AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_rpxx_reg_300.orf -o00240_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: RP655 24 30S RIBOSOMAL PROTEIN S19 (rpsS) Input sequences: #1 RP053 300 ADP,ATP CARRIER PROTEIN (tlc1) #2 RP054 72 GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT) #3 RP055 162 NUCLEOSIDE DIPHOSPHATE KINASE (ndk) #4 RP069 266 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (dcd) #5 RP140 300 DNA-DIRECTED RNA POLYMERASE BETA CHAIN (rpoB) #6 RP141 156 DNA-DIRECTED RNA POLYMERASE BETA PRIME CHAIN (rpoC) #7 RP171 300 DNA-BINDING PROTEIN HU (hupA) #8 RP172 110 DNA POLYMERASE III, DELTA SUBUNIT (holB) #9 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #10 RP379 300 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE (kdsB) #11 RP396 140 unknown #12 RP397 187 THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA (tlpA) #13 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #14 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #15 RP443 300 unknown #16 RP444 57 unknown #17 RP445 120 THIOREDOXIN REDUCTASE (trxB1) #18 RP501 215 TRNA PSEUDOURIDINE 55 SYNTHASE (truB) #19 RP503 21 30S RIBOSOMAL PROTEIN S15 (rpsO) #20 RP504 154 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (pnp) #21 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #22 RP513_RP514 600 RP513: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA), RP514: THIOREDOXIN REDUCTASE (trxB2) #23 RP522 300 CYTIDYLATE KINASE (cmk) #24 RP636 23 30S RIBOSOMAL PROTEIN S11 (rpsK) #25 RP637 57 30S RIBOSOMAL PROTEIN S13 (rpsM) #26 RP641 24 50S RIBOSOMAL PROTEIN L30 (rpmD) #27 RP649 60 50S RIBOSOMAL PROTEIN L14 (rplN) #28 RP658 241 50S RIBOSOMAL PROTEIN L4 (rplD) #29 RP660 93 30S RIBOSOMAL PROTEIN S10 (rpsJ) #30 RP661 300 ELONGATION FACTOR TU (tuf) #31 RP684 300 THYMIDYLATE KINASE (tmk) #32 RP730 300 unknown #33 RP774 93 unknown #34 RP775 191 CELL DIVISION PROTEIN FTSY (ftsY) #35 RP776 153 DNA POLYMERASE I (polA) #36 RP778 127 DNA POLYMERASE III, ALPHA CHAIN (dnaE) #37 RP779 245 UDP-GLUCOSE 6-DEHYDROGENASE (udg) #38 RP857 72 PSEUDOURIDYLATE SYNTHASE I (truA) #39 RP860 270 unknown #40 RP864 66 unknown #41 RP865 149 DNA POLYMERASE III SUBUNITS GAMMA AND TAU (dnaX) Motif number 1 AAATAAATAGAAAATTTAATT 1 290 1 AAAATTTAAT 0.896245 -11 AATTTGTAAAAAAATATAAAAAAGCTTCTA 2 11 1 AAAATATAAA 0.877254 -62 TCTCTGTGTTAAAATTTATATCTTGAGCCT 3 13 1 AAAATTTATA 0.725366 -150 TTTTGTATAGTAAATTTATTATTTAAATAA 4 26 0 TAAATTTATT 0.639308 -241 CAACTACGCTAAAATATAATATACTTTGCA 4 82 1 AAAATATAAT 0.90466 -185 TTTACTGTTTAAAATATAATAATTTAAATT 5 67 1 AAAATATAAT 0.90466 -234 GGTTCTATATAAAATTTAAATTATTATATT 5 79 0 AAAATTTAAA 0.866777 -222 TACAAAGTTTAAAATATATATGTTATTATA 7 132 0 AAAATATATA 0.743685 -169 AACTCATATCAAAATATATTGATGTATATT 7 203 1 AAAATATATT 0.793812 -98 ATGTTTTTATAAAAAATAAATACCAACTTC 7 238 0 AAAAAATAAA 0.896129 -63 TTTTATTTAAAAAAATTATAGAAAAAGTTT 9 18 1 AAAAATTATA 0.761237 -72 ATTTAAAATTAAAAAATAATTGTTGACAGA 10 270 0 AAAAAATAAT 0.919707 -31 CAAATGAGAATAAAAATAATTTGATTAATA 11 68 1 TAAAAATAAT 0.852723 -73 ATTTGATTAATAAAAATAATTGATTTAAAT 11 86 1 TAAAAATAAT 0.852723 -55 GTTCTAAATCTAAATTTAAATCAATTATTT 11 99 0 TAAATTTAAA 0.766831 -42 ATACCACAACTAAATATAAATACTAATATG 12 129 1 TAAATATAAA 0.783202 -59 TACTAATATGAAAAAATAATAAAATGCCTT 12 149 1 AAAAAATAAT 0.919707 -39 TTCATTATAGTAAATTTAAAGAAATTTGCT 13 251 1 TAAATTTAAA 0.766831 -50 ATCTAAAAACAAAAAATAATT 14 96 1 AAAAAATAAT 0.919707 -11 AATTAAATGAAAAAATTAAATCTAAAGATT 15 93 0 AAAAATTAAA 0.887056 -208 TTCATTAGACAAAAATTAATTTCAAATCAA 15 204 0 AAAAATTAAT 0.912492 -97 TTTAGTGAAAAAAAAATAAAACCTCATATA 