AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i227_rna_methyltransferase_aful_reg_300.orf -o227_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG25045 74 Archaeoglobus_fulgidus #2 RAG47972 56 Archaeoglobus_fulgidus #3 RAG50012 30 Archaeoglobus_fulgidus #4 RAG46510 204 Archaeoglobus_fulgidus #5 RAG07110 278 Archaeoglobus_fulgidus Motif number 1 ATATCAACTTTTACCCGAATAACGTAAATAT 1 31 0 TTACCGAATA 0.943324 -44 AATTTTTAAACCCATGACCGTTCTCTA 3 7 1 TAACCCATGA 0.905918 -24 AACATTTAGGTTAACCTAAGAGACG 4 5 0 TTACCTAAGA 0.982758 -200 CGAAAAAGTGTTATCCTCCGAGAAATTCGGA 4 123 1 TTACCTCCGA 0.948131 -82 TTGCACTTTTTTAACCGACGATAAAATAGAA 5 20 0 TTACCGACGA 0.993582 -259 CGGTGGGATTTGAACCCACGACTGGCGGGTC 5 86 1 TGACCCACGA 0.990508 -193 GTTGGAGCTCTGACCCGAAGAGACCCGCCAG 5 107 0 TGACCGAAGA 0.988558 -172 GTGAAAGAACTTATCCCAAAAAATTTAATAT 5 239 0 TTACCCAAAA 0.943272 -40 *** ******* Masking position 3 Map Score: 9.92115 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 32 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 GGGTTCAAATCCCACCGGCCCCATTTTTATTT 5 71 0 CCCCGGCCCC 0.99587 -208 GAGCTCTGACCCGAAGAGACCCGCCAGTCGTG 5 102 0 CGAGAGACCC 0.973751 -177 GTCTGCTGAGCGGTGATGACCCGTTGGAGCTC 5 128 0 CGGATGACCC 0.923936 -151 GTCATCACCGCTCAGCAGACCCGTCAATCATC 5 140 1 CCGCAGACCC 0.997995 -139 ATCATCACGCCGCTGGAGCCCGCCGCGCTTCC 5 166 1 CCGGAGCCCG 0.990383 -113 TTCCTGGCTACGCCACGACCCCTCGTTAAATG 5 194 1 CCACGACCCC 0.973926 -85 TAAGTTCTTTCACCGCAGCCCCAACTACTGAT 5 257 1 CCGCAGCCCC 0.999028 -22 * * ******** Masking position 10 Map Score: 7.13925 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 206 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 TCGAAAGCTCCAACAAATCGC 1 64 1 CAACAAATCG 0.838054 -11 TTTAACTGAACAGCAAAGTTTATATTCATC 2 17 1 CAGCAAAGTT 0.820487 -40 ATTCATCGTCCAGAAAAGTCAGCATAA 2 40 1 CAGAAAAGTC 0.935333 -17 CTTTTGGTAACAAAAAATTGCGAAAAAGTG 4 103 1 CAAAAAATTG 0.975494 -102 CAAAAAATTGCGAAAAAGTGTTATCCTCCG 4 113 1 CGAAAAAGTG 0.966776 -92 TGTTATCCTCCGAGAAATTCGGAAATAAAT 4 131 1 CGAGAAATTC 0.694918 -74 TTAATTACAGGAAAAAAGAGTAGCCAGAAA 4 171 1 GAAAAAAGAG 0.816359 -34 AAAGAGTAGCCAGAAAAGAGGTGATTTGTA 4 185 1 CAGAAAAGAG 0.955559 -20 TATCGTCGGTTAAAAAAGTGCAACCTTCTA 5 28 1 TAAAAAAGTG 0.868834 -251 ATTTAAATGTCAAGAAATAGAAGGTTGCAC 5 45 0 CAAGAAATAG 0.898196 -234 GAACTTATCCCAAAAAATTTAATATCCTAT 5 234 0 CAAAAAATTT 0.886998 -45 ********** Masking position 5 Map Score: 8.60927 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 494 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TAAATATCAGAAGCTTGAGGTTCTTGC 1 6 0 AAGTTGAGTT 0.929154 -69 CGATTTGTTGGAGCTTTCGAATATATCAACTT 1 52 0 GAGTTTCGAT 0.906886 -23 GATGAATATAAACTTTGCTGTTCAGTTAAATA 2 15 0 