AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_mgen_mpneu_300.orf -o193_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 RMG02589 300 Mycoplasma #2 RMG02591 234 Mycoplasma #3 RMP00460 300 Mycoplasma_pneumoniae Motif number 1 TTTTTTATTTGTTTAATAGTTAA 1 3 1 TTTTATTGTT 0.873386 -298 ATAACGCTTTTTTTAACTATTAAACAAATAA 1 15 0 TTTTAACATT 0.982778 -286 AAGCGTTATGTTTTATCTATTTTATTAGTTA 1 37 1 TTTTATCATT 0.990468 -264 TTCAAAACTTTTTTAACTAATAAAATAGATA 1 50 0 TTTTAACAAT 0.924929 -251 AGTTTTGAATTTTTATCTATTTTTAGTTAAT 1 72 1 TTTTATCATT 0.990468 -229 AACATAAGACTTTTATTAACTAAAAATAGAT 1 86 0 TTTTATTACT 0.891078 -215 AGTCTTATGTTTTTATCAAATTTTTATCTGT 1 106 1 TTTTATCAAT 0.956567 -195 TTTATCAAATTTTTATCTGTTTTTTGGTTAA 1 117 1 TTTTATCGTT 0.953073 -184 TCTAAAACTTTTTTAACCAAAAAACAGATAA 1 129 0 TTTTAACAAA 0.70071 -172 TCTTTCTTAAATTTATTTATTAAATAGTTAA 1 163 1 ATTTATTATT 0.702387 -138 TTAACACTTTTATTAACTATTTAATAAATAA 1 175 0 TATTAACATT 0.8781 -126 AAGTGTTAAGTTTTATCTATTTTTAATTAAT 1 197 1 TTTTATCATT 0.990468 -104 GGGGTCGAGGTTTTATTAATTAAAAATAGAT 1 211 0 TTTTATTATT 0.965902 -90 ATTTTTTTGTTATTAACAATTTAA 2 4 0 TATTAACATT 0.877356 -231 TTAAAGTTGGTTTTTTTAATAGAGATTTTTT 2 28 0 TTTTTTTATA 0.458335 -207 TATTAATAAATTTTATTAATATAAGCAAGAA 2 159 1 TTTTATTATA 0.798677 -76 TTTATTAGAATTTAAACGATTTCATCTAATA 2 201 1 TTTAAACATT 0.884092 -34 ATGTGATTTGAACTATTAGATGAAATC 2 218 0 TTTGAACATT 0.865045 -17 tagaaataattttaatcgactgaagttgtgt 3 39 1 tttaatcact 0.76423 -262 cagtttcctattttttttattccaacttgtc 3 85 1 tttttttatt 0.816817 -216 ******* *** Masking position 3 Map Score: 33.2183 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 385 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 TTTTTTATTTGTTTAATAGT 1 1 1 TTTTTTATTT 0.80125 -300 CATAACGCTTTTTTTAACTATTAAACAAAT 1 17 0 TTTTTAACTA 0.756013 -284 TTTATCTATTTTATTAGTTAAAAAAGTTTT 1 48 1 TTATTAGTTA 0.820078 -253 TTTTTATCTATTTTTAGTTAATAAAAGTCT 1 81 1 TTTTTAGTTA 0.948382 -220 TTTTATCTGTTTTTTGGTTAAAAAAGTTTT 1 127 1 TTTTTGGTTA 0.938399 -174 GTTTTAGATTTTCTTTCTTAAATTTATTTA 1 152 1 TTCTTTCTTA 0.937808 -149 TTTCTTAAATTTATTTATTAAATAGTTAAT 1 165 1 TTATTTATTA 0.903798 -136 GTTTTATCTATTTTTAATTAATAAAACCTC 1 206 1 TTTTTAATTA 0.951338 -95 TAATAGAGATTTTTTTGTTATTAACAATTT 2 13 0 TTTTTTGTTA 0.972549 -222 TAAAGTTGGTTTTTTTAATAGAGATTTTTT 2 28 0 TTTTTTAATA 0.801233 -207 AATTAGATTGTTCTTGCTTATATTAATAAA 2 170 0 TTCTTGCTTA 0.866378 -65 AACAATCTAATTCTTTATTAGAATTTAAAC 2 188 1 TTCTTTATTA 0.95491 -47 gtttcctattttttttattccaacttgtcg 3 87 1 ttttttattc 0.856632 -214 tcttctcaacttttttcttaaccttttgtg 3 202 1 ttttttctta 0.964251 -99 ********** Masking position 5 Map Score: 18.99 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 254 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 AATAGTTAAAAAAAGCGTTATGTTTTATCT 1 25 1 AAAAGCGTTA 0.926057 -276 TTTAACTAATAAAATAGATAAAACATAACG 1 40 0 AAAATAGATA 0.963865 -261 TTATTAACTAAAAATAGATAAAAATTCAAA 1 75 0 AAAATAGATA 0.963865 -226 TTTAGTTAATAAAAGTCTTATGTTTTTATC 1 93 1 AAAAGTCTTA 0.816461 -208 AAACAGATAAAAATTTGATAAAAACATAAG 1 109 0 AAATTTGATA 0.772244 -192 TTTTAACCAAAAAACAGATAAAAATTTGAT 1 120 0 