cut-off is now inclusive

[COTRASIF]

This change affected both online search methods, and is implemented in
downloadable versions since initial public release.

Previously, cut-off was not inclusive - that is, only scores strictly
"greater than" cut-off were written to the results file. Furthermore,
it was impossible to specify 1.0 as a cut-off - it was automatically
converted to 0.99.

Now it is possible to specify cut-off=1.0, and thus include only
perfect matches in the results file.