AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_mpneu_reg_300.orf -o321_mpneu_300.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMP00152 101 Mycoplasma_pneumoniae #2 RMP00154 300 Mycoplasma_pneumoniae Motif number 1 ctttcaattttcggtattcgttttaaataccg 1 50 0 tggtattgtt 0.975873 -52 atatcatttcccggtcttgtttgttgattaaa 2 78 0 cggtcttttt 0.930557 -223 atgatacatgtatatatcatttcccggtcttg 2 91 0 ttatatcttt 0.829075 -210 atgtatcatgtatatattctttccgatggtac 2 114 1 ttatattttt 0.958775 -187 atattatccgtaggtctttattttcggtttaa 2 154 1 tggtcttatt 0.971186 -147 tcggtttaattagatattaattcataaatatg 2 177 1 tgatattatt 0.977396 -124 aattattttattgatattaattcatatttatg 2 199 0 tgatattatt 0.977396 -102 tgtaaaccggtaggtattatttattttagttt 2 242 1 tggtattttt 0.99245 -59 ttttagtttatttgttttgtttttcgtttttt 2 265 1 ttgttttttt 0.869228 -36 tttcgtttttttgatatttttcccg 2 286 1 tgatattttc 0.945027 -15 * ****** *** Masking position 7 Map Score: 12.5383 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 133 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 2 atatggtgtaatttttaattcgctaa 1 7 0 atttttaatt 0.847396 -95 accgcttaggtttgttaatatggtgtaatt 1 24 0 tttgttaata 0.970724 -78 taatttaccttctgttaatt 1 92 1 tctgttaatt 0.938544 -10 gttctaccaatttgttacttcttttaatca 2 56 1 tttgttactt 0.938544 -245 cccggtcttgtttgttgattaaaagaagta 2 71 0 tttgttgatt 0.98626 -230 ttaattcatatttatgaattaatatctaat 2 185 0 tttatgaatt 0.856519 -116 aaacaattattttattgatattaattcata 2 205 0 tttattgata 0.92703 -96 accggtaggtattatttattttagtttatt 2 247 1 attatttatt 0.775859 -54 attatttattttagtttatttgttttgttt 2 257 1 ttagtttatt 0.817604 -44 tgtttttcgtttttttgatatttttcccg 2 282 1 ttttttgata 0.898643 -19 ********** Masking position 5 Map Score: 8.7925 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 276 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 ttgttaatatggtgtaatttttaattcgct 1 13 0 ggtgtaattt 0.962887 -89 ttcggtattcgttttaaataccgcttaggt 1 43 0 gttttaaata 0.896068 -59 cacgtgcaacctttcaattttcggtattcg 1 62 0 ctttcaattt 0.882074 -40 aaaggttgcacgtgtaatttaccttctgtt 1 78 1 cgtgtaattt 0.951814 -24 tttgttacttcttttaatcaacaaacaaga 2 66 1 cttttaatca 0.955077 -235 ctttattttcggtttaattagatattaatt 2 169 1 ggtttaatta 0.980415 -132 taaaataattgttttaatcactgtaaaccg 2 221 1 gttttaatca 0.965409 -80 ********** Masking position 6 Map Score: 5.13594 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 132 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 caacctttcaattttcggtattcgttttaa 1 56 0 attttcggta 0.981031 -46 cagaaggtaaattacacgtgcaacctttca 1 76 0 attacacgtg 0.720102 -26 tcgagattgaattatagggaaattatggtt 2 29 1 attataggga 0.877086 -272 tgtatatatcatttcccggtcttgtttgtt 2 85 0 atttcccggt 0.929935 -216 tgtaatatatattatccgtaggtctttatt 2 146 1 attatccgta 0.951957 -155 gtaggtctttattttcggtttaattagata 2 163 1 attttcggtt 0.985368 -138 ggtattatttattttagtttatttgttttg 2 254 1 attttagttt 0.857565 -47 atttgttttgtttttcgtttttttgatatt 2 274 1 tttttcgttt 0.734061 -27 ********** Masking position 3 Map Score: 3.56185 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 212 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 cgggaaatgatatatacatgtatcatgtat 2 97 1 tatatacatg 0.975897 -204 tcggaaagaatatatacatgatacatgtat 2 110 0 tatatacatg 0.975897 -191 ********** Masking position 5 Map Score: 0.598903 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: 6.84553e-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: 6.84553e-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: 6.84553e-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