This tool identifies potential interactions between small RNAs and unigenes. The program allows users to input a small RNA sequence or mRNA sequence, it then searches against the SGN tomato unigenes (if the input is small RNA) or the tomato small RNAs (if the input is mRNA) and reports all possible sRNA:mRNA interactions which meet the user specified cutoff criteria. Here is the scoring matrix the program used according to Jones-Rhoades and Bartel (2004):

	score
Perfect match	0
G:U wobble	0.5
Non-G:U mismatch	1
Indel	2

The program can search for both strand of mRNA if you are not sure the direction of your input mRNA. If you input sequence is a sRNA, then search for both strand of SGN tomato unigene is encouraged.

Jones-Rhoades MW, Bartel DP. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787-99