AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_mjan_reg_300.orf -o00340_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: MJ0302 117 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) MJ1425 25 malate dehydrogenase MJ0703 24 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA2) MJ1430 88 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) MJ1532 34 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA1) Input sequences: #1 MJ0303 44 riboflavin synthase beta chain (ribH) #2 MJ0304 89 ferripyochelin binding protein (fbp) #3 MJ0406 154 ribokinase (rbsK) #4 MJ0408 118 conserved hypothetical protein #5 MJ0409 62 M. jannaschii predicted coding region MJ0409 #6 MJ0411 41 imidazoleglycerol-phosphate synthase, cyclase subunit (hisF) #7 MJ0507 142 transcription initiation factor IID, TATA-box binding protein #8 MJ0508 126 LSU ribosomal protein L12A (P1) #9 MJ0509 25 LSU ribosomal protein L10E #10 MJ0510 300 LSU ribosomal protein L1P (rplA) #11 MJ0535 300 acetylpolyamine aminohydrolase (aphA) #12 MJ0697 68 fibrillarin (fib) #13 MJ0698 167 imidazoleglycerol-phosphate dehydrogenase/histidinol-phosphatase (hisB) #14 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #15 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #16 MJ1000 202 histidyl-tRNA synthetase (hisS) #17 MJ1027 125 formate hydrogenlyase, subunit 5 #18 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #19 MJ1029 47 dimethyladenosine transferase (ksgA) #20 MJ1204 21 ATP phosphoribosyltransferase (hisG) #21 MJ1206 300 conserved hypothetical protein #22 MJ1391 300 putative aminotransferase #23 MJ1424 202 tRNA intron endonuclease (endA) #24 MJ1427 97 M. jannaschii predicted coding region MJ1427 #25 MJ1456 77 histidinol dehydrogenase (hisD) #26 MJ1521 88 Na+/H+ antiporter #27 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #28 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #29 MJ1575 300 GMP synthase (guaA) #30 MJ1576 80 LemA protein #31 MJ1577 29 M. jannaschii predicted coding region MJ1577 #32 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) Motif number 1 ACTAAATAGAAATAACAAAAATCCTTTGAAG 1 18 1 AAAACAAAAA 0.889155 -27 ACATTTAAAAAAGTATAAAAAATGTGA 2 7 0 AATATAAAAA 0.837933 -83 AACTACATATAACATTTAAAAAAGTATAAAA 2 18 0 AAATTTAAAA 0.847432 -72 AATATCTAAAAATAACATAAAAAACTTTTTG 2 61 1 AAAACATAAA 0.858889 -29 CTAAAAATCTTTAAGTAGTAGTTC 3 4 1 AAATCTTTAA 0.700639 -151 GTAGTAGTTCAATAATTTTAACTTTAAAGTT 3 25 1 AAAATTTTAA 0.843881 -130 TGTCTTTCAAAAAATAAAAATTTATTAATG 4 10 1 AAAATAAAAA 0.925371 -109 AGGCGTTCAAAAGTTCATTAATAAATTTTTA 4 25 0 AATTCATTAA 0.593182 -94 GAAATATAATAAAAAGTAAGTA 6 2 1 AATATAATAA 0.816114 -40 AATAAAAAGTAAGTATAATAAAAATAGGGAT 6 18 1 AATATAATAA 0.816114 -24 TGTAATATTTAAAAATAAAAAAAGAAAGTAG 7 16 0 AAAATAAAAA 0.925371 -127 TTGTATATTTAACTTAATAAATGTAATATTT 7 37 0 AATTAATAAA 0.457615 -106 AATTTTATGTAATATTTAAAAGTATTTATAT 7 67 1 AAATTTAAAA 0.847432 -76 CCGAAAAATATAAATAACTAATTA 8 4 1 AAAATATAAA 0.903925 -123 GTAATATCTAAACAATATTAATTTGAAGTAG 8 55 0 AAAATATTAA 0.889822 -72 GGTTAAAACAAATAAATAAAACACAAAGGAG 