15 253 1 AAAAAATAAA 0.896129 -48 GTAATGAGCTAAATATAATTAATTATAAT 15 282 0 TAAATATAAT 0.827479 -19 ATGATTTCTAAAAATTTATTCTAAATTGGT 16 24 1 AAAATTTATT 0.777994 -34 ACATAATCCAAAAATTTAAAAAGACTAAAA 17 31 0 AAAATTTAAA 0.866777 -90 TAATTTAATTTAAAATTATTAAGTTATTGT 17 87 0 TAAAATTATT 0.681485 -34 TAGCCAATTTTAAAATTAAACGAGTATATC 18 77 0 TAAAATTAAA 0.798792 -139 ATTACATGCAAAAAATTATTCTATAATTTC 21 95 1 AAAAATTATT 0.808796 -70 TTATTGTTGAAAAAAATAATACAAAAGAAC 22 308 0 AAAAAATAAT 0.919707 -293 AAAATCTAAAAAAAAATAAAATATTTATAT 22 471 1 AAAAAATAAA 0.896129 -130 TTATATAATCAAAAATTAATTATTTGCAGT 23 215 0 AAAAATTAAT 0.912492 -86 AATTCTGTATTAAATATAAATAATTATTAT 23 252 1 TAAATATAAA 0.783202 -49 ACCTATTATTAAAAAATAATAGGTATTTGT 29 25 1 AAAAAATAAT 0.919707 -69 TGGACACTATTAAATATATAACAGTGCTAT 30 123 0 TAAATATATA 0.594637 -178 TTTTTTTTGCTAAATTTATTTGTTACCACT 30 234 0 TAAATTTATT 0.639308 -67 TATTACAGGAAAAAATTAAATGTAGAATCA 31 82 0 AAAAATTAAA 0.887056 -219 TCATGCAATAAAAAAATAATAGTAAATATT 31 233 1 AAAAAATAAT 0.919707 -68 ATATCTTTAAAAAAAATATTTACTATTATT 31 247 0 AAAAAATATT 0.82292 -54 AAAATCTAGATAAAATTAAATTT 33 81 1 TAAAATTAAA 0.798792 -13 TTAGGTGCATAAAAAATATTTAGTATTTTT 34 53 0 AAAAAATATT 0.82292 -139 TTTAAAATTAATTTAATAAGTA 36 116 0 TAAAATTAAT 0.840533 -12 GTATAATTTAAAAATTTAATATAAAAATCA 37 217 1 AAAATTTAAT 0.896245 -29 ********** Masking position 4 Map Score: 45.4299 Number of sites scoring better than the average of aligned sites = 1014 Number in coding regions = 653 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 2 AACAGTTAATATATAGAAATCAAAATTAAGTAAAA 1 145 1 ATAAAAAAAA 0.86741 -156 TTTATTATATATAAAGGTTATAAAA 3 148 1 ATAGTTAAAA 0.690035 -15 TATACTTAAAATTAAGAATTTAATAGTTTCTTATT 4 120 0 ATAAATAATA 0.925762 -147 AAATTTTTCTTTAAAAAATCTAAAACTACTTCCAT 4 182 0 TTAAATAAAA 0.816668 -85 ACGCATAATTATTTACAATACAAAATTTTTCTTTA 4 204 0 ATAAATAAAA 0.935402 -63 ATTTGTCTTGTTGTATAATTTAAAAATTGTTATTG 6 32 1 TTAAATAAAA 0.802809 -125 GGCTACATTTTTCTATAAATTAATATAATAACATA 7 109 1 TTAAAAAATA 0.633237 -192 ATACTAACATATATATGATCTAAAATAAACTTTTT 9 39 0 ATAGATAAAA 0.81483 -51 AACTGCCTATATTTAAAATTAAAAAATAATTGTTG 10 275 0 ATAAATAAAA 0.934513 -26 CCACAACTAAATATAAATACTAATATGAAAAAATA 12 132 1 ATAATAAATA 0.73983 -56 TAACATTTTAATTGATATATAAATAAGTATCCTAA 13 101 0 ATAATAAATA 0.73983 -200 ACTATAATGAATTGAGGATAAAATATAGACTATTA 13 227 0 ATAGATAATA 0.790838 -74 AATGTTTTACATATTAAAAATTTGTATTA 13 282 0 TTAATAAAAA 0.485496 -19 TTGAGATAAAATCTAAAAACAAAAAATAATT 14 86 1 ATAAAAAAAA 0.86741 -21 TATTTTAGATATCTATAATAGAAAATAAACCTAAT 15 151 0 ATAAATAAAA 0.93554 -150 TTAATTTCAAATCAAAATTTGAAAATCTTATATTA 15 184 0 ATAATTAAAA 0.880129 -117 ACCATATAACATACATAATCCAAAAATTTAAAAAG 17 38 0 ATAAATAAAA 0.935541 -83 TTTAAATTAAATTAATAAACAAATAATT 17 103 1 ATAAAAAATA 0.848967 -18 GAATATATGATATAAAATGCAAAATTGATAGACA 18 192 0 ATAAATAAAA 0.93554 -24 TGATCTCATTATATATATTGCAATATGAGATTAAG 20 69 1 ATAATTAATA 0.863176 -86 ACTGAATGATATCTTTAATAGAATATAAATTATGA 20 116 1 ATTAATAATA 0.435695 -39 TAAAAAACCTTTAAACAATGTAATATTAGTAATAA 21 137 1 TTAAATAATA 0.792977 -28 TTTGATCTTTATTTAAATTAAAATAT 22 2 0 ATAATTAATA 0.863162 -599 GAATTAGAAAATGCATGTTTCAAAAACTATAATAT 22 109 0 ATAGTTAAAA 0.690035 -492 CGCATTATTGTTGAAAAAAATAATACAAAAGAACC 22 307 0 TTAAAAAATA 0.633237 -294 CAAGTCAAAAATCTAAAAAAAAATAAAATATTTAT 22 464 1 ATAAAAAATA 0.848967 -137 ACCTTTCTGCATCAAGATTAAAATAAGCTTTTTAA 23 76 0 ATAATTAATA 0.863176 -225 ATTAAGCCTATTATATAATCAAAAATTAATTATTT 23 220 0 TTAAATAAAA 0.815886 -81 TGTTATTCAGATTTAGGATTTAAAATTAACAAAGC 28 154 1 ATAGATAAAA 0.814667 -88 TTTTTCAGATATTAAAATACAAATACCTATTATTT 29 38 0 ATAATAAATA 0.73983 -56 CTATATCATTTTTCAGATTATAAAAAATAACATAT 