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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";

When given your sample input data you get:

Bad bond type '5C' given 0, 21
True laziness is hard work

In reply to Re: recursive algorithm by GrandFather
in thread recursive algorithm by Anonymous Monk

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