AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifnr_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 AF0154 139 conserved hypothetical protein #2 AF0155 62 A. fulgidus predicted coding region AF0155 #3 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #4 AF0176 58 molybdopterin oxidoreductase, molybdopterin binding subunit #5 AF0177 300 tungsten formylmethanofuran dehydrogenase, subunit E (fwdE) #6 AF0396 154 A. fulgidus predicted coding region AF0396 #7 AF0400 84 NADH oxidase (noxA-3) #8 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #9 AF0499 300 molybdopterin oxidoreductase, iron-sulfur binding subunit #10 AF0883 71 argininosuccinate lyase (argH) #11 AF0950 177 carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #12 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #13 AF1858 145 NADH oxidase (noxA-5) #14 AF1860 282 A. fulgidus predicted coding region AF1860 #15 AF1868 51 A. fulgidus predicted coding region AF1868 #16 AF1869 78 A. fulgidus predicted coding region AF1869 #17 AF2191 300 A. fulgidus predicted coding region AF2191 #18 AF2371 170 A. fulgidus predicted coding region AF2371 #19 AF2374 159 A. fulgidus predicted coding region AF2374 #20 AF2377 115 conserved hypothetical protein #21 AF2378 47 conserved hypothetical protein #22 AF2383 33 conserved hypothetical protein #23 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 ATATAAACACTGTTAGGTAACAGTGTTTGGGG 1 21 0 TGTTAGGAAA 0.919815 -119 TCAAAACCGATTTTAGGCCAACCAAAAACTTT 1 90 1 TTTTAGGCAC 0.923816 -50 TATTCGAAGATTTTAGGGAAAAGGTAGATGTT 2 20 1 TTTTAGGAAA 0.985322 -43 TTCCCTAAAATATTAGGAAAAATTG 4 4 0 TATTAGGAAA 0.888838 -55 TTTCCTAATATTTTAGGGAAAAACCTTATGAC 4 16 1 TTTTAGGAAA 0.985322 -43 AACTTAACATTTTTGGGTAAGCTGAAAATAGC 7 30 1 TTTTGGGAAC 0.957103 -55 GTCCCCCTCTTTTTAGGCAATATATAAGAATT 8 34 1 TTTTAGGAAA 0.985169 -105 TTGCAGATATTTTTAGGTAAGCTTAAACCAGA 8 81 0 TTTTAGGAAC 0.986031 -58 CTTACCTTTATTTTGGAAAAGAGTTC 18 155 1 TTTTGGAAAA 0.734809 -16 ATCCTCCGTTTTTTAGAAAAGCCTAAAAGTCT 20 42 1 TTTTAGAAAC 0.899372 -74 ATTTTAGGCAATCCGAAAAGTTA 21 2 1 TTTTAGGAAC 0.986027 -46 CTATTTTTAGGATAAATTGCTGGCTA 22 5 1 TTTTAGGTAA 0.889241 -29 GTATTCTCAATTTTAGGTAATAACCTATAAAC 23 92 1 TTTTAGGAAA 0.983851 -99 ******* ** * Masking position 10 Map Score: 21.9108 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 GTTAATTTCCAAAACCCTTATATTTTATCAAG 3 31 1 AAAACTTATA 0.829161 -69 TTATCTTAAAGAAAAATTTAAATATCGTCAGT 6 43 0 