AAAACAGATA 0.891434 -181 TTTTGGTTAAAAAAGTTTTAGATTTTCTTT 1 138 1 AAAAGTTTTA 0.749844 -163 ATTTATTTATTAAATAGTTAATAAAAGTGT 1 173 1 TAAATAGTTA 0.86967 -128 AATAGTTAATAAAAGTGTTAAGTTTTATCT 1 185 1 AAAAGTGTTA 0.971706 -116 TTATTAATTAAAAATAGATAAAACTTAACA 1 200 0 AAAATAGATA 0.963865 -101 TTAAATTGTTAATAACAAAAA 2 2 1 TAAATTGTTA 0.886337 -233 ********** Masking position 3 Map Score: 12.0195 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 232 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 AGATAAAAATTCAAAACTTTTTTAACTAAT 1 60 0 TCAAAACTTT 0.92166 -241 AGAAAGAAAATCTAAAACTTTTTTAACCAA 1 140 0 TCTAAAACTT 0.921005 -161 AGATTTTCTTTCTTAAATTTATTTATTAAA 1 157 1 TCTTAAATTT 0.93204 -144 GGACTTGAACCCATAACCTTCTGGTCCGAA 2 93 1 CCATAACCTT 0.902417 -142 tctttgatcttctcaacttttttcttaacc 3 195 1 tctcaacttt 0.98028 -106 tcaacttttttcttaaccttttgtggaaac 3 207 1 tcttaacctt 0.989595 -94 cggtgcatggtcttaactttaatttgcact 3 238 1 tcttaacttt 0.983596 -63 cactttagtttctcaaccttgcatttgatt 3 264 1 tctcaacctt 0.987476 -37 ********** Masking position 5 Map Score: 12.2568 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 GAAAGAAAATCTAAAACTTTTTTAACCAAA 1 139 0 CTAAAACTTT 0.808374 -162 CCATCCATAACACCAACCTGTTTGTGTTGT 1 267 1 CACCAACCTG 0.965116 -34 CTATTAAAAAAACCAACTTTAAAGTTGGTT 2 37 1 AACCAACTTT 0.936348 -198 TAGAATTTCAAACCAACTTTAAAGTTGGTT 2 47 0 AACCAACTTT 0.936348 -188 attttttttattccaacttgtcgaacttgg 3 94 1 ttccaacttg 0.957329 -207 tcaaaatttactacaacttgatctactgta 3 163 1 ctacaacttg 0.969638 -138 actttagtttctcaaccttgcatttgattc 3 265 1 ctcaaccttg 0.907642 -36 ********** Masking position 5 Map Score: 2.82839 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 90 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTATGGATGGTTTGGTCAGCGATTTGATAGG 1 246 0 TTTGGTCACG 0.878944 -55 ATCCCTAGACTTGAACAACACAAACAGGTT 1 281 0 CTTGAACACA 0.840912 -20 TTAAAGTTGGTTTGAAATTCTAAATGGCGCG 2 55 1 TTTGAAATCT 0.823115 -180 ATGTGATTTGAACTATTAGATGAAATC 2 218 0 TTTGAACTTT 0.823115 -17 acttgtcgaacttggtcatctggaaaaactc 3 109 1 cttggtcact 0.958556 -192 actcgcctgattcgatctcctgtgggttcaa 3 136 1 ttcgatctct 0.946683 -165 tttactacaacttgatctactgtagttcttt 3 169 1 cttgatctct 0.984968 -132 actgtagttctttgatcttctcaactttttt 3 187 1 tttgatctct 0.985262 -114 ******** ** Masking position 2 Map Score: 2.92448 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 82 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CAGAAGGTTATGGGTTCAAGTCCTATTGGG 2 86 0 TGGGTTCAAG 0.984506 -149 GATTGAGCTATGGGCGCATATATTAATAAA 2 139 1 TGGGCGCATA 0.972928 -96 cgatctcctgtgggttcaaaatttactaca 3 148 1 tgggttcaaa 0.976223 -153 ttgtggaaactcggtgcatggtcttaactt 3 227 1 tcggtgcatg 0.973446 -74 ********** Masking position 8 Map Score: 0.0510107 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 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 8 ********** No masking Map Score: -1.34049e-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: -1.34049e-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 10 ********** No masking Map Score: -1.34049e-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