AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ipurR_aful_opreg_300.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0252 251 CTP synthase (pyrG) #2 AF0841 80 adenylosuccinate synthetase (purA) #3 AF0842 65 A. fulgidus predicted coding region AF0842 #4 AF0875 300 snRNP, putative #5 AF0971 101 conserved hypothetical protein #6 AF0973 108 bile acid-inducible operon protein F (baiF-1) #7 AF0977 173 ammonium transporter (amt-1) #8 AF1157 163 phosphoribosylamine--glycine ligase (purD) #9 AF1186 139 conserved hypothetical protein #10 AF1189 283 A. fulgidus predicted coding region AF1189 #11 AF1191 32 dihydroxynaphthoic acid synthase (menB) #12 AF1192 50 conserved hypothetical protein #13 AF1195 27 activator 1, replication factor C, 53 KD subunit #14 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #15 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #16 AF1215 101 cell division protein, putative #17 AF1269 300 A. fulgidus predicted coding region AF1269 #18 AF1270 33 transcriptional regulatory protein, ArsR family #19 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #20 AF1420 216 membrane protein #21 AF1421 49 conserved hypothetical protein #22 AF1422 35 aspartate racemase #23 AF1423 112 conserved hypothetical protein #24 AF1693 45 phosphoribosylformylglycinamidine cyclo-ligase (purM) #25 AF1746 122 ammonium transporter (amt-2) #26 AF1749 95 ammonium transporter (amt-3) #27 AF1941 201 conserved hypothetical protein #28 AF2242 61 adenylosuccinate lyase (purB) #29 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #30 AF2244 300 acyl-CoA dehydrogenase (acd-11) Motif number 1 ACACAAGTCGAAAACATTTTTAACCCTGAAGC 4 181 0 AAAATTTTTA 0.856086 -120 TTCATAAATGAAAAAATTTAAAT 5 2 0 AAAATTTAAA 0.944698 -100 GTGTATCTGCAAAAGCTTTATATTGCCAGATT 5 65 1 AAAATTTATA 0.890093 -37 TTTTCGATTTCAAACTTTAAAAAATTGTAGAA 6 14 0 CAAATTAAAA 0.739973 -95 TTTGAAATCGAAAAACTTATACATTTGAAAAT 6 32 1 AAAATTATAC 0.676471 -77 GCCAATTTAGAAAATGTTAAAATCGACATCAA 7 45 0 AAAATTAAAA 0.827856 -129 ATTCATGCAAAAAACTTTTAAATCTGGCATGA 7 140 1 AAAATTTAAA 0.944699 -34 TCAAACATTACAAAAGTTTATATACCTCAGCC 9 105 1 CAAATTTATA 0.827357 -35 GAAAAGTGTTAAAAGCTTTAAAATATCCCCAA 10 119 1 AAAATTTAAA 0.944699 -165 AAAGTTGGGAAAAAGGTTTAAATAAAAAGCGT 16 61 1 AAAATTTAAA 0.944699 -41 AAACTCATGAAAAACCTTATTAGCCTCTTGTT 20 183 1 AAAATTATTA 0.626188 -34 GGTAGCACAGCAAACTTTTTAACATTCAAAGC 21 17 1 CAAATTTTAA 0.881339 -33 CCAAAGCTTTATCTTGTTAGGCG 22 2 1 CAAATTTATC 0.739302 -34 CACCCAACCTAAAAAATTTTAACCTCAACTTC 23 23 0 AAAATTTTAA 0.926166 -90 AGTTATTCACAAAATTTTTAAACAGCCTTGTG 25 22 0 AAAATTTAAA 0.944699 -101 