30 92 0 TTAATTAAAA 0.670376 -209 AAAAGAAACAATATACAATAAAATATTACAGGAAA 31 100 0 ATAAATAATA 0.925763 -201 TCTACAATAAATATAGATTTAAATAATGATATTAT 31 147 0 ATAATTAATA 0.863176 -154 AATGTTTAGAATGCTCAATTAAAAACTTAATT 32 279 1 ATTAATAAAA 0.473294 -22 TAACACCAACATACATAAAACAAAAACTAGCTAAT 34 167 1 ATAAAAAAAA 0.86741 -25 AGAACCAAAGATCCATAATATAAAAAGCTGAAGCT 37 122 0 ATAAATAAAA 0.93554 -124 TAACGTATAATTTAAAAATTTAATATAAAAATCAC 37 213 1 TTAAATAATA 0.792867 -33 TTATTATGAGATCCATGTAAAAATACAAATTTGAG 39 203 0 ATAGTAAATA 0.462996 -68 TTTAAACATAATTTAAAATACAAAACAATAAAA 40 44 1 ATAAATAAAA 0.935402 -23 ** * *** **** Masking position 12 Map Score: 42.2613 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 364 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 CCTATAGTTAATAAAATGTTTATTGAGTTCTTTC 1 199 1 AAAATTTTAT 0.918345 -102 CTTTATATATAATAAATTATTAGATTTACTGCAT 3 130 0 AAAATATTAA 0.894726 -33 GATAAAGTAAAACATATTTTTGAATATATTCAAT 10 221 0 AATATTTTGA 0.621342 -80 ATTTAAAATTAAAAAATAATTGTTGACAGATTAG 10 266 0 AAAATATTGT 0.585599 -35 TATTCATATCATGAAATCTTTAGATTTAATTTTT 15 79 1 AAAATTTTAA 0.948817 -222 ATTATTGACAAGGATATAATTATTATATGGAATT 15 119 0 AATATATTAT 0.632283 -182 CTAATGAAATAAAAAATCTTTATAAAATTTAGTG 15 226 1 AAAATTTTAA 0.948817 -75 ACCAATTTAGAATAAATTTTTAGAAATCATTGTC 16 20 0 AAAATTTTAA 0.947619 -38 ATAATTTTAAATTAAATTAATAAACAAATAATT 17 98 1 AAAATAATAA 0.516762 -23 ACTTAAATGTAGAAAATCTTTAATATATAATTCT 18 39 0 AAAATTTTAT 0.918345 -177 TGATTACTGAATGATATCTTTAATAGAATATAAA 20 111 1 AATATTTTAT 0.789459 -44 TTAAATAAAGATCAAATTTATAAAAAATGAAGAG 22 21 1 AAAATTATAA 0.699881 -580 TTCAAAAACTATAATATCATTACAAAAAACTCTT 22 92 0 AATATATTAA 0.735808 -509 TCAATATGAAATCAAATATTTATATTGTAATTCA 22 166 0 AAAATTTTAA 0.919739 -435 CTAAAAAAAAATAAAATATTTATATTGAATAAAT 22 476 1 AAAATTTTAA 0.947428 -125 ATTTATATTGAATAAATTATTATTCTCGTGTCTA 22 493 1 AAAATATTAT 0.83894 -108 TGATGTTGTTACAAAATGTTTACTGCGCAAGTTA 23 116 1 AAAATTTTAT 0.918345 -185 CAAAGCGTACATCATATCTTTAATTGTTTGCATC 23 164 1 AATATTTTAT 0.786386 -137 ACTATAAATCACTAAATATTTATAGTATTTATGT 28 72 0 AAAATTTTAA 0.856788 -170 CATATTCATGATAATATCATTATTTAAATCTATA 31 137 1 AATATATTAT 0.6324 -164 ATATCTTTAAAAAAAATATTTACTATTATTTTTT 31 243 0 AAAATTTTAT 0.819904 -58 AAGACGACGCAGCAAATTTTTGAAGTTCATCGAG 32 83 1 AAAATTTTGA 0.833284 -218 ATTGGCTTATAATAAATGTTTAGAATGCTCAATT 32 265 1 AAAATTTTAA 0.947619 -36 TTAGGTGCATAAAAAATATTTAGTATTTTTGATC 34 49 0 AAAATTTTAT 0.819904 -143 AGGATGACTTAGCAAATTTTTGGAGTTCTATCTG 37 56 0 AAAATTTTGA 0.833284 -190 TGATTTTTATATTAAATTTTTAAATTATACGTTA 37 213 0 AAAATTTTAA 0.947619 -33 TACTAAAATTACTAAATCTATACAATATAATTT 39 10 0 AAAATTATAA 0.699666 -261 CTAGGGAAACACTAAATAATTAAAAAGGCTTATT 39 101 0 AAAATATTAA 0.893595 -170 ATTTGTTTTAATAATATAATTAAAGTATTTTAAA 40 16 1 AATATATTAA 0.735806 -51 * **** **** * Masking position 7 Map Score: 36.2782 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 196 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 TTATAACCTTTATATATAATAAATTATTAGAT 3 139 0 TTATATAATA 0.894781 -24 TTCCATATTATTTAAATAATAAATTTACTATA 4 19 1 TTAAATAATA 0.949935 -248 TTTAGCGTAGTTGATTTAATTAACTAATCTAA 4 63 0 TGATTTAATA 0.508287 -204 AATTTTGTATTGTAAATAATTATGCGTTATAA 4 212 1 TTAAATAATA 0.949935 -55 CAAAACTTTATTTAATTAATAAACTAATGATT 4 242 0 TTAATTAATA 0.846215 -25 ATTTATTATAAATTATAAGTAATTTATT 5 7 1 TTAAATTATA 0.880105 -294 CTATATAAAATTTAAATTATTATATTTTAAAC 5 73 0 TTAAATTATA 0.880105 -228 TCCTTGTAGCTGTAAATCATAAGATTTTTTTG 5 195 0 TTAAATCATA 0.69313 -106 AACGGGGTTTTAGAAATTATCAGTACTATACA 8 24 0 TGAAATTATA 0.754711 -87 CCTTCATTACTATAAATTATTAT 12 175 1 TTAAATTATA 0.880105 -13 TATCCTAAGATTGATATAATAAAGTCTAATAA 