c:\@Work\Perl\monks>perl -wMstrict -le
"my @stops = (2,6);
 ;;
 my $tag = '___';
 ;;
 for ('ATCGGATCTGGC', 'A-C-G--CTGGC') {
   my $seq = $_;
   printf qq{'$seq' -> };
   ;;
   for our $s (@stops) {
     local our $q = $s - 1;
     $seq =~ s/
       ((?:[TAGC][^TAGC]*){$q} [TAGC])
       /$1$tag/x;
     }
   print qq{'$seq'};
   }
"
'ATCGGATCTGGC' -> 'AT___CGGA___TCTGGC'
'A-C-G--CTGGC' -> 'A-C___-G--CTG___GC'