AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_mgen_mpneu_100.orf -o301_mgen_mpneu_100.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 Purged sequences: RMP00371 18 Mycoplasma_pneumoniae Input sequences: #1 RMG00037 202 Mycoplasma #2 RMG04456 38 Mycoplasma #3 RMG03425 36 Mycoplasma #4 RMG04443 58 Mycoplasma #5 RMP00126 20 Mycoplasma_pneumoniae #6 RMP00127 32 Mycoplasma_pneumoniae #7 RMP00368 300 Mycoplasma_pneumoniae Motif number 1 AAAAAACTCATTTTGAAAATAGATTAATTT 1 1 0 TTAAATTTTT 0.974075 -202 CAAAATGAGTTTTTTCAACATTTATTAATTAAAAATTAAT 1 26 1 TTCAAATATT 0.803664 -177 AAGATTCAACTTTAAAAAGCATTAATTTTTAATTAATAAA 1 46 0 TTAAAAATTT 0.958618 -157 TAAAAAAGTATTGAAAAATGAATTAAGATTCAACTTTAAA 1 70 0 TTAAATAATT 0.962898 -133 ACTTTTACTTTTAGAAAAGCGTATTAATTTAATTAAAGAA 1 119 0 TTAAATTTTT 0.974075 -84 AAAGTAAAAGTTAAGAAAAGTACTTTTATTCAAACAAAAA 1 148 1 TTAAATTATT 0.970633 -55 ATCTCTAAAATTATAAAAACGTTTTTGTTTGAATAAAAGT 1 169 0 TTAAATTTTT 0.974003 -34 AGCTAATAATTAAAAGTCTAATTTTTATTGTTAATT 3 11 0 TAAAAAATTT 0.871455 -26 TTTATAAGACTTTTAAAATGTTTAATTATTAATATATAGC 4 28 1 TTAAAAAATT 0.953221 -31 aagttttcagaaaatattagaatttctatcaa 6 5 1 ttgaataatt 0.916477 -28 atgagttgcttgagcaaactttgttcgtttaagttttcgt 7 28 0 tgaaattttt 0.922304 -273 aagcaactcatgcccaaaacccgtaacattaccctagaac 7 57 1 tgaaataatt 0.891294 -244 tgttacgttctaggggaactgttattgtttcccttgttgg 7 96 0 tagaaatttt 0.784975 -205 gaacgtaacattgtagaacgtagtttctttggcgaattag 7 126 1 ttgaattttt 0.940782 -175 ttagatcagttagagaaagaacaatcaattcgcaattttt 7 162 1 taaaaatatt 0.883657 -139 caactccaagttcataaaccgcaaaccgttgatctaaca 7 272 1 ttaaaaagtt 0.84405 -29 ** *** ** *** Masking position 8 Map Score: 20.2874 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 439 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 CATTTATTAATTAAAAATTAATGCTTTTTA 1 44 1 TTAAAAATTA 0.946343 -159 AGATTCAACTTTAAAAAGCATTAATTTTTA 1 55 0 TTAAAAAGCA 0.869946 -148 ATAGGAAGCCTAAAAAAGTATTGAAAAATG 1 90 0 TAAAAAAGTA 0.963785 -113 AATACGCTTTTCTAAAAGTAAAAGTTAAGA 1 134 1 TCTAAAAGTA 0.956644 -69 TTTTTGTTTGAATAAAAGTACTTTTCTTAA 1 158 0 AATAAAAGTA 0.90442 -45 AACTATCTCTAAAATTATAAAAACGTT 1 186 0 TCTAAAATTA 0.908987 -17 GAATATTAGATAAATAAGTATATTATC 2 8 0 TAAATAAGTA 0.856315 -31 AATTAACAATAAAAATTAGACTTTTAAT 3 9 1 ATAAAAATTA 0.86246 -28 AGCTAATAATTAAAAGTCTAATTTTTAT 3 19 0 ATTAAAAGTC 0.827621 -18 TTAAAAGTCTTATAAAATTAAATAATCGAA 4 14 0 TATAAAATTA 0.923352 -45 AATTAAACATTTTAAAAGTCTTATAAAATT 4 25 0 TTTAAAAGTC 0.931054 -34 AGCTATATATTAATAATTAAACATTTTAA 4 40 0 TTAATAATTA 0.798013 -19 ********** Masking position 6 Map Score: 13.7357 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 262 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 TTTTAGAAAAGCGTATTAATTTAATTAAAGA 1 120 0 GCGTATAATT 0.945648 -83 tacgaaatagatagaattag 5 9 0 acgaatagat 0.945197 -12 agtttctttggcgaattagatcagttagaga 7 147 1 gcgaatagat 0.989012 -154 gaaaaaaattgcgaattgattgttctttctc 7 174 0 gcgaatgatt 0.984076 -127 gagttggttagcgaagtggtttaacacatca 7 247 0 gcgaatggtt 0.992869 -54 ***** ***** Masking position 5 Map Score: 3.07047 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CATTTTGAAAATAGATTAATTT 1 3 0 ATAGATTAAT 0.83286 -200 TTTTTTCAACATTTATTAATTAAAAATTAA 1 35 1 ATTTATTAAT 0.713017 -168 TTTATTAATTAAAAATTAATGCTTTTTAAA 1 46 1 AAAAATTAAT 0.713998 -157 ATCTTAATTCATTTTTCAATACTTTTTTAG 1 81 1 ATTTTTCAAT 0.793192 -122 TAGGCTTCCTATTCTTTAATTAAATTAATA 1 108 1 ATTCTTTAAT 0.890757 -95 TAATTCGATTATTTAATTTTATAAGAC 4 8 1 ATTATTTAAT 0.711427 -51 AGACTTTTAAAATGTTTAATTATTAATATA 4 34 1 AATGTTTAAT 0.863874 -25 AGCTATATATTAATAATTAAACAT 4 45 0 ATATATTAAT 0.895683 -14 ********** Masking position 8 Map Score: 4.50671 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 143 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAAAGTACTTTTATTCAAACAAAAACGTTTT 1 163 1 TTATTCAACA 0.965301 -40 TATTTATCTAATATTCCAACATAATCC 2 22 1 ATATTCAACA 0.923684 -17 CTATATATTAATAATTAAACATTTTAAAAGT 4 36 0 ATAATTAACA 0.745495 -23 tgacgaaaacttaaacgaacaaagtttgctc 7 26 1 ttaaacaaca 0.957596 -275 cgaacaaagtttgctcaagcaactcatgccc 7 41 1 ttgctcagca 0.896793 -260 aacattaccctagaaccaacaagggaaacaa 7 81 1 tagaacaaca 0.849886 -220 ccgcaaaccgttgatctaaca 7 290 1 ttgatcaaca 0.984298 -11 ****** **** Masking position 8 Map Score: 1.55709 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 93 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: -1.36892e-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 7 ********** No masking Map Score: -1.36892e-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: -1.36892e-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