AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i266_mgen_mpneu_300.orf -o266_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 = 0.36 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 taaaatgggaatttttcccattaatagactag 1 43 0 atttcccatt 0.878328 -152 atctcacgattttttacacaatgttaaatcgt 2 23 1 ttttcacaat 0.903541 -48 tcgtactgaaatcgtccccaattaaacaatat 4 47 1 atgtcccaat 0.953744 -100 ttttatggttttctttgccaaaataacttt 4 127 1 ttttgccaaa 0.984207 -20 aaatagagaattggtggccaaacttatcaatt 6 46 1 ttgtgccaaa 0.953744 -255 taactcgacgattttgccgaaaaatcacagaa 6 77 1 atttccgaaa 0.969428 -224 aaatcacagaatattcgcgaatctttcggaaa 6 98 1 atttgcgaat 0.969587 -203 ttttaccgtgtcttttccgaaagattcgcgaa 6 111 0 tcttccgaaa 0.845531 -190 aaacccccgaatgttcgccaataattgtaaca 6 178 1 atttgccaat 0.98416 -123 tttgttacaattattggacaattttgttacaa 6 202 0 ttttgacaat 0.903923 -99 aaacgtcacaattttggcgaaatttcgaatat 6 256 1 atttgcgaaa 0.969428 -45 tttcgaaatttttttccgcaaatt 6 287 1 ttttcgcaaa 0.888029 -14 ** ** ****** Masking position 10 Map Score: 14.0186 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 69 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 gatcttctcctgctgccgttttctcacgacat 1 113 1 tgctgctttt 0.907106 -82 ccttggcgtcttctgcgtttattcgcacttta 4 79 0 ttctggttat 0.932684 -68 aacaaatatgttttatggttttctttgccaaa 4 117 1 ttttagtttt 0.955441 -30 gtattctgttttttatgtttttcgtaagtcgc 6 14 1 ttttagtttt 0.955441 -287 tatcaattaactcgacgattttgccgaaaaat 6 70 1 ctcgagtttt 0.904034 -231 ttcgcgaatattctgtgatttttcggcaaaat 6 87 0 ttctggtttt 0.974982 -214 aaaatccgagttcgatccttttaccgtgtctt 6 129 0 ttcgactttt 0.943548 -172 ttggcgaacattcgggggttttgccggacatc 6 167 0 ttcgggtttt 0.978328 -134 tggacaattttgttacaattattggcgaacat 6 188 0 tgttaattat 0.638931 -113 cggaaaattttgttacaattattggacaattt 6 210 0 tgttaattat 0.638931 -91 tcgccaaaattgtgacgtttttactcgattac 6 244 0 tgtgagtttt 0.953345 -57 tttcgaatatttcgaaatttttttccgcaaat 6 278 1 ttcgaatttt 0.939333 -23 ***** * **** Masking position 9 Map Score: 11.4524 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 214 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 acgaatggaacgtgtcgtttgtgaggcgtcgtt 1 159 1 cgtgtctttg 0.984736 -36 tcgtttgtgaggcgtcgttttggacgacccac 1 173 1 ggcgtctttg 0.99024 -22 ttaaatccttggcgtcttctgcgtttattcgca 4 84 0 ggcgtctctg 0.96422 -63 tatcaattaactcgacgattttgccgaaaaatc 6 70 1 ctcgacattg 0.948542 -231 ccgaaagattcgcgaatattctgtgatttttcg 6 94 0 cgcgaaattg 0.974193 -207 atccttttaccgtgtcttttccgaaagattcgc 6 114 0 cgtgtctttg 0.984735 -187 tacaattattggcgaacattcgggggttttgcc 6 174 0 ggcgaaattg 0.958689 -127 cgagtaaaaacgtcacaattttggcgaaatttc 6 249 1 cgtcacattg 0.914379 -52 ****** *** * Masking position 10 Map Score: 6.6977 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 4 aaaaatggttaagtcctgaagttccacgga 1 11 1 aagtcctgaa 0.964151 -184 ttttctcacgacatcctgaatgaataaaac 1 131 1 acatcctgaa 0.964151 -64 attgtgtaaaaaatcgtgagattatgaaac 2 15 0 aaatcgtgag 0.980774 -56 acacaatgttaaatcgtaagaagttggaga 2 38 1 aaatcgtaag 0.945166 -33 tgtttttcgtaagtcgcaaatagagaattg 6 29 1 aagtcgcaaa 0.882825 -272 gttttgccggacatcccgagtaaaatccga 6 152 0 acatcccgag 0.972269 -149 ********** Masking position 4 Map Score: 2.94482 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 5 taatgggaaaaattcccattttaccagtagt 1 52 1 aattccattt 0.919073 -143 cgattgtgaatattctttacttaatcaaatt 1 83 0 tattcttact 0.838795 -112 tcaataattctattctccaacttctt 2 55 0 aattctttct 0.911378 -16 tttcagtacgaattccgatctgaatgatata 4 27 0 aattccatct 0.900342 -120 cttctgcgtttattcgcactttaatattgtt 4 71 0 tattcgactt 0.846105 -76 acggtattctgttttttatgttttt 6 5 1 tattcttttt 0.910045 -296 tttggccaccaattctctatttgcgacttac 6 37 0 aattcttatt 0.88558 -264 aaaaggatcgaactcggattttactcgggat 6 139 1 aactcgattt 0.7913 -162 aatttcgaaatattcgaaatttcgccaaaat 6 266 0 tattcgaatt 0.898827 -35 ****** **** Masking position 4 Map Score: 2.57952 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 99 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 atttaacattgtgtaaaaaatcgtgagatt 2 22 0 gtgtaaaaaa 0.913122 -49 cgccaaggatttaaaacaaatatgttttat 4 103 1 ttaaaacaaa 0.876441 -44 tcgccaataattgtaacaaaattgtccaat 6 192 1 ttgtaacaaa 0.986116 -109 tgtccaataattgtaacaaaattttccgag 6 214 1 ttgtaacaaa 0.986116 -87 ********** Masking position 5 Map Score: 0.874809 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 13 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 taagtaaagaatattcacaatcgatcttct 1 91 1 atattcacaa 0.913769 -104 atatacataaatatacataat 4 2 0 atatacataa 0.977599 -145 gatctgaatgatatacataaatatacataa 4 12 0 atatacataa 0.977599 -135 gcgacttacgaaaaacataaaaaacagaat 6 16 0 aaaaacataa 0.877382 -285 ********** Masking position 7 Map Score: 0.497754 Number of sites scoring better than the average of aligned sites = 1 Number in coding regions = 1 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 Motif number 10 ********** 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