AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i025_1_2_1_2_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 fdhD 193 affects formate dehydrogenase-N #2 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #3 yjcQ 140 putative enzyme #4 yjcR 300 putative membrane protein #5 HI0005 300 fdhD protein (fdhD) Motif number 1 AACTCCCACTCCCTGCACACGCAGCAAGCGAATGT 1 48 0 CCTGCCGCGC 0.995906 -146 TATTTTTCTTTGCGGAAGGGGCCGCAAAGGTCCAG 1 82 1 TCGGGGGCGC 0.875763 -112 TACCGCGTGACAGCCATCACGCGGCAGACATT 2 8 0 CGCCCCGCGC 0.978106 -190 TGAGCGCGCTCAACTCCCTGCCATTACCGGT 3 7 1 CCTCCCCCGC 0.996042 -134 CTGCCATTACCGGTGGTCAGGCTGCTGGCGTTCTT 3 28 1 CGTGCGGCGC 0.987976 -113 CAGAGTTGCACGGTCTGCGGCACGCGACCTGGTCG 3 85 0 CGTCCGCAGC 0.967942 -56 GACCGTGCAACTCTGGGTAGGCTGCCTGCTGGTGA 3 105 1 CCTGTGGCGC 0.976498 -36 ACAGTTCTCTCTCGCATGGCGATGCAACTCAAAAA 4 23 1 CCGCGCGAGC 0.971757 -278 CTGGTTTTTCTGCGCCATTGCCAGCCTTATTTTGA 4 142 1 TCGCTGCCGC 0.820067 -159 CTTATTTTGACGCTCATCACGAGGCGAGTTATTCA 4 167 1 CCTCCCGAGC 0.993728 -134 GCCCTTTTTGCTCTCTACGCCATGCTGTTCTGGCT 4 245 1 CCTCCCCAGC 0.9893 -56 * *** * *** ** Masking position 15 Map Score: 14.1444 Number of sites scoring better than the average of aligned sites = 2428 Number in coding regions = 2334 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 AAAATAACTCCCACTCCCTGCACACGCAGC 1 58 0 CCACTCCCTG 0.958961 -136 TCAAAACTGACGACAGCCTGTTTTTCGTCA 2 58 1 CGACAGCCTG 0.980577 -140 ACTATTTATTCAAAACTCTGACGAAAAACA 2 76 0 CAAAACTCTG 0.725598 -122 TGAGCGCGCTCAACTCCCTGCCATTACCGG 3 11 1 CAACTCCCTG 0.97951 -130 GAAAGAACGCCAGCAGCCTGACCACCGGTA 3 35 0 CAGCAGCCTG 0.97536 -106 AACTCTGGGTAGGCTGCCTGCTGGTGATTC 3 113 1 AGGCTGCCTG 0.894286 -28 CAACTCAAAAAAACAGCCTGGATAATTCCC 4 47 1 AAACAGCCTG 0.974324 -254 TTTTTCTGCGCCATTGCCAGCCTTATTTTG 4 146 1 CCATTGCCAG 0.756071 -155 ATAATTCCGACAAATGCCAGATTGATATTT 4 208 0 CAAATGCCAG 0.95426 -93 ATAGATTAGAAAAATGCCAGCCAGAACAGC 4 268 0 AAAATGCCAG 0.884593 -33 AGTTAAATGTAAAAAGTCTGTTAAATTATT 5 265 0 AAAAAGTCTG 0.71386 -36 ********** Masking position 8 Map Score: 10.8726 Number of sites scoring better than the average of aligned sites = 3263 Number in coding regions = 2984 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 GACGTGACAATGTCGAAACAAGGAGCAATCC 1 10 0 TGCGAAACAG 0.958671 -184 TTGCGGCCCCTTCCGCAAAGAAAAATAACTCC 1 77 0 TTCGCAAAAA 0.801438 -117 AGTTTTGACGTGACGAAACGAAATACCGCGTG 2 34 0 TGCGAAACAA 0.965661 -164 TTCAAAACTCTGACGAAAAACAGGCTGTCGTC 2 66 0 TGCGAAAACA 0.94339 -132 CCAGGTCGCGTGCCGCAGACCGTGCAACTCTG 3 88 1 TGCGCAGACG 0.97025 -53 TCACCGGGATTGCCGGAGATAATGAGCATCCC 4 91 0 TGCGGAGAAA 0.967923 -210 AGGCTGGCAATGGCGCAGAAAAACCAGCTGGG 4 137 0 TGCGCAGAAA 0.987788 -164 CAGAACAGCATGGCGTAGAGAGCAAAAAGGGC 4 245 0 TGCGTAGAAG 0.943799 -56 TCACAATATTTGTTGAAGCTAATGTCATTTGA 5 214 0 TGTGAAGCAA 0.844152 -87 ** ****** ** Masking position 7 Map Score: 5.49819 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 1048 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 4 TTTCTCTTAACCAGATAAGAACACACAC 1 176 0 CTCTTAAAAA 0.978247 -18 CGCATACGCGCTCTCGACTACAGTATGCATCTTTT 2 147 0 CTCTCAAATA 0.986156 -51 GCTCGCTTAACTCTTCATGAAAGAACGCCAGCAGC 3 48 0 CTCTTAAAAA 0.978032 -93 GAGCGCGTCTCAAATAGATTAGAAAAATGCC 4 280 0 GTCTCAAATA 0.973883 -21 GATTATGCAGGTCTCAAGAAGAAAATTCTTCAAG 5 10 0 GTCTCAAAAA 0.985821 -291 TAAAATAATACTCTCTAGTATATAAATCATCGTAA 5 124 1 CTCTCAAAAA 0.99214 -177 ***** * * * ** Masking position 7 