13 77 0 TGATATAATA 0.780915 -224 TTCATTTAATTCCATATAATAATTATATCCTT 15 112 1 TCATATAATA 0.730729 -189 ATGAGCTAAATATAATTAATTATAATATATGA 15 276 0 TTAATTAATA 0.846215 -25 CATATTGCAATATATATAATGAGATCAAATGG 20 64 0 TTATATAATA 0.894781 -91 TTTAATAGAATATAAATTATGAAATGAGATAA 20 129 1 TTAAATTATA 0.880105 -26 CGCATCCTCTTATAAATAATCAATATGAAATC 22 187 0 TTAAATAATA 0.949935 -414 ACACTAAAACTGCAAATAATTAATTTTTGATT 23 207 1 TCAAATAATA 0.858254 -94 CTGTATTAAATATAAATAATTATTATTTGTAA 23 256 1 TTAAATAATA 0.949935 -45 TTATCGTAAGTTTATTTAATAATAATCTCTTA 28 120 1 TTATTTAATA 0.7115 -122 TAAATATAGATTTAAATAATGATATTATCATG 31 143 0 TTAAATAATA 0.949935 -158 ACTTGTTAGATCCAAATAATTAATGTCT 34 7 0 TCAAATAATA 0.858254 -185 AGTGTTTCCCTAGATATAATAATTGTGATTGA 39 122 1 TGATATAATA 0.780915 -149 GTTTTCATCATGTAATTTATTATGAGATCCAT 39 222 0 TTAATTTATA 0.680392 -49 * ******** * Masking position 7 Map Score: 20.6527 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 178 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 TTAACTAACTAAATGAAAATTTAGTGAACTTTAAATTG 1 109 0 AAATTTTATA 0.860992 -192 GAAGTCAAACAAATTGATTTTTTCTAGAAAGAACTCAA 1 221 0 AAATTTTTTA 0.840336 -80 AATTAAATTTTCTATTTATTTGAAGATAAACAT 1 278 0 AATTTTTATA 0.748331 -23 TCTCCAATTCAAATTCCTCTTTATAAGATAGTTTATGC 3 96 1 AAATTTTAAA 0.928068 -67 TTGTATAGTAAATTTATTATTTAAATAATATGGAATTA 4 16 0 AATTTTTAAA 0.860992 -251 TTACTATACAAAATAAACTTTTAGATTAGTTAATTAAA 4 43 1 AAATTTTAAA 0.928068 -224 GAAACTATTAAATTCTTAATTTTAAGTATATAGCGTTG 4 125 1 AATTTTTTAA 0.840336 -142 TTACAATACAAAATTTTTCTTTAAAAAATCTAAAACTA 4 189 0 AAATTTTAAA 0.928068 -78 AAATCGTATTAATTTTCGCTTTAAAATATTGCCTAATA 5 137 0 AATTTTTAAA 0.860992 -164 TGTAATAATGAATTTTTGGTTTTAATCACTTGATTAAG 7 41 1 AATTTTTTAA 0.840336 -260 ATATGATCTAAAATAAACTTTTTCTATAATTTTTTTAA 9 24 0 AAATTTTTTA 0.840336 -66 ATAGAGTTCTAAATCTAAATTTAAATCAATTATTTTTA 11 96 0 AAATTTTAAA 0.928046 -45 AATCATTGCTAAATAACATTTTAATTGATATATAAATA 13 111 0 AAATTTTATA 0.860993 -190 ATTTTTTATAAATTTGATCTTTATTTAAATTAAAATAT 22 11 0 AATTTTTATA 0.748331 -590 TAGAATTAGAAAATGCATGTTTCAAAAACTATAATATC 22 108 0 AAATTTTCAA 0.653026 -493 CTTTATGGAGAAATGCAGCTTTTAATTACCAATGTATA 22 405 1 AAATTTTTAA 0.916411 -196 TATAGTAACTAAATCTTATTTTTGTCAAGTCAAAAATC 22 439 1 AAATTTTTTA 0.840336 -162 ATCAAGATTAAAATAAGCTTTTTAAAAAAGTATAAATT 23 63 0 AAATTTTTAA 0.916411 -238 AATAACATATAAATCTATCTTTTAAATAGATATATTTC 30 64 0 AAATTTTTAA 0.916411 -237 AATCTACAATAAATATAGATTTAAATAATGATATTATC 31 146 0 AAATTTTAAA 0.928068 -155 AAATAATAGTAAATATTTTTTTTAAAGATATGATTATG 31 246 1 AAATTTTTAA 0.916411 -55 TAAAAATTGCAATTTTAAAAACTAAAGCATA 31 280 0 AAATTTTTAA 0.916411 -21 GTAAAATAAGAATTCTAGATTTATATTAAAAATTGGCT 32 234 1 AATTTTTAAA 0.860972 -67 AATTAAGTTTTTAATTGAGCATTCTAAA 32 283 0 AATTTTTATA 0.748331 -18 AAAATATTTGTTTTAATAATATAATTAAA 40 2 1 AAATTTTTAA 0.916411 -65 **** **** * * Masking position 10 Map Score: 34.5626 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 135 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 AGAAAACAATTTTTACTTAATTTTGATTTCT 1 159 0 TTTTACTTAT 0.782897 -142 TAAGTTATGATTCGATTTTATAGGCTCAAGA 3 33 0 TTCGATTTAT 0.694776 -130 TGTTTGATTTTATTTAAAAAAAT 9 3 1 TTTGATTTAT 0.939775 -87 CAAAAATATGTTTTACTTTATCGCCGAAAAA 10 233 1 TTTTACTTAT 0.782897 -68 TGAATTGATTTTATTTCATGTTGTTAGTG 13 9 1 TTTTATTTAT 0.867019 -292 TGGTGTTTTATTAGACTTTATTATATCAATC 13 70 1 TTAGACTTAT 0.803601 -231 TTTTTTGTTTTTAGATTTTATCTCAACATTG 14 81 0 TTAGATTTAT 0.880921 -26 CATGAAATCTTTAGATTTAATTTTTTCATTT 15 88 1 TTAGATTTAT 0.880921 -213 TATAAAGATTTTTTATTTCATTAGACAAAAA 15 219 0 TTTTATTTAT 0.867019 -82 AACTTGACCATTTGATCTCATTATATATATT 20 57 1 TTTGATCTAT 