GTTGTTTTTAAAAATCTTTTAATATTTTTTTG 25 85 0 AAAATTTTAA 0.926208 -38 CGAATTTAAAAAAATATTTAACAAAAACTCAT 26 57 0 AAAATTTAAC 0.909981 -39 TTTATAAGTAAAAAAATTTTACTAAAATAAAA 27 89 0 AAAATTTTAC 0.881299 -113 TATCACCCTGCAAACGTTTTTCAAATAATAAA 29 15 0 CAAATTTTTC 0.675707 -24 **** ****** Masking position 7 Map Score: 20.7845 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 75 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 TTCCAGATATAATCTCCTCTTCGTTCTCCTCAACCACTTCA 1 142 0 AATCTCCCCC 0.99569 -110 CGATATTTTTAAATAACTCCTCCTGCAACGAACCTTAGATA 4 252 1 AAACTCCCCA 0.970225 -49 ATACTCCTCCACACTACTCAATACAATCCCT 6 88 0 ATTCTCCACA 0.749615 -21 ACAAAAGTTTATATACCTCAGCCCACTTCACATTAC 9 114 1 ATACTCCCCC 0.967896 -26 GGAAGTCCAGAACTTTCTCTGCTACCGTCGAGGTATCCGGG 15 17 0 AATCTCCCCA 0.980767 -284 GCAAAGTATAAATCTCCTTGACGATCCTCTGGTTGGGATAG 17 235 1 AATCTTCCCG 0.790999 -66 TCGTTTTGTCAAGTTATTCTGCTGGCAACGCTTCAAGACTT 20 110 1 AATTTCCCCC 0.93833 -107 TAACGGAATTAACTACCTCATTCAACCACCCTTAGTTGAGA 27 29 1 AAACTCTCCC 0.906738 -173 TTCCGGCAAAAATCTGCTCCTCGCAATGCCCACAGCGGCGG 30 21 0 AATCTCCACC 0.985164 -280 TTTTGCCGGAAAAGACCTTCTCCACCGCCTCAGCCTGAGGC 30 51 1 AAACTTCCCC 0.949177 -250 CCTGAGGCGGAAACAGCTCTTCTATACCCTCCTCCTTTAAA 30 84 1 AAACTCCACC 0.976974 -217 TGCTTTCAGCAAGCTCCTCCACCTTCACCACTTCAAGTTTT 30 147 1 AATCTCCCCC 0.99569 -154 GGTGCATTAAAAATTGCTCCTCGTTAAACTCATGATATATA 30 192 1 AATCTCCACC 0.985164 -109 ** * *** * * * * Masking position 1 Map Score: 16.6128 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 676 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GTTTATTTGGTTTGCGATTTTTGGAAAAATGGTAG 2 33 0 TTTGCTTTTA 0.839834 -48 ATTTAAATTTTTTCATTTATGAACACAACTAAT 5 9 1 TTTTTTTATA 0.75814 -93 TTTTTCTTTTTTTAAAAAGAATATT 7 1 1 TTTTTTTTTA 0.964366 -173 AAAAAGAATATTTTTTATTTTTTGATGTCGATTTT 7 24 1 TTTTTTTTTA 0.964366 -150 GTATTTAAGCTTTGTTATTTTTACACAGGTAGAAT 8 58 1 TTTGTTTTTA 0.938002 -106 TTTTAATTTTTATTTTTTCCAACAGATAGTT 14 7 1 TTTTTTTTTA 0.964366 -59 CCTCCTTCACTTTTTTCTTATTAAAATACCATCCG 15 270 0 TTTTTTTTTA 0.964366 -31 ATTCTTCAGTTTTTTAGTTTTTTTCTAAAAAGTTT 26 11 0 TTTTTTTTTC 0.903655 -85 ACTCTTTTTTCTTTTTAACGAAAAGGAGT 28 5 1 TTTTTTTTTC 0.903655 -57 ATTTTTTATTATTTGAAAAACGTTTG 29 2 1 TTTTTTTTTA 0.964366 -37 TTTAAATCCTTTTTCAATTGTTTAACTTGGCAAAA 30 250 1 TTTTCTTTTA 0.903655 -51 GCAGGCTCTTTTTGTGATTATTTAAATTTTGCCAA 30 276 0 TTTGTTTTTA 0.938002 -25 ***** ** ** * Masking position 8 Map Score: 13.9257 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 21 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 GTTCTCCTCAACCACTTCAACTTCCAATTCCGA 1 128 0 ACCTTCACTT 0.889334 -124 CCAACCACCTCATGTTTTATCACTAC 