AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i297_bsub_mtub_300.orf -o297_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 Purged sequences: kdtB 85 kdtB Input sequences: #1 ylbH 300 similar to hypothetical proteins #2 ylbI 63 similar to lipopolysaccharide core biosynthesis #3 Rv2966c 195 hypothetical protein Rv2966c #4 pca 24 pca #5 Rv2969c 96 hypothetical protein Rv2969c #6 lipN 300 lipN Motif number 1 AGGATGTTGTTGCCAACCGCGGAGAAGACT 1 98 0 TGCCAACCGC 0.935672 -203 TCTATGTACATAGCGGCGTCCGGCCGAATA 1 243 1 TAGCGGCGTC 0.828817 -58 CCGCCCCGGCGACGATGCAG 3 1 1 CCGCCCCGGC 0.985592 -195 GCAGGCGGTACCCCCACTGCATCGTCGCCG 3 17 0 CCCCCACTGC 0.963141 -179 GCAGTGGGGGTACCGCCTGCTTGCGGGGGA 3 27 1 TACCGCCTGC 0.954885 -169 CTCATCGCTTCGTCCCCCGCAAGCAGGCGG 3 39 0 CGTCCCCCGC 0.968833 -157 GCGGGCGGTACCCCCACCTCATCGCTTCGT 3 56 0 CCCCCACCTC 0.982217 -140 GAGGTGGGGGTACCGCCCGCTTGCGGAGGA 3 66 1 TACCGCCCGC 0.99185 -130 CGCAGATGAGCACCGCCGGCGACGATGCAG 3 100 1 CACCGCCGGC 0.994657 -96 GCGGGCGGTACCCCCACTGCATCGTCGCCG 3 116 0 CCCCCACTGC 0.963141 -80 GCAGTGGGGGTACCGCCCGCTTGCGGGGGA 3 126 1 TACCGCCCGC 0.99185 -70 CTCATCGCTTCGTCCCCCGCAAGCGGGCGG 3 138 0 CGTCCCCCGC 0.968833 -58 GCGGGCGGTACCCCCACCTCATCGCTTCGT 3 155 0 CCCCCACCTC 0.982217 -41 GAGGTGGGGGTACCGCCCGCTTGCGAGGGA 3 165 1 TACCGCCCGC 0.99185 -31 GTGCGCCGCTCTCCCTCGCAAGC 3 183 0 CGCCGCTCTC 0.886988 -13 ACCGGCGGCAAGCCAGCCTCGAC 5 4 0 AGCCAGCCTC 0.590024 -93 GCCTCTAGCGTACCGGCGGCAAGCCAGCCT 5 15 0 TACCGGCGGC 0.970863 -82 GGCCGCGGTCAGGCGACGGCGCCTCTAGCG 5 35 0 AGGCGACGGC 0.843257 -62 CGTCGCCTGACCGCGGCCGCGACAAGCCGA 5 47 1 CCGCGGCCGC 0.990047 -50 AATATCGTGATCCCCAAGTCGGTGAACCCA 6 21 0 TCCCCAAGTC 0.478686 -280 GGCTGTGGCTCAGCACCTGCCCAGGTGTTG 6 75 0 CAGCACCTGC 0.772399 -226 TCGCGGCTTACGCCGCCGTCGCCGAAGGCT 6 101 0 CGCCGCCGTC 0.991885 -200 GCGTGCCCAACGGCCAACTCTACGTGGTGA 6 160 0 CGGCCAACTC 0.703825 -141 CCGTTGGGCACGCCGGACTCGCGGCACCTA 6 177 1 CGCCGGACTC 0.909667 -124 GGACTCGCGGCACCTACCGCTTGCCCGGTG 6 191 1 CACCTACCGC 0.901441 -110 TTTCGGGTCCTGCCGGCCGACACCGGGCAA 6 211 0 TGCCGGCCGA 0.771871 -90 GACACTCGATCCGCGCCGTCAGGCTGGATG 6 243 0 CCGCGCCGTC 0.974891 -58 ********** Masking position 4 Map Score: 54.9502 Number of sites scoring better than the average of aligned sites = 3807 Number in coding regions = 3503 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 GGATGTTGTTGCCAACCGCGGAGAAGACTT 1 97 0 GCCAACCGCG 0.866586 -204 