0.610743 -98 AATATAAATATTTGATTTCATATTGATTATT 22 174 1 TTTGATTTAT 0.939775 -427 AAGATTGGTATTTTATTAGATCTAGATACGA 22 377 0 TTTTATTAAT 0.693372 -224 ATAATTAATTTTTGATTATATAATAGGCTTA 23 222 1 TTTGATTAAT 0.844045 -79 TAATAATTATTTATATTTAATACAGAATTAA 23 250 0 TTATATTTAT 0.755557 -51 CTTTTGACTTAATAATGTAAATT 27 3 1 TTTGACTTAT 0.896166 -58 ATATTTGATTAGATTGTTTTGATT 28 4 1 TTTGATTAAT 0.844046 -238 TTGGTGTTATTTTTACTTCATTATAATTCCA 34 145 0 TTTTACTTAT 0.782897 -47 TTTAGATTTTATTTATATAGGT 35 142 0 TTAGATTTAT 0.880921 -12 TTTTATACTGTTTGATTAGATTTTTAGGTTC 36 64 1 TTTGATTAAT 0.844046 -64 TTTGTGATTTTTATATTAAATTTTTAAATTA 37 220 0 TTATATTAAT 0.517377 -26 ******** ** Masking position 2 Map Score: 18.2437 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 141 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 ACCTTCAATATTTTGTATTGTCATAAGAAT 1 47 1 TTTTGTATTG 0.900242 -254 TCTAATAATTTATTATATATAAAGGTTATA 3 140 1 TATTATATAT 0.502958 -23 TAAAAGTTTATTTTGTATAGTAAATTTATT 4 36 0 TTTTGTATAG 0.858995 -231 CTGCAAAGTATATTATATTTTAGCGTAGTT 4 83 0 TATTATATTT 0.599837 -184 TAAAGAAAAATTTTGTATTGTAAATAATTA 4 204 1 TTTTGTATTG 0.900242 -63 AAATTTAAATTATTATATTTTAAACAGTAA 5 68 0 TATTATATTT 0.599837 -233 ATAATTTAAATTTTATATAGAACCTAGGTT 5 85 1 TTTTATATAG 0.566202 -216 CATAATGTTATTTTGTATTTAAGCTATGGA 6 95 1 TTTTGTATTT 0.768347 -62 AGCATTCACTTATTGTATAGTACTGATAAT 8 11 1 TATTGTATAG 0.927798 -100 TTATATATTGTATACAGGATCAACA 14 6 1 TATTGTATAC 0.55643 -101 GGATCAACAATATTGTATTGATTCACTGGA 14 27 1 TATTGTATTG 0.950088 -80 ATTATTAAGTTATTGTATTGAATTTATATA 17 73 0 TATTGTATTG 0.950088 -48 GACACCATTTTAGTGTATAGAACTTCAATT 22 530 0 TAGTGTATAG 0.71491 -71 TTTGCAGTTTTAGTGTATTTTTAACGATGC 23 193 0 TAGTGTATTT 0.577222 -108 TGTAATATTTTATTGTATATTGTTTCTTTT 31 105 1 TATTGTATAT 0.825264 -196 ATCTAACAAGTATTGTATTGGGATCAAAAA 34 28 1 TATTGTATTG 0.950088 -164 AGATTTCAGCTATTATATTGTATCTTGACC 35 95 0 TATTATATTG 0.803088 -59 AAATTATATTGTATAGATTTAGTAAT 39 7 1 TATTGTATAG 0.927798 -264 CTGTATATTTTGTTGTATTGTGGCAAGTGT 39 154 1 TGTTGTATTG 0.735223 -117 TTTTATTGTTTTGTATTTTAAATTATGT 40 49 0 TTTTGTATTT 0.768347 -18 ********** Masking position 6 Map Score: 17.4215 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 54 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 GGATGAAATTTTAATATTTTACCTTCAATATTTTGTATTG 1 27 1 TTATTTAATA 0.58546 -274 AAATAAGCCTTTACAATTTAAAGTTCACTAAATTTTCATT 1 96 1 TTAATAAATA 0.792604 -205 CAGTTAATATATAGAAATCAAAATTAAGTAAAAATTGTTT 1 147 1 ATAACAAATA 0.662585 -154 AATAATAAATTTACTATACAAAATAAACTTTTAGATTAGT 4 33 1 TTATCAAATT 0.408466 -234 AACTTTTAGATTAGTTAATTAAATCAACTACGCTAAAATA 4 58 1 TTATTTAATA 0.58546 -209 TTTTGTTGGGATAGATACCTATTTCCAATAAATTACTTAT 5 25 0 ATAACTAATA 0.361901 -276 AACAAAAGCTTTACTGTTTAAAATATAATAATTTAAATTT 5 58 1 TTATTAAATA 0.83022 -243 CTATGCACTCTTAATAAATAACCATAATTATGGTTCCTTG 5 221 0 TTATTAAATA 0.83022 -80 AATTTTTAAATTATACAACAAGACAAATTATGTACAACAT 6 20 0 TTAACAAATA 0.928033 -137 ACTCCATAGCTTAAATACAAAATAACATTATGGCTCACTA 6 87 0 TTAAAAAATA 0.770737 -70 AATCAAGTGATTAAAACCAAAAATTCATTATTACAACTCT 7 36 0 TTAAAAAATA 0.770737 -265 CTGTCAACAATTATTTTTTAATTTTAAATATAGGCAGTTT 10 271 1 TTATTAAATA 0.83022 -30 AATCAATTCATTAATAATCAAATGAGAATAAAAATAATTT 11 50 1 TTATCAAATA 0.94287 -91 AAAGGCTTTTTTATACCACAACTAAATATAAATACTAATA 12 117 1 TTAACAATTA 0.35051 -71 AATTAAAATGTTATTTAGCAATGATTATTATCTTTATTTT 13 123 1 TTATCAAATA 0.942867 -178 ATGCTTCTTATTACTTCACAATAACTAGTATTTTAAAAAA 13 177 0 TTATCAAATA 0.94287 -124 ATTTTTTCATTTAATTCCATATAATAATTATATCCTTGTC 15 107 1 TTATATAATA 0.55403 -194 GATATCTATAATAGAAAATAAACCTAATTATTGACAAGGA 15 139 0 ATAATAAATA 0.36782 -162 AGCAAAAAGTTTATAATGCAAGGAGCATTATTAATGCATG 