I'm currently trying out exists, thanks for that! In the example above, I would have to put the "filter" keys in the exists, because the $x becomes the sequence that gets augmented and compared to all $x's. So, if the key in %two exists as a key in %one, then the key from %one becomes the target. Which then gets assigned to a new variable with each option from the base list. Those are then checked against the $x keys for matches.

foreach my $sql1 (@{$sql1}) {
    $table1{$sql1->[1]}{$sql1->[0]}=undef;  #rearranges the sql pull -
+ large table of sequences and id's - These get used to create the alt
+s and house the entire list that needs to be searched
}

foreach my $sql2 (@{$sql2}) {                
    $table2{$sql2->[1]}{$sql2->[0]}=undef;  #rearranges the sql pull -
+ "filter" table of sequences and id's - Only used to dictate which se
+quences get used from the large table

my @bases = ('A','C','G','T');

foreach my $x (keys %table1){    

    if (exists $table2 ({$x})) {

my $found_alt = 0;

foreach my $bases (@bases) {
        my $alt = $x;
        substr($alt, 20, 1) = $opt;
        next if ($alt eq $x);
        if (exists $table1{$alt}) {
            $found_alt = 1;
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