Map Score: 4.11625 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TAATGGCAGGGAGTTGAGCGCGCTCA 3 7 0 GAGTTGAGCG 0.996335 -134 CTTTCATGAAGAGTTAAGCGAGCGGCGACC 3 60 1 GAGTTAAGCG 0.985594 -81 AGCCTACCCAGAGTTGCACGGTCTGCGGCA 3 98 0 GAGTTGCACG 0.975691 -43 AACTCGCCTCGTGATGAGCGTCAAAATAAG 4 167 0 GTGATGAGCG 0.977055 -134 ********** Masking position 5 Map Score: 1.88276 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 86 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CTGTAGTCGAGAGCGCGTATGCGTGATTTG 2 159 1 GAGCGCGTAT 0.953727 -39 TGATTAACTGGAGCGAGACCG 2 187 1 GAGCGAGACC 0.985988 -11 TGAGCGCGCTCAACTCCCTGC 3 2 1 GAGCGCGCTC 0.499657 -139 ACGGTCTGCGGCACGCGACCTGGTCGCCGC 3 81 0 GCACGCGACC 0.914436 -60 ATCGCCATGCGAGAGAGAACTGTTGGCATA 4 16 0 GAGAGAGAAC 0.853824 -285 GAGCGCGTCTCAAATAGATT 4 291 0 GAGCGCGTCT 0.973511 -10 ********** Masking position 5 Map Score: 2.18906 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 535 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TTTAATATGCCAACAGTTCTCTCT 4 4 1 AATATCCAAC 0.977902 -297 ATCGGCGCTTATTATCCCAGCTGGTTTTTCT 4 122 1 ATTATCCAGC 0.928338 -179 ATAGATTAGAAAAATGCCAGCCAGAACAGCA 4 267 0 AAAATCCAGC 0.860767 -34 TACTATCTATAATATCTCAACAACTTGTTGT 5 55 0 AATATTCAAC 0.973436 -246 ACTAGAGAGTATTATTTTAACGAAATCAACA 5 112 0 ATTATTTAAC 0.812921 -189 CTAGCCATCCAATAAATCAACGTTTTTACGA 5 153 0 AATAATCAAC 0.94097 -148 TAAATATAAAAATAATTTAACAGACTTTTTA 5 255 1 AATAATTAAC 0.812944 -46 ***** ***** Masking position 4 Map Score: 1.75601 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 197 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 TTCGTTTCGTCACGTCAAAACTGACGACAG 2 44 1 CACGTCAAAA 0.923262 -154 CCTCGTGATGAGCGTCAAAATAAGGCTGGC 4 161 0 AGCGTCAAAA 0.957353 -140 TTATGTTGATTTCGTTAAAATAATACTCTC 5 109 1 TTCGTTAAAA 0.882623 -192 TATATAAATCATCGTAAAAACGTTGATTTA 5 142 1 ATCGTAAAAA 0.961147 -159 TTATGGATTTATCGTTAAAAAATCGTTACT 5 184 0 ATCGTTAAAA 0.961151 -117 CCATTAGTTAAATGTAAAAAGTCTGTTAAA 5 270 0 AATGTAAAAA 0.727601 -31 ********** Masking position 5 Map Score: 0.728859 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 216 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 GCAGGGAGTGGGAGTTATTTTTCTTTGCGG 1 67 1 GGAGTTATTT 0.976551 -127 TGATATTACGGGCACTATTTATTCAAAACT 2 89 0 GGCACTATTT 0.89 -109 AGAGCGCGTATGCGTGATTTGATTAACTGG 2 168 1 TGCGTGATTT 0.893604 -30 TCAGGCTGCTGGCGTTCTTTCATGAAGAGT 3 44 1 GGCGTTCTTT 0.959911 -97 GGCATTTGTCGGAATTATTTATACCGCCCT 4 220 1 GGAATTATTT 0.933653 -81 GTTGTTGAAAGGAGTGATTATGCAGGTCTC 5 30 0 GGAGTGATTA 0.894934 -271 ********** Masking position 8 Map Score: 0.703501 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 547 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 TGGTGTGTGTGTTCTTATCTGGTTAAGAGA 1 172 1 GTTCTTATCT 0.911518 -22 CCTGCTGGTGATTCTGATCTCG 3 129 1 ATTCTGATCT 0.979878 -12 GGCTGGCATTTTTCTAATCTATTTGAGACG 4 276 1 TTTCTAATCT 0.924566 -25 TTCAACAAATATTGTGATCTAGATCATAAA 5 229 1 ATTGTGATCT 0.947824 -72 TATTTTTATATTTATGATCTAGATCACAAT 5 239 0 TTTATGATCT 0.924566 -62 ********** Masking position 5 Map Score: 0.190429 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 27 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ********** No masking Map Score: -3.12396e-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: -3.12396e-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: -3.12396e-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