3 50 0 ACCCTCAGTT 0.953963 -16 ATTTTTAAATAACTCCTCCTGCAACGAACCTTA 4 256 1 ACCCTCCGCA 0.925446 -45 ACTCAATACAATCCCTCCATGCAGTATTAATAA 6 71 0 ACCTCCAGCA 0.679812 -38 TTAATTATATATCCGCCCCTGCTGACCGAAAAC 8 112 1 ACGCCCCGCT 0.880893 -52 AAGTAATGAGAAATCTCCCTGTTGGCT 14 49 1 AACTCCCGTT 0.518195 -17 AATACACCTCCTTCACTTTTTTCTTATT 15 283 0 ACCCTTCCTT 0.796353 -18 TAAAAACAGCAACGCCTCAGCTTGACCG 16 6 0 ACCCTCACTT 0.958766 -96 ACAGATTGCAAGCTCTCTCACCTCTCACAGGGA 17 159 1 ACCTCTCCCT 0.633994 -142 AAGCCCTTCCTCTTTTTTTGATTC 19 2 1 ACCTTCCCTT 0.935484 -23 GTAAATTTTTATCGGCCCAACCAGAACAACATC 23 89 1 ACGCCCACCA 0.515472 -24 GTAACCTTTTATCGCCCCCTGTTAACTTCGCTT 28 38 1 ACCCCCCGTT 0.97092 -24 GACCTTCTCCACCGCCTCAGCCTGAGGCGGAAA 30 64 1 ACCCTCACCT 0.970908 -237 CAGCTCTTCTATACCCTCCTCCTTTAAAATGCC 30 97 1 AACCTCCCCT 0.848775 -204 GCTTGCTGAAAGCATCTCAAGTTATGCTGTTGG 30 128 0 ACTCTCAGTT 0.539692 -173 GCTTTCAGCAAGCTCCTCCACCTTCACCACTTC 30 148 1 ACCCTCCCCT 0.983665 -153 CTCCACCTTCACCACTTCAAGTTTTCAACGGTG 30 163 1 ACCTTCAGTT 0.877477 -138 * * ***** *** Masking position 1 Map Score: 12.4335 Number of sites scoring better than the average of aligned sites = 1952 Number in coding regions = 1854 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 GGTTGAGGAGAACGAAGAGGAGATTATATCT 1 148 1 AACGAGAGGA 0.980806 -104 ATTTGTAATTAAAAACGAGGATTAATTATAT 8 91 1 AAAAAGAGGA 0.893489 -73 GGATTGAGATAAGATTGAGCAAAGAAGTGTG 9 38 0 AAGATGAGCA 0.636835 -102 TTGATGAGCAAACGAAGAGAATGAAGCTCTT 15 108 1 AACGAGAGAA 0.816995 -193 TGAAGGACGTAACGTTGAGGACGTGTTGAAT 15 148 1 AACGTGAGGA 0.973766 -153 TAATAAGAAAAAAGTGAAGGAGGTGTATT 15 282 1 AAAGTAAGGA 0.724132 -19 GAATCAAAAAAAGAGGAAGGGCTT 19 8 0 AAAAAGAGGA 0.893489 -17 TACTAAAATAAAAATTGAGGATAGCTTGCTG 27 71 0 AAAATGAGGA 0.859027 -131 TTTTCTTTTTAACGAAAAGGAGTAACCTTTT 28 17 1 AACGAAAGGA 0.876538 -45 TGGCATTTTAAAGGAGGAGGGTATAGAAGAG 30 100 0 AAGGAGAGGG 0.843546 -201 TGAAGTGGTGAAGGTGGAGGAGCTTGCTGAA 30 151 0 AAGGTGAGGA 0.958009 -150 TCATGAGTTTAACGAGGAGCAATTTTTAATG 30 196 0 AACGAGAGCA 0.92411 -105 ***** ***** Masking position 8 Map Score: 9.41201 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 692 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 CACCTCATGTTTTATCACTACATTTTACTTTAGTGT 3 35 0 TTTCAATTTT 0.960386 -31 TATTTCTACAATTTTTTAAAGTTTGA 6 1 1 TATCATTTTT 0.614373 -108 AGAAATCTTCAATTTCTACAAATTTTCTTAAAAATT 7 87 1 AATCAATTTT 0.852163 -87 GAATTAGAGAATTTACTGAAGAATTTTTAAGAAAAT 7 108 0 ATTCAAATTT 0.588595 -66 AAGGCTTTCGAATGTCTTTAAAGTTTAGAGTTTGAT 8 15 0 AATCAAGTTT 0.558224 -149 TCATCTAAAATTTTCAATACTTTTTTCATACGACT 10 10 1 ATTCATTTTT 0.783314 -274 GAATATCTTTTTTCTCAGAATATTTTTTTATTAGTC 