TCTTTATTCGGCCGGACGCCGCTATGTACA 1 247 0 GCCGGACGCC 0.816304 -54 CTGCATCGTCGCCGGGGCGG 3 1 0 GCCGGGGCGG 0.87286 -195 GGTACCGCCTGCTTGCGGGGGACGAAGCGA 3 35 1 GCTTGCGGGG 0.989597 -161 CCGCTCCTCCGCAAGCGGGCGGTACCCCCA 3 70 0 GCAAGCGGGC 0.95102 -126 GATGAGCACCGCCGGCGACGATGCAGTGGG 3 104 1 GCCGGCGACG 0.929969 -92 GGTACCGCCCGCTTGCGGGGGACGAAGCGA 3 134 1 GCTTGCGGGG 0.989597 -62 GCTCTCCCTCGCAAGCGGGCGGTACCCCCA 3 169 0 GCAAGCGGGC 0.95102 -27 GTCGAGGCTGGCTTGCCGCCGGTACGCTAG 5 11 1 GCTTGCCGCC 0.984614 -86 CCGCCGGTACGCTAGAGGCGCCGTCGCCTG 5 26 1 GCTAGAGGCG 0.935959 -71 AGGCGCCGTCGCCTGACCGCGGCCGCGACA 5 41 1 GCCTGACCGC 0.922746 -56 CGATTTGTCGGCTTGTCGCGGCCGCGGTCA 5 54 0 GCTTGTCGCG 0.945533 -43 CTGAGCCACAGCCTTCGGCGACGGCGGCGT 6 92 1 GCCTTCGGCG 0.936429 -209 CGACGGCGGCGTAAGCCGCGAATAGTGCTG 6 110 1 GTAAGCCGCG 0.683189 -191 CGCGAATAGTGCTGGTCGGCATTCAACACT 6 126 1 GCTGGTCGGC 0.674697 -175 CGTAGAGTTGGCCGTTGGGCACGCCGGACT 6 166 1 GCCGTTGGGC 0.720584 -135 CGTTGGGCACGCCGGACTCGCGGCACCTAC 6 178 1 GCCGGACTCG 0.824961 -123 GGCACCTACCGCTTGCCCGGTGTCGGCCGG 6 199 1 GCTTGCCCGG 0.960716 -102 CTTGCCCGGTGTCGGCCGGCAGGACCCGAA 6 210 1 GTCGGCCGGC 0.53009 -91 AAGACATCCAGCCTGACGGCGCGGATCGAG 6 239 1 GCCTGACGGC 0.75771 -62 ********** Masking position 1 Map Score: 36.8923 Number of sites scoring better than the average of aligned sites = 3029 Number in coding regions = 2814 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 3 CTCTCCCTTTGCCTTCTCCTTAACATATTAA 1 33 0 GCTTCTCCTT 0.836588 -268 CCTCCGGTTTCTCCTCTCCCTTTGCCTTCTC 1 46 0 CCCTCTCCCT 0.958856 -255 GGAAACGTAAGTCTTCTCCGCGGTTGGCAAC 1 89 1 GCTTCTCCGC 0.961519 -212 TTTTATAAATCGCTACACCTGTTAACCCATA 2 28 0 CCTACACCTG 0.75142 -36 GCGGTACCCCCACTGCATCGTCGCCGGGGCG 3 12 0 CCTGCATCGT 0.935078 -184 GCGGTACCCCCACCTCATCGCTTCGTCCCCC 3 51 0 CCCTCATCGC 0.960156 -145 TGCTCATCTGCGCCGCTCCTCCGCAAGCGGG 3 81 0 CCCGCTCCTC 0.988276 -115 GCGGTACCCCCACTGCATCGTCGCCGGCGGT 3 111 0 CCTGCATCGT 0.935078 -85 GCGGTACCCCCACCTCATCGCTTCGTCCCCC 3 150 0 CCCTCATCGC 0.960156 -46 GTGCGCCGCTCTCCCTCGCAAGCG 3 182 0 CCCGCTCTCC 0.82379 -14 GTGTGGCTCCCTTATCCGGATGTC 4 6 0 CCTTATCCGG 0.831089 -19 GAGGCGCCGTCGCCTGACCGCGGCCGCGACA 5 40 1 CCCTGACCGC 0.908802 -57 AGTTTCGCTGATCCTCACGTGCTCGA 5 81 0 CCTGATCCTC 0.889572 -16 AAGGCTGTGGCTCAGCACCTGCCCAGGTGTT 6 76 0 CCAGCACCTG 0.810149 -225 GGGCTGCTCCCTACAAAACTCT 6 289 0 GCTGCTCCCT 0.889538 -12 * ********* Masking position 3 Map Score: 13.8027 Number of sites