i want to remove the  PCR2rc from the subject, but it is can not recognized
if i set the mismatch =0.2
how can i sent parameter to let trimLRPatterns works

   GATCGGAAGAGCACACGTCTGAACTCCA
TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG

subject<- DNAString("
GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC")
PCR2rc <-
DNAString("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
max.mismatchs <- 0.25*1:nchar(PCR2rc)

trimLRPatterns( Lpattern = PCR2rc, subject = subject,
max.Lmismatch=0.2,with.Rindels=T)
88-letter "DNAString" instance
seq:
ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC

trimLRPatterns( Lpattern = PCR2rc, subject = subject,
max.Lmismatch=0.5,with.Rindels=T)
  27-letter "DNAString" instance
seq: AAAAAAAAAAAAAAACGACACAAGCCC

countPattern(PCR2rc, subject, max.mismatch= 0.2, min.mismatch=0,
with.indels=TRUE)
[1] 0

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