AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifhlA_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0443 43 conserved hypothetical protein #2 MJ0444 265 conserved hypothetical protein #3 MJ0445 300 translation initiation factor aIF-1A #4 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #5 MJ0519 181 M. jannaschii predicted coding region MJ0519 #6 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #7 MJ0522 108 NADH dehydrogenase I #8 MJ0524 123 conserved hypothetical protein #9 MJ0525 122 conserved hypothetical protein #10 MJ0528 74 conserved hypothetical protein #11 MJ0529 132 repressor protein, putative #12 MJ0676 108 hydrogenase expression/formation protein (hypE) #13 MJ0677 69 ethylene-inducible protein #14 MJ0678 62 conserved hypothetical protein #15 MJ0679 39 transketolase'' #16 MJ0680 23 pentose-5-phosphate-3-epimerase #17 MJ0681 156 transketolase' #18 MJ0682 26 conserved hypothetical protein #19 MJ0683 29 conserved hypothetical protein #20 MJ0684 68 aspartate aminotransferase (aspB2) #21 MJ0995 57 VAR1 protein isolog #22 MJ1027 125 formate hydrogenlyase, subunit 5 #23 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #24 MJ1310 83 conserved hypothetical protein #25 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 GGGGGCTTCGCCCCCTATTGGCACAGAACT 2 223 0 CCCCCTATTG 0.997514 -43 GGGGGCGAAGCCCCCTATGGAAAGAAAAGG 2 238 1 CCCCCTATGG 0.998448 -28 AATAGGGCGAAGCCCTATGGTTTCTGAATA 4 26 0 AGCCCTATGG 0.929431 -88 CATAGGGCTTCGCCCTATTGGGATACCCAG 4 37 1 CGCCCTATTG 0.991333 -77 ATAGGGGGTTTCCCCTATGGATACAATGTA 5 21 0 TCCCCTATGG 0.987874 -161 ATAGGGGAAACCCCCTATTGGGATGAACCT 5 33 1 CCCCCTATTG 0.997514 -149 GGGGCTTCGCCCCTCTATTGGGATACTCCC 5 133 0 CCCTCTATTG 0.990476 -49 GGGGCGAAGCCCCTCTATGGGTCTTATACA 5 150 1 CCCTCTATGG 0.99397 -32 TAGGAGGTCTCCTCCTATGCTTTGTCAA 7 9 0 CCTCCTATGC 0.880239 -100 TAGGAGGAGACCTCCTATTGCTATACCACC 7 22 1 CCTCCTATTG 0.980682 -87 TAGAGGGTTTCCCTCTATGGTTTCCAAGTT 8 29 0 CCCTCTATGG 0.99397 -95 TAGAGGGAAACCCTCTATTGGGATACACCC 8 42 1 CCCTCTATTG 0.990476 -82 AGGGCTTCGCCCTATTGGGATACCCAG 10 58 0 CGCCCTATTG 0.991333 -17 TTTATCACCTATGGGAACTTTTAA 11 5 1 TCACCTATGG 0.853916 -128 ********** Masking position 7 Map Score: 39.7165 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 22 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 TCCGAGCGTAGCAAGGAGGTGTTAGCTTTGAT 2 77 0 GCGGAGGTGT 0.999356 -189 TCCTTGCTACGCTCGGAGGTGTAAATTAAATT 2 92 1 GCGGAGGTGT 0.999356 -174 CCGAGCGTAAGCGAGGAGGTGTTAGGTTTTGG 5 79 0 GCGGAGGTGT 0.999356 -103 CCTCGCTTACGCTCGGAGGTGTAAATTAGTAA 5 95 1 GCGGAGGTGT 0.999356 -87 TCCGAGCGAAGCGAGGAGGTGTTAGTTTTTGA 6 142 0 GCGGAGGTGT 0.999356 -51 TCCTCGCTTCGCTCGGAAGTGTAAATTTACAA 6 157 1 GCGGAAGTGT 0.99426 -36 CCGAGCGTAAGCGAGGAGGTGTTAGGGTGTAT 8 64 0 GCGGAGGTGT 0.999356 -60 CCTCGCTTACGCTCGGAGGTGTAAATTAATTT 8 80 1 GCGGAGGTGT 0.999356 -44 ** ******** Masking position 7 Map Score: 37.7747 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 0 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 GAAAGTTCTGTGGATATACCCCCAAATTTAAT 2 116 0 TGGTATCCCC 0.828167 -150 TTTCCATAGGGGGCTTCGCCCCCTATTGGCAC 2 229 0 GGGTTCCCCC 0.998434 -37 AGAAACCATAGGGCTTCGCCCTATTGGGATAC 4 31 1 GGGTTCCCCT 0.998341 -83 ATCCCAATAGGGGGTTTCCCCTATGGATACAA 5 25 0 GGGTTTCCCT 0.98437 -157 CCCCTCTATTGGGATACTCCCCAAATCTTACT 5 122 0 GGGTACCCCC 0.993789 -60 ACCCATAGAGGGGCTTCGCCCCTCTATTGGGA 5 140 0 GGGTTCCCCC 0.998434 -42 TCCCAATAGAGGGTTTCCCTCTATGGTTTCCA 8 33 0 GGGTTCCTCT 0.990539 -91 ACCCTCTATTGGGATACACCCTAACACCTCCT 8 51 1 GGGTACCCCT 0.993662 -73 ACCCAGAGCGGGGCTTCACTACGTTCAGCCCC 10 32 0 GGGTTCCTAC 0.935838 -43 AGGGCTTCGCCCTATTGGGATAC 10 62 0 GGGTTCCCCT 0.998341 -13 *** *** **** Masking position 5 Map Score: 26.7627 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 6 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 CTTATTTCTAATTTTTATTTTATATGGTTTT 1 20 1 ATTTTATTTT 0.967221 -24 AATAACACTAAATTTTATTGTCAATCAACAC 3 21 1 ATTTTATTGT 0.921415 -280 TGATATTAATAGTTTTGTTATCCTATCAAAA 3 235 0 ATTTTGTTAT 0.831729 -66 TATTTTTAATATTTTTATTTTGTGTTTGTTG 3 264 0 ATTTTATTTT 0.967221 -37 TTATCACCTTTTTTTTATTTTTAATATTTTT 3 279 0 TTTTTATTTT 0.921786 -22 CCTCACCCAGATTTTTATTTTAATATTT 6 8 0 ATTTTATTTT 0.967221 -185 TATCTCACCTAATTTTATTAAATAATGGACA 7 86 0 ATTTTATTAA 0.808892 -23 GGTGTAAATTAATTTTGATTAATTTGTTTGG 8 97 1 ATTTTGATTA 0.595571 -27 TTGGATATGCACTATTAATTATTGGAACTCT 9 60 1 ATATTAATTA 0.557727 -63 TCATTTTTTTAATTTTGTTTTAAAATTTTAT 12 25 1 ATTTTGTTTT 0.926875 -84 TTTGTTTTAAAATTTTATTGAAAGATTGTAA 12 38 1 ATTTTATTGA 0.811785 -71 AATACTTAAATATTTTGATATATTTTTTACA 12 64 0 TTTTTGATAT 0.384059 -45 TCACTCTTTAACTTTTATTGAATACTTAAAT 12 84 0 ATTTTATTGA 0.811785 -25 ATAGAATAATAATTTTATTTTATTTATTTTA 14 14 0 ATTTTATTTT 0.967219 -49 TTTCAAATAAACTTTTATTGTTGGGATT 14 45 1 ATTTTATTGT 0.921417 -18 AAATAATTAATTTATTATTTTTGTTT 15 6 0 TTATTATTTT 0.812563 -34 AATTTTATTTTTTGGTGATTT 16 1 1 ATTTTATTTT 0.967219 -23 CTATTTACTATCTATTATTTTTAGGTGTAAG 17 18 1 TTATTATTTT 0.812563 -139 TCATTATGGATTTTTTGTTTTTGCTTTTTTT 17 84 1 TTTTTGTTTT 0.83505 -73 TGTTTTTGCTTTTTTTATTAATTCATTGAGT 17 99 1 TTTTTATTAA 0.628325 -58 ATTGAGTAATGATATTATTTTTTAAATCTTA 17 123 1 GTATTATTTT 0.624599 -34 CACCACGAAAAGTATTATTAATTAATAATAA 20 18 1 ATATTATTAA 0.608907 -51 ACTAAAAGGAATTATTATTAATTAATAATAC 20 29 0 ATATTATTAA 0.608906 -40 