AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_bsub_mtub_300.orf -o039_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 sigW 300 RNA polymerase ECF-type sigma factor (sigma-W) #2 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #3 yhxA 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #4 glpP 27 transcription antiterminator #5 glpF 178 glycerol uptake facilitator #6 glpD 140 glycerol-3-phosphate dehydrogenase #7 yhxB 131 similar to phosphomannomutase #8 pmmA 101 pmmA #9 Rv3258c 122 hypothetical protein Rv3258c Motif number 1 CCAGCCCTCTCAGCCCGCAAAAAAAGAGCA 2 27 0 CAGCCCGCAA 0.985768 -134 GTGGTATAATGGGCTCGCTATGTAAAGTAC 2 82 1 GGGCTCGCTA 0.89893 -79 GGGCTGCAGACAGCCCGTTATGAT 7 5 0 CAGCCCGTTA 0.973806 -127 GGGCTGTCTGCAGCCCGTTATTTCTTTTTA 7 19 1 CAGCCCGTTA 0.973806 -113 CTCCCCCTTTCGGCACGTAAAAAGAAATAA 7 36 0 CGGCACGTAA 0.814176 -96 GAGACCGATTCGGCCCGCGTCGTTCGCGGG 8 27 1 CGGCCCGCGT 0.990349 -75 GCCAGCCTATCGGCCCGCGAACGACGCGGG 8 40 0 CGGCCCGCGA 0.998872 -62 AGGTTGTCAGGAGCCCGCGC 8 92 1 GAGCCCGCGC 0.948483 -10 GCAATCCGGCGGGGCCGCGAG 9 2 0 GGGGCCGCGA 0.981911 -121 CCGGATTGCTCGCCGCGCTACCGACCCGCC 9 23 1 CGCCGCGCTA 0.960427 -100 GCTACCGACCCGCCCCGCGACCGACGGCTC 9 39 1 CGCCCCGCGA 0.996408 -84 CCGTTACCATCGGCGCGTGAGCGATTCCCG 9 81 0 CGGCGCGTGA 0.983789 -42 CCGTCCACGCCGCGATGTTTAACCG 9 108 0 CACGCCGCGA 0.955696 -15 ********** Masking position 6 Map Score: 26.9084 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 391 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 AGCGCGTTAGCCGCTTTGCTCTTTTTTTGCGGG 2 10 1 GCGTTGCTCT 0.902975 -151 GCCGTAAAGAGCTGCTGTGGTCTCCGAGTTCTCC 5 60 0 GCGGTGGTCC 0.994181 -119 CTTACACTTTGGTGCTGTGGTCTCTCCTCATCTC 6 56 0 GGGGTGGTCC 0.992803 -85 ATGCACTTTGGCTGTTGTGGTCTCTTTTTCTATT 6 91 1 GCGGTGGTCC 0.994184 -50 ATATGAAGCGGGTGCCTCTGTCACTTGATAACCT 7 71 0 GGGTCTGTCC 0.964274 -61 AACGACGCGGGCCGAATCGGTCTCGAACAGCATG 8 17 0 GCGTCGGTCC 0.997395 -85 TCGCGGCCCCGCCGGATTGCTCGCCGCGCTACCG 9 12 1 GCGTTGCTCC 0.990699 -111 TCGGTCGCGGGGCGGGTCGGTAGCGCGGCGAGCA 9 29 0 GGGTCGGTAC 0.964292 -94 GCTCCTCGTGGAGCCGTCGGTCGCGGGGCGGGTC 9 45 0 GACTCGGTCC 0.884545 -78 CGAGGAGCTGCGGGAATCGCTCACGCGCCGATGG 9 71 1 CGGTCGCTCC 0.94669 -52 ** * ****** * Masking position 11 Map Score: 14.4878 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 185 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 GTAAAACACAAAATACGAAATGACTGAAATCT 2 125 1 AAAACGAAAG 0.731707 -36 TTTCTGTATGATATAGGAAATGGCGA 3 5 0 ATAAGGAAAG 0.971583 -296 TTCCTATATCATACAGAAAACGGCTAGGCTTC 3 18 1 ATAAGAAAAG 0.955281 -283 TTCCAAAGCAAAACAGGCAAAGTGACAATGCT 3 112 0 AAAAGGCAAG 0.877839 -189 TTTCTCAAGAAGAAAGAGGATGCAGCTTCCAA 3 138 0 AGAAGAGGAG 0.930335 -163 TTTCTTCTTGAGAAAGGGGATGTTTTATTATT 3 155 1 AGAAGGGGAG 0.955306 -146 AAGACATCACATAAAGAGAAGGTCTGTTTCAA 3 248 1 ATAAGAGAAG 0.966293 -53 TGAATTGGCATTATAGGGAACGCTAATGAA 3 281 1 TTAAGGGAAG 0.841634 -20 AAAAAGCATGATAGAGAAGAAGAGAATAAAAA 5 131 0 ATAAGAAGAG 0.94616 -48 TTGTCACGGTAAATAGAAAAAGAGACCACAAC 6 104 0 AAAAGAAAAG 0.935861 -37 CCGTGACAACAAGGAGGAAACGTA 6 127 1 AAGAGGAAAG 0.800364 -14 GCATAAGCTGATACATAGGAGGACGAAT 7 114 1 ATAATAGGAG 0.65013 -18 *** ****** * Masking position 5 Map Score: 8.47986 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 748 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 4 GATGCAGCTTCCAAAGCAAAACAGGCAAAGTG 3 120 0 CCAAAGCAAC 0.944399 -181 GAAATCATCACCAAGACATCACATAAAGAGAA 3 236 1 CCAAGACACC 0.942652 -65 AACTCGGAGACCACAGCAGCTCTTTACGGCAA 5 64 1 CCACAGCACC 0.996929 -115 AATAAAAAAACCACAACAAACCGCTTTACGGG 5 107 0 CCACAACAAC 0.966697 -72 TGAGGAGAGACCACAGCACCAAAGTGTAAGCA 6 60 1 CCACAGCACA 0.986713 -81 GAAAAAGAGACCACAACAGCCAAAGTGCATGC 6 89 0 CCACAACACA 0.966697 -52 GCCCCGCGACCGACGGCTCCACGAGGAGCTGC 9 50 1 CGACGGCTCC 0.917625 -73 TGAGCGATTCCCGCAGCTCCTCGTGGAGCCGT 9 62 0 CCGCAGCTCC 0.969279 -61 ******** * * Masking position 7 Map Score: 6.625 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 211 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CCGTTGCCTTACCGCTTGGCTATAGCC 1 8 0 ACCGCTTGGC 0.99382 -293 GATTCGAACCAACGCATGACGGAGTCAAAG 1 39 0 AACGCATGAC 0.756367 -262 AGCGCGTTAGCCGCTTTGCTCTTTTTTTG 2 10 1 GCCGCTTTGC 0.990093 -151 CATACAGAAAACGGCTAGGCTTCACATTGC 3 27 1 ACGGCTAGGC 0.907586 -274 ACCACAACAAACCGCTTTACGGGTGCATAA 5 100 0 ACCGCTTTAC 0.935454 -79 TCGTTCGCGGGCCGATAGGCTGGCGGCCAA 8 46 1 GCCGATAGGC 0.80183 -56 GATTTTCTGCGACTCTTGGCCGCCAGCCTA 8 61 0 GACTCTTGGC 0.867429 -41 TCGCGGCCCCGCCGGATTGCTCGCCGCGCT 9 12 1 GCCGGATTGC 0.876123 -111 ********** Masking position 10 Map Score: 3.47154 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 900 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 ACTTCTAACTGTTCAGTCTGTATAATAATTTTA 1 136 1 GTTCAGTTAT 0.913316 -165 TGCCTTCACCGGTCTGTATGTATACGAGCTTCG 1 264 0 GGTCTGTTAT 0.992229 -37 AGCCAGACCGGGTCAGAGTCAATAAACCGCGTA 3 187 0 GGTCAGTAAT 0.973439 -114 ACTCTGACCCGGTCTGGCTTTATATTGAAGGCA 3 201 1 GGTCTGTTAT 0.992229 -100 ATAAAGAGAAGGTCTGTTTCAATTGAATTGGCA 3 258 1 GGTCTGTAAT 0.985599 -43 TGGCTGTTGTGGTCTCTTTTTCTATTTACCGTG 6 99 1 GGTCTCTTCT 0.914569 -42 ****** * *** Masking position 9 Map Score: 2.95304 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 57 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 