#! perl -slw
use strict;

my @seqs = (
    "CAG GTR CAG CTG AAG SAG TCA GG",
    "GAK GTG CAG CTT CAG CAG TCR GG",
);

for my $seq ( @seqs ) {
    print $seq;
    $seq =~ tr[ ][_];
    $seq =~ s[R][{A,G}]g;
    $seq =~ s[S][{C,G}]g;
    $seq =~ s[K][{G,T}]g;
    tr[_][ ] and print "\t$_" while glob $seq;
}
__END__
CAG GTR CAG CTG AAG SAG TCA GG
        CAG GTA CAG CTG AAG CAG TCA GG
        CAG GTA CAG CTG AAG GAG TCA GG
        CAG GTG CAG CTG AAG CAG TCA GG
        CAG GTG CAG CTG AAG GAG TCA GG
GAK GTG CAG CTT CAG CAG TCR GG
        GAG GTG CAG CTT CAG CAG TCA GG
        GAG GTG CAG CTT CAG CAG TCG GG
        GAT GTG CAG CTT CAG CAG TCA GG
        GAT GTG CAG CTT CAG CAG TCG GG