10 42 0 TTTCAATTTT 0.960386 -242 ACTAAATTAAAGTAGTCTTAAATTTTTCGTTCCATA 10 241 0 AGTTAATTTT 0.470959 -43 GTATTTTCCAGTACATTTTTCCCTGCCCG 11 4 1 TTTCAATTTT 0.960386 -29 TATATTACTATTTTGCTGTAATTTTTAAT 12 4 0 TTTCATTTTT 0.831082 -47 AAAAGAACCCTTTAACAGGAAATTTTCTACTGTCTA 17 273 0 TTTCAATTTT 0.960386 -28 TGAGTGACAGAGTATCGTGAGATTTTCCGAGCCCGC 20 27 0 AGTCAATTTT 0.827047 -190 AGACAGGCCTTTTAGCGGTAAATTTTTATCGGCCCA 23 72 1 TTTCAATTTT 0.960386 -41 AAATTGAGAGTTATTCACAAAATTTTTAAACAGCCT 25 26 0 TTACAATTTT 0.634304 -97 ATGTCAAAAAAATATTAAAAGATTTTTAAAAACAAC 25 81 1 AATTAATTTT 0.517735 -42 TTTTTTAGTTTTTTTCTAAAAAGTTT 26 1 0 TTTCAAGTTT 0.841551 -95 AGTTATGAGTTTTTGTTAAATATTTTTTTAAATTCG 26 53 1 TTTTAATTTT 0.818616 -43 CTCAATTTTTATTTTAGTAAAATTTTTTTACTTATA 27 83 1 ATTAAATTTT 0.501965 -119 GTAAAATTTTTTTACTTATAAATTTTATCCTTCAGA 27 99 1 TTTTAATTTT 0.818616 -103 *** * * ***** Masking position 14 Map Score: 12.0753 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 121 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 GCTTTTTTGCGGTATTTAAAATTAAGGCGG 1 19 1 GGTATTTAAA 0.566863 -233 GGTTCAGCGATATTTTTAAATAACTCCTCC 4 245 1 TATTTTTAAA 0.579398 -56 GCAGATACACTCATTTTAAATATCAATCAA 5 45 0 TCATTTTAAA 0.731121 -57 TAAAAAATATTCTTTTTAAAAAAAGAAAAA 7 11 0 TCTTTTTAAA 0.950492 -163 GGCTTTCGAATGTCTTTAAAGTTTAGAGTT 8 19 0 TGTCTTTAAA 0.694295 -145 GCTTGGACAATCTATTGAAAAGTGTTAAAA 10 103 1 TCTATTGAAA 0.615792 -181 GAATAACAGCTCTTTTGAAATTATCATCCC 15 175 1 TCTTTTGAAA 0.807915 -126 TTCACTTTTTTCTTATTAAAATACCATCCG 15 270 0 TCTTATTAAA 0.592313 -31 GAGGCGTTGCTGTTTTTAAACTTGCCTTTA 16 21 1 TGTTTTTAAA 0.877882 -81 TAATACGCTTTTTATTTAAACCTTTTTCCC 16 67 0 TTTATTTAAA 0.480136 -35 GTCGGAAAAGTCTTTTTAAAAGGTTGCCCA 24 19 0 TCTTTTTAAA 0.950492 -27 AACACACAAGGCTGTTTAAAAATTTTGTGA 25 18 1 GCTGTTTAAA 0.611578 -105 GTTTTAGTGTTGTTTTTAAAAATCTTTTAA 25 95 0 TGTTTTTAAA 0.877882 -28 TTGTTAAATATTTTTTTAAATTCGGGCTTA 26 65 1 TTTTTTTAAA 0.708363 -31 TTTTGCTCATGCTCTTTAAAAATCAAGCGA 27 175 0 GCTCTTTAAA 0.743435 -27 ACTCTTTTTTCTTTTTAACGAAAAGGAGT 28 10 1 TCTTTTTAAC 0.682885 -52 TATGCTGTTGGCATTTTAAAGGAGGAGGGT 30 109 0 GCATTTTAAA 0.565031 -192 ACAATTGTGTTCTATTTAAATCCTTTTTCA 30 236 1 TCTATTTAAA 0.879736 -65 ********** Masking position 6 Map Score: 11.5573 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 50 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 TGTCTCAACTCCGGAGGGCGCAAATCTG 1 234 0 ACTCCGGAGG 0.977992 -18 ACACTGACAGTCCTTCGCAGGGGTTTATTTGG 2 58 0 TCTTCGCAGG 0.832416 -23 CTATAAAAGTTTCTTCGGATGGAGGCAATTAA 4 55 1 TCTTCGGAGG 0.9678 -246 AACCTTAGATAATTCTGGAGGGAAAGAAT 4 282 1 ATTCTGGAGG 0.895101 -19 