AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i089_mgen_mpneu_100.orf -o089_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 RMG01413 173 Mycoplasma #2 RMG01415 125 Mycoplasma #3 RMP00021 23 Mycoplasma_pneumoniae #4 RMP00022 300 Mycoplasma_pneumoniae Motif number 1 GAAAAATTGGGTAACAATGG 1 1 0 GTAACAATGG 0.902393 -173 GGGAAGTGGTTGAAAAATTGGGTAACAATG 1 12 0 TGAAAAATTG 0.945629 -162 TTGTTAAAAAATAACAATTTATAGAGTGGG 1 40 0 ATAACAATTT 0.682675 -134 TTGTTATTTTTTAACAATTTGAACAATTAA 1 53 1 TTAACAATTT 0.944232 -121 TAATAACCACTTAAACATTG 2 1 0 TTAAACATTG 0.886097 -125 aacacgtgatttaaaactgtggaaccaaaa 4 58 0 ttaaaactgt 0.884283 -243 gcgagaatcgttaacacgtgatttaaaact 4 70 0 ttaacacgtg 0.910481 -231 tttttgccaattaaaaatcgttaaattcat 4 121 0 ttaaaaatcg 0.923291 -180 tttaaccggattaaaactgggattttgatt 4 154 0 ttaaaactgg 0.959502 -147 ttttcatctctaaaaaatttttttctttcg 4 187 0 taaaaaattt 0.672845 -114 tttttagagatgaaaaatgggggatttatt 4 201 1 tgaaaaatgg 0.94208 -100 ttaaatagatttaacaagtggcatcaatca 4 266 1 ttaacaagtg 0.947898 -35 ********** Masking position 4 Map Score: 10.6008 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 401 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 TAGAGTGGGGAAGTGGTTGAAAAATTGGGT 1 19 0 AAGTGGTTGA 0.893525 -155 GTTAAAAAATAACAATTTATAGAGTGGGGA 1 38 0 AACAATTTAT 0.600296 -136 GTTATTTTTTAACAATTTGAACAATTAAAT 1 55 1 AACAATTTGA 0.789377 -119 TCTCAAAAACAACCAGTTAAGCTTGTTAGC 1 116 0 AACCAGTTAA 0.924691 -58 CAATGTTTAAGTGGTTATTAAAACATCA 2 9 1 AAGTGGTTAT 0.770815 -117 ACTGGAGGCTATGAGGTTGATTATGATGTT 2 32 0 ATGAGGTTGA 0.920336 -94 ccagaacggtatgtagttaatttacgaact 4 26 1 atgtagttaa 0.961715 -275 tctcattttgatgaatttaacgatttttaa 4 111 1 atgaatttaa 0.902202 -190 cccagttttaatccggttaaagggcgaaag 4 163 1 atccggttaa 0.932911 -138 atctatttaaatgtaattaacccttaatta 4 246 0 atgtaattaa 0.737195 -55 cacttgttaaatctatttaaatgtaattaa 4 256 0 atctatttaa 0.902238 -45 agtggcatcaatcaagttaaatccatttc 4 282 1 atcaagttaa 0.961713 -19 ********** Masking position 1 Map Score: 10.581 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 320 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TTTGGTTTTAAAAACCCTTTCATCTCAAAAA 1 137 0 AAAACCCTTC 0.983914 -37 AAGGGTTTTTAAAACCAAATTTCTCGCTCGG 1 149 1 AAAACCAATT 0.899202 -25 TACCGTTCTGAAAGCCCTTTTTGTTGTTCCT 2 83 1 AAAGCCCTTT 0.944458 -43 ctgtggaaccaaaactagttcgtaaattaac 4 41 0 aaaactattc 0.951645 -260 gcggacatataaatctcattttgatgaattt 4 98 1 aaatctcttt 0.950388 -203 ttaattggcaaaaacttaatcaaaatcccag 4 137 1 aaaacttatc 0.686515 -164 aacttaatcaaaatcccagttttaatccggt 4 149 1 aaatcccgtt 0.922429 -152 gccacttgttaaatctatttaaatgtaatta 4 257 0 aaatctatta 0.790385 -44 caatcaagttaaatccatttc 4 290 1 aaatccattc 0.974748 -11 ******* *** Masking position 3 Map Score: 5.80777 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 220 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 ACTCTATAAATTGTTATTTTTTAACAATTT 1 43 1 TTGTTATTTT 0.887972 -131 TACATTAATATAGTTATTTTTTGCAATTTA 1 80 0 TAGTTATTTT 0.919073 -94 TTAAGCTTGTTAGCTAAATTTACATTAATA 1 100 0 TAGCTAAATT 0.912736 -74 actttcgtcaaatttggtcgtta 3 5 1 tcgtcaaatt 0.918646 -19 gaacggtatgtagttaatttacgaactagt 4 29 1 tagttaattt 0.962981 -272 caattaaaaatcgttaaattcatcaaaatg 4 114 0 tcgttaaatt 0.973468 -187 ttgatgccacttgttaaatctatttaaatg 4 263 0 ttgttaaatc 0.879515 -38 ********** Masking position 6 Map Score: 4.9606 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 89 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TCCCCACTCTATAAATTGTTATTTTTTAAC 1 38 1 ATAAATTGTT 0.708598 -136 TTTTTTGCAATTTAATTGTTCAAATTGTTA 1 64 0 TTTAATTGTT 0.955141 -110 CAATGTTTAAGTGGTTATTAAAACAT 2 7 1 TTAAGTGGTT 0.865579 -119 ATGAGGTTGATTATGATGTTTTAATAACCA 2 22 0 TTATGATGTT 0.886094 -104 TGAAAGCCCTTTTTGTTGTTCCTCCCTGCG 2 91 1 TTTTGTTGTT 0.954886 -35 tttcgtcaaatttggtcgtta 3 13 1 tttggtcgtt 0.842233 -11 tctggcggctttttaatgtt 4 1 0 ttttaatgtt 0.857345 -300 gggattttgattaagtttttgccaattaaa 4 136 0 ttaagttttt 0.706562 -165 gggggatttattggattgttgatgtgttaa 4 219 1 ttggattgtt 0.839716 -82 gttaaatctatttaaatgtaattaaccctt 4 251 0 tttaaatgta 0.575662 -50 ********** Masking position 2 Map Score: 3.29792 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 508 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 ********** No masking Map Score: 1.63668e-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: 1.63668e-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: 1.63668e-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