TTATAAAAAGTATTTTAATGTCTTTGGTGAT 21 14 0 TTTTTAATGT 0.596638 -44 AAATATTTTAACTATTATTATAAG 21 44 1 ATATTATTAT 0.80889 -14 CCTTTTATATAGTTTTGTTTTAATAAAGTTA 22 16 0 ATTTTGTTTT 0.926875 -110 GCTAATTATCATTATTAATTATGATAAATTA 22 51 1 ATATTAATTA 0.557727 -75 ATTAATATTTATGTTTTTAATAGCTTT 24 7 1 ATTATGTTTT 0.475399 -77 TTATGAGTTTGTTTTTATTTTGTATGTTTTA 25 29 0 GTTTTATTTT 0.818946 -272 TCAATTTTAAAGTTTTATTTTTAAGAGAATT 25 59 0 ATTTTATTTT 0.967222 -242 AGTAATACTTTTTATTAATTTTCCAATACCA 25 96 1 TTATTAATTT 0.577924 -205 GCATAATAGATTTTTTAATTTAATTTCTTGC 25 199 0 TTTTTAATTT 0.788244 -102 CTTTATTGAGAATTTTAATATGCATAATAGA 25 220 0 ATTTTAATAT 0.784218 -81 AGCATAATCTATTTATATTTTATACATCACT 25 249 1 ATTATATTTT 0.678422 -52 * ********* Masking position 6 Map Score: 36.1937 Number of sites scoring better than the average of aligned sites = 1907 Number in coding regions = 1250 Number in noncoding regions = 657 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 5 GTTTCATCAAAGCTAACACCTCCTTGCTAC 2 72 1 AGCTAACACC 0.89262 -194 CCCCAAATTTAATTTACACCTCCGAGCGTA 2 99 0 AATTTACACC 0.980875 -167 ATATCCACAGAACTTTCACAGCTTTATAAT 2 131 1 AACTTTCACA 0.906927 -135 ATTGGCACAGAACTTTCACAGGAAAGTATC 2 207 0 AACTTTCACA 0.906927 -59 TATTAATATCAACAAACACAAAATAAAAAT 3 255 1 AACAAACACA 0.665575 -46 CTTCACCAAAACCTAACACCTCCTCGCTTA 5 74 1 ACCTAACACC 0.89262 -108 AAATCTTACTAATTTACACCTCCGAGCGTA 5 102 0 AATTTACACC 0.980875 -80 TTTCATCAAAAACTAACACCTCCTCGCTTC 6 137 1 AACTAACACC 0.977847 -56 ATCAGTTGTAAATTTACACTTCCGAGCGAA 6 164 0 AATTTACACT 0.817542 -29 AATCAAAATTAATTTACACCTCCGAGCGTA 8 87 0 AATTTACACC 0.980875 -37 GAGTTCCATAAATATTCACCATACTTTTTC 9 11 0 AATATTCACC 0.829042 -112 GATTTTTCACCCAAAATAATT 15 29 0 ATTTTTCACC 0.751047 -11 TCATATTTAAAACTTACACCTAAAAATAAT 17 31 0 AACTTACACC 0.989621 -126 ********** Masking position 8 Map Score: 14.3995 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 40 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 AATTTTTATTTTATATGGTTTTTAT 1 29 1 TTATAGGTTT 0.701971 -15 ATGAAAACTCTTTAAGAGTTTTCATGTAACT 2 22 0 TTTAAAGTTT 0.805644 -244 TTTTTTTTATTTTTAATATTTTTATTTTGTG 3 271 0 TTTTATATTT 0.859413 -30 CAGATTTTTATTTTAATATTT 6 1 0 TTTTATATTT 0.859413 -192 TTAATTTTGATTAATTTGTTTGGAAAAAT 8 105 1 TTAATTGTTT 0.740785 -19 GTGGGTAACTTTTATATATTTCCCAGAGGAT 11 70 1 TTTATTATTT 0.719929 -63 TTTACTTCATTTTTTTAATTTTGTTTTAAAA 12 19 1 TTTTTAATTT 0.819624 -90 TTTAATTTTGTTTTAAAATTTTATTGAAAGA 12 32 1 TTTTAAATTT 0.846628 -77 TTTATTTTATTTATTTTATTT 14 1 0 TTATTTATTT 0.791914 -62 AATAAAATTATTATTCTATTTTCAAATAAAC 14 26 1 TTATTTATTT 0.791914 -37 AGTTTCACCTTTTTAAGATTTAAAAAATAAT 17 136 0 TTTTAGATTT 0.679344 -21 TGCATCACCATTAATGTGTTTTTA 18 4 0 TTAATTGTTT 