• Mismatch vs. incomplete data

The current version does not distinguish between a failure to match due to a true mismatch and a failure to match due to missing sequence data at the target position.

• Ambiguities near the probe 3'-end

Specifying mismatches, insertions or deletions near the probe 3'-end can increase the search time towards infinity. This tendency is due to the internal workings of the underlying pattern matching program. To avoid this problem, break the probe into fragments (example here).

• Organism selection

There ought to be an easy way of selecting organisms.

• Base pair weighting

Attaching weights to each match would be a desired feature.

• Td formulae are not precise

The three different Td formulae give only approximate values, and they are provided only for preliminary comparisons. Your probe will have to be tested empirically.