AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_3_mtub_reg_100.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 Rv0264c 95 hypothetical protein Rv0264c #2 fecB2 21 fecB2 #3 Rv0266c 176 hypothetical protein Rv0266c Motif number 1 CAGGGATTTTCGAGACTGCCAGAGGTGCCTTAGCA 1 16 0 CGGACTCCGG 0.855989 -80 AATCCCTGGCCGAGCCGAAGATTGCAGCGCTACCG 1 43 1 CGGCCGAGGC 0.995353 -53 ATCACACTCATGCGTCGACGGTAGCGCTGCAATCT 1 61 0 TGGTCGCGGC 0.955896 -35 AGCGTGAGGGTATCGCGCGCG 2 5 0 CGGAGGTACG 0.889125 -17 GGTTAGGTCTCCTGTCGACAAGCGGGCGACATCAG 3 12 1 CCGTCGCAGG 0.900839 -165 TCTTTAGCGTCGAGCCGTCATTACCGCTGATGTCG 3 38 0 CGGCCGCACC 0.992535 -139 AGCGCGCATCCGGGCCGGTAACAGGGTCTCTTTAG 3 66 0 CGGCCGTAGG 0.936902 -111 GGCCCGGATGCGCGCTGTTACAGCGGAGATACCTT 3 85 1 CGGCTGTACG 0.976312 -92 CAACGGCAGACGGGCCGAAGCCACCTAAAGGTATC 3 112 0 CGGCCGAGCC 0.940009 -65 CTTCGGCCCGTCTGCCGTTGTGAGGACGGGACCGG 3 127 1 TCGCCGTGGG 0.966644 -50 GGACCGGCTGCGAGCGTGAAGGGGGAGTCCGG 3 155 1 CGGCGTAAGG 0.953178 -22 ** **** ** ** Masking position 4 Map Score: 16.9878 Number of sites scoring better than the average of aligned sites = 19719 Number in coding regions = 18129 Number in noncoding regions = 1590 Number of orfs with sites within 600 bp upstream = 958 Fraction of orfs with sites within 600 bp upstream = 0.153871 Motif number 2 GCATTTGCTAAGGCACCTCTGGCAGTC 1 7 1 GCTAAGCACC 0.926491 -89 TCTGGCAGTCTCGAAAATCCCTGGCCGAGCC 1 28 1 TCGAAATCCC 0.91893 -68 CCTGGCCGAGCCGAAGATTGCAGCGCTACCG 1 47 1 CCGAAGTTGC 0.945139 -49 CACTCATGCGTCGACGGTAGCGCTGCAATCT 1 61 0 TCGACGTAGC 0.885037 -35 CGACAAGCGGGCGACATCAGCGGTAATGACG 3 27 1 GCGACACAGC 0.929319 -150 TAGCGTCGAGCCGTCATTACCGCTGATGTCG 3 38 0 CCGTCATACC 0.971222 -139 CGCTGTTACAGCGGAGATACCTTTAGGTGGC 3 97 1 GCGGAGTACC 0.985437 -80 GGCAGACGGGCCGAAGCCACCTAAAGGTATC 3 112 0 CCGAAGCACC 0.997116 -65 GCAGCCGGTCCCGTCCTCACAACGGCAGACG 3 135 0 CCGTCCCACA 0.835411 -42 CCGGACTCCCCCTTCACGCTC 3 166 0 CCGGACCCCC 0.96627 -11 ****** **** Masking position 2 Map Score: 10.6875 Number of sites scoring better than the average of aligned sites = 23176 Number in coding regions = 22067 Number in noncoding regions = 1109 Number of orfs with sites within 600 bp upstream = 723 Fraction of orfs with sites within 600 bp upstream = 0.116126 Motif number 3 GAGACTGCCAGAGGTGCCTTAGCAAATGC 1 10 0 GAGGTGCCTT 0.875244 -86 GAAGATTGCAGCGCTACCGTCGACGCATGA 1 59 1 GCGCTACCGT 0.892415 -37 CGCGCGCGATACCCTCACGCT 2 6 1 GCGATACCCT 0.987509 -16 CTCGACGCTAAAGAGACCCTGTTACCGGCC 3 59 1 AAGAGACCCT 0.966764 -118 TGTTACAGCGGAGATACCTTTAGGTGGCTT 3 100 1 GAGATACCTT 0.941568 -77 CGTTGTGAGGACGGGACCGGCTGCGAGCGT 3 142 1 ACGGGACCGG 0.708907 -35 ********** Masking position 7 Map Score: 5.48523 Number of sites scoring better than the average of aligned sites = 1335 Number in coding regions = 1238 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 ATTTTCGAGACTGCCAGAGGTGCCTTAGCA 1 16 0 CTGCCAGAGG 0.96921 -80 ATCTTCGGCTCGGCCAGGGATTTTCGAGAC 1 35 0 CGGCCAGGGA 0.983364 -61 GGTCTCCTGTCGACAAGCGGGCGACATCAG 3 17 1 CGACAAGCGG 0.99258 -160 GTCTCTTTAGCGTCGAGCCGTCATTACCGC 3 46 0 CGTCGAGCCG 0.803454 -131 GCATCCGGGCCGGTAACAGGGTCTCTTTAG 3 66 0 CGGTAACAGG 0.92683 -111 GTCCTCACAACGGCAGACGGGCCGAAGCCA 3 124 0 CGGCAGACGG 0.947061 -53 CGGCTGCGAGCGTGAAGGGGGAGTCCGG 3 159 1 CGTGAAGGGG 0.977152 -18 ********** Masking position 1 Map Score: 3.89558 Number of sites scoring better than the average of aligned sites = 9366 Number in coding regions = 8620 Number in noncoding regions = 746 Number of orfs with sites within 600 bp upstream = 574 Fraction of orfs with sites within 600 bp upstream = 0.092194 Motif number 5 ********** No masking Map Score: -1.17788e-14 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: -1.17788e-14 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: -1.17788e-14 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