`Avoid Special Cases`

    33            for ($i=0;$i<@{$chain[3]};$i++){

This is the sort of thing that drives maintenance programmers bats
3? Why 3???
My guess: The choice was arbitrary because all the chains have the same length
If that's true, we might check the condition and report an error if not:

        my $BAD_LENGTH;
        for my $n (1 .. $#chains) {
          unless (@{$chains[$n]} == @{$chains[1]}) {
            warn "Chain 1 and chain $n have different lengths!\n";
            $BAD_LENGTH = 1;
          }
        }
        exit 1 if $BAD_LENGTH;

The maintenance programmer would no longer have to wonder why one chain was special
Alternative:

      for ($i=0;$i<@{$chain[1]};$i++){

If you must choose arbitrarily, choose the first item