The context++ score (CS) for a specific site is the sum of the contribution of 14 features (Agarwal et al., 2015):

• site type
• supplementary pairing
• local AU
• minimum distance
• sRNA1A*
• sRNA1C*
• sRNA1G*
• sRNA8A*
• sRNA8C*
• sRNA8G*
• site8A*
• site8C*
• site8G*
• 3' UTR length*
• SA*
• ORF length*
• ORF 8mer count*
• 3' UTR offset 6mer count*
• TA (target site abundance)
• SPS (seed-pairing stability)
• P_CT (probability of conserved targeting)*

*new for TargetScanHuman 7 and TargetScanMouse 7

Since overlapping sites cannot be occupied at the same time, some are removed from this table to create a set of non-overlapping sites while maximizing the total context score. These non-overlapping sites are used to calculate the total context score. All sites are still shown on the gene-centric detail pages.

To calculate the cumulative weighted context++ score (CWCS; Agarwal et al., 2015), for each site i, from 1 to n, the cumulative predicted repression at that site (C_i) was calculated as C_i = C_(i-1) + (1-2^CSi)(AIR_i-C_(i-1)), in which CS_i and AIR_i were the context++ score and AIR of site i, and the (1-2^CSi)(AIR_i-C_(i-1)) term predicted the marginal repression of site i, in which the predicted repression at the site (1-2^CSi) was modified based on the fraction of mRNAs containing that site (AIR_i) as reduced by the mRNA depletion predicted to occur from the action of any more distal sites (C_(i-1), assigning C₀ as 0). The CWCS was then calculated as log₂(1-C_n), in which C_n was the C_i at the most proximal site of the reference 3' UTR.

Predicted targets of each miRNA family are sorted by CWCS.

For each reference 3' UTR, CWCSs were calculated for each member of a miRNA family, and the score from the member with the greatest predicted repression was chosen to represent that family as the representative miRNA. If more than one miRNA have the most favorable CWCS, the miRNA with the lowest number and/or letter is shown. Poorly conserved sites are given the same weight as conserved sites. Although only one miRNA is chosen as the representative miRNA, all the other miRNAs of the miRNA family are also predicted to target the same target gene at the same target site(s).

Total context++ scores are also shown for each representative transcript. These were calculated by summing the context++ scores for the sites to the representative miRNA.