AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_mgen_mpneu_300.orf -o299_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 tagtctattaatgggaaaaattcccattttac 1 44 1 atgggaaatt 0.895807 -151 cgatttaacattgtgtaaaaaatcgtgagatt 2 22 0 ttgtgaaaaa 0.8385 -49 tattgtttaattggggacgatttcagtacgaa 4 46 0 ttgggacatt 0.962582 -101 aaagttattttggcaaagaaaaccataaaac 4 126 0 ttggcaaaaa 0.973375 -21 attgataagtttggccaccaattctctatttg 6 45 0 ttggcacaat 0.972701 -256 ctcgacgattttgccgaaaaatcacagaatat 6 80 1 ttgccaaaat 0.978552 -221 ttccgaaagattcgcgaatattctgtgatttt 6 97 0 ttcgcaaatt 0.960792 -204 gttacaattattggcgaacattcgggggtttt 6 177 0 ttggcaaatt 0.990369 -124 tgtaacaaaattgtccaataattgtaacaaaa 6 203 1 ttgtcaaaat 0.952939 -98 tattcgaaatttcgccaaaattgtgacgtttt 6 255 0 ttcgcaaatt 0.960792 -46 cggaaaaaaatttcgaaatattcgaaatttcg 6 273 0 tttcgaaatt 0.742084 -28 aatttgcggaaaaaaatttcgaaat 6 286 0 ttgcgaaaaa 0.92131 -15 ***** ** *** Masking position 7 Map Score: 14.7935 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 77 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 aaaaatggttaagtcctgaagtt 1 2 1 aaaaggtaag 0.846018 -193 atgtcgtgagaaaacggcagcaggagaagatc 1 113 0 aaaaggcgca 0.899754 -82 cattgtgtaaaaaatcgtgagattatgaaact 2 14 0 aaaacgtaga 0.951545 -57 tacacaatgttaaatcgtaagaagttggagaa 2 37 1 taaacgtaga 0.694616 -34 taaagtgcgaataaacgcagaagacgccaagg 4 79 1 ataacgcgaa 0.874455 -68 tttggcaaagaaaaccataaaacatatttgtt 4 117 0 aaaacataaa 0.943756 -30 gcgacttacgaaaaacataaaaaacagaatac 6 14 0 aaaacataaa 0.943756 -287 atttttcggcaaaatcgtcgagttaattgata 6 70 0 aaaacgtgag 0.962026 -231 attttgccgaaaaatcacagaatattcgcgaa 6 87 1 aaaacacgaa 0.956698 -214 aagacacggtaaaaggatcgaactcggatttt 6 129 1 aaaagatgaa 0.903123 -172 gatgtccggcaaaacccccgaatgttcgccaa 6 167 1 aaaacccgaa 0.9087 -134 gtaatcgagtaaaaacgtcacaattttggcga 6 244 1 aaaacgtaca 0.951545 -57 **** *** *** Masking position 4 Map Score: 10.2663 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 163 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 tactactggtaaaatgggaatttttcccatt 1 53 0 aaaatggaat 0.914082 -142 taatttgattaagtaaagaatattcacaatc 1 82 1 aagtaagaat 0.774755 -113 tcctgaatgaataaaacgaatggaacgtgtc 1 144 1 ataaacgaat 0.855847 -51 aaacaatattaaagtgcgaataaacgcagaa 4 70 1 aaagtcgaat 0.954343 -77 gaaaaacataaaaaacagaataccgt 6 6 0 aaaaaagaat 0.936393 -295 cgtaagtcgcaaatagagaattggtggccaa 6 36 1 aaataagaat 0.936393 -265 catcccgagtaaaatccgagttcgatccttt 6 140 0 aaaatcgagt 0.915549 -161 aattttggcgaaatttcgaatatttcgaaat 6 265 1 aaattcgaat 0.978903 -36 ttgcggaaaaaaatttcgaaatattcgaaat 6 277 0 aaattcgaaa 0.87973 -24 ***** ***** Masking position 9 Map Score: 5.82944 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 21 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 atcttctcctgctgccgttttctcacgaca 1 114 1 gctgccgttt 0.946452 -81 acgaatggaacgtgtcgtttgtgaggcgtc 1 159 1 cgtgtcgttt 0.99156 -36 tcgtttgtgaggcgtcgttttggacgaccc 1 173 1 ggcgtcgttt 0.993 -22 ttaaatccttggcgtcttctgcgtttattc 4 87 0 ggcgtcttct 0.946027 -60 atccttttaccgtgtcttttccgaaagatt 6 117 0 cgtgtctttt 0.975427 -184 tcgccaaaattgtgacgtttttactcgatt 6 246 0 tgtgacgttt 0.929032 -55 ********** Masking position 8 Map Score: 4.13778 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 3 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 accaattctctatttgcgacttacgaaaaa 6 31 0 tatttgcgac 0.952141 -270 tgttcgccaataattgtaacaaaattgtcc 6 189 1 taattgtaac 0.98227 -112 aattgtccaataattgtaacaaaattttcc 6 211 1 taattgtaac 0.98227 -90 aatttcgccaaaattgtgacgtttttactc 6 250 0 aaattgtgac 0.97136 -51 ********** Masking position 5 Map Score: 1.60631 Number of sites scoring better than the average of aligned sites = 1 Number in coding regions = 0 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 gagaattggtggccaaacttatcaattaac 6 51 1 ggccaaactt 0.975056 -250 acagaatattcgcgaatctttcggaaaaga 6 103 1 cgcgaatctt 0.949257 -198 tacaattattggcgaacattcgggggtttt 6 177 0 ggcgaacatt 0.946079 -124 tacaattattggacaattttgttacaatta 6 199 0 ggacaatttt 0.946041 -102 cgattacctcggaaaattttgttacaatta 6 221 0 ggaaaatttt 0.865371 -80 tcacaattttggcgaaatttcgaatatttc 6 261 1 ggcgaaattt 0.981394 -40 ********** Masking position 5 Map Score: 1.4732 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 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