AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_mjan_reg_300.orf -o00230_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0191 25 SSU ribosomal protein S11P (rpsK) MJ0194 31 LSU ribosomal protein L13P (rplM) MJ0885 38 DNA polymerase B1 MJ1648 143 phosphoribosylformylglycinamidine synthase I, (purQ) Input sequences: #1 MJ0102 300 Phenylacrylic acid decarboxylase #2 MJ0107 167 dihydropteroate synthase #3 MJ0189 300 SSU ribosomal protein S13P (rpsM) #4 MJ0190 57 SSU ribosomal protein S4P (rpsD) #5 MJ0193 77 LSU ribosomal protein L18E #6 MJ0196 57 DNA-directed RNA polymerase, subunit N (rpoN) #7 MJ0197 140 DNA-directed RNA polymerase, subunit K (rpoK) #8 MJ0202 56 conserved hypothetical protein #9 MJ0203 120 phosphoribosylformylglycinamidine cyclo-ligase (purM) #10 MJ0204 99 amidophosphoribosyltransferase (purF) #11 MJ0388 90 conserved hypothetical protein #12 MJ0397 300 DNA-directed RNA polymerase, subunit E' (rpoE1) #13 MJ0478 300 protein translocase, subunit SEC61 alpha (secY) #14 MJ0479 142 adenylate kinase (adk) #15 MJ0561 281 adenylosuccinate synthetase (purA) #16 MJ0616 108 phosphoribosylaminoimidazole carboxylase, (purE) #17 MJ0640 158 conserved hypothetical protein #18 MJ0641 166 phosphoglycerate kinase (pgk) #19 MJ0667 91 thymidine phosphorylase (deoA) #20 MJ0831 93 conserved hypothetical protein #21 MJ0832 259 anaerobic ribonucleoside-triphosphate reductase (nrdD) #22 MJ0888 88 conserved hypothetical protein #23 MJ0929 300 adenylosuccinate lyase (purB) #24 MJ0934 300 polyferredoxin (mvhB) #25 MJ0936 94 conserved hypothetical protein #26 MJ0937 63 phosphoribosylamine--glycine ligase (purD) #27 MJ1036 300 M. jannaschii predicted coding region MJ1036 #28 MJ1037 62 tryptophan synthase beta subunit (trpB) #29 MJ1038 176 tryptophan synthase alpha subunit (trpA) #30 MJ1039 174 DNA-directed RNA polymerase, subunit H (rpoH) #31 MJ1041 85 DNA-directed RNA polymerase, subunit B' (rpoB1) #32 MJ1042 108 DNA-directed RNA polymerase, subunit A' (rpoA1) #33 MJ1043 74 DNA-directed RNA polymerase, subunit A'' (rpoA2) #34 MJ1132 188 conserved hypothetical protein #35 MJ1149 59 mutator MutT protein, putative (mutT) #36 MJ1264 76 phosphoribosylformylglycinamidine synthase II (purL) #37 MJ1265 189 nucleoside diphosphate kinase, (ndk) #38 MJ1368 122 sulfate transport system permease protein (cysT) #39 MJ1390 187 DNA-directed RNA polymerase, subunit I (rpoI) #40 MJ1391 300 putative aminotransferase #41 MJ1456 77 histidinol dehydrogenase (hisD) #42 MJ1458 61 conserved hypothetical protein #43 MJ1459 137 adenine deaminase (adeC) #44 MJ1575 300 GMP synthase (guaA) #45 MJ1592 300 phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC) #46 MJ1616 228 inosine-5'-monophosphate dehydrogenase, (guaB) #47 MJ1642 300 conserved hypothetical protein #48 MJ1644 147 M. jannaschii predicted coding region MJ1644 #49 MJ1646 24 pyrimidine biosynthesis protein, putative #50 MJ1647 65 DNA binding protein #51 MJ1652 76 DNA topoisomerase I (topA) {Bacillus subtilis #52 MJ1654 64 M. jannaschii predicted coding region MJ1654 #53 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 ********** No masking Map Score: -2.52076e-11 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 2 TCGGCACCATTTTATTATTTTATTTTAGGT 1 188 1 TTTATTATTT 0.784491 -113 GGTTGTTATATTTATTTTTTTAGATTTATG 1 215 1 TTTATTTTTT 0.910707 -86 TTAAATAGTATTTATTTTTTAAATCTTAAC 1 257 1 TTTATTTTTT 0.910707 -44 TTTAATTACATTTATAGTTTTCATTTTAAG 2 39 1 TTTATAGTTT 0.843423 -129 TACCATATTATATATTATTTTCGGTTTTTA 3 49 0 TATATTATTT 0.568215 -252 ATATATTCTTTTTATATATTCCCACAATAC 3 99 0 TTTATATATT 0.882322 -202 TGTTTCATTTTTTATATATTCTTTTTATAT 3 112 0 TTTATATATT 0.882322 -189 GCCACTTCTTTTTATTTTTTAATATCTATT 3 236 1 TTTATTTTTT 0.910707 -65 TCAAACCTTTTATAATTATTATAAGGTTTG 5 38 0 TATAATTATT 0.650376 -40 CATTTGATATTTTATATATTTCAGAGGTGA 7 117 1 TTTATATATT 0.882322 -24 CTTTCTGTAGTTTAAATATTCCATAATGCA 9 29 1 TTTAAATATT 