8 86 1 AAAAATAAAA 0.727273 -41 TTTGCTATTAAAGATTTATAAAATAGCCTCA 10 236 1 AAATTTATAA 0.826628 -65 AATCTAATGCAATATAAATAATAACTTATAT 12 28 0 AAATAAATAA 0.695962 -41 TTTATCACCAAAAAATAATAAATCTAATGCA 12 48 0 AAAATAATAA 0.914117 -21 TTTACTAAAAAATAATTTTAAATTTATCTAA 13 146 0 AAAATTTTAA 0.843881 -22 TTTTAATTGTAATTTTATAAAATCGTAAG 14 70 1 AATTTATAAA 0.724192 -19 TTTAACCAAAAATATTTTAAATAAGATTTCT 15 24 0 AAATTTTAAA 0.808231 -25 GTTTATATAGAATTTCATTAACATATACATA 16 41 0 AATTCATTAA 0.593182 -162 AAGTTGATTCAACATCAATAACTGTAAATAT 16 88 1 AAATCAATAA 0.821701 -115 CAATAACTGTAAATATATAAATACTTATATC 16 103 1 AATATATAAA 0.796876 -100 TGATGAAACAAAGATTTATAAGATAGCTTTG 16 148 1 AAATTTATAA 0.826628 -55 CTCGATAACTTTATTAAAACAAAACTA 17 7 1 AATTTATTAA 0.692676 -119 ATTAAAACAAAACTATATAAAAGGTTAAGCT 17 23 1 AATATATAAA 0.796876 -103 CCAACAATTATAAACATGATAAT 17 113 0 AAAATTATAA 0.876905 -13 AAATATCAGTAAAATAAATAATGTAACAAAA 18 39 0 AAATAAATAA 0.695962 -22 AAAAAGAGAAAAGAAAATAAAAAT 19 4 0 AAAAAATAAA 0.751442 -44 TCTTTTTTAGAATAAATAAAAAGTGAAACA 19 28 1 AAAAATAAAA 0.727273 -20 ACATACTCAGAACTACTATAAATACTTTTCG 21 129 1 AATACTATAA 0.657727 -172 TTATTGTATTAAATATTTTAATTAATGTCTT 21 163 1 AATATTTTAA 0.692676 -138 TAGGCGTCAAAATAAAAATAATTTTTTATAC 21 206 1 AAAAAAATAA 0.773761 -95 AAACAAATCAAAGTATAAAAAATTATTTTTA 21 218 0 AATATAAAAA 0.837933 -83 TCGCAGGAATAAAATCTTTAAAAGAAATC 22 9 0 AAATCTTTAA 0.700639 -292 AAATTTTATAAAGATTATTAATAAAGTTAAT 22 47 0 AAATTATTAA 0.843881 -254 ATCTTTCAAAAATAATAAAAATTTTATAAAG 22 65 0 AAAATAAAAA 0.925371 -236 AAATTTTAACAAATATAAAAATTTCGCTATT 22 144 0 AATATAAAAA 0.837933 -157 AAAAGTTATTAAAATTAAAAAATACCTTACT 22 202 1 AAATTAAAAA 0.892461 -99 AATGCTCCGCAAAAACTAAAAATGCCAATTT 22 271 1 AAAACTAAAA 0.842985 -30 ATTCCTGCGAAAGTTCTATAATATTGAGGTG 23 16 0 AATTCTATAA 0.562583 -187 TATGTTATTTAACAAAATTAATGAATGAATT 23 122 0 AAAAAATTAA 0.721844 -81 AATTTTGTTAAATAACATAAACCATATGTTA 23 134 1 AAAACATAAA 0.858889 -69 TATTGTGGATAATAAAATAAATAACATATGG 23 155 0 AAAAAATAAA 0.751442 -48 TATTATTTATAAAATCTTAAAATTTATTGTG 23 179 0 AAATCTTAAA 0.731654 -24 ATTTACAACAAAAAATAAAAAGTTTGAAGC 24 10 0 AAAATAAAAA 0.925371 -88 TTTTGTTGTAAATATTTATAATTTATAGAAC 24 28 1 AAATTTATAA 0.826628 -70 TTTTAAAGATAATAACAATAACAACCAGATG 24 58 0 AAAACAATAA 0.873188 -40 CTTATACAGTAAATAATATAAGCACTGACTA 25 30 1 AATAATATAA 0.488354 -48 TCCAGATATTAAAAACTAAAAGATTGGTGGG 26 65 1 AAAACTAAAA 0.842985 -24 ATTTTGAATTAAAAATTTAAAAATTGAAA 27 9 0 AAAATTTAAA 0.862959 -138 AATATAAAATAAGAATATAAAAATATAAGTT 27 42 0 AAAATATAAA 0.903925 -105 ATATCAGAATAAGAATATAAAATAAGAATAT 27 55 0 AAAATATAAA 0.903925 -92 AAATATCAATAAAATTAAAAAGATAAGGTAA 27 88 0 AAATTAAAAA 0.892461 -59 ACTCTATAAAAAGAATTTAAAATAATACTAA 28 77 1 AAAATTTAAA 0.862959 -102 ATTAAAATAGAATTTAATAAATTACACAACA 28 109 1 AATTAATAAA 0.457615 -70 AAAGCCTTTGAATAATTTTAATCAATGAATG 28 138 0 AAAATTTTAA 0.843881 -41 ATAATAAAAGAAATTTTAAAATATAGTGTCT 29 41 1 AATTTTAAAA 0.698437 -260 TGTTAAAATTAATATTAATAATGGATATTTG 29 80 1 AAATTAATAA 0.876905 -221 CTAATAATAAAATTTATATAAGTTGATATCA 30 11 1 AATTATATAA 0.389808 -70 AAAATCCCCTAAAAATTAAAATTAATAA 31 