0.740785 -23 TATTAGCCCCTTATAAAGTTTTTGCTTAT 19 9 0 TTATAAGTTT 0.859886 -21 TAATAATTCCTTTTAGTGTTTATAAATGGTG 20 43 1 TTTTATGTTT 0.899862 -26 ATAATAATAGTTAAAATATTTTATAAAAAGT 21 34 0 TTAAATATTT 0.702532 -24 GCTTAACCTTTTATATAGTTTTGTTTTAATA 22 22 0 TTATAAGTTT 0.859886 -104 CATATACCTATTATCATGTTTATAATTGTTG 22 104 1 TTATCTGTTT 0.538469 -22 TTTAAGAGAATTTATGAGTTTGTTTTTATTT 25 40 0 TTTATAGTTT 0.773355 -261 AATTTTTCAATTTTAAAGTTTTATTTTTAAG 25 65 0 TTTTAAGTTT 0.890286 -236 AGTAATACTTTTTATTAATTTTCCAATACCA 25 96 1 TTTATAATTT 0.698904 -205 GCATAATAGATTTTTTAATTTAATTTCTTGC 25 199 0 TTTTTAATTT 0.819624 -102 ***** ***** Masking position 9 Map Score: 17.4017 Number of sites scoring better than the average of aligned sites = 1646 Number in coding regions = 1154 Number in noncoding regions = 492 Number of orfs with sites within 600 bp upstream = 399 Fraction of orfs with sites within 600 bp upstream = 0.0640861 Motif number 7 CTAAATAACCTTTTCTTTCCATAGGG 2 250 0 AACCTTTTCT 0.917506 -16 CGCAGTAATAAATCTTTTCTATTGAATATT 3 175 0 AATCTTTTCT 0.752111 -126 TATTGGGATGAACCTTTTAGTAAAAGCTTC 5 48 1 AACCTTTTAG 0.968224 -134 ACTATAAACGAAACTTTTAGAAAAAGTTGA 6 62 1 AAACTTTTAG 0.96764 -131 AGTTGAACGAAAACTCTTAGAGTTTTCATA 6 86 1 AAACTCTTAG 0.802261 -107 TCTAATATATAAACTTTTCGTCTTATTTTT 11 39 1 AAACTTTTCG 0.957244 -94 TTTTTGTGGGTAACTTTTATATATTTCCCA 11 65 1 TAACTTTTAT 0.836176 -68 TCTCACTCTTTAACTTTTATTGAATACTTA 12 87 0 TAACTTTTAT 0.836176 -22 ATTTCATAACAAACTTTTATCAATGATTAT 13 38 1 AAACTTTTAT 0.935807 -32 ATTTTCAAATAAACTTTTATTGTTGGGATT 14 43 1 AAACTTTTAT 0.935807 -20 TTAATTAATAATACTTTTCGTGGTGGCATA 20 13 0 ATACTTTTCG 0.78327 -56 TTAATAATAATTCCTTTTAGTGTTTATAAA 20 39 1 TTCCTTTTAG 0.632645 -30 TAATTAGCTTAACCTTTTATATAGTTTTGT 22 29 0 AACCTTTTAT 0.936929 -97 TTCTCCCTCCAATCTTTTAGAGAAAGTTAA 23 17 0 AATCTTTTAG 0.892615 -21 ATGTTTTTAATAGCTTTTAGCTTTTTGGTT 24 21 1 TAGCTTTTAG 0.70982 -63 AGATTTCTAAAACCTGTTCGCTATGCTCAC 25 164 1 AACCTGTTCG 0.755821 -137 ********** Masking position 5 Map Score: 17.6644 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 131 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 TAGCCCGAAGCTACGCTTCGGTTTCATCAA 2 52 1 CTACGCTTCG 0.931842 -214 CACCTCCTTGCTACGCTCGGAGGTGTAAAT 2 88 1 CTACGCTCGG 0.996789 -178 ACCTCCTCGCTTACGCTCGGAGGTGTAAAT 5 91 1 TTACGCTCGG 0.990672 -91 CACCTCCTCGCTTCGCTCGGAAGTGTAAAT 6 153 1 CTTCGCTCGG 0.98726 -40 ACCTCCTCGCTTACGCTCGGAGGTGTAAAT 8 76 1 TTACGCTCGG 0.990672 -48 CGGGGCTTCACTACGTTCAGCCCCACTTTC 10 26 0 CTACGTTCAG 0.903066 -49 ********** Masking position 7 Map Score: 7.42291 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 1 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CATGTAACTTTCTTAAAGTT 