AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_rpxx_reg_100.orf -o00970_rpxx_100.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 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 RP307 130 CATIONIC AMINO ACID TRANSPORTER-1 (atrc1) #10 RP308 80 HISTIDYL-TRNA SYNTHETASE (hisS) #11 RP325 107 GLUTAMYL-TRNA SYNTHETASE (gltX1) #12 RP371 252 LYSYL-tRNA SYNTHETASE (lysS) #13 RP384 141 PROLYL-TRNA SYNTHETASE (proS) #14 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #15 RP420 300 unknown #16 RP421 64 LEUCYL-TRNA SYNTHETASE (leuS) #17 RP468 74 TRYPTOPHANYL-TRNA SYNTHETASE (trpS) #18 RP556 300 TYROSYL-TRNA SYNTHETASE (tyrS) #19 RP617 300 PROBABLE ISOLEUCYL-TRNA SYNTHETASE (ileS) #20 RP623 114 GLUTAMYL-TRNA SYNTHETASE (gltX2) #21 RP684 300 THYMIDYLATE KINASE (tmk) #22 RP687 300 VALYL-TRNA SYNTHETASE (valS) #23 RP782 175 unknown #24 RP849 40 GLYCYL-TRNA SYNTHETASE BETA CHAIN (glyS) #25 RP850 186 GLYCYL-TRNA SYNTHETASE ALPHA SUBUNIT (glyQ) #26 RP856 190 ALANYL-TRNA SYNTHETASE (alaS) Motif number 1 AAATACAAGAATTTTAAAGATAAAAGTTGA 1 151 0 ATTTTAAAGA 0.884484 -99 AAATTCTTGTATTTTAAGTTGCTTTATACT 1 167 1 ATTTTAAGTT 0.560739 -83 CTCTAGTACTAATTTAAAAGCTACTAGTTC 2 83 1 AATTTAAAAG 0.525442 -218 TAGTAGTGCGATTATAAATTTTGTTCATAT 3 101 1 ATTATAAATT 0.767286 -200 ATGAGATTTAATTTTAAGTTGATTATAATA 3 221 1 ATTTTAAGTT 0.560739 -80 AAGTTTGATCAATATAAATAAAATTATCAA 3 257 1 AATATAAATA 0.818486 -44 TATAAATAAAATTATCAAAATTCAAAATAT 3 269 1 ATTATCAAAA 0.833223 -32 CAAAATTCAAAATATAAGGAATTAGGT 3 284 1 AATATAAGGA 0.769021 -17 AATTATAAAAATATAACGGAA 4 81 0 ATTATAAAAA 0.892274 -11 AATTGATGAGAATTTAAAAGGTTCTAAAGA 7 18 0 AATTTAAAAG 0.525442 -283 AATATCATGCATTATCAATGCTAGAAAAAT 7 45 0 ATTATCAATG 0.609732 -256 TTTATTGTATATTATAAGTAAAAGATTAAG 7 269 1 ATTATAAGTA 0.804558 -32 GTTGATGTAAAATATAAAGATAGTGTACTA 8 41 1 AATATAAAGA 0.862447 -260 TAGATAGAGCATTTTCAAGAATTATATCGT 8 242 1 ATTTTCAAGA 0.822108 -59 ATTATTCTTTATTATAAATATACTCTTGCC 10 31 1 ATTATAAATA 0.88567 -50 ATGGTTTAATATCAAATTATTACTATA 11 8 1 AATATCAAAT 0.564975 -100 TCGCACTGTCATTATAAGAAGTAATTAAGT 12 61 1 ATTATAAGAA 0.814961 -192 GAGTTCGTGTAATTTAAAAAAATAAAACAT 12 96 1 AATTTAAAAA 0.760852 -157 AAGCTCAGTCATTATAAGGAGCATTACGCA 12 161 0 ATTATAAGGA 0.851224 -92 TTATTTGTAAAATATCAAATTAAGCTCAGT 12 182 0 AATATCAAAT 0.564975 -71 AGACAAATCGATTATCAAGATT 13 3 0 ATTATCAAGA 0.866494 -139 TTTTCCTATTATTATAAGGAAAAACCATTA 13 101 0 ATTATAAGGA 0.851224 -41 AAAAGTCAGAATTTTAAAAGCGAAATAAAC 15 171 1 ATTTTAAAAG 0.651443 -130 TATTTTACTCATTATAAAATTATGTTATAA 17 43 0 ATTATAAAAT 0.772596 -32 TATTTAATTTATTATAAAGTATATGAAAAC 18 100 0 ATTATAAAGT 0.827834 -201 TTAAGGCCTTATTTTAAAGGGTCTAGTTTT 18 151 0 ATTTTAAAGG 0.719477 -150 CTTAAGGTTAATTTTAAAAAGCAGCAATAA 18 176 1 ATTTTAAAAA 0.838958 -125 AACCAAAAACAATATAAATAAT 18 289 1 AATATAAATA 0.818486 -12 TATCTTCAAAAATATCAATTTCGTATTACT 19 99 1 AATATCAATT 0.548341 -202 TAAACTAATAAATTTCAAGAGTGCAATGCA 19 210 0 AATTTCAAGA 0.728941 -91 