How can I fix it?

By giving better examples :) I had assumed on the basis of the sample supplied, that the overlapping sections were identical as in both cases supplied. I think javafans make that same assumption.

You'd need to accumulate the overlaps in a third array in the while, and then add another for loop to process them is the same way as @heads & @tails. (There obviously scope there for making the for loop a subroutine.

I'm done for today, but I'll be back tonight.