AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i204_dna_repair1_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 yejH 148 putative ATP-dependent helicase #2 HI1285 91 type I restriction enzyme (hsdR) #3 HI1287 300 type I modification enzyme (hsdM) Motif number 1 ACCGCTATACTGGGCAGACAACAGTTCAGAT 1 58 0 TGGGCGACAA 0.952442 -91 GGTAGATTATTCTGCTAATAGTATGCCATGG 1 117 0 TCTGCAATAG 0.942605 -32 TGATTTCACTTCTGCCAATAAACGAAGAAAT 2 24 1 TCTGCAATAA 0.984085 -68 ACTTTGGGCATCTGCTGATAAACTCCGCAAA 3 52 1 TCTGCGATAA 0.993717 -249 GCTGATAAACTCCGCAAACAACTTGATGCCG 3 65 1 TCCGCAACAA 0.976067 -236 TATCAAAAAAAGTGCGGTCAAGATAGAGGGG 3 203 0 AGTGCGTCAA 0.880265 -98 GTTTTCTAGTTCTGCGGTTAAGGCTTCTTGA 3 247 0 TCTGCGTTAA 0.983024 -54 TGATTATTACACCGCTGATAACGTATTTTGG 3 280 1 ACCGCGATAA 0.97498 -21 ***** ***** Masking position 10 Map Score: 9.79459 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 496 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 CTCCGTTTTTACAGGCAAAATCACACAC 1 8 0 ACAGGAAAAT 0.656397 -141 GGTCGGGCATTGACCCGAAAATCTGAACTGT 1 38 1 TGACCGAAAA 0.880962 -111 ATAACATCCCTCAAGGGAAAAAGATCCATGG 1 92 1 TCAAGGAAAA 0.884258 -57 GTTTATTGGCAGAAGTGAAATCAATCTCGTG 2 16 0 AGAAGGAAAT 0.862483 -76 TTCTGCCAATAAACGAAGAAATTAATCTATT 2 33 1 AAACGAGAAA 0.675451 -59 CAGCAAATACACAAAAGGAACACCT 2 77 1 ACAAAGGAAC 0.728942 -15 TAAATGAWTTAGACGAAAAACTTTGGGCATC 3 33 1 AGACGAAAAC 0.903385 -268 TAAGAAGATAAGACCAAGAACGATATGTTTA 3 103 0 AGACCAGAAC 0.926188 -198 GTTTCACCCATCAACAGGAAAAAATTCAGGC 3 150 1 TCAACGGAAA 0.911132 -151 AGGAAAAAATTCAGGCGGAACTCTCCACACC 3 165 1 TCAGGGGAAC 0.897055 -136 GGAACTCTCCACACCTGAAAATCCCCTCTAT 3 181 1 ACACCGAAAA 0.920521 -120 TTTTTGATACTGAAGAAGAATATCAAGAAGC 3 225 1 TGAAGAGAAT 0.800305 -76 CCTTAACCGCAGAACTAGAAAACCGTGATTA 3 255 1 AGAACAGAAA 0.896163 -46 ***** ***** Masking position 3 Map Score: 6.9265 Number of sites scoring better than the average of aligned sites = 2501 Number in coding regions = 2232 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 3 GGATGTTATTAGACCGCTATACTGGGCAGA 1 71 0 AGACCGCTAT 0.962972 -78 TAGGTAGATTATTCTGCTAATAGTATGCCA 1 120 0 ATTCTGCTAA 0.903398 -29 AGCTCCCCAAAGACAGCAAATACACAAAAG 2 64 1 AGACAGCAAA 0.917427 -28 CTGCTGATAAACTCCGCAAACAACTTGATG 3 63 1 ACTCCGCAAA 0.975776 -238 AAACAACTTGATGCCGCTAACTATAAACAT 3 80 1 ATGCCGCTAA 0.976148 -221 CGTGATTATTACACCGCTGATAACGTATTT 3 278 1 ACACCGCTGA 0.974903 -23 ********** Masking position 1 Map Score: 2.76975 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 394 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GTATGCCATGGATCTTTTTCCCTTGAGGGA 1 98 0 GATCTTTTTC 0.963442 -51 TTACTCACGAGATTGATTTCACTTCTGCCA 2 11 1 GATTGATTTC 0.956479 -81 GGAGCTAATAGATTAATTTCTTCGTTTATT 2 40 0 GATTAATTTC 0.914842 -52 AGTTCCGCCTGAATTTTTTCCTGTTGATGG 3 157 0 GAATTTTTTC 0.844709 -144 AAGGCTTCTTGATATTCTTCTTCAGTATCA 3 229 0 GATATTCTTC 0.888064 -72 ********** Masking position 8 Map Score: 0.818836 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 264 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 ********** No masking Map Score: 3.7902e-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 6 ********** No masking Map Score: 3.7902e-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: 3.7902e-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