AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_mgen_mpneu_100.orf -o228_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 AGTTTCTTTTAATAATACTGATTCTTTTAA 2 154 1 AATAATACTG 0.856462 -147 TAATGGAATCACTAATATCACTACCATTAA 2 180 0 ACTAATATCA 0.765842 -121 CAAATAGACACATAATATCAGACCCTCAAA 2 210 1 CATAATATCA 0.944621 -91 tagcataatactaaataaatact 3 4 1 cataatacta 0.972728 -297 ataatactaaataaatactaataatattaa 3 15 1 ataaatacta 0.919883 -286 ctactaatagcttaatattattagtattta 3 26 0 cttaatatta 0.95232 -275 ataatattatcttaatattatttacctact 3 51 0 cttaatatta 0.95232 -250 ttttctttaacataatattatcttaatatt 3 62 0 cataatatta 0.931193 -239 ccgtttactattaaatactaatcttctata 3 107 0 ttaaatacta 0.783935 -194 ttccattttcctatataccactttcttttt 3 151 1 ctatatacca 0.66517 -150 ttgggcacattttaataccacgttggtagc 3 186 1 tttaatacca 0.928865 -115 ttggtagcatcttaataccctgatggtatt 3 208 1 cttaataccc 0.906308 -93 taccgacgaaattaataccatcagggtatt 3 221 0 attaatacca 0.976371 -80 ttcgtcggtaaataataccggaataatact 3 241 1 aataataccg 0.882608 -60 ataataccggaataatactaaataaatatt 3 252 1 aataatacta 0.956945 -49 ataatactaaataaatattagaatttaagc 3 263 1 ataaatatta 0.813351 -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 AAAGGCGATGTTAATGAAAAAGATAAACTCT 2 44 1 TTAATGAAAA 0.735365 -257 TTTTCTTGCTAAAAAGAGTTTATCTTTTTCA 2 58 0 AAAAAGAGTT 0.799887 -243 AGAGGTATTTTAAAAGCATATGGAGAAGCCA 2 89 1 TAAAAGCATT 0.898246 -212 ATATTGCTGAAAAAAGAATTTATAAAGGGTT 2 120 1 AAAAAGAATT 0.950412 -181 TCAGTATTATTAAAAGAAACTGCTAACCCTT 2 144 0 TAAAAGAAAT 0.976921 -157 TCACTACCATTAAAAGAATCAGTATTATTAA 2 162 0 TAAAAGAATA 0.966569 -139 GATGGTTTAATTAAAGAAACTATCTCA 2 284 1 TTAAAGAAAT 0.966569 -17 taatattatgttaaagaaaaagtttctctat 3 72 1 ttaaagaaaa 0.951804 -229 cccaaccgcgaaaaagaaagtggtatatagg 3 160 0 aaaaagaaat 0.950414 -141 aattaaacacttaaagaattataaaagga 4 9 0 ttaaagaata 0.951802 -59 ********* * Masking position 4 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 ATAATCACCTGATTAATTGTTTC 1 13 1 GTTATGTTTC 0.949224 -13 GCTAAAAAGAGTTTATCTTTTTCATTAACATCG 2 49 0 GTTACTTTTC 0.993142 -252 ATTTATAAAGGGTTAGCAGTTTCTTTTAATAAT 2 137 1 GTTACGTTTC 0.991794 -164 atatagtatagagaaactttttctttaacataa 3 77 0 ggaacttttc 0.925856 -224 aaacaaatttgtttgccgtttactattaaatac 3 119 0 gttgctttac 0.941869 -182 aaacaaatttgttttccattttcctatatacca 3 138 1 gtttcttttc 0.977929 -163 * *** * ***** Masking position 10 Map Score: 1.71547 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 41 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 GGGAATGGTTTTGTTTTGGTTATCACCACT 2 11 0 TTGTTTTGGT 0.823937 -290 CCTCAAAACCTTATTTATGATGCTAGTGGT 2 233 1 TTATTTATGA 0.767863 -68 ACCTTCTAGGTTATTTTGCTGATGGTTTAA 2 264 1 TTATTTTGCT 0.940517 -37 ttattagtatttatttagtattatgcta 3 9 0 ttatttagta 0.917765 -292 tatcttaatattatttacctactaatagct 3 44 0 ttatttacct 0.950767 -257 gcaaacaaatttgttttccattttcctata 3 136 1 ttgttttcca 0.898744 -165 tattccggtattatttaccgacgaaattaa 3 236 0 ttatttaccg 0.918882 -65 attctaatatttatttagtattattccggt 3 257 0 ttatttagta 0.917765 -44 ********** Masking position 5 Map Score: 2.68001 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 152 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 AAAGAATTTATAAAGGGTTAGCAGTTTCTTTTA 2 132 1 TAAAGTAGCA 0.94687 -169 CAAAATAACCTAGAAGGTTACCACTAGCATCAT 2 249 0 TAGAATACCA 0.960985 -52 TTTCTTTAATTAAACCATCAGCAAAATAACCTA 2 270 0 TAAACTAGCA 0.979498 -31 ctaataatattaagctattagtaggtaaataat 3 32 1 taagctagta 0.821372 -269 ctatactatatagaagattagtatttaatagta 3 99 1 tagaatagta 0.887651 -202 tatttaatagtaaacggcaaacaaatttgtttt 3 120 1 taaaccaaca 0.783206 -181 aacgtggtattaaaatgtgcccaaccgcgaaaa 3 177 0 taaaatccca 0.874987 -124 atcagggtattaagatgctaccaacgtggtatt 3 199 0 taagacacca 0.877416 -102 aaataaatattagaatttaagcaaacttatacg 3 271 1 tagaatagca 0.97573 -30 ***** * **** Masking position 2 Map Score: 1.40853 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 198 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTATAATCACCTGATTAATTG 1 2 1 TATAATCACC 0.827885 -24 TTGTTTTGGTTATCACCACT 2 1 0 TATCACCACT 0.873863 -300 ACCAAAACAAAACCATTCCCCGCAAAGGCG 2 21 1 AACCATTCCC 0.832326 -280 GAATCACTAATATCACTACCATTAAAAGAA 2 175 0 TATCACTACC 0.955913 -126 CCTAGAAGGTTACCACTAGCATCATAAATA 2 244 0 TACCACTAGC 0.971505 -57 TCTTTAATTAAACCATCAGCAAAATAACCT 2 271 0 AACCATCAGC 0.962074 -30 acgaaattaataccatcagggtattaagat 3 216 0 taccatcagg 0.930411 -85 ********** Masking position 5 Map Score: 0.415443 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 240 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 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 Motif number 9 ********** 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