AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -irpoH_mgen_opreg_300.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MG249 44 RNA polymerase sigma-43 factor (rpoD) #2 MG254 175 DNA ligase #3 MG305 87 heat shock protein 70 (dnaK) #4 MG309 53 lipoprotein, putative Motif number 1 CTAGCATTATAATTTTAGCTTATATAACTT 1 8 0 ATTTTAGCTT 0.968313 -37 TGTTACTTTAATATTTAGTATATTTTAACTTGC 2 11 0 AATTTAGTTT 0.941202 -165 TTTACAAAGAAGTTTTAATTTGGAGCAGATAAC 2 107 0 ATTTTAATTG 0.938807 -69 CTAAGTCAGGATTTTTCTTATTTATAGTA 2 157 1 ATTTTCTTTT 0.932605 -19 TTTAATTAGCACTTTTAGTGTTTGAGTGCTAAT 3 18 1 ATTTTAGTTT 0.991383 -70 TTTGAGTGCTAATTTTTGTTTATAATTACTGAG 3 38 1 ATTTTTGTTT 0.9837 -50 ACTTTTTTTTTAGATCAATAACA 3 75 0 ATTTTTTTTG 0.920202 -13 TAAAATTTATATTTTTATTATTACCAC 4 5 0 ATTTTATTTA 0.889619 -49 AAATTTCAATAATTTTAAAATTTATATTTTTAT 4 20 0 ATTTTAAATT 0.889298 -34 AAATTATTGAAATTTTTGACTGTGCA 4 38 1 ATTTTTGATT 0.950144 -16 * ******* * * Masking position 6 Map Score: 11.8268 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 137 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AATTTTAGCTTATATAACTT 1 1 0 TATATAACTT 0.829636 -44 TGCGACTAGCATTATAATTTTAGCTTATAT 1 16 0 ATTATAATTT 0.966301 -29 TATTTAGTATATTTTAACTTGC 2 3 0 ATTTTAACTT 0.905629 -173 CTGCGTTGTTACTTTAATATTTAGTATATT 2 20 0 ACTTTAATAT 0.797341 -156 TTACAAAGAAGTTTTAATTTGGAGCAGATA 2 109 0 GTTTTAATTT 0.863676 -67 TACTATAAATAAGAAAAATCC 2 165 0 ACTATAAATA 0.888564 -11 AACAAACTTTAATTAGCACTTTTAG 3 6 1 ACTTTAATTA 0.928806 -82 CTAATTTTTGTTTATAATTACTGAGTAATT 3 46 1 TTTATAATTA 0.879669 -42 TAATAATAAAAATATAAATTTTAAAATTAT 4 15 1 AATATAAATT 0.77426 -39 GTCAAAAATTTCAATAATTTTAAAATTTAT 4 28 0 TCAATAATTT 0.783027 -26 ********** Masking position 5 Map Score: 5.80483 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 252 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 CTAAAATTATAATGCTAGTCGCATTGAGCT 1 23 1 AATGCTAGTC 0.94085 -22 TTCTTTGTAAAATCCTGATTGGTATCAACT 2 129 1 AATCCTGATT 0.885469 -47 AAATAAGAAAAATCCTGACTTAGTTGATAC 2 150 0 AATCCTGACT 0.861799 -26 AAACACTAAAAGTGCTAATTAAAGTTTGTT 3 11 0 AGTGCTAATT 0.987904 -77 TTAGTGTTTGAGTGCTAATTTTTGTTTATA 3 32 1 AGTGCTAATT 0.987904 -56 ********** Masking position 6 Map Score: 3.68922 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 56 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 ATGCTAGTCGCATTGAGCTAA 1 34 1 CATTGAGCTA 0.990455 -11 TATGTTCTACCATTGAACTATATCTGCGTT 2 43 0 CATTGAACTA 0.991553 -133 GAGTAATTGTTATTGATCTAAAAAAAAAGT 3 68 1 TATTGATCTA 0.978122 -20 ATTTTAAAATTATTGAAATTTTTGACTGTG 4 32 1 TATTGAAATT 0.880911 -22 ********** Masking position 6 Map Score: 2.31409 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 AATGGTAGAACATAACCTTGCCAAGGTTAA 2 59 1 CATAACCTTG 0.994301 -117 GAACCCGCATCTTAACCTTGGCAAGGTTAT 2 70 0 CTTAACCTTG 0.9947 -106 ********** Masking position 5 Map Score: 0.293653 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: -7.15216e-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: -7.15216e-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: -7.15216e-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