2 1 0 TCTTAAAGTT 0.951139 -265 ACATGAAAACTCTTAAAGAGTTTTCATAGC 2 26 1 TCTTAAAGAG 0.841489 -240 AAAATAAAAATATTAAAAATAAAAAAAAGG 3 274 1 TATTAAAAAT 0.652019 -27 AAGCAATGCCTCTTAAAATTTATTGGGAGG 4 87 1 TCTTAAAATT 0.93373 -27 TTCAACTTTTTCTAAAAGTTTCGTTTATAG 6 63 0 TCTAAAAGTT 0.799031 -130 GAACGAAAACTCTTAGAGTTTTCATAGCTG 6 90 1 TCTTAGAGTT 0.754319 -103 TTTAATTTTGTTTTAAAATTTTATTGAAAG 12 32 1 TTTTAAAATT 0.684609 -77 ATTTTTTAAATCTTAAAAAGGTGAAACT 17 139 1 TCTTAAAAAG 0.793492 -18 TTTAACTTTCTCTAAAAGATTGGAGGGAGA 23 16 1 TCTAAAAGAT 0.774368 -22 TCATAAATTCTCTTAAAAATAAAACTTTAA 25 54 1 TCTTAAAAAT 0.924026 -247 AATTTTTCAATTTTAAAGTTTTATTTTTAA 25 66 0 TTTTAAAGTT 0.749937 -235 CTACTTATAATCTTAAAAATCCGAAAGATT 25 139 1 TCTTAAAAAT 0.924026 -162 CTATTATGCATATTAAAATTCTCAATAAAG 25 221 1 TATTAAAATT 0.684608 -80 ********** Masking position 5 Map Score: 11.327 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 174 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 GTTTGTTGATATTAATAGTTTTGTTATCCTATC 3 239 0 ATAATATTTG 0.811072 -62 AAAAAGTATGGTGAATATTTATGGAACTCGTTG 9 12 1 GTAATATATG 0.864182 -111 CGATAATATAATGATTGATTATGAAAA 11 116 1 ATATTGTATG 0.905836 -17 ACAAACTTTTATCAATGATTATGGAGGGAGAGT 13 46 1 ATAATGTATG 0.977239 -24 AAAACAAAAAATCCATAATGATGTTATGCTAAA 17 72 0 ATCATATATG 0.864182 -85 TAAAAACACATTAATGGTGATGCATA 18 10 1 ATAATGTATG 0.977239 -17 AGTATTATTAATTAATAATAATTCCTTTTAGTG 20 28 1 ATAATATATT 0.726731 -41 TTTAGTGTTTATAAATGGTGATGTC 20 54 1 ATAATGTATG 0.977239 -15 GCTAATTATCATTATTAATTATGATAAATTATC 22 51 1 ATATTATATG 0.892524 -75 ATTAATATTTATGTTTTTAATAG 24 1 1 ATAATATATG 0.973729 -83 ATCATTAATGACAAATAGTGATGTATAAAATAT 25 263 0 ACAATATATG 0.864182 -38 ACTATTTGTCATTAATGATAATGATAAATTACT 25 277 1 ATAATGTATG 0.977239 -24 ** **** * *** Masking position 6 Map Score: 14.2199 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TCTGTGGATATACCCCCAAATTTAATTTAC 2 112 0 TACCCCCAAA 0.954797 -154 TTTGGGGGTATATCCACAGAACTTTCACAG 2 122 1 TATCCACAGA 0.611376 -144 AAACTATTAATATCAACAAACACAAAATAA 3 251 1 TATCAACAAA 0.814546 -50 CCATAGGGGAAACCCCCTATTGGGATGAAC 5 31 1 AACCCCCTAT 0.64563 -151 CTATTGGGATACTCCCCAAATCTTACTAAT 5 119 0 ACTCCCCAAA 0.884145 -63 TTTATCTCACCTAATTTTATTAAA 7 95 0 TCTCACCTAA 0.800495 -14 CGAAGTTGATAATCCCCTAATTAGG 9 108 1 AATCCCCTAA 0.921407 -15 TTTATCACCTATGGGAACTTTT 11 3 1 TATCACCTAT 0.721756 -130 ATATAAAAGTTACCCACAAAAAATAAGACG 11 57 0 TACCCACAAA 0.839542 -76 TTAAATCACCAAAAAATAAAATT 16 11 0 AATCACCAAA 0.912698 -13 GTTATCACCAAAGACATTAAAA 21 3 1 TATCACCAAA 0.946614 -55 ********** Masking position 4 Map Score: 4.0483 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 378 