ATCAAATTATAATTTAAAAAGTTCTGAGTA 20 58 1 AATTTAAAAA 0.760852 -57 TATTATTATTATTTTAAATATATATAACTC 20 94 0 ATTTTAAATA 0.837112 -21 TTTATTGTAGATTTTAAAGTAAAGTATTTG 21 171 1 ATTTTAAAGT 0.751714 -130 AAAAATTGCAATTTTAAAAACTAAAGCATA 21 280 0 ATTTTAAAAA 0.838958 -21 TATGCATTCAATTATAAAAAAGTAATTTAA 22 166 1 ATTATAAAAA 0.892274 -135 TAAGAATATTATTATAAAGATTATGTATGA 22 266 0 ATTATAAAGA 0.915072 -35 GAAATTGTTAATTTTAAATATCAATATTAT 25 32 0 ATTTTAAATA 0.837112 -155 TTAATAATGAAATATAAGTTCTGTAATTAT 25 80 0 AATATAAGTT 0.516971 -107 TGTCATTACAAATATCAGTAAGAGGATACG 26 61 1 AATATCAGTA 0.590656 -130 AGGATACGGCAATATCAGAACTTTGATACG 26 83 1 AATATCAGAA 0.606883 -108 CCCCGTCACAATTTTCAATTTTCCAGCTCA 26 119 1 ATTTTCAATT 0.591041 -72 ********** Masking position 5 Map Score: 26.6301 Number of sites scoring better than the average of aligned sites = 1287 Number in coding regions = 810 Number in noncoding regions = 477 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 ATATTAAGATATATTATATAATTTATAAGATTT 1 28 0 AATTATAATT 0.811861 -222 ATGAGATATAATATTTGTTAATTTATATATTCA 2 200 1 AATTTTAATT 0.811861 -101 TATCACTAACATTTTATGTAATAAAGCTTGATA 3 33 0 ATTTATAATA 0.796845 -268 ATATATAATAACTTTAGTTAATACAAGTATAAC 3 63 1 ATTTATAATA 0.796845 -238 TCATTAAGTAATATTTAATAATTACTCTATTAA 3 192 0 AATTTTAATT 0.811861 -109 TTACTTAATGAGATTTAATTTTAAGTTGATTAT 3 214 1 AATTTTTTTA 0.568969 -87 TTATATTTTGAATTTTGATAATTTTATTTATAT 3 268 0 ATTTTTAATT 0.871639 -33 AAAGTTATAAAGTATATATAATATAACGTGCAA 5 44 1 ATATATAATA 0.508403 -55 AACTTTAGTTTTTATTTGCACAAG 6 2 1 ATTTATTTTA 0.675598 -71 TTATCACACTATAATATATTATTAATCTTCCTT 7 110 1 AAATATTATT 0.441909 -191 CTATTTTTCTATTTTATATATTAACGATATAAT 8 262 0 ATTTATATTA 0.749532 -39 TTTTATTCTAATTTATCTATTTTTCTATTTTA 8 279 0 ATTTATATTT 0.838558 -22 CGTATATGCTAAAATTCCTAATAAAGCAATACA 9 71 0 AAATTTAATA 0.395954 -60 ACATTTTTTCATTATTCTTTATTATAAATATAC 10 21 1 ATATTTTATT 0.555409 -60 AAATAACTAATTTTATTAATTGCTATACGTG 11 87 0 ATTTTTAATT 0.871639 -21 CAATATACTAAATTTATTTATTTGTAAAATATC 12 196 0 ATTTATATTT 0.838383 -57 TTTTTCTTGCACTTTAATTAATAATCAGTGACA 12 227 0 ATTTATAATA 0.796845 -26 CAATCTAATAAATTTTATTATTTCATGAGATTG 13 56 0 ATTTTTATTT 0.838383 -86 TTAGTTTAATAATTTTCCTATTATTATAAGGAA 13 110 0 ATTTTTATTA 0.749532 -32 AATTATTTTTTGTTTTTAGATTTTATC 14 90 0 ATTTTTTTTT 0.783308 -17 CACAAACTCAAAATTATCTTATTATACTTTATA 15 35 0 AATTATTATT 0.750195 -266 TGATAAGACCAGTTTAGATATTTAATGAAAAAA 15 66 1 ATTTATATTT 0.838559 -235 AACATATGGAAGATTTAATTATTTCTTAGCATA 15 131 0 AATTTTTATT 0.750196 -170 GAAAAAACAAAGTTTTGTTTATTTCGCTTTTAA 15 184 0 ATTTTTTATT 0.825725 -117 ACATACAATTAGTTTAAATAATTTTTGACTAAT 15 229 1 ATTTATAATT 0.871928 -72 TATAAATACCATTTTTATTAATATAATTATTTT 17 15 0 ATTTTTAATA 0.796845 -60 ACTCATTATAAAATTATGTTATAAATACCATTT 17 34 0 AATTATTATA 0.633723 -41 CACTATATATTATATTAACATGAT 18 2 1 ATATATTATA 0.418512 -299 TAACATTACCATTATATTTAATTTATTATAAAG 18 111 0 ATATATAATT 0.642228 -190 TTAAAAGTTAATATTTGTTATTTTTGCTTGTG 19 10 0 AATTTTATTT 