This writes out a text file for every primary and secondary motif which has a significant spacing. The text file contains fields which from left to right are:

1. A portion of the sequence in lower case with the motif matches in upper case.
2. The position of the secondary match within the sequence portion.
3. The fragment of the sequence which matched the primary motif.
4. The strand which matched the primary motif.
5. The fragment of the sequence which matched the secondary motif.
6. The strand which matched the secondary motif.
7. Secondary site is on the same (s) or opposite (o) strand to the primary site.
8. Secondary site is upstream (u) or downstream (d) of the primary site.
9. The gap between the primary and secondary site.
10. The name of the sequence.
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