You could try something like this:

my $seq = "012345678WW89YYabcdeZZ";
my $start = 'WW';
my @ends = qw (XX YY ZZ);
my $end = '(' . join ( '|', @ends ) . ')';

if ( $seq =~ /$start.*?$end/ ) {
  print "start: $-[0] end: $-[1]";
}
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dave