0.856749 -92 TAAATTATCTTTTTAATTTTACTAATTCTT 10 14 1 TTTTAATTTT 0.804352 -86 CTTCTTTCTTTTTATTTATTTGCTAAAAGT 10 53 1 TTTATTTATT 0.865792 -47 TAAAAACCCTTTTTTAGTTTTTTAGACTTT 10 78 0 TTTTTAGTTT 0.700787 -22 GCTATGGTAATTTATAAATTTACTTTATTA 11 58 1 TTTATAAATT 0.727968 -33 ATAAATTTACTTTATTATTTTGGTGATACT 11 71 1 TTTATTATTT 0.784491 -20 TTAATGTAATTATTAATTTTGCCACAAACC 12 194 0 TATTAATTTT 0.597788 -107 ACATTAATTATTTATTGTTTTTTATAATCT 12 217 1 TTTATTGTTT 0.822528 -84 TTAGTTACTCTTTTTTTATTAAATTTAACT 12 261 1 TTTTTTTATT 0.737184 -40 TTTTAATATCTTTATTTTTTTGTAAAAAAA 13 75 0 TTTATTTTTT 0.910707 -226 TAAGTTACTCTTTAAATTTTTAATATCTTT 13 92 0 TTTAAATTTT 0.904356 -209 TCCATTTTTCTATTTTATTTCATTTTTAGT 13 168 1 TATTTTATTT 0.363941 -133 TAATTAGGAGTATAAATTTTTAGTGAAATT 13 212 0 TATAAATTTT 0.773665 -89 TTTTTTAAGATTTTAAGATTTATGTTTTAT 13 259 0 TTTTAAGATT 0.541641 -42 ACTTTCGCAGTTTATATATTTTTTAGAATA 14 89 0 TTTATATATT 0.882322 -54 GTTGTTATGGTTTATTATTTGAAGGTTTAA 15 28 1 TTTATTATTT 0.784491 -254 TATGTTATACTATTTATATTCCAAAATATA 15 156 1 TATTTATATT 0.540972 -126 TTTATAGTTCTATATATTTTGGAATATAAA 15 168 0 TATATATTTT 0.810795 -114 ATTAATTAACTTTAAATATTACAATTACAA 15 241 1 TTTAAATATT 0.856749 -41 TTCAAAACCTTATATTTTTTTGTAATTGTA 15 260 0 TATATTTTTT 0.786647 -22 AGTAAATTAATTTAATTTTTAATTTTAATA 17 13 1 TTTAATTTTT 0.890537 -146 TAATTTTTAATTTTAATATTCTACTAGTTT 17 25 1 TTTTAATATT 0.722255 -134 ATATCGTCTTTTTAATTTTTAATACCATTT 17 117 0 TTTAATTTTT 0.890537 -42 AAGATTTCTTTATATTTATTCTTTCTGCAA 18 43 1 TATATTTATT 0.699881 -124 TAATTATCATTTTAAAGTTTTTAAGGTTTT 18 72 0 TTTAAAGTTT 0.811205 -95 CCTCTAAGATTTTTATGTTTTTAGAAGTTT 18 146 0 TTTTATGTTT 0.616482 -21 TTTTCTAAACTTTATATATTTTCTTTAATA 19 32 0 TTTATATATT 0.882322 -60 CTATTAAATTTTTATATTTTCTAAACTTTA 19 48 0 TTTATATTTT 0.922202 -44 GAATAATATATTTAATAATTTCTAAAATTG 20 31 0 TTTAATAATT 0.647469 -63 AAGAGCAATTTATATTGATTTATTATGTTG 21 39 0 TATATTGATT 0.514513 -221 TAGGAATGTGTATTTAGTTTTTCAGTAATA 21 170 0 TATTTAGTTT 0.458493 -90 TACAAATAATTTTATTTTTTACTATTTTTT 21 230 1 TTTATTTTTT 0.910707 -30 ATAAATAAAGTATAAATATTGTTAAAAACT 22 38 0 TATAAATATT 0.683742 -51 ATATTTATACTTTATTTATTTATAATTTAT 22 49 1 TTTATTTATT 0.865792 -40 TAGATAATTATTTAATTTTTATTTTCAAAA 23 12 1 TTTAATTTTT 0.890537 -289 AAAGGATTTTTATTTAATTTCTAAGGGTTT 23 89 0 TATTTAATTT 0.399404 -212 GTTTTAGGATTTTTAATTTTGTTGTTTGGT 23 188 0 TTTTAATTTT 0.804352 -113 TAGAAGTCTGTTTATAATTTATTATTTGGG 23 217 0 TTTATAATTT 0.808823 -84 GCTAATGATTTTTATAGTTTGATGTTTATT 23 275 0 TTTATAGTTT 0.843423 -26 CCGGCCACTTTTTATTATTTTAAATTCTCA 24 110 1 TTTATTATTT 0.784491 -191 GCCGGGCTTCTTTTTATTTTAGAACAATTA 24 243 1 TTTTTATTTT 0.837504 -58 AATCGATAAATTTAAATATTTTTAAAATAT 24 272 1 TTTAAATATT 0.856749 -29 TTTTTTACTTTTTTATTATTACATTAATCC 26 25 1 TTTTATTATT 0.691113 -39 AAATAATAGTTATTATTTTTTAATAACAAA 27 13 0 TATTATTTTT 0.561169 -288 AAATAATAACTATTATTTTTATTTAAGTTA 27 25 1 TATTATTTTT 0.561169 -276 TTTTTGTTAATTTAAAAATTCAAATTGTAT 27 200 0 TTTAAAAATT 0.680981 -101 ATTCACATTATTTTATTTTTGTTAATTTAA 27 215 0 TTTTATTTTT 0.779606 -86 CTAAATTTTATATTTTATCTTATATT 27 285 0 TTTATATTTT 0.922202 -16 TTTTCTCATATTTATTTTTTACTTTTATTG 30 45 0 TTTATTTTTT 0.910707 -130 AAGAAACTTTATTTATTATGTTTTTTC 31 8 1 TTTATTTATT 0.865792 -78 AAGAGAGATTTTTATTGATTTTGAAAAGAT 31 64 0 TTTATTGATT 0.745647 -22 AGCAAGGTCTTTTAATGTTTCTCT 32 5 0 TTTAATGTTT 0.787097 -104 TTATTTTTACTTTTTATTTTTCTAAAAATA 32 60 0 TTTTTATTTT 0.837504 -49 AAGGATTTGCTTTTATTTTTACTTTTTATT 32 72 0 TTTTATTTTT 0.779606 -37 TTTTACATCTTTTAATTTTTTAAGGTGAGA 33 51 1 TTTAATTTTT 0.890537 -24 CACCAAAGTTTTTATAGTTTTTTGCAAAGT 34 16 1 TTTATAGTTT 0.843423 -173 TGCAAAAAACTATATATATTTCTTAGCCAA 34 124 1 TATATATATT 0.730479 -65 TCTTAGCCAATTTTAATATTAATCTTATTC 34 144 1 TTTTAATATT 0.722255 -45 GTTATCACTTTAAATATTAAGCAAAGAA 34 171 0 TTTAAATATT 0.856749 -18 GGGAGAGATATTTAAAATTT 35 1 0 TTTAAAATTT 0.771416 -59 ATGAGCAATATTTAAATTTTTCGAGATAGA 37 65 1 TTTAAATTTT 0.904356 -125 ATATAATTACTATTATTATTACTAATACTT 37 149 0 TATTATTATT 0.447163 -41 