AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_mpneu_reg_100.orf -o030_mpneu_100.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 0.797912 -166 ttgattttcaaagtatttaaataagagtta 1 61 1 aagtatttaa 0.844394 -122 gttttttaaaaaacatttaactcttattta 1 78 0 aaacatttaa 0.959563 -105 cagctctgcaaaactttaaacgataaaagc 1 116 1 aaactttaaa 0.845082 -67 ttacgtcaacaaacatttaaatagtcggtt 2 54 0 aaacatttaa 0.959563 -247 taaatcgtgaaaacattttacccgtttacg 2 79 0 aaacatttta 0.959551 -222 ttcccgaaataaacttttaactgggcaatt 2 110 1 aaacttttaa 0.980865 -191 tttaactgggcaatttttcaattaattacc 2 125 1 caatttttca 0.872589 -176 tattcgttcgaaatttttcgcgttttatcg 2 159 1 aaatttttcg 0.919932 -142 gttttatcgcaaattttttgtggatgacaa 2 180 1 aaattttttg 0.921392 -121 agtcaaaataaaactttttaagatttattc 2 211 1 aaacttttta 0.980865 -90 ctatcgaaaagaattttttattgaaaaact 2 256 1 gaatttttta 0.927843 -45 aaaagcgggagagtttttcaataaaaaatt 2 267 0 gagtttttca 0.799273 -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 0.804023 -168 attagatcgttgattttcaaagtatttaaat 1 52 1 tattttcaaa 0.776649 -131 aacatttaactcttatttaaatactttgaaa 1 66 0 tttatttaaa 0.583524 -117 aagagttaaatgttttttaaaaaaccacttt 1 83 1 tttttttaaa 0.942627 -100 tttattctcgaagatccgaaaa 2 2 1 tattctcgaa 0.885389 -299 aatagtcggttctttttcgacattatttact 2 34 0 ttttttcgac 0.861973 -267 actatttaaatgtttgttgacgtaaacgggt 2 59 1 ttttgttgac 0.732917 -242 tttcgggaactaaatcgtgaaaacattttac 2 88 0 taatcgtgaa 0.769177 -213 gttaaaagtttatttcgggaactaaatcgtg 2 100 0 ttttcgggaa 0.776789 -201 tttttcgcgttttatcgcaaattttttgtgg 2 172 1 ttatcgcaaa 0.781499 -129 ttatcgcaaattttttgtggatgacaaaagt 2 183 1 tttttgtgga 0.78558 -118 cttaaaaagttttattttgacttttgtcatc 2 202 0 ttattttgac 0.829077 -99 atatagagaataaatcttaaaaagttttatt 2 217 0 taatcttaaa 0.788651 -84 agatttattctctatattaaaatgactatcg 2 231 1 ttatattaaa 0.706196 -70 cgaaaagaattttttattgaaaaactctccc 2 260 1 ttttattgaa 0.893029 -41 taatcatttttcttaaaagcgggagag 2 284 0 ttttcttaaa 0.957691 -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 taaatgttttttaaaaaaccactttttcag 1 89 1 ttaaaaaacc 0.843225 -94 ttttgcagagctgaaaaagtggttttttaa 1 99 0 ctgaaaaagt 0.976257 -84 tttttcagctctgcaaaactttaaacgata 1 111 1 ctgcaaaact 0.949489 -72 aaactttaaacgataaaagcatcggcgtgt 1 126 1 cgataaaagc 0.860953 -57 ctcgaagatccgaaaaaagtaaataatgtc 2 17 1 cgaaaaaagt 0.971912 -284 gggtaattaattgaaaaattgcccagttaa 2 126 0 ttgaaaaatt 0.730793 -175 aaaaaatttgcgataaaacgcgaaaaattt 2 169 0 cgataaaacg 0.730897 -132 tttttgtggatgacaaaagtcaaaataaaa 2 194 1 tgacaaaagt 0.893183 -107 gagaataaatcttaaaaagttttattttga 2 213 0 cttaaaaagt 0.887378 -88 gaattttttattgaaaaactctcccgcttt 2 266 1 ttgaaaaact 0.934065 -35 ********** Masking position 5 Map Score: 7.47426 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 283 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 attttttagaaagggtgtaatttt 1 5 0 aagggtgtaa 0.957562 -178 gtatttaaataagagttaaatgttttttaa 1 73 1 aagagttaaa 0.819303 -110 ttgttgacgtaaacgggtaaaatgttttca 2 72 1 aaacgggtaa 0.976857 -229 tcgggaactaaatcgtgaaaacattttacc 2 87 0 aatcgtgaaa 0.951976 -214 tcgaacgaataggagggtaattaattgaaa 2 140 0 aggagggtaa 0.928514 -161 atttgcgataaaacgcgaaaaatttcgaac 2 164 0 aaacgcgaaa 0.953461 -137 tttttcttaaaagcgggagagtttttcaat 2 275 0 aagcgggaga 0.980412 -26 ********** Masking position 1 Map Score: 2.71182 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 136 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 atgcgtaatagtaacttattagatcgttga 1 35 1 gtaacttatt 0.94836 -148 taactcttatttaaatactttgaaaatcaa 1 61 0 ttaaatactt 0.886491 -122 aaaggcttaactaattaatagttaca 1 167 0 ttaactaatt 0.964051 -16 tccgaaaaaagtaaataatgtcgaaaaaga 2 25 1 gtaaataatg 0.946227 -276 gaataggagggtaattaattgaaaaattgc 2 134 0 gtaattaatt 0.956807 -167 ********** Masking position 6 Map Score: 0.856725 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 55 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 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 Motif number 8 ********** 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