18 134 0 TTAACAAATA 0.92805 -82 AGTATTATACTTATACCGCAACTTAAATTAGTGTAAGCAC 20 15 1 TTAACAAATA 0.92805 -140 AATGCAGCTTTTAATTACCAATGTATAGTAACTAAATCTT 22 416 1 TTATCAAATA 0.94287 -185 TACAAAATGTTTACTGCGCAAGTTACAATAGTAAGAATGC 23 125 1 TTATCAAATA 0.94287 -176 TAATTCTGTATTAAATATAAATAATTATTATTTGTAACTT 23 251 1 TTAAAAAATA 0.770737 -50 AAATAATCTCCAAATTTTACTAGTAACTAGAA 25 36 0 ATATCAAATA 0.715312 -22 TTTGTTAATTTTAAATCCTAAATCTGAATAACATCTAAGA 28 147 0 TTAATAAATA 0.792604 -95 AGCAAATACTTTACTTTAAAATCTACAATAAATATAGATT 31 163 0 TTATAAAATA 0.811375 -138 TAAATTACGTTTATTACTATAGCTATATTAGCACCAAATA 32 165 1 TTATATAATA 0.553216 -136 TAAACATTTATTATAAGCCAATTTTTAATATAAATCTAGA 32 247 0 TTAACAAATA 0.92805 -54 TTTAGTAATTTTAGTATACTATTTTCAATAATATTGATTT 39 28 1 TTATCTAATA 0.826589 -243 TTAAAAAGGCTTATTTGACAAATTTAACTATTACAAATAT 39 76 0 TTATCAAATA 0.94287 -195 GAGATCCATGTAAAAATACAAATTTGAGTATTTTAATTGT 39 191 0 TAAACAAATA 0.35051 -80 AATATTTGTTTTAATAATATAATTAAAGTATTTTAAACAT 40 13 1 TTATATAATA 0.554041 -54 *** * *** * ** Masking position 11 Map Score: 32.2319 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 136 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 AATTTGTAAAAAAATATAAAAAA 2 1 1 AATTTTAAAA 0.73729 -72 AAAAAGTAACATTATCTCAAAAATCGTATTAAT 5 162 0 ATTATTAAAA 0.848427 -139 AAATCATAAGATTTTTTTGAAAAAGTAACATTA 5 181 0 ATTTTTAAAA 0.872757 -120 TTATTATATTAATTTATAGAAAAATGTAGCCAT 7 107 0 AATTTTAAAA 0.73729 -194 GTTGGTATTTATTTTTTATAAAAACATCAATAC 7 241 1 ATTTTTAAAA 0.872758 -60 TATAGTACTGATAATTTCTAAAACCCCGTTACA 8 26 1 ATAATTAAAA 0.729638 -85 TGTTTGATTTTATTTAAAAAAATTATAGA 9 7 1 ATTTTTAAAA 0.872758 -83 TTATTTAAAAAAATTATAGAAAAAGTTTATTTT 9 20 1 AAATTTAAAA 0.575028 -70 AATAACCTGAAAAACTATTTTCGT 9 76 0 ATAACTAAAA 0.529454 -14 TCGAATATTGAATATATTCAAAAATATGTTTTA 10 215 1 AATATTAAAA 0.696073 -86 GTCTTACTGCAAATTTTTTAAAATACTAGTTAT 13 164 1 AAATTTAAAA 0.575028 -137 ATTATATGGAATTAAATGAAAAAATTAAATCTA 15 99 0 ATTAATAAAA 0.54293 -202 TCTTTATAAAATTTAGTGAAAAAAAAATAAAAC 15 242 1 ATTTATAAAA 0.59276 -59 TATGATGACAATGATTTCTAAAAATTTATTCTA 16 14 1 ATGATTAAAA 0.36013 -44 TTGTTTATTAATTTAATTTAAAATTATTAAGTT 17 92 0 ATTTATAAAA 0.592764 -29 TTGGTGTAAGATTACATGCAAAAAATTATTCTA 21 85 1 ATTACTAAAA 0.70004 -80 ATAAAGATCAAATTTATAAAAAATGAAGAGTAA 22 25 1 AATTTTAAAA 0.73729 -576 TAACATTGAAATAATGTTGAAAACATCTTCAAG 22 249 0 ATAATTAAAA 0.729638 -352 AGATATCAAAATTTTTTAAAAAAACTGTTTAAG 22 345 0 ATTTTTAAAA 0.872753 -256 TGTCAAGTCAAAAATCTAAAAAAAAATAAAATA 22 461 1 AAAATTAAAA 0.524763 -140 TGGAATTTATACTTTTTTAAAAAGCTTATTTTA 23 60 1 ACTTTTAAAA 0.396031 -241 TAAACACCTTATTTCGTAAAAAAAAGCTCTTGG 28 35 0 ATTTCTAAAA 0.740913 -207 TTTGTATTTTAATATCTGAAAAACATCTTGCTG 29 50 1 AATATTAAAA 0.696073 -44 GTTATTTTTTATAATCTGAAAAATGATATAGCA 30 96 1 ATAATTAAAA 0.729638 -205 CTGATCAAGAATTACATTTAAAACT 31 3 0 ATTACTAAAA 0.70004 -298 AAGCATAATCATATCTTTAAAAAAAATATTTAC 31 254 0 ATATCTAAAA 0.579621 -47 TAATTTAAAAATTTAATATAAAAATCACAAAAA 37 220 1 ATTTATAAAA 0.592764 -26 GCTGAAATCAATATTATTGAAAATAGTATACTA 39 39 0 ATATTTAAAA 0.767821 -232 TGTATTTTAAATTATGTTTAAAATACTTTAATT 40 33 0 ATTATTAAAA 0.848427 -34 ***** * **** Masking position 7 Map Score: 24.6395 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 390 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 10 TTAGAAGCTTTTTTATATTTTTTTACAAATT 2 8 0 TTTATATTTT 0.917831 -65 ATATATATGTTATTATATTAATTTATAGAAAAAT 7 115 0 TTTATATTTT 0.917831 -186 GTGGGTAGTTTGTTATAATTAACTCATATCAAAA 7 183 1 TTTATATACT 0.69594 -118 ATGAATTGATTGTTATAGTAAACTTTGTTATAAT 11 27 0 TTTATATACT 0.69594 -114 ATCAAATTATTTTTATTCTCATTTGATTATTAAT 11 59 0 TTTATTTTTT 0.713727 -82 