TargetFinder searches query sequences of less then 1000nt for potential small RNA targets. A query is submitted in the form of a locus identifier or FASTA formatted sequence. Multiple queries are made by listing more than one identifier or sequence, separated by returns. The results from this search should not be considered proof of targeting, but rather preliminary data for potential target-small RNA interaction.

TargetFinder does FASTA3 searches of the query sequence(s) against small RNAs in the database. Potential small RNA target sites are scored using a position-weighted, mispair penalty system as follows:

• Mispair, bulge or gap - 1.0
• G:U pair - 0.5
• Mispair, bulge, gap, or G:U pair occurring within position 2 to 13 relative to the 5' end of the small RNA - double penalty listed above
• Single-nucleotide bulge or gap - maximum of one allowed

Predicted scores of 4 or less are considered plausible small RNA/target hits. Scores of zero may be due to small RNAs that derive from the query sequence, and are listed separately.