CATTTGATAGTATAATATTTTCATTAAAAA 38 20 0 TATAATATTT 0.512126 -103 TACCTAATTATATAAAATTTGTGTTAAACA 38 60 0 TATAAAATTT 0.549553 -63 TTTTATTTATTTTAAATTTTTCATATTTTT 39 16 1 TTTAAATTTT 0.904356 -172 ATTTTTCATATTTTTATTTTTACTATTCTT 39 31 1 TTTTTATTTT 0.837504 -157 CTATTCTTTATTTATATATTCGGATTAATA 39 53 1 TTTATATATT 0.882322 -135 AGGTTTTAGATATTTTTATTAATCCGAATA 39 69 0 TATTTTTATT 0.503478 -119 GATTTCTTTTAAAGATTTTATTCCTGC 40 8 1 TTTAAAGATT 0.731023 -293 ATAAAAATTTTATAAAGATTATTAATAAAG 40 52 0 TATAAAGATT 0.49559 -249 TTATAAAATTTTTATTATTTTTGAAAGATA 40 67 1 TTTATTATTT 0.784491 -234 AATAGCGAAATTTTTATATTTGTTAAAATT 40 144 1 TTTTTATATT 0.765259 -157 GTAAGGTATTTTTTAATTTTAATAACTTTT 40 202 0 TTTTAATTTT 0.804352 -99 CAAATTGGCATTTTTAGTTTTTGCGGAGCA 40 273 0 TTTTTAGTTT 0.700787 -28 AGTCAGTGCTTATATTATTTACTGTATAAG 41 30 0 TATATTATTT 0.568215 -48 TTTTAAATAATATTATTTTTGATGATTTTC 42 12 1 TATTATTTTT 0.561169 -50 AGATAATTTAATAATTTTTGATGAAA 43 7 1 TTTAATAATT 0.647469 -131 ATGATTTTCATTTAATTTTTTCCTATTAAT 43 68 1 TTTAATTTTT 0.890537 -70 AATTTTTTCCTATTAATTTTCTCCTAAAAA 43 81 1 TATTAATTTT 0.597788 -57 GACACTATATTTTAAAATTTCTTTTATTAT 44 41 0 TTTAAAATTT 0.771416 -260 CCATTATTAATATTAATTTTAACAACTTTG 44 74 0 TATTAATTTT 0.597788 -227 TTGATATATTTTTATTTTTTATTTCACTGT 45 72 1 TTTATTTTTT 0.910707 -229 GTTAATAAAGTTTATTAATTAAGTTTGAAC 45 174 0 TTTATTAATT 0.697198 -127 AACTATAAATTTTTTATATTACATTGTAAG 45 214 1 TTTTTATATT 0.765259 -87 ACATTGTAAGTATAAAGATTAAAAATTAAA 45 234 1 TATAAAGATT 0.49559 -67 AAAACTCTCATTTAATTTTTAATCTTTATA 45 244 0 TTTAATTTTT 0.890537 -57 AAATGAGAGTTTTAATAATTAAAATTTAAA 45 261 1 TTTAATAATT 0.647469 -40 TAGCTATAACTTTAAATTTTAATTATTAAA 45 271 0 TTTAAATTTT 0.904356 -30 AGATAATTATTTTATTTTTTGTCAATCAAT 46 46 1 TTTATTTTTT 0.910707 -183 TGTCAATCAATTTTTATATTATTGATGCCC 46 65 1 TTTTTATATT 0.765259 -164 TTAACTTTATTTTATTTTTTATTGAATTAA 46 102 1 TTTATTTTTT 0.910707 -127 AAGAGGCTTATTTTTAGTTTATTTTTAG 48 130 1 TTTTTAGTTT 0.700787 -18 TATCTTTATTTTTATTATTTTTATTTCAAA 50 25 1 TTTATTATTT 0.784491 -41 AAAGAAATCATATATAAATTATAATATATT 51 44 1 TATATAAATT 0.491716 -33 AGTCCATTGTTATATAGATTAGGATTTTTC 53 13 0 TATATAGATT 0.551916 -288 AAGAGATTGTTTTATAATTTTAGAGGACTA 53 217 1 TTTATAATTT 0.808823 -84 ********** Masking position 3 Map Score: 111.5 Number of sites scoring better than the average of aligned sites = 3296 Number in coding regions = 2179 Number in noncoding regions = 1117 Number of orfs with sites within 600 bp upstream = 648 Fraction of orfs with sites within 600 bp upstream = 0.10408 Motif number 3 CAAACGAAACTTTTAGAAAAAGTTAAACAAAATC 1 144 0 TTTAAAAATT 0.899678 -157 GCATAAATTTTCTTTAAAAAATTTATTTCTACGA 2 113 1 TTTTAAAATT 0.941535 -55 ACCTTATAATAATTATAAAAGGTTTGAAGGAAAA 5 41 1 ATTAAAAATT 0.851124 -37 ATTTATTTTACAATTTTTGGAAAGATA 6 4 1 TTTTACAATT 0.865339 -54 GCAAATTGGATGTTTAAAAAATTTTTATTCCTAC 9 56 1 TTTTAAAATT 0.941535 -65 TACTCTTTAAATTTTTAATATCTTTATTTTTTTG 13 83 0 ATTTAATATT 0.851124 -218 CTTAAAAGGAATTTACAAAATGTTGGCTGATTTT 13 118 1 ATTAAAAATT 0.851124 -183 TTTATATATTTTTTAGAATATATTGAGAAATATG 14 75 0 TTTAAATATT 0.833165 -68 ACTATAAAAAACTTATAATAACTTACTTGCCATA 15 190 1 ATTAAATATT 0.760972 -92 TAATACCATTTCTTTTAAAACTTTCGATTTGTTC 17 94 0 TTTTAAAATT 0.941535 -65 TGTTTTTAGAAGTTTTAATAGATTATCGTCATTT 18 127 0 ATTTAATATT 0.851124 -40 ATTTATATACTATTTTAAAAGATTATCGCACTTA 21 92 1 TTTTAAAATT 0.941535 -168 AATAATTTTATTTTTTACTATTTTTTGGGTGATT 21 234 1 TTTTACTATT 0.781587 -26 TTAACTTAAGTTTTTAACAATATTTATACTTTAT 22 30 1 TTTTACAATT 0.865339 -59 TACTTAAGATATTTTAAAAATATTTAAATTTATC 24 276 0 ATTTAAAATT 0.91124 -25 ACATAGATAGTGTTATAAAATATTCTCCATTATA 25 50 1 TTTAAAAATT 0.899678 -45 CGAACAACCTTTTTAGAAAAGGTTGATCAAAATC 29 134 0 TTTAAAAATT 0.899678 -43 ATTTTTATTGATTTTGAAAAGATTAAAATTAAAC 31 53 0 ATTTAAAATT 0.91124 -33 AATCTTGCCTTATTACAATATTTTTAGAAAAATA 32 42 1 TTTAAATATT 0.833165 -67 TAAATTCAAAAATTTCAAAACTTTTTCAAAACAA 33 16 1 ATTTAAAATT 0.91124 -59 TATTATCATTATTTTTAATAACTTCCGTATCAAA 37 107 1 ATTTAATATT 0.851124 -83 