AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ndkA 42 ndkA #2 valS 87 valS #3 Rv2449c 89 hypothetical protein Rv2449c #4 Rv2450c 81 hypothetical protein Rv2450c #5 aspS 239 aspS #6 Rv2581c 50 hypothetical protein Rv2581c Motif number 1 CAAGATGTATGCCCAAACCGG 1 2 0 GCCCAAACCG 0.989074 -41 CATGAAAGCGCCCGAAACCGCCCGGAT 2 8 0 CCCGAAACCG 0.933204 -80 GTGAGGGCTGGCGGTCACCGATCAATTCTA 2 56 0 GCGGTCACCG 0.996724 -32 GTGACCGCCAGCCCTCACCCTGCCGCCGAT 2 68 1 GCCCTCACCC 0.984231 -20 GCGTCTGCTCGCGCACCCCGGAGTAGCGTC 3 64 1 GCGCACCCCG 0.994081 -26 GCTTTGGCGCGCGCGCACCGCGAAAGGAAC 4 58 1 GCGCGCACCG 0.998686 -24 CGGCGAGACGGCGCAGACCCCATC 5 5 0 GCGCAGACCC 0.979427 -235 CACTCCGCGCGCCGGGATCGAGCTCCGGCG 5 30 0 GCCGGGATCG 0.976412 -210 CCGCTGTTGTGCGGCCACACTCCGCGCGCC 5 47 0 GCGGCCACAC 0.819837 -193 GTGCAACAGCGCGGCGACCGTCGTTCCGAC 5 92 1 GCGGCGACCG 0.990383 -148 CCGTCGTTCCGACGGCACCGGGTCCGACTA 5 109 1 GACGGCACCG 0.969927 -131 AACAGGCATTGCCCTAGTCGGACCCGGTGC 5 123 0 GCCCTAGTCG 0.74918 -117 GGTGCCCGCGGCGCACATCGGTCACGCAGG 5 183 0 GCGCACATCG 0.992122 -57 GATGTGCGCCGCGGGCACCTCTAGACTGAG 5 194 1 GCGGGCACCT 0.980902 -46 GTTCGCGGCCCGCCTCGTCCCCGGACG 6 8 1 GCCCGCCTCG 0.974607 -43 CGCCTCGTCCCCGGACGCCGGGGATGGGAA 6 21 1 CCGGACGCCG 0.962913 -30 ********** Masking position 2 Map Score: 36.6745 Number of sites scoring better than the average of aligned sites = 21213 Number in coding regions = 19992 Number in noncoding regions = 1221 Number of orfs with sites within 600 bp upstream = 765 Fraction of orfs with sites within 600 bp upstream = 0.122872 Motif number 2 CCGGTTTGGGCATACATCTTG 1 1 1 CCGGTTGGGC 0.94677 -42 CTTGCGGCATCTAGTGTTGGGCACC 1 28 1 CTAGGTTGGG 0.801552 -15 ATCCGGGCGGTTTCGGGCGCTTTCATG 2 7 1 GCGGTTCGGG 0.966256 -81 CGCTTTCATGCCGGTGTGAAGCGGTTCCTAG 2 28 1 CCGGGTGAAG 0.963226 -60 ATCGGCGGCAGGGTGAGGGCTGGCGGTC 2 70 0 GCAGGTGAGG 0.85189 -18 GGGAGCTTTTGCGTCTTTTCGCGGTGG 3 7 0 GCGTTTTTCG 0.651675 -83 CCAAATCCGACCGGATTTGGGAGCTTTTGCG 3 25 0 CCGGTTTGGG 0.995132 -65 CCAAATCCGGTCGGATTTGGGAGCTTTTGCG 3 36 1 TCGGTTTGGG 0.927917 -54 CTCGCGCACCCCGGAGTAGCGTCAAACCC 3 71 1 CCGGGTAGCG 0.985502 -19 TAACCCATGCCCGTGGGTTGGCTTTGGCGCG 4 38 1 CCGTGGTTGG 0.901998 -44 GGATCGAGCTCCGGCGAGACGGCGCAGACCC 5 15 0 CCGGGAGACG 0.971116 -225 ATCCCGGCGCGCGGAGTGTGGCCGCACAACA 5 42 1 GCGGGTGTGG 0.984941 -198 GTATTCGCCGCTGTTGTGCGGCCACACTCCG 5 53 0 CTGTGTGCGG 0.736164 -187 TTGCACAAGGCCGGGTATTCGCCGCTGTTGT 5 67 0 CCGGTATTCG 0.917196 -173 AGCGCGGCGACCGTCGTTCCGACGGCACCGG 5 99 1 CCGTGTTCCG 0.924184 -141 GTCGGTTAATCCGGTTGAAGGGGA 5 226 1 CCGGTGAAGG 0.845576 -14 TCCCCGGCGTCCGGGGACGAGGCGGGCCGCG 6 14 0 CCGGGACGAG 0.909567 -37 TCCCCGGACGCCGGGGATGGGAAACTGGGAA 6 28 1 CCGGGATGGG 0.994618 -23 **** ****** Masking position 11 Map Score: 25.4911 Number of sites scoring better than the average of aligned sites = 18666 Number in coding regions = 17214 Number in noncoding regions = 1452 Number of orfs with sites within 600 bp upstream = 875 Fraction of orfs with sites within 600 bp