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 12 TTTCCAAGTTTTTTCATTATTTCCCCCT 8 9 0 TTTTCATTAT 0.896097 -115 TTTTCATAATCAATCATTAT 11 123 0 TTTTCATAAT 0.896097 -10 CTTATAATAATAGTTAAAATA 21 47 0 TTATAATAAT 0.713416 -11 GTTAAGCTAATTATCATTATTAATTATGAT 22 46 1 TTATCATTAT 0.941491 -80 AATAGATAATTTATCATAATTAATAATGAT 22 58 0 TTATCATAAT 0.941491 -68 CAGTAATTTATCATTATCATTAATGAC 25 284 0 TTATCATTAT 0.941491 -17 ********** Masking position 6 Map Score: 3.24687 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 57 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 GCTAACACCTCCTTGCTACGCTCGGAGGTG 2 83 1 CCTTGCTACG 0.905132 -183 ACCCAGGATGCATTGCTTCTGCAAAGAAGC 4 61 1 CATTGCTTCT 0.92075 -53 TTTTAAGAGGCATTGCTTCTTTGCAGAAGC 4 75 0 CATTGCTTCT 0.92075 -39 CCTAACACCTCCTCGCTTACGCTCGGAGGT 5 85 1 CCTCGCTTAC 0.938064 -97 ACTAACACCTCCTCGCTTCGCTCGGAAGTG 6 148 1 CCTCGCTTCG 0.982306 -45 CCTAACACCTCCTCGCTTACGCTCGGAGGT 8 70 1 CCTCGCTTAC 0.938064 -54 TAATTTAATTTCTTGCTTCTTGTGAGCATA 25 185 0 TCTTGCTTCT 0.846727 -116 ********** Masking position 7 Map Score: 2.61143 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 13 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TCTTAAAGAGTTTTCATAGCCCGAAGCTAC 2 36 1 TTTTCATAGC 0.955324 -230 TAACCTTTTCTTTCCATAGGGGGCTTCGCC 2 241 0 TTTCCATAGG 0.902348 -25 AAATTGAGTGTTTTAATAGGTCTTACGCAG 3 200 0 TTTTAATAGG 0.966453 -101 AATTTTGAAATTTTGATAGGATAACAAAAC 3 225 1 TTTTGATAGG 0.928459 -76 TCCCAATAAATTTTAAGAGGCATTGCTTCT 4 85 0 TTTTAAGAGG 0.884418 -29 ACTCTTAGAGTTTTCATAGCTGGAAAGCAT 6 98 1 TTTTCATAGC 0.955324 -95 ATATTTATGTTTTTAATAGCTTTTAGCTTT 24 15 1 TTTTAATAGC 0.946545 -69 TTATTGAGAATTTTAATATGCATAATAGAT 25 219 0 TTTTAATATG 0.762871 -82 ********** Masking position 6 Map Score: 5.82449 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 80 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 ATCAACACATATATATAGTGAGAGTATATA 3 44 1 ATATATAGTG 0.808134 -257 TAGTGAGAGTATATAAAGTAGATATTACAA 3 59 1 ATATAAAGTA 0.885095 -242 CAAATGTCCAATATAAAGTGCTTAAGTCCT 3 123 0 ATATAAAGTG 0.902931 -178 CGAAACTTTTAGAAAAAGTTGAACGAAAAC 6 70 1 AGAAAAAGTT 0.689508 -123 CAGGGAAATAAAAGAAAGTGGGGCTGAACG 10 13 1 AAAGAAAGTG 0.668108 -62 ATTAAACATATATAGTTGGAGACTATA 13 8 1 ATATATAGTT 0.728155 -62 CCTAAAAATAATAGATAGTAAATAGAGGAA 17 13 0 ATAGATAGTA 0.808134 -144 AAAATATTTTATAAAAAGTATTTTAATGTC 21 23 0 ATAAAAAGTA 0.855401 -35 CCAATCTTTTAGAGAAAGTTAAATAGAA 23 9 0 AGAGAAAGTT 0.777376 -29 TGGAAAATTAATAAAAAGTATTACTAATTT 25 91 0 ATAAAAAGTA 0.855401 -210 ********** Masking position 5 Map Score: 2.18229 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 150 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281