TTTTTATAACTATCTTTATAGAGTT 11 126 0 TTTATACTCT 0.653729 -15 AATGAAGGCATTTTATTATTTTTTCATATTAGTA 12 149 0 TTTATTTTTT 0.713727 -39 TATTAGACTTTATTATATCAATCTTAGGATACTT 13 78 1 TTTATACTCT 0.653729 -223 TAGCAATGATTATTATCTTTATTTTTGTCTTACT 13 138 1 TTTATCTTTT 0.798165 -163 AAATATAGACTATTATACTAATTTCATGCTTCTT 13 208 0 TTTATATTTT 0.917831 -93 ATAGTCTATATTTTATCCTCAATTCATTATAGTA 13 229 1 TTTATCTATT 0.539374 -72 TAAAAATTTGTATTATAGCAAATTTCTTTAAATT 13 263 0 TTTATACATT 0.446849 -38 CTTTGTGAAGTGTTATCATCTTTTA 15 2 0 TTTATCTTTT 0.798165 -299 GTTTATTTTCTATTATAGATATCTAAAATAATAT 15 156 1 TTTATAATCT 0.545585 -145 AATTTGAAAATCTTATATTATTTTAGATATCTAT 15 170 0 TTTATATTTT 0.917831 -131 TTTCACTAAATTTTATAAAGATTTTTTATTTCAT 15 229 0 TTTATAATTT 0.63437 -72 ATATATGAGGTTTTATTTTTTTTTCACTAAATTT 15 250 0 TTTATTTTTT 0.713727 -51 AAACCTCATATATTATAATTAATTATATTTAGCT 15 271 1 TTTATATATT 0.767848 -30 ATTATTTCAATGTTATATTACTCTAGAGCCGTAT 22 267 1 TTTATATTCT 0.885449 -334 AATATAAATATTTTATTTTTTTTTAGATTTTTGA 22 468 0 TTTATTTTTT 0.713727 -133 TTATAGTCGTTATTATAATGCTTTTTTGCAAAAA 22 561 0 TTTATATTTT 0.917831 -40 CATCAAAGATTTTTATATTATTTTCTAGTTACTA 25 14 1 TTTATATTTT 0.917831 -44 CGTAAGTTTATTTAATAATAATCTCTTAGATGTT 28 124 1 TTAATATTCT 0.277912 -118 TGAAGAAGTATATTATAATCTTTTAATAAAATCT 33 54 1 TTTATATTTT 0.917831 -40 AAATTTAATTTTATCTAGATTTTATTAAAAGA 33 72 0 TTTATCATTT 0.380515 -22 TGAAGTTGATTCTTATACTACTCTTCATTTATTT 37 160 1 TTTATATTCT 0.885449 -86 TTTTTGTGATTTTTATATTAAATTTTTAAATTAT 37 219 0 TTTATATATT 0.767848 -27 * ***** * *** Masking position 6 Map Score: 28.6096 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 114 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 TGATTAGGCTCTATGCACTCTTAATAAATAACCATA 5 235 0 CTGTCTTATA 0.97154 -66 TAAAGAATGGCTACGTTGTCTTAATAAAGTTTGTAG 10 173 0 CTGTCTTATA 0.97154 -128 TTTTAGAAATCATTGTCATCATATTA 16 1 0 CAGTCATATA 0.86634 -57 TTAAAATTGGCTAAGTTGTCTTAATAAGCTCTGTAG 18 94 1 CTGTCTTATA 0.97154 -122 AACCTTTAAACAATGTAATATTAGTAATAAATT 21 142 1 CAGTATTATA 0.670745 -23 ATGATGTACGCTTTGCATTCTTACTATTGTAACTTG 23 143 0 CTGTCTTATA 0.97154 -158 CAAAAATTTGCTGCGTCGTCTTATTAAGTGCTGTGG 32 69 0 CTGTCTTATA 0.97154 -232 CGTTCTTGGACACTGAATACTTATTAAATTAATTTT 36 99 1 CAGACTTATA 0.766406 -29 TGGACCTCAGAATTCTTGCTATGATACAATA 38 52 0 CTGTCTTGTA 0.876836 -21 TGTATTTTTACATGGATCTCATAATAAATTACATGA 39 211 1 CAGTCATATA 0.86634 -60 ** * ***** ** Masking position 12 Map Score: 5.34404 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 1 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 Motif number 12 TCATAACTTATATCTATGTACTGCAGTATGAG 3 54 1 TATTATGTAT 0.814707 -109 CCACTATATTTATGGAAGTAGTTTTAGATTTT 4 171 1 TATGAAGTAT 0.460404 -96 TTACTGCCCGTATTTAAGTTTGATTAGGCTCT 5 259 0 TATTAAGTTG 0.648442 -42 AGTGTATATATGTTGTACATAATTTG 6 5 1 TATTATGTTT 0.931951 -152 AAGTTTAAAATATATATGTTATTATATTAATT 7 126 0 TATTATGTTT 0.931951 -175 GGTTAATATGTATTGATGTTTTTATAAAAAAT 7 251 0 TATGATGTTT 0.900804 -50 TTTTAGATCATATATATGTTAGTATAAACGAA 9 49 1 TATTATGTTG 0.863059 -41 ATTTTTGGATTATGTATGTTATATGGTTATAT 17 46 1 TATTATGTTT 0.931951 -75 AGAAAGGTGATTTTGATGTTGTTACAAAATGT 23 103 1 TTTGATGTTT 0.630188 -198 ATATTTATAGTATTTATGTAATGTAAACACCT 28 59 0 TATTATGTAT 0.814707 -183 AAATGATTTATATAGAAGTTTTAGATAAGACT 28 202 1 TATGAAGTTT 0.726602 -40 AAAAGATAGATTTATATGTTATTTTTTATAAT 30 79 1 TTTTATGTTT 0.719885 -222 AGTGCTGTGGTATTTATGTGTTCAGTAACTGC 32 47 0 TATTATGTGT 0.7206 -254 GTTTTTGTTTTATGTATGTTGGTGTTATTTTT 34 162 0 TATTATGTTG 0.863059 -30 *** ****** * Masking position 6 Map Score: 5.56952 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 32 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 