AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_mgen_mpneu_300.orf -o257_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 RMG04338 167 Mycoplasma #2 RMG05439 300 Mycoplasma #3 RMP00268 300 Mycoplasma_pneumoniae #4 RMP00269 187 Mycoplasma_pneumoniae Motif number 1 TTTGTATTTAAAAATTAACAATATCTCA 1 9 1 TAAAAATTAA 0.91502 -159 CTAATATCAGATAAATTTAAGATAACTTTT 1 63 1 ATAAATTTAA 0.752635 -105 ACTAATTTAAAAGAAAGTAAAAGTTATCTT 1 81 0 AAGAAAGTAA 0.756886 -87 TTTTAATAATTAAAAACTAATTTAAAAGAA 1 96 0 TAAAAACTAA 0.921389 -72 ATTAAAACCAAAAAAATTAATCCCGTTAGA 2 35 0 AAAAAATTAA 0.960144 -266 AAAGTTAAAAATGAAAATAGAACTACTATT 2 85 0 ATGAAAATAG 0.482926 -216 GCAACCATCAAAAAAGTTAAAAATGAAAAT 2 97 0 AAAAAGTTAA 0.904895 -204 GAAGCTAATGAAAAAACTAATGAAAGCAAA 2 128 0 AAAAAACTAA 0.963171 -173 AATTAAAAAGAAGAAGCTAATGAAAAAACT 2 140 0 AAGAAGCTAA 0.894316 -161 TTAGTTTTAGATGCAATTAAAAAGAAGAAG 2 154 0 ATGCAATTAA 0.827195 -147 TTAATTGCATCTAAAACTAAGCAGAATAAA 2 164 1 CTAAAACTAA 0.6916 -137 ACTAAGCAGAATAAAAATAATTAAATTTAT 2 179 1 ATAAAAATAA 0.823548 -122 CTTTTCACTGATAAATTTAATTATTTTTAT 2 189 0 ATAAATTTAA 0.752635 -112 TCAATTATTTTTGAAGCTAAAGCCTAAGTT 2 225 1 TTGAAGCTAA 0.732082 -76 CCTTTAATTAATGAAGTTAAGAAGCACTTG 2 258 0 ATGAAGTTAA 0.84886 -43 tttaaaccctaaaaaattaattggactcgc 3 42 0 aaaaaattaa 0.960144 -259 tagggtttaaaagaaattagcattaggctt 3 61 1 aagaaattag 0.828209 -240 gcattaggcttaaaaattaaattttcctgt 3 80 1 taaaaattaa 0.91502 -221 gtttcaacaataaaaactaaaaactctacg 3 124 0 taaaaactaa 0.921389 -177 caaatacttaaaacaactaaaaaaccaatg 3 258 0 aaacaactaa 0.897991 -43 tggttagtaattaaaactaa 4 1 0 ttaaaactaa 0.893866 -187 taaagtgcaaataaaaataatttagcaaca 4 123 0 ataaaaataa 0.823548 -65 tttgcactttaagcatttaactgctaattg 4 142 1 aagcatttaa 0.559563 -46 taccaattattaacaattagcagttaaatg 4 155 0 taacaattag 0.470256 -33 ********** Masking position 8 Map Score: 31.0639 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 795 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 TATTGTTAATTTTTAAATACAAA 1 1 0 TTTTAATAAA 0.655342 -167 TTAAATTAGTTTTTAATTATTAAAATATTTTTA 1 101 1 TTTTATTAAA 0.966434 -67 TATTAAAATATTTTTATTATGAACATAACGCCA 1 118 1 TTTTATTAAA 0.965462 -50 AGTAGTTCTATTTTCATTTTTAACTTTTTTGAT 2 88 1 TTTTATTTAA 0.912404 -213 TGAGTTCATCTTTTCACTGATAAATTTAATTAT 2 195 0 TTTTACTGAA 0.912108 -106 ATTTCAAAACCTTTAATTAATGAAGTTAAGAAG 2 264 0 CTTTATTAGA 0.852883 -37 gttaaaaccgttttcattagcgagtccaattaa 3 23 1 ttttattaga 0.930903 -278 taacaggaaaatttaatttttaagcctaatgct 3 79 0 atttatttaa 0.847629 -222 gagtttttagtttttattgttgaaactttttaa 3 128 1 ttttattgga 0.955681 -173 tggttaggaaatttaattgaaaaactaccacaa 3 184 0 atttattgaa 0.936005 -117 gaaaaatatttgtttggaaataacaaatac 3 281 0 attttttgaa 0.705358 -20 ttagttttaattactaaccacatatac 4 5 1 ttttattaaa 0.966434 -183 gtagattaagcgtttattgccaataaggcactc 4 44 0 cgttattgaa 0.746292 -144 cactttaagcatttaactgctaattgttaataa 4 146 1 atttactgaa 0.884849 -42 **** **** ** Masking position 13 Map Score: 16.4204 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 258 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 