AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_bsub_mtub_100.orf -o215_bsub_mtub_100.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 obg 33 GTPase activity #2 spo0B 300 sporulation initiation phosphoprotein #3 rplU 146 ribosomal protein L21 (BL20) #4 obg 85 obg #5 rplU 300 rplU Motif number 1 CTCATTCTTGGCGGGGTCTGCTCGCACATACT 2 69 0 GCGGGTCGCT 0.840055 -232 TAGTCTAATAGGAGGTGCAGAGA 3 134 1 GGAGGGCGAG 0.788628 -13 CAGTGGGCGCACACGCGCGACGC 4 2 0 ACACGGCACG 0.779127 -84 TCGCGCGTGTGCGCCCACTGCGAAGATTCACG 4 14 1 GCGCCACGCG 0.997072 -72 TGCGGAGTGTGCAGCTACTGCGGGTTTTGCCC 4 48 0 GCAGCACGCG 0.990181 -38 TGCACACTCCGCAGATGAAGGGGAGCTCG 4 67 1 GCAGAGAGGG 0.799489 -19 GCCCCGGAGTGCGCCGGTAGCGTCGAGATCGA 5 55 1 GCGCCGTGCG 0.991989 -246 ACACGAAAGTGCGCCGGTAGCGTCGATCTCGA 5 77 0 GCGCCGTGCG 0.991989 -224 TCAAACCAGCGGGGCCTCAGCGAGATCGACGC 5 113 0 GGGGCTCGCG 0.969415 -188 TACGTGACCTGCAACTACGGGGTCAAACCAGC 5 135 0 GCAACACGGG 0.887996 -166 CGTCAGCCTGGCGACAACTGGTCAAGGGTACG 5 163 0 GCGACACGGT 0.626963 -138 GCTGACGGCTGGAGACGATGCGGGGTCCGTTG 5 188 1 GGAGAGAGCG 0.786551 -113 TCTTGGGCGGGCACCTACAACGGACCCCGCAT 5 205 0 GCACCACACG 0.933132 -96 CAGCGGCGGGACGCGTGCTGGGTCTTGGGCGG 5 227 0 ACGCGGCGGG 0.967306 -74 CTTCGCGCGCGGGCCAGCGGCGGGACGCGTGC 5 241 0 GGGCCGCGCG 0.997056 -60 CCGCTGGCCCGCGCGCGAAGCGCAACGCATGC 5 253 1 GCGCGGAGCG 0.990119 -48 GCGAAGCGCAACGCATGCAGCGGAAGTATGAA 5 267 1 ACGCAGCGCG 0.971139 -34 ***** ** *** Masking position 10 Map Score: 25.2729 Number of sites scoring better than the average of aligned sites = 3369 Number in coding regions = 3127 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 TTCTTGGCGGGGTCTGCTCGCACATACTCTGC 2 65 0 GGTCGCCGCA 0.865053 -236 GAGCTTTTACAGCCCCCTGGTATCTGGCGAGT 3 100 1 AGCCCCGGTA 0.853349 -47 GCGTCGCGCGTGTGCGCCCACTGCGAAGAT 4 9 1 CGTGGCCCCA 0.988622 -77 TCATCTGCGGAGTGTGCAGCTACTGCGGGTTT 4 53 0 AGTGGCGCTA 0.971711 -33 ACCCGGATGACGTCACCACCCGGGCCCCGGAG 5 32 1 CGTCCCCCCG 0.957445 -269 CGGGCCCCGGAGTGCGCCGGTAGCGTCGAGAT 5 52 1 AGTGGCGGTA 0.97554 -249 AGCACACGAAAGTGCGCCGGTAGCGTCGATCT 5 80 0 AGTGGCGGTA 0.97554 -221 GGCGCACTTTCGTGTGCTGGCGTCGATCTCGC 5 94 1 CGTGGCGGCG 0.725053 -207 GTCAAGGGTACGTGACCTGCAACTACGGGGTC 5 143 0 CGTGCCGCAA 0.953515 -158 GACCCCGCATCGTCTCCAGCCGTCAGCCTGGC 5 183 0 CGTCCCGCCG 0.985798 -118 CGTGCTGGGTCTTGGGCGGGCACCTACAACGG 5 214 0 CTTGGCGGCA 0.960611 -87 AGACCCAGCACGCGTCCCGCCGCTGGCCCGCG 5 234 1 CGCGCCGCCG 0.970068 -67 CGTTGCGCTTCGCGCGCGGGCCAGCGGCGGGA 5 248 0 CGCGGCGGCC 0.557538 -53 **** ** **** Masking position 7 Map Score: 20.5724 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 898 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 CTAGGTGTTTACTCCGCATATTGCAAAAAA 2 27 0 ACTCCGCATA 0.860279 -274 GTGCGAGCAGACCCCGCCAAGAATGAGAAT 2 74 1 ACCCCGCCAA 0.943587 -227 TTGATTTGCAGCCAGGCAGAACATTTTATG 2 146 0 GCCAGGCAGA 0.968871 -155 TTAGACTAAGACTCGCCAGATACCAGGGGG 3 112 0 ACTCGCCAGA 0.898819 -35 GTAGCTGCACACTCCGCAGATGAAGGGGAG 4 62 1 ACTCCGCAGA 0.968862 -24 CAGCGGTCCAACCCGGATGACGTCACCACC 5 22 1 ACCCGGATGA 0.914358 -279 GCACTCCGGGGCCCGGGTGGTGACGTCATC 5 