TTTTCACATCCTATAGTTAATAAAATGTTTA 1 190 1 CTATATTAAT 0.790234 -111 AAGATAAACATTATACTAAAATATATGATAG 1 258 0 TTATATAAAA 0.624463 -43 TACTTATAATTTATAATAAAT 5 1 0 TTATATAAAT 0.765155 -300 ATTAGAGTTGTAATAATGAATTTTTGGTTTT 7 33 1 TAATATGAAT 0.608849 -268 AAACTGCCTATATTTAAAATTAAAAAAT 10 283 0 CTATATTAAA 0.658052 -18 AATAAAACACCAATACTTAAAAAGACGTGTT 13 51 0 CAATATTAAA 0.495727 -250 TTTAAATTTACTATAATGAATTGAGGATAAA 13 240 0 CTATATGAAT 0.714119 -61 CTTCGACCATCTATAGTGAATAGCTTCTCTT 15 42 1 CTATATGAAT 0.714119 -259 ACCTCATATATTATAATTAATTATATTTAGC 15 273 1 TTATATTAAT 0.821282 -28 CCAATTTAAGTTATAGTTAATAGAATTAGAA 22 135 0 TTATATTAAT 0.821282 -466 AATAAAATATTTATATTGAATAAATTATTAT 22 485 1 TTATATGAAT 0.75291 -116 TAATAATTATTTATATTTAATACAGAATTAA 23 250 0 TTATATTAAT 0.821282 -51 TTATTTACTCTATACTTAAACTA 24 4 0 CTATATTAAA 0.658052 -20 AAGCGTCATGCAATATTAAATGATTTATATA 28 185 1 CAATATAAAT 0.577069 -57 TCATTAAACCTAATATTTAAACAGCAAGATG 29 73 0 TAATATTAAA 0.545282 -21 AATAAAAAAATAATAGTAAATATTTTTTTTA 31 239 1 TAATATAAAT 0.624683 -62 AATTCTAGATTTATATTAAAAATTGGCTTAT 32 244 1 TTATATAAAA 0.624463 -57 AAAAATTGGCTTATAATAAATGTTTAGAATG 32 261 1 TTATATAAAT 0.765155 -40 TTTGTGATTTTTATATTAAATTTTTAAATTA 37 220 0 TTATATAAAT 0.765155 -26 TAATACTTAATACTGTCATTT 38 1 1 TAATATTAAT 0.701268 -72 AGTATATTTGTAATAGTTAAATTTGTCAAAT 39 73 1 TAATATTAAA 0.545282 -198 ***** ***** Masking position 7 Map Score: 14.1771 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 182 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 14 AAGAAATATCAAATAAGCCTTTACAATTTAAA 1 86 1 AAAAGCCTTT 0.945006 -215 TTTATAGAAAAATGTAGCCATTTTACATCAGT 7 96 0 AATAGCCATT 0.899114 -205 TTATTAAGACAACGTAGCCATTCTTTAAACAG 10 182 1 AATAGCCATT 0.899116 -119 AATTGTTGACAGATTAGCCTTTTTCGGCGATA 10 251 0 AGTAGCCTTT 0.781832 -50 GTTGTGGTATAAAAAAGCCTTTAGAAGCACCG 12 107 0 AAAAGCCTTT 0.945005 -81 TTAATATATAATTCTAGCCAATAGACATAGGT 18 22 0 ATTAGCCAAT 0.440153 -194 TTATTAAGACAACTTAGCCAATTTTAAAATTA 18 89 0 AATAGCCAAT 0.760113 -127 ATCAAGATTAAAATAAGCTTTTTAAAAAAGTA 23 69 0 AAAAGCTTTT 0.552165 -232 TTTAATACAGAATTAAGCCTATTATATAATCA 23 234 0 AAAAGCCTAT 0.859341 -67 GAGAAGATATATCTAAGCCTTTTGCTTATTCT 31 36 1 ATAAGCCTTT 0.810017 -265 TAAATTTGTCAAATAAGCCTTTTTAATTATTT 39 90 1 AAAAGCCTTT 0.945006 -181 TAGCATAATTAACATAACCTTT 41 1 0 AATAACCTTT 0.552165 -149 ** ******** Masking position 6 Map Score: 3.3367 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 35 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 AATCAAAACTTTATTTAATTAATA 4 253 0 CAAACTTTAT 0.476091 -14 TTTTGGTTTTAATCACTTGATTAAGATAATG 7 54 1 AACACTTGAT 0.687942 -247 TTTCATTAGACAAAAATTAATTTCAAATCAA 15 204 0 CAAAATTAAT 0.467505 -97 TCCAGCACTTTATTTACATGTTT 17 3 1 CACACTTTAT 0.73994 -118 AATTCAATACAATAACTTAATAATTTTAAAT 17 79 1 AAAACTTAAT 0.816961 -42 AGTAATCATCAAACACTTAATCTCATATTGC 20 88 0 AACACTTAAT 0.933232 -67 ATTATATAATCAAAAATTAATTATTTGCAGT 23 215 0 CAAAATTAAT 0.467505 -86 TTGCACTATAAATCACTAAATATTTATAGTA 28 79 0 AACACTAAAT 0.708097 -163 CTTCTATATAAATCATTTAATATTGCATGAC 28 189 0 AACATTTAAT 0.500717 -53 CTTCTCCCTCCACCACTTAATGGTTCAGGGA 30 35 1 CACACTTAAT 0.938128 -266 TTACTTGAATAACCACTTAATTATTAGCAAA 31 197 0 AACACTTAAT 0.933232 -104 ATAAATACCACAGCACTTAATAAGACGACGC 32 62 1 CACACTTAAT 0.938128 -239 ATGCTCAATTAAAAACTTAATT 32 289 1 AAAACTTAAT 0.816982 -12 ATATCTAGGGAAACACTAAATAATTAAAAAG 39 108 0 AACACTAAAT 0.708097 -163 ATCATTGCTTAACCAATTAATAGTCATTGCC 41 112 1 AACAATTAAT 0.717036 -38 ** ******** Masking position 5 Map Score: 7.80006 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 54 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727