8 0 AAAATTAAAA 0.892461 -22 TAGGTCTTTCAAAATTAATAAAATTTACTTA 32 17 0 AAATTAATAA 0.876905 -50 GACCTACTATAAAAACAAAAACAAGAGGAGA 32 42 1 AAAACAAAAA 0.889155 -25 ** ******** Masking position 2 Map Score: 78.9356 Number of sites scoring better than the average of aligned sites = 3300 Number in coding regions = 2290 Number in noncoding regions = 1010 Number of orfs with sites within 600 bp upstream = 594 Fraction of orfs with sites within 600 bp upstream = 0.0954064 Motif number 2 TCACATTTTTTATACTTTTTTAAA 2 4 1 CATTTTTATA 0.876513 -86 GATTAGCAAAAATTGTTTATATAGAGTAACT 3 52 0 AATGTTTATA 0.637513 -103 GTTCATTAATAAATTTTTATTTTTTGAAAGA 4 13 0 AATTTTTATT 0.883826 -106 AATATCACTATTTATTAGTGTCTTTC 4 103 0 CATATTTATT 0.764429 -16 TTATTATACTTACTTTTTATTATATTTC 6 8 0 TATTTTTATT 0.682715 -34 TAATATTTAAAAGTATTTATATATAAAGTAT 7 76 1 AATATTTATA 0.936603 -67 TTTATATATAAAGTATTTATATATGGGGTTT 7 91 1 AATATTTATA 0.936603 -52 GTTTGCAATTCACTATTTATAATTAGTTATT 8 23 0 CATATTTATA 0.869927 -104 TCAAAATCCGTAGATTTTATAAGATTATAGG 10 104 0 TAATTTTATA 0.728843 -197 CACTCAACCGAAAATTTTATATATGGTTTCT 10 165 1 AAATTTTATA 0.904794 -136 GAAATTTTGAAAAATTTTATATTGCTAAGAT 10 199 0 AAATTTTATA 0.904794 -102 ATTTGCTATTAAAGATTTATAAAATAGCCTC 10 235 1 AAGATTTATA 0.722159 -66 TTTTTAAGTAAAATATTTATATCAGATACCA 10 270 1 AATATTTATA 0.936603 -31 TATCCTAAATAATTTTTTATATCCCAAAAGA 11 254 1 AATTTTTATA 0.940046 -47 GCATATAAGTTATTATTTATATTGCATTAGA 12 26 1 TATATTTATA 0.806729 -43 GTCACCAAAAATTTATTGTCAATTTAG 14 7 1 AAAATTTATT 0.812612 -82 TGTAAGATATAAGTATTTATATATTTACAGT 16 108 0 AATATTTATA 0.936603 -95 CTGATGAAACAAAGATTTATAAGATAGCTTT 16 147 1 AAGATTTATA 0.722159 -56 TATTTTGTTACATTATTTATTTTACTGATAT 18 37 1 CATATTTATT 0.764422 -24 TGTTTCACTTTTTATTTATTCTAAAA 19 32 0 CATTTTTATT 0.774976 -16 TAAAACCGAAAAGTATTTATAGTAGTTCTGA 21 135 0 AATATTTATA 0.936603 -166 AAATAAAAATAATTTTTTATACTTTGATTTG 21 215 1 AATTTTTATA 0.940046 -86 ATTTCTTTTAAAGATTTTATTCCTGCGAAAG 22 12 1 AAATTTTATT 0.82178 -289 AAAAATAATAAAAATTTTATAAAGATTATTA 22 58 0 AAATTTTATA 0.904794 -243 AACAATAGCGAAATTTTTATATTTGTTAAAA 22 141 1 AATTTTTATA 0.940047 -160 TAGAACTTCGCAGTTTTTATATTAAAAAGGT 23 87 0 CATTTTTATA 0.876513 -116 AATAAATTTTAAGATTTTATAAATAATAACT 23 182 1 AAATTTTATA 0.904794 -21 GCTTCAAACTTTTTATTTTTTGTTGTA 24 7 1 AATTTTTATT 0.883826 -91 TTTTTGTTGTAAATATTTATAATTTATAGAA 24 27 1 AATATTTATA 0.936603 -71 ATTACCACCAAAAAATTTATATGCTTTCTAA 26 11 1 AAAATTTATA 0.899453 -78 TTCACATTCAAATAATTTATTACTATTATGT 27 123 0 AAAATTTATT 0.783558 -24 TTTATCACCTTATATTTTATTAGTATCTTTC 29 280 0 TAATTTTATT 0.565593 -21 CTAATAATAAAATTTATATAAGTTGATA 30 8 1 TAAATTTATA 0.716778 -73 TTTTCATAAGTAAATTTTATTAATTTTGAAA 32 11 1 TAATTTTATT 0.566002 -56 ** ******** Masking position 6 Map Score: 54.793 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 427 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 3 AATTTTTATTTTTTGAAAGACA 4 3 0 TTTTGAAAGA 0.977086 -116 ATCCAAGAAGTTTTGAAAGACACTAATAAA 4 89 1 TTTTGAAAGA 0.977086 -30 ATTATTAAGTCTTTAAAATAAATAT 5 6 0 CTTTAAAATA 0.792788 -57 TCTTTTTTTATTTTTAAATATTACATTTAT 7 22 1 TTTTTAAATA 0.778811 -121 TATATAAATACTTTTAAATATTACATAAAA 7 69 0 CTTTTAAATA 0.603749 -74 AATCCGTAGATTTTATAAGATTATAGGAAA 10 101 0 TTTTATAAGA 0.687856 -200 TTTCAGGAAATTTTGAAAAATTTTATATTG 10 206 0 TTTTGAAAAA 0.732695 -95 CAGAAATCTTATTTAAAATATTTTTGGTTA 15 23 1 ATTTAAAATA 0.56386 -26 ATCAGCATAATTTTGTAAGATATAAGTATT 16 122 0 TTTTGTAAGA 0.829505 -81 GGAATAAAATCTTTAAAAGAAATC 22 5 0 CTTTAAAAGA 0.890985 -296 TTTTTATTATTTTTGAAAGATACTATACGA 22 75 1 TTTTGAAAGA 0.977086 -226 TTGCGGAGCATTTTAAAAGAATATATGGGT 22 253 0 TTTTAAAAGA 0.950454 -48 ATAAGTTAAATTTTGAATTAAAAATTTAAA 27 19 0 TTTTGAATTA 0.552149 -128 TACTATTATGTTTTTAAATATCAATAAAAT 27 104 0 TTTTTAAATA 0.778811 -43 TTTTAAAACATTTTGAAATACTAAGGACCA 28 46 0 TTTTGAAATA 0.952403 -133 TTTCAAAATGTTTTAAAAGACTCTATAAAA 28 58 1 TTTTAAAAGA 0.950454 -121 TATAAAAAGAATTTAAAATAATACTAAAAT 28 81 1 ATTTAAAATA 0.56386 -98 ATAAAAGAAATTTTAAAATATAGTGTCTTT 29 44 1 TTTTAAAATA 0.900541 -257 ATTTTAACAACTTTGAAAGACACTATATTT 29 59 0 CTTTGAAAGA 0.947251 -242 TTCAAAAACATTTTGAAAGAACCTTTTAGT 29 253 0 TTTTGAAAGA 0.977086 -48 TTCAAAATGTTTTTGAAAGATACTAATAAA 29 266 1 TTTTGAAAGA 0.977086 -35 ATTTTATTAATTTTGAAAGACCTACTATAA 32 24 1 TTTTGAAAGA 0.977086 -43 ********** Masking position 4 Map Score: 35.9596 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 309 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 AAATTAAACTAAATAGAAAT 1 1 1 AAATTAAACT 0.559548 -44 GTCTTTCAAAAAATAAAAATTTATTAATGA 4 12 1 AAATAAAAAT 0.895949 -107 AAAGTAAGTATAATAAAAATAGGGATAGG 6 23 1 TAATAAAAAT 0.837055 -19 TAATATTTAAAAATAAAAAAAGAAAGTAGA 7 15 0 AAATAAAAAA 0.864518 -128 TATAAATAACTAATTATAAATAGTGAATTG 8 19 1 TAATTATAAA 0.379552 -108 TAAAACAAATAAATAAAACACAAAGGAGAA 8 89 1 AAATAAAACA 0.640639 -38 GCTTCATAGAAAATAAAACTATTTTAGCCA 10 36 1 AAATAAAACT 0.706367 -265 TATCACCAAAAAATAATAAATCTAATGCAA 12 47 0 AAATAATAAA 0.660055 -22 TTTTTAGATAAATTTAAAATTATTTTTTAG 13 143 1 AATTTAAAAT 0.697305 -25 TTTTACTAAAAAATAATTTTAAA 13 155 0 TACTAAAAAA 0.378771 -13 TAATAAAAAATCCAGAAATC 15 1 1 TAATAAAAAA 0.791966 -48 CCAGAAATCTTATTTAAAATATTTTTGGTT 15 22 1 TATTTAAAAT 0.578909 -27 TCGATAACTTTATTAAAACAAAACTATATA 17 12 1 TATTAAAACA 0.350298 -114 AATTTATCATAATTAATAATGATAATTAGC 17 51 0 AATTAATAAT 0.570492 -75 AGAGAAAAGAAAATAAAAAT 19 1 0 AAATAAAAAT 0.895949 -47 TTTTTAGAATAAATAAAAAGTGAAACA 19 31 1 AAATAAAAAG 0.614395 -17 TTCAAGACATTAATTAAAATATTTAATACA 21 167 0 TAATTAAAAT 0.730666 -134 ATAGGCGTCAAAATAAAAATAATTTTTTAT 21 205 1 AAATAAAAAT 0.895949 -96 TAACATAATCTAATAAAACAAATCAAAGTA 21 234 0 TAATAAAACA 0.5154 -67 CCATTAACTTTATTAATAATCTTTATAAAA 22 45 1 TATTAATAAT 0.442096 -256 CTTTCAAAAATAATAAAAATTTTATAAAGA 22 64 0 TAATAAAAAT 0.837055 -237 AAAGTTATTAAAATTAAAAAATACCTTACT 22 203 1 AAATTAAAAA 0.771158 -98 GCTCCGCAAAAACTAAAAATGCCAATTTGG 22 274 1 AACTAAAAAT 0.579669 -27 TTACAACAAAAAATAAAAAGTTTGAAGC 24 9 0 AAATAAAAAG 0.614395 -89 GATGTTCTATAAATTATAAATATTTACAAC 24 32 0 AAATTATAAA 0.506267 -66 AAACTTTGTCAATTAAAAATCT 25 66 1 AATTAAAAAT 0.81361 -12 TTAAATTTTGAATTAAAAATTTAAAAATTG 27 14 0 AATTAAAAAT 0.81361 -133 AATATCAATAAAATTAAAAAGATAAGGTAA 27 88 0 AAATTAAAAA 0.771158 -59 