AACTTGCTTT 0.898988 -42 AAGCTTTAATAACATTTAGGTTAACCTAAGAG 4 14 0 AACTTTAGTT 0.951105 -191 AATGTTATTAAAGCTTTCGGTTGTCCTAAATT 4 30 1 AAGTTTCGTT 0.987841 -175 TGCCATTCCGGAGCTTTAATTTAGGACAACCG 4 47 0 GAGTTTAATT 0.852743 -158 TGTAATTAAGAACTTTTCGATTTATTTCCGAA 4 148 0 AACTTTCGTT 0.983301 -57 CAAGAAATAGAAGGTTGCACTTTTTTAACCGA 5 33 0 AAGTTGCATT 0.962387 -246 *** ***** ** Masking position 2 Map Score: 6.33166 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 179 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TTTTTATTTAACTGAACAGC 2 1 1 TTTTTATTTA 0.96631 -56 AACAGCAAAGTTTATATTCATCGTCCAGAA 2 25 1 TTTATATTCA 0.777403 -32 CATTCCGGAGCTTTAATTTAGGACAACCGA 4 46 0 CTTTAATTTA 0.826445 -159 ATTAAGAACTTTTCGATTTATTTCCGAATT 4 146 0 TTTCGATTTA 0.942831 -59 TTTTACTTTTTCTATTTTATCGTCGGTT 5 9 1 TTTCTATTTT 0.917541 -270 AAAGTGCAACCTTCTATTTCTTGACATTTA 5 42 1 CTTCTATTTC 0.917339 -237 ACCGGCCCCATTTTTATTTAAATGTCAAGA 5 60 0 TTTTTATTTA 0.96631 -219 ********** Masking position 6 Map Score: 2.88759 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 32 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TGACGGGTCTGCTGAGCGGTGATGACCCGTTGGAG 5 131 0 GCGAGGATGA 0.989109 -148 GCGGCGGGCTCCAGCGGCGTGATGATTGACGGGTC 5 157 0 CCGCGGATGA 0.992654 -122 ACGAGGGGTCGTGGCGTAGCCAGGAAGCGCGGCGG 5 185 0 GTGCGGAGGA 0.995167 -94 CTCGTTAAATGCTTCGCAGATAGGATATTAAATTT 5 215 1 GCTCGGAGGA 0.994941 -64 AGTAGTTGGGGCTGCGGTGAAAGAACTTATCCCAA 5 251 0 GCGCGGAGAA 0.995168 -28 ** *** * **** Masking position 12 Map Score: 2.44105 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 150 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ATTTAGAGAACGGTCATGGGTTTAAAAATT 3 11 0 CGGTCATGGG 0.992578 -20 AGAGACCCGCCAGTCGTGGGTTCAAATCCC 5 90 0 CAGTCGTGGG 0.997069 -189 ATTTAACGAGGGGTCGTGGCGTAGCCAGGA 5 195 0 GGGTCGTGGC 0.986655 -84 ATCAGTAGTTGGGGCTGCGGTG 5 267 0 CAGTAGTTGG 0.956072 -12 ********** Masking position 4 Map Score: 1.68089 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 GCGATTTGTTGGAGCTTTCGAATAT 1 60 0 TTGTTGGAGC 0.989146 -15 CGGTGATGACCCGTTGGAGCTCTGACCCGA 5 120 0 CCGTTGGAGC 0.997405 -159 AATCATCACGCCGCTGGAGCCCGCCGCGCT 5 165 1 CCGCTGGAGC 0.995574 -114 ATCAGTAGTTGGGGCTGCGGTGAAA 5 264 0 TAGTTGGGGC 0.981637 -15 ********** Masking position 5 Map Score: 4.5007 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 43 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 9 ********** No masking Map Score: 1.82142e-12 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 10 ********** No masking Map Score: 1.82142e-12 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 11 ********** No masking Map Score: 1.82142e-12 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