GAAATTTAAA 0.901772 -112 TCTTTAAGATAAAAACTTAAAACTAATTTGCT 6 63 1 AAAATTAAAA 0.85095 -92 TCTGTACGTCGGAAAATTTATATTGCAATATT 6 119 1 GGAATTTATA 0.819238 -36 CGCAAATTTCGAAATTCTTATATATTGCCTAA 8 46 0 GAAACTTATA 0.819238 -93 GGGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 8 113 0 GGAATTAAAA 0.665605 -26 ATGTATAGAGGAAAACTTTAAATATAATGGGG 9 94 0 GAAATTTAAA 0.901772 -207 ATAAAAAAGCAAAAGGTTAATATAAGCTAAAT 9 223 1 AAAATTAATA 0.883025 -78 CATCATCTCCAAAACATAAATACATTTGCGGT 10 18 1 AAAATAAATA 0.564075 -54 CTTGAATGCAAAAAAATATATATCGAA 11 6 0 AAAATATATA 0.690234 -172 ATTTAATGGGAAAAAACTTAAATAAAATGA 12 9 0 AAAACTTAAA 0.785897 -73 TCTCAGCAAGAAAACATTTAAAACGAATTGGA 12 49 1 AAAATTTAAA 0.907675 -33 CGTTCCGTTGAAAATATTTAGAGCATTATAAT 13 26 1 AAAATTTAGA 0.672162 -120 AAATATTCACAAAAGGTTTATAACTGAAAGAT 13 80 1 AAAATTTATA 0.928568 -66 TAAACTTATAAGAATATTAATAAATAAAATCT 13 108 0 AGAATTAATA 0.738115 -38 AAGAATTTTTAAAGCGAGTTTGA 14 2 1 AGAATTTAAA 0.785897 -281 AAGCGAGTTTGAAAAATTTATAGAAATGAATG 14 22 1 GAAATTTATA 0.923888 -261 AGCACATTTCGAAAGCTTAATATTTTCCTTTG 15 23 1 GAAATTAATA 0.875762 -29 ATTGGTAGCAGAAAGATTTATATTAAATGAAG 16 12 0 GAAATTTATA 0.923889 -67 TTTAAAATTTAAAAAATAAAAATAAAAAA 20 8 0 AAAATAAAAA 0.494599 -108 CGTTTTTTAGAAAAGCCTAAAAGTCTTGAGGT 20 48 1 AAAACTAAAA 0.680674 -68 TGGAAATTGCAAAAAGTTTATAGGTTATTACC 23 107 0 AAAATTTATA 0.928567 -84 **** ****** Masking position 4 Map Score: 22.8781 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 110 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 GCTTATAATGTTAAATATAAACACTGTTAG 1 37 0 TTAAATATAA 0.841451 -103 TACTACTTGATAAAATATAAGGGTTTTGGA 3 38 0 TAAAATATAA 0.873861 -62 AAAAACACCGTTAAATTTAAATACAGCGTT 5 203 0 TTAAATTTAA 0.492536 -98 TTTTACATGATTAAAAATAATCGAATTAGG 5 229 1 TTAAAAATAA 0.786865 -72 GAGGAAAACTTTAAATATAATGGGGGATAA 9 89 0 TTAAATATAA 0.841451 -212 GGGAAAAAACTTAAATAAAATGA 12 4 0 TTAAATAAAA 0.860215 -78 TTTCGATAGATTAATTATAATGCTCTAAAT 13 41 0 TTAATTATAA 0.770662 -105 TTTTAGGACGTTAAACATAATCTGGCAGGG 14 145 0 TTAAACATAA 0.853723 -138 ACTTCATTTAATATAAATCTTTCTGC 16 7 1 TTTAATATAA 0.758628 -72 GAGGATTGTTTAAAATTTAAAAAATAAAAA 20 18 0 TAAAATTTAA 0.541125 -98 TGATTAGCAATTAAATATAACTCAGTATTC 23 68 1 TTAAATATAA 0.841451 -123 AAAGTTCTTATTAAATAAAATCAAAAAAAC 23 166 1 TTAAATAAAA 0.860215 -25 ********** Masking position 4 Map Score: 11.7396 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 AAGGTTCTGGCAAGAGGAGGTGGAAA 3 84 1 CAAGAGGAGG 0.983321 -16 