TargetRank scores the seed matches in a UTR relative to a given siRNA or miRNA, and then calculates an overall score for the mRNA as a whole by summing the scores for all seed matches present in the 3' UTR.
The score for each seed match is based on (1) its seed match type, (2) the base composition at position t9, (3) flanking AU content (of the 50 nt immediately 3' of the seed match), and (4) flanking conservation (of the 50 nt immediately 5' of the seed match). In cases where multiple input siRNA/miRNA sequences are provided and the seed match type is ambiguous (i.e. the same 3' UTR sequence can be interpreted as a different seed match type depending on which input siRNA/miRNA is considered), then the TargetRank score for each possible seed match type is calculated separately and the final score for the seed match is the average of the possible scores.
Only targets with scores above 0.2 are reported.
Additional details of the parameters used in TargetRank can be found in Nielsen et al. 2007 and related Supplementary Material. The relative ranking given by TargetRank is probably more useful than the score itself, since the overall magnitude of miRNA- or siRNA-associated repression will vary in different systems.