use Modern::Perl qw/2015/; my $seq = 'A-C-G--CTGGC'; my $tag = '___'; $seq =~ s/([ATGC]-*[ATGC])-*/$1$tag/; $seq =~ s/($tag[ATGC]-*[ATGC]-*[ATGC]-*[ATGC])-*/$1$tag/; say $seq;