AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iilvY_ecoli_hinf_300.orf -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ilvY 149 positive regulator for ilvC #2 HI0681 300 transcriptional activator (ilvY) Motif number 1 CTATATGACAGGAAATTTATTGCGGAAATT 1 72 1 GGAAATTTAT 0.980918 -78 AATTTATTGCGGAAATTGATATATTCACAA 1 85 1 GGAAATTGAT 0.958061 -65 TTAGTTTTCTGGTATTTTTCAAAATACGCT 2 23 1 GGTATTTTTC 0.899848 -278 AAAGAAGGGAGCTAATTTATTCTTTCTTCA 2 75 0 GCTAATTTAT 0.837032 -226 CTGAAAAATTGGAAATTTGTAGGAAATTTT 2 110 1 GGAAATTTGT 0.944885 -191 GAAATTTGTAGGAAATTTTCGTCTGTTTGA 2 121 1 GGAAATTTTC 0.79189 -180 TTTGCTTAACGGAAATTTTCTGAACTCGCT 2 155 0 GGAAATTTTC 0.79189 -146 CTGAAAAATTGGAAATTTGCTTAACGGAAA 2 170 0 GGAAATTTGC 0.592018 -131 ********** Masking position 4 Map Score: 15.8751 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 140 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 ACGTCACATTGCAATTTTTGCAACGTCAACA 1 114 1 GCAATTTTTC 0.839788 -36 GAAAACTAACCGCACTTTTTA 2 1 0 CGCACTTTTA 0.966158 -300 TAAAATTTAGCGTATTTTGAAAAATACCAGA 2 30 0 CGTATTTTGA 0.937242 -271 AAATTTTACCCGCACTTTAAATTGAAGAAAG 2 53 1 CGCACTTTAA 0.855638 -248 AAATTAGCTCCCTTCTTTGCCGCCTGAAAAA 2 87 1 CCTTCTTTGC 0.946521 -214 CTACAAATTTCCAATTTTTCAGGCGGCAAAG 2 101 0 CCAATTTTTA 0.962175 -200 AAGCAAATTTCCAATTTTTCAGGAAATAAGG 2 178 1 CCAATTTTTA 0.962175 -123 GAAAACACGCCCTACTTTGCCTTATTTCCTG 2 197 0 CCTACTTTGC 0.992111 -104 TTTCTTTTTGCCTACTTTTGCTTTGCACGAG 2 224 1 CCTACTTTTC 0.993483 -77 CCGATGGCGACCTACTTTTTCTTTGCTCGTG 2 249 0 CCTACTTTTC 0.993485 -52 ********* * Masking position 6 Map Score: 14.3291 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 461 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 3 ACTTTAAATTGAAGAAAGAATAAATTAGCTCC 2 66 1 GAAAAGAATA 0.941987 -235 TGAGCGTAGCGAGTTCAGAAAATTTCCGTTAA 2 148 1 GGTCAGAAAA 0.974472 -153 CAGAAAATTTCCGTTAAGCAAATTTCCAATTT 2 163 1 CGTAAGCAAA 0.952026 -138 GCAAAAGTAGGCAAAAAGAAAACACGCCCTAC 2 213 0 GAAAAGAAAA 0.985034 -88 TTCTTTGCTCGTGCAAAGCAAAAGTAGGCAAA 2 230 0 GGAAAGCAAA 0.993846 -71 TGCTTTGCACGAGCAAAGAAAAAGTAGGTCGC 2 242 1 GGAAAGAAAA 0.994892 -59 * * ******** Masking position 7 Map Score: 4.93815 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 209 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TGATTCCTCGTGATGTTGTGCTTCTTATTG 1 13 1 TGATGTTGTG 0.990587 -137 AATTGCAATGTGACGTTGTGAATATATCAA 1 100 0 TGACGTTGTG 0.996528 -50 CCCTCGATGTTGACGTTGCAAAAATTGCAA 1 122 0 TGACGTTGCA 0.988799 -28 ********** Masking position 3 Map Score: 2.00203 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 45 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TCAATCTCGCAAACGCGAACCGAACAATAAGAAGC 1 32 0 AAACACCGAC 0.99458 -118 AAAAATACCAGAAAACTAACCGCACTTTTTA 2 7 0 GAACACCGAC 0.996547 -294 AAAATACGCTAAATTTTACCCGCACTTTAAATTGA 2 43 1 AAATACCGAC 0.972356 -258 AAGAAAGAATAAATTAGCTCCCTTCTTTGCCGCCT 2 77 1 AAAACCCCTC 0.93937 -224 GAAATTTTCTGAACTCGCTACGCTCAAACAGACGA 2 139 0 GAACCACGTC 0.973965 -162 TAGGCAAAAAGAAAACACGCCCTACTTTGCCTTAT 2 203 0 GAACCCCCAC 0.9958 -98 *** * * *** ** Masking position 3 Map Score: 2.28095 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 298 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 GCTTCTTATTGTTCGGTTCGCGTTTGCGAG 1 32 1 GTTCGGTTCG 0.989196 -118 TAAAAAGTGCGGTTAGTTTTCTGGTA 2 7 1 GTGCGGTTAG 0.996643 -294 TCAATTTAAAGTGCGGGTAAAATTTAGCGT 2 48 0 GTGCGGGTAA 0.989159 -253 ********** Masking position 8 Map Score: 0.823274 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 29 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: 8.764e-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: 8.764e-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: 8.764e-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