ATAAAATTTGTGTTAAACAAAATTGATGACATTT 38 45 0 TTTAACAATT 0.781587 -78 TTTTTTCATTTCTTTCAAAAATTTGAAAAATTTT 39 163 0 TTTTAAAATT 0.941535 -25 GGTATTTTTTAATTTTAATAACTTTTGCAAAAAC 40 194 0 ATTTAATATT 0.851113 -107 ATTAATATTAATTTTAACAACTTTGAAAGACACT 44 65 0 ATTTACAATT 0.80379 -236 ACTAAAAGGTTCTTTCAAAATGTTTTTGAAAGAT 44 253 1 TTTTAAAATT 0.941535 -48 GTGCCTTAGTTATTACAAAATATTTTAAAAAGAA 45 113 0 TTTAAAAATT 0.899678 -188 AGTATATGATTATTTAAATAGTTTATGAACTTAA 46 134 0 TTTTAATATT 0.899678 -95 CTTTATAACCTTTTTAACTATATTTAGAAGAGGG 46 197 0 TTTTACTATT 0.781587 -32 TTATTATTTTTATTTCAAAAATTTTTGGAGGTAT 50 36 1 TTTTAAAATT 0.941535 -30 ATCATATATAAATTATAATATATTCAGTTAGATA 51 50 1 ATTAAATATT 0.760972 -27 * *** **** ** Masking position 7 Map Score: 43.0365 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 605 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 4 AAATTCACCATTAAAAACTGTTAAGTT 1 284 0 ACCATAAAAA 0.603416 -17 AGCATAAATTTTCTTTAAAAAATTTATTTCT 2 112 1 TTCTTAAAAA 0.823033 -56 TAGCATAACATTCAACAAAAAATTATTGAAG 4 29 1 TTCACAAAAA 0.92426 -29 AAATTTTTATTCCTACAAAAATCGTATAGTT 9 74 1 TCCTCAAAAA 0.862893 -47 ATCAGTTAAATTTAATAAAAAAAGAGTAACT 12 263 0 TTTATAAAAA 0.742075 -38 GTATCTATTTTTTTACAAAAAAATAAAGATA 13 68 1 TTTTCAAAAA 0.839943 -233 GGGATTAAATTTCACTAAAAATTTATACTCC 13 205 1 TTCATAAAAA 0.847963 -96 CTTTTCACCAAAAAGGTCTAAATT 16 95 0 TTCACAAAAA 0.92426 -14 AAAAGACGATATTACCAAAAAGAAAGGGGAT 17 135 1 ATTACAAAAA 0.735753 -24 TATTTATTCTTTCTGCAAAAACCTTAAAAAC 18 55 1 TTCTCAAAAA 0.91074 -112 ATCTATTAAAACTTCTAAAAACATAAAAATC 18 138 1 ACTTTAAAAA 0.396245 -29 TTTAATTTTTATTTTCAAAAATCTGAATAAT 23 22 1 ATTTCAAAAA 0.699193 -279 GAATTTTTAAATTAACAAAAATAAAATAATG 27 209 1 ATTACAAAAA 0.735753 -92 TTAATAATATTCCAACAAAAACCGGATTTAA 27 256 0 TCCACAAAAA 0.882723 -45 TTGATCAACCTTTTCTAAAAAGGTTGTTCGG 29 138 1 TTTTTAAAAA 0.706036 -39 TCGGGCAGCTTTTACTAAAAAG 29 165 1 TTTATAAAAA 0.742075 -12 ACTTTTATTGTCCTATAAAAATATTTCTTTA 30 24 0 TCCTTAAAAA 0.74203 -151 AAAATTAAACATCAACAAAAACTCAGAAAAA 31 32 0 ATCACAAAAA 0.843687 -54 TCTTTTCAAAATCAATAAAAATCTCTCTTAG 31 65 1 ATCATAAAAA 0.711554 -21 TACTTTTTATTTTTCTAAAAATATTGTAATA 32 52 0 TTTTTAAAAA 0.706036 -57 TCCTAAAATGTTTTGCAAAAAACTATATATA 34 111 1 TTTTCAAAAA 0.839943 -78 ATATAAAAACTTCATTAAAAATATAGGGAGA 35 25 0 TTCATAAAAA 0.847959 -35 GTATAATATTTTCATTAAAAATTTATTAAA 38 10 0 TTCATAAAAA 0.847959 -113 ATATATTCGGATTAATAAAAATATCTAAAAC 39 66 1 ATTATAAAAA 0.559968 -122 TTTTTTCATTTCTTTCAAAAATTTGAAAAAT 39 166 0 TCTTCAAAAA 0.764148 -22 TCGTATAGTATCTTTCAAAAATAATAAAAAT 40 74 0 TCTTCAAAAA 0.764148 -227 TTTTAATAACTTTTGCAAAAACTACTTGTTT 40 185 0 TTTTCAAAAA 0.839943 -116 ATTGATGAAAATCATCAAAAATAATATTATT 42 17 0 ATCACAAAAA 0.843687 -45 ACGCTTCGGTTTCATCAAAAATTATTAAATT 43 15 0 TTCACAAAAA 0.924256 -123 TAGTAAAAGGTTCATCAAAAATCTAACACCT 44 226 0 TTCACAAAAA 0.924256 -75 TTTATTAGTATCTTTCAAAAACATTTTGAAA 44 265 0 TCTTCAAAAA 0.764148 -36 TTAACATTAATTCAATAAAAAATAAAATAAA 46 107 0 TTCATAAAAA 0.847963 -122 AAATATATACCTCCAAAAATTTTTGAAAT 50 47 0 ACCTCAAAAA 0.735704 -19 **** ****** Masking position 7 Map Score: 42.6485 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 383 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 5 CAACCTAAAATAAAATAATAAAATGGTGCCGAGG 1 186 0 TATAATAAAT 0.603182 -115 GTTAATCCATAAATCTAAAAAAATAAATATAACA 1 218 0 AATAAAAAAT 0.884186 -83 CTGTTAAGTTAAGATTTAAAAAATAAATACTATT 1 260 0 AATTAAAAAT 0.782818 -41 TGAAAACTATAAATGTAATTAAATTAAAACATAA 2 28 0 AATAATTAAT 0.838149 -140 CAAACCTTATAATAATTATAAAAGGTTTGAAGGA 5 38 1 AATTATAAAG 0.374635 -40 TATTTGCTAAAAGTCTAAAAAACTAAAAAAGGGT 10 69 1 AATAAAAAAT 0.884186 -31 GATTATAAAAAACAATAAATAATTAATGTAATTA 12 212 0 AATAAATAAT 0.900667 -89 TAAATCTTAAAATCTTAAAAAAAGGTGGTACCTT 13 267 1 AATAAAAAAG 0.689617 -34 AATTTCACAAAATGATAAATAATTTAAACCTTCA 15 47 0 AATAAATAAT 0.899958 -235 GGTTCTTTTCAAAACTAATAAAATCTATTTATGA 15 85 1 AATAATAAAT 0.813437 -197 AAATATATAGAACTATAAAAAACTTATAATAACT 15 179 1 AATAAAAAAT 0.884182 -103 GGAAATTCTTAATATTAATTAACTTTAAATATTA 15 228 1 