You can use the look ahead assertion (found in Extended Patterns), which makes perl search for a pattern and return to the previous position after the match (and /g doesn't allow perl to match exactly at the same position, so it will move by at least one char on the next attempt).

($myseq =~ /(?=AA)/gi ), or (?=(AA)) if you want to capture the matches (which isn't really useful when the pattern is AA).

In reply to Re: Identifying Overlapping Matches in Nucleotide Sequence by Eily
in thread Identifying Overlapping Matches in Nucleotide Sequence by FIJI42

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