scoring better than the average of aligned sites = 2377 Number in coding regions = 2102 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 4 TACCCCCACCTCATCGCTTCGTCCCCCGCAA 3 47 0 TCATCGCTTG 0.98727 -149 TACCCCCACCTCATCGCTTCGTCCCCCGCAA 3 146 0 TCATCGCTTG 0.98727 -50 CGCATTGGGTTCACCGACTTGGGGATCACGA 6 16 1 TCACCGACTG 0.980937 -285 GATCACGATATTACCGAGTTGGATATGCCAC 6 39 1 TTACCGAGTG 0.869701 -262 TGCCACCTAATCAACACCTGGGCAGGTGCTG 6 64 1 TCAACACCTG 0.975924 -237 TGGTCGGCATTCAACACTTTGGTCACCACGT 6 138 1 TCAACACTTG 0.97406 -163 AACACTTTGGTCACCACGTAGAGTTGGCCGT 6 150 1 TCACCACGTG 0.989168 -151 ********* * Masking position 3 Map Score: 6.76531 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 130 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ATAAGTTCTTCCTCCGGTTTCTCCTCTCCC 1 57 0 CCTCCGGTTT 0.861845 -244 TGCTGCCTATACACCTGTTTATCAAGATTA 1 163 1 ACACCTGTTT 0.969663 -138 GTTCCACACCACTTTTTCTAAAAGC 1 286 0 ACACCACTTT 0.869778 -15 ATAAATCGCTACACCTGTTAACCCATAGGT 2 25 0 ACACCTGTTA 0.888093 -39 CTCACTACCCCCTCTTTTTATAAATCG 2 47 0 CCCCCTCTTT 0.967841 -17 AGTGGGGGTACCGCCTGCTTGCGGGGGACG 3 29 1 CCGCCTGCTT 0.916696 -167 GGCGGTACCCCCACCTCATCGCTTCGTCCC 3 53 0 CCACCTCATC 0.960151 -143 GGCGGTACCCCCACCTCATCGCTTCGTCCC 3 152 0 CCACCTCATC 0.960151 -44 ********** Masking position 9 Map Score: 3.77526 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 362 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 6 CAAGGATCATGCTGCCTATACACCTGTTTAT 1 154 1 GCTGCCTTAC 0.898938 -147 GCTCATCTGCGCCGCTCCTCCGCAAGCGGGC 3 80 0 GCCGCTCTCC 0.929228 -116 AGGCTGGCTTGCCGCCGGTACGCTAGAGGCG 5 15 1 GCCGCCGTAC 0.989879 -82 GTCAGGCGACGGCGCCTCTAGCGTACCGGCG 5 27 0 GGCGCCTTAG 0.962841 -70 TAGAGGCGCCGTCGCCTGACCGCGGCCGCGA 5 38 1 GTCGCCTACC 0.827182 -59 CCTGACCGCGGCCGCGACAAGCCGACAAATC 5 52 1 GCCGCGAAAG 0.958587 -45 GGCGGCGTAAGCCGCGAATAGTGCTGGTCGG 6 114 1 GCCGCGATAG 0.986532 -187 AGCGGTAGGTGCCGCGAGTCCGGCGTGCCCA 6 181 0 GCCGCGATCC 0.991511 -120 CCAGCCTGACGGCGCGGATCGAGTGTCCGTT 6 246 1 GGCGCGGTCG 0.972968 -55 ******* *** Masking position 5 Map Score: 8.65226 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 663 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 ********** No masking Map Score: 3.56936e-12 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: 3.56936e-12 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: 3.56936e-12 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