0.767023 -291 ATTAACTTTTAATTTAACTTATTACAAATTCAT 19 31 1 ATTTATTATT 0.825724 -270 AGAAAATAACAATTTTTCTTTTTCAGTAATACG 19 120 0 ATTTTTTTTT 0.783308 -181 TTTTCTTTTAAATATACCTTATACAAAAATATT 19 147 1 ATATATTATA 0.418512 -154 AGTTTAGTATAAATTATGTATTTATCTCTTAGT 19 234 1 AATTATATTT 0.767023 -67 TTATTATTATTATTTTAAATATATA 20 100 0 ATATTTATTT 0.577977 -15 GATTGATTCTACATTTAATTTTTTCCTGTAATA 21 79 1 AATTTTTTTT 0.696161 -222 TTTAAAAAAAATATTTACTATTATTTTTTTATT 21 239 0 AATTTTATTA 0.654787 -62 TATCGTCGTTAAATTACTTTTTTATAATTGAAT 22 171 0 AATTATTTTT 0.696131 -130 CTTGGTATCAATTTTTCATATTAAACAAGTATA 23 42 0 ATTTTTATTA 0.749532 -134 CCACCTATCTACTTTTCATTATTTACTTATT 23 155 1 ATTTTTTATT 0.825725 -21 GTGAATAAATAATATTGATATTTAAAATTAACA 25 24 1 ATATTTATTT 0.577892 -163 TACAGAACTTATATTTCATTATTAATATTTAAT 25 85 1 AATTTTTATT 0.750196 -102 TAGTTCTAATATATTAACTTTTT 25 174 1 AATTATTTTT 0.696161 -13 GAATGCAATAACATTAAATAATATATCTTACC 26 169 1 AATTATAATA 0.713148 -22 * **** ***** Masking position 5 Map Score: 38.0356 Number of sites scoring better than the average of aligned sites = 1756 Number in coding regions = 1076 Number in noncoding regions = 680 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 3 TTATGTTATGTTTTTTCTTGTGATAGTTTTACTTACTA 2 27 1 TTTTTCTATT 0.961822 -274 CTATGTATATTTCTTTCATTGTATACATATACATAAAA 6 42 0 TTTTTCTATT 0.961709 -31 CTACTTTCAATCATTTATTTGCATGATTATAACAAATA 7 172 0 TCTTTATATT 0.670787 -129 GCATTTAATTTTATTGTATATTATAAGTAAAAGATTAA 7 260 1 TTTTGTTATT 0.394228 -41 ACAAGTTATTTTCTTTATTAGTATATTTGAGTTATGGC 8 133 0 TTTTTATATT 0.957187 -168 ATAACTAATTTTATTAATTGCTATACGTGTGTGGCTTA 11 78 0 TTTTAATATT 0.578903 -30 TTTTTCTGGATTGTTTCATCGAATTACTGCGTAATGCT 12 134 1 TTTTTCTATT 0.961822 -119 ATAAATTTTATTATTTCATGAGATTGCTAAATTGTGTT 13 44 0 TTTTTCTATT 0.961822 -98 AAAATTGTTTTAGTTTAATAATTTTCCTATTAT 13 119 0 TGTTTATATT 0.789463 -23 TTTAAAAAAATTTTTTCATTAAATATCTAAACTGGTCT 15 71 0 TTTTTCTATT 0.961819 -230 GAAGATTTAATTATTTCTTAGCATAAATTTTAAATCTG 15 118 0 TTTTTCTATT 0.961805 -183 CAAAACTTTGTTTTTTCTATATATGTATGACATACAAT 15 200 1 TTTTTCAATT 0.796463 -101 TATAAATACCATTTTTATTAATATAATTATTTTAATA 17 10 0 ATTTTATATT 0.698314 -65 TATTATAATTTGGTTTAATATAATAGATAATGACTAAG 19 261 0 TGTTTATATT 0.78936 -40 CTACATTTAATTTTTTCCTGTAATATTTTATTGTATAT 21 87 1 TTTTTCTATT 0.961822 -214 GATAATATCATTATTTAAATCTATATTTATTGTAGATT 21 146 1 TTTTTAAATT 0.776465 -155 TATTATTTTTTTATTGCATGATATACTTACTTGAATAA 21 216 0 TTTTGCTATT 0.808585 -85 TTTAAAAAAAATATTTACTATTATTTTTTTATTGCATG 21 234 0 ATTTTATATT 0.698387 -67 AGTAAATATTTTTTTTAAAGATATGATTATGCTTTAGT 21 253 1 TTTTTAAATT 0.776467 -48 ATAAGTGTTCTTATTTTATACCATGACTCCTTCCAGCA 22 19 0 TTTTTTTATT 0.795134 -282 TAAATTACTTTTTTATAATTGAATGCATAAAAGTTTCT 22 157 0 TTTATATATT 0.556892 -144 TCAGATATACTTGTTTAATATGAAAAATTGATACCAAG 23 37 1 TTTTTATAAT 0.548785 -139 AATATCAATATTATTTATTCACATAATATGCAGTT 25 8 0 TTTTTATATA 0.698388 -179 GTAAGATATATTATTTAATGTTATTGCATTCTAACTGG 26 162 0 TTTTTATATA 0.698388 -29 ** **** * ** * Masking position 4 Map Score: 20.1662 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 147 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CTAGATAATCAACTTTTATCTTTAAAATTCTTGTAT 1 143 1 AATTTATTAA 0.501201 -107 TTTGAGTTGGAATTTTTTAGTTTAAATGTCTATTAA 2 149 1 AATTTTTTAA 0.808493 -152 AATGTCTATTAATTGTTTTTTTTATAAATGAGATAT 2 173 1 AATTTTTTAA 0.808493 -128 TAATGCCATCAACAATTTTTTGTAAATA 2 283 1 AAATTTTTAA 0.934459 -18 GTGATATATAATAACTTTAGTTAATACAAGTATAAC 3 60 1 ATATTTTAAA 0.509294 -241 TTTGAATTTTGATAATTTTATTTATATTGATCAAAC 3 259 0 GAATTTTTAA 0.512707 -42 CATTTCATTAAAGTTTTTCTTGTATAAAGTTATAAA 5 19 1 AATTTTTTAA 0.808493 -80 TGCACAAGCTAATAATTTTATGTATATGTATACAAT 6 27 1 AAATTTTTAA 0.934458 -46 AGTTTATAGTAATAATTTGATATTAAACCAT 11 6 0 AAATTTTTTA 0.41517 -102 GTAACACCGTATATTTTTAGTTTATAGTAATAATTT 11 24 0 ATTTTTTTAA 0.603095 -84 TTGTTACAACATAACTTTGCTAAATAGTCCAGTGAA 14 48 0 ATATTTTAAA 0.509294 -59 ATATTTAATGAAAAAATTTTTTTAAATCAGGACTCC 15 83 1 AAAATTTTAA 0.41517 -218 TATTAAAATAATTATATTAATAAAAATGGTAT 17 7 1 AAATTATAAA 0.406997 -68 TACTCATTATAAAATTATGTTATAAATACCATTTTT 17 32 0 AAATATTTAA 0.41517 -43 TTTTTCTATAAACAGTTTTCTCTACAGACACTTTAT 18 255 0 AAATTTTTAA 0.934459 -46 ATTTTTGAAGATAATTTTTGTAGAAAAATATATTCA 19 76 0 ATATTTTGAA 0.462493 -225 CTAAAGTTGTAATATTTTTGTATAAGGTATATTTAA 19 154 0 AAATTTTTAG 0.512707 -147 CTTGAAATTTATTAGTTTAGTATAAATTATGTATTT 19 221 1 ATATTTTTAA 0.83691 -80 TATATTGCAAATTATTTTCCTAGATACTCTAATCAA 20 27 1 ATATTTTGAA 0.462493 -88 TCTCCTGATCAAGAATTACATTTAAAACT 21 4 0 AAATTATTAA 0.772388 -297 TATTACAGGAAAAAATTAAATGTAGAATCAATCAAA 21 76 0 AAATTATTAA 0.772388 -225 TTTTTCCTGTAATATTTTATTGTATATTGTTTCTTT 21 98 1 AAATTTTTAA 0.934459 -203 TGATAATATCATTATTTAAATCTATATTTATTGTAG 21 145 1 ATATTATTAA 0.549827 -156 ATTATTAGCAAATACTTTACTTTAAAATCTACAATA 21 173 0 AAATTTTTAA 0.934459 -128 AAATAATAGTAAATATTTTTTTTAAAGATATGATTA 21 246 1 AATTTTTTAA 0.808493 -55 TTGAATGCATAAAAGTTTCTTTAATATCTTTAACCT 22 141 0 AAATTTTAAA 0.742509 -160 ATTTAAAATTAACAATTTCATTTACAAAGATATGGA 25 43 1 AAATTTTTAA 0.934459 -144 ** * *** * ** * Masking position 11 Map Score: 26.7455 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 294 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TCTTGAAAAATATTAAGATATATTATATAATTTATAAGATT 1 29 0 TTAAGTAATT 0.523479 -221 TCTAGTACTAATTTAAAAGCTACTAGTTCATAAACATATTG 2 84 1 ATAAATAATT 0.694795 -217 AATTTTTTAGTTTAAATGTCTATTAATTGTTTTTTTTATAA 2 159 1 TTAATTAATT 0.618463 -142 AAATCTCATTAAGTAATATTTAATAATTACTCTATTAAGTA 3 189 0 AGAATTAATT 0.566506 -112 ACTTAATGAGATTTAATTTTAAGTTGATTATAATACTTGCA 3 216 1 ATAATAATTT 0.658608 -85 TAACGTGCAAAATTAATCTGTTTAAACTTATAAGAGAAACA 5 67 1 ATAATTTATT 0.841268 -32 TACTTCATCTTTAGAACCTTTTAAATTCTCAT 7 2 1 ATCATTAATT 0.792055 -299 ACATAATTCAATCTTAATCTTTTACTTATAATATAC 7 275 0 ATAATAATTT 0.64206 -26 TACATCAACTACTAAAGAATTACCATCTTTTAATTCAGA 8 9 0 ATAAGTAATT 0.920377 -292 AACTTCAATTACATTTTTTCATTATTCTTTATTATAAA 10 8 1 ATCATTTTTT 0.349383 -73 