GCACAGTAGCAGTGCGGAGGGGATAGG 6 8 0 AGTGCGGAGG 0.901772 -147 TATTGCCTAAAAAGAGGGGGACTTGCAATT 8 26 0 AAAGAGGGGG 0.983321 -113 TACCTGCAGGCAAGCGTAGGTAAATCTGAA 11 52 1 CAAGCGTAGG 0.891451 -126 GTAAGGATGAAAAGAGGGAGGGTGGAACAG 14 193 1 AAAGAGGGAG 0.837417 -90 ACTACGAGAGAATGAGGAGGTTGAGGT 14 266 1 AATGAGGAGG 0.960998 -17 CAGTAAAAAGCATGCGGGGGGCGGGATTCG 17 187 1 CATGCGGGGG 0.97877 -114 CAAATTTTTCCAAGCGGGGGTTGCCGAGCC 17 266 0 CAAGCGGGGG 0.990277 -35 GCTTTTCTAAAAAACGGAGGATTGTTTAAA 20 34 0 AAAACGGAGG 0.88347 -82 GTTCCGAGTTACAGAGGAGGA 20 105 1 ACAGAGGAGG 0.927081 -11 ********** Masking position 6 Map Score: 10.9847 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 262 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TTCAAAACCGATTTTAGGCCAACCAAAAAC 1 89 1 ATTTTAGGCC 0.918503 -51 ATATTCGAAGATTTTAGGGAAAAGGTAGAT 2 19 1 ATTTTAGGGA 0.940579 -44 TTTTCCTAATATTTTAGGGAAAAACCTTAT 4 15 1 ATTTTAGGGA 0.940579 -44 AAACTTAACATTTTTGGGTAAGCTGAAAAT 7 29 1 TTTTTGGGTA 0.735506 -56 AGTCCCCCTCTTTTTAGGCAATATATAAGA 8 33 1 TTTTTAGGCA 0.949277 -106 ATTGCAGATATTTTTAGGTAAGCTTAAACC 8 84 0 TTTTTAGGTA 0.922492 -55 GAGGATTGAGTTTTTAGGACGTTAAACATA 14 156 0 TTTTTAGGAC 0.697197 -127 ATTTTAGGCAATCCGAAAAG 21 1 1 ATTTTAGGCA 0.958432 -47 AGTATTCTCAATTTTAGGTAATAACCTATA 23 91 1 ATTTTAGGTA 0.936157 -100 ********** Masking position 5 Map Score: 8.64079 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 13 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TCGCAGATGAGAGGCGTGAGGTTGAGAAGGGGAAGCCTGA 5 40 0 GAGTGAGGGG 0.842079 -261 GTATTGGGAAGAGCTGGGAAAGAGACTGGGAAGTTTCGAG 5 138 0 GAGGGAAAGG 0.993437 -163 ATCTGGTGATGAGTATGGAGATAAGACCTGTAATTGAGAT 9 44 0 GAGGGAGATG 0.972398 -257 TTTCATTTACGATTGTGGATAGGCTTTCGGCATTCATTTC 14 44 0 GATGGATAGG 0.898656 -239 TGAAAAGAGGGAGGGTGGAACAGAGTAATGATGGGAGTAT 14 200 1 GAGGGAACTG 0.918993 -83 CACCTGGATTGAGGTGGGAAATTAAAGCGGTGATTCGCCT 17 13 0 GAGGGAAAGG 0.993437 -288 GGGGGTTGCCGAGCCAGGAAAAGGCGCAGGGCTTAAGACC 17 241 0 GAGGGAAAGG 0.993437 -60 GAACGTAAACGATTCCGGAAAAATGAATGGATTTTCGGAG 18 112 0 GATGGAAAGG 0.977123 -59 TATTGTCCCCGATCGGGGAAGAGGCAGAGGTGGCAGTGCC 19 31 1 GATGGAAGGG 0.954292 -129 GCTTCTCTGCGAGCTCGGGGACACACCATGTCGATAGGTC 19 80 1 GAGGGGGATG 0.8802 -80 *** ***** ** Masking position 2 Map Score: 7.43112 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 288 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 7 ATCACCACCCCAAACACTGTTACCTAACAG 1 14 1 CAAACACTGT 0.850264 -126 ATGTTAAATATAAACACTGTTAGGTAACAG 