CCTCTGCCTTCACCGGTCTGTATGTATACG 1 271 0 CACCGGTCTG 0.973695 -30 AGCGCGTTAGCCGCTTTGCTCTTTTTTT 2 9 1 AGCCGCTTTG 0.977722 -152 TGTGAAGCCTAGCCGTTTTCTGTATGATAT 3 23 0 AGCCGTTTTC 0.806698 -278 ATTGACTCTGACCCGGTCTGGCTTTATATT 3 197 1 ACCCGGTCTG 0.912736 -104 CACCGCTTTCATGCACTGAT 5 1 1 CACCGCTTTC 0.95631 -178 AACCACAACAAACCGCTTTACGGGTGCATA 5 101 0 AACCGCTTTA 0.859033 -78 ACGCGGGCCGAATCGGTCTCGAACAGCATG 8 17 0 AATCGGTCTC 0.554925 -85 CTCGCGGCCCCGCCGGATTGCTCGCCGCGC 9 11 1 CGCCGGATTG 0.91012 -112 CCGGATTGCTCGCCGCGCTACCGACCCGCC 9 23 1 CGCCGCGCTA 0.923146 -100 CCGTCCACGCCGCGATGTTTAACCGTT 9 106 0 CGCCGCGATG 0.891695 -17 ********** Masking position 9 Map Score: 3.18687 Number of sites scoring better than the average of aligned sites = 1464 Number in coding regions = 1356 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 8 GCGCGTTAGCCGCTTTGCTCTTTTTTTGCGGG 2 12 1 CGCTTTCCTT 0.946275 -149 AGAGGGCTGGCACATTTCACTTGCTAAATCGA 2 47 1 CACATTCCTT 0.992286 -114 CCCATTATACCACATTTCGATTTAGCAAGTGA 2 63 0 CACATTCATT 0.982786 -98 GGCTAGGCTTCACATTGCTATTGCAATGGCTG 3 39 1 CACATTCATT 0.982786 -262 AGCACATTCCTCCTAAAGTCACGA 5 165 0 CACATTCCCT 0.983036 -14 ****** * *** Masking position 6 Map Score: 2.01628 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 9 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 TGTCTTTTTTCTTTTCGGAAAAATCATTCC 1 105 1 CTTTTCGGAA 0.880004 -196 ATGTGCCAGCCCTCTCAGCCCGCAAAAAAA 2 32 0 CCTCTCAGCC 0.921288 -129 CACAGCAGCTCTTTACGGCAAATGTTTATG 5 75 1 CTTTACGGCA 0.921229 -104 GAGATCTCCCCCTTTCGGCACGTAAAAAGA 7 41 0 CCTTTCGGCA 0.990724 -91 TGTTCGAGACCGATTCGGCCCGCGTCGTTC 8 22 1 CGATTCGGCC 0.939234 -80 TGGCCGCCAGCCTATCGGCCCGCGAACGAC 8 45 0 CCTATCGGCC 0.980787 -57 ********** Masking position 6 Map Score: 0.767648 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 282 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 CCTTTTGATCAAAGGTGTCTGTGACTGGGCTA 1 73 0 AAAGGTTCTT 0.985354 -228 CCTTTGATCAAAAGGTGTCTTTTTTCTTTTCG 1 90 1 AAAGGTTCTT 0.965135 -211 CTTCGTTTCAAAAGGTTTCAATTTTTTTATAA 1 237 0 AAAGGTTCAT 0.986876 -64 TCGTACTGATAAAGGTCGCACTCGAAACAACT 3 75 0 AAAGGTGCAT 0.977912 -226 ****** *** * Masking position 6 Map Score: 0.761615 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 22 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 ********** No masking Map Score: 3.35619e-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 12 ********** No masking Map Score: 3.35619e-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 13 ********** No masking Map Score: 3.35619e-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