TATAAGAAGTAATTAAGTCGTAGGAGTTCGTGTAATTTAAA 12 73 1 ATAAGTAATT 0.920388 -180 TAAATAGTCCAGTGAATCAATACAATATTGTTGATCCTGTA 14 23 0 ATAATTAATT 0.944623 -84 GAACATATTAAATAGTTAATAGCTTATAAAGTATAAT 15 7 1 ATAATTAATT 0.944618 -294 CAGTTTAGATATTTAATGAAAAAATTTTTTTAAATCAGGAC 15 75 1 ATAATAATTT 0.658541 -226 TAATTAACTCACTTAATTTATAAATCATGTTAATATAATAT 18 17 0 ATAATTATTT 0.885612 -284 AAATTAAGTGAGTTAATTAATATGAGCTTGTATGATAATCA 18 39 1 ATAATTAATT 0.944625 -262 TTTATAATAAATTAAATATAATGGTAATGTTATTGCTATAA 18 112 1 ATAATATTTT 0.374752 -189 TTTTCCTGCTAATAAATTTATTGCTGCTTTTTAAAATTAAC 18 182 0 ATAATTTTTT 0.706346 -119 TAATAAGTTAAATTAAAAGTTAATATTTGTTATTTTTGCTT 19 14 0 ATAAATAATT 0.694602 -287 TGCAATGCACAATCAAGAACTTTCTAATGCTAAAGTTGTAA 19 178 0 ATAAGTTTTT 0.619791 -123 TTGAATAACCACTTAATTATTAGCAAATACTTTACTTTAAA 21 183 0 ATAATTAATT 0.944618 -118 AATTTTAAAAACTAAAGCATAATCATATCTTTAAAAAAAAT 21 260 0 ATAAGAAATT 0.742097 -41 TCAAGTAAAGAATCAAGGACTAAAAATTTCTATGATTGATT 22 100 1 ATAAGTAATT 0.920388 -201 CTTTTTTATAATTGAATGCATAAAAGTTTCTTTAATATCTT 22 147 0 ATAATTAATT 0.944623 -154 TATGGAGATAATTACAGAACTTATATTTCATTATTAATATT 25 73 1 ATCAGTTATT 0.445019 -114 CATTATTAATATTTAATGAGTATTAGATAATGAATTAGATG 25 101 1 ATAATTAATT 0.944625 -86 * * *** ** * * * Masking position 18 Map Score: 18.9934 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 276 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTAAAGATCTAGTAAGTAAAACTATCACAAG 2 43 0 ATAAGTAAAA 0.957121 -258 TAATTACTCTATTAAGTAATACTATTCCGAT 3 176 0 ATAAGTAATA 0.951529 -125 ATTAAATCTCATTAAGTAATATTTAATAATT 3 202 0 ATAAGTAATA 0.951529 -99 TATTGTATATTATAAGTAAAAGATTAAGATT 7 271 1 TTAAGTAAAA 0.671385 -30 ATTAAGTAAAATTGATACACC 9 1 1 ATAAGTAAAA 0.957111 -130 CTCCTATTTTAGTGAGTAATATCTCCATTCT 9 104 0 ATGAGTAATA 0.892497 -27 TGGTTCTCACACTAAGTAATACAACCGTAAA 16 14 0 ATAAGTAATA 0.95154 -51 ATAATTTTATAATGAGTAAAATAAAAAGGTA 17 50 1 ATGAGTAAAA 0.904192 -25 ATGAATTTGTAATAAGTTAAATTAAAAGTTA 19 33 0 ATAAGTTAAA 0.671149 -268 ATCTGAGAAGAATAAGCAAAAGGCTTAGATA 21 45 0 ATAAGCAAAA 0.751777 -256 TGGTTATTCAAGTAAGTATATCATGCAATAA 21 213 1 ATAAGTATAT 0.402041 -88 AATAAGTAAATAATGAAAAGT 23 165 0 ATAAGTAAAT 0.794742 -11 ATATTATGTGAATAAATAATATTGATATTTA 25 17 1 ATAAATAATA 0.678211 -170 ATTAATATTTAATGAGTATTAGATAATGAAT 25 105 1 ATGAGTATTA 0.590309 -82 ATGCAATAACATTAAATAATATATCTTACC 26 171 1 ATAAATAATA 0.67821 -20 * ********* Masking position 5 Map Score: 8.98866 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 68 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TTGTAAAAATCTTATAAATTATATAATATA 1 22 1 CTTATAAATT 0.768371 -228 GACATTTAAACTAAAAAATTCCAACTCAAA 2 149 0 CTAAAAAATT 0.68287 -152 AATTTATTGACTAATAATTTTCAAACAAAA 2 232 1 CTAATAATTT 0.930261 -69 TAGTAGTGCGATTATAAATTTTGTTCATAT 3 101 1 ATTATAAATT 0.462351 -200 TTTGCACAAGCTAATAATTTTATGTATATG 6 25 1 CTAATAATTT 0.930261 -48 TTAGTTTATAGTAATAATTTGATATTAAAC 11 14 0 GTAATAATTT 0.609034 -94 ATGAAGCAATCTAATAAATTTTATTATTTC 13 65 0 CTAATAAATT 