TATACTCCTTTGGACGACTGGATTTGA 13 6 1 TCTTTGGAGA 0.622127 -22 AAAGTTCTGGACTTCCGGAAGGCACTGGCCCC 15 42 1 ATTCCGGAGG 0.908282 -259 CACGTCAATCTTCTCCGTAAGGTAAAAA 17 7 0 TCTCCGTAGG 0.95445 -294 TAGTTTATGGTGCTCTGTACGGTCTGAATAAA 17 70 1 TCTCTGTAGG 0.929356 -231 TCCTTGACGATCCTCTGGTTGGGATAGACAGT 17 249 1 TCTCTGGTGG 0.948899 -52 TGATGTTGTTCTGGTTGGGCCGATAAAA 23 95 0 TTTCTGGTGG 0.839745 -18 * ******* ** Masking position 4 Map Score: 4.95372 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 205 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 GCGGTATTTAAAATTAAGGCGGAAATCGTTAT 1 27 1 AATAAGGCGG 0.933861 -225 TCGGAATTGGAAGTTGAAGTGGTTGAGGAGAA 1 128 1 AATGAAGTGG 0.972883 -124 GTAGTGATAAAACATGAGGTGGTTGG 3 50 1 AATGAGGTGG 0.974918 -16 TACCAACAGTAATTTAAAGCAGCTCAAACATT 9 82 1 AATAAAGCAG 0.7862 -58 GTAATGTGAAGTGGGCTGAGGTAT 9 126 0 AATGAAGTGG 0.972883 -14 TTGCTATACTAAATTAAAGTAGTCTTAAATTT 10 252 0 AATAAAGTAG 0.740681 -32 TAATAAGAAAAAAGTGAAGGAGGTGTATT 15 282 1 AATGAAGGAG 0.787298 -19 CGGTCAAGCTGAGGCGTTGCTGTTTTT 16 6 1 AATGAGGCGT 0.813851 -96 TTTCCGCCTCAGGCTGAGGCGGTGGAGAAGGT 30 65 0 AGTGAGGCGG 0.912558 -236 CACCGTTGAAAACTTGAAGTGGTGAAGGTGGA 30 164 0 AATGAAGTGG 0.972883 -137 ** ******** Masking position 7 Map Score: 5.9691 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 181 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 CAAACGAGCTTTCCAGATATAATCTCCTCT 1 163 0 TTCCAGATAT 0.930003 -89 GAGGATGGGATTCCAGATTTGCGCCCTCCG 1 221 1 TTCCAGATTT 0.973185 -31 AGCTTTATATTGCCAGATTTGTTAATTATA 5 78 1 TGCCAGATTT 0.953599 -24 CAGGATTTCATGCCAGATTTAAAAGTTTTT 7 149 0 TGCCAGATTT 0.953599 -25 CTTTCCCCAATTCCTGATTGGGGATATTTT 10 138 0 TTCCTGATTG 0.864406 -146 ATATGATGAGTTCCAGCTATCGAGGGGTTA 10 173 0 TTCCAGCTAT 0.779196 -111 AAATTTTTCGTTCCATATTGCATTCTTTCA 10 228 0 TTCCATATTG 0.798892 -56 TTGGGCAGCATTACAGATTGCAAGCTCTCT 17 147 1 TTACAGATTG 0.798892 -154 ********** Masking position 8 Map Score: 2.4725 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 105 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 GCAAACCAAATAAACCCCTGCGAAGGACTGTCA 2 53 1 TAACCCTGCA 0.848083 -28 TTTTTAAATAACTCCTCCTGCAACGAACCTTAG 4 257 1 ACCTCCTGCA 0.73992 -44 CTCAATACAATCCCTCCATGCAGTATTAATAAT 6 70 0 TCCCCATGCG 0.925607 -39 TAATTATATATCCGCCCCTGCTGACCGAAAACG 8 113 1 TCGCCCTGCG 0.974784 -51 ATGTCACACCTTGCTATACTAAATTA 10 268 0 TCCCCTTGCA 0.919723 -16 AGTAATGAGAAATCTCCCTGTTGGCT 14 50 1 AACCCCTGTG 0.865322 -16 CAATCTGCGTTATCACCCTGTAGGGGCCAGTGC 15 63 0 TACCCCTGTG 0.95853 -238 ACCATTCTTCTCTGTCCCTGTGAGAGGTGAGAG 17 173 0 TCGCCCTGTA 0.938374 -128 TAACCTTTTATCGCCCCCTGTTAACTTCGCTTC 28 39 1 TCCCCCTGTA 0.980376 -23 