AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_mpneu_reg_300.orf -o030_mpneu_300.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMP00104 182 Mycoplasma_pneumoniae #2 RMP00112 300 Mycoplasma_pneumoniae Motif number 1 actattacgcatattttttagaaagggtgt 1 17 0 atatttttta 0.763999 -166 ttgattttcaaagtatttaaataagagtta 1 61 1 aagtatttaa 0.816487 -122 gttttttaaaaaacatttaactcttattta 1 78 0 aaacatttaa 0.951116 -105 cagctctgcaaaactttaaacgataaaagc 1 116 1 aaactttaaa 0.817272 -67 ttacgtcaacaaacatttaaatagtcggtt 2 54 0 aaacatttaa 0.951116 -247 taaatcgtgaaaacattttacccgtttacg 2 79 0 aaacatttta 0.951106 -222 ttcccgaaataaacttttaactgggcaatt 2 110 1 aaacttttaa 0.97676 -191 tttaactgggcaatttttcaattaattacc 2 125 1 caatttttca 0.848834 -176 tattcgttcgaaatttttcgcgttttatcg 2 159 1 aaatttttcg 0.904033 -142 gttttatcgcaaattttttgtggatgacaa 2 180 1 aaattttttg 0.905754 -121 agtcaaaataaaactttttaagatttattc 2 211 1 aaacttttta 0.97676 -90 ctatcgaaaagaattttttattgaaaaact 2 256 1 gaatttttta 0.913366 -45 aaaagcgggagagtttttcaataaaaaatt 2 267 0 gagtttttca 0.765521 -34 ********** Masking position 6 Map Score: 16.655 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 174 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 ctattacgcatattttttagaaagggtgtaa 1 15 0 tttttttaga 0.808273 -168 attagatcgttgattttcaaagtatttaaat 1 52 1 tattttcaaa 0.781331 -131 aacatttaactcttatttaaatactttgaaa 1 66 0 tttatttaaa 0.590081 -117 aagagttaaatgttttttaaaaaaccacttt 1 83 1 tttttttaaa 0.94408 -100 tttattctcgaagatccgaaaa 2 2 1 tattctcgaa 0.88812 -299 aatagtcggttctttttcgacattatttact 2 34 0 ttttttcgac 0.865177 -267 actatttaaatgtttgttgacgtaaacgggt 2 59 1 ttttgttgac 0.738206 -242 tttcgggaactaaatcgtgaaaacattttac 2 88 0 taatcgtgaa 0.773969 -213 gttaaaagtttatttcgggaactaaatcgtg 2 100 0 ttttcgggaa 0.781468 -201 tttttcgcgttttatcgcaaattttttgtgg 2 172 1 ttatcgcaaa 0.786104 -129 ttatcgcaaattttttgtggatgacaaaagt 2 183 1 tttttgtgga 0.790125 -118 cttaaaaagttttattttgacttttgtcatc 2 202 0 ttattttgac 0.832896 -99 atatagagaataaatcttaaaaagttttatt 2 217 0 taatcttaaa 0.793147 -84 agatttattctctatattaaaatgactatcg 2 231 1 ttatattaaa 0.71167 -70 cgaaaagaattttttattgaaaaactctccc 2 260 1 ttttattgaa 0.895598 -41 taatcatttttcttaaaagcgggagag 2 284 0 ttttcttaaa 0.958773 -17 * ********* Masking position 1 Map Score: 11.5375 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 464 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 gcaaaactttaaacgataaaagcatcggcgt 1 123 1 aaacgaaaaa 0.965627 -60 aagatccgaaaaaagtaaataatgtcgaaaa 2 21 1 aaaagtaata 0.823556 -280 ttacgtcaacaaacatttaaatagtcggttc 2 53 0 aaacattaaa 0.843926 -248 ttgttgacgtaaacgggtaaaatgttttcac 2 72 1 aaacggtaaa 0.938434 -229 tcgggaactaaatcgtgaaaacattttaccc 2 86 0 aatcgtaaaa 0.976574 -215 atttgcgataaaacgcgaaaaatttcgaacg 2 163 0 aaacgcaaaa 0.976546 -138 tgtggatgacaaaagtcaaaataaaactttt 2 198 1 aaaagtaaaa 0.963025 -103 atagagaataaatcttaaaaagttttatttt 2 215 0 aatcttaaaa 0.843926 -86 ****** **** Masking position 9 Map Score: 6.64173 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 135 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 attacgcatattttttagaaagggtgtaat 1 14 0 ttttttagaa 0.819319 -169 ttagatcgttgattttcaaagtatttaaat 1 53 1 gattttcaaa 0.85157 -130 tgaaaaagtggttttttaaaaaacatttaa 1 88 0 gttttttaaa 0.87839 -95 taaaaaaccactttttcagctctgcaaaac 1 100 1 ctttttcagc 0.896559 -83 atcgtttaaagttttgcagagctgaaaaag 1 110 0 gttttgcaga 0.911338 -73 tttattctcgaagatccgaaaa 2 3 1 tattctcgaa 0.641457 -298 cattatttacttttttcggatcttcgagaa 2 15 0 ttttttcgga 0.963885 -286 atagtcggttctttttcgacattatttact 2 34 0 ctttttcgac 0.896559 -267 tatcgcaaattttttgtggatgacaaaagt 2 184 1 tttttgtgga 0.722983 -117 caaaataaaactttttaagatttattctct 2 214 1 ctttttaaga 0.816407 -87 aagcgggagagtttttcaataaaaaattct 2 265 0 gtttttcaat 0.782752 -36 taatcatttttcttaaaagcgggagag 2 284 0 ttttcttaaa 0.659758 -17 ********** Masking position 4 Map Score: 6.53382 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 590 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 ********** No masking Map Score: 6.84553e-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: 6.84553e-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: 6.84553e-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