1 30 0 TAAACACTGT 0.955316 -110 GTTTTGGAAATTAACACCGTAAAAAAAACG 3 16 0 TTAACACCGT 0.957778 -84 TATCAAGTAGTAAACATTGTTAGCCAGAAA 3 56 1 TAAACATTGT 0.830219 -44 TAATCATGTAAAAACACCGTTAAATTTAAA 5 212 0 AAAACACCGT 0.940586 -89 ATTAGGCAACTTAACACCGTTCAAAAATAA 5 253 1 TTAACACCGT 0.957778 -48 AAGAAAAATTTAAATATCGTCAGTGAGAGG 6 37 0 TAAATATCGT 0.664522 -118 TGCTTTCAAATTAACAACGTGT 16 67 1 TTAACAACGT 0.838408 -12 GATGAAATTATAAATAACGTGGAAATTGCA 23 128 0 TAAATAACGT 0.664522 -63 TAAAATCAAAAAAACACTGT 23 181 1 AAAACACTGT 0.871066 -10 ********** Masking position 6 Map Score: 6.8177 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 97 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ACTTTTTAAATTTAGGCTATCCTAAACATAACG 1 117 1 TTGGCTTCCT 0.973518 -23 GCCTTATAAGCTCAGGCTTCCCCTTCTCAACCT 5 29 1 CTGGCTCCCC 0.926128 -272 GGGAGCAATCCTGTAGCTGACCTTATCCTTCTT 5 102 1 CTAGCTACCT 0.794808 -199 CGCACTGCTACTGTGCCTCTCACTGACGATATT 6 22 1 CTGCCTTCAC 0.666216 -133 GGCTTGCTATTTTCAGCTTACCCAAAAATGTTA 7 34 0 TTAGCTACCC 0.872357 -51 CGCTTTCTGGTTTAAGCTTACCTAAAAATATCT 8 76 1 TTAGCTACCT 0.809838 -63 TTTCGATATATTTTGGCTCTCCTAAGTCCGCAG 9 175 1 TTGGCTTCCT 0.973518 -126 ATTCCTCCGATTACGGCTTTTCTGTAAACTTCA 9 274 0 TTGGCTTTCT 0.928666 -27 GAAAGCAATATTTAGCCTTTTCCGATGTATATT 16 41 0 TTGCCTTTCC 0.921867 -38 GTCTTAAGCCCTGCGCCTTTTCCTGGCTCGGCA 17 242 1 CTGCCTTTCC 0.914759 -59 ATCGTTTACGTTCCGGCTTACCTTTATTTTGGA 18 139 1 TTGGCTACCT 0.959167 -32 GCACTGCCACCTCTGCCTCTTCCCCGATCGGGG 19 37 0 CTGCCTTTCC 0.914759 -123 ATCGTAAGGCTTTCGCCTCACTCCTAAGGGGAC 19 117 0 TTGCCTACTC 0.583719 -43 CCTCAAGACTTTTAGGCTTTTCTAAAAAACGGA 20 46 0 TTGGCTTTCT 0.928666 -70 ** **** **** Masking position 8 Map Score: 11.9897 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 458 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 AATGCAATCAAAAATGCATAATGCTTATAA 1 59 0 AAAATGCATA 0.822496 -81 ATCGGTTTTGAAAATGCAATCAAAAATGCA 1 71 0 AAAATGCAAT 0.878811 -69 CTACAAACTTAAAAAGCAAATTAGTTTTAA 6 79 0 AAAAAGCAAA 0.951762 -76 GGTAAGCTGAAAATAGCAAGCCATATAATA 7 45 1 AAATAGCAAG 0.84316 -40 GAATCGAATAAAAAAGCAAAAGGTTAATAT 9 216 1 AAAAAGCAAA 0.951762 -85 ATCGAAACAGAAAAAGAAATATTCACAAAA 13 64 1 AAAAAGAAAT 0.752876 -82 TTACTGCAGTAAAAAGCATGCGGGGGGCGG 17 181 1 AAAAAGCATG 0.885099 -120 ATAAACAGCAATTCTCAAATTT 17 289 0 AAACAGCAAT 0.741842 -12 CGATTCCGGAAAAATGAATGGATTTTCGGA 18 113 0 AAAATGAATG 0.529419 -58 CTTAAAAGACAAAAAGAAAATTATTAAATT 23 38 0 AAAAAGAAAA 0.830144 -153 