AATAATTAAT 0.838149 -54 TTTTAAAACTAATTATAAATAAATTATGGTTTTG 16 48 0 AATAAATAAT 0.899958 -61 AGTAGAATATTAAAATTAAAAATTAAATTAATTT 17 16 0 TATTAAAAAT 0.556856 -143 ATTATTAAGTTAATTTTAATAACTGAT 18 4 0 TATTAATAAT 0.598793 -163 AATATAAAGAAATCTTAAATAATTATTAAGTTAA 18 25 0 AATAAATAAT 0.900071 -142 CTTTCTGCAAAAACCTTAAAAACTTTAAAATGAT 18 63 1 AATTAAAAAT 0.782819 -104 GATGGAATAATATATTTAATAATTTCTAAAATTG 20 31 0 TATTAATAAT 0.598685 -63 ATAAAAAGTTAAAGATAAAGAAATAGGGGGAAGA 20 68 1 AATAAAGAAT 0.410237 -26 TCCGCTTAAATATTTTAAATAAGTGCGATAATCT 21 111 0 TATAAATAAT 0.759682 -149 ATAAATTTGAAAATTTAATTAACTTAAGTTTTTA 22 12 1 AATAATTAAT 0.838149 -77 AAAGTATAAATATTGTTAAAAACTTAAGTTAATT 22 28 0 TATTAAAAAT 0.556856 -61 AAAAAGTATAAATTATAAATAAATAAAGTATAAA 22 52 0 AATAAATAAT 0.899958 -37 TTTGAAAATAAAAATTAAATAATTATCTAA 23 7 0 AATAAATAAT 0.900668 -294 TTATTTTCAAAAATCTGAATAATTCAATAAACTT 23 30 1 AATGAATAAT 0.608918 -271 GGATTAATGTAATAATAAAAAAGTAAAAAAGTGG 26 21 0 AATAAAAAAT 0.884182 -43 ATATTCTACAAATATTAATTAATTATACAATTTG 27 176 1 AATAATTAAT 0.838145 -125 CATTTTGTTTAAATATAATTAATGACAAAAATTA 30 135 0 AATAATTAAG 0.601126 -40 GCAAAGTAATAAAATTTATTAAGGAAAGTTTAAA 34 39 1 AATTATTAAG 0.415722 -150 ATCCACAAATAATATTAATTAACTAATAAGGTGT 36 49 1 AATAATTAAT 0.838149 -28 ATATTATCATTATTTTTAATAACTTCCGTATCAA 37 106 1 TATTAATAAT 0.598685 -84 GTTTAACACAAATTTTATATAATTAGGTAATTTA 38 61 1 AATATATAAT 0.184752 -62 TAATCATTTTTAAGGTAATTAAATTACCTAATTA 38 80 0 TATAATTAAT 0.643541 -43 GTAAAAATAAAAATATGAAAAATTTAAAATAAAT 39 20 0 AATGAAAAAT 0.567178 -168 GTGGAGATTTTAGTATAAATAAATTTTAGAACAG 39 97 0 TATAAATAAT 0.759686 -91 TTTCTTTCAAAAATTTGAAAAATTTTACATCCTC 39 155 0 AATGAAAAAT 0.567195 -33 CTTTATTAATAATCTTTATAAAATTTTTATTATT 40 52 1 AATTATAAAT 0.673042 -249 AGGTATTTTTTAATTTTAATAACTTTTGCAAAAA 40 195 0 TATTAATAAT 0.598793 -106 GATTTTCATCAATATTAAATAAATTTAATGTGAG 42 35 1 AATAAATAAT 0.900668 -27 CGGTTTCATCAAAAATTATTAAATTATCT 43 6 0 AATTATTAAT 0.709715 -132 AAAGTTTCTTTAACATAAATAAGGTTAAAGGGAG 43 108 1 TATAAATAAG 0.479162 -30 TTTGGAGGATAATCATAATAAAAGAAATTTTAAA 44 27 1 AATAATAAAG 0.559254 -274 GTTCTTTTCAAATGTTAATAAAGTTTATTAATTA 45 183 0 AATAATAAAT 0.813437 -118 ACTTACAATGTAATATAAAAAATTTATAGTTCTT 45 211 0 TATAAAAAAT 0.726893 -90 TTGTAAGTATAAAGATTAAAAATTAAATGAGAGT 45 237 1 AATTAAAAAT 0.782675 -64 ATATAGTTAAAAAGGTTATAAAGGTGAGACT 46 208 1 AATTATAAAG 0.374635 -21 TAATAAAAATAAAGATAATAAAATGTTTATT 50 8 0 AATAATAAAT 0.813437 -58 ** ******* * Masking position 6 Map Score: 47.196 Number of sites scoring better than the average of aligned sites = 1026 Number in coding regions = 720 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 6 GCCTCGCTACGCTCGGCAATGCCTCTTA 1 4 0 GCGGCAGCCC 0.997268 -297 GCCGAGCGTAGCGAGGCAATGCATCCTATTTTGAT 1 22 1 GCGGCAGCAC 0.990383 -279 CCACGCCTTGGCCGGGCTAGGCTACCTCCGCTCTG 3 147 0 GCGGCAGCTC 0.986277 -154 TTGAACCCCCGCGGGGCAAAGCCCCATGGGATCTC 3 187 0 GCGGCAGCCC 0.997263 -114 GCACAGGATATCCAGGCTACCCCACGGCCCCGTTA 7 38 0 TCGGCACCCC 0.965582 -103 CGGGTTCAAGTCCCGGCGGCCCCACCATTTGATAT 7 92 1 TCGGCGCCCC 0.958424 -49 CGGTGCCCTATCCAGGCTAGGCTACGGGTCCTCTT 12 60 1 TCGGCAGCTC 0.958646 -241 CGTATGATAGGCCGGGCTACACCACCAGGGCATAG 24 158 0 GCGGCAACCC 0.969587 -143 CGGGTTCAAATCCCGGCCAGGGCGCCATTTGCCGG 24 213 1 TCGGCAGGCC 0.926033 -88 CCTCGCTTACGCTCGGAGGTGCAACTCAGAAGGAT 44 191 0 GCGGAGGCAC 0.858736 -110 CCTCGCTAACGCTTGGCAGTGCCTCTTAAACC 48 8 0 GCGGCGGCCC 0.996679 -140 CCAAGCGTTAGCGAGGCAGTGCATCCCGGATATTC 48 27 1 GCGGCGGCAC 0.98833 -121 ** *** * *** * Masking position 2 Map Score: 20.9997 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 5 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TGAGTAAATTTGAACTCCTTCCTAATGGAAGG 15 116 1 TGAACCCTCC 0.995608 -166 ATAACATAGATAAACTCCTTCCATTAGGAAGG 15 132 0 TAAACCCTCC 0.975121 -150 AAGGAAAGTTTAAACGCCTTCCAAAAGGAAGG 34 59 1 TAAACCCTCC 0.975115 -130 AAGGTATTTATGAACGCCTTCCTTTTGGAAGG 34 75 0 TGAACCCTCC 0.995541 -114 TGGGTAGTAATGAATGCCTTCCTTTAGTAAGG 40 226 0 TGAATCCTCC 0.975055 -75 