AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_bsub_mtub_300.orf -o223_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ypuL 91 similar to hypothetical proteins #2 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #3 ypuI 54 similar to hypothetical proteins from B. subtilis #4 ypuG 280 similar to hypothetical proteins #5 Rv1707 300 hypothetical protein Rv1707 Motif number 1 GTTTGCTCACGTCCTTGTGGTGG 2 110 0 TTGCTCACTC 0.987111 -13 CAAAGGCTTTTTCTCCCGCTTCTGCGCTCCGA 4 111 1 TTTCCCGCTC 0.949738 -170 ACAAGAGGTGTTTGCTCGGAGCGCAGAAGCGG 4 126 0 TTGCTCGGGC 0.995416 -155 GCGTTCAAGCTTGGCTGGCTGCTATCCGCGAT 5 32 0 TTGCTGGCGC 0.990311 -269 TCTACATGGGCTCGCTCGCAGCGTTCAAGCTT 5 52 0 CTGCTCGCGC 0.997138 -249 CCATGGCAAGTTGGCCCACCGATCGGTTTGGT 5 93 0 TTGCCCACGA 0.974306 -208 CAACTTGCCATGGGCTCACAGCGGCTATCGCG 5 112 1 TGGCTCACGC 0.982014 -189 GGTCGGCAACCTGGCCCGCTGCGGGTTGGGTT 5 247 1 CTGCCCGCGC 0.996527 -54 TGGGTTCGGATTCGCTCGGCTAGTAAGGTGCT 5 273 1 TTGCTCGGTA 0.933399 -28 ** ****** ** Masking position 5 Map Score: 13.7013 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 395 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 AAACGGCGTTTTTTTTAGATTTGGCA 1 7 1 CGTTTTTTTT 0.632536 -85 TTAACAAACAAGCTTTTTCAAATTCCTATG 1 35 0 AGCTTTTTCA 0.985895 -57 GTATTATCTTACTTTTTTCAACCTTAACAA 1 58 0 ACTTTTTTCA 0.948702 -34 CGTTTACTCTCCCTTTTTCAGGGAGAGTTT 2 11 1 CCCTTTTTCA 0.985537 -112 TTTCAGGGAGAGTTTTTTTATGTTTGCTTC 2 26 1 AGTTTTTTTA 0.818538 -97 TAATGAATCGCGCTTTTTCATCATCATAAG 3 16 1 CGCTTTTTCA 0.988291 -39 CAGAAGCAAAGGCTTTTTCTCCCGCTTCTG 4 105 1 GGCTTTTTCT 0.948217 -176 CATCTCACCATTTTCAAGTATCACTC 4 265 0 ACCATTTTCA 0.898943 -16 GGCAGGGGTTGCCTTATTCATCCTCTTGCG 5 185 1 GCCTTATTCA 0.880592 -116 ********** Masking position 5 Map Score: 8.99152 Number of sites scoring better than the average of aligned sites = 2005 Number in coding regions = 1740 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 3 AAAAAGAACGCCCGGCCTCTAGTGCTTCTT 4 63 1 CCCGGCCTCT 0.94599 -218 GTATCACTCTCATTGCCGGAAAAACTGGCT 4 244 0 CATTGCCGGA 0.873786 -37 GCCATGGGCTCACAGCGGCTATCGCGAGCG 5 118 1 CACAGCGGCT 0.962861 -183 ATAAGGCAACCCCTGCCGCTCAGGCCACCG 5 172 0 CCCTGCCGCT 0.996024 -129 CCTGCGGCAACCATGCCGCAAGAGGATGAA 5 201 0 CCATGCCGCA 0.979626 -100 TACCGGCACTCCCTGCGGCAACCATGCCGC 5 212 0 CCCTGCGGCA 0.995588 -89 CAACCTGGCCCGCTGCGGGTTGGGTTCGGA 5 253 1 CGCTGCGGGT 0.971891 -48 ********** Masking position 5 Map Score: 7.38513 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 500 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 CCGGAAAAACTGGCTACCCTATAGTATAAG 4 229 0 TGGCTACCCT 0.921194 -52 CCAGTTTTTCCGGCAATGAGAGTGATACTT 4 246 1 CGGCAATGAG 0.820474 -35 GCTTGGCTGGCTGCTATCCGCGATGGCACC 5 26 0 CTGCTATCCG 0.862588 -275 GGGCTCACAGCGGCTATCGCGAGCGTGTAG 5 123 1 CGGCTATCGC 0.967745 -178 GGACGATGATCGGCTACACGCTCGCGATAG 5 