AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i195_mgen_mpneu_300.orf -o195_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 RMP00490 206 Mycoplasma_pneumoniae #2 RMP00491 129 Mycoplasma_pneumoniae #3 RMP00492 300 Mycoplasma_pneumoniae #4 RMP00495 140 Mycoplasma_pneumoniae #5 RMP00496 62 Mycoplasma_pneumoniae #6 RMP00500 243 Mycoplasma_pneumoniae Motif number 1 tttgaaatcgtaattgttagatctacttataatgt 1 81 1 tattgtttta 0.866782 -126 cggttttttctgttttttaaatctaccacttttat 1 138 1 tgttttttta 0.928314 -69 tctaccacttttatttttgtgtttaccgactcttt 1 159 1 ttttttttta 0.955561 -48 caattgttgttaattttacagctaaaga 1 189 0 ttttgtttta 0.957083 -18 tgagatctcttggtcgttttctgttgatcttcatt 2 77 1 tgtcgttttt 0.785604 -53 cgaaagttcgtactttttaataattaagggattat 3 120 1 tatttttatt 0.771005 -181 gattatctactgctttttaaatttttcaaaaggct 3 149 1 tgtttttttt 0.941603 -152 gcaaacaagtttgtttttccacgttcattagcctt 3 178 0 tttttttctt 0.807979 -123 tgacgagttattgttgtaccctattggaatttctt 3 228 1 ttttgtattt 0.676807 -73 ctattggaatttcttttttcctttagtcattctcc 3 248 1 ttttttttta 0.955561 -53 gacgataattttttctttaacattattatttttac 4 18 1 tttctttata 0.670144 -123 tttaacattattatttttacttgttcaaaaatggt 4 33 1 tttttttttt 0.96387 -108 ggttaaattattgattttaattttaggaataatta 4 65 1 ttatttttta 0.619375 -76 tcaacaataatgattgttaattattcctaaaatta 4 82 0 tgttgttttt 0.943585 -59 ttaacaatcattattgttgaaagttgtattgattt 4 97 1 ttttgttatt 0.922696 -44 cattagacaatattttttccctattttac 5 5 0 tatttttttt 0.886462 -58 gtgattaatttttttgttagaatttggatcatga 5 39 1 ttttgttatt 0.922696 -24 cgagaaactcttttttttatcactagaaaccacca 6 155 0 tttttttata 0.902679 -89 ** ***** * ** Masking position 7 Map Score: 22.0664 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 445 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 ttacaaagactatctaatttcggttttttctg 1 118 1 tttaatttcg 0.969474 -89 ttttatccgcaaggtcatttcggtttatttta 2 17 0 agtcatttcg 0.953765 -113 gctaatttcgtagattagttcgtgcaaatcgt 6 11 0 tgttagttcg 0.928498 -233 aaaaatttagtggctaatttcgtagattagtt 6 23 0 tgtaatttcg 0.992849 -221 tgaaacatggttgacgatttcggaaaaaattt 6 47 0 tgcgatttcg 0.943225 -197 tcgtcaaccatgtttcatttcgaaaacacgaa 6 62 1 tttcatttcg 0.963409 -182 cacgacatgttcggtaatttcgtgttttcgaa 6 80 0 tgtaatttcg 0.992849 -164 caatcttaatttgttaaattcgagaaactctt 6 178 0 tgtaaattcg 0.966472 -66 * * ******** Masking position 7 Map Score: 8.26265 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 3 ttgctttggaaagtttgtttgaaatcgtaa 1 64 1 aagtttgttt 0.973598 -143 ttataagtgaaagtttttatccgcaaggtc 2 33 0 aagtttttat 0.828003 -97 tttcacttataagtctgttcttagtttgag 2 51 1 aagtctgttc 0.903097 -79 ttctatgaataattttgttttccttccggt 3 64 0 aattttgttt 0.912319 -237 cacttaatttaagtttctatgaataatttt 3 78 0 aagtttctat 0.838626 -223 ttaagtggtgaagttagttcgaaagttcgt 3 101 1 aagttagttc 0.886381 -200 gttagttcgaaagttcgtactttttaataa 3 113 1 aagttcgtac 0.894468 -188 aaacgcaaacaagtttgtttttccacgttc 3 187 0 aagtttgttt 0.973598 -114 accctattggaatttcttttttcctttagt 3 245 1 aatttctttt 0.594536 -56 gtttgaaaattttcttctcaaactgtt 3 284 0 aattttcttc 0.831656 -17 attagccactaaattttttccgaaatcgtc 6 37 1 aaattttttc 0.644278 -207 ********** Masking position 2 Map Score: 8.66125 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 221 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 aagattcagtttagtaaagactaatgttgct 1 38 1 ttgtaaagac 0.943199 -169 ttagatagtctttgtaaaaacattataagta 1 104 0 ttgtaaaaac 0.965879 -103 gatttaaaaaacagaaaaaaccgaaattaga 1 130 0 acgaaaaaac 0.90312 -77 agctaaagagtcggtaaacacaaaaataaaa 1 167 0 tcgtaaacac 0.98924 -40 gttgacgatttcggaaaaaatttagtggcta 6 39 0 tcgaaaaaat 0.853464 -205 catgtttcatttcgaaaacacgaaattaccg 6 70 1 ttgaaaacac 0.971579 -174 actatcgatgtcggtaaacacgacaggtcca 6 221 1 tcgtaaacac 0.98924 -23 ** ******** Masking position 6 Map Score: 5.71195 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 20 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 tttaaatctaccacttttatttttgtgtttac 1 153 1 ccactttttt 0.967919 -54 ttcatttaaaccactttaataagtatggatat 2 106 1 ccacttttaa 0.936583 -24 ataaacggttctactttccttactccaataat 3 22 1 ctacttttta 0.949622 -279 cttccggtaactacttatattattggagtaag 3 40 0 ctacttatta 0.949623 -261 actaacttcaccacttaatttaagtttctatg 3 87 0 ccacttatta 0.988009 -214 gtttgtttttccacgttcattagccttttgaa 3 173 0 ccacgtttta 0.979022 -128 acgaaattagccactaaattttttccgaaatc 6 32 1 ccactaattt 0.843916 -212 ctagaaaccaccacgtaaactaggggaggtgg 6 136 0 ccacgtacta 0.925349 -108 ******* *** Masking position 3 Map Score: 6.18746 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 34 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 aaactgaatcttttgagaaactcctaaata 1 20 0 ttttgagaaa 0.897136 -187 tggaaagtttgtttgaaatcgtaattgtta 1 70 1 gtttgaaatc 0.942561 -137 ttttttctgttttttaaatctaccactttt 1 141 1 tttttaaatc 0.55665 -66 tctgttcttagtttgagatctcttggtcgt 2 64 1 gtttgagatc 0.922861 -66 aagtacgaactttcgaactaacttcaccac 3 105 0 tttcgaacta 0.646349 -196 ttcattagccttttgaaaaatttaaaaagc 3 160 0 ttttgaaaaa 0.902403 -141 tctcctaacagtttgagaagaaaattttca 3 278 1 gtttgagaag 0.833089 -23 gtttgaaaattttcttctca 3 291 0 gtttgaaaat 0.824138 -10 atttaaccatttttgaacaagtaaaaataa 4 43 0 ttttgaacaa 0.860577 -98 ccatgtttcatttcgaaaacacgaaattac 6 69 1 tttcgaaaac 0.882928 -175 ********** Masking position 6 Map Score: 3.99654 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 347 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: 2.12695e-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: 2.12695e-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: 2.12695e-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