AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i044_bsub_mtub_300.orf -o044_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 Rv3371 191 hypothetical protein Rv3371 #2 otsB2 41 otsB2 #3 Rv3488 300 hypothetical protein Rv3488 #4 Rv3489 81 hypothetical protein Rv3489 Motif number 1 CCGCCCAGCTCGGCGGCCCGTTGCTCCACC 1 13 1 CGGCGGCCCG 0.941114 -179 GTGGAATGTGGGGTGGAGCAACGGGCCGCC 1 24 0 GGGTGGAGCA 0.926792 -168 TGTTCTTAACCGTTTGGGCCTTCTGCTTCC 1 115 1 CGTTTGGGCC 0.816611 -77 CTTCTGCTTCCGGTGCGGTCCGGCGGACAC 1 134 1 CGGTGCGGTC 0.943242 -58 CGGTGCGGTCCGGCGGACACTTATACCTGG 1 144 1 CGGCGGACAC 0.973069 -48 CGCAAAACGACGGTGGGGACTTGTC 1 177 1 CGGTGGGGAC 0.995781 -15 CCATCTCCGTCGGCGTTGACCCCCGTGAGA 2 13 1 CGGCGTTGAC 0.950966 -29 TTGATAAATCGGGCGGTGACG 3 2 0 GGGCGGTGAC 0.978647 -299 GGCTGCGTCTGGTTGGAGCAACTACGTAAA 3 53 0 GGTTGGAGCA 0.558603 -248 AGCCCGAATTGGGCTGCGTCTGGTTGGAGC 3 64 0 GGGCTGCGTC 0.914274 -237 GATTGATGGGGGGAGGAGCCCGAATTGGGC 3 80 0 GGGAGGAGCC 0.927016 -221 ATCAATCATTCGGTGGCGCGAAGTTCACCA 3 103 1 CGGTGGCGCG 0.985056 -198 TGCGGGTAGCCGGCGGCGAATTCGCACTTA 3 233 0 CGGCGGCGAA 0.9874 -68 AAGCCGATATCGGCTTGGTCACCTGAGGTG 3 277 1 CGGCTTGGTC 0.790883 -24 ACCGCGTCGACGGTACCCATC 4 2 1 CCGCGTCGAC 0.919809 -80 CGGTACCCATCGCCGGGGCCAAACCGTGAC 4 21 1 CGCCGGGGCC 0.976213 -61 CGGGGCCAAACCGTGACGACGTCTGCAGCG 4 34 1 CCGTGACGAC 0.715577 -48 GCCCGCATTGCGCTGCAGACGTCGTCACGG 4 44 0 CGCTGCAGAC 0.801006 -38 ********** Masking position 8 Map Score: 25.058 Number of sites scoring better than the average of aligned sites = 3476 Number in coding regions = 3229 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 GCAACGGGCCGCCGAGCTGGGCGGAA 1 3 0 GCCGGTGCGG 0.98886 -189 TCGATATACTGTGGAATGTGGGGTGGAGCAACGG 1 30 0 GTGGAGGGGT 0.718031 -162 TGTTTCGCAGGTGAAGATGTGCTGAACAACTGCG 1 81 0 GTGAGTGCTG 0.800433 -111 CCTTCTGCTTCCGGTGCGGTCCGGCGGACACTTA 1 133 1 CCGGGGCCGG 0.696916 -59 ACCTGGGGTCGCAAAACGACGGTGGGGACTTGTC 1 168 1 GCAAAGGGTG 0.706116 -24 GGCGTTGACCCCCGTGAGAGGGTGGGTC 2 24 1 CCCGGGGGTG 0.986558 -18 GGGGGAGGAGCCCGAATTGGGCTGCGTCTGGTTG 3 68 0 CCCGATGCTG 0.989489 -233 GTGAGCGTGTCCGGGACTCTGGTGAACTTCGCGC 3 118 0 CCGGATGGTG 0.990296 -183 ACGCGAACTACCTGCATTTAGGGGATCACAGGCA 3 150 1 CCTGATGGGG 0.936778 -151 CGGTGTATGACTGGGAGTTTGCTGTACGTCTATT 3 197 1 CTGGATGCTG 0.959438 -104 TCTACGGGGTGCGGGTAGCCGGCGGCGAATTCGC 3 238 0 GCGGTGGGCG 0.926197 -63 ATATCGGCTTGCGATTCTACGGGGTGCGGGTAGC 3 253 0 GCGATTGGGG 0.915935 -48 AGGTGACCAAGCCGATATCGGCTTGCGATTCTAC 3 267 0 GCCGTTGCTT 0.832027 -34 