[BioC] questions about matchPattern and vmatchPattern

[wang peter]

dear ALL:
       Please this sample
subject = "TGCATTT"
Rpattern = "TGCAATTT"
result <- matchPattern(Rpattern, subject, max.mismatch= 4, min.mismatch=0)
result
  Views on a 7-letter BString subject
subject: TGCATTT
views:
    start end width
[1]     0   7     8 [ TGCATTT]
[2]     1   8     8 [TGCATTT ]



is the start position and end position on the subject or pattern?

and for vmatchPattern result
if one pattern has many hits on one sequence, does it return only
one hit or all of hits as results?

thank u
-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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