AGTGAGATATTGTTAATTTTTAAATACAAA 1 10 0 TGTTATTTTT 0.713974 -158 TTAAATTAGTTTTTAATTATTAAAATATTTT 1 101 1 TTTTATTATT 0.95372 -67 TATTAAAATATTTTTATTATGAACATAACGC 1 118 1 TTTTATTATG 0.877181 -50 ACGGGATTAATTTTTTTGGTTTTAATTTAGT 2 39 1 TTTTTTGGTT 0.68505 -262 AGTAGTTCTATTTTCATTTTTAACTTTTTTG 2 88 1 TTTTATTTTT 0.940569 -213 TTTTTAACTTTTTTGATGGTTGCATTTGCTT 2 104 1 TTTTATGGTT 0.953357 -197 AGCTTCTTCTTTTTAATTGCATCTAAAACTA 2 152 1 TTTTATTGCA 0.619089 -149 AATTTAATTATTTTTATTCTGCTTAGTTTTA 2 175 0 TTTTATTCTG 0.762885 -126 tccaattaattttttagggtttaaaagaaat 3 47 1 ttttagggtt 0.865905 -254 taacaggaaaatttaatttttaagcctaatg 3 81 0 atttattttt 0.627449 -220 gagtttttagtttttattgttgaaacttttt 3 128 1 ttttattgtt 0.975897 -173 tttttagttgttttaagtatttgttatttcc 3 265 1 ttttagtatt 0.866854 -36 ttagttttaattactaaccacatat 4 5 1 ttttattact 0.866854 -183 **** ****** Masking position 4 Map Score: 9.10997 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 322 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 AAGTGAAACCAAGACGTTGTCATGA 1 153 0 AAACCAAGAC 0.959813 -15 AGTAGTTATCAAGCCAATGCAAATTCTAAC 2 11 1 AAGCCAATGC 0.974282 -290 AAACTAATGAAAGCAAATGCAACCATCAAA 2 115 0 AAGCAAATGC 0.959813 -186 AGCCTAAGTTTAACAAGTGCTTCTTAACTT 2 245 1 TAACAAGTGC 0.874737 -56 ttaaatttcctaaccaagatacgatagatt 3 201 1 taaccaagat 0.773 -100 aacaactaaaaaaccaatgctgacagtagt 3 247 0 aaaccaatgc 0.985273 -54 tgtttggaaataacaaatacttaaaacaac 3 271 0 taacaaatac 0.943103 -30 tgttatttccaaacaaatatttttc 3 286 1 aaacaaatat 0.858798 -15 ********** Masking position 6 Map Score: 5.52875 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 106 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTTGTATTTAAAAATTAACAAT 1 2 1 TTGTATTAAA 0.870892 -166 GAAAGTAAAAGTTATCTTAAATTTATCTGAT 1 68 0 GTTATTTAAA 0.509027 -100 TAACTTTTACTTTCTTTTAAATTAGTTTTTA 1 85 1 TTTCTTTAAA 0.907774 -83 ATTAATTTTTTTGGTTTTAATTTAGTTAGTT 2 44 1 TTGGTTTAAT 0.432462 -257 TTCTTTTTAATTGCATCTAAAACTAAGCAGA 2 158 1 TTGCACTAAA 0.9574 -143 TCAATTATTTTTGAAGCTAAAGCCTAAGTTT 2 225 1 TTGAACTAAA 0.794229 -76 AGTTTAACAAGTGCTTCTTAACTTCATTAAT 2 251 1 GTGCTCTTAA 0.728414 -50 TTGAAATATTTTTGTATTAAA 2 290 1 TTTGTTTAAA 0.725995 -11 ctaatgctaatttcttttaaaccctaaaaaa 3 56 0 tttctttaaa 0.907774 -245 tgtggtagtttttcaattaaatttcctaacc 3 185 1 tttcattaaa 0.871588 -116 tatatgtggttagtaattaaaactaa 4 6 0 tagtattaaa 0.540685 -182 taccgaaatagtgctgctaaattagcgtgcc 4 91 0 gtgctctaaa 0.939224 -97 tatttcggtagtgttgctaaattatttttat 4 112 1 gtgttctaaa 0.792875 -76 ttatttttatttgcactttaagcatttaact 4 133 1 ttgcatttaa 0.826125 -55 tattaacaattagcagttaaatgcttaaagt 4 147 0 tagcattaaa 0.826147 -41 ***** ***** Masking position 10 Map Score: 11.695 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 775 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 ********** No masking Map Score: 2.65333e-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: 2.65333e-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: 2.65333e-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