Hi, you assign to the variable each time through the loop, so it only ever holds one key. Just pass the value if it exists:

for my $found_key ( sort keys %hash1 ) {
    if ( exists $hash2{ $found_key } ) {
        ntSpacer( $hash2{ $found_key } );
    }
}

sub ntSpacer {
    my $seq = shift;
    ...
}
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Hope this is all you were looking for ... I didn't check the sub (although it seems you are using the undefined value as a spacer)