hello every one,

i have such coding

> subject1 =
"ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAATATT"

> pattern1 =
"AATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG"
> matchPattern(pattern1, subject1, max.mismatch=0.2, min.mismatch=0,
with.indels=TRUE)
  Views on a 81-letter BString subject
subject:
ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAATATT
views: NONE
> trimLRPatterns(Lpattern = pattern1, subject = subject,
max.Lmismatch=0,with.Lindels=TRUE)
[1] "AAAAAAAAAAAATATT"
>

i already allow the indels,but why matchPattern cannot find the pattern in
subject
what does with.indels mean?
i am confused
thx
shan gao

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