I have not been able to make a regex that matches a discontinuous string and still follows the numeric range set in {}. See below, the first example gives correct behavior only when the string is continuous and the second demonstrates its flaws when the string is interrupted by dashes. Example one: 

$seq = 'ATCGGATCTGGC';
$tag = '___';

$seq =~ s/[ATGC]{2}/$&$tag/;
$seq =~ s/$tag[ATGC]{4}/$&$tag/;

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printing $seq will output:

AT___CGGA___TCTGGC

And that’s exactly what they should do, BUT, if $seq has dashes, the regexes are not appropriate. In example 2 below, say that all is the same as above, except that 

$seq = 'A-C-G--CTGGC';

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Printing $seq now outputs:

A-C-G--CT___GGC

instead of the desired output where it effectively ignores dashes and only count letters:

A-C___G--CTG___GC

Any ideas on how I can write the regexes to match when gaps are included?

In reply to Regex to match range of characters broken by dashes by Q.and

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