTTAATGAAA 13 109 0 TATTAGTTTG 0.965761 -192 CTCATTACATTATCTATGGTATTATGCATTACTTTT 13 261 0 TATTAGTTTG 0.965761 -40 TTATATATTGTATACAGGATCAACAAT 18 2 1 TATTAGTTAG 0.886888 -105 AATTATTTTTTGTTTTTAGATTTTATCTC 18 88 0 TATTTGTTTG 0.886888 -19 ATTATTTATATTGTTTTTGGTTTTTCTATA 22 281 0 TTTTAGTTTG 0.798749 -20 GAGTATATTATATATAGTGTGTTGCGTCATCAAGTT 24 13 1 TATTAGTTTG 0.965761 -62 ATATTTATCTTATCTACGGTGTTCAGTAAAACAATA 33 18 1 TATTAGTTTG 0.965761 -146 GGTCCAGATATATTAATAGTTTTTAGTATTTTATTG 33 49 0 TATAAGTTTG 0.798749 -115 *** ** ** ** * Masking position 10 Map Score: 7.98971 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432