Here is a solution using a dynamic regex construct. I've never used it before and learned more about it here.

A fly in the ointment was in the code for our $s (@stops). The code wouldn't work here with a 'my' declaration. 'our' was necessary.

This is fairly readable and should work for any number of groups (provided they don't exceed the count of fasta characters in a string of them. I didn't test for that to see how it behaved).

The dynamic regex form was necessary because the count of the quantifier changed for each iteration of the 'for' loop ($s-1).

The printout after the __END__ token shows the results of the run.

Update: Added a final substitution to remove dashes preceding and following the double underscore (as he desired in his post. Missed that.) 

#!/usr/bin/perl
use strict;
use warnings;
use 5.014;

my @stops = (2,6); # group by 2 then 4 (6 == 2 + 4)

my $tag = '___';

for ('ATCGGATCTGGC', 'A-C-G--CTGGC') {
    my $seq = $_;
    
    for our $s (@stops) { # necessary to use 'our' instead of 'my'
        $seq =~ s/
             ( # begin capture
                    
                  (??{                       # dynamic regex
                      "(?:[TAGC][^TAGC]*)" . # group to apply quantifi
+er to
                      "{" . ($s-1) . "}"   . # quantifier
                      "[TAGC]"               # end token
                  })                         # end dynamic reference
                    
              ) # end capture
        /$1$tag/x; # end of substitution
    }
    $seq =~ s/__-+/__/g;
    say $seq;
}

__END__
C:\Old_Data\perlp>perl dynamic_regex.pl
AT___CGGA___TCTGGC
A-C___G--CTG___GC

C:\Old_Data\perlp>

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In reply to Re: Regex to match range of characters broken by dashes by Cristoforo
in thread Regex to match range of characters broken by dashes by Q.and

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