ATTTTATTGATATTTAAAAACATAATAGTA 27 104 1 TATTTAAAAA 0.504703 -43 CTATAAAAAGAATTTAAAATAATACTAAAA 28 80 1 AATTTAAAAT 0.697305 -99 AATAATACTAAAATTAAAATAGAATTTAAT 28 97 1 AAATTAAAAT 0.81973 -82 TTAAAATTAATATTAATAATGGATATTTGA 29 82 1 TATTAATAAT 0.442096 -219 CTAATAATAAAATTTATATAA 30 2 1 TAATAATAAA 0.536689 -79 AATCCCCTAAAAATTAAAATTAATAA 31 7 0 AAATTAAAAT 0.81973 -23 GGTCTTTCAAAATTAATAAAATTTACTTAT 32 16 0 AATTAATAAA 0.496048 -51 ********** Masking position 6 Map Score: 32.2665 Number of sites scoring better than the average of aligned sites = 2272 Number in coding regions = 1491 Number in noncoding regions = 781 Number of orfs with sites within 600 bp upstream = 464 Fraction of orfs with sites within 600 bp upstream = 0.0745262 Motif number 5 TTATCTTTATACAAACTACATATAACATTTAAAA 2 28 0 AACACATATA 0.853159 -62 TTAACTTTAAAGTTACTCTATATAAACAATTTTT 3 42 1 AACCTATATA 0.883583 -113 ATTTTTGCTAATCTACTATATAAAGGGTTCAAAC 3 70 1 AACATATAAA 0.893181 -85 CCCCATATATAAATACTTTATATATAAATACTTT 7 85 0 AACTTATATA 0.540052 -58 GATATTATATAAAAACCCCATATATAAATACTTT 7 100 0 AACCCATATA 0.728778 -43 AGAGTTTGCAATTCACTATTTATAATTAGTTATT 8 23 0 AACATTTATA 0.47979 -104 AGCCAGTTGAATTTACTATATAAAGTCAGAATAG 10 61 1 AACATATAAA 0.893181 -240 CTAAGATATCAGAAACCATATATAAAATTTTCGG 10 172 0 AACATATATA 0.942566 -129 TATTTATATCAGATACCATATAATATGG 10 283 1 AACATATAAT 0.779304 -18 TGTTCTTCTTAAACACGAAATATAGGGTTGGACA 11 183 0 AACAAATATA 0.526818 -118 AATACCACCATATATGCATATAAG 12 1 1 ACCCCATATA 0.310605 -68 ATGGTTGGAGAAAGACCACATATTATGTTTGTTG 13 88 1 AACACATATT 0.710447 -80 ATTTAGCTAAATTGACAATAAATTTTTGGTGAC 14 10 0 AACATAAATT 0.595261 -79 TTTTTAGATAACTTACTATATAAATTTAGCTAAA 14 33 0 AACATATAAA 0.893181 -56 TATGTTAATGAAATTCTATATAAACCTTTCGGTT 16 47 1 ATCATATAAA 0.339506 -156 TTTATTAAAACAAAACTATATAAAAGGTTAAGCT 17 20 1 CACATATAAA 0.410541 -106 ACATACTCAGAACTACTATAAATACTTTTCGGTT 21 129 1 AACATAAATA 0.776918 -172 GGCATTCATTACTACCCATATATTCTTTTAAAAT 22 240 1 ACCATATATT 0.537481 -61 GTTAAATAACATAAACCATATGTTATTTATTTTA 23 140 1 AACATATGTT 0.365992 -63 TTATTTTATTATCCACAATAAATTTTAAGATTTT 23 166 1 AACATAAATT 0.595261 -37 TAATATAAGCACTGACTATATATAAACTTTGTCA 25 43 1 AACATATATA 0.942566 -35 AAATGTTTTAAAAGACTCTATAAAAAGAATTTAA 28 63 1 AACCTATAAA 0.794536 -116 AACAACTTTGAAAGACACTATATTTTAAAATTTC 29 50 0 AACCTATATT 0.762198 -251 ATTTTGAAAGACCTACTATAAAAACAAAAACAAG 32 33 1 AACATAAAAA 0.639565 -34 * ** ******* Masking position 6 Map Score: 17.0592 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 226 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 ATATGTAGTTTGTATAAAGATAAATATCTAAAA 2 39 1 TTATAAAAAA 0.626158 -51 TATTTCACCAAAAAGTTTTTTAT 2 77 0 TTTTCACAAA 0.790755 -13 CTAAAAATCTTTAAGTAGTAGTTCAATAAT 3 8 1 TTTTAAGATA 0.8083 -147 AATTTTTAAGAATAACTTAATGATT 3 140 0 TTTTAAGAAA 0.956595 -15 ATAAATGTAATATTTAAAAATAAAAAAAGAAAG 7 19 0 TTTTAAAAAA 0.863726 -124 CTATTTAACAACTAACTTAGATAT 7 129 0 TTTTAACATA 0.76738 -14 AGCCTCATCTTTTTTAAGTAAAATATTTATATC 10 260 1 TTTTAAGAAA 0.956433 -41 TCTGATAGTCTGTTTAAGAAGAACATTGTTGTA 11 39 1 TTTTAAGAAA 0.956617 -262 TCTCTAAAATTGTTTAAGGAGAACAGTATTGTA 