AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i289_bsub_mtub_100.orf -o289_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 yeaC 152 similar to methanol dehydrogenase regulation #2 yeaD 300 similar to hypothetical proteins from B. subtilis #3 Rv3163c 29 hypothetical protein Rv3163c #4 Rv3166c 79 hypothetical protein Rv3166c #5 Rv3167c 44 hypothetical protein Rv3167c Motif number 1 TTTTTTGTGTGTTTTGGCCAGCTTTATTGGT 1 34 1 GTTTGGCCAG 0.892725 -119 TATTTTCCTCCTAGTCATCTACAA 1 139 0 TTTCTCCTAG 0.849465 -14 ATGTTTCAGGGCGGCTTTGTCAGC 2 4 1 TTTCGGGCGG 0.929717 -297 CAGGGCGGCTTTGTCAGCTGGTTTTTGTTTT 2 17 1 TTGTAGCTGG 0.899705 -284 CCCTTTTGTCTTGTATGCCGGGCTGTTGGCC 2 58 1 TTGTTGCCGG 0.965287 -243 TATGCCGGGCTGTTGGCCTTGTATCCGCTCC 2 71 1 TGTTGCCTTG 0.622584 -230 GCTCCGTTCTTTTCAGGCTTCAGGCAAATGG 2 97 1 TTTCGGCTTC 0.709997 -204 TAAAACACAATTGCATGCGGGGGACAGGCTG 2 129 1 TTGCTGCGGG 0.924005 -172 TGCATGCGGGGGACAGGCTGGGCGTAACGGT 2 140 1 GGACGGCTGG 0.845064 -161 TGATTGAAGATTGCCTGCCAGAAGGTATCGA 2 213 1 TTGCTGCCAG 0.91978 -88 AAAACGAGCCGTTTGGCGCGGCCTCCGTCTC 2 255 0 GTTTGCGCGG 0.8008 -46 CAAACGGCTCGTTTTTCCTTGGTTTAAACGG 2 271 1 GTTTTCCTTG 0.73843 -30 CGGGTTGGCTGGATGAACTACG 3 2 1 GGGTGGCTGG 0.955507 -28 ACCTGGCTTGGTTCATACTGGCACG 4 5 0 GTTCTACTGG 0.82123 -75 CTGGGGGTTGGTTCAACCTGGCTTGGTTCAT 4 20 0 GTTCACCTGG 0.917976 -60 CCTGCCGCCGTTGCGGCCTGGGGGTTGGTTC 4 37 0 TTGCGCCTGG 0.986244 -43 ACTCGACCGGTTGCCTGCCGCCGTTGCGGCC 4 50 0 TTGCTGCCGC 0.901167 -30 **** ****** Masking position 8 Map Score: 15.1024 Number of sites scoring better than the average of aligned sites = 5405 Number in coding regions = 4971 Number in noncoding regions = 434 Number of orfs with sites within 600 bp upstream = 305 Fraction of orfs with sites within 600 bp upstream = 0.0489881 Motif number 2 GTCACAGGAAGCTTTTTTGTGTGTTTTGGC 1 22 1 GCTTTTTTGT 0.918689 -131 TATACAGATTGCTTTTTTGTGGTAAAGTTA 1 90 1 GCTTTTTTGT 0.918689 -63 GGCTTTGTCAGCTGGTTTTTGTTTTACGCG 2 23 1 GCTGGTTTTT 0.906872 -278 CCTTGTATCCGCTCCGTTCTTTTCAGGCTT 2 87 1 GCTCCGTTCT 0.983252 -214 GGAAATGGCAGCTCTCTTCTCAGCGTAACC 2 168 0 GCTCTCTTCT 0.939194 -133 GCGCCAAACGGCTCGTTTTTCCTTGGTTTA 2 267 1 GCTCGTTTTT 0.971661 -34 CGTCATGCTCCGTTTAAACCAAGGAA 2 285 0 GCTCCGTTTA 0.93715 -16 GTTCAACCTGGCTTGGTTCATACTGGCACG 4 11 0 GCTTGGTTCA 0.973786 -69 GCGGCCTGGGGGTTGGTTCAACCTGGCTTG 4 26 0 GGTTGGTTCA 0.843688 -54 ********** Masking position 7 Map Score: 7.35339 Number of sites scoring better than the average of aligned sites = 1285 Number in coding regions = 1103 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 3 AAAAACGATTCTAGCAAATTGTTACCAATAA 