AATGGATATTTGAACGCTCTCCTATAGGGAGG 44 99 1 TGAACCTTCC 0.975119 -202 AAGGCATTAATGAACACCTCCCTATAGGAGAG 44 115 0 TGAACCCCCC 0.979289 -186 AAGGCACTGATGAACTCCTTCCATTAGGAAGG 45 140 1 TGAACCCTCC 0.995608 -161 TAATTAAGTTTGAACTCCCTTCCTAATGGAAG 45 157 0 TGAACCCTTC 0.951943 -144 GGATTTCATCTGAATCCTCTCCGAGCTAAAGC 47 35 0 TGAATCTTCC 0.871393 -266 ***** ** *** Masking position 4 Map Score: 17.6788 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 4 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TAAGAGGCATTGCCGAGCGTAGCG 1 2 1 AAGAGGCGCC 0.901414 -299 TGGAGATCCCATGGGGCTTTGCCCCGCGGGGGT 3 185 1 ATGGGGCGCC 0.995577 -116 CCTAGCCTGGATAGGGCACCGGCCTTCTAAGCC 12 48 0 ATAGGGCGGC 0.987945 -253 TCTGGCGGGAAAGGGGCGACGCCGCCGGCCACT 24 86 1 AAGGGGCGCC 0.986351 -215 AGCCCGGCAAATGGCGCCCTGGCCGGGATTTGA 24 218 0 ATGGCGCGGC 0.927565 -83 GGGTATCCCAATAGGGCGAAGTCCTATGGTGTC 29 90 0 ATAGGGCGTC 0.965148 -87 AATAAAGTTAATGGGGCTTTCGCAGGAATAAAA 40 26 0 ATGGGGCCGC 0.927565 -275 TCCAGAAACCATAGGGCTTCGCCTATTGGTATA 44 153 1 ATAGGGCGCC 0.99294 -148 ACGCTCGAAGATAGGGAGGCGGCGAGACAAACA 47 93 1 ATAGGGAGGC 0.843704 -208 GGTTGGTGTCATCGGGCAGAGTCAGAGCTACCC 47 166 0 ATCGGGCGTC 0.894971 -135 GGTTTAAGAGGCACTGCCAAGCGTTAGC 48 6 1 AAGAGGCGCC 0.901414 -142 TTTTCACACCATAGGGCTCTGCCCTATTGGAAT 48 58 0 ATAGGGCGCC 0.99294 -90 GTAGCTTACCATAGGGCTCCGCCTTA 52 49 1 ATAGGGCGCC 0.99294 -16 ******* *** Masking position 1 Map Score: 18.2348 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 17 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 ATTTAGCTAAGTATAAATTATGTTTTAA 2 9 1 AAGTATAAAT 0.826807 -159 TTAAAATGAAAACTATAAATGTAATTAAAT 2 38 0 AACTATAAAT 0.87123 -130 ACCTTATAATAATTATAAAAGGTTTGAAGG 5 41 1 AATTATAAAA 0.631328 -37 AAGTCTAAAAAACTAAAAAAGGGTTTTTAA 10 79 1 AACTAAAAAA 0.774067 -21 TTGTATGGTTAATTATAAATATAGGTTTGT 12 171 1 AATTATAAAT 0.771592 -130 TCCCATAATGAACTAAAAATGAAATAAAAT 13 179 0 AACTAAAAAT 0.871232 -122 AAATATATAGAACTATAAAAAACTTATAAT 15 179 1 AACTATAAAA 0.774067 -103 TTTTAAAACTAATTATAAATAAATTATGGT 16 52 0 AATTATAAAT 0.771592 -57 AGAATATTAAAATTAAAAATTAAATTAATT 17 17 0 AATTAAAAAT 0.77178 -142 AAAGTTTAGAAAATATAAAAATTTAATAGA 19 49 1 AAATATAAAA 0.699759 -43 AAATATAAATTAATCCTTAT 21 1 1 AAATATAAAT 0.821511 -259 TAAATAAATAAAGTATAAATATTGTTAAAA 22 41 0 AAGTATAAAT 0.826807 -48 ACCAACTAAAAAGTATAAATTATAAATAAA 22 63 0 AAGTATAAAT 0.826807 -26 AGATTTTTGAAAATAAAAATTAAATAATTA 23 16 0 AAATAAAAAT 0.821512 -285 CTTAGAAATTAAATAAAAATCCTTTGAACT 23 94 1 AAATAAAAAT 0.821512 -207 CAAACAACAAAATTAAAAATCCTAAAACCC 23 190 1 AATTAAAAAT 0.77178 -111 ATAAACATCAAACTATAAAAATCATTAGCA 23 276 1 AACTATAAAA 0.774067 -25 AATAATAAAAAAGTAAAAAAGTGGTTTAAA 26 15 0 AAGTAAAAAA 0.707382 -49 TATATAACTTAAATAAAAATAATAGTTATT 27 29 0 AAATAAAAAT 0.821512 -272 AAAATCTAATAACTATAAATGACTATAAAT 27 63 1 AACTATAAAT 0.87123 -238 ATATAAGATAAAATATAAAATTTAG 27 286 1 AAATATAAAA 0.699759 -15 AGGACAATAAAAGTAAAAAATAAATATGAG 30 41 1 AAGTAAAAAA 0.707382 -134 GAAAAATAAAAAGTAAAAATAAAAGCAAAT 32 68 1 AAGTAAAAAT 0.826809 -41 CTTTGCAAAAAACTATAAAAACTTTGGTGG 34 15 0 AACTATAAAA 0.774067 -174 AATTTAAAATAAATAAAAATCAA 39 4 0 AAATAAAAAT 0.821512 -184 AGAATAGTAAAAATAAAAATATGAAAAATT 39 30 0 AAATAAAAAT 0.821512 -158 AAATTTTAACAAATATAAAAATTTCGCTAT 40 145 0 AAATATAAAA 0.699759 -156 AAGTTATTAAAATTAAAAAATACCTTACTA 40 204 1 AATTAAAAAA 0.63133 -97 GCTCCGCAAAAACTAAAAATGCCAATTTGG 40 274 1 AACTAAAAAT 0.871232 -27 AAACTTTGTCAATTAAAAATCT 41 66 1 AATTAAAAAT 0.77178 -12 GTGAAATAAAAAATAAAAATATATCAAAGA 45 69 0 AAATAAAAAT 0.821512 -232 ATTTGAAAAGAACTATAAATTTTTTATATT 45 204 1 AACTATAAAT 0.87123 -97 ATCATATAAAAAGTATAAATACCCCTCTTC 46 175 1 AAGTATAAAT 0.826807 -54 CTAAAAATAAACTAAAAATAAGCCTCTTA 48 129 0 AACTAAAAAT 0.871232 -19 AAAATTTTTGAAATAAAAATAATAAAAATA 50 31 0 AAATAAAAAT 0.821512 -35 AGTCCTCTAAAATTATAAAACAATCTCTTA 53 216 0 AATTATAAAA 0.631328 -85 ********** Masking position 5 Map Score: 57.5599 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 414 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 