0.930261 -77 TTGTTTTAGTTTAATAATTTTCCTATTATT 13 118 0 TTAATAATTT 0.512442 -24 CATATACTTTATAATAAATTAAATATAATG 18 105 1 ATAATAAATT 0.775683 -196 TATTTTCCTGCTAATAAATTTATTGCTGCT 18 195 0 CTAATAAATT 0.930261 -106 TTATACTAAACTAATAAATTTCAAGAGTGC 19 216 0 CTAATAAATT 0.930261 -85 AAACCAAATTATAATAATTTCTAGAATA 19 283 1 ATAATAATTT 0.775682 -18 CTCTAATCAAATTATAATTTAAAAAGTTCT 20 53 1 ATTATAATTT 0.462351 -62 AAAGTATTTGCTAATAATTAAGTGGTTATT 21 191 1 CTAATAATTA 0.533009 -110 GAATCAAGGACTAAAAATTTCTATGATTGA 22 109 1 CTAAAAATTT 0.68287 -192 AATTTTAGTTCTAATATATTAACTTTTT 25 169 1 CTAATATATT 0.533008 -18 ********** Masking position 6 Map Score: 12.5095 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 99 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TATAATTTATAAGATTTTTACAAGGTAATTTTA 1 12 0 AAATTTACAA 0.689659 -238 CCAAGGTATAATGAATATGGCAATTTCTAAACT 1 84 0 ATATATGCAA 0.607283 -166 TCTAGTAAGTAAAACTATCACAAGAAAAAACAT 2 34 0 AAATATACAA 0.957589 -267 GTGTAAATACTGTAACAAGCTCTATCAA 3 6 1 AAATGTACAA 0.858386 -295 CAATATAAATAAAATTATCAAAATTCAAAATAT 3 266 1 AAATATAAAA 0.789813 -35 ATTTATTTGCATGATTATAACAAATATCAGACA 7 165 0 ATATATACAA 0.913798 -136 TTAGTGATACAAGAGTATTAAAATTTATGAATG 8 101 1 AAATATAAAA 0.789813 -200 GGTAATAGTTAAAAGTATTACAAATGTTAGTGT 8 172 1 AAATATACAA 0.957589 -129 TGTCTCTAGTATGAGTAACACAATTTAGCAATC 13 28 1 ATATAAACAA 0.475629 -114 ATTTTATCTCAACATTGTTACAACATAACTTTG 14 65 0 AAATGTACAA 0.858386 -42 CTATTAGTCAAAAATTATTTAAACTAATTGTAT 15 231 0 AAATATTAAA 0.394731 -70 TTGTATGATAATCAATATATCAAGTATAGACAA 18 66 1 ATATATTCAA 0.647861 -235 GTATATTTAAAAGAAAATAACAATTTTTCTTTT 19 131 0 AAAAATACAA 0.658931 -170 TACCTTATACAAAAATATTACAACTTTAGCATT 19 161 1 AAATATACAA 0.957589 -140 AAGATTATGTATGATTATGACAAGATGTGTTGT 22 247 0 ATATATACAA 0.913798 -54 TCGTGTTAAGAATATTATTATAAAGATTATGTA 22 269 0 AAATATATAA 0.597937 -32 ** * *** **** Masking position 4 Map Score: 9.17151 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 122 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 TCTAAACTACAAAACAACACCATCTTGAAAAA 1 60 0 AAAACAACCA 0.605699 -190 GATACAGTGTAAAGCTAGATAATCAACTTTTA 1 129 1 AAAGCAATAA 0.919198 -121 ATCACAGTATAAAGCAACTTAAAATACAAGAA 1 170 0 AAAGCATTAA 0.493255 -80 CTACATGGGCAATGCCTTACAAAACAAAGGAT 1 224 1 AATGCTACAA 0.577787 -26 ATGCATTATCAATGCTAGAAAAATTGATGAGA 7 37 0 AATGCAAAAA 0.643303 -264 TCAACACATTATAGCAATATCATGCATTATCA 7 58 0 ATAGCAATCA 0.795986 -243 AATTCCTAATAAAGCAATACAATTAGAATAAG 9 60 0 AAAGCAACAA 0.94018 -71 AATTTATTAGATTGCTTCATCAAAACTAATGG 13 75 1 ATTGCTATCA 0.253573 -67 CAGAATTTTAAAAGCGAAATAAACAAAACTTT 15 177 1 AAAGCAATAA 0.919198 -124 GTCTAGTTTTATAGCAATAACATTACCATTAT 18 129 0 ATAGCAAACA 0.638555 -172 AGAAAAACCAAAAACAATATAAATAAT 18 284 1 AAAACAATAA 0.531623 -17 TTTAAAAACTAAAGCATAATCATATCTTTAAA 21 266 0 AAAGCTATCA 0.734836 -35 AAGTGGTAATATAGCAAAACAAATTTGTTCTC 22 70 1 ATAGCAACAA 0.846221 -231 TCTCTAAACCAAAGCGAAACAACACATCTTGT 22 229 1 AAAGCAACAA 0.94018 -72 