$element2 at least is running away and therefore you are trying to read beyond the end of @contigfile in your substr call. Hence the warning message.

If you must do it using this algorithm (and TIMTOWTDI but it wouldn't have been my choice) it would be wise to test that both $element1 and $element2 are not outside the bounds of the array. I'd also suggest you use strict.

In reply to Re: Uninitialized value in substr command by hippo
in thread Uninitialized value in substr command by lmtaylor

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