Your index function always starts from the beginning of the string, so at best has only two distinct values.

You probably want the pos function and a while loop. Collecting an array of K's and R's is not getting you much. I'm going to rewrite the regex as a character class, though there's nothing wrong with yours.

my $string = 'LPNTGVTNNAYMPLLGIIGLVTSFSLLGLXKARRD';

while ($string =~ /([KR])/g) {
    print pos($string) - length($1), $/;
}

__END__
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