ATCAAAAGGCAAAGCTAGACAATTTTAGTTCT 25 149 1 AAAGCAACAA 0.94018 -38 CTCCAGTTAGAATGCAATAACATTAAATAATA 26 160 1 AATGCAAACA 0.638555 -31 ***** * **** Masking position 1 Map Score: 6.98368 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 197 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 ATACAGTGTAAAGCTAGATAATCAACTTTTA 1 130 1 AAGCAGATAA 0.751504 -120 TCTCATTTATAAAAAAAACAATTAATAGACA 2 175 0 AAAAAAACAA 0.613357 -126 TTAAACTTATAAGAGAAACAA 5 88 1 AAGAAAACAA 0.911482 -11 ATTCCTAATAAAGCAATACAATTAGAATAAG 9 60 0 AAGCATACAA 0.926958 -71 ATTAAAGTGCAAGAAAAATAA 12 242 1 AAGAAAATAA 0.694479 -11 TAGTCCAGTGAATCAATACAATATTGTTGAT 14 29 0 AATCATACAA 0.525785 -78 AGAATTTTAAAAGCGAAATAAACAAAACTTT 15 178 1 AAGCAAATAA 0.860859 -123 TTCTCACACTAAGTAATACAACCGTAAAAAA 16 11 0 AAGTATACAA 0.586291 -54 TGAATATGGTAAAAGAAACAATATACAATAA 21 114 0 AAAAAAACAA 0.613357 -187 AGTGGTAATATAGCAAAACAAATTTGTTCTC 22 71 1 TAGCAAACAA 0.764498 -230 CTCTAAACCAAAGCGAAACAACACATCTTGT 22 230 1 AAGCAAACAA 0.965549 -71 TCAAAAGGCAAAGCTAGACAATTTTAGTTCT 25 150 1 AAGCAGACAA 0.931971 -37 **** ****** Masking position 6 Map Score: 3.17732 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 91 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TCTTGAAAAATATTAAGATATATTATATAATT 1 38 0 TATTAAATAA 0.934348 -212 TAAGTAATACTATTCCGATATATCTTCTCATC 3 163 0 TATTCCATAA 0.772379 -138 AATTATAAAAATATAACGGAATCTG 4 77 0 TATAAAATAA 0.711723 -15 TCTTTCATTGTATACATATACATAAAATTATT 6 37 0 TATACAATAA 0.669833 -36 GATACAAGAGTATTAAAATTTATGAATGCCAT 8 106 1 TATTAAATTA 0.711844 -195 AATATCAAATTATTACTATAAACTAAAAATAT 11 18 1 TATTACATAA 0.805129 -90 ATAGGAAAATTATTAAACTAAAACAATTTT 13 122 1 TATTAACTAA 0.658849 -20 ATACCATTTTTATTAATATAATTATTTTAATA 17 11 0 TATTAAATAT 0.792846 -64 TAGAAAAATATATTCAAATATTGAACACATGA 19 60 0 TATTCAATAT 0.758657 -241 GTGTTAAGAATATTATTATAAAGATTATGTAT 22 268 0 TATTATATAA 0.602344 -33 AGGTTTATAATATTCAGATATACTTGTTTAAT 23 24 1 TATTCAATAA 0.921194 -152 ACTGGTAATGTATTAATATACACTCTACTCCT 23 86 1 TATTAAATAA 0.934356 -90 CAATATTATTTATTCACATAATATGCAGTT 25 9 0 TATTCAATAT 0.758657 -178 TATATTTCATTATTAATATTTAATGAGTATTA 25 94 1 TATTAAATTA 0.711844 -93 TGATGTCCAGTATTAAAATACACTGAATT 26 8 0 TATTAAATAA 0.934357 -183 ****** *** * Masking position 2 Map Score: 8.04947 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 47 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 TAACATTTTCTAAAATTATGTTATGTTTTT 2 12 1 TAAAATTATG 0.780722 -289 AATTCCAACTCAAAAATATGTTTTCACTTT 2 133 0 CAAAAATATG 0.656149 -168 CAGACAGCATAAAATATATGTATCAATTAA 7 141 0 AAAATATATG 0.511032 -160 CCTTTAATGATAAAGTTATGTAGAAGATTT 8 72 1 TAAAGTTATG 0.917177 -229 CAAGAGTATTAAAATTTATGAATGCCATAA 8 110 1 AAAATTTATG 0.732679 -191 ATGTGGATTAAATAGTTATGGCAAGAGTAT 10 50 0 AATAGTTATG 0.50339 -31 GACTATTTAGCAAAGTTATGTTGTAACAAT 14 55 1 CAAAGTTATG 0.94486 -52 CTCCAGATTTAAAATTTATGCTAAGAAATA 15 115 1 AAAATTTATG 0.732679 -186 ATTTCGCTTTTAAAATTCTGACTTTTGCTA 15 167 0 TAAAATTCTG 0.621692 -134 