AATAACGTGGAAATTGCAAAAAGTTTATAG 23 116 0 AAATTGCAAA 0.763804 -75 ********** Masking position 3 Map Score: 4.0568 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 132 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 TTCTTCACCTCGAAACTTCCCAGTCTCTTTC 5 130 1 CGAACTTCCC 0.722013 -171 GGGAAGGTTAAAAAACTTCTCGATTGCAGAT 8 105 0 AAAACTTCTC 0.619174 -34 TTAACCTTCCCACAACTCCCCCTT 8 125 1 CAAACTCCCC 0.927834 -14 ATTATGAGGTCAAAAATCATCATTTTTCGAT 9 151 1 CAAAATCATC 0.667317 -150 CAGGTAATTTAACAAATCCCCTTGAATGCAA 11 27 0 AAAAATCCCC 0.881204 -151 GAAAAATCTTCACCAATTCTCAAATACATAC 11 79 1 CACAATTCTC 0.912626 -99 ATTTTAACAACACAAATCCTCATGTATCCTG 11 122 1 CAAAATCCTC 0.965464 -56 CGTCCTAAAAACTCAATCCTCATTCACTGTA 14 165 1 ACCAATCCTC 0.709338 -118 TTTCCTGGCTCGGCAACCCCCGCTTGGAAAA 17 260 1 CGCAACCCCC 0.741229 -41 ATAAACAGCAATTCTCAAATTTTTCC 17 285 0 CACAATTCTC 0.912619 -16 GCTCACTCAACGGAAATCCTCTCTAACTGAC 18 67 0 CGAAATCCTC 0.945969 -104 TTTAAATTTTAAACAATCCTCCGTTTTTTAG 20 27 1 AACAATCCTC 0.912626 -89 ** ******** Masking position 5 Map Score: 4.53099 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 695 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 GTGGGAAGTACGGCTCGAAAACTTAACATTTT 7 11 1 CGGCTCAAAC 0.983334 -74 AGTCCGCAGACGGCTCAGAATCGAATAAAAAA 9 199 1 CGGCTCAATC 0.955751 -102 ATATTTTCAACGGAACGCAATCAACAACAAAA 13 11 0 CGGAACAATC 0.931245 -135 ACAGTGACGGCGACACATCAACTGACCTGTTG 17 74 1 CGACACCAAC 0.911973 -227 CGCCTTTTCCTGGCTCGGCAACCCCCGCTTGG 17 255 1 TGGCTCCAAC 0.865916 -46 AAAGGTAAGCCGGAACGTAAACGATTCCGGAA 18 132 0 CGGAACAAAC 0.973683 -39 GCTTCATCGTCGGCACTGCCACCTCTGCCTCT 19 50 0 CGGCACCCAC 0.981321 -110 CTCTGTAACTCGGAACGCACACCTTCATGTTT 20 89 0 CGGAACACAC 0.954444 -27 ****** **** Masking position 6 Map Score: 3.42181 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 108 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 CCAACTTAGTCAGCAATCAACATCTACCTT 2 40 0 CAGCAATCAA 0.666103 -23 ATAATAAGCGCTGCAGTCGGGGGTCC 7 69 1 CTGCAGTCGG 0.985714 -16 CTAAAAATATCTGCAATCGAGAAGTTTTTT 8 97 1 CTGCAATCGA 0.875241 -42 TCTCCTAAGTCCGCAGACGGCTCAGAATCG 9 192 1 CCGCAGACGG 0.90333 -109 GCTAAATATACAGCAGACAGAGAATTTGAA 9 248 1 CAGCAGACAG 0.896436 -53 GTTAAATTACCTGCAGGCAAGCGTAGGTAA 11 45 1 CTGCAGGCAA 0.948231 -133 GCCTCGTATAGTGCAGGCGGTCTGAAGTTT 14 82 0 GTGCAGGCGG 0.934503 -201 ATGCTTTTTACTGCAGTAAGAGTCTCATGT 17 170 0 CTGCAGTAAG 0.842018 -131 TAAAGGATTAGTGCAGTCAAATTTAATAAT 23 19 1 GTGCAGTCAA 0.893946 -172 ********** Masking