11 107 1 TTTTAAGAAA 0.956617 -194 CTATATTTCGTGTTTAAGAAGAACAATATTGTA 11 192 1 TTTTAAGAAA 0.956617 -109 AAAAGAGAAATATTAAACTAAAAACCTATTTT 11 279 1 TTTAAACAAA 0.685184 -22 TTTATCACCAAAAAATAATAAAT 12 56 0 TTATCACAAA 0.499685 -13 TTTAAAATTATTTTTTAGTAAAA 13 155 1 TTTTTAGAAA 0.755447 -13 AATTTTTAACCAAAAATATTTTAAA 15 34 0 TTTTAACAAA 0.945208 -15 TCGATAACTTTATTAAAACAAAACTATATAAAA 17 12 1 TTTAAAAAAA 0.444333 -114 TTCTTTTCTCTTTTTTAGAATAAATAAAAAGTG 19 20 1 TTTTTAGAAA 0.757215 -28 ATGTAAGTAAATTTTAACAAATATAAAAATTTC 22 150 0 ATTTAACATA 0.182869 -151 TGGTTTATGTTATTTAACAAAATTAATGAATGA 23 125 0 TTTTAACAAT 0.539247 -78 TATTATTTACTGTATAAGAAAAAATCAAGGTGA 25 15 0 TTATAAGAAA 0.853522 -63 TTTAAAAGACTCTATAAAAAGAATTTAAAATAA 28 69 1 TTATAAAAAA 0.626158 -110 * ****** * ** Masking position 3 Map Score: 16.6509 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 204 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 AAGTTTTTTATGTTATTTTTAGATATTTAT 2 58 0 TGTTATTTTT 0.791851 -32 GGGTTCAAACAGTTATTGTTCTAATACTTA 3 94 1 AGTTATTGTT 0.953165 -61 CAAATCATTAAGTTATTCTTAAAAATT 3 138 1 AGTTATTCTT 0.796436 -17 ATTTATAATTAGTTATTTATATTTTTCGG 8 10 0 AGTTATTTAT 0.835111 -117 GATAAAAAAGAGTTTTTGATACAATATTGT 11 214 0 AGTTTTTGAT 0.865954 -87 TATGCATATAAGTTATTATTTATATTGCAT 12 23 1 AGTTATTATT 0.896746 -46 TATCTAAAAAAGTTTTTAATTGTAATTTTA 14 57 1 AGTTTTTAAT 0.733823 -32 ATATATTTACAGTTATTGATGTTGAATCAA 16 91 0 AGTTATTGAT 0.939222 -112 GTTCTGAGTATGTTATTGTTGCTTGCAATG 21 112 0 TGTTATTGTT 0.920682 -189 ATAAACCATATGTTATTTATTTTATTATCC 23 150 1 TGTTATTTAT 0.742842 -53 AGTTATTATTTATAAAATCT 23 193 0 AGTTATTATT 0.896746 -10 AACATCTGGTTGTTATTGTTATTATCTTTA 24 56 1 TGTTATTGTT 0.920682 -42 CCAATCTTTTAGTTTTTAATATCTGGATAT 26 62 0 AGTTTTTAAT 0.733823 -27 TTTCTCCTCTTGTTTTTGTTTTTATAGTAG 32 45 0 TGTTTTTGTT 0.82913 -22 ********** Masking position 6 Map Score: 12.7925 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 255 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 TTAGATAAAGGATATTGAGGTGGAGTAA 5 45 1 GATTGAGGTG 0.860417 -18 CAAAGGAGAACATTTGGAGGTGTAAATT 8 109 1 CATGGAGGTG 0.987156 -18 TGTTGTATGGAAACGGGAGGTGTGAGGGCGGC 11 65 1 AAAGGAGGTG 0.979796 -236 TCGTGGAAAAAGAGAGGAGGTGACTATGATGG 11 147 0 AGAGGAGGTG 0.971855 -154 GGAGGTATCCCAATAGGAGGTCTCCTCCTATG 13 59 1 CAAGGAGGTC 0.908764 -109 AATAAGGTAACAATCTGAGGTGAGAAG 16 6 0 CAATGAGGTG 0.955955 -197 AAAGTTCTATAATATTGAGGTGAATCT 23 6 0 AATTGAGGTG 0.931897 -197 AACGCTCTCCTATAGGGAGGTGTTCATTAATG 29 111 1 TATGGAGGTG 0.936469 -190 TCCTCGCTTACGCTCGGAGGTGCAACTCAGAA 29 195 0 CGCGGAGGTG 0.97845 -106 TCCGAGCGTAAGCGAGGAGGTGTTAGATTTTT 29 209 1 AGCGGAGGTG 0.966246 -92 *** ******* Masking position 8 Map Score: 7.62977 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 7 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 ATAAATATCTAAAAATAACATAAAAAACTTTTTG 2 58 1 AAATAACAAA 0.628069 -32 ATATAGAGATAAAATTAGCTTCATAGAAAATAAA 10 19 1 AAATAGCCAT 0.652919 -282 AATAGTAGAATAAAGTCTCAAAATCCGTAGATTT 10 118 0 TAATCTCAAT 0.701192 -183 TTTATATTGCTAAGATATCAGAAACCATATATAA 10 181 0 TAATATCAAA 0.904825 -120 