AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_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 Rv0225 35 hypothetical protein Rv0225 #2 gmdA 300 gmdA Motif number 1 CTGGCACACCCTACGGCCCGC 1 1 1 CTGGCACACC 0.967199 -35 GGCTCTCAGCGACAGCTGTCTGACCTG 2 7 1 CAGCGACACT 0.951515 -294 CAATCCCGCACAGCCACGACCAACTTGGGAA 2 46 0 CAGCCACGCC 0.998433 -255 CGCGACCCCCACGCCACCTCCAATCCCGCAC 2 66 0 ACGCCACCCC 0.991533 -235 AATCCATACGACGCGACCCCCACGCCACCTC 2 77 0 ACGCGACCCC 0.988861 -224 CCGCGCGAAACGGCCGCAGGCGCAATGGTCA 2 121 1 CGGCCGCAGC 0.970457 -180 AGGCTAGACTCCACCGCGGCCAAGTTGGTGA 2 149 0 CCACCGCGCC 0.982669 -152 TCCTGGTTGTCGGGGGCGACCAGGAAAATGT 2 181 0 CGGGGGCGCC 0.996284 -120 GCCCGTTCTGCAGCGACCTCCTGGTTGTCGG 2 199 0 CAGCGACCCC 0.997445 -102 AGATGTGGGTAGGGAACGCCCGTTCTGCAGC 2 216 0 AGGGAACGCC 0.919333 -85 TATGAAGCGACAGCGGCGCCCCGCTGTGATG 2 249 1 CAGCGGCGCC 0.998062 -52 ******** ** Masking position 7 Map Score: 24.049 Number of sites scoring better than the average of aligned sites = 14965 Number in coding regions = 14114 Number in noncoding regions = 851 Number of orfs with sites within 600 bp upstream = 555 Fraction of orfs with sites within 600 bp upstream = 0.0891423 Motif number 2 CACCCTACGGCCCGCTAGGCTATCGACCA 1 17 1 CCCGCTAGGC 0.990561 -19 CACCTCCAATCCCGCACAGCCACGACCAAC 2 53 0 CCCGCACAGC 0.980722 -248 TACGACGCGACCCCCACGCCACCTCCAATC 2 72 0 CCCCCACGCC 0.985295 -229 TATGGATTCTCCTCCTCGGTTCCGCGCGAA 2 100 1 CCTCCTCGGT 0.992218 -201 AGGCTAGACTCCACCGCGGCCAAGTTGGTG 2 150 0 CCACCGCGGC 0.960892 -151 CTCACATTTTCCTGGTCGCCCCCGACAACC 2 178 1 CCTGGTCGCC 0.950025 -123 TCTGCAGCGACCTCCTGGTTGTCGGGGGCG 2 194 0 CCTCCTGGTT 0.772975 -107 GTAGGGAACGCCCGTTCTGCAGCGACCTCC 2 209 0 CCCGTTCTGC 0.968223 -92 ACAGCGGCGCCCCGCTGTGATGGCTGAGCA 2 258 1 CCCGCTGTGA 0.913192 -43 CTCTGTCGGTCATGCTCAGCCATCACAGCG 2 270 0 CATGCTCAGC 0.908188 -31 TGTCTTCCCGCCTCTGTCGGTCATGCT 2 284 0 CCGCCTCTGT 0.950435 -17 ********** Masking position 1 Map Score: 13.323 Number of sites scoring better than the average of aligned sites = 16182 Number in coding regions = 14981 Number in noncoding regions = 1201 Number of orfs with sites within 600 bp upstream = 776 Fraction of orfs with sites within 600 bp upstream = 0.124639 Motif number 3 CAGACAGCTGTCGCTGAGAGCC 2 3 0 TCGCTGAGAG 0.92107 -298 CTCTCAGCGACAGCTGTCTGACCTGTGGTT 2 13 1 CAGCTGTCTG 0.932598 -288 AAGTTGGTCGTGGCTGTGCGGGATTGGAGG 2 51 1 TGGCTGTGCG 0.977192 -250 TGTGCGGGATTGGAGGTGGCGTGGGGGTCG 2 65 1 TGGAGGTGGC 0.869724 -236 ACCAACTTGGCCGCGGTGGAGTCTAGCCTC 2 151 1 CCGCGGTGGA 0.969902 -150 AGCGACCTCCTGGTTGTCGGGGGCGACCAG 2 189 0 TGGTTGTCGG 0.943788 -112 CGCTTCATAGTAGATGTGGGTAGGGAACGC 2 228 0 TAGATGTGGG 0.951148 -73 CAGCGGGGCGCCGCTGTCGCTTCATAGTAG 2 245 0 CCGCTGTCGC 0.992765 -56 CAGCGGCGCCCCGCTGTGATGGCTGAGCAT 2 259 1 CCGCTGTGAT 0.944918 -42 TGTCTTCCCGCCTCTGTCGGTCATGCTCAG 2 281 0 CCTCTGTCGG 0.971509 -20 ********** Masking position 6 Map Score: 10.0543 Number of sites scoring better than the average of aligned sites = 12698 Number in coding regions = 11797 Number in noncoding regions = 901 Number of orfs with sites within 600 bp upstream = 616 Fraction of orfs with sites within 600 bp upstream = 0.0989399 Motif number 4 TGGTCGATAGCCTAGCGGGCCGTAGGGTGT 1 16 0 CCTAGCGGGC 0.92618 -20 GGTTTTGTTCCCAAGTTGGTCGTGGCTGTG 2 39 1 CCAAGTTGGT 0.986716 -262 TCGCGCGGAACCGAGGAGGAGAATCCATAC 2 99 0 CCGAGGAGGA 0.992567 -202 TCCACCGCGGCCAAGTTGGTGACCATTGCG 2 141 0 CCAAGTTGGT 0.986716 -160 ACCAACTTGGCCGCGGTGGAGTCTAGCCTC 2 151 1 CCGCGGTGGA 0.985823 -150 GCCCCCGACAACCAGGAGGTCGCTGCAGAA 2 195 1 ACCAGGAGGT 0.927465 -106 ********** Masking position 5 Map Score: 4.08198 Number of sites scoring better than the average of aligned sites = 2633 Number in coding regions = 2477 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 GGAGAATCCATACGACGCGACCCCCACGCC 2 82 0 TACGACGCGA 0.992674 -219 GAGGCTAGACTCCACCGCGGCCAAGTTGGT 2 151 0 TCCACCGCGG 0.979536 -150 GAACGCCCGTTCTGCAGCGACCTCCTGGTT 2 204 0 TCTGCAGCGA 0.992649 -97 CCACATCTACTATGAAGCGACAGCGGCGCC 2 239 1 TATGAAGCGA 0.982649 -62 ********** Masking position 1 Map Score: 1.70666 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 811 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 ********** No masking Map Score: 9.48026e-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: 9.48026e-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 8 ********** No masking Map Score: 9.48026e-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