1 57 0 CTAGCAATTG 0.893917 -96 TTACCACAAAAAAGCAATCTGTATAAAAAAA 1 84 0 AAAGCAACTG 0.91574 -69 TTTCAGGCTTCAGGCAAATGGATAAAACACA 2 107 1 CAGGCAATGG 0.994728 -194 CTGTCCCCCGCATGCAATTGTGTTTTATCCA 2 125 0 CATGCAATGT 0.908039 -176 TACCTTCTGGCAGGCAATCTTCAATCACCAT 2 209 0 CAGGCAACTT 0.985394 -92 GTAGTTCATCCAGCCAACCCG 3 1 0 CAGCCAACCG 0.964933 -29 GCAACGGCGGCAGGCAACCGGTCGAGTGGTG 4 54 1 CAGGCAACGG 0.996866 -26 ******* *** Masking position 6 Map Score: 5.83771 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 496 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GCTTCCTGTGACAGGAAGCTCCA 1 4 0 ACAGGAAGCT 0.992083 -149 GCTTCCTGTCACAGGAAGCTTTTTTGTGTG 1 15 1 ACAGGAAGCT 0.992083 -138 TTACCACAAAAAAGCAATCTGTATAAAAAA 1 85 0 AAAGCAATCT 0.938548 -68 GCGTAAAACAAAAACCAGCTGACAAAGCCG 2 22 0 AAAACCAGCT 0.942815 -279 CATCAGCGGAAATGGCAGCTCTCTTCTCAG 2 175 0 AATGGCAGCT 0.974416 -126 ********** Masking position 7 Map Score: 3.45392 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 322 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CAGCTGACAAAGCCGCCCTGAAACAT 2 7 0 AGCCGCCCTG 0.923651 -294 GATACAAGGCCAACAGCCCGGCATACAAGA 2 66 0 CAACAGCCCG 0.904766 -235 TTGGCCTTGTATCCGCTCCGTTCTTTTCAG 2 83 1 ATCCGCTCCG 0.962585 -218 TTCTCAGCGTAACCGTTACGCCCAGCCTGT 2 152 0 AACCGTTACG 0.82037 -149 TTGGCGCGGCCTCCGTCTCGATTTAATGAC 2 244 0 CTCCGTCTCG 0.969282 -57 AGGCCGCGCCAAACGGCTCGTTTTTCCTTG 2 262 1 AAACGGCTCG 0.92681 -39 TAGTTCATCCAGCCAACCCG 3 1 0 AGCCAACCCG 0.899105 -29 GCTGGATGAACTACGGCGCGAT 3 18 1 CTACGGCGCG 0.961838 -12 GGTTGCCTGCCGCCGTTGCGGCCTGGGGGT 4 43 0 CGCCGTTGCG 0.952082 -37 ********** Masking position 4 Map Score: 3.12637 Number of sites scoring better than the average of aligned sites = 2087 Number in coding regions = 1932 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 ATAAAGCTGGCCAAAACACACAAAAAAGCT 1 31 0 CCAAAACACA 0.970907 -122 AGCAATCTGTATAAAAAAAACGATTCTAGC 1 73 0 ATAAAAAAAA 0.889053 -80 CCTAACTTTACCACAAAAAAGCAATCTGTA 1 92 0 CCACAAAAAA 0.832596 -61 GGAGAAACGCGTAAAACAAAAACCAGCTGA 2 30 0 GTAAAACAAA 0.932934 -271 AGCCCGGCATACAAGACAAAAGGGAGAAAC 2 52 0 ACAAGACAAA 0.931671 -249 AGGCAAATGGATAAAACACAATTGCATGCG 2 118 1 ATAAAACACA 0.951599 -183 ********** Masking position 6 Map Score: 0.449728 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 461 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 7 ********** No masking Map Score: 1.44541e-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: 1.44541e-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: 1.44541e-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