Adding a little sanity checking to evalRna may help you figure out the problem:

sub evalRna {
    my ($l, $r) = @_;
    my %bonds    = (GU => 1, UG => 1, AU => 2, UA => 2, CG => 3, GC =>
+ 3);
    my $lu = "$bases[$l]$bases[$r]";
    my $numBonds = $bonds{$lu} || die "Bad bond type '$lu' given $l, $
+r\n";
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When given your sample input data you get:

Bad bond type '5C' given 0, 21
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