136 0 CGGCTACACG 0.95333 -165 CCTGCCGCTCAGGCCACCGTCGCCTGGACG 5 161 0 AGGCCACCGT 0.798973 -140 AGGATGAATAAGGCAACCCCTGCCGCTCAG 5 179 0 AGGCAACCCC 0.975855 -122 GCACTCCCTGCGGCAACCATGCCGCAAGAG 5 207 0 CGGCAACCAT 0.972673 -94 CCAGACTTACCGGCACTCCCTGCGGCAACC 5 219 0 CGGCACTCCC 0.9482 -82 TAAGTCTGGTCGGCAACCTGGCCCGCTGCG 5 240 1 CGGCAACCTG 0.976551 -61 ********** Masking position 4 Map Score: 6.62308 Number of sites scoring better than the average of aligned sites = 1315 Number in coding regions = 1236 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 AGCTTGTTTGTTAAGGTTGAAAAAAGTAAGA 1 51 1 TTAAGGTGAA 0.947886 -41 AAGATAATACTTGAGGTGAAAGAC 1 78 1 TTGAGGTAAA 0.856987 -14 CTTATATCTTATGATGATGAAAAAGCGCGAT 3 22 0 ATGATGAGAA 0.895036 -33 ATCATAAGATATAAGGAAGAAGCTATC 3 38 1 ATAAGGAGAA 0.981965 -17 AAAAGCACATTAAAGGAGGAAGCACC 4 6 0 TAAAGGAGAA 0.9698 -275 TAGAAGGGATAAAAGGAAAAAAGAACGCCCG 4 46 1 AAAAGGAAAA 0.919399 -235 ACCATGCCGCAAGAGGATGAATAAGGCAACC 5 191 0 AAGAGGAGAA 0.98058 -110 ******* *** Masking position 4 Map Score: 4.47293 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 572 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 6 CTTAACAAACAAGCTTTTTCAAATTCCTAT 1 36 0 AAGCTTTTTC 0.786757 -56 TTTTTTATGTTTGCTTCCAGAAATATAATT 2 39 1 TTGCTTCCAG 0.781237 -84 TTAATGAATCGCGCTTTTTCATCATCATAA 3 15 1 GCGCTTTTTC 0.927607 -40 GATAGCTTCTTCCTTATATCTT 3 43 0 TAGCTTCTTC 0.936973 -12 GGTGCTTCCTCCTTTAATGTG 4 2 1 GTGCTTCCTC 0.960042 -279 CTCCTTTAATGTGCTTTTAGTGTACCATAG 4 19 1 GTGCTTTTAG 0.940796 -262 CCGGCCTCTAGTGCTTCTTAGAAAGGAAAA 4 74 1 GTGCTTCTTA 0.914594 -207 GAAAAAGCCTTTGCTTCTGGTTTTCCTTTC 4 94 0 TTGCTTCTGG 0.927781 -187 TATTGGACGAGAGCTTTTTGGTGGCTTATA 4 205 1 GAGCTTTTTG 0.972401 -76 AGCCCATGTAGAGCGTTTGGTACCAAACCG 5 72 1 GAGCGTTTGG 0.806231 -229 ********** Masking position 6 Map Score: 6.48888 Number of sites scoring better than the average of aligned sites = 1328 Number in coding regions = 1238 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 ATTTGGCATAGGAATTTGAAAAAGCTTGTT 1 29 1 GGAATTTGAA 0.839169 -63 CGTCCTTGTGGTGGTTTGTACAAGTTTATG 2 94 0 GTGGTTTGTA 0.96401 -29 AACACCTCTTGTGTTTTGAATATTCTGTAC 4 146 1 GTGTTTTGAA 0.961259 -135 CTGTTTTGAAGGAGTTTGTACAGAATATTC 4 163 0 GGAGTTTGTA 0.934348 -118 ATTTCATATCCTGTTTTGAAGGAGTTTGTA 4 173 0 CTGTTTTGAA 0.928413 -108 GCCCACCGATCGGTTTGGTACCAAACGCTC 5 82 0 CGGTTTGGTA 0.881748 -219 ********** Masking position 5 Map Score: 0.197285 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 198 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ********** No masking Map Score: -8.2833e-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 9 ********** No masking Map Score: -8.2833e-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 10 ********** No masking Map Score: -8.2833e-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