I'm using pairwiseAlignment() in the Biostrings package as follows:


library('Biostrings')

pattern <- DNAString('GCGAGAG')
subject <- DNAString('AGCTTTAGAGGCGAGAGGCAT')

myalign <- pairwiseAlignment(pattern, subject)
subject(myalign)

> subject(myalign)
[11] GCGAGAG

I'm interested in the position where the pattern starts aligning with the
subject.  In this case, subject(myalign) gives 11 as the starting position
as part of the print out.  Is there a way to pull out this starting position
information from subject(myalign)?

Thanks,
Andrew

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