rogerd,
If you need to put more than one match on a line using the fewest number of total lines, you have a variation on Bin Packing Problem which is NP hard. I can write you a solution, but I don't have time at the moment (you can search this site and CPAN for examples that you could adapt).

Update: Following paragraph added
The bit mask isn't going to help by itself. It was just an idea for determining overlap. Because you require the matches on as fewest lines as possible, you have to try all possible combinations. This is why the problem is NP hard. I am assuming that for a given DNA sequence, the number of strands to place is quite large. If this assumption is correct, your perfect solution is going to be slow so you might want to look at a heuristic approach instead.

Cheers - L~R

In reply to Re^3: formatting output question (use of recursive subroutine?) by Limbic~Region
in thread formatting output question (use of recursive subroutine?) by rogerd

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