AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_mgen_mpneu_100.orf -o217_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 RMG05344 25 Mycoplasma #2 RMG04236 300 Mycoplasma #3 RMP00155 300 Mycoplasma_pneumoniae #4 RMP00158 67 Mycoplasma_pneumoniae #5 RMP00161 22 Mycoplasma_pneumoniae Motif number 1 CAAGAAAAAGAGGTATTTTAAAAGCATATG 2 81 1 AGGTATTTTA 0.573519 -220 TTAAAAGAATCAGTATTATTAAAAGAAACT 2 154 0 CAGTATTATT 0.861202 -147 TTTGAGGGTCTGATATTATGTGTCTATTTG 2 210 0 TGATATTATG 0.923504 -91 agtatttatttagtattatgcta 3 4 0 tagtattatg 0.975453 -297 ttaatattattagtatttatttagtattat 3 15 0 tagtatttat 0.911743 -286 taaatactaataatattaagctattagtag 3 26 1 taatattaag 0.922402 -275 agtaggtaaataatattaagataatattat 3 51 1 taatattaag 0.922402 -250 aatattaagataatattatgttaaagaaaa 3 62 1 taatattatg 0.913833 -239 tatagaagattagtatttaatagtaaacgg 3 107 1 tagtatttaa 0.875869 -194 aaaaagaaagtggtatataggaaaatggaa 3 151 0 tggtatatag 0.637049 -150 gctaccaacgtggtattaaaatgtgcccaa 3 186 0 tggtattaaa 0.949013 -115 aataccatcagggtattaagatgctaccaa 3 208 0 gggtattaag 0.888771 -93 aataccctgatggtattaatttcgtcggta 3 221 1 tggtattaat 0.964602 -80 agtattattccggtattatttaccgacgaa 3 241 0 cggtattatt 0.875932 -60 aatatttatttagtattattccggtattat 3 252 0 tagtattatt 0.955309 -49 gcttaaattctaatatttatttagtattat 3 263 0 taatatttat 0.733897 -38 atacagcgctaagtattataa 5 2 0 aagtattata 0.732608 -21 ********** Masking position 5 Map Score: 23.0274 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 172 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 AGAGTTTATCTTTTTCATTAACATCGCCTTT 2 44 0 TTTTCATTAA 0.755438 -257 TGAAAAAGATAAACTCTTTTTAGCAAGAAAA 2 58 1 AACTCTTTTT 0.816288 -243 TGGCTTCTCCATATGCTTTTAAAATACCTCT 2 89 0 AATGCTTTTA 0.907518 -212 AACCCTTTATAAATTCTTTTTTCAGCAATAT 2 120 0 AATTCTTTTT 0.955168 -181 AAGGGTTAGCAGTTTCTTTTAATAATACTGA 2 144 1 ATTTCTTTTA 0.97919 -157 TTAATAATACTGATTCTTTTAATGGTAGTGA 2 162 1 TATTCTTTTA 0.969825 -139 TGAGATAGTTTCTTTAATTAAACCATC 2 284 0 ATTTCTTTAA 0.969825 -17 atagagaaactttttctttaacataatatta 3 72 0 ttttctttaa 0.956432 -229 cctatataccactttctttttcgcggttggg 3 160 1 atttcttttt 0.955169 -141 tccttttataattctttaagtgtttaatt 4 9 1 tattctttaa 0.95643 -59 * ********* Masking position 8 Map Score: 11.4541 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 235 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 GGGAATGGTTTTGTTTTGGTTATCACCACT 2 11 0 TTGTTTTGGT 0.869986 -290 CCTCAAAACCTTATTTATGATGCTAGTGGT 2 233 1 TTATTTATGA 0.689318 -68 ACCTTCTAGGTTATTTTGCTGATGGTTTAA 2 264 1 TTATTTTGCT 0.938614 -37 ttattagtatttatttagtattatgcta 3 9 0 ttatttagta 0.837105 -292 tatcttaatattatttacctactaatagct 3 44 0 ttatttacct 0.958905 -257 gaaaacaaatttgtttgccgtttactatta 3 124 0 ttgtttgccg 0.834334 -177 gcaaacaaatttgttttccattttcctata 3 136 1 ttgttttcca 0.930961 -165 cctgatggtattaatttcgtcggtaaataa 3 226 1 ttaatttcgt 0.620927 -75 tattccggtattatttaccgacgaaattaa 3 236 0 ttatttaccg 0.950847 -65 attctaatatttatttagtattattccggt 3 257 0 ttatttagta 0.837105 -44 ********** Masking position 5 Map Score: 2.77776 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 224 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 ********** No masking Map Score: -3.95472e-13 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 5 ********** No masking Map Score: -3.95472e-13 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 6 ********** No masking Map Score: -3.95472e-13 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