position 5 Map Score: 2.82935 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 292 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TAATGTTAAATATAAACACTGTTAGGTAACAGTGT 1 27 0 TATAAAATTG 0.647211 -113 TTTGGTTGGCCTAAAATCGGTTTTGAAAATGCAAT 1 81 0 CTAAAACTTG 0.521728 -59 ATAGCCTAAATTTAAAAAGTTTTTGGTTGGCCTAA 1 102 0 TTTAAAATTG 0.955431 -38 ACTCATTAGCTTTAAATTATTTTTGAACGGTGTTA 5 264 0 TTTAAATTTG 0.841744 -37 GGACTCTTAAAAACTCATTAGCTTTAAATTA 5 280 0 TTAAAACTTG 0.758919 -21 TAAAGAAAAATTTAAATATCGTCAGTGAGAGGCAC 6 34 0 TTTAAAATCG 0.85198 -121 AAGATAAAAACTTAAAACTAATTTGCTTTTTAAGT 6 68 1 CTTAAACTTG 0.87111 -87 AGAGGAAAACTTTAAATATAATGGGGGATAAGTAT 9 85 0 TTTAAAATGG 0.757729 -216 GATTTGTGTTGTTAAAATTGGTTTGTATTGGTATG 11 105 0 GTTAAATTTG 0.779125 -73 GACGGTAAGGTTTAAATACACTTAGAGTTGAAGCC 11 152 1 TTTAAAATTG 0.955438 -26 CAAGAAAACATTTAAAACGAATTGGAGAGAGCGAA 12 55 1 TTTAAACTTG 0.951222 -27 ATTGCGTTCCGTTGAAAATATTTAGAGCATTATAA 13 22 1 GTTGAAATTG 0.643231 -124 AAATCTTTCAGTTATAAACCTTTTGTGAATATTTC 13 79 0 GTTATAATTG 0.548829 -67 TTCTTATAAGTTTAAATATTCATCGAGAGC 13 126 1 TTTAAAAATG 0.647212 -20 AAGAATTTTTAAAGCGAGTTTGAAAAATTTAT 14 8 1 TTTAAACTTG 0.951222 -275 TTTTTAGGACGTTAAACATAATCTGGCAGGGACGA 14 141 0 GTTAAAATCG 0.792384 -142 ****** * ** * Masking position 6 Map Score: 6.85295 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 28 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 14 TTCCACCTCCTCTTGCCAGAACCTTTCTGG 3 79 0 TCTTGCCAGA 0.709818 -21 AACCTTATGACCTTGCCAAAAAGACACTAT 4 37 1 CCTTGCCAAA 0.952975 -22 TCACATCGTCCCTTGCAAGATTTGCCTCGT 14 105 0 CCTTGCAAGA 0.727072 -178 GGACTCTCGTCCCTGCCAGATTATGTTTAA 14 135 1 CCCTGCCAGA 0.966448 -148 ATCTCTACGACCTTGCAGGACCAGGGCTGG 17 130 1 CCTTGCAGGA 0.800982 -171 ********** Masking position 4 Map Score: 1.73915 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 40 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 15 AAAACTTTTTAAATTTAGGCTATCCTAAAC 1 114 1 AAATTTAGGC 0.827201 -26 CGAAATTCTTATATATTGCCTAAAAAGAGG 8 39 0 ATATATTGCC 0.767351 -100 GGTTATTATAAGATTTTGGCTTATGTATAG 9 118 0 AGATTTTGGC 0.909319 -183 ATTTTTCGATATATTTTGGCTCTCCTAAGT 9 172 1 ATATTTTGGC 0.923638 -129 TGTCTGCTGTATATTTAGCTTATATTAACC 9 237 0 ATATTTAGCT 0.728505 -64 TTTGAAAGCAATATTTAGCCTTTTCCGATG 16 47 0 ATATTTAGCC 0.95389 -32 TCAGATTTAGCCAGCAATTTAT 22 22 0 AGATTTAGCC 0.944904 -12 ********** Masking position 3 Map Score: 1.01001 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274