TAAAGATTTATAAAATAGCCTCATCTTTTTTAAG 10 244 1 TAATAGCCAT 0.746449 -57 TTATCCACTCTAAAATATCCTAAATAATTTTTTA 11 239 1 TAATATCAAA 0.904825 -62 AAATAATTTTAAATTTATCTAAAAAAGCTTTATC 13 134 0 AAATATCAAA 0.858654 -34 CTTACTATATAAATTTAGCTAAATTGACAATAAA 14 22 0 AAATAGCAAT 0.856206 -67 ATTTATATAGTAAGTTATCTAAAAAAGTTTTTAA 14 42 1 TAATATCAAA 0.904825 -47 AATGAATAGATAATTTATCATAATTAATAATGAT 17 58 0 TAATATCAAT 0.93702 -68 GTAAAATAAATAATGTAACAAAATAGAAATTAAC 18 28 0 TAATAACAAT 0.805288 -33 AAGATAAGGTAAAGATATCAGAATAAGAATATAA 27 66 0 AAATATCAAT 0.904825 -81 TCAAACATACTAAACTATCCAAATAATTCAAATT 30 39 1 TAATATCAAT 0.93702 -42 *** **** *** Masking position 3 Map Score: 6.39251 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 106 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 ATCTACTATATAAAGGGTTCAAACAGTTAT 3 80 1 TAAAGGGTTC 0.924755 -75 TCTTCCTTTGGAAGGCGTTCAAAAGTTCAT 4 38 0 GAAGGCGTTC 0.913675 -81 CCTTCCAAAGGAAGACGTTCGTTAGTGCAA 4 53 1 GAAGACGTTC 0.94876 -66 CTTACTAAAGGAAGGCATTCATTACTACCC 22 227 1 GAAGGCATTC 0.791391 -74 CCCCCTTTATGAAAGCGTTCAAAATTCA 28 9 0 GAAAGCGTTC 0.914027 -170 CTCCCTATAGGAGAGCGTTCAAATATCCAT 29 100 0 GAGAGCGTTC 0.928773 -201 AACCTTTTAGTAAAAGGTTCATCAAAAATC 29 234 0 TAAAAGGTTC 0.827829 -67 AACCTTTTACTAAAAGGTTCTTTCAAAATG 29 245 1 TAAAAGGTTC 0.827829 -56 ********** Masking position 2 Map Score: 4.11014 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 16 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 ACAATAACTGTTTGAACCCTTTATATAGTA 3 83 0 TTTGAACCCT 0.975757 -72 TTAATGAACTTTTGAACGCCTTCCAAAGGA 4 35 1 TTTGAACGCC 0.971744 -84 GCCTCCGGGATTTGAACCCGGGGTCCGGGC 21 41 1 TTTGAACCCG 0.959366 -260 TGAATTTTGAACGCTTTCATAAAGG 28 6 1 TTTGAACGCT 0.98323 -173 ATAATGGATATTTGAACGCTCTCCTATAGG 29 97 1 TTTGAACGCT 0.98323 -204 ********** Masking position 5 Map Score: 3.95192 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 AAATTAAACTAAATAGAAATAACAAAAA 1 8 1 ACTAAAAGAA 0.81328 -37 TAAATAAAACACAAAGGAGAACATTTGGAGG 8 98 1 ACAAAGAGAA 0.865871 -29 TTTTTATATCCCAAAAGAGAAATATTAAACT 11 267 1 CCAAAAAGAA 0.928738 -34 TTTATCACCAAAAAATAATAAATCTAAT 12 51 0 CCAAAAATAA 0.667531 -18 TCAACTTTACACAAAACCGAAAGGTTTATAT 16 64 0 ACAAAACGAA 0.954592 -139 CTATTTATTTACAAAAAACAAAACGTATTTA 16 179 1 ACAAAAACAA 0.829623 -24 AAATAATGTAACAAAATAGAAATTAACTAAA 18 24 0 ACAAAAAGAA 0.974096 -37 TATTTATTCTAAAAAAGAGAAAAGAAAATAA 19 15 0 AAAAAAAGAA 0.747664 -33 ATTTAATACAATAAAACCGAAAAGTATTTAT 21 146 0 ATAAAACGAA 0.623557 -155 TTAATACAAAACAATAGCGAAATTTTTATAT 22 132 1 ACAATACGAA 0.708878 -169 AATATTTACAACAAAAAATAAAAAGTTTGAA 24 13 0 ACAAAAATAA 0.852797 -85 AATTTCACCACAAAAAAGAATTTGAATTAT 30 61 0 ACAAAAAGAA 0.974096 -20 ****** **** Masking position 4 Map Score: 7.46108 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 144 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 CACTATTTATTAGTGTCTTTCAAAACTTCT 4 94 0 TAGTGTCTTT 0.820902 -25 ACTTACTTTTTATTATATTTC 6 2 0 TATTATATTT 0.634334 -40 TTACATCTGATAGTCTGTTTAAGAAGAACA 11 34 1 TAGTCTGTTT 0.713517 -267 GCATTAGATTTATTATTTTTTGGTGATAAA 12 49 1 TATTATTTTT 0.753632 -20 AAAGACCACATATTATGTTTGTTGGAGTTT 