%reverse= reverse(%CodonMap)
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This does not do what you think it does.

A hash key in Perl can only have one value. Use Data::Dumper to look at the result:

use Data::Dumper;
%reverse= reverse(%CodonMap)
print Dumper \%reverse;
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You will need to construct your reverse map manually, for example by looping through all keys and values:

use Data::Dumper;
my %reverse;

while( my( $k,$v )= each %CodonMap) {
    $reverse{ $v }||= [];
    push @{ $reverse{ $v }}, $k;
};
print Dumper \%reverse;
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Then, you will need to adapt your program logic to cater for the fact that you don't have simple scalars in %reverse anymore.