AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_mgen_mpneu_100.orf -o216_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 Input sequences: #1 RMG04129 91 Mycoplasma #2 RMG03233 300 Mycoplasma #3 RMP00094 55 Mycoplasma_pneumoniae #4 RMP00182 150 Mycoplasma_pneumoniae #5 RMP00183 81 Mycoplasma_pneumoniae #6 RMP00184 65 Mycoplasma_pneumoniae Motif number 1 ATTGCAATATTGTTTTATTAAAACAT 1 7 1 ATATTGTTTT 0.907924 -85 TTTTATTAAAACATTATTTAATAATAAATA 1 23 1 ACATTATTTA 0.959896 -69 ACATGATTTTTAATTATTTATTATTAAATA 1 37 0 TAATTATTTA 0.859975 -55 ATTGCTTTGAACATGATTTTTAATTATTTA 1 47 0 ACATGATTTT 0.859967 -45 ATGCTTGATAACATTGCTTTGAACATGATT 1 59 0 ACATTGCTTT 0.849024 -33 TAAGGCGTTAAACTTGTTTTCAGAATTAAT 2 25 0 AACTTGTTTT 0.917009 -276 GTTGTTTAGCATATTATTTTAAGGCGTTAA 2 44 0 ATATTATTTT 0.955117 -257 AACAAAGTCTTAATTATTTTCTGTTGTTTA 2 66 0 TAATTATTTT 0.909516 -235 TAAAGATAAGAACTTATTTATCTAAAAAAA 2 101 1 AACTTATTTA 0.931832 -200 ATCTGCAAACTCATTATTTTTTTAGATAAA 2 117 0 TCATTATTTT 0.946069 -184 CAATCTTATTTTGACCAATGAT 2 289 0 ATCTTATTTT 0.951191 -12 ggtgctttaattatttatttttttatt 3 39 0 taattattta 0.859975 -17 taatcttatttttaccaatcaa 5 70 0 atcttatttt 0.951191 -12 aggtagtttgaccttacttaaacgcttcga 6 44 1 accttactta 0.863752 -22 ********** Masking position 4 Map Score: 18.622 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 222 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TTATTTAATAATAAATAATTAAAAATCATGTTCAA 1 36 1 ATATTAAAAA 0.966728 -56 TGTTTTCAGAATTAATGATGAAATAGTTGT 2 6 0 ATATGAAATA 0.906199 -295 ACTTTGTTAGATATAAAGATAAGAACTTATTTATC 2 88 1 ATAATAAGAA 0.922875 -213 ATAAGAACTTATTTATCTAAAAAAATAATGAGTTT 2 106 1 ATAAAAAAAA 0.860866 -195 TGCAGATGACATGCAAAATGAAAATCGGGCCTTAT 2 140 1 ATATGAAAAT 0.758881 -161 AATTTATTAACTAGACGAATAAAAAATAGCTGATT 2 185 1 CTAATAAAAA 0.965992 -116 GTTCTATTTTATCTATGCTTAAGAATAACTTAATC 2 216 0 ATATTAAGAA 0.909665 -85 CATAGATAAAATAGAACTTTAAAAAGTTATAATTA 2 234 1 ATATTAAAAA 0.966728 -67 TAATTAGCCGCTTTATTAAGAAAAAAATCATTGGT 2 263 1 CTAAGAAAAA 0.963717 -38 ctagctttatctatacgtagaaataataaaaaaat 3 15 1 ctaagaaata 0.904254 -41 cgtagaaataataaaaaaataaataattaaagcac 3 30 1 ataataaata 0.924674 -26 taaaaggagacttgattggtaaaaataagatta 5 59 1 ctagtaaaaa 0.897331 -23 ** * ******* Masking position 5 Map Score: 10.3201 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 188 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 AAAAATCATTGGTCAAAATAAGATTG 2 285 1 GGTCAAAATA 0.990926 -16 agttaggtaaaactacctaacggca 5 6 1 ggtaaaacta 0.98705 -76 agacttgattggtaaaaataagatta 5 66 1 ggtaaaaata 0.986034 -16 gttcaaagagggttaaaacagtgattttca 6 14 0 ggttaaaaca 0.947347 -52 gtttaagtaaggtcaaactacctgttcaaa 6 37 0 ggtcaaacta 0.991589 -29 ********** Masking position 5 Map Score: 7.17181 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 