13 98 1 TATTATGTTT 0.93043 -70 ATATACCTATTATCATGTTTATAATTGTTG 17 105 1 TATCATGTTT 0.644707 -21 ATTTTTATTTTCTTTTCTCTTTTTT 19 6 1 TATTTTCTTT 0.6077 -42 ATAAAATTTTTATTATTTTTGAAAGATACT 22 69 1 TATTATTTTT 0.753632 -232 GACTTTCGTATAGTATCTTTCAAAAATAAT 22 80 0 TAGTATCTTT 0.935518 -221 TTGTTATTGTTATTATCTTTAAAACCTTAA 24 65 1 TATTATCTTT 0.93043 -33 AATTTATTACTATTATGTTTTTAAATATCA 27 111 0 TATTATGTTT 0.93043 -36 AAATTTCTTTTATTATGATTATCCTCCAAA 29 27 0 TATTATGATT 0.550419 -274 TTTTAAAATATAGTGTCTTTCAAAGTTGTT 29 54 1 TAGTGTCTTT 0.820902 -247 TATATTTTATTAGTATCTTTCAAAAACATT 29 271 0 TAGTATCTTT 0.935518 -30 TTGGATAGTTTAGTATGTTTGATATCAACT 30 31 0 TAGTATGTTT 0.935518 -50 ********** Masking position 2 Map Score: 13.1795 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 73 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 TTTTTATGTTATTTTTAGATATTTATCTTTA 2 53 0 ATTTTAGATA 0.718673 -37 ATAATTATCTTATATTAGATAAAGGATATTG 5 31 1 TATTTAGATA 0.889198 -32 ATTTAACAACTAACTTAGATATTATATAAAA 7 120 0 TAATTAGATA 0.645533 -23 CAAATTAATATTGTTTAGATATTACGGTTAA 8 61 1 TTGTTAGATA 0.804646 -66 GTAAAATATTTATATCAGATACCATATAATA 10 277 1 TATTCAGATA 0.78796 -24 AGGATAAAGCTTTTTTAGATAAATTTAAAAT 13 132 1 TTTTTAGATA 0.94726 -36 AATTAAAAACTTTTTTAGATAACTTACTATA 14 47 0 TTTTTAGATA 0.94726 -42 TAACCAAAAATATTTTAAATAAGATTTCTGG 15 22 0 TATTTAAATA 0.5467 -27 TCAGCATAATTTTGTAAGATATAAGTATTTA 16 120 0 TTTTAAGATA 0.836576 -83 GAAACAAAGATTTATAAGATAGCTTTGCTAT 16 152 1 TTTTAAGATA 0.836576 -51 TTTATTAGATTATGTTAGATATTGTGAGATT 21 247 1 TATTTAGATA 0.889198 -54 ATTCATTAATTTTGTTAAATAACATAAACCA 23 127 1 TTTTTAAATA 0.75114 -76 GATAGTTTAGTATGTTTGATATCAACTTATA 30 27 0 TATTTTGATA 0.686983 -54 *** ******* Masking position 9 Map Score: 8.86724 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 132 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 CTTTTACTTCAAAGGATTTTTGTTATTTCT 1 25 0 AAAGGATTTT 0.585607 -20 ATTTCACCAAAAAGTTTTTTATGTTATTTT 2 69 0 AAAGTTTTTT 0.777859 -21 ACTACTACTTAAAGATTTTTAG 3 3 0 AAAGATTTTT 0.777079 -152 ACTGGCTAAAATAGTTTTATTTTCTATGAA 10 38 0 ATAGTTTTAT 0.364873 -263 ATTTGCTATTAAAGATTTATAAAATAGCCT 10 235 1 AAAGATTTAT 0.71277 -66 TAAACGTTTATCGATAATATC 11 2 1 AAACGTTTAT 0.751066 -299 AAAATAGGTTTTTAGTTTAATAT 11 288 0 ATAGGTTTTT 0.802747 -13 TGGGAAGGATAAAGCTTTTTTAGATAAATT 13 127 1 AAAGCTTTTT 0.672633 -41 TTACAATTAAAAACTTTTTTAGATAACTTA 14 52 0 AAACTTTTTT 0.458602 -37 CACAAAACCGAAAGGTTTATATAGAATTTC 16 56 0 AAAGGTTTAT 0.925787 -147 CTGATGAAACAAAGATTTATAAGATAGCTT 16 147 1 AAAGATTTAT 0.71277 -56 ACAAAAAACAAAACGTATTTAAGG 16 189 1 AAACGTATTT 0.496003 -14 AAACATGATAATAGGTATATGACTCACTAA 17 95 0 ATAGGTATAT 0.400284 -31 TTTATATTAAAAAGGTATTTAGATGCCTAA 23 73 0 AAAGGTATTT 0.802688 -130 CCTTTTAGTAAAAGGTTCATCAAAAATCTA 29 232 0 AAAGGTTCAT 0.744351 -69 CCTTTTACTAAAAGGTTCTTTCAAAATGTT 29 247 1 AAAGGTTCTT 0.804172 -54 GGTTCTTTCAAAATGTTTTTGAAAGATACT 29 260 1 AAATGTTTTT 0.517042 -41 ********** Masking position 3 Map Score: 7.86301 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 817 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987