AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_mixed14_mpneu_reg_300.orf -o299_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 RMP00504 194 Mycoplasma_pneumoniae #2 RMP00505 70 Mycoplasma_pneumoniae #3 RMP00506 24 Mycoplasma_pneumoniae #4 RMP00512 146 Mycoplasma_pneumoniae #5 RMP00513 23 Mycoplasma_pneumoniae #6 RMP00517 300 Mycoplasma_pneumoniae Motif number 1 tgaggcgtcgttttggacgacccac 1 180 1 ttttggacga 0.908466 -15 aaagttattttggcaaagaaaaccata 4 130 0 ttttggcaaa 0.935745 -17 aactcgacgattttgccgaaaaatcacaga 6 78 1 ttttgccgaa 0.975128 -223 aatcacagaatattcgcgaatctttcggaa 6 99 1 tattcgcgaa 0.959755 -202 ttcgcgaatctttcggaaaagacacggtaa 6 111 1 tttcggaaaa 0.802713 -190 cattcgggggttttgccggacatcccgagt 6 161 0 ttttgccgga 0.957689 -140 ttgttacaattattggcgaacattcggggg 6 181 0 tattggcgaa 0.988914 -120 ttgttacaattattggacaattttgttaca 6 203 0 tattggacaa 0.91281 -98 aacgtcacaattttggcgaaatttcgaata 6 257 1 ttttggcgaa 0.993241 -44 tcgaaatttttttccgcaaatt 6 289 1 tttccgcaaa 0.881454 -12 ********** Masking position 3 Map Score: 15.0076 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 124 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 agtctattaatgggaaaaattcccattttac 1 45 1 tggaaaaatt 0.792666 -150 agaagatcgattgtgaatattctttacttaa 1 90 0 ttggaatatt 0.935819 -105 attctccaacttcttacgatttaacattgtg 2 39 0 ttctacgatt 0.742666 -32 attgtttaattggggacgatttcagtacgaa 4 46 0 tgggacgatt 0.984311 -101 gtcgagttaattgataagtttggccaccaat 6 55 0 ttgtaagttt 0.880025 -246 tccgaaagattcgcgaatattctgtgatttt 6 97 0 tcggaatatt 0.817737 -204 ttacaattattggcgaacattcgggggtttt 6 177 0 tgggaacatt 0.929961 -124 ttggacaattttgttacaattattggcgaac 6 190 0 ttgtacaatt 0.939688 -111 tcggaaaattttgttacaattattggacaat 6 212 0 ttgtacaatt 0.939688 -89 ttcgccaaaattgtgacgtttttactcgatt 6 246 0 ttggacgttt 0.958448 -55 gtcacaattttggcgaaatttcgaatatttc 6 260 1 tgggaaattt 0.921508 -41 *** ******* Masking position 6 Map Score: 8.4192 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 69 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 cgattgtgaatattctttacttaatcaaatta 1 82 0 tattcttttt 0.960977 -113 tcacaatcgatcttctcctgctgccgttttct 1 105 1 tcttctccct 0.945768 -90 tcaataattctattctccaacttcttacgatt 2 49 0 tattctccct 0.96855 -22 cgcactttaatattgtttaattggggacgatt 4 56 0 tattgttttt 0.80297 -91 atccttggcgtcttctgcgtttattcgcactt 4 81 0 tcttctgctt 0.968551 -66 acggtattctgttttttatgtttttc 6 5 1 tattctgttt 0.982296 -296 tttggccaccaattctctatttgcgacttacg 6 36 0 aattctcttt 0.90862 -265 gattcgcgaatattctgtgatttttcggcaaa 6 89 0 tattctgttt 0.982296 -212 ******** ** Masking position 6 Map Score: 5.36739 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 tacttaatcaaattactactggtaaaatgg 1 67 0 aattactact 0.841148 -128 gggacgatttcagtacgaattccgatctga 4 35 0 cagtacgaat 0.928886 -112 aacaatattaaagtgcgaataaacgcagaa 4 71 1 aagtgcgaat 0.950302 -76 ggcaataattactaatcggttaa 5 7 1 aattactaat 0.94508 -17 tctatttgcgacttacgaaaaacataaaaa 6 23 0 acttacgaaa 0.894117 -278 attttggcgaaatttcgaatatttcgaaat 6 266 1 aatttcgaat 0.971271 -35 tgcggaaaaaaatttcgaaatattcgaaat 6 277 0 aatttcgaaa 0.936341 -24 ********** Masking position 8 Map Score: 2.5378 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 39 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ctcctgctgccgttttctcacgacatcctga 1 119 1 cgtttttcac 0.966897 -76 cataatctcacgattttttacacaatgttaa 2 19 1 cgatttttac 0.912612 -52 caacttcttacgatttaacattgtgtaaaaa 2 33 0 cgatttacat 0.940229 -38 aagacgccaaggatttaaaacaaatatgttt 4 99 1 ggatttaaac 0.91005 -48 gatcgaactcggattttactcgggatgtccg 6 144 1 ggatttactc 0.966081 -157 aaaattgtgacgtttttactcgattacctcg 6 240 0 cgttttactc 0.966897 -61 ****** **** Masking position 6 Map Score: 1.0187 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 68 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 tgtcgtgagaaaacggcagcaggagaagat 1 114 0 aaacggcagc 0.962071 -81 tgaatgaataaaacgaatggaacgtgtcgt 1 147 1 aaacgaatgg 0.895382 -48 gacgcctcacaaacgacacgttccattcgt 1 159 0 aaacgacacg 0.992843 -36 gggtcgtccaaaacgacgcctcacaaacga 1 173 0 aaacgacgcc 0.970294 -22 aatctttcggaaaagacacggtaaaaggat 6 117 1 aaaagacacg 0.974255 -184 aagacacggtaaaaggatcgaactcggatt 6 129 1 aaaaggatcg 0.821015 -172 aatcgagtaaaaacgtcacaattttggcga 6 246 1 aaacgtcaca 0.889864 -55 ********** Masking position 3 Map Score: 3.04421 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.26009e-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 8 ********** No masking Map Score: 1.26009e-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 9 ********** No masking Map Score: 1.26009e-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