AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_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 Rv0225 35 hypothetical protein Rv0225 #2 gmdA 300 gmdA Motif number 1 CTGGCACACCCTACGGCCCGCT 1 3 1 GGCACACCCT 0.823729 -33 GCACACCCTACGGCCCGCTAGGCTATCGAC 1 14 1 CGGCCCGCTA 0.937999 -22 GGCTCTCAGCGACAGCTGTCTGACCTGT 2 9 1 GCGACAGCTG 0.985595 -292 CCTCCAATCCCGCACAGCCACGACCAACTT 2 51 0 CGCACAGCCA 0.977556 -250 CGACCCCCACGCCACCTCCAATCCCGCACA 2 65 0 GCCACCTCCA 0.985975 -236 TCCATACGACGCGACCCCCACGCCACCTCC 2 76 0 GCGACCCCCA 0.978539 -225 GTATGGATTCTCCTCCTCGGTTCCGCGCGA 2 99 1 TCCTCCTCGG 0.818829 -202 GGTGACCATTGCGCCTGCGGCCGTTTCGCG 2 124 0 GCGCCTGCGG 0.940398 -177 GAGGCTAGACTCCACCGCGGCCAAGTTGGT 2 151 0 TCCACCGCGG 0.987252 -150 TTTCCTGGTCGCCCCCGACAACCAGGAGGT 2 185 1 GCCCCCGACA 0.947206 -116 CCGTTCTGCAGCGACCTCCTGGTTGTCGGG 2 198 0 GCGACCTCCT 0.945592 -103 GCGTTCCCTACCCACATCTACTATGAAGCG 2 228 1 CCCACATCTA 0.899538 -73 CTACTATGAAGCGACAGCGGCGCCCCGCTG 2 245 1 GCGACAGCGG 0.992426 -56 GCGACAGCGGCGCCCCGCTGTGATGGCTGA 2 255 1 CGCCCCGCTG 0.968899 -46 CTGTCGGTCATGCTCAGCCATCACAGCGGG 2 268 0 TGCTCAGCCA 0.79248 -33 CTGAGCATGACCGACAGAGGCGGGAAGACA 2 281 1 CCGACAGAGG 0.894578 -20 ********** Masking position 5 Map Score: 24.4779 Number of sites scoring better than the average of aligned sites = 51417 Number in coding regions = 48191 Number in noncoding regions = 3226 Number of orfs with sites within 600 bp upstream = 1267 Fraction of orfs with sites within 600 bp upstream = 0.203501 Motif number 2 ACACCCTACGGCCCGCTAGGCTATCGACCA 1 16 1 GCCGCTAGGC 0.961308 -20 GATTCTCCTCCTCGGTTCCGCGCGAAACGGC 2 104 1 CCGGTTCCGC 0.989455 -197 TTGCGCCTGCGGCCGTTTCGCGCGGAACCGA 2 115 0 GCCGTTTCGC 0.997586 -186 CCAAGTTGGTGACCATTGCGCCTGCGGCCGT 2 130 0 GCCATTGCGC 0.981279 -171 GGTAGGGAACGCCCGTTCTGCAGCGACCTCC 2 209 0 GCCGTTCTGC 0.989959 -92 ACAGCGGGGCGCCGCTGTCGCTTCATAGTAG 2 245 0 GCGCTGTCGC 0.962735 -56 TCCCGCCTCTGTCGGTCATGCTCAGCCATCA 2 275 0 GCGGTCATGC 0.974907 -26 * ********* Masking position 3 Map Score: 6.56294 Number of sites scoring better than the average of aligned sites = 4590 Number in coding regions = 4299 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 3 CGATAGCCTAGCGGGCCGTAGGGTGTGCCA 1 12 0 GCGGGCCGTA 0.981509 -24 TTGTTCCCAAGTTGGTCGTGGCTGTGCGGG 2 43 1 GTTGGTCGTG 0.986165 -258 GAGGTGGCGTGGGGGTCGCGTCGTATGGAT 2 77 1 GGGGGTCGCG 0.989492 -224 TGGTCACCAACTTGGCCGCGGTGGAGTCTA 2 146 1 CTTGGCCGCG 0.98279 -155 CTCACATTTTCCTGGTCGCCCCCGACAACC 2 178 1 CCTGGTCGCC 0.996767 -123 GCAGCGACCTCCTGGTTGTCGGGGGCGACC 2 191 0 CCTGGTTGTC 0.954284 -110 AGCCATCACAGCGGGGCGCCGCTGTCGCTT 2 253 0 GCGGGGCGCC 0.995574 -48 ********** Masking position 5 Map Score: 10.9213 Number of sites scoring better than the average of aligned sites = 8889 Number in coding regions = 8336 Number in noncoding regions = 553 Number of orfs with sites within 600 bp upstream = 431 Fraction of orfs with sites within 600 bp upstream = 0.0692258 Motif number 4 GGCTCTCAGCGACAGCTGTCTG 2 3 1 CTCTCAGCGA 0.954874 -298 ACGACGCGACCCCCACGCCACCTCCAATCC 2 71 0 CCCCACGCCA 0.964999 -230 GGAGAATCCATACGACGCGACCCCCACGCC 2 82 0 TACGACGCGA 0.960914 -219 TCCTCCTCGGTTCCGCGCGAAACGGCCGCA 2 109 1 TTCCGCGCGA 0.962925 -192 AGTTGGTGACCATTGCGCCTGCGGCCGTTT 2 128 0 CATTGCGCCT 0.738329 -173 GAACGCCCGTTCTGCAGCGACCTCCTGGTT 2 204 0 TCTGCAGCGA 0.93421 -97 CCACATCTACTATGAAGCGACAGCGGCGCC 2 239 1 TATGAAGCGA 0.864297 -62 CTGTCGGTCATGCTCAGCCATCACAGCGGG 2 268 0 TGCTCAGCCA 0.886148 -33 TGTCTTCCCGCCTCTGTCGGTCA 2 288 0 CTTCCCGCCT 0.89461 -13 ********** Masking position 8 Map Score: 2.46937 Number of sites scoring better than the average of aligned sites = 14340 Number in coding regions = 13103 Number in noncoding regions = 1237 Number of orfs with sites within 600 bp upstream = 820 Fraction of orfs with sites within 600 bp upstream = 0.131706 Motif number 5 ********** 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 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