37 0 GCCCGGGTGG 0.901237 -264 TCTCGCTGAGGCCCCGCTGGTTTGACCCCG 5 120 1 GCCCCGCTGG 0.983362 -181 ACCAGTTGTCGCCAGGCTGACGGCTGGAGA 5 173 1 GCCAGGCTGA 0.961926 -128 CCTACAACGGACCCCGCATCGTCTCCAGCC 5 194 0 ACCCCGCATC 0.853104 -107 CGTTGTAGGTGCCCGCCCAAGACCCAGCAC 5 215 1 GCCCGCCCAA 0.864494 -86 ********** Masking position 2 Map Score: 8.63296 Number of sites scoring better than the average of aligned sites = 1808 Number in coding regions = 1675 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 CGGAGTTTTTAACGGTTTAG 1 1 1 CGGAGTTTTT 0.793225 -33 GATGATGACTGGAGTTTTTTTTGCAATAT 2 10 1 TGGAGTTTTT 0.925746 -291 TCAAACCCACTGGATATGTTCCCCAAGCAG 2 111 1 TGGATATGTT 0.696176 -190 TCCTTTTTTCTGGCTTTGGTTGATTTGCAG 2 165 0 TGGCTTTGGT 0.940737 -136 ATAACAGAGAAGGCTTTGTTAGAAAAACAA 2 219 0 AGGCTTTGTT 0.873346 -82 TTTCTTATTTAGGAGTCTGTATAAGTGTGT 2 259 0 AGGAGTCTGT 0.895357 -42 CCAAAATACAAGGCGTTTGTCAATCAGTT 3 10 0 AGGCGTTTGT 0.92644 -137 AGTGCGCCGGTAGCGTCGATCTCGACGCTA 5 72 0 TAGCGTCGAT 0.772034 -229 TTTCGTGTGCTGGCGTCGATCTCGCTGAGG 5 101 1 TGGCGTCGAT 0.974851 -200 GGCTGACGGCTGGAGACGATGCGGGGTCCG 5 187 1 TGGAGACGAT 0.871083 -114 ********** Masking position 10 Map Score: 4.60375 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 1173 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 GATGATGACTGGAGTTTTTT 2 1 1 GATGATGACT 0.942014 -300 GGGTTGGACCGCTGATGGCTGCGGC 5 6 0 GCTGATGGCT 0.990083 -295 GTCCAACCCGGATGACGTCACCACCCGGGC 5 27 1 GATGACGTCA 0.962328 -274 ACTTTCGTGTGCTGGCGTCGATCTCGCTGA 5 99 1 GCTGGCGTCG 0.974638 -202 TTGTCGCCAGGCTGACGGCTGGAGACGATG 5 178 1 GCTGACGGCT 0.995574 -123 ********** Masking position 3 Map Score: 2.48402 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 376 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTTCGCACTCCCAATCATTTAAT 2 288 0 CGCACTCCCA 0.979486 -13 GCAGTGGGCGCACACGCGCGACGC 4 5 0 CACACGCGCG 0.759235 -81 GCAGTAGCTGCACACTCCGCAGATGAAGGG 4 59 1 CACACTCCGC 0.963423 -27 ACGCTACCGGCGCACTCCGGGGCCCGGGTG 5 48 0 CGCACTCCGG 0.995466 -253 ACGCTACCGGCGCACTTTCGTGTGCTGGCG 5 86 1 CGCACTTTCG 0.920403 -215 CGTTGCGCTTCGCGCGCGGGCCAGCGGCGG 5 250 0 CGCGCGCGGG 0.605078 -51 CCTGCCTCTTCATACTTCCGCTGCATGCGT 5 277 0 CATACTTCCG 0.842167 -24 ********** Masking position 5 Map Score: 4.65971 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 282 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TTAATGTTATGGATGTAGCACCATTGCTAC 3 48 1 GGATGTAGCA 0.981635 -99 TGTACTGAGCGGTTGTAGCAATGGTGCTAC 3 62 0 GGTTGTAGCA 0.979866 -85 GATACCAGGGGGCTGTAAAAGCTCTTAACA 3 94 0 GGCTGTAAAA 0.948951 -53 CCAGGCTGACGGCTGGAGACGATGCGGGGT 5 184 1 GGCTGGAGAC 0.967454 -117 AGTATGAAGAGGCAGGAGCA 5 291 1 GGCAGGAGCA 0.985566 -10 ********** Masking position 7 Map Score: 2.32594 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 248 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ********** No masking Map Score: -4.87842e-13 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: -4.87842e-13 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: -4.87842e-13 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