ATAGAAAAAACAAAGTTTTGTTTATTTCGC 15 190 0 CAAAGTTTTG 0.660073 -111 TTACTCATTATAAAATTATGTTATAAATAC 17 39 0 TAAAATTATG 0.780722 -36 TTATAATTTAAAAAGTTCTGAGTATATTCT 20 64 1 AAAAGTTCTG 0.835992 -51 ATATTTTTTTTAAAGATATGATTATGCTTT 21 258 1 TAAAGATATG 0.808457 -43 ATTTCATTTACAAAGATATGGAGATAATTA 25 57 1 CAAAGATATG 0.869554 -130 AACCTCGTATCAAAGTTCTGATATTGCCGT 26 88 0 CAAAGTTCTG 0.890109 -103 ********** Masking position 4 Map Score: 8.21014 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 83 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 13 AAGCTAGATAATCAACTTTTATCTTTAAAAT 1 140 1 ATCAACTTTA 0.661747 -110 TTATAATGCCATCAACAATTTTTTGTAAATA 2 280 1 ATCAACATTT 0.761152 -21 AACAAGCTCTATCAAGCTTTATTACATAAAA 3 24 1 ATCAAGTTTA 0.81514 -277 TTATAGCAATATCATGCATTATCAATGCTAG 7 51 0 ATCATGATTA 0.690597 -250 TATATTTTACATCAACTACTAAAGAATTACC 8 26 0 ATCAACACTA 0.884056 -275 ATAGAGCATTTTCAAGAATTATATCGTTAAT 8 245 1 TTCAAGATTA 0.690597 -56 TATGATTTCCATCAAGCACTTTAATTAAATT 15 276 1 ATCAAGACTT 0.886128 -25 GCAATGCACAATCAAGAACTTTCTAATGCTA 19 187 0 ATCAAGACTT 0.886128 -114 TCTTCTCCTGATCAAGAATTACATTTAAAAC 21 12 0 ATCAAGATTA 0.940698 -289 CAAGTAAAGAATCAAGGACTAAAAATTTCTA 22 101 1 ATCAAGACTA 0.945012 -200 ****** **** Masking position 4 Map Score: 2.80693 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 GTATAATGAATATGGCAATTTCTAAACTAC 1 82 0 TATGGCAATT 0.858889 -168 CTCAACACATTATAGCAATATCATGCATTA 7 61 0 TATAGCAATA 0.820236 -240 ATATTTGAGTTATGGCATTCATAAATTTTA 8 119 0 TATGGCATTC 0.83439 -182 TTGCGGTAGATAGAGCATTTTCAAGAATTA 8 236 1 TAGAGCATTT 0.626076 -65 TACACCATAGTTTGGCAATTATATCCATTT 9 26 1 TTTGGCAATT 0.760084 -105 GCCACACACGTATAGCAATTAATAAAATTA 11 81 1 TATAGCAATT 0.906542 -27 AATAAAACATTATAGCATTTTTTCTGGATT 12 116 1 TATAGCATTT 0.906993 -137 AGTAACACAATTTAGCAATCTCATGAAATA 13 41 1 TTTAGCAATC 0.80666 -101 GGTCTAGTTTTATAGCAATAACATTACCAT 18 132 0 TATAGCAATA 0.820236 -169 ATATTACAACTTTAGCATTAGAAAGTTCTT 19 175 1 TTTAGCATTA 0.726283 -126 GGTTTAGAGATTTAGCATTTGTACAGCATG 22 209 0 TTTAGCATTT 0.834944 -92 TATTTAATGTTATTGCATTCTAACTGGAGT 26 159 0 TATTGCATTC 0.558813 -32 ********** Masking position 7 Map Score: 6.01269 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 159 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 15 TTTGCATGATTATAACAAATATCAGACAGC 7 163 0 TATAACAAAT 0.769464 -138 TAGTTAAAAGTATTACAAATGTTAGTGTTT 8 177 1 TATTACAAAT 0.949038 -124 CATTATTCTTTATTATAAATATACTCTTGC 10 30 1 TATTATAAAT 0.675291 -51 TAATTTGATATTTTACAAATAAATAAATTT 12 190 1 TTTTACAAAT 0.769344 -63 TAATTTAACTTATTACAAATTCATGTGTTC 19 40 1 TATTACAAAT 0.949038 -261 TATACAAAAATATTACAACTTTAGCATTAG 19 166 1 TATTACAACT 0.831844 -135 CAACAGTATATATTGCAAATTATTTTCCTA 20 19 1 TATTGCAAAT 0.831796 -96 TAAGAACTGTCATTACAAATATCAGTAAGA 26 54 1 CATTACAAAT 0.83184 -137 ********** Masking position 7 Map Score: 2.09589 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 32 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678