Scoring

We incorporate the latest Cas9, Cpf1 and TALEN findings into CHOPCHOP's algorithm for scoring and ranking potential target sites. See the instructions page for more information about how we rank our results.

Scoring for each sgRNA/individual TALE target:

More than 100 off-targets: 20000
MM0 off-target: 1000
MM1 off-target: 800
MM2 off-target: 600
MM3 off-target: 400

Additional CRISPR/Cas9 and CRISPR/Cpf1 scoring:

Bad GC (<40 or >70): 500
Efficiency: lower score by efficiency value * 100
4nt self-complementary stem found: 1 for each
CRISPR color thresholds: Green < 0>= Yellow > 1000 >= Red
CPF1 color thresholds: Green < 300>= Yellow > 1000 >= Red

Additional TALEN/NICKASE scoring:

Off-target pair: 10000 (5000 if on same strand, not counted in NICKASE)
MM0 in off-target pair: 5000
MM1 in off-target pair: 3000
MM2 in off-target pair: 2000
MM2 in off-target pair: 1000
TALEN color thresholds: Green < 10000>= Yellow > 15000 >= Red
NICKASE color thresholds: Green < 3000>= Yellow > 6000 >= Red

MM0 = 0 mismatches, MM1 = 1 mismatch, MM2 = 2 mismatches, MM3 = 3 mismatches