TCTATCACCCTGCAAACGTTTTTCA 29 24 0 TACCCCTGCA 0.980388 -15 ** * ****** * Masking position 9 Map Score: 4.51397 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 277 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CAAACCTACCATTTTTCCAAAAATCGCAAA 2 28 1 ATTTTTCCAA 0.911207 -53 CTGAACCCGAATTTTGCCAGATGCTGAGAG 4 222 0 ATTTTGCCAG 0.9618 -79 CAAAAGCTTTATATTGCCAGATTTGTTAAT 5 74 1 ATATTGCCAG 0.931009 -28 AATAAAAATAATATTGCCAAGAA 9 4 0 ATATTGCCAA 0.942121 -136 TTAATTTTTATTTTTTCCAACAGATAGTTA 14 13 1 TTTTTTCCAA 0.716852 -53 GATTATTTAAATTTTGCCAAGTTAAACAAT 30 266 0 ATTTTGCCAA 0.968123 -35 ********** Masking position 5 Map Score: 1.9943 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 22 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 CCAATGTGCGCGGGCCGGGATTCGAACCCG 4 90 1 CGGGCCGGGA 0.973074 -211 GGCGTTAGCCCGGGTTCGAATCCCGGCCCG 4 100 0 CGGGTTCGAA 0.889896 -201 TGGCAAAATTCGGGTTCAGCGATATTTTTA 4 233 1 CGGGTTCAGC 0.872128 -68 CTCCGGGCAGGGAAAAATGTACT 11 20 0 CGGGCAGGGA 0.977271 -13 GTTATCTGCTCGGGCACGTCAATCTTCTCC 17 23 0 CGGGCACGTC 0.845355 -278 TGACGATCCTCTGGTTGGGATAGACAGTAG 17 253 1 CTGGTTGGGA 0.934435 -48 AATTCAACTGCGGGCTCGGAAAATCTCACG 20 18 1 CGGGCTCGGA 0.989983 -199 TGATGTTGTTCTGGTTGGGCCGATAAAAAT 23 93 0 CTGGTTGGGC 0.933198 -20 ********** Masking position 4 Map Score: 2.78218 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 144 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 ATGGGAAATTCAGCACGACAACTGCTGCAAACG 1 187 0 CACACAAACT 0.981382 -65 CAAGGGCTTCCATCATCCTAACTAAGGTTCTTT 17 103 0 CACATCAACT 0.916658 -198 GAAGCGTTGCCAGCAGAATAACTTGACAAAACG 20 111 0 CACAGAAACT 0.973109 -106 GTATTTAGCGCATCACCCAACCTAAAAAATTTT 23 35 0 CACACCACCT 0.941102 -78 TTTTTAAAAACAACACTAAAACTTGAGTTC 25 103 1 CACACAAACT 0.981382 -20 TTTAAAATGCCAACAGCATAACTTGAGATGCTT 30 119 1 CACAGAAACT 0.973109 -182 ** *** * **** Masking position 5 Map Score: 0.855384 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TCCAGATTTGCGCCCTCCGGAGTTGAGACA 1 232 1 CGCCCTCCGG 0.987857 -20 TTTTAATTGCCTCCATCCGAAGAAACTTTT 4 59 0 CTCCATCCGA 0.917896 -242 ATTCTTTCCCTCCAGAATTATCTAA 4 286 0 TTCCCTCCAG 0.91532 -15 AATACAATCCCTCCATGCAGTATTAATAAT 6 70 0 CTCCATGCAG 0.789149 -39 TAGGGGCCAGTGCCTTCCGGAAGTCCAGAA 15 46 0 TGCCTTCCGG 0.888939 -255 GTGTACTCGACTTCCTCCGGGATGATAATT 15 193 0 CTTCCTCCGG 0.931038 -108 CTTATTAAAATACCATCCGGGTCCAATTCT 15 259 0 TACCATCCGG 0.906144 -42 CTATTTCACACTCCATCAGGGCTATTCGTT 20 85 1 CTCCATCAGG 0.917884 -132 ********** Masking position 6 Map Score: 0.749929 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 258 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617