10 TTTTCTTTAAAAAATTTATTTCTACGAAAGT 2 120 1 AAATTTATTT 0.932597 -48 TTTATTTTTTAATATCTATTTACTATAAAAC 3 246 1 AAATCTATTT 0.806211 -55 TAAGAGTTTGAAGATTTATTTATAACTTATC 8 29 1 AAATTTATTT 0.932597 -28 AATTAAAAAGATAATTTATTT 10 1 0 ATATTTATTT 0.725708 -99 TTCTCATCTAAAAATTTATTTACTTCAAAAT 13 33 0 AAATTTATTT 0.932597 -268 TGTTCAATGAAATATTTACTTCTGCGAAAGT 14 25 0 AAATTTACTT 0.729738 -118 CAAAACTAATAAAATCTATTTATGAGTAAAT 15 94 1 AAATCTATTT 0.806211 -188 AATCAAAACCATAATTTATTTATAATTAGTT 16 45 1 ATATTTATTT 0.725708 -64 ATAATTATTTAAGATTTCTTTATATTTATTC 18 33 1 AAATTTCTTT 0.897987 -134 AATAATTTCTAAAATTGATTTCTAAAATTAC 20 17 0 AAATTGATTT 0.806211 -77 GTCCTATAAAAATATTTCTTTATTTGAATAT 30 15 0 AAATTTCTTT 0.897987 -160 CATCCTTACAAATATTTTTTTCTCATATTTA 30 61 0 AAATTTTTTT 0.705997 -114 AAAAGATGTAAAAATTGTTTTGAAAAAGTTT 33 33 0 AAATTGTTTT 0.419284 -42 AACCTGTTCTAAAATTTATTTATACTAAAAT 39 94 1 AAATTTATTT 0.932597 -94 TATATTTGTTAAAATTTACTTACATTAAAAC 40 158 1 AAATTTACTT 0.729738 -143 ACTATATTTTAAAATTTCTTTTATTATGATT 44 37 0 AAATTTCTTT 0.897987 -264 AAATATTTATTTACCACAACTA 51 2 1 AAATTTATTT 0.932597 -75 TAATTTATATATGATTTCTTTGTAATTAGTT 51 34 0 ATATTTCTTT 0.627316 -43 ACTATCTCTTAATATTGATTTTGAGGAGGAA 53 110 1 AAATTGATTT 0.806211 -191 TGGGAACTTTAAAATCTCTTTTTTAACAGCT 53 148 0 AAATCTCTTT 0.725785 -153 ** ******** Masking position 5 Map Score: 19.9435 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 135 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 TAAGAGGCATTGCCGAGCGTAGCG 1 4 1 GAGGCTTGCC 0.951118 -297 ATCAAAATAGGATGCATTGCCTCGCTACGCT 1 26 0 GATGCTTGCC 0.711137 -275 GAGATCCCATGGGGCTTTGCCCCGCGGGGGT 3 187 1 GGGGCTTGCC 0.985441 -114 TAGCCTGGATAGGGCACCGGCCTTCTAAGCC 12 48 0 AGGGCCCGGC 0.867574 -253 ATAGCGGGGGGGCCACACCCGAACCCATC 24 9 1 GGGGCACACC 0.752004 -292 GGCAGTACTCGGGGCATCGCTGGGGGGCTTA 24 54 0 GGGGCTCGCT 0.892337 -247 TGGCGGGAAAGGGGCGACGCCGCCGGCCACT 24 88 1 GGGGCACGCC 0.978732 -213 AAGACACCATAGGACTTCGCCCTATTGGGAT 29 88 1 AGGACTCGCC 0.767108 -89 CAGAAACCATAGGGCTTCGCCTATTGGTATA 44 155 1 AGGGCTCGCC 0.980394 -146 GGTTTAAGAGGCACTGCCAAGCGTTAGC 48 8 1 GAGGCCTGCC 0.963115 -140 GAATATCCGGGATGCACTGCCTCGCTAACGC 48 31 0 GATGCCTGCC 0.767644 -117 TTCACACCATAGGGCTCTGCCCTATTGGAAT 48 58 0 AGGGCCTGCC 0.973044 -90 AGCTTACCATAGGGCTCCGCCTTA 52 51 1 AGGGCCCGCC 0.985316 -14 ***** ***** Masking position 5 Map Score: 14.4128 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 12 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 TAGGATGCATTGCCTCGCTACGCTCGGCAA 1 20 0 TGCCTCGCTA 0.793527 -281 CCGGGTCGCACGCCCCCCAAGCGCACAGGA 7 65 0 CGCCCCCCAA 0.710235 -76 TAAATTTGAACTCCTTCCTAATGGAAGGAG 15 120 1 CTCCTTCCTA 0.932253 -162 CATAGATAAACTCCTTCCATTAGGAAGGAG 15 130 0 CTCCTTCCAT 0.790923 -152 GGTTACTCCTCCCTACCATTTTGTT 30 160 0 CTCCTCCCTA 0.965784 -15 AAAGTTTAAACGCCTTCCAAAAGGAAGGCG 34 63 1 CGCCTTCCAA 0.898033 -126 TATTTATGAACGCCTTCCTTTTGGAAGGCG 34 73 0 CGCCTTCCTT 0.951809 -116 TAGTAATGAATGCCTTCCTTTAGTAAGGTA 40 224 0 TGCCTTCCTT 0.810608 -77 CATTAATGAACACCTCCCTATAGGAGAGCG 44 113 0 CACCTCCCTA 0.834936 -188 AATCTAACACCTCCTCGCTTACGCTCGGAG 44 208 0 CTCCTCGCTT 0.88396 -93 GATTTCGATGTGCCTCCCTTAAAGGGTTCG 45 41 0 TGCCTCCCTT 0.897742 -260 CACTGATGAACTCCTTCCATTAGGAAGGGA 45 144 1 CTCCTTCCAT 0.790923 -157 TTCATTAACTCTCCTTGCTACGCTCGAAGA 47 74 1 CTCCTTGCTA 0.825477 -227 TTTGTCTCGCCGCCTCCCTATCTTCGAGCG 47 94 0 CGCCTCCCTA 0.980987 -207 GTGTTGGAACCTCCACCCTTTAGGTGGAGA 47 241 1 CTCCACCCTT 0.66984 -60 CGGGATGCACTGCCTCGCTAACGCTTGGCA 48 25 0 TGCCTCGCTA 0.793527 -123 ********** Masking position 4 Map Score: 15.871 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 119 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 AAATTATGTTTTAATTTAATTACATTTATAG 2 25 1 TTAATTAATT 0.626085 -143 TAACTATCCTTTAACCTTACTAAAAACCGAA 3 29 1 TTAACTTACT 0.529363 -272 TTAGATTTTTAAACTTATTATTCTTTTTA 7 9 1 TTAACTTATT 0.836978 -132 AATTATCTTTTTAATTTTACTAATTCTTCTT 10 16 1 TTAATTTACT 0.606488 -84 TCTGAATCAGTTAAATTTAATAAAAAAAGAG 