AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i333_bsub_mtub_300.orf -o333_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 yjbQ 234 similar to Na+/H+ antiporter #2 tenA 248 transcriptional regulator #3 Rv0415 129 hypothetical protein Rv0415 Motif number 1 ATTATGAAGCAAAGTGTTGTGAGTCATCAC 1 41 1 AAAGTGTTGT 0.811636 -194 ATCATTTTCTAAACAGGATTAAGACCTTAT 1 101 1 AAACAGGATT 0.884041 -134 GTTTTTTAAAAATGAGGTTTTGTTCTCTGA 1 172 1 AATGAGGTTT 0.954522 -63 CTGACTTAAAAAGGAGGTTCTGATT 1 220 1 AAGGAGGTTC 0.950428 -15 TCGTGTTAATATAGAGGTGCAGAACAATTC 2 30 1 ATAGAGGTGC 0.916718 -219 CTCATAACTTGAACAGGTTCAGACCTGCGT 2 129 1 GAACAGGTTC 0.938803 -120 CCTGCGTAGGGAAGTGGAGCGGTATTTGTG 2 152 1 GAAGTGGAGC 0.913607 -97 CCCGCAAGGAAAAGTGGTTTGGAATTGGCA 2 193 0 AAAGTGGTTT 0.977958 -56 TCCTTGCGGGAAAGTGGTTTTTTTATTTTC 2 213 1 AAAGTGGTTT 0.977958 -36 GCATGATCCGGATCAGGTGTGACGGTAAGG 3 91 0 GATCAGGTGT 0.877928 -39 ********** Masking position 6 Map Score: 9.03681 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 931 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 ATAAAACAATCGGTAAGGAGGAGACCGC 1 6 0 CGAAGGAGGG 0.985653 -229 AGGTTCAGACCTGCGTAGGGAAGTGGAGCGGTA 2 143 1 CGGTAGGGAG 0.973839 -106 AACCACTTTCCCGCAAGGAAAAGTGGTTTGGAA 2 199 0 CGAAGGAAAG 0.950298 -50 TTTTTATTTTCAGAGGGGGAATGATTT 2 232 1 CGGGGGGAAG 0.985031 -17 CACGGGAGTCCCGGGAGCGGGGTCTGAGAGTGG 3 48 1 CGGAGCGGGT 0.942844 -82 GGAGCGGGGTCTGAGAGTGGGCGCGCCTGCCCT 3 61 1 CGGAGTGGGG 0.990066 -69 TCAGGTGTGACGGTAAGGGCAGGCGCGCCCACT 3 76 0 CGAAGGGCAG 0.985967 -54 CGGATCATGCCGGCGAAGGGAGGTCAAGG 3 111 1 CGGAAGGGAG 0.994454 -19 * * ******* * Masking position 3 Map Score: 6.33711 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 245 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TCCTTACCGATTGTTTTATTTATTATGAAGC 1 20 1 TTTTTTATTT 0.966512 -215 TAAAATCGCGTTATGTTTTTTAAAAATGAGG 1 158 1 TTTGTTTTTT 0.962598 -77 AAAAATGAGGTTTTGTTCTCTGAGTGAGAAC 1 179 1 TTTGTTCTCT 0.945005 -56 GGAGCGGTATTTGTGTTATTTTACTATGCCA 2 167 1 TTTGTTATTT 0.984855 -82 GGGAAAGTGGTTTTTTTATTTTCAGAGGGGG 2 220 1 TTTTTTATTT 0.966512 -29 ** ******** Masking position 6 Map Score: 2.95418 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 230 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 TTTATTTTTCATCATCACCCTTGTTAAAATC 1 134 1 ATCATCCCCT 0.985116 -101 AGTGAGAACTAGCATAACCCTGACTTAAAAA 1 201 1 AGCATACCCT 0.980205 -34 GCCCTTATGAAGGACACCCCTAGTGGTTAAA 2 72 0 AGGACACCCT 0.976153 -177 TCACACTTTTATCTCAGCCCTTATGAAGGAC 2 88 0 ATCTCACCCT 0.963332 -161 CAAATACCGCTCCACTTCCCTACGCAGGTCT 2 149 0 TCCACTCCCT 0.945416 -100 AAATCATTCCCCCTCTGAAAATA 2 236 0 ATCATTCCCC 0.929414 -13 CCTTGACCTCCCTTCGCCGGCAT 3 117 0 TTGACCCCCT 0.961679 -13 ****** **** Masking position 8 Map Score: 3.54172 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 165 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GTTTTATTTATTATGAAGCAAAGTGTTGTG 1 32 1 TTATGAAGCA 0.946352 -203 TAACGCGATTTTAACAAGGGTGATGATGAA 1 141 0 TTAACAAGGG 0.928209 -94 GTTATGTTTTTTAAAAATGAGGTTTTGTTC 1 167 1 TTAAAAATGA 0.840829 -68 TAACCCTGACTTAAAAAGGAGGTTCTGATT 1 215 1 TTAAAAAGGA 0.971548 -20 ATCTCAGCCCTTATGAAGGACACCCCTAGT 2 79 0 TTATGAAGGA 0.987166 -170 CCTGTTCAAGTTATGAGGGTCTAAAAGTCA 2 116 0 TTATGAGGGT 0.895295 -133 ********** Masking position 6 Map Score: 1.35083 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 262 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 ********** No masking Map Score: -2.10731e-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: -2.10731e-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: -2.10731e-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