AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_mgen_mpneu_300.orf -o217_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 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 TTAAAAGAATCAGTATTATTAAAAGAAACT 2 154 0 CAGTATTATT 0.842425 -147 TTAATGGTAGTGATATTAGTGATTCCATTA 2 180 1 TGATATTAGT 0.745575 -121 TTTGAGGGTCTGATATTATGTGTCTATTTG 2 210 0 TGATATTATG 0.938588 -91 agtatttatttagtattatgcta 3 4 0 tagtattatg 0.969658 -297 ttaatattattagtatttatttagtattat 3 15 0 tagtatttat 0.911406 -286 taaatactaataatattaagctattagtag 3 26 1 taatattaag 0.947078 -275 agtaggtaaataatattaagataatattat 3 51 1 taatattaag 0.947078 -250 aatattaagataatattatgttaaagaaaa 3 62 1 taatattatg 0.923818 -239 tatagaagattagtatttaatagtaaacgg 3 107 1 tagtatttaa 0.764754 -194 aaaaagaaagtggtatataggaaaatggaa 3 151 0 tggtatatag 0.640283 -150 gctaccaacgtggtattaaaatgtgcccaa 3 186 0 tggtattaaa 0.921258 -115 aataccatcagggtattaagatgctaccaa 3 208 0 gggtattaag 0.896557 -93 aataccctgatggtattaatttcgtcggta 3 221 1 tggtattaat 0.973701 -80 agtattattccggtattatttaccgacgaa 3 241 0 cggtattatt 0.870742 -60 aatatttatttagtattattccggtattat 3 252 0 tagtattatt 0.952186 -49 gcttaaattctaatatttatttagtattat 3 263 0 taatatttat 0.796102 -38 ********** Masking position 5 Map Score: 23.0955 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 129 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 AGAGTTTATCTTTTTCATTAACATCGCCTTT 2 44 0 TTTTCATTAA 0.732445 -257 TGAAAAAGATAAACTCTTTTTAGCAAGAAAA 2 58 1 AACTCTTTTT 0.797483 -243 TGGCTTCTCCATATGCTTTTAAAATACCTCT 2 89 0 AATGCTTTTA 0.896872 -212 AACCCTTTATAAATTCTTTTTTCAGCAATAT 2 120 0 AATTCTTTTT 0.949703 -181 AAGGGTTAGCAGTTTCTTTTAATAATACTGA 2 144 1 ATTTCTTTTA 0.976581 -157 TTAATAATACTGATTCTTTTAATGGTAGTGA 2 162 1 TATTCTTTTA 0.966083 -139 TGAGATAGTTTCTTTAATTAAACCATC 2 284 0 ATTTCTTTAA 0.966083 -17 atagagaaactttttctttaacataatatta 3 72 0 ttttctttaa 0.951113 -229 cctatataccactttctttttcgcggttggg 3 160 1 atttcttttt 0.949704 -141 tccttttataattctttaagtgtttaatt 4 9 1 tattctttaa 0.951111 -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 AAGAAAAAGAGGTATTTTAAAAGCATATGG 2 82 1 GGTATTTTAA 0.930156 -219 TAAAAGAATCAGTATTATTAAAAGAAACTG 2 153 0 AGTATTATTA 0.871155 -148 GGTTACCACTAGCATCATAAATAAGGTTTT 2 237 0 AGCATCATAA 0.961367 -64 ttaacataatattatcttaatattatttac 3 56 0 attatcttaa 0.720218 -245 ctaccaacgtggtattaaaatgtgcccaac 3 185 0 ggtattaaaa 0.792904 -116 ccacgttggtagcatcttaataccctgatg 3 203 1 agcatcttaa 0.939438 -98 aaacacttaaagaattataaaagga 4 6 0 agaattataa 0.902987 -62 tacagcgctaagtattataa 5 1 0 agtattataa 0.974179 -22 ********** Masking position 4 Map Score: 5.33482 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 40 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GGGAATGGTTTTGTTTTGGTTATCACCACT 2 11 0 TTGTTTTGGT 0.889111 -290 ACCTTCTAGGTTATTTTGCTGATGGTTTAA 2 264 1 TTATTTTGCT 0.940245 -37 tatcttaatattatttacctactaatagct 3 44 0 ttatttacct 0.952349 -257 gaaaacaaatttgtttgccgtttactatta 3 124 0 ttgtttgccg 0.943876 -177 gcaaacaaatttgttttccattttcctata 3 136 1 ttgttttcca 0.931908 -165 cctgatggtattaatttcgtcggtaaataa 3 226 1 ttaatttcgt 0.765627 -75 tattccggtattatttaccgacgaaattaa 3 236 0 ttatttaccg 0.943082 -65 ********** Masking position 5 Map Score: 1.92685 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 118 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 tagcataatactaaataaatactaataat 3 10 1 actaaataaa 0.980458 -291 gtttctctatactatatagaagattagtat 3 93 1 actatataga 0.871886 -208 ttatttaccgacgaaattaataccatcagg 3 226 0 acgaaattaa 0.921672 -75 ccggaataatactaaataaatattagaatt 3 258 1 actaaataaa 0.980458 -43 ********** Masking position 6 Map Score: 0.698534 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 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 Motif number 7 ********** 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 8 ********** 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