18 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 4 ATCAAGCATCGTTATGCGCACG 1 80 1 GTTATGCGCA 0.968563 -12 CATTTTGCATGTCATCTGCAAACTCATTAT 2 130 0 GTCATCTGCA 0.883179 -171 AAAAGTTATAATTAGCCGCTTTATTAAGAA 2 255 1 ATTAGCCGCT 0.96236 -46 gtttctaacgatcttgcgctttgctattcc 4 79 1 atcttgcgct 0.942009 -72 tctttgcgctgttttccgctgcttatgtct 4 117 1 gttttccgct 0.983319 -34 gcaatgtataattatccgctttattttaaa 5 33 1 attatccgct 0.985904 -49 ********** Masking position 2 Map Score: 3.68678 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 17 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ATTGCAATATTGTTTTATTAAAACA 1 6 1 AATATTGTTT 0.650488 -86 TGCTTTGAACATGATTTTTAATTATTTATT 1 45 0 ATGATTTTTA 0.754031 -47 GAAAATAATTAAGACTTTGTTAGATATAAA 2 75 1 AAGACTTTGT 0.920043 -226 CTGCAAACTCATTATTTTTTTAGATAAATA 2 115 0 ATTATTTTTT 0.83286 -186 GCGGCTAATTATAACTTTTTAAAGTTCTAT 2 244 0 ATAACTTTTT 0.868695 -57 ATTTTGACCAATGATTTTTTTCTTAATAAA 2 274 0 ATGATTTTTT 0.956111 -27 ttgaatcgaaaagactgtttctaacgatct 4 63 1 aagactgttt 0.950165 -88 ctttgctattccgacttttttctttgcgct 4 97 1 ccgacttttt 0.766134 -54 tccgctgcttatgtctttgtggaccaaatt 4 131 1 atgtctttgt 0.755426 -20 gtgtgaaaatcactgttttaaccctctt 6 9 1 atcactgttt 0.874811 -57 ********** Masking position 6 Map Score: 3.04419 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 280 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 AAATAATGTTTTAATAAAACAATATTGCAA 1 12 0 TTAATAAAAC 0.85894 -80 AAAACATTATTTAATAATAAATAATTAAAA 1 30 1 TTAATAATAA 0.916765 -62 ATTAACTAGACGAATAAAAAATAGCTGATT 2 190 1 CGAATAAAAA 0.894977 -111 TTATCTATGCTTAAGAATAACTTAATCAGC 2 213 0 TTAAGAATAA 0.932604 -88 AATAAAGCGGCTAATTATAACTTTTTAAAG 2 250 0 CTAATTATAA 0.755692 -51 AGCCGCTTTATTAAGAAAAAAATCATTGGT 2 268 1 TTAAGAAAAA 0.95738 -33 atacgtagaaataataaaaaaataaataat 3 27 1 ataataaaaa 0.874514 -29 gaaaacagcgcaaagaaaaaagtcggaata 4 103 0 caaagaaaaa 0.849302 -48 ********** Masking position 4 Map Score: 3.56541 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 159 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ACAACTATTTCATCATTAAT 2 1 1 ACAACTATTT 0.90108 -300 ATTAATTCTGAAAACAAGTTTAACGCCTTA 2 25 1 AAAACAAGTT 0.746952 -276 AATAACTTAATCAGCTATTTTTTATTCGTC 2 198 0 TCAGCTATTT 0.935271 -103 acgtatagataaagctagtttc 3 3 0 aaagctagtt 0.972532 -53 tacattgccgttaggtagttttacctaact 5 11 0 ttaggtagtt 0.849066 -71 ccctctttgaacaggtagtttgaccttact 6 32 1 acaggtagtt 0.976581 -34 ********** Masking position 7 Map Score: 0.526042 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 144 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: -4.67335e-15 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: -4.67335e-15 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: -4.67335e-15 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