GTAAGCCAAGCCCGCATTGCGCTGCAGACGTCGT 4 49 0 CCCGATGCTG 0.989489 -33 **** * * **** Masking position 11 Map Score: 12.8724 Number of sites scoring better than the average of aligned sites = 3229 Number in coding regions = 2963 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 3 GAGCAACGGGCCGCCGAGCTGGGCGGAA 1 7 0 CCCCGACTGG 0.836104 -185 GTGCTGAACAACTGCGCTGTATCGAACAATTG 1 65 0 ACGCGCGTAT 0.784462 -127 CACATCTTCACCTGCGAAACATGTTCTTAACC 1 94 1 CCGCGAACAT 0.910906 -98 GACAAGTCCCCACCGTCGTTTTGCGACCCCA 1 171 0 CCCCGTGTTT 0.820052 -21 ACGGGGGTCAACGCCGACGGAGATGGCG 2 7 0 ACCCGAGGAG 0.98024 -35 TCGGCGTTGACCCCCGTGAGAGGGTGGGTC 2 22 1 CCCCGTAGAG 0.86747 -20 CGTCACCGCCCGATTTATCAATCGCAAA 3 7 1 CGCCGATTAT 0.856797 -294 TGGGGGGAGGAGCCCGAATTGGGCTGCGTCTG 3 72 0 AGCCGATTGG 0.578277 -229 GAACTTCGCGCCACCGAATGATTGATGGGGGG 3 97 0 CCCCGATGAT 0.9789 -204 TCCCAGTCATACACCGATGCATTTCAAGGTGC 3 181 0 ACCCGAGCAT 0.983734 -120 CGTACAGCAAACTCCCAGTCATACACCGATGC 3 193 0 ACCCCATCAT 0.620816 -108 GTGCGGGTAGCCGGCGGCGAATTCGCACTTAC 3 232 0 CCGCGGGAAT 0.79006 -69 GGCTACCCGCACCCCGTAGAATCGCAAGCCGA 3 252 1 ACCCGTGAAT 0.867822 -49 GCGATGGGTACCGTCGACGCGGT 4 2 0 CCTCGAGCGG 0.860205 -80 CGGTTTGGCCCCGGCGATGGGTACCGTCGACG 4 15 0 CCGCGAGGGT 0.974987 -67 ** **** **** Masking position 5 Map Score: 8.12259 Number of sites scoring better than the average of aligned sites = 2046 Number in coding regions = 1821 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 4 AGATGTGCTGAACAACTGCGCTGTATCGAA 1 71 0 AACAACTGCG 0.937335 -121 CTACGTAAACGGGAAGTGCGAGATTTGCGA 3 32 0 GGGAAGTGCG 0.994401 -269 GTCTGGTTGGAGCAACTACGTAAACGGGAA 3 47 0 AGCAACTACG 0.951352 -254 CGGGACTCTGGTGAACTTCGCGCCACCGAA 3 111 0 GTGAACTTCG 0.938311 -190 CCCTAAATGCAGGTAGTTCGCGTGAGCGTG 3 143 0 AGGTAGTTCG 0.92567 -158 TACGTCTATTGGTAAGTGCGAATTCGCCGC 3 221 1 GGTAAGTGCG 0.978106 -80 ********** Masking position 5 Map Score: 2.24249 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 232 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TATCGAACAATTGTTCGATATACTGTGGAA 1 48 0 TTGTTCGATA 0.992861 -144 TATCGAACAATTGTTCGATACAGCGCAGTT 1 58 1 TTGTTCGATA 0.992861 -134 ********** Masking position 5 Map Score: 0.157922 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: -2.67574e-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 7 ********** No masking Map Score: -2.67574e-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 8 ********** No masking Map Score: -2.67574e-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