12 268 0 TTAATTTAAT 0.800626 -33 AAATTAAAAATTAAATTAATTTACTAT 17 7 0 TTAATTAATT 0.626085 -152 AATTTAATTTTTAATTTTAATATTCTACTAG 17 21 1 TTAATTTAAT 0.800626 -138 AATTATTAAGTTAATTTTAATAACTGAT 18 8 0 TTAATTTAAT 0.800626 -159 AATTAAATTTTCAAATTTATT 22 1 0 TCAATTTATT 0.632113 -88 TGTTAAAAACTTAAGTTAATTAAATTTTCAA 22 18 0 TTAATTAATT 0.626085 -71 TTTAGAATATTTAAGTTTATTGAATTATTCA 23 45 0 TTAATTTATT 0.875545 -256 GATCAAAATCTTAATTTAAATGGGTATCCCA 29 113 0 TTAATTAAAT 0.488694 -64 AGTCTCTCTTTTAACCTAATTTTTGTCATTA 30 119 1 TTAACTAATT 0.549951 -56 TTGTTGATGTTTAATTTTAATCTTTTCAAAA 31 45 1 TTAATTTAAT 0.800626 -41 AAGACCTTGCTTAACCTTAATCTTGCCTTAT 32 24 1 TTAACTTAAT 0.745589 -85 TGCAAAGTAATAAAATTTATTAAGGAAAGTT 34 38 1 TAAATTTATT 0.522153 -151 AATTTTAATATTAATCTTATTCTTTGCTTAA 34 152 1 TTAACTTATT 0.836978 -37 TATTAGTTAATTAATATTATTTGTGGATATA 36 46 0 TTAAATTATT 0.334808 -31 CTATCCCTAATCAATCTTAATCATTTTTAAG 38 100 0 TCAACTTAAT 0.417175 -23 AAACCTGTTCTAAAATTTATTTATACTAAAA 39 93 1 TAAATTTATT 0.522153 -95 GAAAGCCCCATTAACTTTATTAATAATCTTT 40 38 1 TTAATTTATT 0.875545 -263 AAGGTATTTTTTAATTTTAATAACTTTTGCA 40 199 0 TTAATTTAAT 0.800626 -102 GTTCTCACATTAAATTTATTTAATATTGAT 42 42 0 TTAATTTATT 0.875545 -20 AGCTCTCCCTTTAACCTTATTTATGTTAAAG 43 115 0 TTAACTTATT 0.836978 -23 GGAAGGGAGTTCAAACTTAATTAATAAACTT 45 166 1 TCAACTTAAT 0.417175 -135 ACTTAATTAATAAACTTTATTAACATTTGAA 45 180 1 TAAATTTATT 0.522153 -121 CCCCCATATATTAACTTTATTTTATTTTTTA 46 92 1 TTAATTTATT 0.875545 -137 **** ****** Masking position 7 Map Score: 28.665 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 232 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 14 TCATTTTAAGACTTTCGCAGTATTATATAT 2 59 1 ACTTTCGCAG 0.983839 -109 AAGATTTAGGACTTTCGTAGAAATAAATTT 2 131 0 ACTTTCGTAG 0.974606 -37 ACTTTCATAGTCAATATAAG 2 158 0 ACTTTCATAG 0.897734 -10 ATTGAATAGAACTTTCGCAGAAGTAAATAT 14 15 1 ACTTTCGCAG 0.983839 -128 TTTCAATAGAACTTTCGCAGTTTATATATT 14 99 0 ACTTTCGCAG 0.983839 -44 AGTTAATGGGGCTTTCGCAGGAATAAAATC 40 24 0 GCTTTCGCAG 0.941756 -277 GTATTTTATGACTTTCGTATAGTATCTTTC 40 89 0 ACTTTCGTAT 0.810815 -212 CCATCACCTAACTTTCATAGAATATTGCAG 46 12 1 ACTTTCATAG 0.897734 -217 ********** Masking position 9 Map Score: 9.69579 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 7 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 ATTTATTTTTTTAGATTTATGGATTAACTATTTTTA 1 224 1 TTATTTGATA 0.596379 -77 GCGCCACTTCTTTTTATTTTTTAATATCTATTTACT 3 234 1 TTTTTTTATA 0.730655 -67 CCTCCATAATTTCGTGTTTTATAGTAAATAGATATT 3 256 0 TTCTTTAATA 0.692952 -45 AAACATCCAATTTGCATTATGGAATATTTAAACTAC 9 35 0 TTTTTTGATA 0.951277 -86 TATTTCTAATTTTTGATTTTGAAGTAAATAAATTTT 13 18 1 TTTTTTGATA 0.951277 -283 GATTTTAAGATTTATGTTTTATATTACTGATAATTT 13 245 0 TTTTTTAATA 0.916199 -56 TCGCAGTTTATATATTTTTTAGAATATATTGAGAAA 14 79 0 TATTTTAATA 0.664027 -64 TTTATAGTTCTATATATTTTGGAATATAAATAGTAT 15 162 0 TATTTTGATA 0.779225 -120 TAAATTATGGTTTTGATTATAGAGTAAGCTATAAAA 16 27 0 TTTTTTAATA 0.916198 -82 AGAATCCCCTTTCTTTTTGGTAATATCGTCTTTTT 17 134 0 TTTTTGGATA 0.651138 -25 AAAGGGATTCTTCCATTTATATACTATTTTAAAAGA 21 78 1 TTCTTTAATA 0.692952 -182 GCCGGGCTTCTTTTTATTTTAGAACAATTAATCGAT 24 243 1 TTTTTTAACA 0.52365 -58 TAAACCACTTTTTTACTTTTTTATTATTACATTAAT 26 17 1 TTTTTTTATA 0.730655 -47 AATCTCACCTTTTGCTTTTGGATTAATGTAATAAT 26 39 0 TTTTTTGATA 0.951277 -25 ATTATTTTTATTTAAGTTATATATTAGAAAATCTAA 27 36 1 TTTTTTAATA 0.916199 -265 TAACCAAAGTTTTAGCTTTTGTATAATTGCTTCATG 27 120 1 TTTTTTGAAA 0.569806 -181 ATTATACAATTTGAATTTTTAAATTAACAAAAATAA 27 197 1 TTGTTTAATA 0.550826 -104 AAAAGATAATTTTAGCTTCTGAAATAGTATTTGGTA 28 33 0 TTTTTTGATA 0.951277 -30 TCACCTTGATTTTTTCTTATACAGTAAATAATATAA 41 15 1 TTTTTTAATA 0.916189 -63 GGCGAAGCCCTATGGTTTCTGGAATAACTAAGGCAT 44 140 0 TATTTTGATA 0.779225 -161 AACAATGGACTTTTATTTGTGTATTATTTTAGACAC 53 32 1 TTTTTTGATA 0.951277 -269 *** ** ** * ** Masking position 8 Map Score: 14.4962 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 81 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467