upstream = 0.14054 Motif number 3 AACACTAGATGCCGCAAGATGTATGCCCAA 1 16 0 GCCGCAAGAT 0.8964 -27 GCGCCCGAAACCGCCCGGAT 2 1 0 CCGCCCGGAT 0.90295 -87 CGGGCGCTTTCATGCCGGTGTGAAGCGGTT 2 24 1 CATGCCGGTG 0.74911 -64 ATCGGCGGCAGGGTGAGGGCTGGC 2 74 0 GCGGCAGGGT 0.95023 -14 ACCGCGAAAAGACGCAAAAGCTCCCAAATC 3 13 1 GACGCAAAAG 0.631969 -77 GCTCCCAAATCCGACCGGATTTGGGAGCTT 3 30 0 CCGACCGGAT 0.857447 -60 TGCGCGAGCAGACGCAAAAGCTCCCAAATC 3 49 0 GACGCAAAAG 0.631969 -41 TCTGCTCGCGCACCCCGGAGTAGCGTCAAA 3 67 1 CACCCCGGAG 0.961945 -23 GCATGGGTTAGCTGCCAGGTGCATTCGAGG 4 18 0 GCTGCCAGGT 0.814228 -64 AGCCAACCCACGGGCATGGGTTAGCTGCCA 4 31 0 CGGGCATGGG 0.694481 -51 GCGGTGCGCGCGCGCCAAAGCCAACCCACG 4 49 0 CGCGCCAAAG 0.855887 -33 TCTGCGCCGTCTCGCCGGAGCTCGATCCCG 5 18 1 CTCGCCGGAG 0.964737 -222 CCACACTCCGCGCGCCGGGATCGAGCTCCG 5 33 0 CGCGCCGGGA 0.946362 -207 GCTGTTGCACAAGGCCGGGTATTCGCCGCT 5 72 0 AAGGCCGGGT 0.841907 -168 TCGTTCCGACGGCACCGGGTCCGACTAGGG 5 112 1 GGCACCGGGT 0.903838 -128 GCACATCGGTCACGCAGGATAATTTCGGCT 5 171 0 CACGCAGGAT 0.970436 -69 CTCGTCCCCGGACGCCGGGGATGGGAAACT 6 24 1 GACGCCGGGG 0.993402 -27 ********** Masking position 5 Map Score: 19.5483 Number of sites scoring better than the average of aligned sites = 41613 Number in coding regions = 38803 Number in noncoding regions = 2810 Number of orfs with sites within 600 bp upstream = 1287 Fraction of orfs with sites within 600 bp upstream = 0.206714 Motif number 4 ATACATCTTGCGGCATCTAGTGTTGGGCAC 1 22 1 CGGCATCTAG 0.875751 -21 ATCCGGGCGGTTTCGGGCGCTTTCATG 2 8 1 CGGTTTCGGG 0.609592 -80 CGGTGTGAAGCGGTTCCTAGAATTGATCGG 2 39 1 CGGTTCCTAG 0.862773 -49 GAGGGCTGGCGGTCACCGATCAATTCTAGG 2 54 0 GGTCACCGAT 0.889592 -34 ACGCTACTCCGGGGTGCGCGAGCAGACGCA 3 63 0 GGGGTGCGCG 0.975005 -27 TTTGGCGCGCGCGCACCGCGAAAGGAACAA 4 60 1 GCGCACCGCG 0.969356 -22 GATGGGGTCTGCGCCGTCTCGCCGG 5 6 1 GGTCTGCGCC 0.718669 -234 CTCCGCGCGCCGGGATCGAGCTCCGGCGAG 5 28 0 CGGGATCGAG 0.962389 -212 TCGGAACGACGGTCGCCGCGCTGTTGCACA 5 91 0 GGTCGCCGCG 0.973618 -149 CCGACGGCACCGGGTCCGACTAGGGCAATG 5 117 1 CGGGTCCGAC 0.965168 -123 AGGATAATTTCGGCTCATCTCAACAAACAT 5 156 0 CGGCTCATCT 0.454561 -84 AATTATCCTGCGTGACCGATGTGCGCCGCG 5 177 1 CGTGACCGAT 0.887656 -63 TGTGCGCCGCGGGCACCTCTAGACTGAGCA 5 196 1 GGGCACCTCT 0.928214 -44 CGGGGACGAGGCGGGCCGCGAAC 6 4 0 GCGGGCCGCG 0.955715 -47 CCCCGGCGTCCGGGGACGAGGCGGGCCGCG 6 14 0 CGGGGACGAG 0.892827 -37 ********** Masking position 7 Map Score: 13.1546 Number of sites scoring better than the average of aligned sites = 48708 Number in coding regions = 45556 Number in noncoding regions = 3152 Number of orfs with sites within 600 bp upstream = 1301 Fraction of orfs with sites within 600 bp upstream = 0.208962 Motif number 5 ********** No masking Map Score: 1.60826e-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 6 ********** No masking Map Score: 1.60826e-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 7 ********** No masking Map Score: 1.60826e-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